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Bernstein JM, Voris HK, Stuart BL, Karns DR, McGuire JA, Iskandar DT, Riyanto A, Calderón-Acevedo CA, Brown RM, Gehara M, Soto-Centeno JA, Ruane S. Integrative methods reveal multiple drivers of diversification in rice paddy snakes. Sci Rep 2024; 14:4727. [PMID: 38472264 DOI: 10.1038/s41598-024-54744-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.
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Affiliation(s)
- Justin M Bernstein
- Center for Genomics, University of Kansas, Dyche Hall, 1345 Jayhawk Blvd, Lawrence, KS, 66045, USA.
| | - Harold K Voris
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Bryan L Stuart
- Section of Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA
| | - Daryl R Karns
- Biology Department, Hanover College, Hanover, IN, 47243, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Awal Riyanto
- Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong, 16911, Indonesia
| | - Camilo A Calderón-Acevedo
- State University of New York: College of Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
| | - J Angel Soto-Centeno
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
- Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
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2
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Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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3
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Coelho FEA, Guillory WX, Gehara M. Coalescent simulations indicate that the São Francisco River is a biogeographic barrier for six vertebrates in a seasonally dry South American forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.983134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The riverine barrier hypothesis has been extensively explored in Neotropical rainforests, while its importance in drier regions such as the Caatinga, a seasonally dry tropical forest in northeastern Brazil, has only recently received more attention. The Caatinga is bisected by the São Francisco River (SFR), which has long been suggested to be an important biogeographic feature in the region. However, recent studies have found mixed support for the role of the SFR as a hard barrier, most of them relying on the presence or absence of genetic breaks congruent with its course. Here, we used published multilocus and next-generation data from six vertebrate species to test the SFR’s strength as a barrier. Using model-based approaches (approximate Bayesian computation and supervised machine learning), we tested demographic models incorporating full, intermediate, and zero migration across the SFR, estimating divergence times and migration rates for each species. We found support for the SFR’s role as a barrier, allowing gene flow for some species. Estimated divergence times varied among species but are limited to the late Pleistocene, coherent with one of several proposed paleocourse changes in the river’s geological history. Contrary to the mixed results of previous studies, our study supports the SFR as an important phylogeographic barrier across different taxonomic groups, driving diversification in the Caatinga.
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Thom G, Gehara M, Smith BT, Miyaki CY, do Amaral FR. Microevolutionary dynamics show tropical valleys are deeper for montane birds of the Atlantic Forest. Nat Commun 2021; 12:6269. [PMID: 34725329 PMCID: PMC8560783 DOI: 10.1038/s41467-021-26537-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022] Open
Abstract
Tropical mountains hold more biodiversity than their temperate counterparts, and this disparity is often associated with the latitudinal climatic gradient. However, distinguishing the impact of latitude versus the background effects of species history and traits is challenging due to the evolutionary distance between tropical and temperate assemblages. Here, we test whether microevolutionary processes are linked to environmental variation across a sharp latitudinal transition in 21 montane birds of the southern Atlantic Forest in Brazil. We find that effective dispersal within populations in the tropical mountains is lower and genomic differentiation is better predicted by the current environmental complexity of the region than within the subtropical populations. The concordant response of multiple co-occurring populations is consistent with spatial climatic variability as a major process driving population differentiation. Our results provide evidence for how a narrow latitudinal gradient can shape microevolutionary processes and contribute to broader scale biodiversity patterns. There are many hypotheses for why the tropics are more biodiverse than higher latitudes. Phylogenomic analyses of 21 montane birds finds that tropical birds disperse less and have more genetically structured populations than their counterparts at higher latitudes, possibly due to a larger elevational climate gradient in the tropics
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA. .,Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
| | - Marcelo Gehara
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.,Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ, 07102, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Fábio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Prof. Artur Riedel, 275, Jardim Eldorado, Diadema, SP, CEP 09972-270, Brazil
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7
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Bonatelli IAS, Gehara M, Carstens BC, Colli GR, Moraes EM. Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography. Mol Ecol 2021; 31:331-342. [PMID: 34614269 DOI: 10.1111/mec.16210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.
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Affiliation(s)
- Isabel A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, Brazil
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
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8
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de Oliveira FFR, Gehara M, Solé M, Lyra M, Haddad CFB, Silva DP, de Magalhães RF, Leite FSF, Burbrink FT. Quaternary climatic fluctuations influence the demographic history of two species of sky-island endemic amphibians in the Neotropics. Mol Phylogenet Evol 2021; 160:107113. [PMID: 33610648 DOI: 10.1016/j.ympev.2021.107113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/13/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
We evaluated the role of Quaternary climatic fluctuations on the demographic history and population structure of amphibian species endemic to the 'campo rupestre' in the Neotropics, evaluating their distributional shifts, demographic changes, and lineage formation from the end of Pleistocene to present. We chose two anurans endemic to the high-elevation 'campo rupestre' in the Espinhaço Range (ER) in northeastern and southeastern Brazil (Bokermannohyla alvarengai and Bokermannohyla oxente), as models to test the role of Quaternary climatic fluctuations over their distribution range in this region. We collected tissue samples throughout their distribution range and used statistical phylogeography to examine processes of divergence and population demography. We generated spatial-temporal reconstructions using Bayesian inference in a coalescent framework in combination with hind-cast projections of species distribution models (SDMs). We also used the results and literature information to test alternative diversification scenarios via approximate Bayesian computation (ABC). Our results show that Quaternary climatic fluctuations influenced the geographic ranges of both species showing population expansion during the last glacial maximum (LGM) and range contraction during interglacial periods, as inferred from selected ABC models and from past projections of SDMs. We recovered Pleistocene diversification for both species occuring in distinctly unique periods for each taxon. An older and range-restricted lineage was recovered in a geographically isolated geological massif, deserving conservation and further taxonomic study. The diversification and distribution of these amphibian species endemic to the Neotropical 'campo rupestre' were influenced by Quaternary climatic fluctuations. The expansion of cold adapted species restricted to higher elevations during glacial periods and their concomitant retraction during interglacial periods may have been crucial for producing patterns of species richness and endemism along elevation gradients in tropical and subtropical domains. Such processes may influence the evolution of the biota distributed in heterogeneous landscapes with varied topography.
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Affiliation(s)
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University - Newark, USA
| | - Mirco Solé
- Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Bahia, Brazil; Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Mariana Lyra
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Célio Fernando Baptista Haddad
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Daniel Paiva Silva
- Instituto Federal Goiano - IF Goiano, Departamento de Biologia, Urutaí, Goiás, Brazil
| | - Rafael Félix de Magalhães
- Departamento de Ciências Naturais, Campus Dom Bosco, Universidade Federal de São João del-Rei, São João del Rei, MG 36301-160, Brazil
| | - Felipe Sá Fortes Leite
- Laboratório Sagarana, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa - UFV, Florestal, Minas Gerais, Brazil
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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9
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Abstract
Species are being lost at an unprecedented rate during the Anthropocene. Progress has been made in clarifying how species traits influence their propensity to go extinct, but the role historical demography plays in species loss or persistence is unclear. In eastern North America, five charismatic landbirds went extinct last century, and the causes of their extinctions have been heavily debated. Although these extinctions are most often attributed to post-colonial human activity, other factors such as declining ancestral populations prior to European colonization could have made these species particularly susceptible. We used population genomic data from these extinct birds and compared them with those from four codistributed extant species. We found extinct species harboured lower genetic diversity and effective population sizes than extant species, but both extinct and non-extinct birds had similar demographic histories of population expansion. These demographic patterns are consistent with population size changes associated with glacial-interglacial cycles. The lack of support for overall population declines during the Pleistocene corroborates the view that, although species that went extinct may have been vulnerable due to low diversity or small population size, their disappearance was driven by human activities in the Anthropocene.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, 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 Avenue, Newark, NJ 07102, USA
| | - Michael G Harvey
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Röhr DL, Camurugi F, Paterno GB, Gehara M, Juncá FA, Álvares GF, Brandão RA, Garda AA. Variability in anuran advertisement call: a multi-level study with 15 species of monkey tree frogs (Anura, Phyllomedusidae). CAN J ZOOL 2020. [DOI: 10.1139/cjz-2020-0018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding the variability of acoustic signals is a first important step for the comprehension of the evolutionary processes that led to current diversity. Herein, we evaluate the variability of the advertisement call of the phyllomedusid species from the genera Phyllomedusa Wagler, 1830 and Pithecopus Cope, 1866 at different levels: intra-individual, intra-population, inter-population, intra-species, and inter-specific. An analysis of coefficients of variation showed a continuum of variability between the acoustic parameters analyzed, from static to highly dynamic. The majority of the variation was attributed to the inter-specific level, while call parameters at the intra-individual level varied the least. However, each parameter behaved differently with call interval being the most variable across all levels. Most temporal acoustic parameters were affected by environmental temperature, while pulse rate and dominant frequency were strongly influenced by body size. Only pulse rate was correlated to the geographic distance between populations, while all parameters presented a significant phylogenetic signal. Based on these results, we discuss the possible importance of different evolutionary forces and the usage of vocalizations for taxonomic purposes.
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Affiliation(s)
- David L. Röhr
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Lagoa Nova, 59072-970, Natal, RN, Brazil
| | - Felipe Camurugi
- Programa de Pós-Graduação em Ciências Biológicas (Zoologia), Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, 58059-900, PB, Brazil
| | - Gustavo B. Paterno
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Lagoa Nova, 59072-970, Natal, RN, Brazil
| | - Marcelo Gehara
- Rutgers University–Newark, Department of Biological Sciences, 195 University Avenue, Newark, NJ 07102, USA
| | - Flora A. Juncá
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, BR 116, Km 03, Campus Universitário, 44031-460, Feira de Santana, BA, Brazil
| | - Guilherme F.R. Álvares
- Laboratório de Fauna e Unidades de Conservação, Departamento de Engenharia Florestal, Universidade de Brasília, 70.910-900, Brasília – DF, Brazil
| | - Reuber A. Brandão
- Laboratório de Fauna e Unidades de Conservação, Departamento de Engenharia Florestal, Universidade de Brasília, 70.910-900, Brasília – DF, Brazil
| | - Adrian A. Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, 59072-970, Natal, RN, Brazil
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12
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Lanna FM, Gehara M, Werneck FP, Fonseca EM, Colli GR, Sites JW, Rodrigues MT, Garda AA. Dwarf geckos and giant rivers: the role of the São Francisco River in the evolution of Lygodactylus klugei (Squamata: Gekkonidae) in the semi-arid Caatinga of north-eastern Brazil. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Species diversification can be strongly influenced by geomorphological features, such as mountains, valleys and rivers. Rivers can act as hard or soft barriers to gene flow depending on their size, speed of flow, historical dynamics and regional topographical characteristics. The São Francisco River (SFR) is the largest perennial river in the Caatinga biome in north-eastern Brazil and has been considered a barrier to gene flow and dispersal. Herein, we evaluated the role of the SFR on the evolution of Lygodactylus klugei, a small gecko from the Caatinga. Using a single-locus species delimitation method (generalized mixed Yule coalescent), we defined lineages (haploclades). Subsequently, we evaluated the role of the SFR in structuring genetic diversity in this species using a multilocus approach to quantify migration across margins. We also evaluated genetic structure based on nuclear markers, testing the number of populations found through an assignment test (STRUCTURE) across the species distribution. We recovered two mitochondrial lineages structured with respect to the SFR, but only a single population was inferred from nuclear markers. Given that we detected an influence of the SFR only on mitochondrial markers, we suggest that the current river course has acted as a relatively recent geographical barrier for L. klugei, for ~450 000 years.
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Affiliation(s)
- Flávia M Lanna
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, USA
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
| | - Marcelo Gehara
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Emanuel M Fonseca
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, USA
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Jack W Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Reid BN, Naro-Maciel E, Hahn AT, FitzSimmons NN, Gehara M. Geography best explains global patterns of genetic diversity and postglacial co-expansion in marine turtles. Mol Ecol 2019; 28:3358-3370. [PMID: 31264298 DOI: 10.1111/mec.15165] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 01/07/2023]
Abstract
For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion, while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to postglacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial data set encompassing 23 previously identified lineages from all seven marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian model averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.
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Affiliation(s)
- Brendan N Reid
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
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15
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Rancilhac L, Goudarzi F, Gehara M, Hemami MR, Elmer KR, Vences M, Steinfarz S. Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis. Mol Phylogenet Evol 2019; 133:189-197. [PMID: 30659915 DOI: 10.1016/j.ympev.2019.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/01/2019] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. kaiseri, and N. derjugini) against coalescent-based species-delimitation approaches of our genome-wide genetic data set. While the position of N. strauchii as sister species to all other Neurergus species was consistent in all of our analyses, the phylogenetic relationships between the three remaining species changed depending on the applied method. The concatenation approach, as well as quartet-based species-tree inference, supported a topology with N. kaiseri as the closest relative to N. derjugini, while full-coalescent species-tree inference approaches supported N. crocatus as sister species of N. derjugini. Investigating the individual signal of gene trees highlighted an extensive variation among gene histories, most likely resulting from incomplete lineage sorting. Coalescent-based species-delimitation models suggest that the current taxonomy might underestimate the species richness within Neurergus and supports seven species. Based on the current sampling, our analysis suggests that N. strauchii, N. derjugini and N. kaiseri might each be subdivided into further species. However, as amphibian species are known to be composed of deep conspecific lineages that do not always warrant species status, these results need to be cautiously interpreted in an integrative taxonomic framework. We hypothesize that the rather shallow divergences detected within N. kaiseri and N. derjugini likely reflect an ongoing speciation process and thus require further investigation. On the contrary, the much deeper genetic divergence found between the two morphologically and geographically differentiated subspecies of N. strauchii leads us to propose that N. s. barani should be considered a distinct species, Neurergus barani Öz, 1994.
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Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany.
| | - Forough Goudarzi
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany; Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Marcelo Gehara
- American Museum of Natural History, Department of Herpetology, Central Park West at 79th St, New York, NY 10024, USA
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
| | - Sebastian Steinfarz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
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16
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Abstract
Most phylogenies are typically represented as purely bifurcating. However, as genomic data have become more common in phylogenetic studies, it is not unusual to find reticulation among terminal lineages or among internal nodes (deep time reticulation; DTR). In these situations, gene flow must have happened in the same or adjacent geographic areas for these DTRs to have occurred and therefore biogeographic reconstruction should provide similar area estimates for parental nodes, provided extinction or dispersal has not eroded these patterns. We examine the phylogeny of the widely distributed New World kingsnakes (Lampropeltis), determine if DTR is present in this group, and estimate the ancestral area for reticulation. Importantly, we develop a new method that uses coalescent simulations in a machine learning framework to show conclusively that this phylogeny is best represented as reticulating at deeper time. Using joint probabilities of ancestral area reconstructions on the bifurcating parental lineages from the reticulating node, we show that this reticulation likely occurred in northwestern Mexico/southwestern US, and subsequently, led to the diversification of the Mexican kingsnakes. This region has been previously identified as an area important for understanding speciation and secondary contact with gene flow in snakes and other squamates. This research shows that phylogenetic reticulation is common, even in well-studied groups, and that the geographic scope of ancient hybridization is recoverable.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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17
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Lanna FM, Werneck FP, Gehara M, Fonseca EM, Colli GR, Sites JW, Rodrigues MT, Garda AA. The evolutionary history of Lygodactylus lizards in the South American open diagonal. Mol Phylogenet Evol 2018; 127:638-645. [PMID: 29906606 DOI: 10.1016/j.ympev.2018.06.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/05/2018] [Accepted: 06/06/2018] [Indexed: 11/16/2022]
Abstract
The Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests (SDTF) were interconnected during Pleistocene glacial periods, enabling the expansion of species ranges that were subsequently fragmented in interglacial periods, promoting speciation. The lizard genus Lygodactylus occurs in Africa, Madagascar, and South America. Compared to the high diversity of African Lygodactylus, only two species are known to occur in South America, L. klugei and L. wetzeli, distributed in SDTFs and the Chaco, respectively. We use a phylogenetic approach based on mitochondrial (ND2) and nuclear (RAG-1) markers covering the known range of South American Lygodactylus to investigate (i) if they are monophyletic relative to their African congeners, (ii) if their divergence is congruent with the fragmentation of the PAH, and (iii) if cryptic diversity exists within currently recognized species. Maximum likelihood and Bayesian phylogenetic analyses recovered a well-supported monophyletic South American Lygodactylus, presumably resulting from a single trans-Atlantic dispersal event 29 Mya. Species delimitation analyses supported the existence of five putative species, three of them undescribed. Divergence times among L. klugei and the three putative undescribed species, all endemic to the SDTFs, are not congruent with the fragmentation of the PAH. However, fragmentation of the once broader and continuous SDTFs likely influenced the divergence of L. wetzeli in the Chaco and Lygodactylus sp. 3 (in a SDTF enclave in the Cerrado).
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Affiliation(s)
- Flávia M Lanna
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, 59078-900 Natal, RN, Brazil.
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), 69067-375 Manaus, Amazonas, Brazil
| | - Marcelo Gehara
- American Museum of Natural History, Department of Herpetology, 79th St. Central Park West, New York, NY 10024, United States
| | - Emanuel M Fonseca
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, 59078-900 Natal, RN, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil
| | - Jack W Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT 84602, United States
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, 59078-900 Natal, RN, Brazil
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18
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Oliveira EF, Martinez PA, São-Pedro VA, Gehara M, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Costa GC. Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard. Heredity (Edinb) 2017; 120:251-265. [PMID: 29238076 DOI: 10.1038/s41437-017-0017-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/30/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.
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Affiliation(s)
- Eliana Faria Oliveira
- Pós-Graduação em Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil. .,Universidade Federal de Mato Grosso do Sul, Centro de Ciências Biológicas e da Saúde, Laboratório de Zoologia, Campo Grande, MS, Brazil.
| | - Pablo Ariel Martinez
- Universidade Federal de Sergipe, Laboratório de Pesquisas Integrativas em Biodiversidade (PIBi Lab), Pós-Graduação em Ecologia e Conservação, São Cristovão, SE, Brazil
| | - Vinícius Avelar São-Pedro
- Universidade Federal de São Carlos, Campus Lagoa do Sino, Centro de Ciências da Natureza, Buri, SP, Brazil
| | - Marcelo Gehara
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | | | - Daniel Oliveira Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Natal, RN, Brazil
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19
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Gehara M, Garda AA, Werneck FP, Oliveira EF, Fonseca EM, Camurugi F, Magalhães FDM, Lanna FM, Sites JW, Marques R, Silveira‐Filho R, São Pedro VA, Colli GR, Costa GC, Burbrink FT. Estimating synchronous demographic changes across populations using
hABC
and its application for a herpetological community from northeastern Brazil. Mol Ecol 2017; 26:4756-4771. [DOI: 10.1111/mec.14239] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/30/2017] [Accepted: 07/02/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Marcelo Gehara
- Department of Herpetology American Museum of Natural History New York NY USA
| | - Adrian A. Garda
- Departamento de Botânica e Zoologia Centro de Biociências Universidade Federal do Rio Grande do Norte Lagoa Nova Natal RN Brazil
| | - Fernanda P. Werneck
- Coordenação de Biodiversidade Programa de Coleções Científicas Biológicas Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus AM Brazil
| | - Eliana F. Oliveira
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências Biológicas e da Saúde Laboratório de Zoologia Cidade Universitária Universidade Federal do Mato Grosso do Sul Campo Grand MS Brazil
| | - Emanuel M. Fonseca
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Felipe Camurugi
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Felipe de M. Magalhães
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Flávia M. Lanna
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum Brigham Young University Provo UT USA
| | - Ricardo Marques
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Ricardo Silveira‐Filho
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Vinícius A. São Pedro
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências da Natureza Universidade Federal de São Carlos Buri SP Brazil
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília Brazil
| | - Gabriel C. Costa
- Department of Biology Auburn University at Montgomery Montgomery AL USA
| | - Frank T. Burbrink
- Department of Herpetology American Museum of Natural History New York NY USA
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20
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Menezes L, Canedo C, Batalha-Filho H, Garda AA, Gehara M, Napoli MF. Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest. PLoS One 2016; 11:e0154626. [PMID: 27248688 PMCID: PMC4889069 DOI: 10.1371/journal.pone.0154626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/16/2016] [Indexed: 11/21/2022] Open
Abstract
We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population’s distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.
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Affiliation(s)
- Lucas Menezes
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Clarissa Canedo
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Henrique Batalha-Filho
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Adrian Antonio Garda
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Botânica, Ecologia e Zoologia, Laboratório de Anfíbios e Répteis-LAR, Campus Universitário, Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Gehara
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Felgueiras Napoli
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- * E-mail:
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21
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Oliveira EF, Gehara M, São-Pedro VA, Chen X, Myers EA, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Rodrigues MT, Arias FJ, Zaher H, Santos RML, Costa GC. Speciation with gene flow in whiptail lizards from a Neotropical xeric biome. Mol Ecol 2015; 24:5957-75. [PMID: 26502084 DOI: 10.1111/mec.13433] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/15/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.
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Affiliation(s)
- Eliana F Oliveira
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Marcelo Gehara
- Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Vinícius A São-Pedro
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Xin Chen
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Edward A Myers
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Frank T Burbrink
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA.,Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, 58000-00, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Federico J Arias
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Rodrigo M L Santos
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Gabriel C Costa
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
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22
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Miralles A, Hipsley CA, Erens J, Gehara M, Rakotoarison A, Glaw F, Müller J, Vences M. Distinct patterns of desynchronized limb regression in malagasy scincine lizards (squamata, scincidae). PLoS One 2015; 10:e0126074. [PMID: 26042667 PMCID: PMC4456255 DOI: 10.1371/journal.pone.0126074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/28/2015] [Indexed: 12/27/2022] Open
Abstract
Scincine lizards in Madagascar form an endemic clade of about 60 species exhibiting a variety of ecomorphological adaptations. Several subclades have adapted to burrowing and convergently regressed their limbs and eyes, resulting in a variety of partial and completely limbless morphologies among extant taxa. However, patterns of limb regression in these taxa have not been studied in detail. Here we fill this gap in knowledge by providing a phylogenetic analysis of DNA sequences of three mitochondrial and four nuclear gene fragments in an extended sampling of Malagasy skinks, and microtomographic analyses of osteology of various burrowing taxa adapted to sand substrate. Based on our data we propose to (i) consider Sirenoscincus Sakata & Hikida, 2003, as junior synonym of Voeltzkowia Boettger, 1893; (ii) resurrect the genus name Grandidierina Mocquard, 1894, for four species previously included in Voeltzkowia; and (iii) consider Androngo Brygoo, 1982, as junior synonym of Pygomeles Grandidier, 1867. By supporting the clade consisting of the limbless Voeltzkowia mira and the forelimb-only taxa V. mobydick and V. yamagishii, our data indicate that full regression of limbs and eyes occurred in parallel twice in the genus Voeltzkowia (as hitherto defined) that we consider as a sand-swimming ecomorph: in the Voeltzkowia clade sensu stricto the regression first affected the hindlimbs and subsequently the forelimbs, whereas the Grandidierina clade first regressed the forelimbs and subsequently the hindlimbs following the pattern prevalent in squamates. Timetree reconstructions for the Malagasy Scincidae contain a substantial amount of uncertainty due to the absence of suitable primary fossil calibrations. However, our preliminary reconstructions suggest rapid limb regression in Malagasy scincids with an estimated maximal duration of 6 MYr for a complete regression in Paracontias, and 4 and 8 MYr respectively for complete regression of forelimbs in Grandidierina and hindlimbs in Voeltzkowia.
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Affiliation(s)
- Aurélien Miralles
- Centre d’Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique, Montpellier, France
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- * E-mail:
| | - Christy A. Hipsley
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Berlin, Germany
- University of Melbourne, School of BioSciences, Melbourne, Victoria, Australia
| | - Jesse Erens
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- Biosystematics Group, Wageningen University, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Marcelo Gehara
- Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Andolalao Rakotoarison
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- Département de Biologie Animale, Université d’Antananarivo, Antananarivo, Madagascar
| | - Frank Glaw
- Zoologische Staatssammlung München, München, Germany
| | - Johannes Müller
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Berlin, Germany
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
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Rodríguez A, Börner M, Pabijan M, Gehara M, Haddad CFB, Vences M. Genetic divergence in tropical anurans: deeper phylogeographic structure in forest specialists and in topographically complex regions. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9774-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Gehara M, Crawford AJ, Orrico VGD, Rodríguez A, Lötters S, Fouquet A, Barrientos LS, Brusquetti F, De la Riva I, Ernst R, Urrutia GG, Glaw F, Guayasamin JM, Hölting M, Jansen M, Kok PJR, Kwet A, Lingnau R, Lyra M, Moravec J, Pombal JP, Rojas-Runjaic FJM, Schulze A, Señaris JC, Solé M, Rodrigues MT, Twomey E, Haddad CFB, Vences M, Köhler J. High levels of diversity uncovered in a widespread nominal taxon: continental phylogeography of the neotropical tree frog Dendropsophus minutus. PLoS One 2014; 9:e103958. [PMID: 25208078 PMCID: PMC4160190 DOI: 10.1371/journal.pone.0103958] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/04/2014] [Indexed: 11/24/2022] Open
Abstract
Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.
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Affiliation(s)
- Marcelo Gehara
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- Pós-graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, Natal, RN, Brasil
- * E-mail:
| | - Andrew J. Crawford
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
- Smithsonian Tropical Research Institute, Panamá, Republic of Panama
| | - Victor G. D. Orrico
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, Brasil
| | - Ariel Rodríguez
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
| | - Stefan Lötters
- Trier University, Biogeography Department, Trier, Germany
| | - Antoine Fouquet
- CNRS-Guyane - USR3456, Immeuble Le Relais - 2, Cayenne, French Guiana
| | - Lucas S. Barrientos
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Francisco Brusquetti
- Departamento de Zoologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil; Instituto de Investigación Biológica del Paraguay, Asunción, Paraguay
| | | | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | | | - Frank Glaw
- Zoologische Staatssammlung München, München, Germany
| | - Juan M. Guayasamin
- Universidad Tecnológica Indoamérica, Centro de Investigación de la Biodiversidad y el Cambio Climático (BioCamp), Cotocollao, Quito, Ecuador
| | - Monique Hölting
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Martin Jansen
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Philippe J. R. Kok
- Amphibian Evolution Lab, Department of Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Axel Kwet
- German Herpetological Society (DGHT), Mannheim, Germany
| | - Rodrigo Lingnau
- Universidade Tecnológica Federal do Paraná, Francisco Beltrão, PR, Brasil
| | - Mariana Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil
| | - Jiří Moravec
- Department of Zoology, National Museum, Prague, Czech Republic
| | - José P. Pombal
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Arne Schulze
- Hessisches Landesmuseum Darmstadt, Department of Zoology, Darmstadt, Germany
| | - J. Celsa Señaris
- Laboratorio de Ecología y Genética de Poblaciones, Centro de Ecología, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Mirco Solé
- Universidade Estadual de Santa Cruz, Departamento de Ciências Biológicas, Rodovia Ilhéus-Itabuna, Bahia, Brasil
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, Brasil
| | - Evan Twomey
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
| | - Celio F. B. Haddad
- Departamento de Zoologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
| | - Jörn Köhler
- Hessisches Landesmuseum Darmstadt, Department of Zoology, Darmstadt, Germany
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Vences M, Sanchez E, Hauswaldt JS, Eikelmann D, Rodríguez A, Carranza S, Donaire D, Gehara M, Helfer V, Lötters S, Werner P, Schulz S, Steinfartz S. Nuclear and mitochondrial multilocus phylogeny and survey of alkaloid content in true salamanders of the genus Salamandra (Salamandridae). Mol Phylogenet Evol 2014; 73:208-16. [DOI: 10.1016/j.ympev.2013.12.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/27/2013] [Accepted: 12/29/2013] [Indexed: 11/28/2022]
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26
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Hauswaldt JS, Angelini C, Gehara M, Benavides E, Polok A, Steinfartz S. From species divergence to population structure: A multimarker approach on the most basal lineage of Salamandridae, the spectacled salamanders (genus Salamandrina) from Italy. Mol Phylogenet Evol 2014; 70:1-12. [DOI: 10.1016/j.ympev.2013.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 08/17/2013] [Accepted: 08/20/2013] [Indexed: 11/26/2022]
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Vences M, Hauswaldt JS, Steinfartz S, Rupp O, Goesmann A, Künzel S, Orozco-terWengel P, Vieites DR, Nieto-Roman S, Haas S, Laugsch C, Gehara M, Bruchmann S, Pabijan M, Ludewig AK, Rudert D, Angelini C, Borkin LJ, Crochet PA, Crottini A, Dubois A, Ficetola GF, Galán P, Geniez P, Hachtel M, Jovanovic O, Litvinchuk SN, Lymberakis P, Ohler A, Smirnov NA. Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Mol Phylogenet Evol 2013; 68:657-70. [PMID: 23632031 DOI: 10.1016/j.ympev.2013.04.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 11/26/2022]
Abstract
We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.
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Affiliation(s)
- Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
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Vences M, Gehara M, Köhler J, Glaw F. Description of a new Malagasy treefrog (Boophis) occurring syntopically with its sister species, and a plea for studies on non-allopatric speciation in tropical amphibians. AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/15685381-00002856] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Based on concordant differences in male advertisement call, tadpole morphology, and absence of haplotype sharing in mitochondrial and nuclear DNA markers, we describe a new species of treefrog from Ranomafana National Park in the southern central east of Madagascar. In its adult stage Boophis narinsi sp. n. is highly similar to its sister species, Boophis majori, but appears to differ in having longer hindlimbs. The genetic divergences between these two species (2.5-3.3% in a fragment of the 16S rRNA gene, depending on fragment length and individual haplotype analyzed) are below the threshold typically characterizing distinct species of anurans. Together with their relatively small and largely overlapping ranges and their sympatric occurrence in Ranomafana National Park, this indicates that they potentially could have originated rather recently by adaptive speciation under parapatric or sympatric conditions. Most studies on amphibian speciation have so far by default assumed vicariant speciation. We suggest that alternative speciation scenarios should be considered in future works and characterize settings in which more reliable assessments of adaptive parapatric or sympatric speciation could be carried out.
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Affiliation(s)
- Miguel Vences
- 1Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Marcelo Gehara
- 1Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Jörn Köhler
- 2Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
| | - Frank Glaw
- 3Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany
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