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Diversity, Volume 12, Issue 11 (November 2020) – 33 articles

Cover Story (view full-size image): The birds of the Galápagos Islands are famous for their role in stimulating Charles Darwin’s conception of evolution by means of natural selection. The Galápagos Rail, a species collected by Darwin and described from the Beagle voyage, has nevertheless gained little attention due to its secretive habits. Using century-old museum specimens and modern samples, Chaves et al. sequenced its full mitochondrial genome and demonstrated that the Galápagos Rail colonized the Galápagos Islands ~1.2 million years ago from the Americas. Its genetic diversity is low, with surprisingly little genetic differentiation between populations on different islands—important information that should guide future conservation efforts. Photo: Michael Dvorak©. View this paper
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Editorial
Biodiversity of Ciliates and Their Symbionts: A Special Issue
Diversity 2020, 12(11), 441; https://doi.org/10.3390/d12110441 - 23 Nov 2020
Cited by 1 | Viewed by 639
Abstract
Interests to estimate and assess the diversity of ciliates have a centuries-long history [...] Full article
(This article belongs to the Special Issue Biodiversity of Ciliates and their Symbionts)
Review
The Role of Hybridisation in the Making of the Species-Rich Arctic-Alpine Genus Saxifraga (Saxifragaceae)
Diversity 2020, 12(11), 440; https://doi.org/10.3390/d12110440 - 23 Nov 2020
Cited by 3 | Viewed by 820
Abstract
Evolutionary processes fuelling rapid species diversification are not yet fully understood, although their major contribution to overall patterns of plant biodiversity is well established. Hybridisation is among the least understood of these processes, despite its multifaceted role in speciation processes being widely accepted. [...] Read more.
Evolutionary processes fuelling rapid species diversification are not yet fully understood, although their major contribution to overall patterns of plant biodiversity is well established. Hybridisation is among the least understood of these processes, despite its multifaceted role in speciation processes being widely accepted. Species of the large arctic-alpine genus Saxifraga are notorious for their ability to hybridise; however, the overall role of hybridisation and polyploidisation for the diversification of this genus remains unknown. Here, we provide a comprehensive genus-wide review of hybridisation accounts and ploidy levels. We find that the sections of Saxifraga vary greatly in their propensity to hybridise. The majority of natural hybridisation accounts are from recent localised events (n = 71). Hybridisation hotspots were located in the Pyrenees and the European Alps, thus contrasting with the overall distribution of species richness in the genus. Hybrids or hybrid populations are often short-lived in Saxifraga due to a multitude of reproductive barriers, most commonly low F1 hybrid fertility. However, these barriers are not always fully effective, allowing for backcrossing and the formation of hybrid swarms. In addition, we find that the incidence of polyploidy varies widely across different sections of Saxifraga, with species-rich sections Porphyrion and Saxifraga showing divergent polyploidy proportions. Overall, we show that hybridisation and polyploidisation played differential roles in the diversification of this large genus. Nevertheless, a significant proportion of species are yet to be scrutinised, particularly among the Asian Saxifraga species, illustrating the need for systematic further study to fully unravel the role of hybridisation during the evolution of Saxifraga. Full article
(This article belongs to the Special Issue Diversity and Paleoecological History of Saxifraga)
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Article
Transporting Biodiversity Using Transmission Power Lines as Stepping-Stones?
Diversity 2020, 12(11), 439; https://doi.org/10.3390/d12110439 - 23 Nov 2020
Viewed by 1580
Abstract
The most common ecological response to climate change is the shifts in species distribution ranges. Nevertheless, landscape fragmentation compromises the ability of limited dispersal species to move following these climate changes. Building connected environments that enable species to track climate changes is an [...] Read more.
The most common ecological response to climate change is the shifts in species distribution ranges. Nevertheless, landscape fragmentation compromises the ability of limited dispersal species to move following these climate changes. Building connected environments that enable species to track climate changes is an ultimate goal for biodiversity conservation. Here, we conducted an experiment to determine if electric power transmission lines could be transformed in a continental network of biodiversity reserves for small animals. We analysed if the management of the habitat located inside the base of the transmission electric towers (providing refuge and planting seedlings of native shrub) allowed to increase local richness of target species (i.e., small mammals and some invertebrates’ groups). Our results confirmed that by modifying the base of the electric transmission towers we were able to increase density and diversity of several species of invertebrates and small mammals as well as number of birds and bird species, increasing local biodiversity. We suggest that modifying the base of the electric towers would potentially facilitate the connection of fragmented populations. This idea would be easily applicable in any transmission line network anywhere around the world, making it possible for the first time to build up continental scale networks of connectivity. Full article
(This article belongs to the Section Biodiversity Conservation)
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Editorial
Practice Must Be Backed up by Theory! A Special Issue on Plant Community Ecology
Diversity 2020, 12(11), 438; https://doi.org/10.3390/d12110438 - 21 Nov 2020
Viewed by 575
Abstract
Plant communities form the structural and functional basis for nearly all terrestrial ecosystems [...] Full article
(This article belongs to the Special Issue Plant Community Ecology: From Theory to Practice)
Editorial
Fungal Diversity
Diversity 2020, 12(11), 437; https://doi.org/10.3390/d12110437 - 19 Nov 2020
Cited by 1 | Viewed by 613
Abstract
Fungi play key roles at two levels of ecological organization: in communities, fungi are symbionts of plants and animals, while in ecosystems, fungi are decomposers that recycle nutrients to other organisms [...] Full article
(This article belongs to the Special Issue Fungal Diversity)
Article
Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota
Diversity 2020, 12(11), 436; https://doi.org/10.3390/d12110436 - 19 Nov 2020
Viewed by 814
Abstract
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) [...] Read more.
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics. Full article
(This article belongs to the Special Issue Ecology of Crop-Associated Communities of Bacteria and Fungi)
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Article
Diatoms in Kamchatka’s Hot Spring Soils
Diversity 2020, 12(11), 435; https://doi.org/10.3390/d12110435 - 18 Nov 2020
Cited by 1 | Viewed by 816
Abstract
Diatoms inhabiting terrestrial habitats that are affected by thermal activity remain poorly studied, despite significant interest in the biodiversity of hot springs. The Kamchatka peninsula is characterized by the presence of 30 active volcanoes associated with hydrotherms. Our study involved a survey of [...] Read more.
Diatoms inhabiting terrestrial habitats that are affected by thermal activity remain poorly studied, despite significant interest in the biodiversity of hot springs. The Kamchatka peninsula is characterized by the presence of 30 active volcanoes associated with hydrotherms. Our study involved a survey of diatom diversity in soils around the Malki, Upper Paratunka, and Dachnie thermal springs on the Kamchatka peninsula. A total of 49 diatom taxa were found. The genera Pinnularia, Planothidium, Fragilariforma, Epithemia, Halamphora, Gomphonema, Nitzschia, Aulocoseira, Sellaphora, Surirella, and Navicula were the most common. Pinnularia cf. subcapitata and Planothidium lanceolatum were dominant in all springs. Diatom communities in the soils near the thermal springs included both aquatic and terrestrial species, which may reflect the transitional nature of habitats at the borders of hot springs and soils. To gain a better understanding of the diversity of diatom communities in soils near thermal springs, broader worldwide studies are necessary. Full article
(This article belongs to the Special Issue Taxonomy, Ecology and Biogeography of Diatoms)
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Article
Seascape Configuration Leads to Spatially Uneven Delivery of Parrotfish Herbivory across a Western Indian Ocean Seascape
Diversity 2020, 12(11), 434; https://doi.org/10.3390/d12110434 - 18 Nov 2020
Cited by 1 | Viewed by 1851
Abstract
Spatial configuration of habitat types in multihabitat seascapes influence ecological function through links of biotic and abiotic processes. These connections, for example export of organic matter or fishes as mobile links, define ecosystem functionality across broader spatial scales. Herbivory is an important ecological [...] Read more.
Spatial configuration of habitat types in multihabitat seascapes influence ecological function through links of biotic and abiotic processes. These connections, for example export of organic matter or fishes as mobile links, define ecosystem functionality across broader spatial scales. Herbivory is an important ecological process linked to ecosystem resilience, but it is not clear how herbivory relates to seascape configuration. We studied how herbivory and bioerosion by 3 species of parrotfish were distributed in a multi-habitat tropical seascape in the Western Indian Ocean (WIO). We surveyed the abundance of three species with different life histories—Leptoscarus vaigiensis (seagrass species), Scarus ghobban (juvenile-seagrass/adults-reefs) and Scarus rubroviolaceus (reef species) —in seagrass meadows and on reefs and recorded their selectivity of feeding substrate in the two habitats. Herbivory rates for L. vaigiensis and S. ghobban and bioerosion for S. rubroviolaceus were then modelled using bite rates for different size classes and abundance and biomass data along seascape gradients (distance to alternative habitat types such as land, mangrove and seagrass). Bioerosion by S. rubroviolaceus was greatest on reefs far from seagrass meadows, while herbivory rates by S. ghobban on reefs displayed the opposite pattern. Herbivory in seagrass meadows was greatest in meadows close to shore, where L. vaigiensis targeted seagrass leaves and S. ghobban the epiphytes growing on them. Our study shows that ecological functions performed by fish are not equally distributed in the seascape and are influenced by fish life history and the spatial configuration of habitats in the seascape. This has implications for the resilience of the system, in terms of spatial heterogeneity of herbivory and bioerosion and should be considered in marine spatial planning and fisheries management. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Herbivorous Fish)
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Article
Spatial Distribution of Phytoplankton Community Composition and Their Correlations with Environmental Drivers in Taiwan Strait of Southeast China
Diversity 2020, 12(11), 433; https://doi.org/10.3390/d12110433 - 18 Nov 2020
Viewed by 784
Abstract
Large-scale dinoflagellate blooms have appeared in recent decades in the Taiwan Strait, Southeast China. To study spatial variability of phytoplankton community composition, physical and chemical environmental drivers in surface seawater of the Taiwan Strait, we conducted cruises in May and July 2019. Cell [...] Read more.
Large-scale dinoflagellate blooms have appeared in recent decades in the Taiwan Strait, Southeast China. To study spatial variability of phytoplankton community composition, physical and chemical environmental drivers in surface seawater of the Taiwan Strait, we conducted cruises in May and July 2019. Cell numbers of dinoflagellates were significantly higher than that of diatoms in most sampling stations during the cruise in May, whereas diatoms were the major contributor to autotrophic biomass in July. Phytoplankton community shifted from a dinoflagellate- and diatom-dominated system in May to diatom dominance in July. The dominant phytoplankton species (genera) were the harmful algal bloom dinoflagellates Prorocentrum donghaiense and Scrippsiella trochoidea and the diatoms Coscinodiscus in May, and Rhizosolenia, Pseudo-nitzschia, and Guinardia in July. Cell densities of dinoflagellates and P. donghaiense reduced exponentially with increasing seawater temperature and salinity and decreasing dissolved inorganic nitrogen (DIN) concentrations. Based on the results of our work and previous studies, it becomes obvious that harmful dinoflagellate blooms are likely to be a major component of the planktonic food web in the Taiwan Strait at a temperature of 17.0–23.0 °C, a salinity of 29.0–33.0 psu, and a DIN concentration higher than 2.0 μmol L–1. Full article
(This article belongs to the Special Issue Linking Plankton Diversity with Ecosystem Functioning and Services)
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Article
Insights into the Fungal Community and Functional Roles of Pepper Rhizosphere Soil under Plastic Shed Cultivation
Diversity 2020, 12(11), 432; https://doi.org/10.3390/d12110432 - 17 Nov 2020
Viewed by 868
Abstract
The rhizosphere fungal community is essential for determining plant health and improving crop productivity. The fungal community structure and functional roles in the plastic shed soils were explored using high throughput sequencing and FUNGuild in this study. The fungal community structures shifted between [...] Read more.
The rhizosphere fungal community is essential for determining plant health and improving crop productivity. The fungal community structure and functional roles in the plastic shed soils were explored using high throughput sequencing and FUNGuild in this study. The fungal community structures shifted between the rhizosphere and non-rhizosphere soils. The greatest abundance variation was observed for the rare fungal members with relative abundances <0.1%. In the rhizosphere soil of pepper, the abundance of the genera Purpureocillium, Metacorgyceps, Arthrobotrys, Cephalotheca, and Scedosporium increased significantly, among which, Purpureocillium, Arthrobotrys and Metacorgyceps exhibited biocontrol characteristics. Co-occurrence network analysis revealed different interactions of fungal communities in the rhizosphere and non-rhizosphere soils, both of which were dominated by low abundance members. More positive correlation was identified among the rare members, the fungal pathotroph functions and phthalate acid ester in the rhizosphere soil. This study highlights the important niche of the rare fungal members in soil microbial ecology under plastic shed cultivation. Full article
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Review
A Review of the Ecomorphology of Pinnotherine Pea Crabs (Brachyura: Pinnotheridae), with an Updated List of Symbiont-Host Associations
Diversity 2020, 12(11), 431; https://doi.org/10.3390/d12110431 - 16 Nov 2020
Viewed by 1811
Abstract
Almost all pea crab species in the subfamily Pinnotherinae (Decapoda: Brachyura: Pinnotheridae) are considered obligatory endo- or ectosymbionts, living in a mutualistic or parasitic relationship with a wide variety of invertebrate hosts, including bivalves, gastropods, echinoids, holothurians, and ascidians. While the subfamily is [...] Read more.
Almost all pea crab species in the subfamily Pinnotherinae (Decapoda: Brachyura: Pinnotheridae) are considered obligatory endo- or ectosymbionts, living in a mutualistic or parasitic relationship with a wide variety of invertebrate hosts, including bivalves, gastropods, echinoids, holothurians, and ascidians. While the subfamily is regarded as one of the most morphologically adapted groups of symbiotic crabs, the functionality of these adaptations in relation to their lifestyles has not been reviewed before. Available information on the ecomorphological adaptations of various pinnotherine crab species and their functionality was compiled in order to clarify their ecological diversity. These include the size, shape, and ornamentations of the carapace, the frontal appendages and mouthparts, the cheliped morphology, the ambulatory legs, and the reproductive anatomy and larval characters. The phylogenetic relevance of the adaptations is also reviewed and suggestions for future studies are made. Based on an updated list of all known pinnotherine symbiont–host associations and the available phylogenetic reconstructions, it is concluded that, due to convergent evolution, unrelated species with a similar host interaction might display the same morphological adaptations. Full article
(This article belongs to the Special Issue Review Papers on Marine Diversity)
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Article
Fish Assemblage Structure in the Northwestern Hawaiian Islands Is Associated with the Architectural Complexity of Coral-Reef Habitats
Diversity 2020, 12(11), 430; https://doi.org/10.3390/d12110430 - 15 Nov 2020
Viewed by 819
Abstract
The architectural complexity of coral-reef habitat plays an important role in determining the assemblage structure of reef fish. We investigated associations between the reef habitats and fish assemblages in the Northwestern Hawaiian Islands (NWHI) using in situ fish counts and data on habitat [...] Read more.
The architectural complexity of coral-reef habitat plays an important role in determining the assemblage structure of reef fish. We investigated associations between the reef habitats and fish assemblages in the Northwestern Hawaiian Islands (NWHI) using in situ fish counts and data on habitat metrics and benthic community composition that were obtained from three-dimensional (3D) photogrammetric reconstructions of the surveyed sites. The structure of fish assemblage as a whole on the basis of Bray–Curtis dissimilarity, species richness and the abundances of herbivores and piscivores were associated with habitat metrics, with higher levels of architectural complexity generally supporting greater numbers of fish species and individuals. Benthic cover did not explain additional variation in these variables after the effects of habitat metrics were taken into account. Corallivorous fish was the only group that showed positive associations with both habitat metrics and benthic cover (Acropora and Pocillopora corals). The total fish abundance and the abundances of planktivores and invertivores did not show associations with either habitat metrics or benthic cover. This study suggests that an appropriate combination of habitat metrics can be used to account sufficiently for the effects of habitat architecture on fish assemblages in reef monitoring efforts in the NWHI. Full article
(This article belongs to the Special Issue Coral Reef Ecology and Biodiversity)
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Article
Stable Isotope Dynamics of Herbivorous Reef Fishes and Their Ectoparasites
Diversity 2020, 12(11), 429; https://doi.org/10.3390/d12110429 - 14 Nov 2020
Cited by 1 | Viewed by 1137
Abstract
Acanthurids (surgeonfishes) are an abundant and diverse group of herbivorous fishes on coral reefs. While their contribution to trophic linkages and dynamics in coral reef systems has received considerable attention, the role of linkages involving their parasites has not. As both consumers of [...] Read more.
Acanthurids (surgeonfishes) are an abundant and diverse group of herbivorous fishes on coral reefs. While their contribution to trophic linkages and dynamics in coral reef systems has received considerable attention, the role of linkages involving their parasites has not. As both consumers of fish tissue and prey to microcarnivores, external parasites may play a significant role in trophic transfer between primary consumers (and hence their predominantly algae-based diet) and the broader coral reef community. Stable isotope analysis is a common tool for studying trophic linkages which can be used for studies involving parasites. We examined the stable isotope ecology (13C and 15N) of copepod (Caligus atromaculatus) and monogenean (Neobenedenia sp.) ectoparasites collected from two species of Caribbean acanthurids (Acanthurus coeruleus and Acanthurus bahianus). There were significant intraspecific differences in isotope discrimination factors between parasites collected from the two different host species as well as interspecific differences between parasites collected from the same host species. Discrimination factors for 15N were consistently positive but varied in magnitude depending on host and parasite species and were slightly lower than what would be expected for consumers. The 13C discrimination factors for both monogeneans and copepods collected from A. coeruleus were consistently positive but were negative for copepods collected from A. bahianus. These findings emphasize the complexity of the stable isotope trophic interactions occurring between parasites and their hosts, highlighting the value of these types of host-parasite isotopic studies. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Herbivorous Fish)
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Article
Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon
Diversity 2020, 12(11), 428; https://doi.org/10.3390/d12110428 - 13 Nov 2020
Viewed by 2208
Abstract
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups [...] Read more.
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment. Full article
(This article belongs to the Section Phylogeny and Evolution)
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Article
Analysis of Rare Plant Occurrence Data for Monitoring Prioritization
Diversity 2020, 12(11), 427; https://doi.org/10.3390/d12110427 - 12 Nov 2020
Cited by 1 | Viewed by 948
Abstract
Efforts to conserve rare plant species can be limited by a lack of time and funding for monitoring. Understanding species occurrence and distribution patterns within existing protected habitat and throughout the entire species range can help stewards prioritize rare plant monitoring. We created [...] Read more.
Efforts to conserve rare plant species can be limited by a lack of time and funding for monitoring. Understanding species occurrence and distribution patterns within existing protected habitat and throughout the entire species range can help stewards prioritize rare plant monitoring. We created a database of rare plant occurrences from public, private, and research sources to analyze the distribution of rare plant species throughout the existing protected area within the Nature Reserve of Orange County in California, USA. We analyzed species occurrence relative to the urban edge, roads, trails, and mean high tide line. We also determined the vegetation community with the highest number of rare plant species to help prioritize habitats for conservation and restoration. We found that some parts of protected areas have more rare plant species and we also found sampling biases on the location of occurrence data. We found that rare species occur close to roads and trails and the mean high tide line. Rare species were in all vegetation communities within the reserve, including degraded areas. Using patterns of distribution and considering the immediate threats to a rare species population can help land managers and stewards prioritize monitoring toward the most threatened species. Full article
(This article belongs to the Special Issue Vascular Plant Diversity at Different Scales)
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Article
The Evolution and Biogeography of Wolbachia in Ants (Hymenoptera: Formicidae)
Diversity 2020, 12(11), 426; https://doi.org/10.3390/d12110426 - 12 Nov 2020
Cited by 3 | Viewed by 1905
Abstract
Wolbachia bacteria are widely distributed across invertebrate taxa, including ants, but several aspects of this host-associated interaction are still poorly explored, especially with regard to the ancestral state association, origin, and dispersion patterns of this bacterium. Therefore, in this study, we explored the [...] Read more.
Wolbachia bacteria are widely distributed across invertebrate taxa, including ants, but several aspects of this host-associated interaction are still poorly explored, especially with regard to the ancestral state association, origin, and dispersion patterns of this bacterium. Therefore, in this study, we explored the association of Wolbachia with Formicidae in an evolutionary context. Our data suggest that supergroup F is the ancestral character state for Wolbachia infection in ants, and there is only one transition to supergroup A, and once ants acquired infection with supergroup A, there have been no other strains introduced. Our data also reveal that the origin of Wolbachia in ants likely originated in Asia and spread to the Americas, and then back to Asia. Understanding the processes and mechanisms of dispersion of these bacteria in Formicidae is a crucial step to advance the knowledge of this symbiosis and their implications in an evolutionary context. Full article
(This article belongs to the Special Issue Diversity, Biogeography and Community Ecology of Ants)
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Article
Evolutionary History of the Galápagos Rail Revealed by Ancient Mitogenomes and Modern Samples
Diversity 2020, 12(11), 425; https://doi.org/10.3390/d12110425 - 12 Nov 2020
Cited by 1 | Viewed by 3393
Abstract
The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing [...] Read more.
The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing to its elusive behavior, cryptic plumage, and restricted distribution, the Galápagos Rail is one of the least studied endemic vertebrates of the Galapagos Islands. To date, there is no genetic data for this species, leaving its origins, relationships to other taxa, and levels of genetic diversity uncharacterized. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here, we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multilocus nuclear and mitochondrial sequencing from both modern and historical samples. We show that the Galápagos Rail is part of the “American black rail clade”, sister to the Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 million years ago. A separate analysis of one nuclear and two mitochondrial markers in the larger population samples demonstrates a shallow population structure across the islands, possibly due to elevated island connectivity. Additionally, birds from the island Pinta possessed the lowest levels of genetic diversity, possibly reflecting past population bottlenecks associated with overgrazing of their habitat by invasive goats. The modern and historical data presented here highlight the low genetic diversity in this endemic rail species and provide useful information to guide conservation efforts. Full article
(This article belongs to the Section Phylogeny and Evolution)
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Article
Being Well-Connected Pays in a Disturbed World: Enhanced Herbivory in Better-Linked Habitats
Diversity 2020, 12(11), 424; https://doi.org/10.3390/d12110424 - 12 Nov 2020
Cited by 1 | Viewed by 995
Abstract
Seascapes are typically comprised of multiple components that are functionally linked by the movement of organisms and fluxes of matter. Changes to the number and spatial arrangement of these linkages affect biological connectivity that, in turn, can alter ecological functions. Herbivory is one [...] Read more.
Seascapes are typically comprised of multiple components that are functionally linked by the movement of organisms and fluxes of matter. Changes to the number and spatial arrangement of these linkages affect biological connectivity that, in turn, can alter ecological functions. Herbivory is one such function, pivotal in controlling excessive algal growth when systems become disturbed. Here, we used microcosm experiments to test how the change to connectivity affects herbivory under different levels of disturbance. We applied network theory to measure types of connectivity at different scales (patch and whole system) and quantified herbivory by a crustacean mesograzer exposed to excess algae, mimicking pulse and press disturbances. We demonstrate that greater connectivity significantly enhances herbivory in Clibanarius virescens: Both the number of linkages and their spatial arrangement interact to shape the response of herbivory in systems to disturbance. Our findings highlight the value of controlled experiments for advancing theories about the potential effects of connectivity on important ecological functions, such as herbivory, and justify further investigation to measure how connectivity might affect the resilience of ecosystems. We posit that the variation in the type, and scale, of spatial linkages might have profound consequences for managing the capacity of ecosystems to respond to disturbance. Full article
(This article belongs to the Section Marine Diversity)
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Article
Sea Slugs—“Rare in Space and Time”—But Not Always
Diversity 2020, 12(11), 423; https://doi.org/10.3390/d12110423 - 11 Nov 2020
Cited by 1 | Viewed by 714
Abstract
The term “rare in space and time” is often used to typify the spatial and temporal patterns of occurrence of heterobranch sea slugs. However, “rare” in this context has not been clearly defined. In an attempt to provide more insight into the concept [...] Read more.
The term “rare in space and time” is often used to typify the spatial and temporal patterns of occurrence of heterobranch sea slugs. However, “rare” in this context has not been clearly defined. In an attempt to provide more insight into the concept of rarity in sea slug assemblages, we analysed abundance data from 209 individual surveys conducted over a 5-year period in a subtropical estuary and a 7-year period on a shallow coastal reef, on the Sunshine Coast, Qld, Australia. Using an ‘intuitive’ method (<10 individuals recorded over the study), and the ‘quartile’ method we assessed numerical rarity (number of individuals of a species seen over the study period) and temporal rarity (frequency of observation). We also assessed numerical rarity using octaves based on log2 abundance bins. The quartile method did not effectively capture either measure of rarity. The octave method, however, fitted closely to subjective classifications of abundance and defined a similar number of species as rare when compared to the intuitive method. Using the octave method, 66% of species in both the estuary and on the reef, were considered as rare. Consequently, we recommend the octave method to allocate abundance classifications. To address the poor fit for temporal classifications based on quartiles, we propose the following as a working model for wider testing: rare ≤25% of surveys; uncommon 26−50%, common 51−75%; and abundant >75%. Full article
(This article belongs to the Section Marine Diversity)
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Article
Recently Naturalized Paraserianthes lophantha subsp. lophantha Displays Contrasting Genetic Diversity and Climate Relationships Compared to Native Populations
Diversity 2020, 12(11), 422; https://doi.org/10.3390/d12110422 - 10 Nov 2020
Viewed by 971
Abstract
Paraseriantheslophantha subsp. lophantha (Leguminosae) is native to southwestern Australia, but has become naturalized in eastern Australia and in countries around the world. Previous studies have investigated the introduction sources for P. lophantha subsp. lophantha overseas, but here, we expand on the knowledge [...] Read more.
Paraseriantheslophantha subsp. lophantha (Leguminosae) is native to southwestern Australia, but has become naturalized in eastern Australia and in countries around the world. Previous studies have investigated the introduction sources for P. lophantha subsp. lophantha overseas, but here, we expand on the knowledge of genetic patterns in its native and naturalized range in Australia. Genetic patterns were examined using nine nuclear microsatellite loci and three chloroplast DNA markers. The native populations exhibited phylogeographic patterns, including north-south differentiation, and a genetic signal related to temperature gradients. Naturalized Australian populations displayed lower overall genetic variation and no phylogeographic patterns. Several naturalized populations separated by large distances (350–650 km) shared multi-locus genotypes, supporting the notion of a shared source of germplasm and possible inbreeding due to human-mediated introductions from a limited number of individuals and/or source populations within the native range. We advocate that management strategies are tailored to the distinct conservation aims underpinning conservation in native or naturalized populations. Within the native distribution, management should have a long-term aim to replicate historical evolutionary processes, whereas in naturalized populations, immediate actions may be required to reduce the abundance of P. lophantha subsp. lophantha and minimize its invasive impact on the recipient vegetation. Full article
(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)
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Article
Landscape and Climate Influence the Patterns of Genetic Diversity and Inbreeding in Cerrado Plant Species
Diversity 2020, 12(11), 421; https://doi.org/10.3390/d12110421 - 06 Nov 2020
Cited by 2 | Viewed by 908
Abstract
The anthropization of the landscape of the Cerrado biome that has occurred over the past few decades has fragmented its natural environments, impacting the connectivity of the plant populations and altering their gene flow. Plant species may also reduce population size in response [...] Read more.
The anthropization of the landscape of the Cerrado biome that has occurred over the past few decades has fragmented its natural environments, impacting the connectivity of the plant populations and altering their gene flow. Plant species may also reduce population size in response to sub-optimal climatic and environmental conditions, and observed distribution patterns may align with theoretical schemes, such as the center–periphery model, that is, it is possible that populations on the edge have lower genetic diversity than center populations, theoretically submitted to environmental conditions closer to the optimum. In this context, we evaluate whether the genetic diversity and inbreeding coefficients of Cerrado plant species are affected by landscape features and climate characteristics, and in particular, if the distribution of the genetic diversity of these plants is consistent with the center–periphery model. To do this, we conducted a literature search for genetic studies of Cerrado plant populations using Scopus, Web of Science, and Scielo databases and the species found were used as a proxy to explore patterns throughout the biome. The data were analyzed using generalized linear mixed models (GLMM) and multiple matrix regressions (MMRRs) to evaluate the effects of landscape features and climatic variables on the observed (HO) and expected heterozygosity (HE), allelic richness (AR) and inbreeding (Fis) patterns of the local populations. The landscape was evaluated in terms of the percentage land cover of agriculture (AG), forestry (FO), remnant vegetation (RV), urban areas (UA), pasture (PA), and water (WA) within buffers of 1 km, 3 km, and 5 km around the study populations. We analyzed 121 populations of 31 plant species. The GLMMs showed that HO was affected by FO regardless of buffer size, while HE was also affected by FO, but also by WA and UA. AR was affected by WA and UA in all three buffer zones while the Fis was affected by FO and AU. The MMRRs showed that WA may affect HO, HE, and Fis within the 1 km buffer, while FO affects HO and UA affects AR within the 5 km buffer. In the case of the 1 km and 3 km buffers, however, the geographic distance between populations was identified as a factor determining the genetic diversity and inbreeding indices, indicating that isolation by distance may be an important factor defining the breeding patterns of the Cerrado plant populations. The GLMMs and MMRRs also showed that the mean annual temperature (MAT) and, to a lesser extent, isothermality (ISO) can explain the variation in genetic diversity observed in the Cerrado plant populations. We also found that the center–periphery model fits the distribution pattern observed in most of the species evaluated, including Annona crassiflora,Annona coriacea, Copaifera langsdorffii, and Eugenia dysenterica. Our results indicate that changes in the climate and the landscape of Brazilian Cerrado must be considered carefully to guarantee minimizing the impacts of these processes on the genetic diversity of Cerrado plant species and ensuring the long-term conservation of these species in this biome. Full article
(This article belongs to the Special Issue Vascular Plant Diversity at Different Scales)
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Article
A Gliriform Tooth from the Eocene of the Erlian Basin (Nei Mongol, China) and the Premolar Morphology of Anagalidan Mammals at a Crossroads
Diversity 2020, 12(11), 420; https://doi.org/10.3390/d12110420 - 05 Nov 2020
Cited by 1 | Viewed by 962
Abstract
The middle Eocene in Nei Mongol (China) was an interval of profound faunal changes as regards the basal Glires and gliriform mammals in general. A major diversification of rodent lineages (ctenodactyloids) and more modern small-sized lagomorphs was accompanied by a decline of mimotonids [...] Read more.
The middle Eocene in Nei Mongol (China) was an interval of profound faunal changes as regards the basal Glires and gliriform mammals in general. A major diversification of rodent lineages (ctenodactyloids) and more modern small-sized lagomorphs was accompanied by a decline of mimotonids (Gomphos and Mimolagus) and anagalids. The latter was an enigmatic group of basal Euarchontoglires endemic to China and Mongolia. Here, we describe the first anagalid tooth (a P4) from the Huheboerhe classic site in the Erlian Basin. The tooth, characterized by its unique morphology intermediate between mimotonids and anagalids is semihypsodont, has a single buccal root typical of mimotonids, a large paracone located anteriorly, and a nascent hypocone, characteristic of advanced anagalids. The new finding of neither an abundant nor speciose group suggests a greater diversity of anagalids in the Eocene of China. This discovery is important because it demonstrates the convergent adaptations in anagalids, possibly of ecological significance. Full article
(This article belongs to the Section Phylogeny and Evolution)
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Article
Urochloa Grasses Swap Nitrogen Source When Grown in Association with Legumes in Tropical Pastures
Diversity 2020, 12(11), 419; https://doi.org/10.3390/d12110419 - 05 Nov 2020
Cited by 6 | Viewed by 1113
Abstract
The degradation of tropical pastures sown with introduced grasses (e.g., Urochloa spp.) has dramatic environmental and economic consequences in Latin America. Nitrogen (N) limitation to plant growth contributes to pasture degradation. The introduction of legumes in association with grasses has been proposed as [...] Read more.
The degradation of tropical pastures sown with introduced grasses (e.g., Urochloa spp.) has dramatic environmental and economic consequences in Latin America. Nitrogen (N) limitation to plant growth contributes to pasture degradation. The introduction of legumes in association with grasses has been proposed as a strategy to improve N supply via symbiotic N2 fixation, but the fixed N input and N benefits for associated grasses have hardly been determined in farmers’ pastures. We have carried out on-farm research in ten paired plots of grass-alone (GA) vs. grass-legume (GL) pastures. Measurements included soil properties, pasture productivity, and sources of plant N uptake using 15N isotope natural abundance methods. The integration of legumes increased pasture biomass production by about 74%, while N uptake was improved by two-fold. The legumes derived about 80% of their N via symbiotic N2 fixation. The isotopic signature of N of grasses in GA vs. GL pastures suggested that sources of grass N are affected by sward composition. Low values of δ15N found in some grasses in GA pastures indicate that they depend, to some extent, on N from non-symbiotic N2 fixation, while δ15N signatures of grasses in GL pastures pointed to N transfer to grass from the associated legume. The role of different soil–plant processes such as biological nitrification inhibition (BNI), non-symbiotic N2 fixation by GA pastures and legume–N transfer to grasses in GL pastures need to be further studied to provide a more comprehensive understanding of N sources supporting the growth of grasses in tropical pastures. Full article
(This article belongs to the Special Issue Plant-Soil Interactions)
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Article
Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota
Diversity 2020, 12(11), 418; https://doi.org/10.3390/d12110418 - 04 Nov 2020
Cited by 1 | Viewed by 1346
Abstract
Plant microbiota support the diversity and productivity of plants. Thus, cultivation-dependent approaches are indispensable for in vitro manipulation of hub taxa. Despite recent advances in high-throughput methods, cultivability is lagging behind other environmental microbiomes, notably the human microbiome. As a plant-based culturing strategy, [...] Read more.
Plant microbiota support the diversity and productivity of plants. Thus, cultivation-dependent approaches are indispensable for in vitro manipulation of hub taxa. Despite recent advances in high-throughput methods, cultivability is lagging behind other environmental microbiomes, notably the human microbiome. As a plant-based culturing strategy, we developed culture media based on a broth of cooked aqueous mixtures of host plants. This improved the in vitro growth of representative isolates of plant microbiota and extended the in situ recovery of plant microbiota. With clover, 16S rRNA gene sequencing of representative isolates confirmed the predominance of Firmicutes, Alphaproteobacteria and Gammaproteobacteria, and less frequently Bacteroidetes and Actinobacteria. Whereas bovine-based culture media (modified R2A) confined the diversity to Firmicutes, the plant broth-based culture media revealed a wider scope of endophytes beyond rhizobia, i.e., multiple genera such as Chryseobacterium, Cronobacter, Kosakonia, Tsukamurella, and a potentially/presumptive novel species. Matrix-assisted laser desorption/ionization time-of-flight (MADI-TOF) analysis clustered isolates according to their plant niches, the endo-phyllosphere/endo-rhizosphere. We recommend the plant broth for simplicity, reproducibility and perdurable storage, supporting future culturomics applications, good laboratory practice (GLP) and good manufacturing practice (GMP). The strategy creates an “in-situ-similis” vegan nutritional matrix to analyze microbial diversity and reveal novel microbial resources pertinent to biotechnological and environmental applications. Full article
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Article
Genetic Patterns and Climate Modelling Reveal Challenges for Conserving Sclerolaena napiformis (Amaranthaceae s.l.) an Endemic Chenopod of Southeast Australia
Diversity 2020, 12(11), 417; https://doi.org/10.3390/d12110417 - 04 Nov 2020
Viewed by 763
Abstract
Sclerolaena napiformis is a perennial chenopod endemic to southeast Australia. Human-mediated habitat loss and fragmentation over the past century has caused a rapid decline in abundance and exacerbated reduced connectivity between remnant populations across three disjunct regions. To assess conservation requirements, we measured [...] Read more.
Sclerolaena napiformis is a perennial chenopod endemic to southeast Australia. Human-mediated habitat loss and fragmentation over the past century has caused a rapid decline in abundance and exacerbated reduced connectivity between remnant populations across three disjunct regions. To assess conservation requirements, we measured the genetic structure of 27 populations using double digest RADseq). We combined our genetic data with habitat models under projected climate scenarios to identify changes in future habitat suitability. There was evidence of regional differentiation that may pre-date (but also may be compounded) by recent habitat fragmentation. We also found significant correlation between genetic and geographic distance when comparing sites across regions. Overall, S. napiformis showed low genetic diversity and a relatively high proportion of inbreeding/selfing. Climate modelling, based on current occupancy, predicts a reduction in suitable habitat for S. napiformis under the most conservative climate change scenario. We suggest that the best conservation approach is to maximise genetic variation across the entire species range to allow dynamic evolutionary processes to proceed. We recommend a conservation strategy that encourages mixing of germplasm within regions and permits mixed provenancing across regions to maximise genetic novelty. This will facilitate shifts in genetic composition driven by individual plant fitness in response to the novel environmental conditions this species will experience over the next 50 years. Full article
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Article
Interactions among Shade, Caching Behavior, and Predation Risk May Drive Seed Trait Evolution in Scatter-Hoarded Plants
Diversity 2020, 12(11), 416; https://doi.org/10.3390/d12110416 - 31 Oct 2020
Cited by 2 | Viewed by 735
Abstract
Although dispersal is critical to plant life history, the relationships between seed traits and dispersal success in animal-dispersed plants remain unclear due to complex interactions among the effects of seed traits, habitat structure, and disperser behavior. We propose that in plants dispersed by [...] Read more.
Although dispersal is critical to plant life history, the relationships between seed traits and dispersal success in animal-dispersed plants remain unclear due to complex interactions among the effects of seed traits, habitat structure, and disperser behavior. We propose that in plants dispersed by scatter-hoarding granivores, seed trait evolution may have been driven by selective pressures that arise from interactions between seedling shade intolerance and predator-mediated caching behavior. Using an optimal foraging model that accounts for cache concealment, hoarder memory, and perceived predation risk, we show that hoarders can obtain cache-recovery advantages by placing caches in moderately risky locations that force potential pilferers to engage in high levels of vigilance. Our model also demonstrates that the level of risk needed to optimally protect a cache increases with the value of the cached food item. If hoarders perceive less sheltered, high-light conditions to be more risky and use this information to protect their caches, then shade-intolerant plants may increase their fitness by producing seeds with traits valued by hoarders. Consistent with this hypothesis, shade tolerance in scatter-hoarded tree species is inversely related to the value of their seeds as perceived by a scatter-hoarding rodent. Full article
(This article belongs to the Special Issue Predators as Agents of Selection and Diversification)
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Review
Predators as Agents of Selection and Diversification
Diversity 2020, 12(11), 415; https://doi.org/10.3390/d12110415 - 31 Oct 2020
Cited by 4 | Viewed by 853
Abstract
Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can [...] Read more.
Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can occur, exploring empirical evidence and suggesting promising areas for future work. We also introduce several papers recently accepted in Diversity that demonstrate just how important and varied predation can be as an agent of natural selection. We conclude that there is still much to be done in this field, especially in areas where multiple predator species prey upon common prey, in certain taxonomic groups where we still know very little, and in an overall effort to actually quantify mortality rates and the strength of natural selection in the wild. Full article
(This article belongs to the Special Issue Predators as Agents of Selection and Diversification)
Editorial
Genetic Diversity of Soil Bacteria
Diversity 2020, 12(11), 414; https://doi.org/10.3390/d12110414 - 29 Oct 2020
Viewed by 593
Abstract
The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, [...] Read more.
The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, at different latitudes and under different types of management. Full article
(This article belongs to the Special Issue Genetic Diversity of Soil Bacterial Communities)
Article
Hypogean Communities as Cybernetic Systems: Implications for the Evolution of Cave Biotas
Diversity 2020, 12(11), 413; https://doi.org/10.3390/d12110413 - 29 Oct 2020
Cited by 3 | Viewed by 606
Abstract
Ramón Margalef proposed in 1968 that ecosystems could be better understood if they were viewed as cybernetic systems. I tested this hypothesis in the case of hypogean ecosystems using available pieces of evidence. I looked on how information on feedbacks, stability, succession, organization, [...] Read more.
Ramón Margalef proposed in 1968 that ecosystems could be better understood if they were viewed as cybernetic systems. I tested this hypothesis in the case of hypogean ecosystems using available pieces of evidence. I looked on how information on feedbacks, stability, succession, organization, diversity, and energy flows in the hypogean environment fit the cybernetics hypothesis. The results were that there are convincing arguments that the application of the concept of cybernetics in biospeleology can be beneficial to broadening our understanding of cave biota in terms of their structure. I also make the case that this approach can provide more clarity about how cave biota has evolved through time and the implications for their conservation. Full article
(This article belongs to the Special Issue Cave Communities: From the Surface Border to the Deep Darkness)
Article
Impacts of Forest Thinning and White-Tailed Deer Herbivory on Translocation of the Rare Terrestrial Orchid Platanthera integrilabia
Diversity 2020, 12(11), 412; https://doi.org/10.3390/d12110412 - 28 Oct 2020
Viewed by 1080
Abstract
Translocation is increasingly being used to supplement existing occurrences and establish new occurrences of rare plant species, but translocation success is dependent on understanding responses to habitat conditions and management. Platanthera integrilabia (white fringeless orchid) is a rare terrestrial orchid species presently found [...] Read more.
Translocation is increasingly being used to supplement existing occurrences and establish new occurrences of rare plant species, but translocation success is dependent on understanding responses to habitat conditions and management. Platanthera integrilabia (white fringeless orchid) is a rare terrestrial orchid species presently found in mostly small occurrences that comprise a fraction of its historical distribution and abundance in the southeastern United States. We investigated the influence of shade and white-tailed deer herbivory, as cited concerns for this species, on the early success of its translocation from tubers as determined through measures of emergence, survival, growth, and reproduction of two cohorts. Our findings suggest that translocation from tubers could be a viable option to assist the conservation of P. integrilabia relative to its propagation from seed, but that low early emergence, survival, and flowering rates should be considered in translocation plans. Our results also indicate that translocation and ongoing habitat management should consider the potential for light availability to differentially impact distinct plant life stages and influence deer herbivory. We recommend that additional translocation studies designed to investigate the influence of site conditions on outcomes could improve the success of such efforts as well as inform the management of extant occurrences. Full article
(This article belongs to the Special Issue The Ecology and Diversity of Orchids)
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