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Fenker J, Melville J, Moritz C. Dragons in the tropics - Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa. Mol Phylogenet Evol 2024; 197:108090. [PMID: 38723791 DOI: 10.1016/j.ympev.2024.108090] [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: 06/13/2023] [Revised: 12/20/2023] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Co-distributed taxa can respond both similarly or differently to the same climatic and geological events, resulting in a range of phylogeographic patterns across the region. Using a nested approach on a taxonomically diverse yet morphologically conservative group of agamid lizards, we first aimed to evaluate more precisely the extent of phylogeographic structuring within the genus. Then, focusing on four lineages within the more widespread species, we assessed the impact of biogeographic barriers on phylogeographic structuring and demographic history of species, comparing to patterns previously observed in co-distributed taxa. These species occur in the Australian Monsoonal Tropics, a vast tropical savanna system with high richness and endemism associated with environmental heterogeneity and past climate fluctuations. The employment of genomic data helped to determine the relationships between specific taxa that were previously difficult to place. We found a local influence of biogeographic and climatic breaks on population dynamics, analogous to other species. We detected high levels of population structure in the West Kimberley and Arnhem Plateau, which are already known for high endemism. However, we also highlighted unique lineages in areas that have been overlooked until recently, in the South Kimberley and West Top End. Climatic and geographical features in the Arnhem Plateau act as a soft barrier between populations in the east and west regions of the Top End. These observations reflect patterns observed for other vertebrates across this rich biome, indicating how climatic variation, species' ecology, and landscape features interact to shape regional diversity and endemism.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton 2601, Canberra, ACT, Australia; Department of Sciences, Museums Victoria, Melbourne Museum, 11 Nicholson StreetCarlton 3053, Melbourne, VIC, Australia.
| | - Jane Melville
- Department of Sciences, Museums Victoria, Melbourne Museum, 11 Nicholson StreetCarlton 3053, Melbourne, VIC, Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton 2601, Canberra, ACT, Australia
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2
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Hurtado-Gómez JP, Vargas-Ramírez M, Iverson JB, Joyce WG, McCranie JR, Paetzold C, Fritz U. Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae). Mol Phylogenet Evol 2024; 197:108083. [PMID: 38679303 DOI: 10.1016/j.ympev.2024.108083] [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: 04/16/2023] [Revised: 04/02/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.
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Affiliation(s)
| | - Mario Vargas-Ramírez
- Grupo Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia; Estación de Biología Tropical Roberto Franco (EBTRF), Universidad Nacional de Colombia, Villavicencio, Colombia
| | - John B Iverson
- Department of Biology, Earlham College, Richmond, IN 47374, USA
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, 1700 Fribourg, Switzerland
| | - James R McCranie
- Smithsonian Research Associate, 10770 SW 164th Street, Miami, FL 33157, USA
| | - Claudia Paetzold
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany.
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3
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Lyu B, Liu Q, Wu Y, Nguyen TQ, Che J, Nguyen SN, Myers EA, Burbrink FT, Guo P, Wang J. Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae). Ecol Evol 2024; 14:e11278. [PMID: 38628918 PMCID: PMC11019134 DOI: 10.1002/ece3.11278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.
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Affiliation(s)
- Bing Lyu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Truong Q. Nguyen
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
- Vietnam Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Sang N. Nguyen
- Institute of Tropical BiologyVietnam Academy of Science and TechnologyHo Chi Minh CityVietnam
| | - Edward A. Myers
- Department of HerpetologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
| | - Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Peng Guo
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
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4
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Deng Z, Zhang X, Wolinska J, Blair D, Hu W, Yin M. Climate has contributed to population diversification of Daphnia galeata across Eurasia. Mol Ecol 2023; 32:5110-5124. [PMID: 37548328 DOI: 10.1111/mec.17094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
Climate is a fundamental abiotic factor that plays a key role in driving the evolution, distribution and population diversification of species. However, there have been few investigations of genomic signatures of adaptation to local climatic conditions in cladocerans. Here, we have provided the first high-quality chromosome-level genome assembly (~143 Mb, scaffold N50 12.6 Mb) of the waterflea, Daphnia galeata, and investigated genomic variation in 22 populations from Central Europe and Eastern China. Our ecological-niche models suggested that the historic distribution of D. galeata in Eurasia was significantly affected by Quaternary climate fluctuations. We detected pronounced genomic and morphometric divergences between European and Chinese D. galeata populations. Such divergences could be partly explained by genomic signatures of thermal adaptation to distinct climate regimes: a set of candidate single-nucleotide polymorphisms (SNPs) potentially associated with climate were detected. These SNPs were in genes significantly enriched in the Gene ontology terms "determination of adult lifespan" and "translation repressor activity", and especially, mthl5 and SOD1 involved in the IIS pathway, and EIF4EBP2 involved in the target of the rapamycin signalling pathway. Our study indicates that certain alleles might be associated with particular temperature regimes, playing a functional role in shaping the population structure of D. galeata at a large geographical scale. These results highlight the potential role of molecular variation in the response to climate variation, in the context of global climate change.
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Affiliation(s)
- Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
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5
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Harrington S, Burbrink F. Complex cycles of divergence and migration shape lineage structure in the common kingsnake species complex. JOURNAL OF BIOGEOGRAPHY 2023; 50:341-351. [PMID: 36817740 PMCID: PMC9937589 DOI: 10.1111/jbi.14536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
Aim The Nearctic is a complex patchwork of habitats and geologic features that form barriers to gene flow resulting in phylogeographic structure and speciation in many lineages. Habitats are rarely stable over geologic time, and the Nearctic has undergone major climatic changes in the past few million years. We use the common kingsnake species complex to study how climate, geography, and history influence lineage formation over a large, complex landscape. Location Nearctic/North America. Taxon Common kingsnake, Lampropeltis getula, species complex. Methods We analyzed genome-wide sequence data from 51 snakes spanning the majority of the species complex's range. We used population clustering, generalized dissimilarity modeling, and coalescent methods to identify the number of genetic clusters within the L. getula complex, infer the environmental correlates of genetic differentiation, and estimate models of divergence and gene flow among lineages. Results We identified three major lineages within the L. getula complex and further continuous spatial structure within lineages. The most important ecological correlates of genetic distance in the complex are related to aridity and precipitation, consistent with lineage breaks at the Great Plains/Desert ecotone and the Cochise Filter Barrier. Lineages are estimated to have undergone multiple rounds of isolation and secondary contact, with highly asymmetric migration occurring at present. Main conclusions Changing climates combined with a large and geologically complex landscape have resulted in a mosaic of discrete and spatially continuous genetic structure. Multiple rounds of isolation and secondary contact as climate fluctuated over the past ~4.4 My have likely driven the evolution of discrete lineages that maintain high levels of gene flow. Continuous structure is strongly shaped by aridity and precipitation, suggesting roles for major precipitation gradients in helping to maintain lineage identity in the face of gene flow when lineages are in geographic contact.
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Affiliation(s)
- Sean Harrington
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
- INBRE Data Science Core, University of Wyoming, Laramie, WY 82071, USA
| | - Frank Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
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6
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Hidalgo-Licona LF, Gutiérrez-Mayén MG, Sandoval-Ruiz CA, de la Vega-Pérez AD, Chollet-Villalpando JG. Ecogeographic and Morphometric Variation in the Mexican Pine Snake, Pituophis deppei (Squamata: Colubridae). ICHTHYOLOGY & HERPETOLOGY 2022. [DOI: 10.1643/h2021105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Luis Fernando Hidalgo-Licona
- Maestría en Ciencias Biológicas, Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Blvd. Valsequillo y Av. San Claudio, Edificio BIO 1, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, México;
| | - María Guadalupe Gutiérrez-Mayén
- Laboratorio de Herpetología, Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Blvd. Valsequillo y Av. San Claudio, Edificio BIO 1, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, México;
| | - César Antonio Sandoval-Ruiz
- Laboratorio de Artropodología y Salud, Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Blvd. Valsequillo y Av. San Claudio, Edificio BIO 1, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, México; Ema
| | - Anibal Díaz de la Vega-Pérez
- Consejo Nacional de Ciencia y Tecnología, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Carretera Tlaxcala-Puebla km 1.5 C.P. 90062, Tlaxcala, México;
| | - Jorge Guillermo Chollet-Villalpando
- Instituto de Ecología, A.C. Red de Biodiversidad y Sistemática, Carretera Antigua a Coatepec 351, El Haya, Xalapa Enríquez, 91070 Veracruz, México;
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7
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MacGuigan DJ, Mount GG, Watkins-Colwell GJ, Near TJ, Lambert MR. Genomic Data Clarify Aquarana Systematics and Reveal Isolation-by-Distance Dominates Phylogeography of the Wide-Ranging Frog Rana clamitans. ICHTHYOLOGY & HERPETOLOGY 2022. [DOI: 10.1643/h2021129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel J. MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260;
| | | | - Gregory J. Watkins-Colwell
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Thomas J. Near
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Max R. Lambert
- Science Division, Habitat Program, Washington Department of Fish & Wildlife, Olympia, Washington 98501;
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8
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Catalan A, Höhna S, Lower SE, Duchen P. Inferring the demographic history of the North American firefly Photinus pyralis. J Evol Biol 2022; 35:1488-1499. [PMID: 36168726 DOI: 10.1111/jeb.14094] [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: 01/20/2022] [Revised: 06/13/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022]
Abstract
The firefly Photinus pyralis inhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Despite its broad distribution, its demographic history is unknown. In this study, we modelled and inferred different demographic scenarios for North American populations of P. pyralis, which were collected from Texas to New Jersey. We used a combination of ABC techniques (for multi-population/colonization analyses) and likelihood inference (dadi, StairwayPlot2, PoMo) for single-population demographic inference, which proved useful with our RAD data. We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. To estimate the age of divergence between of P. pyralis, which provides deeper insights into the history of the entire species, we assembled a multi-locus phylogenetic data covering the genus Photinus. We uncovered that the phylogenetic node leading to P. pyralis lies at the end of the Miocene. Importantly, modelling the demographic history of North American P. pyralis serves as a null model of nucleotide diversity patterns in a widespread native insect species, which will serve in future studies for the detection of adaptation events in this firefly species, as well as a comparison for future studies of other North American insect taxa.
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Affiliation(s)
- Ana Catalan
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Sebastian Höhna
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sarah E Lower
- Department of Biology, Bucknell University, Lewisburg, PA, USA
| | - Pablo Duchen
- Institute for Organismal and Molecular Evolutionary Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
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9
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Rickenback J, Pennington RT, Lehmann CER. Diversity in habit expands the environmental niche of
Ziziphus
(Rhamnaceae). Biotropica 2022. [DOI: 10.1111/btp.13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jess Rickenback
- School of Geosciences University of Edinburgh Edinburgh UK
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
| | - R. Toby Pennington
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
- College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Caroline E. R. Lehmann
- School of Geosciences University of Edinburgh Edinburgh UK
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
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10
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Pease BS, Pacifici K, Kays R. Exploring spatial nonstationarity for four mammal species reveals regional variation in environmental relationships. Ecosphere 2022. [DOI: 10.1002/ecs2.4166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Brent S. Pease
- Forestry Program Southern Illinois University Carbondale Illinois USA
| | - Krishna Pacifici
- Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina USA
| | - Roland Kays
- Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina USA
- North Carolina Museum of Natural Sciences Raleigh North Carolina USA
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11
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Tonione MA, Bi K, Dunn RR, Lucky A, Portik DM, Tsutsui ND. Phylogeography and population genetics of a widespread cold-adapted ant, Prenolepis imparis. Mol Ecol 2022; 31:4884-4899. [PMID: 35866574 DOI: 10.1111/mec.16624] [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: 11/08/2021] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022]
Abstract
As species arise, evolve, and diverge, they are shaped by forces that unfold across short and long time scales and at both local and vast geographic scales. It is rare, however, to be able document this history across broad sweeps of time and space in a single species. Here, we report the results of a continental-scale phylogenomic analysis across the entire range of a widespread species. We analyzed sequences of 1,402 orthologous Ultraconserved Element (UCE) loci from 75 individuals to identify population genetic structure and historical demographic patterns across the continent-wide range of a cold-adapted ant, the winter ant, Prenolepis imparis. We recovered five well-supported, genetically isolated clades representing lineages that diverged from 8.2-2.2 million years ago. These include: 1) an early diverging lineage located in Florida, 2) a lineage that spans the southern United States, 3) populations that extend across the midwestern and northeastern United States, 4) populations from the western United States, and 5) populations in southwestern Arizona and Mexico. Population genetic analyses revealed little or no gene flow among these lineages, but patterns consistent with more recent gene flow among populations within lineages, and localized structure with migration in the western United States. High support for five major geographic lineages and lack of evidence of contemporary gene flow indicate in situ diversification across the species' range, producing relatively ancient lineages that persisted through subsequent climate change and glaciation during the Quaternary.
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Affiliation(s)
- Maria Adelena Tonione
- Department of Environmental Science, Policy, and Management, 130 Mulford Hall, #3114, University of California-, 94720-3114, Berkeley, CA, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.,Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, David Clark Labs, Box 7617, Raleigh, NC 27695, USA
| | - Andrea Lucky
- Entomology and Nematology Department, University of Florida, 32608, Gainesville, FL, USA
| | - Daniel M Portik
- California Academy of Sciences, 94118, San Francisco, CA, USA
| | - Neil Durie Tsutsui
- Department of Environmental Science, Policy, and Management, 130 Mulford Hall, #3114, University of California-, 94720-3114, Berkeley, CA, USA
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12
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Pease BS, Pacifici K, Kays R, Reich B. What drives spatially varying ecological relationships in a wide‐ranging species? DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13594] [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] Open
Affiliation(s)
- Brent S. Pease
- Foresty Program Southern Illinois University Carbondale Illinois USA
| | - Krishna Pacifici
- Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina USA
| | - Roland Kays
- Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina USA
- North Carolina Museum of Natural Sciences Raleigh North Carolina USA
| | - Brian Reich
- Department of Statistics North Carolina State University Raleigh North Carolina USA
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13
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Smith ML, Wallace J, Tank DC, Sullivan J, Carstens BC. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Mol Ecol 2022; 31:4402-4416. [PMID: 35780485 DOI: 10.1111/mec.16595] [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: 05/12/2021] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated Species Distribution Models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the Last Glacial Maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.
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Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Jessica Wallace
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Botany and Rocky Mountain Herbarium, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA.,Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
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14
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Wang Z, Pierce NE. Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol 2022; 32:2695-2714. [PMID: 35377501 DOI: 10.1111/mec.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
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Affiliation(s)
- Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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15
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Singhal S, Colli GR, Grundler MR, Costa GC, Prates I, Rabosky DL. No link between population isolation and speciation rate in squamate reptiles. Proc Natl Acad Sci U S A 2022; 119:e2113388119. [PMID: 35058358 PMCID: PMC8795558 DOI: 10.1073/pnas.2113388119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.
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Affiliation(s)
- Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747;
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Maggie R Grundler
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
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16
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Magalhães FDM, Camurugi F, Lyra ML, Baldo D, Gehara M, Haddad CFB, Garda AA. Ecological divergence and synchronous Pleistocene diversification in the widespread South American butter frog complex. Mol Phylogenet Evol 2022; 169:107398. [PMID: 35031468 DOI: 10.1016/j.ympev.2022.107398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/31/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022]
Abstract
Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importance on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scale. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America.
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Affiliation(s)
- Felipe de M Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba-UFPB, Centro de Ciências Exatas e da Natureza, Cidade Universitária, 58000-000 João Pessoa, Paraiba, Brazil; Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark 195 University Ave, Newark, NJ 07102, USA.
| | - Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Mariana L Lyra
- Instituto de Biociências, Universidade Estadual Paulista, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Cx. Postal 199, 13506-900 Rio Claro, São Paulo, Brazil
| | - Diego Baldo
- Instituto de Biología Subtropical (IBS, CONICET-UNaM), Laboratorio de Genética Evolutiva, Facultad de Ciencias Exactas, Universidad Nacional de Misiones, Félix de Azara 1552, CPA N3300LQF Posadas, Misiones, Argentina
| | - Marcelo Gehara
- Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark 195 University Ave, Newark, NJ 07102, USA
| | - Célio F B Haddad
- Instituto de Biociências, Universidade Estadual Paulista, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Cx. Postal 199, 13506-900 Rio Claro, São Paulo, Brazil
| | - Adrian A Garda
- Laboratório de Anfíbios e Répteis (LAR), Departamento de Botânica e Zoologia da Universidade Federal do Rio Grande do Norte, Campus Universitário. Lagoa Nova, 59078-900 Natal, Rio Grande do Norte, Brazil
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17
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Fontúrbel FE, Rodríguez-Gómez GB, Orellana JI, Cortés-Miranda J, Rojas-Hernández N, Vega-Retter C. Geographical context outweighs habitat disturbance effects in explaining mistletoe population genetic differentiation at a regional scale. Mol Ecol 2022; 31:1389-1402. [PMID: 34995392 DOI: 10.1111/mec.16337] [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: 07/08/2021] [Revised: 11/03/2021] [Accepted: 12/17/2021] [Indexed: 11/29/2022]
Abstract
Genetic differentiation depends on ecological and evolutionary processes that operate at different spatial and temporal scales. While the geographical context is likely to determine large-scale genetic variation patterns, habitat disturbance events will probably influence small-scale genetic diversity and gene flow patterns. Therefore, the genetic diversity patterns that we observe today result from the combination of both processes, but they are rarely assessed simultaneously. We determined the population structure and genetic diversity of a hemiparasitic mistletoe (Tristerix corymbosus) from the temperate rainforests of southern Chile to determine the effects of geographical context and habitat disturbance at a regional scale and if it is affected by the abundance and occurrence of its seed disperser mutualist (the arboreal marsupial Dromiciops gliroides). We genotyped 359 individuals from 12 populations using single nucleotide polymorphisms, across three different geographical contexts and four disturbance conditions. We also used camera traps to estimate the abundance and occurrence of the seed disperser. Our results suggest that genetic differences among populations are related more to geographical context than to habitat disturbance. However, as disturbance increased, D. gliroides abundance and occurrence decreased, and mistletoe inbreeding index (FIS ) increased. We also found highly uneven gene flow among study sites. Despite the high levels of disturbance that these temperate rainforests are facing, our results suggest that mistletoe genetic differentiation at a regional scale was more influenced by historical events. However, habitat disturbance can indirectly affect mistletoe population genetic differentiation via the seed dispersal process, which may increase levels of inbreeding.
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Affiliation(s)
- Francisco E Fontúrbel
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.,Millennium Nucleus of Patagonian Limit of Life (LiLi)
| | - Gloria B Rodríguez-Gómez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José I Orellana
- Laboratorio de Vida Silvestre, Universidad de Los Lagos, Osorno, Chile
| | - Jorge Cortés-Miranda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Noemí Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Caren Vega-Retter
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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18
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Nikolakis ZL, Orton RW, Crother BI. Fine‐scale population structure within an Eastern Nearctic snake complex (
Pituophis melanoleucus
). ZOOL SCR 2021. [DOI: 10.1111/zsc.12522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology Southeastern Louisiana University Hammond Louisina USA
- Department of Biology University of Texas at Arlington Arlington Texas USA
| | - Richard W. Orton
- Department of Biology University of Texas at Arlington Arlington Texas USA
| | - Brian I. Crother
- Department of Biology Southeastern Louisiana University Hammond Louisina USA
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19
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Burbrink FT, Bernstein JM, Kuhn A, Gehara M, Ruane S. Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex). Syst Biol 2021; 71:839-858. [PMID: 35043210 DOI: 10.1093/sysbio/syab093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.].
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Justin M Bernstein
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Sara Ruane
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA.,Amphibian and Reptile Collection, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
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20
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Blais BR, Smith BE, Placyk JS, Casper GS, Spellman GM. Phylogeography of the smooth greensnake, Opheodrys vernalis (Squamata: Colubridae): divergent lineages and variable demographics in a widely distributed yet enigmatic species. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Phylogeographic studies can uncover robust details about the population structure, demographics, and diversity of species. The smooth greensnake, Opheodrys vernalis, is a small, cryptic snake occupying mesic grassland and sparsely wooded habitats. Although O. vernalis has a wide geographical range, many metapopulations are patchy and some are declining. We used mitochondrial DNA and double digest restriction-site associated DNA sequencing to construct the first phylogeographic assessment of O. vernalis. Genomic analysis of 119 individuals (mitochondrial DNA) and a subset of another 45 smooth greensnakes (nuclear DNA; N = 3031 single nucleotide polymorphisms) strongly supports two longitudinally separated lineages, with admixture in the Great Lakes region. Post-Pleistocene secondary contact best explains admixture from populations advancing northwards. Overall, populations expressed low heterozygosity, variable inbreeding rates, and moderate to high differentiation. Disjunct populations in the Rocky Mountains and central Great Plains regions might be contracting relicts, whereas northerly populations in more continuous mesic habitats (e.g., Prairie Pothole region, southern Canada) had signals of population expansion. Broadly, conservation management efforts should be focused on local populations, because habitat connectivity may facilitate gene flow and genetic diversity.
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Affiliation(s)
- Brian R Blais
- School of Natural Sciences, Black Hills State University, Spearfish, SD, USA
| | - Brian E Smith
- School of Natural Sciences, Black Hills State University, Spearfish, SD, USA
| | - John S Placyk
- Department of Biology, University of Texas at Tyler, 3900 University Boulevard, Tyler, TX, USA
| | - Gary S Casper
- University of Wisconsin-Milwaukee Field Station, Saukville, WI, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, CO, USA
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21
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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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22
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Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), Using Multilocus Sanger Sequence and Genomic ddRADseq Data. J HERPETOL 2021. [DOI: 10.1670/20-040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Jaynes KE, Myers EA, Gvoždík V, Blackburn DC, Portik DM, Greenbaum E, Jongsma GFM, Rödel MO, Badjedjea G, Bamba-Kaya A, Baptista NL, Akuboy JB, Ernst R, Kouete MT, Kusamba C, Masudi FM, McLaughlin PJ, Nneji LM, Onadeko AB, Penner J, Vaz Pinto P, Stuart BL, Tobi E, Zassi-Boulou AG, Leaché AD, Fujita MK, Bell RC. Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits. Mol Ecol 2021; 31:3979-3998. [PMID: 34516675 DOI: 10.1111/mec.16169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/18/2021] [Accepted: 09/02/2021] [Indexed: 01/25/2023]
Abstract
Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.
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Affiliation(s)
- Kyle E Jaynes
- Department of Biology, Adrian College, Michigan, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Integrative Biology, W.K. Kellogg Biological Station, Michigan State University, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, Michigan, USA
| | - Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, National Museum, Prague, Czech Republic
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Daniel M Portik
- Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Gregory F M Jongsma
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,Department of Biology, University of Florida, Florida, USA
| | - Mark-Oliver Rödel
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des Ressources Aquatiques, Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, République Démocratique du Congo
| | | | - Ninda L Baptista
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Faculdade de Ciências da, Universidade do Porto, Porto, Portugal.,Instituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento Rodrigues, Lubango, Angola
| | - Jeannot B Akuboy
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Marcel T Kouete
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,School of Natural Resources and Environment, University of Florida, Florida, USA
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, République Démocratique du Congo, Lwiro
| | - Franck M Masudi
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Patrick J McLaughlin
- Bioko Biodiversity Protection Project, Drexel University, Philadelphia, Pennsylvania, USA.,Institute of Conservation Science and Learning, Bristol Zoological Society, Bristol, UK
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
| | - Abiodun B Onadeko
- Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Johannes Penner
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.,Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
| | - Pedro Vaz Pinto
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Fundação Kissama, Luanda, Angola
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, North Carolina, USA
| | - Elie Tobi
- Gabon Biodiversity Program, Smithsonian Conservation Biology Institute, Gamba, Gabon
| | | | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
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24
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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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25
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Burbrink FT, Gehara M, McKelvy AD, Myers EA. Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex). Evolution 2021; 75:260-277. [PMID: 33346918 DOI: 10.1111/evo.14141] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 01/04/2023]
Abstract
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in the environment between lineages. Using population genomic data from the North American ratsnake complex (Pantherophis obsoletus), we connected phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics. We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024
| | - Marcelo Gehara
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, New Jersey, 07102
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, New York, 10016
| | - Edward A Myers
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
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