Diversity

13 pages, 1659 KiB

Open AccessEditor’s ChoiceArticle

Mesocarnivore Distribution along Gradients of Anthropogenic Disturbance in Mediterranean Landscapes

by Ignasi Torre, Tomàs Pulido, Marc Vilella and Mario Díaz

Diversity 2022, 14(2), 133; https://doi.org/10.3390/d14020133 - 14 Feb 2022

Cited by 14 | Viewed by 4062

Wildfires are important sources of landscape change in Mediterranean environments, creating large patches of low-growth natural habitats (i.e., scrublands) inside protected areas, whereas woodland patches remain mostly near well protected human settlements. Landscape patterns resulting from these gradients influence habitat suitability for mesocarnivores [...] Read more.

Wildfires are important sources of landscape change in Mediterranean environments, creating large patches of low-growth natural habitats (i.e., scrublands) inside protected areas, whereas woodland patches remain mostly near well protected human settlements. Landscape patterns resulting from these gradients influence habitat suitability for mesocarnivores regarding food and shelter. In winter and summer 2019, we sampled 16 independent line-transects with four camera traps each (64 cameras overall), covering the main habitats of the study area (woodlands, scrublands, and crops). Cameras were baited to compensate for the low detectability of target species, and mesocarnivore contacts were analysed by means of GLMMs and occupancy models. Our results showed a positive and stronger association of wild species with woodland habitats, despite the low proportion of habitat available, higher presence of competitors (other mesocarnivores), and potential predators (human pets, i.e., dogs), and low natural prey availability than in scrubland (i.e., small mammals). However, mesocarnivores will find protection against predators and resting sites in forests as well as other food opportunities in crops and urban areas, despite the possible interference with humans and their pets. Potential cascading effects linked to ecological roles of Mediterranean mesocarnivores on the succession of Mediterranean landscapes would imply longer-term effects of human disturbance on landscape trends. Full article

(This article belongs to the Special Issue Diversity in 2022)

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12 pages, 1826 KiB

Open AccessEditor’s ChoiceArticle

Three New Species of Absidia (Mucoromycota) from China Based on Phylogeny, Morphology and Physiology

by Heng Zhao, Yong Nie, Tongkai Zong, Yucheng Dai and Xiaoyong Liu

Diversity 2022, 14(2), 132; https://doi.org/10.3390/d14020132 - 13 Feb 2022

Cited by 15 | Viewed by 4959

Abstract

Species of Absidia are distributed widely in the environment, while their diversity is insufficiently studied. Three new species, A. frigida, A. gemella and A. longissima, are proposed herein from Xinjiang and Yunnan in China based on phylogenetic, morphological and physiological evidence. [...] Read more.

Species of Absidia are distributed widely in the environment, while their diversity is insufficiently studied. Three new species, A. frigida, A. gemella and A. longissima, are proposed herein from Xinjiang and Yunnan in China based on phylogenetic, morphological and physiological evidence. According to maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) analyses, the phylogenetical results suggest that A. frigida, A. gemella and A. longissima are closely related to A. psychrophilia, A. turgida and A. zonata and A. koreana, respectively, based on ITS and LSU rDNA sequences. Absidia frigida is characterized by a lower growth temperature, which does not grow above 24 °C. It differs from A. psychrophilia by sporangiophores, sporangia, columellae, collars and projections. Absidia gemella is distinguished from A. turgida by hypha, sporangiospores, sporangia, projections and sporangiophores. Absidia longissima is discriminated from A. zonata and A. koreana by sporangiophores, columellae and collars. The three new species are described and illustrated in this article. Full article

(This article belongs to the Special Issue Diversity and Evolution of Fungi)

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5 pages, 1730 KiB

Open AccessEditor’s ChoiceInteresting Images

Seahorse Predation by Octopuses in the Caribbean and the West Pacific

by Ellen Muller, David Harasti and Bert W. Hoeksema

Diversity 2022, 14(2), 125; https://doi.org/10.3390/d14020125 - 10 Feb 2022

Cited by 5 | Viewed by 5625

Abstract

There is much documentation about seahorses (Hippocampus spp.) being threatened by habitat degradation and overfishing, but relatively few published studies mention their natural predators. The present study documents three cases in which seahorses are being caught by octopuses. In one case, the [...] Read more.

There is much documentation about seahorses (Hippocampus spp.) being threatened by habitat degradation and overfishing, but relatively few published studies mention their natural predators. The present study documents three cases in which seahorses are being caught by octopuses. In one case, the seahorse was partly consumed. These observations made at Bonaire (Caribbean Netherlands) and New South Wales (Australia) suggest that predation on seahorses by octopuses may be more widespread and common than previously thought. Full article

(This article belongs to the Collection Interesting Images from the Sea)

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26 pages, 3641 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Single-Island Endemism despite Repeated Dispersal in Caribbean Micrathena (Araneae: Araneidae): An Updated Phylogeographic Analysis

by Lily Shapiro, Greta J. Binford and Ingi Agnarsson

Diversity 2022, 14(2), 128; https://doi.org/10.3390/d14020128 - 10 Feb 2022

Cited by 11 | Viewed by 4529

Abstract

Island biogeographers have long sought to elucidate the mechanisms behind biodiversity genesis. The Caribbean presents a unique stage on which to analyze the diversification process, due to the geologic diversity among the islands and the rich biotic diversity with high levels of island [...] Read more.

Island biogeographers have long sought to elucidate the mechanisms behind biodiversity genesis. The Caribbean presents a unique stage on which to analyze the diversification process, due to the geologic diversity among the islands and the rich biotic diversity with high levels of island endemism. The colonization of such islands may reflect geologic heterogeneity through vicariant processes and/ or involve long-distance overwater dispersal. Here, we explore the phylogeography of the Caribbean and proximal mainland spiny orbweavers (Micrathena, Araneae), an American spider lineage that is the most diverse in the tropics and is found throughout the Caribbean. We specifically test whether the vicariant colonization via the contested GAARlandia landbridge (putatively emergent 33–35 mya), long-distance dispersal (LDD), or both processes best explain the modern Micrathena distribution. We reconstruct the phylogeny and test biogeographic hypotheses using a ‘target gene approach’ with three molecular markers (CO1, ITS-2, and 16S rRNA). Phylogenetic analyses support the monophyly of the genus but reject the monophyly of Caribbean Micrathena. Biogeographical analyses support five independent colonizations of the region via multiple overwater dispersal events, primarily from North/Central America, although the genus is South American in origin. There is no evidence for dispersal to the Greater Antilles during the timespan of GAARlandia. Our phylogeny implies greater species richness in the Caribbean than previously known, with two putative species of M. forcipata that are each single-island endemics, as well as deep divergences between the Mexican and Floridian M. sagittata. Micrathena is an unusual lineage among arachnids, having colonized the Caribbean multiple times via overwater dispersal after the submergence of GAARlandia. On the other hand, single-island endemism and undiscovered diversity are nearly universal among all but the most dispersal-prone arachnid groups in the Caribbean. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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44 pages, 726 KiB

Open AccessEditor’s ChoiceReview

Purely Australian Essential Oils Past and Present: Chemical Diversity, Authenticity, Bioactivity, and Commercial Value

by Nicholas John Sadgrove

Diversity 2022, 14(2), 124; https://doi.org/10.3390/d14020124 - 9 Feb 2022

Cited by 4 | Viewed by 6920

Abstract

In this comprehensive commentary, Australian essential oils and their components are listed and discussed in the context of their value to industry and aesthetics. The historic and cultural significance of endemic essential oils is explained. Several promising candidates are identified that have commercial [...] Read more.

In this comprehensive commentary, Australian essential oils and their components are listed and discussed in the context of their value to industry and aesthetics. The historic and cultural significance of endemic essential oils is explained. Several promising candidates are identified that have commercial potential and will enter the marketplace in the not-too-distant future. This text elaborates on the current progress in research, and explains the up-to-date view of ‘bioactive,’ with reference to insect repellence, antimicrobial activity, anti-inflammatory activity, and potential toxicity. The concept of chemotypes and chemophenetics is explained in detail to justify why chemically variable species in Australia require standardisation practices to ensure reproducibility of their derived natural products: standardisation practice includes cultivar development and authentication protocols. Thereafter, some of the more significant essential oils are defined and some background information provided. This review concludes with a comprehensive table of aromatic species that were studied by Joseph Brophy over the last 30 years, thereby providing the most comprehensive overview available, on the chemistry of Australian essential oil yielding species. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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14 pages, 6008 KiB

Open AccessEditor’s ChoiceArticle

Seasonal and Interannual Dynamics of Pelagic Rotifers in a Tropical, Saline, Deep Lake

by Rocío Fernández, Javier Alcocer, Alfonso Lugo, Luis A. Oseguera and Sandra Guadarrama-Hernández

Diversity 2022, 14(2), 113; https://doi.org/10.3390/d14020113 - 5 Feb 2022

Cited by 5 | Viewed by 2399

Abstract

This is the first long-term study (monthly samples at two 4-year intervals: 1998 to 2001 and 2013 to 2016) on rotifers in a saline, deep lake. The pelagic rotifer assemblage of Lake Alchichica is simple and comprised by two species, both new and [...] Read more.

This is the first long-term study (monthly samples at two 4-year intervals: 1998 to 2001 and 2013 to 2016) on rotifers in a saline, deep lake. The pelagic rotifer assemblage of Lake Alchichica is simple and comprised by two species, both new and most likely endemic: Brachionus sp. Mexico (related to B. plicatilis) and Hexarthra sp. (related to H. jenkinae). Similar low species richness and composition are found in other saline lakes associated with salinity. Rotifers in Lake Alchichica were an irregular component of the zooplankton community. Rotifers’ overall abundance (471 ± 1211 ind m⁻²) and biomass (24 ± 63 mg DW m⁻²) were low; Brachionus sp. Mexico and Hexarthra sp. contributed similarly to the annual mean abundance (54% and 46%, respectively) and biomass (53% and 47%, respectively). Abundance and biomass were tightly coupled, but there was no regular pattern in their seasonal dynamics. When co-existing, Brachionus sp. Mexico showed a higher abundance than Hexarthra sp. The dominant (≈80%) phytoplankton biomass in Lake Alchichica, the large (35–63 µm) diatom Cyclotella alchichicana, is inedible for rotifers, thus rotifers most probably relied only on nanophytoplankton (≤20 µm). Seasonal and interannual differences in rotifers seem related to food availability (oligotrophy) and probably to biotic interactions (e.g., competition). Rotifer abundance and biomass values in 1998–2001 went down to 12.5% in 2013–2016. Climate change and stochastics events leading to pulses of the rotifers’ food, and biotic interactions seem to be the most plausible explanation. Full article

(This article belongs to the Special Issue Biodiversity of Rotifers)

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25 pages, 8398 KiB

Open AccessFeature PaperEditor’s ChoiceReview

Vegetation Ecology of Debris-Covered Glaciers (DCGs)—Site Conditions, Vegetation Patterns and Implications for DCGs Serving as Quaternary Cold- and Warm-Stage Plant Refugia

by Thomas Fickert, Donald Friend, Bruce Molnia, Friederike Grüninger and Michael Richter

Diversity 2022, 14(2), 114; https://doi.org/10.3390/d14020114 - 5 Feb 2022

Cited by 8 | Viewed by 4388

Abstract

Scientific interest in debris-covered glaciers (DCGs) significantly increased during the last two decades, primarily from an abiotic perspective, but also regarding their distinctive ecology. An increasing body of evidence shows that, given a minimum of debris thickness and sufficient substrate stability, DCGs host [...] Read more.

Scientific interest in debris-covered glaciers (DCGs) significantly increased during the last two decades, primarily from an abiotic perspective, but also regarding their distinctive ecology. An increasing body of evidence shows that, given a minimum of debris thickness and sufficient substrate stability, DCGs host surprisingly diverse plant assemblages, both floristically and structurally, despite being obviously cold and in parts also highly mobile habitats. As a function of site conditions, floristic composition and vegetation structure, DCGs represent a mosaic of environments, including subnival pioneer communities, glacier foreland early- to late-successional stages, morainal locations, and locally, even forest sites. On shallow supraglacial debris layers, cryophilous alpine/subnival taxa can grow considerably below their common elevational niche due to the cooler temperatures within the root horizon caused by the underlying ice. In contrast, a greater debris thickness allows even thermophilous plant species of lower elevations to grow on glacier surfaces. Employing the principle of uniformitarianism, DCGs are assumed to have been important and previously undocumented refugia for plants during repeated Quaternary cold and warm cycles. This review and recent study summarize the current knowledge on the vegetation ecology of DCGs and evaluates their potential function as plant habitat under ongoing climate warming. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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23 pages, 1817 KiB

Open AccessEditor’s ChoiceArticle

Strong Philopatry, Isolation by Distance, and Local Habitat Have Promoted Genetic Structure in Heermann’s Gull

by Misael Daniel Mancilla-Morales, Enriqueta Velarde, Andres Aguilar, Araceli Contreras-Rodríguez, Exequiel Ezcurra, Jesús A. Rosas-Rodríguez, José G. Soñanez-Organis and Enrico A. Ruiz

Diversity 2022, 14(2), 108; https://doi.org/10.3390/d14020108 - 2 Feb 2022

Cited by 5 | Viewed by 5010

Abstract

Philopatry can promote genetic differentiation among populations but remains undescribed in many seabirds. Hence, we explored such associations in Heermann’s Gull. Philopatry was observed monitoring 998 gulls in Rasa Island, while genetic differences were examined in the Cardonosa, Rasa, and Isabel islands using [...] Read more.

Philopatry can promote genetic differentiation among populations but remains undescribed in many seabirds. Hence, we explored such associations in Heermann’s Gull. Philopatry was observed monitoring 998 gulls in Rasa Island, while genetic differences were examined in the Cardonosa, Rasa, and Isabel islands using the cytochrome b of 296 gulls. Adults returned repeatedly to its natal valley or to a very close distance from it under different modelled hypotheses. Likewise, the interaction between sex and distance indicated significant male-biased philopatry. Besides, low to high genetic differentiation was observed between the Rasa and Cardonosa islands (Φ_ST = 0–0.22) (both in the Midriff Islands Region), but higher genetic differentiation against Isabel Island (Φ_ST > 0.25) (in the Mexican Province region). Consistently, genetic structure among regions was observed using different approaches (AMOVA: Φ_CT = 0.49; SAMOVA: F_CT = 0.49; and BAPS: K = 2). Similarly, a pattern of isolation by distance (rM = 0.82, p = 0.03), agrees with lower estimates of scaled migration rates between regions than among islands of the same region. Overall, it is suggested that the genetic structure found in Heermann’s Gull has been promoted by physical and behavioral barriers. Full article

(This article belongs to the Section Biodiversity Conservation)

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Graphical abstract

69 pages, 5932 KiB

Open AccessFeature PaperEditor’s ChoiceReview

The Evolution and Fossil Record of Palaeognathous Birds (Neornithes: Palaeognathae)

by Klara Widrig and Daniel J. Field

Diversity 2022, 14(2), 105; https://doi.org/10.3390/d14020105 - 1 Feb 2022

Cited by 17 | Viewed by 19699

Abstract

The extant diversity of the avian clade Palaeognathae is composed of the iconic flightless ratites (ostriches, rheas, kiwi, emus, and cassowaries), and the volant tinamous of Central and South America. Palaeognaths were once considered a classic illustration of diversification driven by Gondwanan vicariance, [...] Read more.

The extant diversity of the avian clade Palaeognathae is composed of the iconic flightless ratites (ostriches, rheas, kiwi, emus, and cassowaries), and the volant tinamous of Central and South America. Palaeognaths were once considered a classic illustration of diversification driven by Gondwanan vicariance, but this paradigm has been rejected in light of molecular phylogenetic and divergence time results from the last two decades that indicate that palaeognaths underwent multiple relatively recent transitions to flightlessness and large body size, reinvigorating research into their evolutionary origins and historical biogeography. This revised perspective on palaeognath macroevolution has highlighted lingering gaps in our understanding of how, when, and where extant palaeognath diversity arose. Towards resolving those questions, we aim to comprehensively review the known fossil record of palaeognath skeletal remains, and to summarize the current state of knowledge of their evolutionary history. Total clade palaeognaths appear to be one of a small handful of crown bird lineages that crossed the Cretaceous-Paleogene (K-Pg) boundary, but gaps in their Paleogene fossil record and a lack of Cretaceous fossils preclude a detailed understanding of their multiple transitions to flightlessness and large body size, and recognizable members of extant subclades generally do not appear until the Neogene. Despite these knowledge gaps, we combine what is known from the fossil record of palaeognaths with plausible divergence time estimates, suggesting a relatively rapid pace of diversification and phenotypic evolution in the early Cenozoic. In line with some recent authors, we surmise that the most recent common ancestor of palaeognaths was likely a relatively small-bodied, ground-feeding bird, features that may have facilitated total-clade palaeognath survivorship through the K-Pg mass extinction, and which may bear on the ecological habits of the ancestral crown bird. Full article

(This article belongs to the Special Issue Evolution and Palaeobiology of Flightless Birds)

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13 pages, 1012 KiB

Open AccessEditor’s ChoiceArticle

Genetic Differentiation among Subspecies of Banksia nivea (Proteaceae) Associated with Expansion and Habitat Specialization

by Jane Sampson and Margaret Byrne

Diversity 2022, 14(2), 98; https://doi.org/10.3390/d14020098 - 30 Jan 2022

Cited by 7 | Viewed by 3401

Abstract

Subspecies are traditionally defined using phenotypic differences associated with different geographical areas. Yet patterns of morphological and genetic variation may not coincide and thereby fail to reflect species’ evolutionary history. The division of the shrub Banksia nivea Labill. into one widespread (B. [...] Read more.

Subspecies are traditionally defined using phenotypic differences associated with different geographical areas. Yet patterns of morphological and genetic variation may not coincide and thereby fail to reflect species’ evolutionary history. The division of the shrub Banksia nivea Labill. into one widespread (B. nivea subsp. nivea) and two geographically localized subspecies (B. nivea subsp. uliginosa (A.S. George) A.R. Mast & K.R. Thiele and B. nivea subsp. Morangup (M. Pieroni 94/2)) in south-west Australia has been based mainly on variation in leaf shape and pistil length, although flowering time and habitat differences are also evident, and subsp. uliginosa occurs on a different substrate. To assess the genetic divergence of B. nivea subspecies, we genotyped representatives from each subspecies for nuclear microsatellite and non-coding chloroplast sequence variation. We used distance and parsimony-based methods to assess genetic relatedness. Patterns were consistent with the existing taxonomy of subsp. nivea and uliginosa but not subsp. Morangup. Phylogenetic analyses revealed evidence for a more recent divergence of subsp. uliginosa associated with expansion from dryer sandy soils into the winter-wet ironstone soils in the southwest of Western Australia, consistent with progressive long-term climatic drying. Nuclear microsatellites showed low to moderate diversity, high population differentiation overall, and genetic structuring of subspecies in different biogeographical areas. We propose this pattern reflects the predicted impact of a patchy distribution, small populations, and restrictions to gene flow driven by both distance and biogeographic differences in subspecies’ habitats. Full article

(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)

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12 pages, 1560 KiB

Open AccessEditor’s ChoiceArticle

COI Metabarcoding Provides Insights into the Highly Diverse Diet of a Generalist Salamander, Salamandra salamandra (Caudata: Salamandridae)

by Adam J. D. Marques, Vanessa A. Mata and Guillermo Velo-Antón

Diversity 2022, 14(2), 89; https://doi.org/10.3390/d14020089 - 28 Jan 2022

Cited by 10 | Viewed by 4987

Abstract

DNA metabarcoding has proven to be an accessible, cost-effective, and non-invasive tool for dietary analysis of predators in situ. Although DNA metabarcoding provides numerous benefits in characterizing diet—such as detecting prey animals that are difficult to visually identify—this method has seen limited application [...] Read more.

DNA metabarcoding has proven to be an accessible, cost-effective, and non-invasive tool for dietary analysis of predators in situ. Although DNA metabarcoding provides numerous benefits in characterizing diet—such as detecting prey animals that are difficult to visually identify—this method has seen limited application in amphibian species. Here, we used DNA metabarcoding to characterize the diet of fire salamanders (Salamandra salamandra) (Linnaeus, 1758) in three distinct regions across the northwestern Iberian Peninsula. To test the efficiency of COI-based metabarcoding in determining salamanders’ diet diversity, we compared our COI-based results with results from traditional diet studies from neighboring and distant populations, as well as with recent findings obtained in a DNA metabarcoding study using 18S. Two COI primers were used in combination to investigate the potential impact of primer bias in prey detection. Our COI metabarcoding approach increased taxonomic resolution and supported a generalist diet in S. salamandra. Between primers, there were no significant differences in the diversity and richness of prey detected. We observed differences in the prevalence of prey identified between sampling regions both in our study and in other studies of S. salamandra diet. This COI metabarcoding study provides recommendations and resources for subsequent research using DNA metabarcoding to study amphibian diets. Full article

(This article belongs to the Special Issue The Ecological Role of Salamanders as Predators and Prey)

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14 pages, 23970 KiB

Open AccessEditor’s ChoiceArticle

Diversification in the Comoros: Review of the Laccophilus alluaudi Species Group with the Description of Four New Species (Coleoptera: Dytiscidae)

by Johannes Bergsten and Olof Biström

Diversity 2022, 14(2), 81; https://doi.org/10.3390/d14020081 - 25 Jan 2022

Cited by 4 | Viewed by 3968

Abstract

The Laccophilus alluaudi species group is an interesting case of an endemic species radiation of Madagascar and the Comoros. To date, a single species, Laccophilus tigrinus Guignot, 1959 (Anjouan), is known from the Comoro Islands, with eight other species known from Madagascar. Here [...] Read more.

The Laccophilus alluaudi species group is an interesting case of an endemic species radiation of Madagascar and the Comoros. To date, a single species, Laccophilus tigrinus Guignot, 1959 (Anjouan), is known from the Comoro Islands, with eight other species known from Madagascar. Here we review the Laccophilus alluaudi species group from the Comoro Islands based on partly new material. We recognize five species, out of which four are here described as new: L. mohelicus n. sp. (Mohéli), L. denticulatus n. sp. (Grande Comore), L. michaelbalkei n. sp. (Mayotte) and L. mayottei n. sp. (Mayotte). Based on morphology of male genitalia, we hypothesize that the five species form a monophyletic group and originated from a single colonization event from Madagascar. If confirmed, this would constitute one of the few examples of intra-archipelago diversification in the Comoros. The knowledge of species limits in relation to their distribution in the Comoros archipelago is also urgently needed in the face of rapid habitat degradation. Full article

(This article belongs to the Special Issue Aquatic Insects: Biodiversity, Ecology and Conservation Challenges)

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23 pages, 1740 KiB

Open AccessEditor’s ChoiceReview

Conservation and Phylogeography of Plants: From the Mediterranean to the Rest of the World

by Javier Bobo-Pinilla, Esteban Salmerón-Sánchez, Antonio J. Mendoza-Fernández, Juan F. Mota and Julio Peñas

Diversity 2022, 14(2), 78; https://doi.org/10.3390/d14020078 - 24 Jan 2022

Cited by 18 | Viewed by 6969

Abstract

During the last decades, phylogeography has transformed the ways to analyze and understand plant diversity and biogeography. The repeated and increasingly detailed articles made from DNA data with phylogeographical procedures and algorithms have revolutionized biodiversity research, particularly on biodiversity conservation. This paper presents [...] Read more.

During the last decades, phylogeography has transformed the ways to analyze and understand plant diversity and biogeography. The repeated and increasingly detailed articles made from DNA data with phylogeographical procedures and algorithms have revolutionized biodiversity research, particularly on biodiversity conservation. This paper presents a systematic literature review of the different ways in which phylogeography has been applied to plants in Mediterranean-type ecosystems (MTEs), especially to rare, threatened, and endemic plants. Studies ranged from basic research to how phylogeography is actually contributing to management conservation of Mediterranean plants. Finally, new and future phylogeography perspectives with integrative scientific arguments and conceptual bases applied to plant conservation biology are discussed. Full article

(This article belongs to the Special Issue Conservation and Phylogeography of Threatened and Endemic Plants)

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11 pages, 1854 KiB

Open AccessEditor’s ChoiceArticle

Morphology and Molecular Phylogeny of Fuscheriides baugilensis sp. nov. (Protozoa, Ciliophora, Haptorida) from South Korea

by Seok Won Jang, Atef Omar, Seung Won Nam and Jae-Ho Jung

Diversity 2022, 14(2), 70; https://doi.org/10.3390/d14020070 - 21 Jan 2022

Cited by 3 | Viewed by 3234

Abstract

The morphology and molecular phylogeny of a new haptorid ciliate, Fuscheriides baugilensis sp. nov., discovered in a temporary pond in South Korea, were investigated. The new species is characterized by its small body size (30–55 × 15–20 μm in vivo), oblong to rod-shaped [...] Read more.

The morphology and molecular phylogeny of a new haptorid ciliate, Fuscheriides baugilensis sp. nov., discovered in a temporary pond in South Korea, were investigated. The new species is characterized by its small body size (30–55 × 15–20 μm in vivo), oblong to rod-shaped extrusomes in the oral bulge and cytoplasm, 14–16 somatic kineties, two dorsal brush rows, and single subapical ciliary condensation. The phylogenetic analyses based on the 18S rRNA gene sequences show that the family Fuscheriidae is paraphyletic and the species belong to the genera Fuscheriides and Pseudofuscheria cluster together in the same subclade, while Fuscheria is in a different subclade, suggesting that the subapical ciliary condensation characterizing the two former genera has a higher taxonomic value than the shape of extrusomes for genera separation. Full article

(This article belongs to the Collection Collection of Experts’ Researches on Aquatic Life (CEREAL))

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14 pages, 1393 KiB

Open AccessEditor’s ChoiceArticle

Defining Management Units for Wild Nile Tilapia Oreochromis niloticus from Nine River Basins in Ghana

by Gifty Anane-Taabeah Attu, Emmanuel A. Frimpong and Eric M. Hallerman

Diversity 2022, 14(2), 73; https://doi.org/10.3390/d14020073 - 21 Jan 2022

Cited by 6 | Viewed by 3675

Abstract

Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused [...] Read more.

Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused on characterizing genetic differentiation at finer scales. We assessed genetic variation in O. niloticus within and among nine drainage basins in Ghana using nuclear microsatellite DNA markers as the basis for identifying potential units of conservation among wild populations. We screened 312 wild individuals using eight nuclear microsatellite DNA markers. We found moderate genetic diversity within and differentiation among all wild populations studied, with strong signals of recent demographic bottlenecks in several populations. Genetic structure among 11 populations suggested the presence of up to ten management units (MUs). In particular, the Black Volta and the Tano–Asuhyea populations, which were the most genetically distinct and geographically isolated and may be most at risk of loss of genetic diversity over time, may well represent evolutionary significant units. Therefore, at the minimum, the Black Volta and Tano–Asuhyea populations should be prioritized for conservation actions to sustain them over the long-term. Full article

(This article belongs to the Special Issue Ancient and Modern DNA for Diversity and Evolution of Animal and Plant Species)

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20 pages, 9173 KiB

Open AccessEditor’s ChoiceArticle

Improved Chironomid Barcode Database Enhances Identification of Water Mite Dietary Content

by Adrian A. Vasquez, Brittany L. Bonnici, Safia Haniya Yusuf, Janiel I. Cruz, Patrick L. Hudson and Jeffrey L. Ram

Diversity 2022, 14(2), 65; https://doi.org/10.3390/d14020065 - 19 Jan 2022

Cited by 8 | Viewed by 3806

Abstract

Chironomids are one of the most biodiverse and abundant members of freshwater ecosystems. They are a food source for many organisms, including fish and water mites. The accurate identification of chironomids is essential for many applications in ecological research, including determining which chironomid [...] Read more.

Chironomids are one of the most biodiverse and abundant members of freshwater ecosystems. They are a food source for many organisms, including fish and water mites. The accurate identification of chironomids is essential for many applications in ecological research, including determining which chironomid species are present in the diets of diverse predators. Larval and adult chironomids from diverse habitats, including lakes, rivers, inland gardens, coastal vegetation, and nearshore habitats of the Great Lakes, were collected from 2012 to 2019. After morphological identification of chironomids, DNA was extracted and cytochrome oxidase I (COI) barcodes were PCR amplified and sequenced. Here we describe an analysis of biodiverse adult and larval chironomids in the Great Lakes region of North America based on new collections to improve chironomid identification by curating a chironomid DNA barcode database, thereby expanding the diversity and taxonomic specificity of DNA reference libraries for the Chironomidae family. In addition to reporting many novel chironomid DNA barcodes, we demonstrate here the use of this chironomid COI barcode database to improve the identification of DNA barcodes of prey in the liquefied diets of water mites. The species identifications of the COI barcodes of chironomids ingested by Lebertia davidcooki and L. quinquemaculosa are more diverse for L. davidcooki and include Parachironomus abortivus, Cryptochironomus ponderosus. Parachironomus tenuicaudatus, Glyptotendipes senilis, Dicrotendipes modestus, Chironomus riparius, Chironomus entis/plumosus, Chironomus maturus, Chironomus crassicaudatus, Endochironomus subtendens, Cricotopus sylvestris, Cricotopus festivellus, Orthocladius obumbratus, Tanypus punctipennis, Rheotanytarsus exiguus gr., and Paratanytarsus nr. bituberculatus. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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16 pages, 2889 KiB

Open AccessEditor’s ChoiceArticle

New Iguanodon bernissartensis Axial Bones (Dinosauria, Ornithopoda) from the Early Cretaceous of Morella, Spain

by José Miguel Gasulla, Fernando Escaso, Iván Narváez, José Luis Sanz and Francisco Ortega

Diversity 2022, 14(2), 63; https://doi.org/10.3390/d14020063 - 18 Jan 2022

Cited by 12 | Viewed by 7477

Abstract

Iguanodon bernissartensis is the most frequently and widely cited styracosternan ornithopod in Western Europe during the Early Cretaceous, although some of these assignments likely need to be revised to establish the true distribution of the taxon. Here, we describe a new specimen of [...] Read more.

Iguanodon bernissartensis is the most frequently and widely cited styracosternan ornithopod in Western Europe during the Early Cretaceous, although some of these assignments likely need to be revised to establish the true distribution of the taxon. Here, we describe a new specimen of I. bernissartensis from the upper Barremian of the Iberian Peninsula. Based on the unique combination of shared characters, the new specimen from the Arcillas de Morella Formation at Morella locality (Castellón, Spain) can be confidently referred to Iguanodon bernissartensis. These characters include parallel-sided anterior and posterior margins of the dorsal and the caudal neural spines as well as the presence of a ventral keel in the posterior dorsal centra and a broad ventral sulcus in the midline of the central surface of the most posterior sacral vertebrae. This new evidence of Iguanodon bernissartensis reinforces the knowledge about styracosternan ornithopods as the most frequently recorded dinosaur group in the Arcillas de Morella Formation. Full article

(This article belongs to the Special Issue Palaeoecological Analysis and Diversity of Turtles and Other Reptiles)

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15 pages, 23519 KiB

Open AccessEditor’s ChoiceArticle

Morphostructural Characterization of the Heterogeneous Rhodolith Bed at the Marine Protected Area “Capo Carbonara” (Italy) and Hydrodynamics

by Valentina A. Bracchi, Sarah Caronni, Agostino N. Meroni, Esteban Gottfried Burguett, Fabrizio Atzori, Nicoletta Cadoni, Fabio Marchese and Daniela Basso

Diversity 2022, 14(1), 51; https://doi.org/10.3390/d14010051 - 13 Jan 2022

Cited by 21 | Viewed by 2814

Abstract

Mediterranean rhodolith beds are priority marine benthic habitats for the European Community, because of their relevance as biodiversity hotspots and their role in the carbonate budget. Presently, Mediterranean rhodolith beds typically occur within the range of 30–75 m of water depth, generally located [...] Read more.

Mediterranean rhodolith beds are priority marine benthic habitats for the European Community, because of their relevance as biodiversity hotspots and their role in the carbonate budget. Presently, Mediterranean rhodolith beds typically occur within the range of 30–75 m of water depth, generally located around islands and capes, on flat or gently sloping areas. In the framework of a collaboration between the University of Milano-Bicocca and the Marine Protected Area “Capo Carbonara” (Sardinia, Italy), video explorations and sampling collections in three selected sites revealed the occurrence of a well developed and heterogeneous rhodolith bed. This bed covers an area >41 km² around the cape, with live coverage ranging between 6.50 and 55.25%. Rhodoliths showed interesting morphostructural differences. They are small compact pralines at the Serpentara Island, associated with gravelly sand, or bigger boxwork at the Santa Caterina shoal associated with sand, whereas branches are reported mostly in the Is Piscadeddus shoal, associated with muddy sand. Both in the Santa Caterina shoal and the Serpentara Island, rhodoliths generally show a spheroidal shape, associated with a mean value of currents of 4.3 and 7.3 cm/s, respectively, up to a maximum of 17.7 cm/s at Serpentara, whereas in the Is Piscadeddus shoal rhodolith shape is variable and current velocity is significantly lower. The different hydrodynamic regime, with a constant current directed SW, which deviates around the cape towards E, is responsible for such morphostructural heterogeneity, with the site of the Serpentara Island being the most exposed to a constant unidirectional and strong current. We can associate current velocity with specific rhodolith morphotypes. The morphostructural definition of the heterogeneity of rhodoliths across large beds must be considered for appropriate management policies. Full article

(This article belongs to the Special Issue Structure and Biodiversity of Rhodolith Seabeds)

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16 pages, 5630 KiB

Open AccessEditor’s ChoiceArticle

Unrecognized Ant Megadiversity in Monsoonal Australia: Diversity and Its Distribution in the Hyperdiverse Monomorium nigrius Forel Group

by Alan N. Andersen, François Brassard and Benjamin D. Hoffmann

Diversity 2022, 14(1), 46; https://doi.org/10.3390/d14010046 - 11 Jan 2022

Cited by 9 | Viewed by 3959

Abstract

We document diversity and its distribution within the hyperdiverse Monomorium nigrius Forel group of the Australian monsoonal tropics, an unrecognized global centre of ant diversity. The group includes a single described species, but several distinct morphotypes each with multiple clearly recognizable taxa are [...] Read more.

We document diversity and its distribution within the hyperdiverse Monomorium nigrius Forel group of the Australian monsoonal tropics, an unrecognized global centre of ant diversity. The group includes a single described species, but several distinct morphotypes each with multiple clearly recognizable taxa are known. Our analysis is based on 401 CO1-sequenced specimens collected from throughout the Australian mainland but primarily in the monsoonal north and particularly from four bioregions: the Top End (northern third) of the Northern Territory (NT), the Sturt Plateau region of central NT, the Kimberley region of far northern Western Australia, and far North Queensland. Clade structure in the CO1 tree is highly congruent with the general morphotypes, although most morphotypes occur in multiple clades and are therefore shown as polyphyletic. We recognize 97 species among our sequenced specimens, and this is generally consistent (if not somewhat conservative) with PTP analyses of CO1 clustering. Species turnover is extremely high both within and among bioregions in monsoonal Australia, and the monsoonal fauna is highly distinct from that in southern Australia. We estimate that the M. nigrius group contains well over 200 species in monsoonal Australia, and 300 species overall. Our study provides further evidence that monsoonal Australia should be recognized as a global centre of ant diversity. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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8 pages, 602 KiB

Open AccessEditor’s ChoiceCommunication

Underwater Photogrammetry Captures the Initial Recovery of a Coral Reef at Lalo Atoll

by Atsuko Fukunaga, Kailey H. Pascoe, Ashley R. Pugh, Randall K. Kosaki and John H. R. Burns

Diversity 2022, 14(1), 39; https://doi.org/10.3390/d14010039 - 8 Jan 2022

Cited by 11 | Viewed by 3159

Abstract

Recovery of coral reefs after physical damage sustained from storm events can be affected by various factors. Here, we examined the initial recovery of a coral reef at the southern end of uninhabited Lalo Atoll of Papahānaumokuākea Marine National Monument after its complete [...] Read more.

Recovery of coral reefs after physical damage sustained from storm events can be affected by various factors. Here, we examined the initial recovery of a coral reef at the southern end of uninhabited Lalo Atoll of Papahānaumokuākea Marine National Monument after its complete destruction by Hurricane Walaka in 2018. While the site was still mostly (98%) covered by a mixture of rubble and sand, surveys utilizing underwater photogrammetry allowed for detailed quantitative assessments of benthic cover and confirmed colonization of coral (Pocillopora meandrina and Porites lobata), macroalgae and sponges. The proportion of sand in the rubble–sand mixture also decreased from the level observed in 2019. Visual fish surveys confirmed the presence of 35 reef fish species, a large increase from no reef fish in 2019, despite the low biotic benthic cover. Overall, the colonization of benthic organisms and the return of reef fish, which is potentially supported by the benthos and cryptofauna in the rubble bed, offer positive signs of reef recovery. The photogrammetric surveys in the present study captured the subtle changes in the benthic cover and provided us with a procedure to continue monitoring the succession of the site. Continuous monitoring of the site should reveal whether the reef returns to the original state of Acropora coral dominance or progresses towards a coral assemblage with a different composition. Full article

(This article belongs to the Topic Technological Innovation to Support Reef Research and Conservation)
(This article belongs to the Section Marine Diversity)

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21 pages, 2864 KiB

Open AccessEditor’s ChoiceArticle

Aquatic Macrophyte Vegetation Promotes Taxonomic and Functional Diversity of Odonata Assemblages in Intermittent Karst Rivers in the Mediterranean

by Marina Vilenica, Fran Rebrina, Renata Matoničkin Kepčija, Vedran Šegota, Mario Rumišek, Lea Ružanović and Andreja Brigić

Diversity 2022, 14(1), 31; https://doi.org/10.3390/d14010031 - 4 Jan 2022

Cited by 19 | Viewed by 3687

Abstract

Assemblages of adult Odonata were studied in four intermittent karst rivers encompassing macrophyte-rich (MRH) and macrophyte-poor habitats (MPH) in southern Europe, where temporary lotic habitats are the predominant freshwater type but are still understudied. With a total of 25 recorded species, the studied [...] Read more.

Assemblages of adult Odonata were studied in four intermittent karst rivers encompassing macrophyte-rich (MRH) and macrophyte-poor habitats (MPH) in southern Europe, where temporary lotic habitats are the predominant freshwater type but are still understudied. With a total of 25 recorded species, the studied habitats support species-rich Odonata assemblages, as already shown for intermittent rivers in the Mediterranean. Aquatic macrophyte abundance, conductivity, and water velocity are the most significant determinants of Odonata assemblages in the studied IRES. MRH promote higher Odonata abundance and the taxonomic and functional diversity of their assemblages compared to the MPH. Odonata assemblages in MRH are characterized by higher values of body size and a higher share of species preferring lentic and temporary hydrological conditions. Moreover, their assemblages are characterized by various patterns of nymphal development and drought resilience strategies. In contrast, MPH are preferred by lotic species, with nymphal development all year round and with no specific drought-resisting strategies. Our results contribute to the knowledge of diversity and ecological requirements of dragonflies and damselflies in IRES habitats, which could provide scientific background for future conservation activities and bioassessment protocols of such habitats and their biota. Full article

(This article belongs to the Special Issue Aquatic Insects: Biodiversity, Ecology and Conservation Challenges)

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15 pages, 436 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Improving Taxonomic Practices and Enhancing Its Extensibility—An Example from Araneology

by Jason E. Bond, Rebecca L. Godwin, Jordan D. Colby, Lacie G. Newton, Xavier J. Zahnle, Ingi Agnarsson, Chris A. Hamilton and Matjaž Kuntner

Diversity 2022, 14(1), 5; https://doi.org/10.3390/d14010005 - 23 Dec 2021

Cited by 23 | Viewed by 6628

Abstract

Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely [...] Read more.

Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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12 pages, 1277 KiB

Open AccessEditor’s ChoiceReview

Epibiotic Communities of Common Crab Species in the Coastal Barents Sea: Biodiversity and Infestation Patterns

by Alexander G. Dvoretsky and Vladimir G. Dvoretsky

Diversity 2022, 14(1), 6; https://doi.org/10.3390/d14010006 - 23 Dec 2021

Cited by 30 | Viewed by 7521

Abstract

Crabs are important ecosystem engineers in marine habitats worldwide. Based on long-term data, we analyzed the species composition and infestation indices of epibionts and symbionts colonizing the great spider crab, Hyas araneus, and two lithodid crabs—the northern stone crab, Lithodes maja, [...] Read more.

Crabs are important ecosystem engineers in marine habitats worldwide. Based on long-term data, we analyzed the species composition and infestation indices of epibionts and symbionts colonizing the great spider crab, Hyas araneus, and two lithodid crabs—the northern stone crab, Lithodes maja, and the red king crab, Paralithodes camtschaticus—in the coastal zone of the Barents Sea. The epibiotic communities found on great spider crabs were closer to northern stone crabs (33%) compared to red king crabs (25%). The prevalence of mobile symbionts (amphipods, Ischyrocerus, and polychaetes, Harmothoe) and common epibionts, such as barnacles and hydrozoans, was low on great spider crabs and high on the body and in the gills of lithodid crabs. Epiphytes were abundant on great spider crabs but not present on both species of lithodid crabs. Egg symbionts found on H. araneus and P. camtschaticus do not affect their local populations. Differences in the fouling communities found on the three crab species are associated with host size range, surface properties of their carapaces, and behavior patterns. Full article

(This article belongs to the Special Issue Ecology and Management of Crab Species: Recent Advances and New Challenges)

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11 pages, 1927 KiB

Open AccessEditor’s ChoiceArticle

Microbiome Changes of Endemic Lake Baikal Sponges during Bleaching Syndrome Development

by Valeria Itskovich, Oxana Kaluzhnaya, Olga Glyzina, Ragothaman Prathiviraj, George Seghal Kiran and Joseph Selvin

Diversity 2021, 13(12), 653; https://doi.org/10.3390/d13120653 - 8 Dec 2021

Cited by 5 | Viewed by 3179

Abstract

The sponge (Porifera) microbiome is an indicator of both natural and anthropogenic stressors. Studying Baikal sponge microbial communities could help reveal if there is a connection between bacterial symbionts and a mass sponge bleaching event that was recently detected; 16S rRNA sequencing was [...] Read more.

The sponge (Porifera) microbiome is an indicator of both natural and anthropogenic stressors. Studying Baikal sponge microbial communities could help reveal if there is a connection between bacterial symbionts and a mass sponge bleaching event that was recently detected; 16S rRNA sequencing was performed among healthy and diseased freshwater sponges of Lubomirskia baikalensis and Baikalospongia intermedia, which were collected from Lake Baikal, Russia. A phylum-based taxonomic classification showed that Chlorophyta, Acidobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria were most abundant across samples. When comparing healthy and diseased L. baikalensis samples, large variations in microbial composition were found at the phylum level. Comparative analyses, which were performed for the first time for B. intermedia, showed a decrease in Chlorophyta (unicellular green algae) and an increase in Bacteroidetes and Cyanobacteria in diseased specimens. At the genus level, the Opitutus (Verrucomicrobia), Planctomyces, and Nitrospira content increased in all diseased sponges, which reflected a general tendency toward an increase in Cyanobacteria in diseased sponges. Comparative analysis of the diseased and healthy sponge metagenomes showed that diseased sponges underwent various nonspecific changes in bacterial composition. The bacterial community composition is probably influenced by sponge type and degree of disease affection. Full article

(This article belongs to the Special Issue Selected Papers from 1st International Electronic Conference on Biological Diversity, Ecology, and Evolution (BDEE 2021))

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18 pages, 2968 KiB

Open AccessEditor’s ChoiceArticle

Biogeography of Long-Jawed Spiders Reveals Multiple Colonization of the Caribbean

by Klemen Čandek, Ingi Agnarsson, Greta J. Binford and Matjaž Kuntner

Diversity 2021, 13(12), 622; https://doi.org/10.3390/d13120622 - 26 Nov 2021

Cited by 8 | Viewed by 3706

Abstract

Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested [...] Read more.

Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested this prediction on long-jawed spiders (Tetragnatha) of the Caribbean archipelago using phylogenies from a total of 318 individuals delineated into 54 putative species. Our results support a Tetragnatha monophyly (within our sampling) but reject the monophyly of the Caribbean lineages, where we found low endemism yet high diversity. The reconstructed biogeographic history detects a potential early overwater colonization of the Caribbean, refuting an ancient vicariant origin of the Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, the results imply multiple colonization events to and from the Caribbean from the mid-Eocene to late-Miocene. Among arachnids, Tetragnatha uniquely comprises both excellently and poorly dispersing species. A direct test of the IDM would require consideration of three categories of dispersers; however, long-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes. A taxon such as Tetragnatha, one that readily undergoes evolutionary changes in dispersal propensity, can be referred to as a ‘dynamic disperser’. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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46 pages, 4086 KiB

Open AccessEditor’s ChoiceArticle

Italian Vascular Flora: New Findings, Updates and Exploration of Floristic Similarities between Regions

by Adriano Stinca, Carmelo Maria Musarella, Leonardo Rosati, Valentina Lucia Astrid Laface, Wolfgang Licht, Emanuele Fanfarillo, Robert Philipp Wagensommer, Gabriele Galasso, Simonetta Fascetti, Assunta Esposito, Tiberio Fiaschi, Gianluca Nicolella, Giuseppina Chianese, Giampiero Ciaschetti, Giovanni Salerno, Paola Fortini, Romeo Di Pietro, Enrico Vito Perrino, Claudia Angiolini, Leopoldo De Simone and Giacomo Mei Show full author list Hide full author list

Diversity 2021, 13(11), 600; https://doi.org/10.3390/d13110600 - 21 Nov 2021

Cited by 57 | Viewed by 8505

Abstract

The tradition of floristic studies in Italy has made it possible to obtain a good knowledge of plant diversity both on a national and regional scale. However, the lack of knowledge for some areas, advances in plant systematics and human activities related to [...] Read more.

The tradition of floristic studies in Italy has made it possible to obtain a good knowledge of plant diversity both on a national and regional scale. However, the lack of knowledge for some areas, advances in plant systematics and human activities related to globalization, highlight the need for further studies aimed at improving floristic knowledge. In this paper, based on fieldwork and herbaria and literature surveys, we update the knowledge on the Italian vascular flora and analyze the floristic similarities between the administrative regions. Four taxa, all exotic, were recorded for the first time in Italy and Europe. In detail, Elaeodendron croceum, Kalanchoë blossfeldiana, and Sedum spathulifolium var. spathulifolium were found as casual aliens, while Oxalis brasiliensis was reported as historical record based on some herbarium specimens. Furthermore, Kalanchoë laxiflora was confirmed as a casual alien species for Italy and Europe. Status changes for some taxa were proposed at both national and regional levels, as well as many taxa were reported as new or confirmed at the regional level. Currently the Italian vascular flora comprises 9150 taxa of which 7547 are native (of which 1598 are Italian endemics) and 1603 are exotic at the national level. The multivariate analysis of updated floristic data on a regional scale showed a clear distribution along the latitudinal gradient, in accordance with the natural geographical location of the regions in Italy. This pattern of plants distribution was not affected by the introduction of alien species. Despite some taxonomic and methodological issues which are still open, the data obtained confirm the important role of floristic investigations in the field and in herbaria, as well as the collaborative approach among botanists, in order to improve the knowledge of the Italian and European vascular flora. Full article

(This article belongs to the Special Issue Biodiversity and Conservation of Vascular Flora)

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11 pages, 3180 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Evolution of Beak and Feather Disease Virus across Three Decades of Conservation Intervention for Population Recovery of the Mauritius Parakeet

by Deborah J. Fogell, Simon Tollington, Vikash Tatayah, Sion Henshaw, Houshna Naujeer, Carl Jones, Claire Raisin, Andrew Greenwood and Jim J. Groombridge

Diversity 2021, 13(11), 584; https://doi.org/10.3390/d13110584 - 16 Nov 2021

Cited by 10 | Viewed by 4529

Abstract

Emerging infectious diseases (EIDs) are key contributors to the current global biodiversity crisis. Psittaciformes (parrots) are one of the most vulnerable avian taxa and psittacine beak and feather disease (PBFD) is the most common viral disease in wild parrots. PBFD is caused by [...] Read more.

Emerging infectious diseases (EIDs) are key contributors to the current global biodiversity crisis. Psittaciformes (parrots) are one of the most vulnerable avian taxa and psittacine beak and feather disease (PBFD) is the most common viral disease in wild parrots. PBFD is caused by the beak and feather disease virus (BFDV), which belongs to the Circoviridae family and comprises a circular, single-stranded DNA genome. BFDV is considered to have spread rapidly across the world and, in 2005, an outbreak of PBFD was documented in the recovering population of the Mauritius parakeet (Alexandrinus eques). The Mauritius parakeet was once the world’s rarest parrot and has been successfully recovered through 30 years of intensive conservation management. Molecular surveillance for the prevalence of BFDV was carried out across a 24-year sample archive spanning the period from 1993 to 2017, and DNA sequencing of positive individuals provided an opportunity to assess patterns of phylogenetic and haplotype diversity. Phylogenetic analyses show variation in the extent of viral diversification within the replicase protein (Rep). Timeseries of BFDV prevalence and number of haplotypes reveal that two subsequent waves of infection occurred in 2010/2011 and 2013/2014 following the initial outbreak in 2005. Continued disease surveillance to determine the frequency and intensity of subsequent waves of infection may benefit future translocation/reintroduction planning. The continued growth of the Mauritius parakeet population despite the presence of BFDV bodes well for its long-term persistence. Full article

(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)

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20 pages, 5346 KiB

Open AccessEditor’s ChoiceArticle

Algae and Cyanobacteria Diversity and Bioindication of Long-Term Changes in the Hula Nature Reserve, Israel

by Sophia Barinova and Alla Alster

Diversity 2021, 13(11), 583; https://doi.org/10.3390/d13110583 - 14 Nov 2021

Cited by 5 | Viewed by 3095

Abstract

Lake Hula, the core of one of the most extensive wetland complexes in the Eastern Mediterranean, was drained in 1951–1958. However, about 350 hectares of papyrus marshes were allocated in the southwestern part of the previous lake and became the Hula Nature Reserve [...] Read more.

Lake Hula, the core of one of the most extensive wetland complexes in the Eastern Mediterranean, was drained in 1951–1958. However, about 350 hectares of papyrus marshes were allocated in the southwestern part of the previous lake and became the Hula Nature Reserve status, the first of two wetlands in Israel included in the Ramsar List of Wetlands of International Importance. The list of algae and cyanobacteria species of Lake Hula was compiled by us for the first time based on data from publications of 1938–1958, as well as our research in the Hula Nature Reserve, obtained within the framework of the monitoring program for 2007–2013. The list includes 225 species and intraspecies of algae and cyanobacteria belonging to eight phyla. The dynamics of the species richness of algae and cyanobacteria flora for 1938–2013 are shown. Species-bioindicators of water quality have been identified, and the change in their composition by ecological groups for a period of about a hundred years has been shown. Based on the species richness of algae communities, water quality indices were calculated with particular attention to changes in trophic status during the study period. The algae flora of Lake Hula and Hula Nature Reserve was found to be similar, but bioindication has revealed an increase in salinity and organic pollution in recent years. Full article

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33 pages, 5076 KiB

Open AccessFeature PaperEditor’s ChoiceReview

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

by Prashant P. Sharma, Jesús A. Ballesteros and Carlos E. Santibáñez-López

Diversity 2021, 13(11), 568; https://doi.org/10.3390/d13110568 - 6 Nov 2021

Cited by 27 | Viewed by 9400

Abstract

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, [...] Read more.

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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18 pages, 851 KiB

Open AccessEditor’s ChoiceArticle

The Natural Capital Value of the Seagrass Posidonia oceanica in the North-Western Mediterranean

by Ilaria Rigo, Chiara Paoli, Giulia Dapueto, Christine Pergent-Martini, Gerard Pergent, Alice Oprandi, Monica Montefalcone, Carlo Nike Bianchi, Carla Morri and Paolo Vassallo

Diversity 2021, 13(10), 499; https://doi.org/10.3390/d13100499 - 15 Oct 2021

Cited by 21 | Viewed by 4800

Abstract

Posidonia oceanica is an endemic Mediterranean seagrass used as a ‘biological quality element’ in monitoring programmes of the EU Water Framework Directive, providing information about coastal ecosystems status. The regression of P. oceanica meadows caused a growing interest among policy makers to assess [...] Read more.

Posidonia oceanica is an endemic Mediterranean seagrass used as a ‘biological quality element’ in monitoring programmes of the EU Water Framework Directive, providing information about coastal ecosystems status. The regression of P. oceanica meadows caused a growing interest among policy makers to assess the value of seagrasses and to increase their protection. An evaluation of P. oceanica meadows located in the Ligurian-Provençal basin (NW Mediterranean) through a biophysical approach is here developed. Six meadows located in Liguria (Italy) and Corsica (France) were investigated by applying the emergy analysis to assess the natural capital (NC) stocked by leaves and rhizomes components. Results highlighted the importance of carrying out an analysis of the variations in the NC value in both components: rhizomes defined the growth stage and the capacity to store NC over time; leaves provided information on the variability due to disturbances in the water column. Emergy analysis allows defining the NC, in terms of resources needed to maintain the meadows and to provide services to coastal communities. This research is inserted into the effort of incorporating the NC evaluation into marine planning and decision making to achieve nature conservation goals, while ensuring the sustainable exploitation of marine resources. Full article

(This article belongs to the Special Issue Biodiversity Conservation in Mediterranean Sea)

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19 pages, 7208 KiB

Open AccessEditor’s ChoiceArticle

FloCan—A Revised Checklist for the Flora of the Canary Islands

by Carl Beierkuhnlein, Anna Walentowitz and Walter Welss

Diversity 2021, 13(10), 480; https://doi.org/10.3390/d13100480 - 29 Sep 2021

Cited by 24 | Viewed by 7150

Abstract

The flora of the Canary Islands has been subject to botanical studies for more than 200 years. Several biodiversity databases are available for the archipelago. However, there are various drivers of change in real biodiversity and the knowledge about it constantly needs to [...] Read more.

The flora of the Canary Islands has been subject to botanical studies for more than 200 years. Several biodiversity databases are available for the archipelago. However, there are various drivers of change in real biodiversity and the knowledge about it constantly needs to be kept track of. Island floras are both: exposed to species loss and to species introductions, either through natural processes or by anthropogenic drivers. Additionally, the evolution of endemic plant species plays a substantial role. Endemic species are sensitive to population decline due to small population sizes and possible low competitiveness against incoming species. Additionally, there is continuous progress in systematics and taxonomy. Species names or their taxonomic attribution can be modified. Here, we check published plant lists for the Canary Islands and literature, and compile currently accepted taxa into an updated checklist. For this FloCan checklist, several sources were compiled, checked for completeness and quality, and their taxonomy was updated. We illustrate how far plant names are considered in regional or global databases. This work represents the current state of knowledge on Canary Island plant diversity, including introduced and recently described taxa. We provide a comprehensive and updated basis for biogeographical and macroecological studies. Particularly, the number of non-native species is being extended substantially. The adaptation to standard international nomenclature supports integration into large-scale studies. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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16 pages, 1261 KiB

Open AccessEditor’s ChoiceArticle

Exploring Plant Functional Diversity and Redundancy of Mediterranean High-Mountain Habitats in the Apennines

by Alessandro Bricca, Maria Laura Carranza, Marco Varricchione, Maurizio Cutini and Angela Stanisci

Diversity 2021, 13(10), 466; https://doi.org/10.3390/d13100466 - 26 Sep 2021

Cited by 15 | Viewed by 3706

Abstract

We analyzed plant functional diversity (FD) and redundancy (FR) in Mediterranean high-mountain communities to explore plant functional patterns and assembly rules. We focused on three above-ground plant traits: plant height (H), a good surrogate of competition for light strategies, and specific leaf area [...] Read more.

We analyzed plant functional diversity (FD) and redundancy (FR) in Mediterranean high-mountain communities to explore plant functional patterns and assembly rules. We focused on three above-ground plant traits: plant height (H), a good surrogate of competition for light strategies, and specific leaf area (SLA) and leaf dry matter content (LDMC), useful indicators of resource exploitation functional schemes. We used the georeferenced vegetation plots and field-measured plant functional traits of four widely spread vegetation types growing on screes, steep slopes, snowbeds and ridges, respectively. We calculated Rao’s FD and FR followed by analysis of standardized effect size, and compared FD and FR community values using ANOVA and the Tukey post hoc test. Assemblage rules varied across plant communities and traits. The High FR_H registered on snowbeds and ridges is probably linked to climatic filtering processes, while the high FD_H and low FD_SLA and FD_LDMC on steep slopes could be related with underlying competition mechanisms. The absence of FD patterns in scree vegetation pinpoint random assembly processes which are typical of highly unstable or disturbed ecosystems. Improved knowledge about the deterministic/stochastic processes shaping species coexistence on high mountain ecosystems should help researchers to understand and predict vegetation vulnerability to environmental changes. Full article

(This article belongs to the Special Issue Diversity, Ecology and Conservation of Alpine Plants)

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21 pages, 1019 KiB

Open AccessEditor’s ChoiceArticle

Concurrent Butterfly, Bat and Small Mammal Monitoring Programmes Using Citizen Science in Catalonia (NE Spain): A Historical Review and Future Directions

by Ignasi Torre, Adrià López-Baucells, Constantí Stefanescu, Lídia Freixas, Carles Flaquer, Carme Bartrina, Alba Coronado, David López-Bosch, Maria Mas, Sílvia Míguez, Joaquim Muñoz, Ferran Páramo, Xavier Puig-Montserrat, Carme Tuneu-Corral, Andreu Ubach and Antoni Arrizabalaga

Diversity 2021, 13(9), 454; https://doi.org/10.3390/d13090454 - 21 Sep 2021

Cited by 22 | Viewed by 4359

Abstract

The Biodiversity and Bioindicators research group (BiBIO), based at the Natural Sciences Museum of Granollers, has coordinated four long-term faunal monitoring programmes based on citizen science over more than two decades in Catalonia (NE Spain). We summarize the historical progress of these programmes, [...] Read more.

The Biodiversity and Bioindicators research group (BiBIO), based at the Natural Sciences Museum of Granollers, has coordinated four long-term faunal monitoring programmes based on citizen science over more than two decades in Catalonia (NE Spain). We summarize the historical progress of these programmes, describing their main conservation outputs, the challenges overcome, and future directions. The Catalan Butterfly Monitoring Scheme (CBMS) consists of a network of nearly 200 recording sites where butterfly populations have been monitored through visual censuses along transects for nearly three decades. This programme provides accurate temporal and spatial changes in the abundance of butterflies and relates them to different environmental factors (e.g., habitat and weather conditions). The Bat Monitoring Programme has progressively evolved to include passive acoustic monitoring protocols, as well as bat box-, underground- and river-bat surveys, and community ecological indices have been developed to monitor bat responses at assemblage level to both landscape and climatic changes. The Monitoring of common small mammals in Spain (SEMICE), a common small mammal monitoring programme with almost 80 active live-trapping stations, provides information to estimate population trends and has underlined the relevance of small mammals as both prey (of several predators) and predators (of insect forest pests). The Dormouse Monitoring Programme represents the first monitoring programme in Europe using specific nest boxes for the edible dormouse, providing information about biological and demographic data of the species at the southern limit of its distribution range. The combination and complementarity of these monitoring programmes provide crucial data to land managers to improve the understanding of conservation needs and develop efficient protection laws. Full article

(This article belongs to the Special Issue Citizen Science for Biodiversity Conservation: Harnessing the Power of the Public to Address Wicked Conservation Problems)

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24 pages, 7323 KiB

Open AccessEditor’s ChoiceArticle

Taxonomy of the Cryptocephalus heraldicus Group (Coleoptera: Chrysomelidae, Cryptocephalinae) from China

by Wenyuan Duan, Fengyan Wang and Hongzhang Zhou

Diversity 2021, 13(9), 451; https://doi.org/10.3390/d13090451 - 20 Sep 2021

Cited by 3 | Viewed by 3976

Abstract

This is a study on the leaf beetle subgenus Cryptocephalus Geoffroy, 1762 from China, with the particular emphasis upon the species-group classification of the subgenus and the taxonomy of the Cryptocephalus heraldicus species group. A new key is compiled to all the species [...] Read more.

This is a study on the leaf beetle subgenus Cryptocephalus Geoffroy, 1762 from China, with the particular emphasis upon the species-group classification of the subgenus and the taxonomy of the Cryptocephalus heraldicus species group. A new key is compiled to all the species groups found in China. Four new species are described from China: Cryptocephalus (Cryptocephalus) biordopunctatus sp. nov. from Yunnan, C. hani sp. nov. from Shanxi, Hubei, Shaanxi and Gansu, C. incisodentatus sp. nov. from Sichuan and Yunnan, and C. nigroflavusiventerus sp. nov. from Yunnan. Three species are found for the first time in China: C. lacosus Pic, 1922, C. nigriceps Allard, 1891 and C. rajah Jacoby, 1908. The species C. nigrolimbatus Jacoby, 1890 is transferred from the subgenus Burlinius Lopatin to this subgenus and assigned to the Cryptocephalus heraldicus group. The species number of this group is now 30 in total according to our result of taxonomic review. A key to all the mainland China species of this species group is provided as well as high quality color images and line drawings of adult habitus, aedeagus, and other important structures. All the types of the new species are deposited in the collection of Institute of Zoology, Chinese Academy of Sciences (IZ-CAS). Full article

(This article belongs to the Special Issue Diversity and Evolution of Coleoptera)

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19 pages, 3285 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

The Role of Small Lowland Patches of Exotic Forests as Refuges of Rare Endemic Azorean Arthropods

by Noelline Tsafack, Simone Fattorini, Mário Boieiro, François Rigal, Alejandra Ros-Prieto, Maria Teresa Ferreira and Paulo A. V. Borges

Diversity 2021, 13(9), 443; https://doi.org/10.3390/d13090443 - 16 Sep 2021

Cited by 19 | Viewed by 4005

Abstract

Islands have been disproportionately affected by the current biodiversity crisis. In island biotas, one of the most recurrent anthropic alterations is species introduction. Invasion of exotic species may represent a major threat for island biotas, because invasive species may change species composition and [...] Read more.

Islands have been disproportionately affected by the current biodiversity crisis. In island biotas, one of the most recurrent anthropic alterations is species introduction. Invasion of exotic species may represent a major threat for island biotas, because invasive species may change species composition and simplify community dynamics. We investigated diversity patterns of native and introduced species in native and exotic forests of Terceira Island (Azores, Portugal) by using diversity profiles based on Hill numbers. Use of diversity profiles allows for a complete characterization of the community diversity because they combine information on species richness, rarity, and dominance. We found that native forest remnants are crucial for the maintenance of endemic Azorean arthropod diversity. However, we also found that some lowland patches of exotic forests can sustain populations of rare endemic species. Our findings reinforce the importance of the few and small remnants of native forests, which are a pillar to the conservation of Azorean endemic arthropods. However, areas occupied by exotic forests, whether they are large and contiguous or small and isolated, close to native forests, or embedded in a matrix of agriculture activities, can also play a role in the conservation of native species, including endemics. Full article

(This article belongs to the Collection Evolution and Extinctions on Islands)

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20 pages, 852 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

by Nicola Tommasi, Andrea Ferrari, Massimo Labra, Andrea Galimberti and Paolo Biella

Diversity 2021, 13(9), 437; https://doi.org/10.3390/d13090437 - 10 Sep 2021

Cited by 16 | Viewed by 4941

Abstract

Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological [...] Read more.

Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable. Full article

(This article belongs to the Special Issue Advances in HTS-Based Identification of Species and Ecological Interactions)

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12 pages, 2914 KiB

Open AccessFeature PaperEditor’s ChoiceReview

The Number and Distribution of Introduced and Naturalized Parrots

by Carlos E. Calzada Preston and Stephen Pruett-Jones

Diversity 2021, 13(9), 412; https://doi.org/10.3390/d13090412 - 29 Aug 2021

Cited by 33 | Viewed by 6703

Abstract

Parrots have been transported and traded by humans for at least the last 2000 years and this trade continues unabated today. This transport of species has involved the majority of recognized parrot species (300+ of 382 species). Inevitably, some alien species either escape [...] Read more.

Parrots have been transported and traded by humans for at least the last 2000 years and this trade continues unabated today. This transport of species has involved the majority of recognized parrot species (300+ of 382 species). Inevitably, some alien species either escape captivity or are released and may establish breeding populations in the novel area. With respect to parrots, established but alien populations are becoming common in many parts of the world. In this review, we attempt to estimate the total number of parrot species introduced into the wild in non-native areas and assess how many of these have self-sustaining breeding populations. Based the public databases GAVIA, eBird, and iNaturalist, 166 species of Psittaciformes have been introduced (seen in the wild) into 120 countries or territories outside of the native range. Of these, 60 species are naturalized, and an additional 11 species are breeding in at least one country outside of their native range (86 countries or territories total). The Rose-ringed Parakeet (Psittacula krameri) and Monk Parakeet (Myiopsitta monachus) are the most widely distributed and successful of the introduced parrots, being naturalized in 47 and 26 countries or territories, respectively. Far and away, the United States and its territories support the greatest number of naturalized parrots, with 28 different species found in either the continental US, or Hawaii or Puerto Rico. Naturalized species as well as urbanized native species of parrots are likely to continue increasing in numbers and geographical range, and detailed studies are needed to both confirm species richness in each area as well mitigate potential ecological impacts and conflicts with humans. Full article

(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)

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5 pages, 529 KiB

Open AccessEditor’s ChoiceBrief Report

Hitchhiking Exotic Clam: Dreissena polymorpha (Pallas, 1771) Transported via the Ornamental Plant Trade

by Jiří Patoka and Barbora Patoková

Diversity 2021, 13(9), 410; https://doi.org/10.3390/d13090410 - 27 Aug 2021

Cited by 15 | Viewed by 2646

Abstract

Ornamental aquaculture is one of the main sources of non-native species worldwide. Unintentionally transported “hitchhiking” organisms have been previously recorded; although most of these species are transported from tropical regions, here we report on the first accidental transport of the zebra mussel ( [...] Read more.

Ornamental aquaculture is one of the main sources of non-native species worldwide. Unintentionally transported “hitchhiking” organisms have been previously recorded; although most of these species are transported from tropical regions, here we report on the first accidental transport of the zebra mussel (Dreissena polymorpha) in a shipment of ornamental Aegagropila linnaei (Chlorophyta) from Russia to the Czech Republic. This invasive mussel is listed on the national blacklist of alien species in the Czech Republic and can be easily released in outdoor garden ponds together with A. linnaei. Since the Czech Republic is known to be a gateway for aquatic ornamental species from a European perspective, re-export to other European countries is also possible. Thus, the spread of D. polymorpha via this pathway cannot be excluded. This finding should be of importance to conservationists, traders, decision-makers and other stakeholders. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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36 pages, 2556 KiB

Open AccessEditor’s ChoiceReview

Retinoic Acid Signaling in Vertebrate Hindbrain Segmentation: Evolution and Diversification

by Alice M. H. Bedois, Hugo J. Parker and Robb Krumlauf

Diversity 2021, 13(8), 398; https://doi.org/10.3390/d13080398 - 23 Aug 2021

Cited by 7 | Viewed by 7199

Abstract

In metazoans, Hox genes are key drivers of morphogenesis. In chordates, they play important roles in patterning the antero-posterior (A-P) axis. A crucial aspect of their role in axial patterning is their collinear expression, a process thought to be linked to their response [...] Read more.

In metazoans, Hox genes are key drivers of morphogenesis. In chordates, they play important roles in patterning the antero-posterior (A-P) axis. A crucial aspect of their role in axial patterning is their collinear expression, a process thought to be linked to their response to major signaling pathways such as retinoic acid (RA) signaling. The amplification of Hox genes following major events of genome evolution can contribute to morphological diversity. In vertebrates, RA acts as a key regulator of the gene regulatory network (GRN) underlying hindbrain segmentation, which includes Hox genes. This review investigates how the RA signaling machinery has evolved and diversified and discusses its connection to the hindbrain GRN in relation to diversity. Using non-chordate and chordate deuterostome models, we explore aspects of ancient programs of axial patterning in an attempt to retrace the evolution of the vertebrate hindbrain GRN. In addition, we investigate how the RA signaling machinery has evolved in vertebrates and highlight key examples of regulatory diversification that may have influenced the GRN for hindbrain segmentation. Finally, we describe the value of using lamprey as a model for the early-diverged jawless vertebrate group, to investigate the elaboration of A-P patterning mechanisms in the vertebrate lineage. Full article

(This article belongs to the Special Issue Evolution, Development, and Diversification of Vertebrates)

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27 pages, 17708 KiB

Open AccessEditor’s ChoiceArticle

Integrative Descriptions of Two New Tardigrade Species along with the New Record of Mesobiotus skorackii Kaczmarek et al., 2018 from Canada

by Pushpalata Kayastha, Milena Roszkowska, Monika Mioduchowska, Magdalena Gawlak and Łukasz Kaczmarek

Diversity 2021, 13(8), 394; https://doi.org/10.3390/d13080394 - 22 Aug 2021

Cited by 14 | Viewed by 5022

Abstract

Two new tardigrade species from a moss sample collected in Canada, one representing Macrobiotus hufelandi complex and the second one belonging to the genus Bryodelphax, are described. Integrative analysis was undertaken based on morphological and morphometric data (using both light and scanning [...] Read more.

Two new tardigrade species from a moss sample collected in Canada, one representing Macrobiotus hufelandi complex and the second one belonging to the genus Bryodelphax, are described. Integrative analysis was undertaken based on morphological and morphometric data (using both light and scanning electron microscopy (SEM)) combined with multilocus molecular analysis (nuclear sequences, i.e., 18S rRNA, 28S rRNA and ITS-2 as well as mitochondrial COI barcode sequences). Based on COI sequences, Macrobiotus birendrai sp. nov. is most similar to Mac. canaricus (p-distance 17%), whereas Bryodelphax mareki sp. nov. is most similar to Bry. parvulus (p-distance 16%). Both species differ also from their congeners in some morphological and morphometric characters of adults and/or details of egg chorion. Additionally, a large population of Mesobiotus skorackii was found in the sample and this is the first report of this species outside its terra typica in Kirghizia. The original description of this species was prepared based solely on the morphology and morphometry, therefore, here we provide updated data for this species enclosing morphometric and molecular data for the Canadian population. Full article

(This article belongs to the Special Issue Selected Papers from 1st International Electronic Conference on Biological Diversity, Ecology, and Evolution (BDEE 2021))

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24 pages, 7391 KiB

Open AccessEditor’s ChoiceArticle

The Towakkalak System, A Hotspot of Subterranean Biodiversity in Sulawesi, Indonesia

by Louis Deharveng, Cahyo Rahmadi, Yayuk Rahayuningsih Suhardjono and Anne Bedos

Diversity 2021, 13(8), 392; https://doi.org/10.3390/d13080392 - 20 Aug 2021

Cited by 13 | Viewed by 4227

Abstract

The Towakkalak System located in the Maros karst of South Sulawesi is currently the richest of Southeast Asia in obligate subterranean species. It comprises several caves and shafts that give access to the subterranean Towakkalak river as well as many unconnected fossil caves, [...] Read more.

The Towakkalak System located in the Maros karst of South Sulawesi is currently the richest of Southeast Asia in obligate subterranean species. It comprises several caves and shafts that give access to the subterranean Towakkalak river as well as many unconnected fossil caves, stream sinks, and springs located within its footprint. The total length of the caves linked to the active system is 24,319 m and comprises two of the longest caves of Indonesia, Gua Salukkan Kallang and Gua Tanette. Studies of its fauna began in 1985. There are 10 stygobionts and 26 troglobionts that are known from the system. The smaller adjacent system of Saripa has 6 stygobionts and 18 troglobionts, of which 1 and 3, respectively, are absent from Towakkalak. Like all tropical cave inventories, our dataset has limits due to identification uncertainties, gaps in habitat (waters, guano) and taxonomic coverage (micro-crustaceans, mites), sampling methods (pitfall trapping, Karaman–Chappuis), and problems of ecological assignment. A number of additional species are therefore expected to be found in the future. The Towakkalak and Saripa cave systems are included in the Bantimurung-Bulusaraung National Park and are under efficient protection, but parts of the Maros karst outside the park are under serious threat, mainly from quarrying. Full article

(This article belongs to the Special Issue Hotspots of Subterranean Biodiversity)

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14 pages, 775 KiB

Open AccessEditor’s ChoiceArticle

Mires in Europe—Regional Diversity, Condition and Protection

by Franziska Tanneberger, Asbjørn Moen, Alexandra Barthelmes, Edward Lewis, Lera Miles, Andrey Sirin, Cosima Tegetmeyer and Hans Joosten

Diversity 2021, 13(8), 381; https://doi.org/10.3390/d13080381 - 16 Aug 2021

Cited by 56 | Viewed by 13302

Abstract

In spite of the worldwide largest proportional loss of mires, Europe is a continent with important mire diversity. This article analyses the condition and protection status of European mire ecosystems. The overview is based on the system of European mire regions, representing regional [...] Read more.

In spite of the worldwide largest proportional loss of mires, Europe is a continent with important mire diversity. This article analyses the condition and protection status of European mire ecosystems. The overview is based on the system of European mire regions, representing regional variety and ecosystem biodiversity. We combined peatland distribution data with land cover maps of the Copernicus Land Monitoring Service as well as with the World Database on Protected Areas to assess the extent of degraded peatlands and the proportion of peatlands located in protected areas in each European mire region. The total proportion of degraded peatlands in Europe is 25%; within the EU it is 50% (120,000 km²). The proportion of degradation clearly increases from north to south, as does the proportion of peatlands located within protected areas. In more than half of Europe’s mire regions, the target of at least 17% of the area located in protected areas is not met with respect to peatlands. Data quality is discussed and the lessons learned from Europe for peatland conservation are presented. Full article

(This article belongs to the Special Issue Ecology, Biogeography and Evolutionary Biology of Peatlands)

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22 pages, 4635 KiB

Open AccessEditor’s ChoiceArticle

Applying Population Viability Analysis to Inform Genetic Rescue That Preserves Locally Unique Genetic Variation in a Critically Endangered Mammal

by Joseph P. Zilko, Dan Harley, Alexandra Pavlova and Paul Sunnucks

Diversity 2021, 13(8), 382; https://doi.org/10.3390/d13080382 - 16 Aug 2021

Cited by 20 | Viewed by 6147

Abstract

Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland [...] Read more.

Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland population of Leadbeater’s possum from an outbred highland population that would alleviate inbreeding depression and rapidly reach a target population size (N) while maximising the retention of locally unique neutral genetic variation. Using genomic kinship coefficients to model inbreeding in Vortex, we simulated genetic rescue scenarios that included gene pool mixing with genetically diverse highland possums and increased the N from 35 to 110 within ten years. The PVA predicted that the last remaining population of lowland Leadbeater’s possum will be extinct within 23 years without genetic rescue, and that the carrying capacity at its current range is insufficient to enable recovery, even with genetic rescue. Supplementation rates that rapidly increased population size resulted in higher retention (as opposed to complete loss) of local alleles through alleviation of genetic drift but reduced the frequency of locally unique alleles. Ongoing gene flow and a higher N will facilitate natural selection. Accordingly, we recommend founding a new population of lowland possums in a high-quality habitat, where population growth and natural gene exchange with highland populations are possible. We also recommend ensuring gene flow into the population through natural dispersal and/or frequent translocations of highland individuals. Genetic rescue should be implemented within an adaptive management framework, with post-translocation monitoring data incorporated into the models to make updated predictions. Full article

(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)

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15 pages, 2736 KiB

Open AccessEditor’s ChoiceReview

Why Is the Alpine Flora Comparatively Robust against Climatic Warming?

by Christian Körner and Erika Hiltbrunner

Diversity 2021, 13(8), 383; https://doi.org/10.3390/d13080383 - 16 Aug 2021

Cited by 86 | Viewed by 11767

Abstract

The alpine belt hosts the treeless vegetation above the high elevation climatic treeline. The way alpine plants manage to thrive in a climate that prevents tree growth is through small stature, apt seasonal development, and ‘managing’ the microclimate near the ground surface. Nested [...] Read more.

The alpine belt hosts the treeless vegetation above the high elevation climatic treeline. The way alpine plants manage to thrive in a climate that prevents tree growth is through small stature, apt seasonal development, and ‘managing’ the microclimate near the ground surface. Nested in a mosaic of micro-environmental conditions, these plants are in a unique position by a close-by neighborhood of strongly diverging microhabitats. The range of adjacent thermal niches that the alpine environment provides is exceeding the worst climate warming scenarios. The provided mountains are high and large enough, these are conditions that cause alpine plant species diversity to be robust against climatic change. However, the areal extent of certain habitat types will shrink as isotherms move upslope, with the potential areal loss by the advance of the treeline by far outranging the gain in new land by glacier retreat globally. Full article

(This article belongs to the Special Issue Diversity, Ecology and Conservation of Alpine Plants)

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21 pages, 1265 KiB

Open AccessEditor’s ChoiceArticle

Mammoth Cave: A Hotspot of Subterranean Biodiversity in the United States

by Matthew L. Niemiller, Kurt Helf and Rickard S. Toomey

Diversity 2021, 13(8), 373; https://doi.org/10.3390/d13080373 - 12 Aug 2021

Cited by 8 | Viewed by 10851

Abstract

The Mammoth Cave System in the Interior Low Plateau karst region in central Kentucky, USA is a global hotspot of cave-limited biodiversity, particularly terrestrial species. We searched the literature, museum accessions, and database records to compile an updated list of troglobiotic and stygobiotic [...] Read more.

The Mammoth Cave System in the Interior Low Plateau karst region in central Kentucky, USA is a global hotspot of cave-limited biodiversity, particularly terrestrial species. We searched the literature, museum accessions, and database records to compile an updated list of troglobiotic and stygobiotic species for the Mammoth Cave System and compare our list with previously published checklists. Our list of cave-limited fauna totals 49 species, with 32 troglobionts and 17 stygobionts. Seven species are endemic to the Mammoth Cave System and other small caves in Mammoth Cave National Park. The Mammoth Cave System is the type locality for 33 cave-limited species. The exceptional diversity at Mammoth Cave is likely related to several factors, such as the high dispersal potential of cave fauna associated with expansive karst exposures, high surface productivity, and a long history of exploration and study. Nearly 80% of the cave-limited fauna is of conservation concern, many of which are at an elevated risk of extinction because of small ranges, few occurrences, and several potential threats. Full article

(This article belongs to the Special Issue Hotspots of Subterranean Biodiversity)

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17 pages, 327 KiB

Open AccessEditor’s ChoiceReview

Sunscreens’ UV Filters Risk for Coastal Marine Environment Biodiversity: A Review

by Samuele Caloni, Tiziana Durazzano, Giada Franci and Letizia Marsili

Diversity 2021, 13(8), 374; https://doi.org/10.3390/d13080374 - 12 Aug 2021

Cited by 19 | Viewed by 7863

Abstract

Considering the rapid growth of tourism in recent years and the acknowledgement that exposure to solar UV radiation may cause skin cancer, sunscreens have been widely used by beachgoers in recent decades. UV filters contained in sunscreens, however, were recently identified as emerging [...] Read more.

Considering the rapid growth of tourism in recent years and the acknowledgement that exposure to solar UV radiation may cause skin cancer, sunscreens have been widely used by beachgoers in recent decades. UV filters contained in sunscreens, however, were recently identified as emerging pollutants in coastal waters since they accumulate in the marine environment with different adverse effects. In fact, exposure to these components was proven to be toxic to most invertebrate and vertebrate marine species. Some UV filters are linked to the production of significant amounts of reactive oxygen species (ROS), such as hydrogen peroxide, and the release of inorganic micronutrients that may alter the status of coastal habitats. Bioaccumulation and biomagnification have not yet been fully addressed. This review highlights recent progress in research and provides a comprehensive overview of the toxicological and ecotoxicological effects of the most used UV filters both on the abiotic and biotic compartments in different types of coastal areas, to gain a better understanding of the impacts on coastal biodiversity. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

31 pages, 2399 KiB

Open AccessEditor’s ChoiceArticle

The Arthropod Fauna of Oak (Quercus spp., Fagaceae) Canopies in Norway

by Karl H. Thunes, Geir E. E. Søli, Csaba Thuróczy, Arne Fjellberg, Stefan Olberg, Steffen Roth, Carl-C. Coulianos, R. Henry L. Disney, Josef Starý, G. (Bert) Vierbergen, Terje Jonassen, Johannes Anonby, Arne Köhler, Frank Menzel, Ryszard Szadziewski, Elisabeth Stur, Wolfgang Adaschkiewitz, Kjell M. Olsen, Torstein Kvamme, Anders Endrestøl, Sigitas Podenas, Sverre Kobro, Lars O. Hansen, Gunnar M. Kvifte, Jean-Paul Haenni and Louis Boumans Show full author list Hide full author list

Diversity 2021, 13(7), 332; https://doi.org/10.3390/d13070332 - 19 Jul 2021

Cited by 13 | Viewed by 5982

Abstract

(1) We document the invertebrate fauna collected from 24 oak canopies in east and west Norway as a contribution to the Norwegian Biodiversity Information Centre’s ‘The Norwegian Taxonomy Initiative’. (2) A snap-shot inventory of the canopies was recorded by means of emitting a [...] Read more.

(1) We document the invertebrate fauna collected from 24 oak canopies in east and west Norway as a contribution to the Norwegian Biodiversity Information Centre’s ‘The Norwegian Taxonomy Initiative’. (2) A snap-shot inventory of the canopies was recorded by means of emitting a mist of natural pyrethrum into the canopies at night using a petrol-driven fogger and collecting the specimens in butterfly nets spread on the ground under the canopy. (3) Almost the entire catch of more than 6800 specimens was identified to 722 species. Out of 92 species new to the Norwegian fauna, 21 were new to science and, additionally, 15 were new to the Nordic fauna. Diptera alone constituted nearly half of the species represented, with 61 new records (18 new species). Additionally, 24 Hymenoptera (one new species), six oribatid mites (two new species) and one Thysanoptera were new to the Norwegian fauna. (4) Our study emphasizes the importance of the oak tree as a habitat both for a specific fauna and occasional visitors, and it demonstrates that the canopy fogging technique is an efficient way to find the ‘hidden fauna’ of Norwegian forests. The low number of red listed species found reflects how poor the Norwegian insect fauna is still studied. Moreover, the implication of the IUCN red list criteria for newly described or newly observed species is discussed. Full article

(This article belongs to the Special Issue Arthropods Associated with Forest Soil and Wood)

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16 pages, 2401 KiB

Open AccessEditor’s ChoiceReview

Ethnolichenology—The Use of Lichens in the Himalayas and Southwestern Parts of China

by Mei-Xia Yang, Shiva Devkota, Li-Song Wang and Christoph Scheidegger

Diversity 2021, 13(7), 330; https://doi.org/10.3390/d13070330 - 18 Jul 2021

Cited by 36 | Viewed by 9938

Abstract

Lichens are used in traditional medicine, food and various other ethnic uses by cultures across the Himalayas and southwestern parts of China. Evidence-based knowledge from historical and modern literatures and investigation of ethnic uses from 1990 proved that lichen species used as medicine [...] Read more.

Lichens are used in traditional medicine, food and various other ethnic uses by cultures across the Himalayas and southwestern parts of China. Evidence-based knowledge from historical and modern literatures and investigation of ethnic uses from 1990 proved that lichen species used as medicine in the Himalayas and southwestern parts of China totaled to 142 species; furthermore, 42 species were utilized as food. Moreover, some lichens are popularly used for lichen produce in ethnic and modern life. An understanding and clarification of the use of lichens in the Himalayas and southeastern parts of China can therefore be important for understanding uses of lichens elsewhere and a reference for additional research of lichen uses in the future. Full article

(This article belongs to the Special Issue Diversity of Lichens—Morphology, Anatomy, Physiology, Secondary Chemistry, Distribution and Their Use: Recent Aspects of Evergreen Topics)

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11 pages, 1537 KiB

Open AccessEditor’s ChoiceOpinion

The Future of DNA Barcoding: Reflections from Early Career Researchers

by Danielle M. Grant, Ole Bjørn Brodnicke, Ann M. Evankow, André O. Ferreira, João T. Fontes, Aslak Kappel Hansen, Mads Reinholdt Jensen, Tuğba Ergül Kalaycı, Alexandra Leeper, Shalaka Kiran Patil, Sebastian Prati, Anna Reunamo, Aradhana J. Roberts, Rajesh Shigdel, Valentina Tyukosova, Mika Bendiksby, Rakel Blaalid, Filipe O. Costa, Peter M. Hollingsworth, Elisabeth Stur and Torbjørn Ekrem Show full author list Hide full author list

Diversity 2021, 13(7), 313; https://doi.org/10.3390/d13070313 - 9 Jul 2021

Cited by 40 | Viewed by 13810

Abstract

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, [...] Read more.

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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21 pages, 20553 KiB

Open AccessEditor’s ChoiceArticle

Orchids of Mongolia: Taxonomy, Species Richness and Conservation Status

by Shukherdorj Baasanmunkh, Batlai Oyuntsetseg, Petr Efimov, Zagarjav Tsegmed, Sumiya Vandandorj, Khurelpurev Oyundelger, Magsar Urgamal, Altangerel Undruul, Khurelbaatar Khaliunaa, Tugsuu Namuulin and Hyeok Jae Choi

Diversity 2021, 13(7), 302; https://doi.org/10.3390/d13070302 - 2 Jul 2021

Cited by 21 | Viewed by 7121

Abstract

Orchidaceae is a diverse, globally important plant family with high conservation assessment and prioritization requirements. The checklist of Orchidaceae in Mongolia was updated based on herbarium materials, literature, and field observations. Mongolian orchids were revised as comprising 26 taxa belonging to 14 genera [...] Read more.

Orchidaceae is a diverse, globally important plant family with high conservation assessment and prioritization requirements. The checklist of Orchidaceae in Mongolia was updated based on herbarium materials, literature, and field observations. Mongolian orchids were revised as comprising 26 taxa belonging to 14 genera with major updates were conducted on Herminium and Epipactis. In particular, H. alaschanicum, previously noted in the Alashan Gobi region, was added to the flora of Mongolia based on literature and type specimens. Epipactis helleborine and E. palustris were excluded from the Mongolian flora owing to the absence of herbarium specimens and wild collection from Mongolia. Assessment of all orchid species at the national level resulted in 1, 4, 7, 11, and 2 species as critically endangered (CR), endangered (EN), vulnerable (VU), near threatened (NT), and data deficient (DD), respectively, according to IUCN criteria. Species richness and conservation gap analyses of 970 georeferenced orchid records based on 0.5° × 0.5° grid cells across 16 phytogeographical regions of Mongolia, showed that four phytogeographical regions, Khangai, Khuvgul, Khentii and Mongolian Dauria, have a high number of orchids. Regrettably, most orchid-rich locations in Mongolia are not fully within protected areas, highlighting the need for protection management updates. Based on herbarium collections, we prepared grid distribution maps of the 26 taxa using 40 × 40 km² grids. Photographs of 18 taxa taken during fieldwork were included, providing valuable information on species morphology and typical habitat. Full article

(This article belongs to the Special Issue Biodiversity and Conservation of Vascular Flora)

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