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Guillory WX, de Medeiros Magalhães F, Coelho FEA, Bonatelli IAS, Palma-Silva C, Moraes EM, Garda AA, Burbrink FT, Gehara M. Geoclimatic drivers of diversification in the largest arid and semi-arid environment of the Neotropics: Perspectives from phylogeography. Mol Ecol 2024; 33:e17431. [PMID: 38877815 DOI: 10.1111/mec.17431] [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: 02/06/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.
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Affiliation(s)
- Wilson X Guillory
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey, USA
| | | | | | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York City, New York, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
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2
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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] [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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3
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Camurugi F, Oliveira EF, Lima GS, Marques R, Magalhães FM, Colli GR, Mesquita DO, Garda AA. Isolation by distance and past climate resistance shaped the distribution of genealogical lineages of a neotropical lizard. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2084470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Eliana F. Oliveira
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Guilherme S. Lima
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Ricardo Marques
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Felipe M. Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
- Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark, Newark, New Jersey, USA
| | - Guarino R. Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Daniel O. Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Adrian A. Garda
- Departamento Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal, Rio Grande do Norte, Brazil
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4
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Tavares MM, Ferro M, Leal BSS, Palma‐Silva C. Speciation with gene flow between two Neotropical sympatric species (
Pitcairnia
spp.: Bromeliaceae). Ecol Evol 2022; 12:e8834. [PMID: 35509614 PMCID: PMC9055293 DOI: 10.1002/ece3.8834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Marília Manuppella Tavares
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Milene Ferro
- Departamento de Biologia Geral e Aplicada Universidade Estadual Paulista Rio Claro Brazil
| | - Bárbara Simões Santos Leal
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Clarisse Palma‐Silva
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
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5
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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6
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Martins LF, Choueri EL, Oliveira AFS, Domingos FMCB, Caetano GHO, Cavalcante VHGL, Leite RN, Fouquet A, Rodrigues MT, Carnaval AC, Colli GR, Werneck FP. Whiptail lizard lineage delimitation and population expansion as windows into the history of Amazonian open ecosystems. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1953185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lidia F. Martins
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Erik L. Choueri
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Alan F. S. Oliveira
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | | | - Gabriel H. O. Caetano
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 849900 Midreshet Ben-Gurion, Israel
| | | | - Rafael N. Leite
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Bâtiment 4R1, 118 Route de Narbonne 31077, Toulouse, France
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana C. Carnaval
- City College of New York and Biology Ph.D. Program, The Graduate Center City University of New York, New York, NY 10031, USA
| | - Guarino R. Colli
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Fernanda P. Werneck
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
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7
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Rabiee M, Mirarab S. SODA: Multi-locus species delimitation using quartet frequencies. Bioinformatics 2021; 36:5623-5631. [PMID: 33555318 DOI: 10.1093/bioinformatics/btaa1010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 10/19/2020] [Accepted: 11/21/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Species delimitation, the process of deciding how to group a set of organisms into units called species, is one of the most challenging problems in evolutionary computational biology. While many methods exist for species delimitation, most based on the coalescent theory, few are scalable to very large datasets, and methods that scale tend to be not accurate. Species delimitation is closely related to species tree inference from discordant gene trees, a problem that has enjoyed rapid advances in recent years. RESULTS In this paper, we build on the accuracy and scalability of recent quartet-based methods for species tree estimation and propose a new method called SODA for species delimitation. SODA relies heavily on a recently developed method for testing zero branch length in species trees. In extensive simulations, we show that SODA can easily scale to very large datasets while maintaining high accuracy. AVAILABILITY The code and data presented here are available on https://github.com/maryamrabiee/SODA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maryam Rabiee
- Computer Science and Engineering, University of California, San Diego, US
| | - Siavash Mirarab
- Electrical and Computer Engineering, University of California, San Diego, US
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8
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Reproductive behavior of Spix’s Whiptails in the wild: understanding the costs and benefits of mate-guarding. Acta Ethol 2021. [DOI: 10.1007/s10211-020-00360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Rocha SM, De-Carvalho CB, Freitas EBD, Santos RA, Santana DO, Borzani ACN, Faria RG, Colli GR, Mesquita DO. Lizards from the Alto Sertão region of Sergipe state, northeastern Brazil. BIOTA NEOTROPICA 2021. [DOI: 10.1590/1676-0611-bn-2020-1137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract We present the first detailed inventory of the lizard fauna of Alto Sertão region, west of Sergipe state, based on three field expeditions carried out by the authors and specimens deposited at the Herpetological Collection of Universidade Federal de Sergipe. The three inventories were carried out between 2010 and 2016, in the municipalities of Canindé de São Francisco, Poço Redondo, Monte Alegre de Sergipe, Nossa Senhora da Glória, and Porto da Folha. In total, we sampled 9,485 lizards of 19 species (10 families) of which 10 are new records for the study area. The most abundant species were Ameivula ocellifera, Tropidurus hispidus and T. semitaeniatus. Thirteen species were considered as widely distributed in Caatinga, five presented a relictual distribution and one was exotic. We suggest that future research focus mainly on non-sampled areas and should prioritize the municipalities of Gararu, Nossa Senhora da Glória and Nossa Senhora de Lourdes since they are localities with little or no sampling records.
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10
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Cabaña I, Chiaraviglio M, Di Cola V, Guisan A, Broennimann O, Gardenal CN, Rivera PC. Hybridization and hybrid zone stability between two lizards explained by population genetics and niche quantification. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractUnderstanding the factors that affect hybridization is an important issue in the study of species evolution. In this work, we analyse the genetic structure of two lizard species, Salvator merianae and Salvator rufescens, at a microscale within a climatic niche analysis framework, to reveal the main factors that contribute to the stability of their hybrid zone. We assess the effect of climate in hybridization by quantifying and decomposing the niche overlap of both species. Using a mitochondrial and a nuclear marker, we find that hybridization is frequent and is not restricted to the sympatric region. The gene flow is mainly from S. rufescens to S. merianae, with introgression into the range of S. merianae. Also, S. merianae would have long been present in the area, while S. rufescens appears to be a recent colonizer. The climate contributes to the population structure of S. merianae, but not to that of S. rufescens. The niches occupied by S. rufescens in the hybrid zone and the non-hybrid zone are similar, while the niches of S. merianae are different. Our results do not fit previous models of hybrid zone stability, suggesting the need to develop new models that consider the evolutionary factors that can differentially affect parental species and hybrids.
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Affiliation(s)
- Imanol Cabaña
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Margarita Chiaraviglio
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Valeria Di Cola
- Department of Ecology & Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology & Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, Lausanne, Switzerland
| | - Olivier Broennimann
- Department of Ecology & Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, Lausanne, Switzerland
| | - Cristina N Gardenal
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Paula C Rivera
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Universidad Nacional de Chilecito, La Rioja, Argentina
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11
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Dong F, Li SH, Chiu CC, Dong L, Yao CT, Yang XJ. Strict allopatric speciation of sky island Pyrrhula erythaca species complex. Mol Phylogenet Evol 2020; 153:106941. [PMID: 32818596 DOI: 10.1016/j.ympev.2020.106941] [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: 09/12/2019] [Revised: 07/01/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.
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Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Chi-Cheng Chiu
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Endemic Species Research Institute, Minsheng East Road, Jiji Township, Nantou County 552, Taiwan.
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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12
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Xu W, Zhou X, Fang W, Chen X. Genetic diversity of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes). PLoS One 2020; 15:e0233714. [PMID: 32469968 PMCID: PMC7259618 DOI: 10.1371/journal.pone.0233714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Toll-like receptor (TLR) genes have recently been employed to assess genetic diversity, as they can be used to infer both demographic history and adaptation to environments with different pathogen pressure. Here, we sampled 120 individuals of the Chinese egret (Egretta eulophotes), a globally vulnerable species, from four breeding populations across China. We assessed the levels of genetic diversity, selection pressure, and population differentiation at seven TLR loci (TLR1LB, TLR2A, TLR3, TLR4, TLR5, TLR7, and TLR15). Using a variety of metrics (SNPs, heterozygosity, nucleotides, haplotypes), our analyses showed that genetic diversity was lower at 4 of the 7 TLR loci in the vulnerable Chinese egret compared to the more common little egret (Egretta garzetta). The selection test indicated TLRs, except for TLR5, were under purifying selection in TLR evolution, suggesting that low TLR genetic diversity in the Chinese egret may be caused by purifying selection. Moreover, analysis of molecular variance indicated low but significant population differentiation among four populations at all of the TLR loci in this egret. However, some comparisons based on fixation index analyses did not show significant population differentiation, and Bayesian clustering showed admixture. Our finding suggested that these four populations of the Chinese egret in China may be considered a single unit for conservation planning. These results, the new report of TLR genetic diversity in a long-distance migratory vulnerable Ardeid species, will provide fundamental TLR information for further studies on the conservation genetics of the Chinese egret and other Ardeids.
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Affiliation(s)
- Wei Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaoping Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
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13
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Ledo RMD, Domingos FMCB, Giugliano LG, Sites JW, Werneck FP, Colli GR. Pleistocene expansion and connectivity of mesic forests inside the South American Dry Diagonal supported by the phylogeography of a small lizard*. Evolution 2020; 74:1988-2004. [DOI: 10.1111/evo.13978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Roger Maia D. Ledo
- Área de Meio Ambiente Instituto Federal de Educação, Ciência e Tecnologia de Brasília Campus Samambaia Samambaia DF 70860 Brazil
- Departamento de Zoologia Universidade de Brasília Brasília DF 70910 Brazil
| | | | - Lilian G. Giugliano
- Departamento de Genética e Morfologia Universidade de Brasília Brasília DF 70910‐900 Brazil
| | - Jack W. Sites
- Department of Biology and Bean Life Sciences Museum Brigham Young University Provo Utah 84602 USA
| | - Fernanda P. Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus AM 69060 Brazil
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília DF 70910 Brazil
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14
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Myers EA, McKelvy AD, Burbrink FT. Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex). Mol Ecol 2020; 29:797-811. [PMID: 31955477 DOI: 10.1111/mec.15358] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species-specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, USA
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY, USA
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15
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Dong F, Hung CM, Yang XJ. Secondary contact after allopatric divergence explains avian speciation and high species diversity in the Himalayan-Hengduan Mountains. Mol Phylogenet Evol 2020; 143:106671. [DOI: 10.1016/j.ympev.2019.106671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022]
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16
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Mângia S, Oliveira EF, Santana DJ, Koroiva R, Paiva F, Garda AA. Revising the taxonomy of
Proceratophrys
Miranda‐Ribeiro, 1920 (Anura: Odontophrynidae) from the Brazilian semiarid Caatinga: Morphology, calls and molecules support a single widespread species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah Mângia
- Departamento de Sistemática e Ecologia Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Universidade Federal da Paraı́ba João Pessoa Brazil
| | - Eliana Faria Oliveira
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Diego José Santana
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Ricardo Koroiva
- Laboratório de Citotaxonomia e Insetos Aquáticos Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Fernando Paiva
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
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17
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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] [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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18
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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19
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Burbrink FT, Ruane S, Kuhn A, Rabibisoa N, Randriamahatantsoa B, Raselimanana AP, Andrianarimalala MSM, Cadle JE, Lemmon AR, Lemmon EM, Nussbaum RA, Jones LN, Pearson R, Raxworthy CJ. The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar. Syst Biol 2019; 68:918-936. [DOI: 10.1093/sysbio/syz026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world’s mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr.
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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
| | - Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University-Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 Fifth Ave., New York, NY 10016, USA
| | - Nirhy Rabibisoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Bernard Randriamahatantsoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Achille P Raselimanana
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - Mamy S M Andrianarimalala
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - John E Cadle
- Department of Biology, East Georgia State College, Swainsboro, GA 30401, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Ronald A Nussbaum
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Leonard N Jones
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Richard Pearson
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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20
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Sonnenberg BR, Branch CL, Pitera AM, Bridge E, Pravosudov VV. Natural Selection and Spatial Cognition in Wild Food-Caching Mountain Chickadees. Curr Biol 2019; 29:670-676.e3. [DOI: 10.1016/j.cub.2019.01.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/05/2018] [Accepted: 01/02/2019] [Indexed: 12/16/2022]
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21
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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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22
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Luo A, Ling C, Ho SYW, Zhu CD. Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios. Syst Biol 2018; 67:830-846. [PMID: 29462495 PMCID: PMC6101526 DOI: 10.1093/sysbio/syy011] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 02/10/2018] [Indexed: 11/14/2022] Open
Abstract
Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Bayesian Phylogenetics and Phylogeography (BPP) explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Cheng Ling
- Department of Computer Science and Technology, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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23
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Geographical Ecology ofTropidurus hispidus(Squamata: Tropiduridae) andCnemidophorus ocellifer(Squamata: Teiidae) in a Neotropical Region: A Comparison among Atlantic Forest, Caatinga, and Coastal Populations. J HERPETOL 2018. [DOI: 10.1670/16-018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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25
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Zhu C, Chen P, Han Y, Ruan L. Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China. Biochem Genet 2018; 56:586-617. [PMID: 29754387 DOI: 10.1007/s10528-018-9862-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
Abstract
The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu's Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low.
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Affiliation(s)
- Chaoying Zhu
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Peng Chen
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Yuqing Han
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Luzhang Ruan
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China.
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26
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Arias FJ, Recoder R, Álvarez BB, Ethcepare E, Quipildor M, Lobo F, Rodrigues MT. Diversity of teiid lizards from Gran Chaco and Western Cerrado (Squamata: Teiidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Federico José Arias
- Laboratório de Herpetologia; Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; São Paulo Brazil
- Museo de Ciencias Naturales; Universidad Nacional de Salta; Salta Argentina
- IBIGEO; Rosario de lerma, Salta Argentina
| | - Renato Recoder
- Laboratório de Herpetologia; Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; São Paulo Brazil
| | - Blanca Beatriz Álvarez
- Laboratorio de Herpetología; Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Corrientes Argentina
| | - Eduardo Ethcepare
- Laboratorio de Herpetología; Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Corrientes Argentina
| | - Matias Quipildor
- Museo de Ciencias Naturales; Universidad Nacional de Salta; Salta Argentina
- IBIGEO; Rosario de lerma, Salta Argentina
| | - Fernando Lobo
- Museo de Ciencias Naturales; Universidad Nacional de Salta; Salta Argentina
- IBIGEO; Rosario de lerma, Salta Argentina
| | - Miguel Trefaut Rodrigues
- Laboratório de Herpetologia; Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; São Paulo Brazil
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27
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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] [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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28
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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] [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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Lisboa CMCA, Bajer K, Pessoa DMA, Huber MAA, Costa GC. Female Brazilian whiptail lizards (Cnemidophorus ocellifer) prefer males with high ultraviolet ornament reflectance. Behav Processes 2017; 142:33-39. [PMID: 28528929 DOI: 10.1016/j.beproc.2017.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 11/25/2022]
Abstract
Conspicuous colouration is an important way of social communication in many taxa. The role of ultraviolet (UV) signals in intraspecific communication has only recently been studied in lizards, and there is not a general understanding of the adaptive role of UV colouration. Colour ornaments can signal male quality in mate choice and are therefore suitable for reliably predicting the outcome of female preference. Here, we tested the potential role of UV colouration in female spatial preference in a non-territorial teiid lizard, Cnemidophorus ocellifer. We experimentally manipulated the UV reflectance of size-matched male pairs and tested the effects of our treatment on females' spatial distribution. We found that females associated with males of higher UV reflectance, suggesting that UV colour can be an important clue during mate preference decisions. Our results provide the first empirical evidence for the importance of UV colouration in female preference in a mutually ornamented lizard species.
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Affiliation(s)
- Carolina M C A Lisboa
- Laboratory of Biogeography and Macroecology, Department of Ecology, Federal University of Rio Grande do Norte, Campus Universitário Lagoa Nova, Natal RN 59078-900, Brazil.
| | - Katalin Bajer
- Laboratory of Biogeography and Macroecology, Department of Ecology, Federal University of Rio Grande do Norte, Campus Universitário Lagoa Nova, Natal RN 59078-900, Brazil; Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary
| | - Daniel M A Pessoa
- Laboratory of Sensory Ecology, Department of Physiology, Federal University of Rio Grande do Norte, Campus Universitário Lagoa Nova, Natal, RN 59078-900, Brazil
| | - Marc A A Huber
- Laboratory of Biogeography and Macroecology, Department of Ecology, Federal University of Rio Grande do Norte, Campus Universitário Lagoa Nova, Natal RN 59078-900, Brazil
| | - Gabriel C Costa
- Department of Biology, Auburn University at Montgomery, Montgomery, AL 36124, USA
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Branch CL, Jahner JP, Kozlovsky DY, Parchman TL, Pravosudov VV. Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli). ROYAL SOCIETY OPEN SCIENCE 2017; 4:170057. [PMID: 28405402 PMCID: PMC5383859 DOI: 10.1098/rsos.170057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.
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