1
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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2
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Talavera A, Palmada-Flores M, Burriel-Carranza B, Valbuena-Ureña E, Mochales-Riaño G, Adams DC, Tejero-Cicuéndez H, Soler-Membrives A, Amat F, Guinart D, Carbonell F, Obon E, Marquès-Bonet T, Carranza S. Genomic insights into the Montseny brook newt ( Calotriton arnoldi), a Critically Endangered glacial relict. iScience 2024; 27:108665. [PMID: 38226169 PMCID: PMC10788218 DOI: 10.1016/j.isci.2023.108665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/09/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
The Montseny brook newt (Calotriton arnoldi), considered the most endangered amphibian in Europe, is a relict salamandrid species endemic to a small massif located in northeastern Spain. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here, we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (Calotriton asper), combining whole-genome and ddRADseq data. Our results reveal significant demographic oscillations which accurately mirrored Europe's climatic history. Although severe bottlenecks have led to depauperate genomic diversity and long runs of homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of population fragmentation.
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Affiliation(s)
- Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Marc Palmada-Flores
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Museu de Ciències Naturals de Barcelona, Pº Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | | | | | - Dean C. Adams
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Anna Soler-Membrives
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fèlix Amat
- Àrea d’Herpetologia, BiBIO, Museu de Granollers – Ciències Naturals. Palaudàries 102, Granollers, Barcelona, Spain
| | - Daniel Guinart
- Servei de Gestió de Parcs Naturals, Diputació de Barcelona, Spain
| | - Francesc Carbonell
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Elena Obon
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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3
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Saccò M, Mammola S, Altermatt F, Alther R, Bolpagni R, Brancelj A, Brankovits D, Fišer C, Gerovasileiou V, Griebler C, Guareschi S, Hose GC, Korbel K, Lictevout E, Malard F, Martínez A, Niemiller ML, Robertson A, Tanalgo KC, Bichuette ME, Borko Š, Brad T, Campbell MA, Cardoso P, Celico F, Cooper SJB, Culver D, Di Lorenzo T, Galassi DMP, Guzik MT, Hartland A, Humphreys WF, Ferreira RL, Lunghi E, Nizzoli D, Perina G, Raghavan R, Richards Z, Reboleira ASPS, Rohde MM, Fernández DS, Schmidt SI, van der Heyde M, Weaver L, White NE, Zagmajster M, Hogg I, Ruhi A, Gagnon MM, Allentoft ME, Reinecke R. Groundwater is a hidden global keystone ecosystem. GLOBAL CHANGE BIOLOGY 2024; 30:e17066. [PMID: 38273563 DOI: 10.1111/gcb.17066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 01/27/2024]
Abstract
Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.
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Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, Verbania Pallanza, Italy
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
- National Biodiversity Future Center, Palermo, Italy
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Roman Alther
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Rossano Bolpagni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Anton Brancelj
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
- Department for Environmental Science, University of Nova Gorica, Nova Gorica, Slovenia
| | - David Brankovits
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, Verbania Pallanza, Italy
| | - Cene Fišer
- SubBio Lab, Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Vasilis Gerovasileiou
- Faculty of Environment, Department of Environment, Ionian University, Zakynthos, Greece
- Biotechnology and Aquaculture (IMBBC), Thalassocosmos, Institute of Marine Biology, Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Christian Griebler
- Department of Functional & Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Simone Guareschi
- Estación Biologica de Doñana (EBD-CSIC), Seville, Spain
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Grant C Hose
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kathryn Korbel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Elisabeth Lictevout
- International Groundwater Resources Assessment Center (IGRAC), Delft, The Netherlands
| | - Florian Malard
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Univ Lyon, Villeurbanne, France
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, Verbania Pallanza, Italy
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Anne Robertson
- School of Life and Health Sciences, Roehampton University, London, UK
| | - Krizler C Tanalgo
- Ecology and Conservation Research Laboratory (Eco/Con Lab), Department of Biological Sciences, College of Science and Mathematics, University of Southern Mindanao, Kabacan, Cotabato, Philippines
| | - Maria Elina Bichuette
- Laboratory of Subterranean Studies (LES), Department of Ecology and Evolutionary Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Špela Borko
- SubBio Lab, Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Traian Brad
- Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
- Departamento de Biologia Animal, and Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Fulvio Celico
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Steven J B Cooper
- South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- Department of Ecology and Evolutionary Biology, School of Biological Sciences and Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - David Culver
- Department of Environmental Science, American University, Washington, DC, USA
| | - Tiziana Di Lorenzo
- National Biodiversity Future Center, Palermo, Italy
- Research Institute on Terrestrial Ecosystems of the National Research Council of Italy (IRET CNR), Florence, Italy
| | - Diana M P Galassi
- Department of Life, Health and Environmental Sciences (MESVA), University of L'Aquila, L'Aquila, Italy
| | - Michelle T Guzik
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Hartland
- Lincoln Agritech Ltd, Ruakura, Kirikiriroa, Aotearoa, New Zealand
| | - William F Humphreys
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Western Australian Museum, Welshpool, Western Australia, Australia
| | - Rodrigo Lopes Ferreira
- Centro de Estudos em Biologia Subterrânea, Departamento de Ecologia e Conservação, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Enrico Lunghi
- Department of Life, Health and Environmental Sciences (MESVA), University of L'Aquila, L'Aquila, Italy
| | - Daniele Nizzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Perina
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Zoe Richards
- Coral Conservation and Research Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Ana Sofia P S Reboleira
- Departamento de Biologia Animal, and Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Melissa M Rohde
- Rohde Environmental Consulting, LLC, Seattle, Washington, USA
- Graduate Program in Environmental Science, State University of New York College of Environmental Science and Forestry, Syracuse, New York, USA
| | | | - Susanne I Schmidt
- Department of Lake Research, Helmholtz Centre for Environmental Research, Magdeburg, Germany
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Louise Weaver
- Water & Environment Group, Institute of Environmental Science & Research Ltd., Christchurch, New Zealand
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Maja Zagmajster
- SubBio Lab, Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Ian Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
| | - Albert Ruhi
- Department of Environmental Science, Policy & Management, University of California, Berkeley, California, USA
| | - Marthe M Gagnon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert Reinecke
- Institute of Geography, Johannes Gutenberg-University Mainz, Mainz, Germany
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4
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Galmarini E, Vaccarelli I, Fiasca B, Di Cicco M, Parise M, Liso IS, Piccini L, Galassi DMP, Cerasoli F. Regional climate contributes more than geographic distance to beta diversity of copepods (Crustacea Copepoda) between caves of Italy. Sci Rep 2023; 13:21243. [PMID: 38040911 PMCID: PMC10692170 DOI: 10.1038/s41598-023-48440-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Despite the study of subterranean biodiversity facing harsh sampling and mapping challenges, the huge diversity of taxa, ecological adaptations and evolutionary trajectories in subterranean environments is gaining increasing attention. Yet, the spatial and environmental factors driving the composition of groundwater communities are still poorly understood. To partially fill this knowledge gap, we collected copepod crustaceans from 12 caves along the Italian peninsula between 2019 and 2022, sampling each cave twice. The resulting presence-absence data were analysed to assess: (i) between-cave taxonomic beta diversity, also partitioning between turnover and nestedness-resultant dissimilarity; (ii) the relative weight of geographic distance and climatic differences in shaping observed beta diversity. Seventy-one species of copepods were collected overall. Pairwise beta diversity was high for most pairs of caves, with turnover being the major component. Geographic distance-decay models partially explained total beta diversity and turnover patterns. However, in Generalized Dissimilarity Models (GDM), including surface climatic conditions as predictors, the contribution of seasonal temperature averages was generally higher than that of geographic distance. Further, the explanatory and predictive performance of the GDMs notably increased, along with temperature contribution, when widening the spatial extent from which climate data were gathered. Our results confirmed a high spatial turnover in groundwater copepods' assemblages and strengthened the link between regional climate and subterranean biodiversity.
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Affiliation(s)
- Emma Galmarini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Ilaria Vaccarelli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- University Institute of Higher Studies in Pavia, Pavia, Italy
| | - Barbara Fiasca
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Mattia Di Cicco
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Mario Parise
- Department of Earth and Environmental Sciences, University Aldo Moro, Bari, Italy
| | - Isabella Serena Liso
- Department of Earth and Environmental Sciences, University Aldo Moro, Bari, Italy
| | - Leonardo Piccini
- Department of Earth Science, University of Florence, Florence, Italy
| | | | - Francesco Cerasoli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy.
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5
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Adcock ZC, Adcock ME, Forstner MRJ. Development and validation of an environmental DNA assay to detect federally threatened groundwater salamanders in central Texas. PLoS One 2023; 18:e0288282. [PMID: 37428788 DOI: 10.1371/journal.pone.0288282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
The molecular detection of DNA fragments that are shed into the environment (eDNA) has become an increasingly applied tool used to inventory biological communities and to perform targeted species surveys. This method is particularly useful in habitats where it is difficult or not practical to visually detect or trap the target organisms. Central Texas Eurycea salamanders inhabit both surface and subterranean aquatic environments. Subterranean surveys are challenging or infeasible, and the detection of salamander eDNA in water samples is an appealing survey technique for these situations. Here, we develop and validate an eDNA assay using quantitative PCR for E. chisholmensis, E. naufragia, and E. tonkawae. These three species are federally threatened and constitute the Septentriomolge clade that occurs in the northern segment of the Edwards Aquifer. First, we validated the specificity of the assay in silico and with DNA extracted from tissue samples of both target Septentriomolge and non-target amphibians that overlap in distribution. Then, we evaluated the sensitivity of the assay in two controls, one with salamander-positive water and one at field sites known to be occupied by Septentriomolge. For the salamander-positive control, the estimated probability of eDNA occurrence (ψ) was 0.981 (SE = 0.019), and the estimated probability of detecting eDNA in a qPCR replicate (p) was 0.981 (SE = 0.011). For the field control, the estimated probability of eDNA occurring at a site (ψ) was 0.938 (95% CRI: 0.714-0.998). The estimated probability of collecting eDNA in a water sample (θ) was positively correlated with salamander relative density and ranged from 0.371 (95% CRI: 0.201-0.561) to 0.999 (95% CRI: 0.850- > 0.999) among sampled sites. Therefore, sites with low salamander density require more water samples for eDNA evaluation, and we determined that our site with the lowest estimated θ would require seven water samples for the cumulative collection probability to exceed 0.95. The estimated probability of detecting eDNA in a qPCR replicate (p) was 0.882 (95% CRI: 0.807-0.936), and our assay required two qPCR replicates for the cumulative detection probability to exceed 0.95. In complementary visual encounter surveys, the estimated probability of salamanders occurring at a known-occupied site was 0.905 (SE = 0.096), and the estimated probability of detecting salamanders in a visual encounter survey was 0.925 (SE = 0.052). We additionally discuss future research needed to refine this method and understand its limitations before practical application and incorporation into formal survey protocols for these taxa.
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Affiliation(s)
- Zachary C Adcock
- Department of Biology, Texas State University, San Marcos, Texas, United States of America
- Cambrian Environmental, Austin, Texas, United States of America
| | - Michelle E Adcock
- Department of Biology, Texas State University, San Marcos, Texas, United States of America
| | - Michael R J Forstner
- Department of Biology, Texas State University, San Marcos, Texas, United States of America
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6
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Chambers EA, Tarvin RD, Santos JC, Ron SR, Betancourth-Cundar M, Hillis DM, Matz MV, Cannatella DC. 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics. Ecol Evol 2023; 13:e9842. [PMID: 36911313 PMCID: PMC9994478 DOI: 10.1002/ece3.9842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 03/10/2023] Open
Abstract
Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Environmental Science, Policy, and Management and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Rebecca D Tarvin
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Integrative Biology and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Juan C Santos
- Department of Biological Sciences St John's University New York New York USA
| | - Santiago R Ron
- Museo de Zoología, Escuela de Ciencias Biológicas Pontificia Universidad Católica del Ecuador Quito Ecuador
| | | | - David M Hillis
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
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7
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Ortiz D, Pekár S, Bryjová A. Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider. Mol Phylogenet Evol 2023; 180:107682. [PMID: 36574825 DOI: 10.1016/j.ympev.2022.107682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czechia
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8
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Raghavan R, Sundar RL, Arjun C, Britz R, Dahanukar N. Evolution in the dark: Unexpected genetic diversity and morphological stasis in the blind, aquifer-dwelling catfish Horaglanis. VERTEBRATE ZOOLOGY 2023. [DOI: 10.3897/vz.73.e98367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The lateritic aquifers of the southern Indian state of Kerala harbour a unique assemblage of enigmatic stygobitic fishes which are encountered very rarely, only when they surface during the digging and cleaning of homestead wells. Here, we focus on one of the most unusual members of this group, the catfish Horaglanis, a genus of rarely-collected, tiny, blind, pigment less, and strictly aquifer-residing species. A six-year exploratory and citizen-science backed survey supported by molecular phylogenetic analysis reveals novel insights into the diversity, distribution and population structure of Horaglanis. The genus is characterized by high levels of intraspecific and interspecific genetic divergence, with phylogenetically distinct species recovered above a 7.0% genetic-distance threshold in the mitochondrial cytochrome oxidase subunit 1 gene. Contrasting with this deep genetic divergence, however, is a remarkable stasis in external morphology. We identify and describe a new cryptic species, Horaglanis populi, a lineage that is the sister group of all currently known species. All four species are represented by multiple haplotypes. Mismatch distribution reveals that populations have not experienced recent expansions.
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Belaire JA, Higgins C, Zoll D, Lieberknecht K, Bixler RP, Neff JL, Keitt TH, Jha S. Fine-scale monitoring and mapping of biodiversity and ecosystem services reveals multiple synergies and few tradeoffs in urban green space management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157801. [PMID: 35931152 DOI: 10.1016/j.scitotenv.2022.157801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/30/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Urban watersheds can play a critical role in supporting biodiversity and ecosystem services in a rapidly changing world. However, managing for multiple environmental and social objectives in urban landscapes is challenging, especially if the optimization of one ecosystem service conflicts with another. Urban ecology research has frequently been limited to a few indicators - typically either biodiversity or ecosystem service indices - making tradeoffs and synergies difficult to assess. Through a recently established watershed-scale monitoring network in Central Texas, we address this gap by evaluating biodiversity (flora and fauna), habitat quality, and ecosystem service indices of urban green spaces across the watershed. Our results reveal substantial heterogeneity in biodiversity and ecosystem service levels and multiple synergies (stacked benefits or "win-wins"). For example, we found that carbon sequestration positively correlated with tree species richness and the proportion of native trees in a green space, indicating that biodiversity goals for increased tree diversity can also provide carbon sequestration benefits. We also documented correlations between green spaces with greater riparian forest cover and lower particulate matter (PM2.5) concentrations and cooler temperatures. In addition, we found that bee and wasp species richness was positively correlated with carbon sequestration and human visitation rates, meaning that urban green spaces can optimize carbon sequestration goals without losing pollinator habitat or access opportunities for city residents. Overall, our results indicate that many aspects of habitat quality, biodiversity, and ecosystem services can be simultaneously supported in urban green spaces. We conclude that urban design and management can optimize nature-based solutions and strategies to have distinct positive impacts on both people and nature.
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Affiliation(s)
- J Amy Belaire
- The Nature Conservancy, Texas, 3801 Kirby Drive, Suite 740, Houston, TX 77098, United States of America.
| | - Caitlin Higgins
- 16201 Gordon Cummings Road, Canyon, TX 79015, United States of America
| | - Deidre Zoll
- Department of Integrative Biology, University of Texas at Austin, 205 W 24th Street, Austin, TX 78712, United States of America.
| | - Katherine Lieberknecht
- School of Architecture, University of Texas at Austin, 310 Inner Campus Drive, Austin, TX 78712, United States of America
| | - R Patrick Bixler
- LBJ School of Public Affairs, 2315 Red River Street, University of Texas at Austin, Austin, TX 78712, United States of America
| | - John L Neff
- Central Texas Melittological Institute, 7307 Running Rope, Austin, TX 78731, United States of America
| | - Timothy H Keitt
- Department of Integrative Biology, University of Texas at Austin, 205 W 24th Street, Austin, TX 78712, United States of America
| | - Shalene Jha
- Department of Integrative Biology, University of Texas at Austin, 205 W 24th Street, Austin, TX 78712, United States of America; Lady Bird Johnson Wildflower Center, University of Texas at Austin, 205 W 24th Street, Austin, TX 78712, United States of America
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Zhu X, Zheng C, Dong X, Zhang H, Ye Z, Xue H, Bu W. Species boundary and phylogeographical pattern provide new insights into the management efforts of Megacopta cribraria (Hemiptera: Plataspidae), a bean bug invading North America. PEST MANAGEMENT SCIENCE 2022; 78:4871-4881. [PMID: 36181419 DOI: 10.1002/ps.7108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Correct identification together with information on distribution range, geographical origin and evolutionary history are the necessary basis for the management and control of invasive species. The bean bug Megacopta cribraria is a crucial agricultural pest of soybean. Recently, M. cribraria has invaded the United States and spread rapidly, causing severe reductions in soybean yields. However, the species boundary and phylogeographical pattern of this invasive bean bug are still unclear. RESULTS The results of different species delimitation methods (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Bayesian Poisson Tree Processes and Bayesian Phylogenetics and Phylogeography) strongly demonstrated that M. cribraria and Megacopta punctatissima represent the same species. M. punctatissima should not be considered a distinct species but rather a variety of M. cribraria. Phylogenetic analyses revealed three well-supported clades (Southeast Asia [SEA], East Asia continent [EAC] and Japan [JA]) with distinct geographical structures in the M. cribraria-M. punctatissima complex. The SEA clade was at the base of the phylogenetic tree, and the sister relationship between the EAC clade and JA clade was strongly supported. The split between the EAC clade and JA clade occurred at approximately 0.71 Ma, corresponding to the submergence period of the East China Sea land bridge. CONCLUSION This study clarified the species boundary between M. cribraria and its closely related species and revealed the phylogeographical pattern and evolutionary history of M. cribraria. The species delimitation and phylogeography results achieved in this study could provide new insights into the monitoring and management of this agricultural pest. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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Wilson TC, Rossetto M, Bain D, Yap JS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. AMERICAN JOURNAL OF BOTANY 2022; 109:1652-1671. [PMID: 36164832 PMCID: PMC9828017 DOI: 10.1002/ajb2.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C. Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and ScienceNSW Department of Planning and EnvironmentWollongongAustralia
| | - Jia‐Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Peter D. Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Margaret L. Stimpson
- Botany, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Peter H. Weston
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelong3125VictoriaAustralia
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12
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Wilson TC, Rossetto M, Bain D, Yap JYS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. AMERICAN JOURNAL OF BOTANY 2022. [PMID: 36164832 DOI: 10.5061/dryad.69p8cz94x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and Science, NSW Department of Planning and Environment, Wollongong, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Peter D Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Margaret L Stimpson
- Botany, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Peter H Weston
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3125, Victoria, Australia
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13
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Mammola S, Meierhofer MB, Borges PA, Colado R, Culver DC, Deharveng L, Delić T, Di Lorenzo T, Dražina T, Ferreira RL, Fiasca B, Fišer C, Galassi DMP, Garzoli L, Gerovasileiou V, Griebler C, Halse S, Howarth FG, Isaia M, Johnson JS, Komerički A, Martínez A, Milano F, Moldovan OT, Nanni V, Nicolosi G, Niemiller ML, Pallarés S, Pavlek M, Piano E, Pipan T, Sanchez‐Fernandez D, Santangeli A, Schmidt SI, Wynne JJ, Zagmajster M, Zakšek V, Cardoso P. Towards evidence-based conservation of subterranean ecosystems. Biol Rev Camb Philos Soc 2022; 97:1476-1510. [PMID: 35315207 PMCID: PMC9545027 DOI: 10.1111/brv.12851] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 12/18/2022]
Abstract
Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.
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Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS), University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Melissa B. Meierhofer
- BatLab Finland, Finnish Museum of Natural History Luomus (LUOMUS)University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
| | - Paulo A.V. Borges
- cE3c—Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group / CHANGE – Global Change and Sustainability InstituteUniversity of Azores, Faculty of Agrarian Sciences and Environment (FCAA), Rua Capitão João d'ÀvilaPico da Urze, 9700‐042 Angra do HeroísmoAzoresPortugal
| | - Raquel Colado
- Departament of Ecology and HidrologyUniversity of MurciaMurcia30100Spain
| | - David C. Culver
- Department of Environmental ScienceAmerican University4400 Massachusetts Avenue, N.WWashingtonDC20016U.S.A.
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS UMR 7205, MNHN, UPMC, EPHEMuseum National d'Histoire Naturelle, Sorbonne UniversitéParisFrance
| | - Teo Delić
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Tiziana Di Lorenzo
- Research Institute on Terrestrial Ecosystems (IRET‐CNR), National Research CouncilVia Madonna del Piano 10, 50019 Sesto FiorentinoFlorenceItaly
| | - Tvrtko Dražina
- Division of Zoology, Department of BiologyFaculty of Science, University of ZagrebRooseveltov Trg 6Zagreb10000Croatia
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
| | - Rodrigo L. Ferreira
- Center of Studies in Subterranean Biology, Biology Department, Federal University of LavrasCampus universitário s/n, Aquenta SolLavrasMG37200‐900Brazil
| | - Barbara Fiasca
- Department of Life, Health and Environmental SciencesUniversity of L'AquilaVia Vetoio 1, CoppitoL'Aquila67100Italy
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Diana M. P. Galassi
- Department of Life, Health and Environmental SciencesUniversity of L'AquilaVia Vetoio 1, CoppitoL'Aquila67100Italy
| | - Laura Garzoli
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Vasilis Gerovasileiou
- Department of Environment, Faculty of EnvironmentIonian University, M. Minotou‐Giannopoulou strPanagoulaZakynthos29100Greece
- Hellenic Centre for Marine Research (HCMR), Institute of Marine BiologyBiotechnology and Aquaculture (IMBBC)Thalassocosmos, GournesCrete71500Greece
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, Division of LimnologyUniversity of ViennaDjerassiplatz 1Vienna1030Austria
| | - Stuart Halse
- Bennelongia Environmental Consultants5 Bishop StreetJolimontWA6014Australia
| | | | - Marco Isaia
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Joseph S. Johnson
- Department of Biological SciencesOhio University57 Oxbow TrailAthensOH45701U.S.A.
| | - Ana Komerički
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
| | - Alejandro Martínez
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Filippo Milano
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Oana T. Moldovan
- Emil Racovita Institute of SpeleologyClinicilor 5Cluj‐Napoca400006Romania
- Romanian Institute of Science and TechnologySaturn 24‐26Cluj‐Napoca400504Romania
| | - Veronica Nanni
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Giuseppe Nicolosi
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Matthew L. Niemiller
- Department of Biological SciencesThe University of Alabama in Huntsville301 Sparkman Drive NWHuntsvilleAL35899U.S.A.
| | - Susana Pallarés
- Departamento de Biogeografía y Cambio GlobalMuseo Nacional de Ciencias Naturales, CSICCalle de José Gutiérrez Abascal 2Madrid28006Spain
| | - Martina Pavlek
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
- Ruđer Bošković InstituteBijenička cesta 54Zagreb10000Croatia
| | - Elena Piano
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Tanja Pipan
- ZRC SAZUKarst Research InstituteNovi trg 2Ljubljana1000Slovenia
- UNESCO Chair on Karst EducationUniversity of Nova GoricaGlavni trg 8Vipava5271Slovenia
| | | | - Andrea Santangeli
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiViikinkaari 1Helsinki00014Finland
| | - Susanne I. Schmidt
- Institute of Hydrobiology, Biology Centre CASNa Sádkách 702/7České Budějovice370 05Czech Republic
- Department of Lake ResearchHelmholtz Centre for Environmental ResearchBrückstraße 3aMagdeburg39114Germany
| | - J. Judson Wynne
- Department of Biological SciencesCenter for Adaptable Western Landscapes, Box 5640, Northern Arizona UniversityFlagstaffAZ86011U.S.A.
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Valerija Zakšek
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS), University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
- cE3c—Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group / CHANGE – Global Change and Sustainability InstituteUniversity of Azores, Faculty of Agrarian Sciences and Environment (FCAA), Rua Capitão João d'ÀvilaPico da Urze, 9700‐042 Angra do HeroísmoAzoresPortugal
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14
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Hubbs NW, Hurt CR, Niedzwiecki J, Leckie B, Withers D. Conservation genomics of urban populations of Streamside Salamander (Ambystoma barbouri). PLoS One 2022; 17:e0260178. [PMID: 35771804 PMCID: PMC9246143 DOI: 10.1371/journal.pone.0260178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
In Tennessee, populations of the state endangered Streamside Salamander (Ambystoma barbouri) are in decline as their distribution lies mostly within rapidly developing areas in the Nashville Basin. Information regarding the partitioning of genetic variation among populations of A. barbouri and the taxonomic status of these populations relative to northern populations and their congener, the Small-mouthed Salamander (A. texanum), have important implications for management and conservation of this species. Here we combined mitochondrial sequencing and genome-wide single nucleotide polymorphism (SNP) data generated using Genotyping-by-Sequencing (GBS) to investigate patterns of genetic variation within Tennessee populations of A. barbouri, to assess their relationship to populations in Kentucky, and to examine their phylogenetic relationship to the closely related A. texanum. Results from phylogenetic reconstructions reveal a complex history of Tennessee A. barbouri populations with regards to northern populations, unisexual A. barbouri, and A. texanum. Patterns of mitochondrial sequence variation suggest that A. barbouri may have originated within Tennessee and expanded north multiple times into Kentucky, Ohio, Indiana, and West Virginia. Phylogenetic reconstructions based on genome-wide SNP data contradict results based on mitochondrial DNA and correspond to geographic and taxonomic boundaries. Variation in allele frequencies at SNP genotypes, as identified by multivariate analyses and Bayesian assignment tests, identified three evolutionary significant units (ESUs) for A. barbouri within Tennessee. Collectively, these results emphasize the need for prioritizing conservation needs for Tennessee populations of A. barbouri to ensure the long-term persistence of this species.
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Affiliation(s)
- N. Wade Hubbs
- Department of Biology, Tennessee Technological University, Cookeville, TN, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Carla R. Hurt
- Department of Biology, Tennessee Technological University, Cookeville, TN, United States of America
- * E-mail:
| | | | - Brian Leckie
- Department of Biology, Tennessee Technological University, Cookeville, TN, United States of America
| | - David Withers
- Tennessee Department of Environment and Conservation, Nashville, TN, United States of America
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15
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Auteri GG, Marchán-Rivadeneira MR, Olson DH, Knowles LL. Landscape connectivity among coastal giant salamander (Dicamptodon tenebrosus) populations shows no association with land use, fire frequency, or river drainage but exhibits genetic signatures of potential conservation concern. PLoS One 2022; 17:e0268882. [PMID: 35675274 PMCID: PMC9176808 DOI: 10.1371/journal.pone.0268882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Determining the genetic consequences of both historical and contemporary events can clarify the effects of the environment on population connectivity and inform conservation decisions. Historical events (like glaciations) and contemporary factors (like logging) can disrupt gene flow between populations. This is especially true among species with specialized ecological requirements and low dispersal ability, like amphibians. We test for the genetic consequences of historical and contemporary disturbances in the coastal giant salamander (Dicamptodon tenebrosus) in the Pacific Northwest of the United States. We consider predictions based on the contemporary landscape (habitat connectivity, logging, forest fires, and topography), in addition to relatively ancient post-Pleistocene range expansion (following the last glacial retreat). To assess local versus larger-scale effects, we sampled 318 individuals across 23 sites, which were clustered in five sampling regions. Genetic variation was assessed using five microsatellite markers. We found evidence of (i) historical regional isolation, with decreased genetic diversity among more recently colonized northern sites, as well as (ii) high levels of inbreeding and loss of heterozygosity at local scales, despite relatively low overall population differentiation (FST) or strong evidence for population bottlenecks. Genetic diversity was not associated with contemporary disturbances (logging or fire), and there were no detectable effects on the genetic connectivity of populations based on intervening landscape features (habitat fragmentation and topography). However, lower genetic diversity in more northern regions indicates a lag in recovery of genetic diversity following post-Pleistocene expansion. Additionally, some populations had evidence of having undergone a recent genetic bottleneck or had high inbreeding (FIS) values. Lower genetic diversity in more northern sites means populations may be more vulnerable to future environmental changes, and managing for connectivity alone may not be sufficient given low mobility. Recent apparent reductions in some populations were not clearly linked to anthropogenic disturbances we examined. This suggests the type of disturbances this species is sensitive to may not be well understood.
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Affiliation(s)
- Giorgia G. Auteri
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - M. Raquel Marchán-Rivadeneira
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Edison Biotechnology Institute, Ohio University, Athens, Ohio, United States of America
| | - Deanna H. Olson
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, Corvallis, Oregon, United States of America
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Kim D, Taylor AT, Near TJ. Phylogenomics and species delimitation of the economically important Black Basses (Micropterus). Sci Rep 2022; 12:9113. [PMID: 35668124 PMCID: PMC9170712 DOI: 10.1038/s41598-022-11743-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/28/2022] [Indexed: 01/25/2023] Open
Abstract
Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is important in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (Micropterus) are an iconic lineage of freshwater fishes that include some of the world’s most popular species for recreational fishing and world's most invasive species. Despite their popularity, previous studies to delimit species and lineages in Micropterus suffer from insufficient geographic coverage and uninformative molecular markers. Our phylogenomic analyses of ddRAD data result in the delimitation of 19 species of Micropterus, which includes 14 described species, the undescribed but well-known Altamaha, Bartram’s, and Choctaw basses, and two additional undescribed species currently classified as Smallmouth Bass (M. dolomieu). We provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: Micropterus salmoides is retained for the Florida Bass and Micropterus nigricans is elevated from synonymy for the Largemouth Bass. The new understanding of diversity, distribution, and systematics of Black Basses will serve as important basis for the management and conservation of this charismatic and economically important clade of fishes.
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Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.
| | - Andrew T Taylor
- Department of Biology, University of Central Oklahoma, Edmond, OK, 73034, USA.,Department of Biology, University of North Georgia, Dahlonega, GA, 30597, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.,Peabody Museum, Yale University, New Haven, CT, 06511, USA
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17
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Speciation with gene flow in a narrow endemic West Virginia cave salamander (Gyrinophilus subterraneus). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01445-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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Adcock ZC, MacLaren AR, Jones RM, Villamizar-Gomez A, Wall AE, White IV K, Forstner MRJ. Predicting surface abundance of federally threatened Jollyville Plateau Salamanders ( Eurycea tonkawae) to inform management activities at a highly modified urban spring. PeerJ 2022; 10:e13359. [PMID: 35529492 PMCID: PMC9070359 DOI: 10.7717/peerj.13359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/08/2022] [Indexed: 01/13/2023] Open
Abstract
Urban expansion has contributed to the loss of habitat for range restricted species across the globe. Managing wildlife populations within these urban settings presents the challenge of balancing human and wildlife needs. Jollyville Plateau Salamanders (Eurycea tonkawae) are a range restricted, federally threatened, species of neotenic brook salamander endemic to central Texas. Almost the entire geographic range of E. tonkawae is embedded in the Austin, Cedar Park, and Round Rock metropolitan areas of Travis and Williamson counties, Texas. Among E. tonkawae occupied sites, Brushy Creek Spring has experienced some of the most extensive anthropogenic disturbance. Today the site consists of small groundwater outlets that emerge in the seams within a concrete culvert underlying a highway. Salamanders persist within this system though they are rarely detected. Here, we model the occurrence of salamanders within the surface habitat of Brushy Creek Spring using generalized linear models. In the absence of available data regarding the amount of water that is discharged from the spring, we use accumulated rainfall as a proxy for discharge to estimate salamander abundance. Additionally, we present evidence of reproduction, recruitment, and subterranean movement by E. tonkawae throughout this site. Infrastructure maintenance is inevitable at Brushy Creek Spring. We intend for our results to inform when maintenance should occur, i.e., during environmental conditions when salamanders are less likely to be observed in the surface habitat, to avoid unnecessary impacts to this federally threatened species.
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Affiliation(s)
- Zachary C. Adcock
- Department of Biology, Texas State University, San Marcos, Texas, United States
- Cambrian Environmental, Austin, Texas, United States
| | | | - Ryan M. Jones
- Cambrian Environmental, Austin, Texas, United States
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19
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Ballou L, Brankovits D, Chávez-Solís EM, Chávez Díaz JM, Gonzalez BC, Rohret S, Salinas A, Liu A, Simões N, Álvarez F, Miglietta MP, Iliffe TM, Borda E. An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatán Peninsula, Mexico. Sci Rep 2022; 12:5302. [PMID: 35351932 PMCID: PMC8961266 DOI: 10.1038/s41598-022-08779-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/07/2022] [Indexed: 01/24/2023] Open
Abstract
The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed anchialine shrimp genus Typhlatya (Atyidae). Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation (i.e., molecular, morphological, broad geographic and type locality sampling, and environmental data) of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges, syntopy within cave systems and five genetic lineages (of which two are new to science). Despite sampling from the type locality of endangered T. campecheae, specimens (and molecular data) were indistinguishable from vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity ancestor for a post-Paleogene arc Yucatán + Cuba Typhlatya clade within the anchialine Atyidae clade. A secondary adaptation for the coastal-restricted euryhaline (2–37 psu), Typhlatya dzilamensis (unknown conservation status) was identified, while remaining species lineages were low-salinity (< 5 psu) adapted and found within the meteoric lens of inland and coastal caves. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.
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Affiliation(s)
- Lauren Ballou
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Pkwy, Galveston, TX, USA
| | - David Brankovits
- Molecular Ecology Group, Water Research Institute, National Research Council of Italy (IRSA CNR), 28922, Pallanza, Italy
| | - Efraín M Chávez-Solís
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1er piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Ciudad de México, Mexico.,Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - José M Chávez Díaz
- Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, A.P. 70-153, 04510, Coyoacán, México D.F., Mexico
| | - Brett C Gonzalez
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, P.O. Box 37012, Washington D.C., USA
| | - Shari Rohret
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Green Bldg., 77 Massachusetts Ave, Cambridge, MA, USA.,Geology & Geophysics Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS #52, Woods Hole, MA, USA
| | - Alexa Salinas
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN, USA
| | - Arielle Liu
- School of Anthropology, University of Arizona, Emil W. Haury Anthropology Bldg., 1009 E South Campus Dr., Tucson, AZ, USA
| | - Nuno Simões
- Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo S/N, Sisal, Yucatán, Mexico.,National Coastal Resilience Laboratory (LANRESC), Puerto de Abrigo S/N, Sisal, Yucatán, Mexico.,International Chair for Ocean and Coastal Studies in Mexico, Harte Research Institute, Texas A&M at Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX, USA
| | - Fernando Álvarez
- Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, A.P. 70-153, 04510, Coyoacán, México D.F., Mexico
| | - Maria Pia Miglietta
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Pkwy, Galveston, TX, USA
| | - Thomas M Iliffe
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Pkwy, Galveston, TX, USA
| | - Elizabeth Borda
- Department of Life Sciences, Texas A&M University San Antonio, One University Way, San Antonio, TX, USA.
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20
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van Steenderen C, Sutton G. SPEDE‐sampler: an R Shiny application to assess how methodological choices and taxon‐sampling can affect Generalised Mixed Yule Coalescent (GMYC) output and interpretation. Mol Ecol Resour 2022; 22:2054-2069. [PMID: 35094502 PMCID: PMC9306842 DOI: 10.1111/1755-0998.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/01/2022]
Abstract
Species delimitation tools are vital to taxonomy and the discovery of new species. These tools can make use of genetic data to estimate species boundaries, where one of the most widely used methods is the Generalized Mixed Yule Coalescent (GMYC) model. Despite its popularity, a number of factors are known to influence the performance and resulting inferences of the GMYC. Moreover, the few studies that have assessed model performance to date have been predominantly based on simulated data sets, where model assumptions are not violated. Here, we present a user‐friendly R Shiny application, ‘SPEDE‐sampler’ (SPEcies DElimitation sampler), that assesses the effect of computational and methodological choices, in combination with sampling effects, on the GMYC model. Output phylogenies are used to test the effect that (1) sample size, (2) BEAST and GMYC parameters (e.g. prior settings, single vs multiple threshold, clock model), and (3) singletons have on GMYC output. Optional predefined grouping information (e.g. morphospecies/ecotypes) can be uploaded in order to compare it with GMYC species and estimate percentage match scores. Additionally, predefined groups that contribute to inflated species richness estimates are identified by SPEDE‐sampler, allowing for the further investigation of potential cryptic species or geographical substructuring in those groups. Merging by the GMYC is also recorded to identify where traditional taxonomy has overestimated species numbers. Four worked examples are provided to illustrate the functionality of the program's workflow, and the variation that can arise when applying the GMYC model to empirical data sets. The R Shiny program is available for download at https://github.com/clarkevansteenderen/spede_sampler_R.
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Affiliation(s)
- C.J.M. van Steenderen
- Centre for Biological Control Department of Zoology and Entomology Rhodes University Grahamstown/Makhanda 6139 Eastern Cape South Africa
| | - G.F. Sutton
- Centre for Biological Control Department of Zoology and Entomology Rhodes University Grahamstown/Makhanda 6139 Eastern Cape South Africa
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21
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Recknagel H, Trontelj P. From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods. Bioscience 2021; 72:254-266. [PMID: 35241972 PMCID: PMC8888124 DOI: 10.1093/biosci/biab117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species—all plethodontid and proteid salamanders—are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.
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Affiliation(s)
- Hans Recknagel
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
| | - Peter Trontelj
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
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22
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Iannella M, Fiasca B, Di Lorenzo T, Di Cicco M, Biondi M, Mammola S, Galassi DM. Getting the ‘most out of the hotspot’ for practical conservation of groundwater biodiversity. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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23
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Geographic patterns of genomic variation in the threatened Salado salamander, Eurycea chisholmensis. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01364-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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25
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Abstract
The Mammoth Cave System in the Interior Low Plateau karst region in central Kentucky, USA is a global hotspot of cave-limited biodiversity, particularly terrestrial species. We searched the literature, museum accessions, and database records to compile an updated list of troglobiotic and stygobiotic species for the Mammoth Cave System and compare our list with previously published checklists. Our list of cave-limited fauna totals 49 species, with 32 troglobionts and 17 stygobionts. Seven species are endemic to the Mammoth Cave System and other small caves in Mammoth Cave National Park. The Mammoth Cave System is the type locality for 33 cave-limited species. The exceptional diversity at Mammoth Cave is likely related to several factors, such as the high dispersal potential of cave fauna associated with expansive karst exposures, high surface productivity, and a long history of exploration and study. Nearly 80% of the cave-limited fauna is of conservation concern, many of which are at an elevated risk of extinction because of small ranges, few occurrences, and several potential threats.
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26
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Linking Hydrogeology and Ecology in Karst Landscapes: The Response of Epigean and Obligate Groundwater Copepods (Crustacea: Copepoda). WATER 2021. [DOI: 10.3390/w13152106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Groundwater invertebrate communities in karst landscapes are known to vary in response to multiple environmental factors. This study aims to explore the invertebrate assemblages’ composition of an Apennine karst system in Italy mainly described by the Rio Gamberale surface stream and the Stiffe Cave. The stream sinks into the carbonate rock and predominantly feeds the saturated karst into the cave. For a minor portion, groundwater flows from the epikarst and the perched aquifer within it. The spatial distribution of the species belonging to the selected target group of the Crustacea Copepoda between the surface stream and the groundwater habitats inside the cave highlighted a different response of surface-water species and obligate groundwater dwellers to the hydrogeological traits of the karst unit. Our results suggest that fast endorheic infiltration routes promoted the drift of epigean species from the surface to groundwater via the sinking stream while most of the obligate groundwater dwellers come from the perched aquifer in the epikarst from diffuse infiltration pathways.
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27
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Tovar RU, Cantu V, Fremaux B, Gonzalez Jr P, Spikes A, García DM. Comparative development and ocular histology between epigean and subterranean salamanders ( Eurycea) from central Texas. PeerJ 2021; 9:e11840. [PMID: 34395082 PMCID: PMC8325428 DOI: 10.7717/peerj.11840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 07/01/2021] [Indexed: 11/24/2022] Open
Abstract
The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes-the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni.
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Affiliation(s)
- Ruben U. Tovar
- Department of Biology, Texas State University, San Marcos, TX, United States of America
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Valentin Cantu
- San Marcos Aquatic Resources Center, U.S. Fish and Wildlife Service, San Marcos, TX, United States of America
- Uvalde National Fish Hatchery, U.S. Fish and Wildlife Service, Uvalde, TX, United States of America
| | - Brian Fremaux
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Pedro Gonzalez Jr
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Amanda Spikes
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Dana M. García
- Department of Biology, Texas State University, San Marcos, TX, United States of America
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28
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Parker E, Dornburg A, Struthers CD, Jones CD, Near TJ. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Syst Biol 2021; 71:58-77. [PMID: 34247239 DOI: 10.1093/sysbio/syab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/06/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
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Affiliation(s)
- Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, NC 28223, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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29
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Mahbub M, Wahab Z, Reaz R, Rahman MS, Bayzid MS. wQFM: Highly Accurate Genome-scale Species Tree Estimation from Weighted Quartets. Bioinformatics 2021; 37:3734-3743. [PMID: 34086858 DOI: 10.1093/bioinformatics/btab428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging. RESULTS We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL. AVAILABILITY wQFM is available in open source form at https://github.com/Mahim1997/wQFM-2020. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mahim Mahbub
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Zahin Wahab
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Rezwana Reaz
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - M Saifur Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
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30
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McAllister CT, Adcock ZC, Villamizar-Gomez A, Jones RM, Forstner MRJ. A New Host Record for Clinostomum cf. marginatum (Trematoda: Digenea: Clinostomidae) from the Endemic Salado Salamander, Eurycea chisholmensis (Caudata: Plethodontidae), from the Edwards Plateau, Texas, U.S.A. COMP PARASITOL 2021. [DOI: 10.1654/1525-2647-88.1.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chris T. McAllister
- Science and Mathematics Division, Eastern Oklahoma State College, 2805 NE Lincoln Road, Idabel, Oklahoma, 74745, U.S.A. (e-mail: ),
| | - Zachary C. Adcock
- Department of Biology, Texas State University, 601 University Drive, San Marcos, Texas, 78666, U.S.A. (e-mail: ), and
| | - Andrea Villamizar-Gomez
- Department of Biology, Texas State University, 601 University Drive, San Marcos, Texas, 78666, U.S.A. (e-mail: ), and
| | - Ryan M. Jones
- Department of Biology, Texas State University, 601 University Drive, San Marcos, Texas, 78666, U.S.A. (e-mail: ), and
| | - Michael R. J. Forstner
- Department of Biology, Texas State University, 601 University Drive, San Marcos, Texas, 78666, U.S.A. (e-mail: ), and
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31
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Bendik NF, Chamberlain DA, Devitt TJ, Donelson SE, Nissen B, Owen JD, Robinson D, Sissel BN, Sparks K. Subterranean movement inferred by temporary emigration in Barton Springs salamanders ( Eurycea sosorum). PeerJ 2021; 9:e11246. [PMID: 33981501 PMCID: PMC8074841 DOI: 10.7717/peerj.11246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022] Open
Abstract
Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat.
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Affiliation(s)
- Nathan F Bendik
- Watershed Protection Department, City of Austin, Austin, TX, United States of America
| | - Dee Ann Chamberlain
- Watershed Protection Department, City of Austin, Austin, TX, United States of America
| | - Thomas J Devitt
- Watershed Protection Department, City of Austin, Austin, TX, United States of America.,Current affiliation: University of Texas, Department of Integrative Biology and Biodiversity Center, Austin, TX, United States of America
| | - Sarah E Donelson
- Watershed Protection Department, City of Austin, Austin, TX, United States of America
| | - Bradley Nissen
- Watershed Protection Department, City of Austin, Austin, TX, United States of America.,Current affiliation: Tennessee State University, Department of Agricultural and Environmental Sciences, Nashville, TN, United States of America
| | - Jacob D Owen
- Watershed Protection Department, City of Austin, Austin, TX, United States of America.,Current affiliation: Randolph Air Force Base, AFCEC, JBSA ISS Natural Resource Support, San Antonio, TX, United States of America
| | - Donelle Robinson
- Watershed Protection Department, City of Austin, Austin, TX, United States of America.,Current affiliation: United States Fish and Wildlife Service, Austin Ecological Services Field Office, Austin, TX, United States of America
| | - Blake N Sissel
- Watershed Protection Department, City of Austin, Austin, TX, United States of America.,Current affiliation: Travis County, Department of Transportation and Natural Resources, Austin, TX, United States of America
| | - Kenneth Sparks
- Watershed Protection Department, City of Austin, Austin, TX, United States of America.,Current affiliation: Baer Engineering & Environmental Consulting, Inc., Austin, TX, United States of America
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32
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Marshall TL, Chambers EA, Matz MV, Hillis DM. How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake. Mol Phylogenet Evol 2021; 162:107194. [PMID: 33940060 DOI: 10.1016/j.ympev.2021.107194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/12/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one's question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.
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Affiliation(s)
- Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA.
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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33
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Esquerré D, Donnellan SC, Pavón-Vázquez CJ, Fenker J, Keogh JS. Phylogeography, historical demography and systematics of the world's smallest pythons (Pythonidae, Antaresia). Mol Phylogenet Evol 2021; 161:107181. [PMID: 33892100 DOI: 10.1016/j.ympev.2021.107181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022]
Abstract
Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A. perthensis). Our integrative analyses of phylogenetics, population structure, species delimitation, historical demography and morphometrics revealed that the true evolutionary diversity is not well reflected in the current appraisal of the diversity of the group. We find that Antaresia childreni and A. stimsoni comprise a widespread network of populations connected by gene flow and without evidence of species-level divergence among them. However, A. maculosa shows considerable genetic structuring which leads us to recognise two subspecies in northeastern Australia and a new species in Torres Strait and New Guinea. These two contrasting cases of over and under estimation of diversity, respectively, illustrate the power of thorough integrative approaches into understanding evolution of biodiversity. Furthermore, our analyses of historical demographic patterns highlight the importance of the Kimberley, Pilbara and Cape York as origins of biodiversity in Australia.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
| | | | - Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jéssica Fenker
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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34
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Brischoux F, Lillywhite HB, Shine R, Pinaud D. Osmoregulatory ability predicts geographical range size in marine amniotes. Proc Biol Sci 2021; 288:20203191. [PMID: 33823670 PMCID: PMC8059505 DOI: 10.1098/rspb.2020.3191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 12/21/2022] Open
Abstract
Species that are distributed over wide geographical ranges are likely to encounter a greater diversity of environmental conditions than do narrowly distributed taxa, and thus we expect a correlation between size of geographical range and breadth of physiological tolerances to abiotic challenges. That correlation could arise either because higher physiological capacity enables range expansion, or because widely distributed taxa experience more intense (but spatially variable) selection on physiological tolerances. The invasion of oceanic habitats by amniotic vertebrates provides an ideal system with which to test the predicted correlation between range size and physiological tolerances, because all three lineages that have secondarily moved into marine habitats (mammals, birds, reptiles) exhibit morphological and physiological adaptations to excrete excess salt. Our analyses of data on 62 species (19 mammals, 18 birds, 24 reptiles) confirm that more-widely distributed taxa encounter habitats with a wider range of salinities, and that they have higher osmoregulatory ability as determined by sodium concentrations in fluids expelled from salt-excreting organs. This result remains highly significant even in models that incorporate additional explanatory variables such as metabolic mode, body size and dietary habits. Physiological data thus may help to predict potential range size and perhaps a species' vulnerability to anthropogenic disturbance.
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Affiliation(s)
- François Brischoux
- Centre d'Etudes Biologiques de Chizé, CEBC UMR 7372 CNRS-La Rochelle Université, 79360 Villiers en Bois, France
| | | | - Richard Shine
- Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia
| | - David Pinaud
- Centre d'Etudes Biologiques de Chizé, CEBC UMR 7372 CNRS-La Rochelle Université, 79360 Villiers en Bois, France
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35
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Gibson R, Hutchins BT, Krejca JK, Diaz PH, Sprouse PS. Stygobromus bakeri, a new species of groundwater amphipod (Amphipoda, Crangonyctidae) associated with the Trinity and Edwards aquifers of central Texas, USA. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.38.61787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new stygobitic groundwater amphipod species, Stygobromus bakerisp. nov., is described from 4 central Texas limestone karst springs; John Knox Spring (Comal County), Jacob’s Well (Hays County), Mormon Spring (Travis County) and Salado Springs (Bell County). This species belongs to the predominately western Nearctic hubbsi species group of Stygobromus and differs from other species in the group by gnathopod 1 with row of 4 to 5 setae posterior to the defining angle, pereopods 6 and 7 with broadly expanded bases and distinct distoposterior lobes, gnathopods 1 and 2 with 2 rows of 3 singly inserted setae on the inner palm, and uropod 3 with single, slightly distal peduncular seta. Habitat, sympatric groundwater species, and conservation issues are discussed.
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36
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Reliable Evapotranspiration Predictions with a Probabilistic Machine Learning Framework. WATER 2021. [DOI: 10.3390/w13040557] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Evapotranspiration is often expressed in terms of reference crop evapotranspiration (ETo), actual evapotranspiration (ETa), or surface water evaporation (Esw), and their reliable predictions are critical for groundwater, irrigation, and aquatic ecosystem management in semi-arid regions. We demonstrated that a newly developed probabilistic machine learning (ML) model, using a hybridized “boosting” framework, can simultaneously predict the daily ETo, Esw, & ETa from local hydroclimate data with high accuracy. The probabilistic approach exhibited great potential to overcome data uncertainties, in which 100% of the ETo, 89.9% of the Esw, and 93% of the ETa test data at three watersheds were within the models’ 95% prediction intervals. The modeling results revealed that the hybrid boosting framework can be used as a reliable computational tool to predict ETo while bypassing net solar radiation calculations, estimate Esw while overcoming uncertainties associated with pan evaporation & pan coefficients, and predict ETa while offsetting high capital & operational costs of EC towers. In addition, using the Shapley analysis built on a coalition game theory, we identified the order of importance and interactions between the hydroclimatic variables to enhance the models’ transparency and trustworthiness.
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37
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Moon LM, Anderson KA, Glass Campbell L. Discovery of central Texas
Eurycea
eggs in the wild. Ecosphere 2021. [DOI: 10.1002/ecs2.3382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Linda M. Moon
- United States Fish & Wildlife Service San Marcos Aquatic Resources Center 500 East McCarty Lane San Marcos Texas78666USA
| | - Kelsey A. Anderson
- United States Fish & Wildlife Service San Marcos Aquatic Resources Center 500 East McCarty Lane San Marcos Texas78666USA
| | - Lindsay Glass Campbell
- United States Fish & Wildlife Service San Marcos Aquatic Resources Center 500 East McCarty Lane San Marcos Texas78666USA
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38
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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39
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Mussmann SM, Douglas MR, Oakey DD, Douglas ME. Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus) of the Greater Death Valley ecosystem. Ecol Evol 2020; 10:10798-10817. [PMID: 33072297 PMCID: PMC7548178 DOI: 10.1002/ece3.6736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio-Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. F ST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater-fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes.
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Affiliation(s)
- Steven M. Mussmann
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - David D. Oakey
- School of Life SciencesArizona State UniversityTempeAZUSA
- Present address:
Arizona State Veteran HomePhoenixAZUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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40
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Bangs MR, Douglas MR, Brunner PC, Douglas ME. Reticulate evolution as a management challenge: Patterns of admixture with phylogenetic distance in endemic fishes of western North America. Evol Appl 2020; 13:1400-1419. [PMID: 32684966 PMCID: PMC7359839 DOI: 10.1111/eva.13042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Admixture in natural populations is a long-standing management challenge, with population genomic approaches offering means for adjudication. We now more clearly understand the permeability of species boundaries and the potential of admixture for promoting adaptive evolution. These issues particularly resonate in western North America, where tectonism and aridity have fragmented and reshuffled rivers over millennia, in turn promoting reticulation among endemic fishes, a situation compounded by anthropogenic habitat modifications and non-native introductions. The melding of historic and contemporary admixture has both confused and stymied management. We underscore this situation with a case study that quantifies basin-wide admixture among a group of native and introduced fishes by employing double-digest restriction site-associated DNA (ddRAD) sequencing. Our approach: (a) quantifies the admixed history of 343 suckers (10 species of Catostomidae) across the Colorado River Basin; (b) gauges admixture within the context of phylogenetic distance and "ecological specialization"; and (c) extrapolates potential drivers of introgression across hybrid crosses that involve endemic as well as invasive species. Our study extends across an entire freshwater basin and expands previous studies more limited in scope both geographically and taxonomically. Our results detected admixture involving all 10 species, with habitat alterations not only accelerating the breakdown of reproductive isolation, but also promoting introgression. Hybridization occurred across the genus despite phylogenetic distance, whereas introgression was only detected within subgenera, implicating phylogenetic distance and/or ecological specialization as drivers of reproductive isolation. Understanding the extent of admixture and reproductive isolation across multiple species serves to disentangle their reticulate evolutionary histories and provides a broadscale perspective for basin-wide conservation and management.
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Affiliation(s)
- Max R. Bangs
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
- Department of Biological SciencesFlorida State UniversityTallahasseeFLUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Patrick C. Brunner
- Integrative BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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41
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Zheng C, Ye Z, Zhu X, Zhang H, Dong X, Chen P, Bu W. Integrative taxonomy uncovers hidden species diversity in the rheophilic genus
Potamometra
(Hemiptera: Gerridae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | | | - Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Pingping Chen
- Netherlands Biodiversity Centre – Naturalis Leiden The Netherlands
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
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42
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McGaugh SE, Weaver S, Gilbertson EN, Garrett B, Rudeen ML, Grieb S, Roberts J, Donny A, Marchetto P, Gluesenkamp AG. Evidence for rapid phenotypic and behavioural shifts in a recently established cavefish population. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Cave colonization offers a natural laboratory to study an extreme environmental shift, and diverse cave species from around the world often have converged on robust morphological, physiological and behavioural traits. The Mexican tetra (Astyanax mexicanus) has repeatedly colonized caves in the Sierra de El Abra and Sierra de Guatemala regions of north-east Mexico ~0.20–1 Mya, indicating an ability to adapt to the cave environment. The time frame for the evolution of these traits in any cave animal, however, is poorly understood. Astyanax mexicanus from the Río Grande in South Texas were brought to Central Texas beginning in the early 1900s and colonized underground environments. Here, we investigate whether phenotypic and behavioural differences have occurred rapidly between a surface population and a geographically proximate cave population, probably of recent origin. Fish from the cave and surface populations differ significantly in morphological traits, including coloration, lateral line expansion and dorsal fin placement. Striking behavioural shifts in aggression, feeding and wall-following have also occurred. Together, our results suggest that morphological and behavioural changes accompanying cave colonization can be established rapidly, and this system offers an exciting and unique opportunity for isolating the genetic and environmental contributions to colonization of extreme environments.
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Affiliation(s)
- Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Sam Weaver
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Erin N Gilbertson
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Brianna Garrett
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Melissa L Rudeen
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Stephanie Grieb
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Jennifer Roberts
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Alexandra Donny
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Peter Marchetto
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, USA
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43
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Narayan EJ, Forsburg ZR, Davis DR, Gabor CR. Non-invasive Methods for Measuring and Monitoring Stress Physiology in Imperiled Amphibians. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00431] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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44
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Hydrologic variability contributes to reduced survival through metamorphosis in a stream salamander. Proc Natl Acad Sci U S A 2019; 116:19563-19570. [PMID: 31488710 DOI: 10.1073/pnas.1908057116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Changes in the amount, intensity, and timing of precipitation are increasing hydrologic variability in many regions, but we have little understanding of how these changes are affecting freshwater species. Stream-breeding amphibians-a diverse group in North America-may be particularly sensitive to hydrologic variability during aquatic larval and metamorphic stages. Here, we tested the prediction that hydrologic variability in streams decreases survival through metamorphosis in the salamander Gyrinophilus porphyriticus, reducing recruitment to the adult stage. Using a 20-y dataset from Merrill Brook, a stream in northern New Hampshire, we show that abundance of G. porphyriticus adults has declined by ∼50% since 1999, but there has been no trend in larval abundance. We then tested whether hydrologic variability during summers influences survival through metamorphosis, using capture-mark-recapture data from Merrill Brook (1999 to 2004) and from 4 streams in the Hubbard Brook Experimental Forest (2012 to 2014), also in New Hampshire. At both sites, survival through metamorphosis declined with increasing variability of stream discharge. These results suggest that hydrologic variability reduces the demographic resilience and adaptive capacity of G. porphyriticus populations by decreasing recruitment of breeding adults. They also provide insight on how increasing hydrologic variability is affecting freshwater species, and on the broader effects of environmental variability on species with vulnerable metamorphic stages.
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45
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Liu T, Sun K, Csorba G, Zhang K, Zhang L, Zhao H, Jin L, Thong VD, Xiao Y, Feng J. Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Mol Phylogenet Evol 2019; 139:106544. [PMID: 31252069 DOI: 10.1016/j.ympev.2019.106544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.
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Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Vu Dinh Thong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; College of Life Science, Jilin Agricultural University, Changchun, China.
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Walls SC, Gabor CR. Integrating Behavior and Physiology Into Strategies for Amphibian Conservation. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00234] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Frequency and Ecology of Tail Loss in Populations of the Georgetown Salamander (Eurycea naufragia). J HERPETOL 2019. [DOI: 10.1670/17-178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Biodiversity conservation of Morlocks in west-central Texas. Proc Natl Acad Sci U S A 2019; 116:2410-2412. [PMID: 30651309 DOI: 10.1073/pnas.1821145116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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