Diversity

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21 pages, 10166 KiB

Open AccessArticle

Revision of the Global Fauna of Leptochela Stimpson, 1860 (Crustacea: Decapoda), Highlighting Phylogenetic Clades and a New Species

by Alexander L. Vereshchaka, Anastasiia A. Lunina, Dmitry N. Kulagin, Jørgen Olesen and Laure Corbari

Diversity 2024, 16(12), 760; https://doi.org/10.3390/d16120760 (registering DOI) - 12 Dec 2024

Viewed by 251

Abstract

Leptochela Stimpson (1860) is a shallow-water, benthopelagic genus within the predominantly pelagic superfamily Pasiphaeoidea. We inventoried a global fauna of 17 currently valid species of Leptochela and identified a newly discovered eighteenth species. Our analysis combined both morphological and molecular data, using 13 [...] Read more.

Leptochela Stimpson (1860) is a shallow-water, benthopelagic genus within the predominantly pelagic superfamily Pasiphaeoidea. We inventoried a global fauna of 17 currently valid species of Leptochela and identified a newly discovered eighteenth species. Our analysis combined both morphological and molecular data, using 13 characters (including two multistate characters) and 5 gene markers, respectively. The results revealed incongruence between the molecular and morphological datasets. However, our phylogenetic conclusions were based on a consensus approach, integrating morphological, molecular, and total evidence trees, which revealed three robust clades. We discuss the evolutionary development of quantitative and qualitative morphological traits in Leptochela and explore the potential causes of the incongruence between morphological and molecular signals, particularly in the context of pelagic eucarids transitioning from pelagic to benthopelagic habitats. Additionally, we describe the new species from Madagascar and provide a key to all known species of Leptochela. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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13 pages, 1702 KiB

Open AccessArticle

Multiple Speciation and Extinction Rate Shifts Shaped the Macro-Evolutionary History of the Genus Lycium Towards a Rather Gradual Accumulation of Species Within the Genus

by Haikui Chen, Kowiyou Yessoufou, Xiu Zhang, Shouhe Lin and Ledile Mankga

Diversity 2024, 16(11), 680; https://doi.org/10.3390/d16110680 - 6 Nov 2024

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Abstract

The Neotropics are the most species-rich region on Earth, and spectacular diversification rates in plants are reported in plants, mostly occurring in oceanic archipelagos, making Neotropical and island plant lineages a model for macro-evolutionary studies. The genus Lycium in the Solanaceae family, originating [...] Read more.

The Neotropics are the most species-rich region on Earth, and spectacular diversification rates in plants are reported in plants, mostly occurring in oceanic archipelagos, making Neotropical and island plant lineages a model for macro-evolutionary studies. The genus Lycium in the Solanaceae family, originating from the Neotropics and exhibiting a unique disjunct geography across several islands, is therefore expected to experience exceptional diversification events. In this study, we aimed to quantify the diversification trajectories of the genus Lycium to elucidate the diversification events within the genus. We compiled a DNA matrix of six markers on 75% of all the species in the genus to reconstruct a dated phylogeny. Based on this phylogeny, we first revisited the historical biogeography of the genus. Then, we fitted a Compound Poisson Process on Mass Extinction Time model to investigate the following key evolutionary events: speciation rate, extinction rate, as well as mass extinction events. Our analysis confirmed that South America is the origin of the genus, which may have undergone a suite of successive long-distance dispersals. Also, we found that most species arose as recently as 5 million years ago, and that the diversification rate found is among the slowest rates in the plant kingdom. This is likely shaped by the multiple speciation and extinction rate shifts that we also detected throughout the evolutionary history of the genus, including one mass extinction at the early stage of its evolutionary history. However, both speciation and extinction rates remain roughly constant over time, leading to a gradual species accumulation over time. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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19 pages, 3754 KiB

Open AccessArticle

The Vulnerability of Malagasy Protected Areas in the Face of Climate Change

by Qi Lai and Carl Beierkuhnlein

Diversity 2024, 16(11), 661; https://doi.org/10.3390/d16110661 - 27 Oct 2024

Viewed by 901

Abstract

This study examines the vulnerability of Madagascar’s protected areas (PAs) to climate change, focusing on climate change velocity, and its impact on biodiversity. We analyzed current and near future climate data using principal component analysis (PCA) and climate change velocity metrics to predict [...] Read more.

This study examines the vulnerability of Madagascar’s protected areas (PAs) to climate change, focusing on climate change velocity, and its impact on biodiversity. We analyzed current and near future climate data using principal component analysis (PCA) and climate change velocity metrics to predict shifts in climatic conditions from the present to the near future, while under the mild and extreme emission scenarios (SSP 126, SSP 585). Forward velocities, which are characterized by the minimum distances that must be overcome by species to keep in track with their appropriate comparative climate, are most pronounced in western and southern Madagascar. In contrast, the backward velocity, which uses future climatic conditions in grid cells in comparison to current conditions, is more common in the eastern regions of the island, and hints at the minimum distance that organisms would have to overcome in colonizing a new habitat. Even though the correlations between PA size and climate change velocity are weak, there is a tendency for larger PAs to exhibit more stable climatic conditions. Conservation strategies must prioritize enhancing the resilience of PAs through adaptive management to mitigate climate impacts. Our findings provide crucial insights for policymakers and conservation planners to develop climate-smart strategies that ensure the long-term efficacy of Madagascar’s PA network. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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12 pages, 16372 KiB

Open AccessArticle

Monitoring Diversity Profiles of Forested Landscapes in the Mediterranean Spain: Their Contribution to Local and Regional Vascular Plant Diversity

by José M. García del Barrio, David Sánchez de Ron, Francisco Auñón, Raquel Benavides, Rafael Alonso Ponce, Sergio González-Ávila, Francisco Bolaños, Sonia Roig and Marta Ortega Quero

Diversity 2024, 16(10), 626; https://doi.org/10.3390/d16100626 - 10 Oct 2024

Viewed by 661

Abstract

Biodiversity monitoring is key for understanding the delivery of ecosystem functions and services. Mediterranean forests and woodlands harbor many characteristic species of the Mediterranean vascular flora, and hence, they are a good surrogate for detecting changes in biodiversity linked to global change. In [...] Read more.

Biodiversity monitoring is key for understanding the delivery of ecosystem functions and services. Mediterranean forests and woodlands harbor many characteristic species of the Mediterranean vascular flora, and hence, they are a good surrogate for detecting changes in biodiversity linked to global change. In this work, we present a database resulting from the study of vascular plant diversity in multi-scale plots of 0.1 ha, measured around the first decade of this century and located in Mediterranean forest environments. Diversity profiles are calculated from Hill numbers (0, 1 and 2) for local (α) and regional (ϒ) diversity, as well as a multiplicative calculation of differential diversity (β). The main Mediterranean forests sampled had a medium coverage of 51% and stand dominant height of 10.6 m, and they were monospecific in two-thirds of cases. Local diversity reaches its highest values (around 78 species per 0.1 ha) in Holm oak dehesas, with values below 50 species for the most productive forest stands dominated by species of the genus Pinus. As regards the contribution to regional diversity, broadleaf formations contribute the most, with stone pine forests and dehesas in an intermediate position, and pine forests contributing the lowest in species richness terms. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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13 pages, 1386 KiB

Open AccessArticle

Life on the Wire—Plant Growth on Power Lines in the Americas

by Gerhard Zotz and Alfredo Cascante-Marín

Diversity 2024, 16(9), 573; https://doi.org/10.3390/d16090573 - 12 Sep 2024

Viewed by 625

Abstract

There are a number of rather anecdotal reports of plant growth on power cables in the Americas, but until now there has been no systematic attempt to gauge the geographical extension of this phenomenon nor a documentation of the diversity of species found [...] Read more.

There are a number of rather anecdotal reports of plant growth on power cables in the Americas, but until now there has been no systematic attempt to gauge the geographical extension of this phenomenon nor a documentation of the diversity of species found there. Using observations from the participatory science data platform iNaturalist and the scientific literature, we document almost 700 occurrences of more than 40 species of vascular plants and three lichen species on power cables with a geographical distribution over 7000 km from the southern United States to northern Argentina. Based on these observations we discuss the ecological conditions of plant growth on power cables in terms of climate; elevational distribution; and the morphological, physiological, and life history traits that allow the observed set of species to thrive on this anthropic structure. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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22 pages, 1625 KiB

Open AccessArticle

The Diet of Eleonora’s Falcons (Falco eleonorae) during the Autumn Migration of Passerine Birds across the Aegean Sea

by Dietrich Ristow and Michael Wink

Diversity 2024, 16(9), 538; https://doi.org/10.3390/d16090538 - 2 Sep 2024

Viewed by 1784

Abstract

Every year, several hundred million birds cross the Mediterranean on their migration from Eurasia to their wintering quarters in Africa. As many migrants travel at night or at high altitudes, direct observations of bird migration are difficult and thus our information about migrating [...] Read more.

Every year, several hundred million birds cross the Mediterranean on their migration from Eurasia to their wintering quarters in Africa. As many migrants travel at night or at high altitudes, direct observations of bird migration are difficult and thus our information about migrating species, numbers and timing is incomplete. An indirect way to assess autumn migration is the analysis of prey remains of Eleonora’s Falcons (Falco eleonorae). These falcons breed in large colonies on islands in the Mediterranean and on the Canary Islands. Many migrants have to pass these islands on their flight to their African wintering quarters. Eleonora’s Falcons appear to be adapted to the autumn bird migration and raise their young between August and October, when migrating birds are abundant. When nestlings have to be fed, falcons exclusively hunt small birds of 10 to 150 g body mass, whereas they prey mostly on aerial invertebrates (Coleoptera, Hymenoptera, Diptera, Orthoptera, Hemiptera, Odonata, Lepidoptera) from November to July. We studied Eleonora’s Falcons from 1965 to 2001 on a rocky islet, north of Crete, which harboured a colony of about 200 breeding pairs. In 1969, 1971, 1977, and 1988 we systematically monitored and collected the pluckings and cached food items in 22 to 36 nest sites each year. Pluckings were systematically analysed later in Germany using a reference collection of bird feathers for identification. In total, we determined more than 111 prey species (mostly Passerines) comprising more than 13,450 individuals. The top 12 prey species were: Willow Warbler (27.8% of all prey items), Red-backed Shrike (10.7%), Spotted Flycatcher (9.9%), Whinchat (8.8%), Common Whitethroat (5.1%), Wood Warbler (3.8), Tree Pipit (2.9%), Icterine Warbler (2.5%), Greater Short-toed Lark (2.5%), Northern Wheatear (1.8%), Common Nightingale (1.6%), and European Pied Flycatcher (1.5%). Eleonora’s Falcons are selective hunters to some degree; thus, the phenology and abundance data derived from the plucking analyses are biased towards slow-flying species or smaller birds (only up to a body mass of 150 g). When the young falcons develop and grow, food demand increases concomitantly. Comparing the total weight of prey over time indicates a correlation with food demand and in consequence with the number of prey items brought to the nest sites by the falcons. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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27 pages, 3024 KiB

Open AccessArticle

Automated ISSR Fingerprinting Is a Cost-Effective Way to Assess Genetic Diversity and Taxonomic Differentiation—A Case Study on the Encephalartos eugene-maraisii Species Complex

by Deanne Murphy, Nigel Paul Barker and Arnold Frisby

Diversity 2024, 16(8), 507; https://doi.org/10.3390/d16080507 - 20 Aug 2024

Viewed by 1593

Abstract

Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding the conservation of species. The precision and resolution of high throughput sequencing technologies provide valuable insights to aid conservation decisions, but these technologies are often financially unfeasible or [...] Read more.

Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding the conservation of species. The precision and resolution of high throughput sequencing technologies provide valuable insights to aid conservation decisions, but these technologies are often financially unfeasible or unavailable in resource constrained countries. Inter-Simple Sequence Repeat (ISSR) markers, when combined with sensitive automated detection systems, provide a simple, cheap means to investigate genetic diversity and discriminate closely related species. Here, we apply this technology to assess genetic diversity and taxonomic delimitation in the Encephalartos eugene-maraisii species complex, a highly threatened, taxonomically dubious group of cycads in South Africa. Our analyses support the taxonomic singularity of E. dyerianus, E. dolomiticus and E. eugene-maraisii. Relationships between E. nubimontanus and E. cupidus remain uncertain. E. middelburgensis samples showed no clustering but had poor amplification success. This study demonstrates the suitability of automated ISSR fingerprinting as a method for plant conservation studies, especially in resource-constrained countries, and we make recommendations as to how this methodology can be effectively implemented. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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19 pages, 2156 KiB

Open AccessArticle

Exploring the Genetic Structure and Phylogeographic Patterns of the Copepod Genus Eurytemora in Europe

by Céleste Mouth, Flavien Ferreira, Natalia Sukhikh, Elisa Bou, Anaëlle Bernard, Michèle Tackx, Fréderic Azémar, Patrick Meire, Tom Maris and Luc Legal

Diversity 2024, 16(8), 483; https://doi.org/10.3390/d16080483 - 8 Aug 2024

Viewed by 1457

Abstract

The genus Eurytemora is a diverse group of copepods found in coastal, estuarine, brackish, and freshwater environments. The main research has focused on Eurytemora affinis (Poppe, 1880) and revealed it to be a species complex. Eurytemora velox (Liljeborg, 1853) has only recently been [...] Read more.

The genus Eurytemora is a diverse group of copepods found in coastal, estuarine, brackish, and freshwater environments. The main research has focused on Eurytemora affinis (Poppe, 1880) and revealed it to be a species complex. Eurytemora velox (Liljeborg, 1853) has only recently been characterized in the Scheldt estuary but never within a global phylogenetic context. This study integrated nearly all European Eurytemora species sequences available, along with original ones from the Scheldt. A total of 351 sequences were analyzed using one mitochondrial gene (CO1) and one nuclear gene (nITS), with sequencing performed specifically on the CO1 gene. Phylogenetic reconstructions were performed using the Maximum Likelihood method, along with haplowebs and genetic diversity indices. A significant subdivision between six European species was observed. The monophyletic clade status of the E. affinis complex was confirmed alongside the existence of three geographically isolated lineages of the E. affinis species, the East Atlantic, the North Sea/English Channel, and the Baltic lineages, each exhibiting pronounced genetic differentiation. The population of E. velox from the Urals differs significantly from the European ones. These results provide both an overview of the genetic structure of the genus in geographic Europe as well as new insights on E. velox. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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16 pages, 2607 KiB

Open AccessArticle

Archaeological Areas as Habitat Islands: Plant Diversity of Epidaurus UNESCO World Heritage Site (Greece)

by Maria Panitsa, Maria Tsakiri, Dimitra Kampiti and Maria Skotadi

Diversity 2024, 16(7), 403; https://doi.org/10.3390/d16070403 - 12 Jul 2024

Viewed by 1604

Abstract

The Epidaurus UNESCO World Heritage site (EPD) is a famous archaeological area that is located in a small valley in the Peloponnese and receives more than 250,000 visitors annually. The study of the plant diversity of the site is in the framework of [...] Read more.

The Epidaurus UNESCO World Heritage site (EPD) is a famous archaeological area that is located in a small valley in the Peloponnese and receives more than 250,000 visitors annually. The study of the plant diversity of the site is in the framework of a continuous research project concerning archaeological areas of the Peloponnese and in the context of a project by the Ministry of Culture, Education and Religious Affairs of Greece that started during 2023 to study the biodiversity of the archaeological areas of Greece. The main aim of this study is the exploration and analysis of the plant species composition and diversity of the Epidaurus archaeological area, with an emphasis on endemic plants, on ruderal and alien taxa as well as on environmental and disturbance indicators and the cultural ecosystem services they provide. This study revealed a high species richness consisting of 446 plant taxa. Most of them are Mediterranean and widespread, ruderals and medium disturbance indicators, but there are also 12 Greek endemic taxa. The richest in the taxa families are Asteraceae, Fabaceae and Poaceae. Therophytes predominate in the total flora registered and hemicryptophytes predominate in the endemics. Comparisons of the EPD’s plant diversity with other archaeological areas of Greece and the Mediterranean revealed its richness and unique character. Management and protection in archaeological areas such as the Epidaurus must focus on the sustainable conservation of their relationship with their natural environment. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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16 pages, 1663 KiB

Open AccessArticle

Remote Coastal Weed Infestation Management Using Bayesian Networks

by Stuart Kininmonth, Kerry Spencer, Amie Hill, Eric Sjerp and Jethro Bangay

Diversity 2024, 16(7), 382; https://doi.org/10.3390/d16070382 - 30 Jun 2024

Viewed by 745

Abstract

The increasing prevalence of species that are detrimental to biodiversity is a major concern, particularly for managers of national parks. To develop effective programmes for controlling weeds, it is essential to have a thorough understanding of the extent and severity of infestations, as [...] Read more.

The increasing prevalence of species that are detrimental to biodiversity is a major concern, particularly for managers of national parks. To develop effective programmes for controlling weeds, it is essential to have a thorough understanding of the extent and severity of infestations, as well as the contributing factors such as temperature, rainfall, and disturbance. Predicting these factors on a regional scale requires models that can incorporate a wide range of variables in a quantifiable manner, while also assisting with on-ground operations. In this study, we present two Bayesian Network models specifically designed for six significant weed species found along the southern coast of Australia. Our models are based on empirical data collected during a coastal weed survey conducted in 2015 and repeated in 2016. We applied these models to the coastal national parks in the isolated and pristine East Gippsland region. Importantly, the prediction models were developed at two different spatial scales that directly corresponded to the scale of the observations. Our findings indicate that coastal habitats, with their vulnerable environments and prevalence of open dune systems, are particularly susceptible to weed infestations. Moreover, adjacent regions also have the potential for colonization if these infestations are not effectively controlled. Climate-related factors play a role in moderating the potential for colonization, which is a significant concern for weed control efforts in the context of global climate change. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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15 pages, 4720 KiB

Open AccessArticle

Disentangling the Effects of Climate and Land Uses on Small Mammals in Agroecosystems of NE Spain

by Ignasi Torre, Andrés Requejo, Antoni Arrizabalaga and Jordi Baucells

Diversity 2024, 16(6), 343; https://doi.org/10.3390/d16060343 - 13 Jun 2024

Cited by 1 | Viewed by 766

Abstract

We analyzed the two main drivers (climate and land uses) shaping the composition of small mammal communities at 16 localities situated in the confluence of the Mediterranean and Eurosiberian regions (Barcelona, Spain). The study area represents a land use and land cover gradient [...] Read more.

We analyzed the two main drivers (climate and land uses) shaping the composition of small mammal communities at 16 localities situated in the confluence of the Mediterranean and Eurosiberian regions (Barcelona, Spain). The study area represents a land use and land cover gradient showing urbanization and crop intensification in the lowlands and forest encroachment in mountain areas. We identified 2458 small mammal individuals of 12 different species from barn owl (Tyto alba) pellets. Three open-land species (Microtus duodecimcostatus, Crocidura russula, and Mus spretus) and one forest/generalist species (Apodemus sylvaticus) were dominant in the diet, accounting for 93% of prey. In order to disentangle the effects of both main drivers on the small mammal community, we used partial constrained ordination techniques, which allowed us to determine the pure effects (and shared effects) of the environmental factors. Land use predictors explained 33.4% of the variance (mostly crops), followed by 23.4% of the variance explained by the geo-climatic variables (mostly rainfall), and an additional 24.8% of the variance was shared by both groups of predictors, totaling 81.6% of environmental variance. The remaining 18.4% of variance was unexplained by environmental matrices. This pattern was consistent with expected associations of species and biotic influences at small spatial scales and highlighted that the number of species increased from the crops in the lowlands towards the highlands covered by deciduous and coniferous forests. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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10 pages, 1196 KiB

Open AccessArticle

The Role of Experience in the Visual and Non-Visual Prey Recognition of Fire Salamander Populations from Caves and Streams

by Hayes Hoover, Raoul Manenti and Andrea Melotto

Diversity 2024, 16(6), 312; https://doi.org/10.3390/d16060312 - 22 May 2024

Viewed by 822

Abstract

The study of foraging behaviour is crucial for understanding several ecological and adaptive processes, as well as for developing conservation measures. While extensive research has been completed on birds and mammals, few studies have been conducted on the learning capabilities of amphibians, particularly [...] Read more.

The study of foraging behaviour is crucial for understanding several ecological and adaptive processes, as well as for developing conservation measures. While extensive research has been completed on birds and mammals, few studies have been conducted on the learning capabilities of amphibians, particularly those pertaining to foraging behaviour. Amphibians may detect potential prey through distinct sensory systems including visual detection, chemoreception, and mechanoreception. In this study, we tested whether fire salamander larvae shift their prey recognition depending on the prey stimulus typology. We performed behavioural assays to better understand the roles of visual and chemical cues in prey recognition and how a continuative visual stimulus may change behavioural patterns. For this assessment, larvae from different habitats (cave and stream) were reared under laboratory conditions and fed while exposed to accompanying sensory stimuli. Their responses to visual and olfactory cues were measured before and after rearing. Both visual and chemical cues significantly affected the time of approach to the stimulus. The period of rearing significantly interacted with the time of approach for both cues. After rearing, when visual cues occurred, the time of approach was much lower than before rearing. These findings provide a basis for further studies on the role of plasticity in the predator–prey interactions of fire salamander larvae. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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10 pages, 1855 KiB

Open AccessArticle

An Overlooked Group of Citizen Scientists in Non-Indigenous Species (NIS) Information: Shell Collectors and Their Contribution to Molluscan NIS Xenodiversity

by Argyro Zenetos, Christiane Delongueville and Roland Scaillet

Diversity 2024, 16(5), 299; https://doi.org/10.3390/d16050299 - 16 May 2024

Viewed by 926

Abstract

This work reports on 60 marine alien mollusks from nine countries across the Mediterranean Sea and the Sea of Marmara collected by two Belgian citizen scientists. Some of their published observations concerning collection dates are compared with the year of first publication for [...] Read more.

This work reports on 60 marine alien mollusks from nine countries across the Mediterranean Sea and the Sea of Marmara collected by two Belgian citizen scientists. Some of their published observations concerning collection dates are compared with the year of first publication for these alien mollusks reported in the literature, which enable us to backdate some of their introductions and set new first Mediterranean records for two species. This underlines the importance of collaboration between volunteers and institutional scientists in tracing variations and changes in the environment and biodiversity. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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10 pages, 1874 KiB

Open AccessArticle

A Rather Unusual ”Pearl”: Biological Observations of the Hidden Pearlfish Carapus acus (Brünnich, 1768) and Its First Report from Apulian Waters (Salento Peninsula, Southern Italy)

by Alessandra Martines, Michele Solca, Egidio Trainito, Stefano Piraino and Giulia Furfaro

Diversity 2024, 16(5), 296; https://doi.org/10.3390/d16050296 - 14 May 2024

Viewed by 910

Abstract

The Salento peninsula in southern Italy (Mediterranean Sea) is a strip of land between the Adriatic and the Ionian Seas, both characterized by local regimes of currents, different geological and physical backgrounds, and quite diversified fauna. In this area, specimens of the sea [...] Read more.

The Salento peninsula in southern Italy (Mediterranean Sea) is a strip of land between the Adriatic and the Ionian Seas, both characterized by local regimes of currents, different geological and physical backgrounds, and quite diversified fauna. In this area, specimens of the sea cucumber Holothuria tubulosa (Brünnich, 1768) (Echinodermata) were collected at four stations in the spring and autumn of 2020 to investigate a possible symbiotic association with the inquiline fish Carapus acus (Brünnich, 1768). Among the collected holothurians, five pearlfish specimens were found in the body cavity of four H. tubulosa collected at 10 m of depth, in autumn, at “Grotta Verde” in Marina di Andrano, Lecce (Ionian Sea). More than half of the sea cucumbers from the latter station hosted the symbiont, suggesting the presence of a shallow population of C. acus inhabiting this coastal area. Furthermore, morphometric analysis carried out on the collected fish helped to shed light on the population dynamics characterizing this neglected species. This is the first report of C. acus from Apulian waters, allowing us to unite previously disjoined areas and providing essential baseline knowledge for planning future in-depth analysis of this difficult-to-study fish in a geographical area that is strategic in terms of the conservation of Mediterranean biodiversity. Furthermore, the range of preferred host species is extended, as C. acus was previously known to prefer other sea cucumber species such as Parastichopus regalis (Cuvier, 1817) instead of H. tubulosa. Finally, the finding of C. acus in a single station and in only one season is not trivial and delivers baseline useful information for future conservation purposes. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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29 pages, 7447 KiB

Open AccessArticle

Tracing Geographic and Molecular Footprints of Copepod Crustaceans Causing Multifocal Purple Spots Syndrome in the Caribbean Sea Fan Gorgonia ventalina

by Oksana A. Korzhavina, Mikhail A. Nikitin, Bert W. Hoeksema, Maickel Armenteros, James D. Reimer and Viatcheslav N. Ivanenko

Diversity 2024, 16(5), 280; https://doi.org/10.3390/d16050280 - 9 May 2024

Cited by 2 | Viewed by 2447

Abstract

The recent rise in ocean temperatures, accompanied by other environmental changes, has notably increased the occurrence and spread of diseases in Octocorallia, many species of which are integral to shallow tropical and subtropical coral reef ecosystems. This study focuses on the understanding of [...] Read more.

The recent rise in ocean temperatures, accompanied by other environmental changes, has notably increased the occurrence and spread of diseases in Octocorallia, many species of which are integral to shallow tropical and subtropical coral reef ecosystems. This study focuses on the understanding of these diseases, which has been largely limited to symptomatic descriptions, with clear etiological factors identified in only a fraction of cases. A key example is the multifocal purple spots syndrome (MFPS) affecting the common Caribbean octocoral sea fan Gorgonia ventalina, linked to the gall-forming copepods of the genus Sphaerippe, a member of the widespread family, Lamippidae. The specialized nature of these copepods as endoparasites in octocorals suggests the potential for the discovery of similar diseases across this host spectrum. Our investigation employed four molecular markers to study disease hotspots in Saint Eustatius, Curaçao, northwest and southwest Cuba, and Bonaire. This led to the discovery of a group of copepod species in these varied Caribbean locations. Importantly, these species are morphologically indistinguishable through traditional methods, challenging established taxonomic approaches. The observed diversity of symbionts, despite the host species’ genetic uniformity, is likely due to variations in larval dispersal mechanisms. Our phylogenetic analyses confirmed that the Lamippidae copepods belong to the order, Poecilostomatoida (Copepoda), and revealed their sister group relationship with the Anchimolgidae, Rhynchomolgidae, and Xarifiidae clades, known for their symbiotic relationships with scleractinian corals. These results add to our understanding of the evolutionary and ecological interactions of copepods and their hosts, and the diseases that they cause, and are important data in a changing climate. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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11 pages, 5854 KiB

Open AccessArticle

The Taurus Mountains, the Hotspot of Western Palearctic Biodiversity, Is in Danger: Marble Quarries Affect Wildlife

by Tamer Albayrak and Tamer Yılmaz

Diversity 2024, 16(5), 267; https://doi.org/10.3390/d16050267 - 30 Apr 2024

Viewed by 1421

Abstract

The Taurus Mountains in the Mediterranean Coastal Basin, considered a biodiversity hotspot, have a rich biodiversity in the Western Palearctic. The number of marble quarries in the Taurus Mountains has dramatically expanded over the past ten years. The objectives of this study are [...] Read more.

The Taurus Mountains in the Mediterranean Coastal Basin, considered a biodiversity hotspot, have a rich biodiversity in the Western Palearctic. The number of marble quarries in the Taurus Mountains has dramatically expanded over the past ten years. The objectives of this study are to (i) determine the impacts of quarrying on wildlife and (ii) determine the potential impacts of quarrying on the future of Taurus. A total of 57,547 photos and video images were analyzed on 5447 photo-trap days in two areas, the marble quarries and the control areas. Using 97 randomly selected marble quarries, the area they cover and their annual growth rates were determined. The most commonly seen animals were the wolf (Canis lupus), fox (Vulpes vulpes), lynx (Lynx lynx), and wild boar (Sus scrofa) in the control area, and the jackal (Canis aureus) and hare (Lepus europaeus) in the marble quarries (p < 0.001). Additionally, we found a significant positive correlation between the distance from the geographical center of the marble quarries and the number of dates of wolf, fox and wild boar sightings, with a significant negative correlation for hares (p < 0.05). A positive correlation was found between the area of marble quarries and the duration of operation (R = 0.89, p < 0.00). The waste from quarries, which makes up 79.7% of the total land used for this purpose, is the greatest cause of habitat degradation. According to calculations, even if no new marble quarries are built as of right now, 7.14% of the Taurus Mountains may have disappeared by the year 2027, and by the year 2032, 8.25% of the Taurus ecosystems may have disappeared completely. The Taurus Mountains, a center of Western Palearctic biodiversity, are being threatened by marble quarries. This study advances our knowledge of how marble quarries may affect wildlife. New strategies must be developed as soon as possible to protect the Taurus Mountains, the hotspot of the Mediterranean basin. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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15 pages, 1465 KiB

Open AccessArticle

Terrestrial Tardigrada (Water Bears) of the Słowiński National Park (Northern Poland)

by Tomasz Bartylak, Pushpalata Kayastha, Anastasiia Polishchuk, Milena Roszkowska, Magdalena Maria Bartylak, Tomasz Rutkowski, Michał Zacharyasiewicz and Łukasz Kaczmarek

Diversity 2024, 16(4), 239; https://doi.org/10.3390/d16040239 - 17 Apr 2024

Viewed by 1253

Abstract

In this paper, samples of mosses, lichens and cryptogams (mosses mixed with lichens) collected from Słowiński National Park (northern Poland) were studied for water bears (Tardigrada). In total, 27 tardigrade taxa were identified: 21 to the species level, one identified as „cf. [...] Read more.

In this paper, samples of mosses, lichens and cryptogams (mosses mixed with lichens) collected from Słowiński National Park (northern Poland) were studied for water bears (Tardigrada). In total, 27 tardigrade taxa were identified: 21 to the species level, one identified as „cf.” and three to the genus level, with six species (Eremobiotus ginevrae, Hypsibius dujardini, Hypsibius scabropygus, Milnesium beasleyi, Minibiotus intermedius and Notahypsibius pallidoides) being new records for Poland. Two possibly new for science species were also found, belonging to genera Diphascon and Mesobiotus. Additionally, a very rare eutardigrade Pseudohexapodibius degenerans has been found in the samples analyzed in the present study for the first time outside of the type locality. The effects of habitat and substrate on species richness were also investigated and showed no significant differences between mosses and lichens, as well as all substrates except for concrete walls. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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37 pages, 8918 KiB

Open AccessArticle

The Phyloperiodic Approach Removes the “Cryptic Species” and Puts forward Multilevel Organismal Diversity

by Tatiana Korshunova and Alexander Martynov

Diversity 2024, 16(4), 220; https://doi.org/10.3390/d16040220 - 6 Apr 2024

Viewed by 3268

Abstract

The notion of the “cryptic species” has recently become an important agenda in biodiversity research. In this study, we show, by applying a periodic-like morphological and molecular framework to the nudibranch genus Cadlina from the world’s least explored locations in the Kuril Islands [...] Read more.

The notion of the “cryptic species” has recently become an important agenda in biodiversity research. In this study, we show, by applying a periodic-like morphological and molecular framework to the nudibranch genus Cadlina from the world’s least explored locations in the Kuril Islands in the northwestern Pacific, including a description of six new species, that the term “cryptic species” should be removed from biodiversity research terminology. We explicitly show that different species of this complex have various degrees of molecular phylogenetic distances and morphological distinctness, revealing a truly multilevel system of fine-scale differences and similarities. Therefore, to designate any of these species as “cryptic” or “non-cryptic” would be completely arbitrary, non-operational, and generally meaningless. By this, we finally strongly propose to remove the notion of “crypticity” and the term “cryptic species” (in the sense of an “indistinguishable species”) from the arsenal of modern biology, including phylogeny and taxonomy. The importance of fine-scale species differentiation in the multilevel framework is shown for addressing conservation and global warming challenges. Six new species are named after scientists who have not always received the honours they deserve, including two women who did not receive their respective Nobel Prizes. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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13 pages, 4938 KiB

Open AccessArticle

Revealing the Diversity of Thin Filamentous Cyanobacteria, with the Discovery of a Novel Species, Pegethrix qiandaoensis sp. nov. (Oculatellaceae, Oculatellales), in a Freshwater Lake in China

by Kaihui Gao, Yao Cheng, Rouzhen Geng, Peng Xiao, He Zhang, Zhixu Wu, Fangfang Cai and Renhui Li

Diversity 2024, 16(3), 161; https://doi.org/10.3390/d16030161 - 5 Mar 2024

Cited by 2 | Viewed by 1581

Abstract

During the study of diversity in filamentous cyanobacteria in China, two strains (WZU0719 and WZU0723) with the form of thin filaments were isolated from the surface of Qiandao Lake, a large freshwater lake in Zhejiang Province, China. A comprehensive analysis was conducted, incorporating [...] Read more.

During the study of diversity in filamentous cyanobacteria in China, two strains (WZU0719 and WZU0723) with the form of thin filaments were isolated from the surface of Qiandao Lake, a large freshwater lake in Zhejiang Province, China. A comprehensive analysis was conducted, incorporating morphological, ecological, and molecular data. The morphological examination provided an initial identification as a Leptolyngbya-like cyanobacterium. Genetic characterization was also performed by amplifying the 16S rRNA gene and the 16S-23S rRNA internal transcribed spacer (ITS) region. The phylogenetic grouping based on the 16S rRNA gene demonstrates that the examined strain is unequivocally assigned to the Pegethrix genus. However, it possesses distinct phylogenetic divergence from the six described Pegethrix species. Additionally, discrepancies in habitat further differentiate it from other members of this genus. Employing the polyphasic approach, we present a comprehensive account of the newly discovered taxa: Pegethrix qiandaoensis sp. nov. The novel taxonomic finding in this research significantly contributes to enhancing the comprehension of Pegethrix diversity across various habitats. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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9 pages, 4624 KiB

Open AccessEditor’s ChoiceCommunication

Millepora spp. as Substrates of Their Hydrozoan Counterparts Stylaster sp. in the Pacific Ocean

by Chloé Julie Loïs Fourreau, Daniela Pica, Emmeline A. Jamodiong, Guillermo Mironenko Castelló, Iori Mizukami and James Davis Reimer

Diversity 2024, 16(3), 142; https://doi.org/10.3390/d16030142 - 23 Feb 2024

Cited by 1 | Viewed by 2024

Abstract

The association between two hydrozoans, Stylaster sp. and Millepora spp., has been described as a case of pseudo-auto-epizoism, and has only been reported from the Caribbean region of the Atlantic Ocean. Here, we report on the occurrence of this association in the Pacific [...] Read more.

The association between two hydrozoans, Stylaster sp. and Millepora spp., has been described as a case of pseudo-auto-epizoism, and has only been reported from the Caribbean region of the Atlantic Ocean. Here, we report on the occurrence of this association in the Pacific Ocean on coral reefs around Iriomote-jima Island, Japan, suggesting the association to be more widespread than had previously been thought. Moreover, Stylaster sp. colonies were observed living healthily on bleached and dead branches of Millepora spp., indicating that this interaction is facultative. The interaction reported here differs from the relationship between the Caribbean Stylaster roseus and Millepora alcicornis by the connection points between the two partners, which is made evident by the whitening of the Millepora counterpart in Iriomote-jima Island, while being seamless in the Caribbean association. Further research is necessary to fully understand the nature of these relationships, comprehending under what conditions it occurs, and establishing which species are involved in the interactions. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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16 pages, 43442 KiB

Open AccessEditor’s ChoiceArticle

Unrecognised Ant Megadiversity in the Australian Monsoonal Tropics III: The Meranoplus ajax Forel Complex

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

Diversity 2024, 16(2), 126; https://doi.org/10.3390/d16020126 - 16 Feb 2024

Cited by 1 | Viewed by 1562

Abstract

Australia’s monsoonal (seasonal) tropics are a global centre of ant diversity, but are largely unrecognised as such because the vast majority of its species are undescribed. Here we document another case of undescribed hyper-diversity within a taxon that is formally recognised as a [...] Read more.

Australia’s monsoonal (seasonal) tropics are a global centre of ant diversity, but are largely unrecognised as such because the vast majority of its species are undescribed. Here we document another case of undescribed hyper-diversity within a taxon that is formally recognised as a single, widespread species, Meranoplus ajax Forel. We recognise 50 species among 125 specimens of M. ‘ajax’ that we CO1-barcoded, integrating CO1 clustering and divergence, morphological differentiation and geographic distribution. A large proportion (44%) of these species are represented by single records, indicating that very many additional species are yet to be collected in this extremely remote and sparsely populated region. Sampling has been concentrated in the Northern Territory, where 27 of the 50 species occur. If diversity in Western Australia and Queensland were similar to that in the Northern Territory, as appears likely, then the M. ajax complex would comprise >100 species. In 2000, when Australia’s monsoonal ant fauna was estimated to contain 1500 species, Meranoplus ajax was considered to represent a single species. Our previous analyses of a range of other taxa have shown that their diversity has been similarly under-appreciated in this estimate. Our findings suggest that the total number of ant species in monsoonal Australia is several thousand, which would make the region by far the world’s richest known. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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52 pages, 18448 KiB

Open AccessEditor’s ChoiceArticle

A Taxonomic Review of South African Indigenous Meliaceae Using Molecular Systematics and Anatomical Data

by Mariam Oyefunke Oyedeji Amusa, Ross Dylan Stewart, Michelle van der Bank and Ben-Erik van Wyk

Diversity 2024, 16(2), 113; https://doi.org/10.3390/d16020113 - 8 Feb 2024

Cited by 1 | Viewed by 3734

Abstract

The Meliaceae are broadly distributed worldwide, with about 50 genera and over 1400 species. There are 11 genera in South Africa, with 13 indigenous and three naturalized species. Considering the diversity of the indigenous species of this family in South Africa and the [...] Read more.

The Meliaceae are broadly distributed worldwide, with about 50 genera and over 1400 species. There are 11 genera in South Africa, with 13 indigenous and three naturalized species. Considering the diversity of the indigenous species of this family in South Africa and the lack of recent studies encompassing these species, a taxonomic revision of the South African indigenous species of Meliaceae is presented here. Phylogenetic analysis, anatomical data, herbarium collections, and online data sources were used in this study. The results confirm the monophyly of Melioideae and Swietenioideae. The incongruence of Turraea previously reported was resolved in this study. Most representative genera of South African Meliaceae were recovered monophyletic with strong support. However, multiple samplings of species and including more markers could provide a better understanding of the relationships among South African species of Meliaceae. The review of the taxonomy of the South African Meliaceae, and especially the study of diagnostic characters and hitherto recorded natural distributions, have value in providing an up-to-date inventory of the indigenous genera and species and an easy means of identifying the taxa. Anatomical characters may be of systematic value to explore higher-level relationships in the family. This study is a contribution to tropical botany and to a more comprehensive database for the Meliaceae. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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13 pages, 906 KiB

Open AccessArticle

Characterization of Insect–Pollinator Biodiversity in Agrochemical-Contaminated Agricultural Habitats

by Fredrick Ojija and Giovanni Bacaro

Diversity 2024, 16(1), 33; https://doi.org/10.3390/d16010033 - 3 Jan 2024

Cited by 2 | Viewed by 2138

Abstract

The extensive application of agrochemicals in agricultural habitats in the Southern Highlands of Tanzania (SHOT) is supposed to negatively impact the biodiversity community of insect–pollinators (INPOs). However, in light of existing knowledge, there are no studies to back up this claim. We carried [...] Read more.

The extensive application of agrochemicals in agricultural habitats in the Southern Highlands of Tanzania (SHOT) is supposed to negatively impact the biodiversity community of insect–pollinators (INPOs). However, in light of existing knowledge, there are no studies to back up this claim. We carried out field surveys in the SHOT to assess and characterize the INPO biodiversity community in agricultural habitats and compare it with protected habitats. Direct observations, transect counts, sweep netting, and pan trap techniques were used for sampling the INPOs. Overall, the INPOs’ relative abundance (57.14%) and species diversity index in protected habitats were significantly higher compared to agricultural habitats. Similarly, we recorded a higher number of plant–INPO interactions in protected habitats than agricultural habitats. Our results suggest that, in contrast to protected habitats, agrochemicals might have driven out or discouraged INPOs from agricultural habitats, resulting in dwindling species richness, diversity, and abundance. This could be due to agrochemical contamination that impairs the quantity and quality of floral resources (nectar and pollen) required by INPOs. Alternatively, protected habitats seemed healthy and devoid of agrochemical contamination, which attracted many INPOs for foraging and nesting. Thus, in order to maintain healthy agricultural habitats and support INPO biodiversity, conservation agriculture is imperative. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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17 pages, 1850 KiB

Open AccessEditor’s ChoiceArticle

Orthoptera Community Dynamics and Conservation in a Natura 2000 Site (Greece): The Role of Beta Diversity

by Apostolis Stefanidis, Konstantina Zografou, Olga Tzortzakaki and Vassiliki Kati

Diversity 2024, 16(1), 11; https://doi.org/10.3390/d16010011 - 23 Dec 2023

Viewed by 2160

Abstract

Greece is a European hotspot for Orthoptera (378 species), yet it has been scarcely explored. We investigated the diversity patterns of Orthoptera and the ecological mechanisms shaping them by sampling 15 sites (30 plots of 1ha) across five habitats in Mount Mitsikeli, a [...] Read more.

Greece is a European hotspot for Orthoptera (378 species), yet it has been scarcely explored. We investigated the diversity patterns of Orthoptera and the ecological mechanisms shaping them by sampling 15 sites (30 plots of 1ha) across five habitats in Mount Mitsikeli, a Natura 2000 site. The mountain is deemed rich (0.4 species/km²), hosting 34 species, including a species of European interest (Paracaloptenus caloptenoides). The grassy openings in the beech–fir forest and rural mosaics were found to be important habitats for Orthoptera, while the mountain grasslands were poorer but hosted a greater abundance of grasshoppers. The three main environmental factors shaping diversity patterns (with an explained variance of 51.34%) were grass height, the cover of woody vegetation and the cover of bare ground. Beta diversity was high (with a Bray–Curtis of index 0.45 among habitats). Species turnover prevailed among all sites and within agricultural land, beech–fir forest and Mediterranean scrub, while nested patterns prevailed within mountain grasslands and mixed thermophilous forest. Conservation actions should target sites in ecosystems driven by species turnover, but primarily the most species-rich sites are driven by nestedness. Such actions should include the implementation of biodiversity-inclusive grazing schemes to hamper forest encroachment and the restoration of mountain grassland quality from cattle overgrazing. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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Review

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9 pages, 546 KiB

Open AccessReview

Overharvesting Is the Leading Conservation Issue of the Endangered Flagship Species Artemisia granatensis Boiss

by Juan Lorite

Diversity 2024, 16(12), 744; https://doi.org/10.3390/d16120744 - 3 Dec 2024

Viewed by 531

Abstract

Here I examine the overexploitation of Artemisia granatensis, a narrow endemic medicinal plant species from Sierra Nevada, Spain, and the consequences for its conservation. With over 50,000 flowering plant species used for medicinal purposes worldwide, many species face sustainability issues due to [...] Read more.

Here I examine the overexploitation of Artemisia granatensis, a narrow endemic medicinal plant species from Sierra Nevada, Spain, and the consequences for its conservation. With over 50,000 flowering plant species used for medicinal purposes worldwide, many species face sustainability issues due to overharvesting and habitat loss. Historical documentation of A. granatensis use dates back to the 13th century, highlighting its significance in traditional medicine. However, this species has suffered extensive overexploitation, particularly in the 19th and 20th centuries, leading to a significant decline in populations. Conservation concerns were first raised in 1909, and despite the species being legally protected since 1982, illegal collection and environmental pressures persist. Today, A. granatensis is critically endangered, with fewer than 2000 individuals remaining in fragmented populations. The study synthesizes the historical and recent literature to understand the long-standing pressures on this species and the limited conservation efforts made. Cultivation of A. granatensis is proposed as a crucial strategy to reduce pressure on wild populations and ensure the survival of this flagship important plant species. Full article

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10 pages, 11817 KiB

Open AccessReview

The State of the Art of the Global Distribution of the Invasive Mytilid Species Brachidontes pharaonis (P. Fischer, 1870)

by Matteo Battiata, Tiziana Curatolo, Murtada D. Naser, Gianluca Sarà and Sabrina Lo Brutto

Diversity 2024, 16(7), 381; https://doi.org/10.3390/d16070381 - 29 Jun 2024

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Abstract

The studies on the bioinvasion phenomenon focus mainly on the biological and ecological traits of a species, while scattered literature is addressed to a correct systematic assessment and an updated geographical distribution on the whole. It is noteworthy that non-indigenous species should be [...] Read more.

The studies on the bioinvasion phenomenon focus mainly on the biological and ecological traits of a species, while scattered literature is addressed to a correct systematic assessment and an updated geographical distribution on the whole. It is noteworthy that non-indigenous species should be monitored on both sides of their range, i.e., towards the front of dispersal and beyond the original range. The backside range boundaries are not often monitored or well delimited; thus, the novel global distribution of an invasive taxon is not often accurately delimitated. A model species for highlighting criticisms about the scarce knowledge on the novel range was chosen. Brachidontes pharaonis is a mussel that has successfully colonised the Mediterranean Sea, following an immigration pathway through the Suez Canal from the Red Sea, presumably from a wider Indo-Pacific area. In this case, the Indo-Pacific boundaries have been overlooked and are still misunderstood due to diverse causes, principally as the synonymy with the congeneric B. variabilis has created confusion in the taxonomic identification. The present review demonstrates that the borders of the B. pharaonis range are still unclear and that the species should be analysed in a wider geographical area. Records of B. pharaonis from Southeast Asia should be treated with caution as this area is out of its range. The Indian and Pacific Oceans host the taxon B. variabilis, composed of two potential cryptic species. Data from the literature highlight the importance of the integrative taxonomic approach to solving various issues concerning the species group complex, morphological variations and cosmopolitan claims of species. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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14 pages, 4320 KiB

Open AccessEditor’s ChoiceReview

Nanopore Sequencing Technology as an Emerging Tool for Diversity Studies of Plant Organellar Genomes

by Jakub Sawicki, Katarzyna Krawczyk, Łukasz Paukszto, Mateusz Maździarz, Mateusz Kurzyński, Joanna Szablińska-Piernik and Monika Szczecińska

Diversity 2024, 16(3), 173; https://doi.org/10.3390/d16030173 - 7 Mar 2024

Cited by 2 | Viewed by 2863

Abstract

In this comprehensive review, we explore the significant role that nanopore sequencing technology plays in the study of plant organellar genomes, particularly mitochondrial and chloroplast DNA. To date, the application of nanopore sequencing has led to the successful sequencing of over 100 plant [...] Read more.

In this comprehensive review, we explore the significant role that nanopore sequencing technology plays in the study of plant organellar genomes, particularly mitochondrial and chloroplast DNA. To date, the application of nanopore sequencing has led to the successful sequencing of over 100 plant mitochondrial genomes and around 80 chloroplast genomes. These figures not only demonstrate the technology’s robustness but also mark a substantial advancement in the field, highlighting its efficacy in decoding the complex and dynamic nature of these genomes. Nanopore sequencing, known for its long-read capabilities, significantly surpasses traditional sequencing techniques, especially in addressing challenges like structural complexity and sequence repetitiveness in organellar DNA. This review delves into the nuances of nanopore sequencing, elaborating on its benefits compared to conventional methods and the groundbreaking applications it has fostered in plant organellar genomics. While its transformative impact is clear, the technology’s limitations, including error rates and computational requirements, are discussed, alongside potential solutions and prospects for technological refinement. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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16 pages, 1614 KiB

Open AccessEditor’s ChoiceReview

A Comprehensive Review of Disease-Causing Agents in Freshwater Turtles: Implications for Conservation and Public Health

by João Rato, Raquel Xavier, D. James Harris, Filipe Banha and Pedro Anastácio

Diversity 2024, 16(3), 171; https://doi.org/10.3390/d16030171 - 7 Mar 2024

Viewed by 2481

Abstract

Freshwater turtles comprise 81% of all chelonian species despite freshwater systems only occupying 1% of the earth’s surface, and they are commonly exploited as pets and food resources. This contact between humans and turtles may put both sides at risk of disease transmission. [...] Read more.

Freshwater turtles comprise 81% of all chelonian species despite freshwater systems only occupying 1% of the earth’s surface, and they are commonly exploited as pets and food resources. This contact between humans and turtles may put both sides at risk of disease transmission. Additionally, human impact on ecosystems can cause disease outbreaks in turtle populations. In this review, we focused on disease agents affecting freshwater turtles, intending to contribute to conservation and public health efforts. We analysed 423 articles and noted a post-SARS-COVID-19 peak, with most research originating from Asia, North America, and Europe. Emydidae was the most frequently studied family, and there was also a bias towards adults, live specimens, and native species. Since most of the studied turtles were wild-caught, we recommend that captive turtles should also be thoroughly studied since they can transmit diseases to other turtles and humans. We registered 2104 potential disease-causing agents, with Platyhelminthes dominating within Animalia, while Proteobacteria dominated bacterial agents. Viruses’ representation was low, highlighting gaps in reptile virology. Fungi, Chromista, and Protozoa were also underrepresented, but this is changing with the development of molecular tools. This synthesis serves as a foundation for targeted health assessments, conservation strategies, and future research, essential to mitigate ecosystem and public health threats. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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Other

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8 pages, 3163 KiB

Open AccessBrief Report

Mapping Breeding Birds in a Karstic Sinkhole with a Comparison between Different Sampling Methods

by Corrado Battisti, Pierangelo Crucitti, Giuseppe Dodaro, Marco Giardini and Francesca Marini

Diversity 2024, 16(6), 326; https://doi.org/10.3390/d16060326 - 30 May 2024

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Abstract

Karstic sinkholes are peculiar structures hosting specific biological communities. Birds are still little studied in this regard. This note reports, for the first time, original data relating to the density of breeding species occurring within a sinkhole in central Italy obtained with a [...] Read more.

Karstic sinkholes are peculiar structures hosting specific biological communities. Birds are still little studied in this regard. This note reports, for the first time, original data relating to the density of breeding species occurring within a sinkhole in central Italy obtained with a fine-grained and time-expensive sampling technique (mapping method). The results were compared with data sampled with the point counts method carried out in the same phenological period. We recorded 22 breeding species, all typical of meso-thermophilous forests and ecotonal habitats of hilly central Italy. Among them, two species (Turdus merula and Troglodytes troglodytes), typical of shady, undergrowth habitats, were recorded in the deepest part of the sinkhole (−70 m from the top). No significant differences emerged between the relative frequencies of the species obtained with the two methods, except for Luscinia megarhynchos (overestimated with the mapping method) and Aegithalos caudatus (underestimated). At the community level, the comparison of the two methods revealed similar values in univariate diversity metrics, Whittaker plots did not show a significant difference (ANCOVA test), and ordinary least squares regression between the frequencies showed a highly significant correlation. Therefore, in these peculiar habitats, data obtained from the two methods are comparable: since the point counts method needs lower sampling effort, it appeared to be more effective when compared to the mapping method to study these peculiar habitats. Full article

(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)

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