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Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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2
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Villegas-Patraca R, Aguilar-López JL, Hernández-Hernández JC, Muñoz-Jiménez O. Diversity and conservation of terrestrial vertebrates (birds, mammals, and reptiles) of Sierra Cucapá, Mexicali, Baja California, Mexico. Zookeys 2022; 1088:17-39. [PMID: 35437372 PMCID: PMC8901611 DOI: 10.3897/zookeys.1088.76134] [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: 10/05/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
Knowledge about the biodiversity of Baja California has been obtained mainly from natural protected areas (NPAs), while some unprotected natural areas have been poorly studied. The Sierra Cucapá in the northeast of the peninsula is one example. The objectives of this study are 1) to integrate existing knowledge of bird, mammal, and reptile diversity in Cucapá from public databases, citizen science platforms, and information generated from fieldwork, 2) to identify the spatial distribution of records in the study area, 3) to compare the composition of vertebrate species of Cucapá with that of NPAs of northern part of the peninsula, and 4) to assess the biological conservation value of Cucapá. We obtained records of 150 species of native vertebrates (102 birds, 34 mammals, and 14 reptiles) of which 10 species of birds, four mammals, and seven reptiles are included in a risk extinction category. The different sources of information contributed in a complementary way to the species inventories. Large areas in western and northern Cucapá lack records. The total difference in species composition between Cucapá and nearby NPAs ranged between 58 and 69% for birds, 61 and 79% for mammals, and 69 and 87% for reptiles. The species richness of Cucapá, its particular species composition, the presence of species in risk extinction categories, and the number and size of unexplored areas indicate that this area represents an opportunity for biological conservation in the northern part of the Peninsula. This work provides compelling data for the protection of Cucapá.
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Nazareno AG, Knowles LL. There Is No 'Rule of Thumb': Genomic Filter Settings for a Small Plant Population to Obtain Unbiased Gene Flow Estimates. FRONTIERS IN PLANT SCIENCE 2021; 12:677009. [PMID: 34721447 PMCID: PMC8551369 DOI: 10.3389/fpls.2021.677009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
The application of high-density polymorphic single-nucleotide polymorphisms (SNP) markers derived from high-throughput sequencing methods has heralded plenty of biological questions about the linkages of processes operating at micro- and macroevolutionary scales. However, the effects of SNP filtering practices on population genetic inference have received much less attention. By performing sensitivity analyses, we empirically investigated how decisions about the percentage of missing data (MD) and the minor allele frequency (MAF) set in bioinformatic processing of genomic data affect direct (i.e., parentage analysis) and indirect (i.e., fine-scale spatial genetic structure - SGS) gene flow estimates. We focus specifically on these manifestations in small plant populations, and particularly, in the rare tropical plant species Dinizia jueirana-facao, where assumptions implicit to analytical procedures for accurate estimates of gene flow may not hold. Avoiding biases in dispersal estimates are essential given this species is facing extinction risks due to habitat loss, and so we also investigate the effects of forest fragmentation on the accuracy of dispersal estimates under different filtering criteria by testing for recent decrease in the scale of gene flow. Our sensitivity analyses demonstrate that gene flow estimates are robust to different setting of MAF (0.05-0.35) and MD (0-20%). Comparing the direct and indirect estimates of dispersal, we find that contemporary estimates of gene dispersal distance (σ r t = 41.8 m) was ∼ fourfold smaller than the historical estimates, supporting the hypothesis of a temporal shift in the scale of gene flow in D. jueirana-facao, which is consistent with predictions based on recent, dramatic forest fragmentation process. While we identified settings for filtering genomic data to avoid biases in gene flow estimates, we stress that there is no 'rule of thumb' for bioinformatic filtering and that relying on default program settings is not advisable. Instead, we suggest that the approach implemented here be applied independently in each separate empirical study to confirm appropriate settings to obtain unbiased population genetics estimates.
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Affiliation(s)
- Alison G. Nazareno
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
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Sikorski AV, Radashevsky VI, Castelli A, Pavlova LV, Nygren A, Malyar VV, Borisova PB, Mikac B, Rousou M, Martin D, Gil J, Pacciardi L, Langeneck J. Revision of the Laonice bahusiensis complex (Annelida: Spionidae) with a description of three new species. Zootaxa 2021; 4996:253-283. [PMID: 34810532 DOI: 10.11646/zootaxa.4996.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 11/04/2022]
Abstract
The morphological reexamination of specimens previously identified as Laonice bahusiensis Sderstrm, 1920 from North European and Mediterranean collections, supported by the molecular analysis of freshly collected material, enabled the recognition of four different species in the region: the genuine L. bahusiensis, L. irinae n. sp. from North European waters, and L. grimaldii n. sp. and L. mediterranea n. sp. from the Mediterranean Sea. The morphology of these species is described and illustrated, and their distributions are clarified based on old and new materials. A key for their identification is also provided. The Bayesian analysis of the COI sequences (483 bp) showed that these four species form a clade, namely the L. bahusiensis species complex, morphologically characterized by the continuous dorsal crests on postbranchiate chaetigers in the adults. The genetic p-distances between the species of the complex ranged from 13.27% to 17.99%, while the intraspecific variability ranged from 0.6% to 1.57%. Together with the sister species Laonice cirrata (Sars, 1851), the L. bahusiensis complex formed the Laonice (Laonice) clade, which is morphologically characterized by the prostomium fused with the anterior peristomial margin. However, the monophyly of the L. bahusiensis complex, as well as that of the clade Laonice (Laonice), needs to be further supported through the analysis of a greater set of genes from a larger number of species.
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Affiliation(s)
| | - Vasily I Radashevsky
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 17 Palchevsky Street, Vladivostok 690041, Russia. .
| | - Alberto Castelli
- Dipartimento di Biologia, Universit di Pisa, via Derna 1, 56126 Pisa, Italy. .
| | - Lyudmila V Pavlova
- Murmansk Marine Biological Institute, Kola Science Centre, Russian Academy of Sciences, 17 Vladimirskaya Street, Murmansk 183010, Russia. .
| | - Arne Nygren
- Sjfartsmuseet Akvariet, Karl Johansgatan 1-3, 414 59 Gteborg, Sverige. .
| | - Vasily V Malyar
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 17 Palchevsky Street, Vladivostok 690041, Russia. (ii) Laboratory of ecology and evolutionary biology of aquatic organisms (LEEBAO), School of Natural Sciences, Far Eastern Federal University, Vladivostok 690091, Russia. .
| | - Polina B Borisova
- P.P. Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prospekt, Moscow 117997, Russia. .
| | - Barbara Mikac
- University of Bologna, Department of Biological, Geological and Environmental Sciences, Via SantAlberto 163, 48123 Ravenna, Italy. .
| | - Maria Rousou
- Department of Fisheries and Marine Research, P.O. Box 28548, 2080, Nicosia, Cyprus. (ii) Marine and Environmental Research Lab Ltd, 4533, Limassol Cyprus. (iii) School of Biology, Department of Zoology, Aristotle University of Thessaloniki (AUTH), P.O. Box 134, 54124, Thessaloniki, Greece. .
| | - Daniel Martin
- Centre for Advanced Studies of Blanes (CEABCSIC), carrer daccs a la Cala St. Francesc, 14, BlanesGirona17300, Catalunya (Spain). .
| | - Joo Gil
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus Gambelas, 8005-139 Faro, Portugal. .
| | - Lorenzo Pacciardi
- Centro Interuniversitario di Biologia Marina e Ecologia Applicata G. Bacci (CIBM), Viale N. Sauro, 4 57128 Livorno, Italy. .
| | - Joachim Langeneck
- Dipartimento di Biologia, Universit di Pisa, via Derna 1, 56126 Pisa, Italy. .
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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Graham MR, Santibáñez‐López CE, Derkarabetian S, Hendrixson BE. Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq. Mol Ecol 2020; 29:3684-3701. [DOI: 10.1111/mec.15588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | | | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology Museum of Comparative Zoology Harvard University Cambridge MA USA
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Mason NA, Fletcher NK, Gill BA, Funk WC, Zamudio KR. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Brian A. Gill
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - W. Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
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8
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Lukhtanov VA. Species Delimitation and Analysis of Cryptic Species Diversity in the XXI Century. ACTA ACUST UNITED AC 2019. [DOI: 10.1134/s0013873819040055] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae). Mol Phylogenet Evol 2019; 138:89-101. [DOI: 10.1016/j.ympev.2019.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
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10
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Myers EA, Xue AT, Gehara M, Cox CL, Davis Rabosky AR, Lemos‐Espinal J, Martínez‐Gómez JE, Burbrink FT. Environmental heterogeneity and not vicariant biogeographic barriers generate community‐wide population structure in desert‐adapted snakes. Mol Ecol 2019; 28:4535-4548. [DOI: 10.1111/mec.15182] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/23/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology Smithsonian Institution National Museum of Natural History Washington DC USA
- Department of Herpetology The American Museum of Natural History New York NY USA
| | | | - Marcelo Gehara
- Department of Herpetology The American Museum of Natural History New York NY USA
| | - Christian L. Cox
- Department of Biology Georgia Southern University Statesboro GA USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Julio Lemos‐Espinal
- Laboratorio de Ecología, UBIPRO, FES Iztacala Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | | | - Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History New York NY USA
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11
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Mitrovich MJ, Diffendorfer JE, Brehme CS, Fisher RN. Effects of urbanization and habitat composition on site occupancy of two snake species using regional monitoring data from southern California. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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12
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O’Connell KA, Smith EN. New molecular sequence data and species trees for North American whipsnakes. Data Brief 2018; 18:1995-1999. [PMID: 29904706 PMCID: PMC5998179 DOI: 10.1016/j.dib.2018.04.067] [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: 03/28/2018] [Revised: 04/04/2018] [Accepted: 04/18/2018] [Indexed: 11/29/2022] Open
Abstract
In this data article we present species trees based on coalescent species delimitation results for North American whipsnakes, as well as metadata pertaining to the article "The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis)" (MPE-2017-76-R1). Species trees were constructed using SNP data generated from double-digest RADseq, filtered to 80% completeness between species. Tables correspond with the primary manuscript and serve as a repository of genetic sequence information for whipsnakes. These data can be downloaded and combined with future whipsnake datasets.
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