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Sharief A, Joshi BD, Kumar V, Singh H, Singh VK, Dar SA, Graham C, Ramesh C, Quyoom I, Thakur M, Sharma LK. Empirical Data Suggest That the Kashmir Musk Deer ( Moschus cupreus, Grubb 1982) Is the One Musk Deer Distributed in the Western Himalayas: An Integration of Ecology, Genetics and Geospatial Modelling Approaches. BIOLOGY 2023; 12:786. [PMID: 37372071 DOI: 10.3390/biology12060786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
Insufficient research has been conducted on musk deer species across their distribution range, primarily because of their elusive behaviour and the fact they occupy remote high-altitude habitats in the Himalayas above 2500 m. The available distribution records, primarily derived from ecological studies with limited photographic and indirect evidence, fail to provide comprehensive information on the species distribution. Consequently, uncertainties arise when attempting to determine the presence of specific taxonomic units of musk deer in the Western Himalayas. This lack of knowledge hampers species-oriented conservation efforts, as there need to be more species-specific initiatives focused on monitoring, protecting, and combatting the illegal poaching of musk deer for their valuable musk pods. We used transect surveys (220 trails), camera traps (255 cameras), non-invasive DNA sampling (40 samples), and geospatial modelling (279 occurrence records) to resolve the taxonomic ambiguity, and identify the suitable habitat of musk deer (Moschus spp.) in Uttarkashi District of Uttarakhand and the Lahaul-Pangi landscape of Himachal Pradesh. All the captured images and DNA-based identification results confirmed the presence of only Kashmir musk deer (KDM) (Moschus cupreus) in Uttarakhand and Himachal Pradesh. The results suggest that KMD inhabit a narrow range of suitable habitats (6.9%) of the entire Western Himalayas. Since all evidence indicates that only KMD are present in the Western Himalayas, we suggest that the presence of other species of musk deer (Alpine musk deer and Himalayan musk deer) was wrongly reported. Therefore, future conservation plans and management strategies must focus only on KMD in the Western Himalayas.
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Affiliation(s)
- Amira Sharief
- Zoological Survey of India, Kolkata 700053, India
- Wildlife Institute of India, Dehradun 248001, India
- WSL Swiss Federal Research Institute, 8903 Zurcherstrasse, Switzerland
| | | | - Vineet Kumar
- Zoological Survey of India, Kolkata 700053, India
- Wildlife Institute of India, Dehradun 248001, India
| | - Hemant Singh
- Zoological Survey of India, Kolkata 700053, India
| | | | | | - Catherine Graham
- WSL Swiss Federal Research Institute, 8903 Zurcherstrasse, Switzerland
| | | | - Iyaz Quyoom
- Department of Zoology, University of Kashmir, Srinagar 19006, India
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Vieira JPS, Selbach-Schnadelbach A, Braz M, Ribeiro PL, van den Berg C, Oliveira RP. Coalescent-Based Species Delimitation in Herbaceous Bamboos (Bambusoideae, Olyreae) from Eastern Brazil: Implications for Taxonomy and Conservation in a Group with Weak Morphological Divergence Coupled with Low Genetic Diversity. PLANTS (BASEL, SWITZERLAND) 2022; 12:107. [PMID: 36616235 PMCID: PMC9824829 DOI: 10.3390/plants12010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Species delimitation in herbaceous bamboos has been complex and, in some genera, a great part of its diversity has been confirmed only based on genetic information, as is the case of the genus Raddia. It includes nine species, all occurring in Brazil, but only R. portoi predominates in dry forests of the Northeast associated with the Caatinga phytogeographic domain. This species is morphologically close to R. angustifolia, which is known for a single location in the Atlantic Forest in Southern Bahia, and is considered to be threatened by extinction. Besides problems with taxonomic focus, actions for its conservation are complicated because it is not certain if it must be considered an independent species or included in the more widespread R. portoi. In this study, we used coalescent multispecies (MSC) theory approaches combined with genetic structure analyses in an attempt to delimit these two species. Different analyses were congruent and the species delimitation using MSC inferred distinct lineages supporting their recognition as two species. These results solved the taxonomic doubts and also showed the power of these approaches to delimit species as lineages, even in groups with weak morphological divergence and low genetic variability, and also impacting our knowledge for conservation purposes.
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Affiliation(s)
- João Paulo S. Vieira
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana 44031-460, Bahia, Brazil
| | - Alessandra Selbach-Schnadelbach
- Instituto de Biologia, Universidade Federal da Bahia, Av. Barão de Jeremoabo s.n., Ondina, Salvador 40150-170, Bahia, Brazil
| | - Marcos Braz
- Instituto de Biologia, Universidade Federal da Bahia, Av. Barão de Jeremoabo s.n., Ondina, Salvador 40150-170, Bahia, Brazil
| | - Patrícia L. Ribeiro
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, Bahia, Brazil
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana 44031-460, Bahia, Brazil
| | - Reyjane P. Oliveira
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana 44031-460, Bahia, Brazil
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Mosher CM, Johnson CJ, Murray BW. Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat specialization,
Ascaphus truei
, resolved using two types of genetic markers. Ecol Evol 2022; 12:e8716. [PMID: 35342604 PMCID: PMC8931771 DOI: 10.1002/ece3.8716] [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: 04/24/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Reconstruction of historical relationships between geographic regions within a species’ range can indicate dispersal patterns and help predict future responses to shifts in climate. Ascaphus truei (coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques—microsatellite and genotype‐by‐sequencing (GBS)—to compare the within‐region genetic diversity of populations near the northern extent of the species’ range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving toward the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of A. truei to climate change.
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Affiliation(s)
- Cherie M. Mosher
- University of Northern British Columbia Prince George British Columbia Canada
| | - Chris J. Johnson
- University of Northern British Columbia Prince George British Columbia Canada
| | - Brent W. Murray
- University of Northern British Columbia Prince George British Columbia Canada
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Buckley SJ, Brauer C, Unmack PJ, Hammer MP, Beheregaray LB. The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages. Mol Ecol 2021; 30:4866-4883. [PMID: 34265125 DOI: 10.1111/mec.16082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022]
Abstract
While the influence of Pleistocene climatic changes on divergence and speciation has been well-documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. We investigated the role of hydrological and coastal topographic changes brought about by Plio-Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7958 ddRAD-seq (double digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to assess the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea-level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter- and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types.
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Affiliation(s)
- Sean James Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, ACT, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Nottingham S, Pelletier TA. The impact of climate change on western Plethodon salamanders' distribution. Ecol Evol 2021; 11:9370-9384. [PMID: 34306628 PMCID: PMC8293714 DOI: 10.1002/ece3.7735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
AIM Given that salamanders have experienced large shifts in their distributions over time, we determined how each species of Plethodon in the Pacific Northwest would respond to climate change. We incorporated several greenhouse scenarios both on a species-by-species basis, and also using phylogenetic groups, with the aim to determine the best course of action in managing land area to conserve diversity in this group. LOCATION Pacific Northwest of the United States (northern CA, OR, WA, ID, and MT). MAJOR TAXA STUDIED Western Plethodon salamanders. METHODS Species distribution models were estimated using MaxEnt for the current time period and for several future climate scenarios using bioclimatic data layers. We used several methods to quantify the change in habitat suitability over time from the models. We explored aspects of the climate layers to determine whether we can expect a concerted response to climate change due to similarity in ecological niche or independent responses that could be harder to manage. RESULTS The distribution of western Plethodon salamander species is strongly influenced by precipitation and less so by temperature. Species responses to climate change resulted in both increases and decreases in predicted suitable habitat, though most species ranges do not contract, especially when taken as a phylogenetic group. MAIN CONCLUSIONS While some established habitats may become more or less climatically suitable, the overall distribution of species in this group is unlikely to be significantly affected. Clades of Plethodon species are unlikely to be in danger of extirpation despite the possibility that individual species may be threatened as a result of limited distributions. Grouping species into lineages with similar geographic ranges can be a viable method of determining conservation needs. More biotic and dispersal information is needed to determine the true impact that changes in climate will have on the distribution of Plethodon species.
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Košuthová A, Bergsten J, Westberg M, Wedin M. Species delimitation in the cyanolichen genus Rostania. BMC Evol Biol 2020; 20:115. [PMID: 32912146 PMCID: PMC7488055 DOI: 10.1186/s12862-020-01681-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/31/2020] [Indexed: 11/24/2022] Open
Abstract
Background In this study, we investigate species limits in the cyanobacterial lichen genus Rostania (Collemataceae, Peltigerales, Lecanoromycetes). Four molecular markers (mtSSU rDNA, β-tubulin, MCM7, RPB2) were sequenced and analysed with two coalescent-based species delimitation methods: the Generalized Mixed Yule Coalescent model (GMYC) and a Bayesian species delimitation method (BPP) using a multispecies coalescence model (MSC), the latter with or without an a priori defined guide tree. Results Species delimitation analyses indicate the presence of eight strongly supported candidate species. Conclusive correlation between morphological/ecological characters and genetic delimitation could be found for six of these. Of the two additional candidate species, one is represented by a single sterile specimen and the other currently lacks morphological or ecological supporting evidence. Conclusions We conclude that Rostania includes a minimum of six species: R. ceranisca, R. multipunctata, R. occultata 1, R. occultata 2, R. occultata 3, and R. occultata 4,5,6. Three distinct Nostoc morphotypes occur in Rostania, and there is substantial correlation between these morphotypes and Rostania thallus morphology.
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Affiliation(s)
- Alica Košuthová
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden.
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Martin Westberg
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36, Uppsala, Sweden
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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Jacobs SJ, Kristofferson C, Uribe‐Convers S, Latvis M, Tank DC. Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult. Mol Ecol 2018; 27:2397-2413. [DOI: 10.1111/mec.14590] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Sarah J. Jacobs
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Casey Kristofferson
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Simon Uribe‐Convers
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Maribeth Latvis
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - David C. Tank
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
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Luque-Montes I, Austin JD, Weinfurther KD, Wilson LD, Hofmann EP, Townsend JH. An integrative assessment of the taxonomic status of putative hybrid leopard frogs (Anura: Ranidae) from the Chortís Highlands of Central America, with description of a new species. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2017.1415232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ileana Luque-Montes
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida 32611, USA
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705–1081, USA
| | - James D. Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida 32611, USA
| | - Kayla D. Weinfurther
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705–1081, USA
| | - Larry David Wilson
- Centro Zamorano de Biodiversidad, Escuela Agrícola Panamericana Zamorano, Departamento Francisco Morazán, Honduras
| | - Erich P. Hofmann
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705–1081, USA
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705–1081, USA
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Espíndola A, Ruffley M, Smith ML, Carstens BC, Tank DC, Sullivan J. Identifying cryptic diversity with predictive phylogeography. Proc Biol Sci 2017; 283:rspb.2016.1529. [PMID: 27798300 DOI: 10.1098/rspb.2016.1529] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/27/2016] [Indexed: 01/14/2023] Open
Abstract
Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.
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Affiliation(s)
- Anahí Espíndola
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA .,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
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Abstract
Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the "microgeographic races" of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography.
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Newman CE, Gregory TR, Austin CC. The dynamic evolutionary history of genome size in North American woodland salamanders. Genome 2017; 60:285-292. [DOI: 10.1139/gen-2016-0166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5–20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.
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Affiliation(s)
- Catherine E. Newman
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - T. Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Christopher C. Austin
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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Aguilar C, Wood PL, Belk MC, Duff MH, Sites JW. Different roads lead to Rome: Integrative taxonomic approaches lead to the discovery of two new lizard lineages in theLiolaemus montanusgroup (Squamata: Liolaemidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cesar Aguilar
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
- Departamento de Herpetologia; Museo de Historia Natural de San Marcos (MUSM); Av. Arenales 1256, Jesus Maria Lima Peru
- Facultad de Ciencias Biologicas; Instituto de Ciencias Biologicas Antonio Raimondi; Universidad Nacional Mayor de San Marcos; Lima Peru
| | - Perry L. Wood
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mark C. Belk
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mike H. Duff
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
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Hope AG, Malaney JL, Bell KC, Salazar-Miralles F, Chavez AS, Barber BR, Cook JA. Revision of widespread red squirrels (genus: Tamiasciurus) highlights the complexity of speciation within North American forests. Mol Phylogenet Evol 2016; 100:170-182. [PMID: 27083861 DOI: 10.1016/j.ympev.2016.04.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 11/27/2022]
Abstract
Integration of molecular methods, ecological modeling, and statistical hypothesis testing are increasing our understanding of differentiation within species and phylogenetic relationships among species by revealing environmental connections to evolutionary processes. Within mammals, novel diversity is being discovered and characterized as more complete geographic sampling is coupled with newer multi-disciplinary approaches. North American red squirrels exemplify a forest obligate genus whose species are monitored as indicators of forest ecosystem condition, yet phylogenetic relationships reflecting evolutionary history within this genus remain tentative. Through testing of competing systematic and niche-based divergence hypotheses, we recognize three species, Tamiasciurus douglasii, T. hudsonicus, and T. fremonti. Our data provide evidence of regional differences in evolutionary dynamics and continental gradients of complexity that are important both for future management and for investigating multiple pathways that can lead to the formation of new species.
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Affiliation(s)
- Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
| | - Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA.
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Fernando Salazar-Miralles
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
| | - Brian R Barber
- Biodiversity Institute, University of Wyoming, Laramie, WY 82071, USA.
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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Kuchta SR, Brown AD, Converse PE, Highton R. Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods. PLoS One 2016; 11:e0150022. [PMID: 26974148 PMCID: PMC4790894 DOI: 10.1371/journal.pone.0150022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 02/08/2016] [Indexed: 11/29/2022] Open
Abstract
Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8-19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed.
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Affiliation(s)
- Shawn R. Kuchta
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Ashley D. Brown
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Paul E. Converse
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Richard Highton
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
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Affiliation(s)
- Jean-François Flot
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom
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