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Pavón-Vázquez CJ, Rana Q, Farleigh K, Crispo E, Zeng M, Liliah J, Mulcahy D, Ascanio A, Jezkova T, Leaché AD, Flouri T, Yang Z, Blair C. Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards. Syst Biol 2024; 73:323-342. [PMID: 38190300 DOI: 10.1093/sysbio/syae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/18/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Colonia Los Reyes Ixtacala, Tlalnepantla, Estado de México, C.P. 54090, México
| | - Qaantah Rana
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
| | - Keaka Farleigh
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Erika Crispo
- Department of Biology, Pace University, One Pace Plaza, New York, NY 10038, USA
| | - Mimi Zeng
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
| | - Jeevanie Liliah
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
| | - Daniel Mulcahy
- Collection Future, Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin 10115, Germany
| | - Alfredo Ascanio
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
- Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
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2
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Meghana R, Anand PP, Vardhanan YS. Molecular and morphometric analyses reveal host-specific cryptic speciation in a mite species, Tetranychus neocaledonicus (Andre, 1933) (Acari: Tetranychidae). Zootaxa 2023; 5306:61-96. [PMID: 37518535 DOI: 10.11646/zootaxa.5306.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 08/01/2023]
Abstract
Host- and habitat-induced morphological shape and size variations are common in phytophagous and parasitic taxa. Several integrated morphological and molecular techniques have been commonly used to understand host-induced morpho-cryptic species forms. Compared to other arthropods, cryptic speciation was more common in Acari. This study focused on the host-specific morphological cryptic shape and size variations of Tetranychus neocaledonicus, collected from moringa and cassava hosts. We used geometric morphometric analysis to uncover the shape and size of inter-and intra-spider mite populations, and discovered that host-specific shape and size variations existed in spider mites regardless of sex. Interestingly, there was no phylogenetic signal in spider mites, implying that the morpho-cryptic speciation of T. neocaledonicus is solely based on the host-induced selection. The molecular clock hypothesis was accepted in our CO1 and 18s rRNA phylogeny analyses, and spider mites collected from both hosts were genetically less diverse. We conclude that T. neocaledonicus exhibited morphologically detectable cryptic population diversity in each host but that these populations are evolutionarily young form. Apart from these host-induced variations, we also monitored the impact of the clearing agent (lactic acid) on the shape and size of T. neocaledonicus; from this study, we proved that the clearing agent significantly alters the taxonomically important morphological traits of spider mites irrespective of the mites' sex, as confirmed by multivariate statistical analysis. This is the first study report to investigated the host-induced morphological variations of spider mites and the impact of a clearing agent.
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Affiliation(s)
- R Meghana
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
| | - P P Anand
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
| | - Y Shibu Vardhanan
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
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3
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Villegas-Patraca R, Aguilar-López JL, Hernández-Hernández JC, Muñoz-Jiménez O. Diversity and conservation of terrestrial vertebrates (birds, mammals, and reptiles) of Sierra Cucapá, Mexicali, Baja California, Mexico. Zookeys 2022; 1088:17-39. [PMID: 35437372 PMCID: PMC8901611 DOI: 10.3897/zookeys.1088.76134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
Knowledge about the biodiversity of Baja California has been obtained mainly from natural protected areas (NPAs), while some unprotected natural areas have been poorly studied. The Sierra Cucapá in the northeast of the peninsula is one example. The objectives of this study are 1) to integrate existing knowledge of bird, mammal, and reptile diversity in Cucapá from public databases, citizen science platforms, and information generated from fieldwork, 2) to identify the spatial distribution of records in the study area, 3) to compare the composition of vertebrate species of Cucapá with that of NPAs of northern part of the peninsula, and 4) to assess the biological conservation value of Cucapá. We obtained records of 150 species of native vertebrates (102 birds, 34 mammals, and 14 reptiles) of which 10 species of birds, four mammals, and seven reptiles are included in a risk extinction category. The different sources of information contributed in a complementary way to the species inventories. Large areas in western and northern Cucapá lack records. The total difference in species composition between Cucapá and nearby NPAs ranged between 58 and 69% for birds, 61 and 79% for mammals, and 69 and 87% for reptiles. The species richness of Cucapá, its particular species composition, the presence of species in risk extinction categories, and the number and size of unexplored areas indicate that this area represents an opportunity for biological conservation in the northern part of the Peninsula. This work provides compelling data for the protection of Cucapá.
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4
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De la Mora-Curiel M, Piñero D, Oyama K, Núñez-Farfán J. A single genealogical lineage from the Sonoran Desert and the Mexican Pacific Coast explains the haplotype distribution of Trichobaris compacta. REV MEX BIODIVERS 2021. [DOI: 10.22201/ib.20078706e.2021.92.3370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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5
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Leavitt DH, Hollingsworth BD, Fisher RN, Reeder TW. Introgression obscures lineage boundaries and phylogeographic history in the western banded gecko, Coleonyx variegatus (Squamata: Eublepharidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe geomorphological formation of the Baja California peninsula and the Gulf of California is a principal driver of diversification for the reptiles of North America’s warm deserts. The western banded gecko, Coleonyx variegatus, is distributed throughout the Mojave, Sonoran and Peninsular deserts. In this study we use multilocus sequence data to address deep phylogeographic structure within C. variegatus. Analyses of mtDNA data recover six divergent clades throughout the range of C. variegatus. Topology of the mtDNA gene tree suggests separate origins of peninsular populations with an older lineage in the south and a younger one in the north. In contrast, analyses of multilocus nuclear data provide support for four lineages, corresponding to the subspecies C. v. abbotti, C. v. peninsularis, C. v. sonoriensis and C. v. variegatus. Phylogenetic analyses of the nuclear data recover C. v. abbotti and C. v. peninsularis as a clade, indicating a single origin of the peninsular populations. Discordance between the nuclear and mtDNA data is largely the result of repeated episodes of mtDNA introgression that have obscured both lineage boundaries and biogeographic history. Dating analyses of the combined nuclear and mtDNA data suggest that the peninsular clade diverged from the continental group in the Late Miocene.
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Affiliation(s)
| | - Bradford D Hollingsworth
- San Diego State University, San Diego, CA, USA
- San Diego Natural History Museum, El Prado, San Diego, CA, USA
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Galina‐Tessaro P, Álvarez‐Cárdenas S, Valdez‐Villavicencio JH, Villagrán‐SantaCruz M. Reproduction in
Sceloporus licki
(Reptilia: Phrynosomatidae) in the Cape Region, Baja California Sur. ACTA ZOOL-STOCKHOLM 2020. [DOI: 10.1111/azo.12342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | - Maricela Villagrán‐SantaCruz
- Laboratorio de Biología Tisular y Reproductora Departamento de Biología Comparada Facultad de Ciencias Universidad Nacional Autónoma de México Ciudad de México México
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Díaz‐Cárdenas B, Ruiz‐Sanchez E, Gadsden H, García‐Enriquez JM, Castro‐Felix P, Castañeda‐Gaytán G, Santerre A. Physiographic and climatic events in the Chihuahuan Desert lead to the speciation and distinct demographic patterns of two sister Sceloporuslizards. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brenda Díaz‐Cárdenas
- Red de Diversidad Biológica del Occidente Mexicano Instituto de Ecología A. C., Centro Regional del Bajío Pátzcuaro México
- Departamento de Ecología Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | - Eduardo Ruiz‐Sanchez
- Departamento de Botánica y Zoología Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | - Héctor Gadsden
- Red de Diversidad Biológica del Occidente Mexicano Instituto de Ecología A. C., Centro Regional del Bajío Pátzcuaro México
| | - José Manuel García‐Enriquez
- Departamento de Biología Celular y Molecular Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | - Patricia Castro‐Felix
- Departamento de Biología Celular y Molecular Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | | | - Anne Santerre
- Departamento de Biología Celular y Molecular Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
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8
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Schield DR, Perry BW, Adams RH, Card DC, Jezkova T, Pasquesi GIM, Nikolakis ZL, Row K, Meik JM, Smith CF, Mackessy SP, Castoe TA. Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Tereza Jezkova
- Department of Biology, Miami University of Ohio, Oxford, OH, USA
| | | | | | - Kristopher Row
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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9
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Provost KL, Mauck WM, Smith BT. Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is linked to behavioral differentiation. Ecol Evol 2018; 8:12456-12478. [PMID: 30619558 PMCID: PMC6309012 DOI: 10.1002/ece3.4596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 01/22/2023] Open
Abstract
Biogeographic barriers are considered important in initiating speciation through geographic isolation, but they rarely indiscriminately and completely reduce gene flow across entire communities. Explicitly demonstrating which factors are associated with gene-flow levels across barriers would help elucidate how speciation is initiated and isolation maintained. Here, we investigated the association of behavioral isolation on population differentiation in Northern Cardinals (Cardinalis cardinalis) distributed across the Cochise Filter Barrier, a region of transitional habitat which separates the Sonoran and Chihuahuan deserts of North America. Using genomewide markers, we modeled demographic history by fitting the data to isolation and isolation-with-migration models. The best-fit model indicated that desert populations diverged in the Pleistocene with low, historic, and asymmetric gene flow across the barrier. We then tested behavioral isolation using reciprocal call-broadcast experiments to compare song recognition between deserts, controlling for song dialect changes within deserts. We found that male Northern Cardinals in both deserts were most aggressive to local songs and failed to recognize across-barrier songs. A correlation of genomic differentiation and strong song discrimination is consistent with a model where speciation is initiated across a barrier and maintained by behavioral isolation.
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Affiliation(s)
- Kaiya L. Provost
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkNew York
- Department of Ecology, Evolution, and Environmental BiologyColumbia UniversityNew YorkNew York
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNew York
| | - William M. Mauck
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkNew York
- Present address:
New York Genome CenterNew YorkNew York
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10
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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11
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Welton LJ, Siler CD, Grismer LL, Diesmos AC, Sites JW, Brown RM. Archipelago-wide survey of Philippine forest dragons (Agamidae:Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Luke J. Welton
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology; 2401 Chautauqua Ave., University of Oklahoma; Norman OK 73072-7029 USA
| | - L. L. Grismer
- Department of Biology; 4500 Riverwalk Parkway, La Sierra University; Riverside CA 92515-8247 USA
| | - Arvin C. Diesmos
- Herpetology Section; Zoology Division; National Museum of the Philippines; Rizal Park Padre Burgos Avenue Manila Philippines
| | - Jack W. Sites
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
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12
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González-Rubio C, García-De León FJ, Rodríguez-Estrella R. Phylogeography of endemic Xantus' hummingbird (Hylocharis xantusii) shows a different history of vicariance in the Baja California Peninsula. Mol Phylogenet Evol 2016; 102:265-77. [PMID: 27261252 DOI: 10.1016/j.ympev.2016.05.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 01/21/2023]
Abstract
Studies of phylogeographic patterns provide insight into the processes driving lineage divergence in a particular region. To identify the processes that caused phylogeographic breaks, it is necessary to use historical information and a set of appropriate molecular data to explain current patterns. To understand the influence of geological or ecological processes on the phylogeography of the only species of hummingbird endemic to the Baja California Peninsula, Hylocharis xantusii, mitochondrial DNA sequences of three concatenated genes (Cyt-b, COI and ND2; 2297bp in total) in 100 individuals were analyzed. The spatial analyses of genetic variation showed phylogeographic structure consisting of a north, central and south regions. According to estimated divergence times, two vicariant events are supported, permanent separation of the peninsula and formation of the Gulf of California at 5mya and temporary isolation of the southern region at the Isthmus of La Paz at 3mya. The temporal frame of genetic differentiation of intraspecific haplotypes indicates that 90% of haplotypes diverged within the last 500,000years, with a population expansion 80,000years ago. Only four haplotypes diverged ∼2.2 my and occurred in the south (Hxan_36, 38 and 45), and north (Hxan_45 and 56) regions; only haplotype 45 is shared between south and north populations. These regions also have the most recent haplotypes from 12,500 to 16,200years ago, and together with high levels of genetic diversity, we suggest two refuge areas, the Northern and Southern regions. Our results indicate that the phylogeographic pattern first results from vicariance processes, then is followed by historical and recent climate fluctuations that influenced conditions on the peninsula, and it is also related to oases distribution. This study presents the first investigation of phylogeography of the peninsular' endemic Xantus' hummingbird.
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Affiliation(s)
- Cristina González-Rubio
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN #195, La Paz, BCS 23096, Mexico
| | - Francisco J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN #195, La Paz, BCS 23096, Mexico.
| | - Ricardo Rodríguez-Estrella
- Laboratorio de Análisis Espacial, Ecología y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN #195, La Paz, BCS 23096, Mexico
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13
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Leaché AD, Banbury BL, Linkem CW, de Oca ANM. Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)? BMC Evol Biol 2016; 16:63. [PMID: 27000803 PMCID: PMC4802581 DOI: 10.1186/s12862-016-0628-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/29/2016] [Indexed: 01/25/2023] Open
Abstract
Background Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. Results The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Conclusions Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA. .,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA.
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B402, Seattle, 98109, Washington, USA
| | - Charles W Linkem
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México
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14
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Mott BM, Gadau J, Anderson KE. Phylogeography of Pogonomyrmex barbatus and P. rugosus harvester ants with genetic and environmental caste determination. Ecol Evol 2015; 5:2798-826. [PMID: 26306168 PMCID: PMC4541987 DOI: 10.1002/ece3.1507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 11/11/2022] Open
Abstract
We present a phylogeographic study of at least six reproductively isolated lineages of new world harvester ants within the Pogonomyrmex barbatus and P. rugosus species group. The genetic and geographic relationships within this clade are complex: Four of the identified lineages show genetic caste determination (GCD) and are divided into two pairs. Each pair has evolved under a mutualistic system that necessitates sympatry. These paired lineages are dependent upon one another because their GCD requires interlineage matings for the production of F1 hybrid workers, and intralineage matings are required to produce queens. This GCD system maintains genetic isolation among these interdependent lineages, while simultaneously requiring co-expansion and emigration as their distributions have changed over time. It has also been demonstrated that three of these four GCD lineages have undergone historical hybridization, but the narrower sampling range of previous studies has left questions on the hybrid parentage, breadth, and age of these groups. Thus, reconstructing the phylogenetic and geographic history of this group allows us to evaluate past insights and hypotheses and to plan future inquiries in a more complete historical biogeographic context. Using mitochondrial DNA sequences sampled across most of the morphospecies' ranges in the U.S.A. and Mexico, we conducted a detailed phylogeographic study. Remarkably, our results indicate that one of the GCD lineage pairs has experienced a dramatic range expansion, despite the genetic load and fitness costs of the GCD system. Our analyses also reveal a complex pattern of vicariance and dispersal in Pogonomyrmex harvester ants that is largely concordant with models of late Miocene, Pliocene, and Pleistocene range shifts among various arid-adapted taxa in North America.
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Affiliation(s)
- Brendon M Mott
- USDA-ARS Carl Hayden Bee Research CenterTucson, Arizona, 85719
- School of Life Sciences, Arizona State UniversityTempe, Arizona, 85287
| | - Jürgen Gadau
- School of Life Sciences, Arizona State UniversityTempe, Arizona, 85287
| | - Kirk E Anderson
- USDA-ARS Carl Hayden Bee Research CenterTucson, Arizona, 85719
- Center for Insect Science, University of ArizonaTucson, Arizona, 85721
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15
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Edwards T, Berry KH, Inman RD, Esque TC, Nussear KE, Jones CA, Culver M. Testing Taxon Tenacity of Tortoises: evidence for a geographical selection gradient at a secondary contact zone. Ecol Evol 2015; 5:2095-114. [PMID: 26045959 PMCID: PMC4449762 DOI: 10.1002/ece3.1500] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai. The taxa were isolated from a common ancestor during the formation of the Colorado River (4–8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California (n - 103), G. morafkai in Arizona (n - 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co-occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; University of Arizona Genetics Core, University of Arizona 1657 E. Helen Street, Tucson, Arizona, 85721
| | - Kristin H Berry
- Western Ecological Research Center, U.S. Geological Survey Falcon Business Park, 21803 Cactus Avenue, Suite F, Riverside, California, 92518
| | - Richard D Inman
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Todd C Esque
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Kenneth E Nussear
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Cristina A Jones
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Game and Fish Department, Nongame Wildlife Branch Phoenix, Arizona, 85086
| | - Melanie Culver
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Arizona Tucson, Arizona, 85721
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16
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Nelson BJ, Andersen JJ, Brown JM. Deflating Trees: Improving Bayesian Branch-Length Estimates using Informed Priors. Syst Biol 2015; 64:441-7. [DOI: 10.1093/sysbio/syv003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/08/2015] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bradley J. Nelson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - John J. Andersen
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeremy M. Brown
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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17
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Gottscho AD. Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America. Biol Rev Camb Philos Soc 2014; 91:235-54. [DOI: 10.1111/brv.12167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 10/28/2014] [Accepted: 11/11/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew D. Gottscho
- Department of Biology; San Diego State University; 5500 Campanile Drive San Diego CA 92182 U.S.A
- Department of Biology; University of California; Riverside CA 92521 U.S.A
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18
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Leaché AD, Harris RB, Maliska ME, Linkem CW. Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data. Genome Biol Evol 2014; 5:2410-9. [PMID: 24259316 PMCID: PMC3879974 DOI: 10.1093/gbe/evt186] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation–migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean = 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation.
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19
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Bezy RL, Cole CJ. Amphibians and Reptiles of the Madrean Archipelago of Arizona and New Mexico. AMERICAN MUSEUM NOVITATES 2014. [DOI: 10.1206/3810.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Torstrom SM, Pangle KL, Swanson BJ. Shedding subspecies: The influence of genetics on reptile subspecies taxonomy. Mol Phylogenet Evol 2014; 76:134-43. [DOI: 10.1016/j.ympev.2014.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/08/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
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21
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Li HS, Xue XF, Hong XY. Cryptic diversity in host-associated populations of Tetra pinnatifidae (Acari: Eriophyoidea): what do morphometric, mitochondrial and nuclear data reveal and conceal? BULLETIN OF ENTOMOLOGICAL RESEARCH 2014; 104:221-32. [PMID: 24401188 DOI: 10.1017/s0007485313000746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Traditional morphology-based taxonomy of eriophyoid mites (Acari: Eriophyoidea) has been challenged by molecular-based technologies in the detection of cryptic species. However, the implications of such cryptic diversity appear to differ when methods based on different types of data are used. Here, samples of a host-associated eriophyoid mite species, Tetra pinnatifidae, collected from different host plants and localities are evaluated. The congruence of results based on morphometric (32 characters), mitochondrial (16S), and nuclear (28S) data were evaluated and showed a host-associated cryptic diversity dividing this morphospecies into several groups/clades that were morphometrically indistinguishable. In comparison, the 16S data confirmed cryptic speciation and intra-clade host-associated diversity, while 28S did not. In contrast, 28S data revealed potential gene flow between host-associated populations. High mitochondrial divergence, as well as low nuclear and morphological divergence indicated very recent stage of cryptic diversity of this eriophyoid mite.
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Affiliation(s)
- Hao-Sen Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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22
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Welton LJ, Siler CD, Oaks JR, Diesmos AC, Brown RM. Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards. Mol Ecol 2013; 22:3495-510. [DOI: 10.1111/mec.12324] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 03/17/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- L. J. Welton
- Department of Biology; Brigham Young University; Provo UT 84602 USA
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| | - C. D. Siler
- Department of Biology; University of South Dakota; Vermillion SD 57069 USA
| | - J. R. Oaks
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| | - A. C. Diesmos
- Herpetology Section; Zoology Division; Philippine National Museum; Rizal Park, Burgos Street Manila Philippines
| | - R. M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
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23
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Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12084] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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25
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Wood DA, Vandergast AG, Barr KR, Inman RD, Esque TC, Nussear KE, Fisher RN. Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the
M
ojave and
S
onoran Deserts. DIVERS DISTRIB 2012. [DOI: 10.1111/ddi.12022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Amy G. Vandergast
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Kelly R. Barr
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Rich D. Inman
- U.S. Geological Survey Western Ecological Research Center Las Vegas Field Station, 160 North Stephanie Street Henderson NV 89074 USA
| | - Todd C. Esque
- U.S. Geological Survey Western Ecological Research Center Las Vegas Field Station, 160 North Stephanie Street Henderson NV 89074 USA
| | - Kenneth E. Nussear
- U.S. Geological Survey Western Ecological Research Center Las Vegas Field Station, 160 North Stephanie Street Henderson NV 89074 USA
| | - Robert N. Fisher
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
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26
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Anderson CG, Greenbaum E. Phylogeography of Northern Populations of the Black-Tailed Rattlesnake (Crotalus molossus Baird And Girard, 1853), With the Revalidation of C. ornatus Hallowell, 1854. HERPETOLOGICAL MONOGRAPHS 2012. [DOI: 10.1655/herpmonographs-d-11-00012.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Brown RP, Tejangkura T, El Mouden EH, Ait Baamrane MA, Znari M. Species delimitation and digit number in a North African skink. Ecol Evol 2012; 2:2962-73. [PMID: 23301164 PMCID: PMC3538992 DOI: 10.1002/ece3.326] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 06/13/2012] [Accepted: 06/18/2012] [Indexed: 11/10/2022] Open
Abstract
Delimitation of species is an important and controversial area within evolutionary biology. Many species boundaries have been defined using morphological data. New genetic approaches now offer more objective evaluation and assessment of the reliability of morphological variation as an indicator that speciation has occurred. We examined geographic variation in morphology of the continuously distributed skink Chalcides mionecton from Morocco and used Bayesian analyses of nuclear and mitochondrial DNA (mtDNA) loci to examine: (i) their concordance with morphological patterns, (ii) support for species delimitation, (iii) timing of speciation, and (iv) levels of gene flow between species. Four digit individuals were found at sites between Cap Rhir (in the south) and the northern extreme of the range, whereas five-digit individuals were found in two disjunct areas: (i) south of Cap Rhir and (ii) the north of the range where they were often syntopic with four-digit individuals. The pattern of variation in generalized body dimensions was largely concordant with that in digit number, suggesting two general morphotypes. Bayesian analyses of population structure showed that individuals from sites south of Cap Rhir formed one genetic cluster, but that northern four- and five-digit individuals clustered together. Statistical support for delimitation of these genetic clusters into two species was provided by a recent Bayesian method. Phylogenetic-coalescent dating with external time calibrations indicates that speciation was relatively recent, with a 95% posterior interval of 0.46-2.66 mya. This postdates equivalent phylogenetic dating estimates of sequence divergence by approximately 1 Ma. Statistical analyses of a small number of independent loci provide important insights into the history of the speciation process in C. mionecton and support delimitation of populations into two species with distributions that are spatially discordant with patterns of morphological variation.
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Affiliation(s)
- R P Brown
- School of Natural Sciences and Psychology, Liverpool John Moores University Liverpool, L3 3AF
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28
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Harding LE, Dragoo JW. Out of the tropics: a phylogeographic history of the long-tailed weasel,Mustela frenata. J Mammal 2012. [DOI: 10.1644/11-mamm-a-280.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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29
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Lee YH, Lin CP. Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands. Mol Ecol 2012; 21:3739-56. [PMID: 22650764 DOI: 10.1111/j.1365-294x.2012.05654.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Climatic oscillations during the Pleistocene period could have had a profound impact on the origin of tropical species by the alternation of allopatric isolation and interpopulation gene flow cycles. However, whether tropical speciation involves strictly allopatric isolation, or proceeds in the face of homogenizing gene flow, is relatively unclear. Here, we investigated geographical modes of speciation in four closely related Euphaea damselfly species endemic to the subtropical and tropical East Asian islands using coalescent analyses of a multilocus data set. The reconstructed phylogenies demonstrated distinct species status for each of the four species and the existence of two sister species pairs, Euphaea formosa/E. yayeyamana and E. decorata/E. ornata. The species divergence time of the sibling Euphaea damselflies dates back to within the last one Mya of the Middle to Lower Pleistocene. The speciation between the populous E. formosa of Taiwan and the less numerous E. yayeyamana of the Yaeyama islands occurred despite significant bidirectional, asymmetric gene flow, which is strongly inconsistent with a strictly allopatric model. In contrast, speciation of the approximately equal-sized populations of E. decorata of the southeast Asian mainland and E. ornata of Hainan is inferred to have involved allopatric divergence without gene flow. Our findings suggest that differential selection of natural or sexual environments is a prominent driver of species divergence in subtropical E. formosa and E. yayeyamana; whereas for tropical E. decorata and E. ornata at lower latitudes, allopatric isolation may well be a pivotal promoter of species formation.
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Affiliation(s)
- Yat-Hung Lee
- Department of Life Science & Center for Tropical Ecology and Biodiversity, Tunghai University, Taichung 40704, Taiwan
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30
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Refugia and geographic barriers of populations of the desert poppy, Hunnemannia fumariifolia (Papaveraceae). ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0089-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Wilson JS, Pitts JP. Identifying Pleistocene refugia in North American cold deserts using phylogeographic analyses and ecological niche modelling. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00902.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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32
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Zhang C, Rannala B, Yang Z. Robustness of Compound Dirichlet Priors for Bayesian Inference of Branch Lengths. Syst Biol 2012; 61:779-84. [DOI: 10.1093/sysbio/sys030] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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33
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Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico. Mol Phylogenet Evol 2012; 62:447-57. [DOI: 10.1016/j.ympev.2011.10.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 10/13/2011] [Accepted: 10/19/2011] [Indexed: 11/24/2022]
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34
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Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape. Mol Phylogenet Evol 2012; 62:87-96. [DOI: 10.1016/j.ympev.2011.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/01/2011] [Accepted: 09/11/2011] [Indexed: 11/22/2022]
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35
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BRYSON JR ROBERTW, RIDDLE BRETTR. Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01798.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Leaché AD. Multi-locus estimates of population structure and migration in a fence lizard hybrid zone. PLoS One 2011; 6:e25827. [PMID: 21980539 PMCID: PMC3183087 DOI: 10.1371/journal.pone.0025827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 09/12/2011] [Indexed: 11/18/2022] Open
Abstract
A hybrid zone between two species of lizards in the genus Sceloporus (S. cowlesi and S. tristichus) on the Mogollon Rim in Arizona provides a unique opportunity to study the processes of lineage divergence and merging. This hybrid zone involves complex interactions between 2 morphologically and ecologically divergent subspecies, 3 chromosomal groups, and 4 mitochondrial DNA (mtDNA) clades. The spatial patterns of divergence between morphology, chromosomes and mtDNA are discordant, and determining which of these character types (if any) reflects the underlying population-level lineages that are of interest has remained impeded by character conflict. The focus of this study is to estimate the number of populations interacting in the hybrid zone using multi-locus nuclear data, and to then estimate the migration rates and divergence time between the inferred populations. Multi-locus estimates of population structure and gene flow were obtained from 12 anonymous nuclear loci sequenced for 93 specimens of Sceloporus. Population structure estimates support two populations, and this result is robust to changes to the prior probability distribution used in the Bayesian analysis and the use of spatially-explicit or non-spatial models. A coalescent analysis of population divergence suggests that gene flow is high between the two populations, and that the timing of divergence is restricted to the Pleistocene. The hybrid zone is more accurately described as involving two populations belonging to S. tristichus, and the presence of S. cowlesi mtDNA haplotypes in the hybrid zone is an anomaly resulting from mitochondrial introgression.
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Affiliation(s)
- Adam D Leaché
- Department of Biology and Burke Museum, University of Washington, Seattle, Washington, United States of America.
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37
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Burbrink FT, Pyron RA. THE IMPACT OF GENE-TREE/SPECIES-TREE DISCORDANCE ON DIVERSIFICATION-RATE ESTIMATION. Evolution 2011; 65:1851-61. [PMID: 21729043 DOI: 10.1111/j.1558-5646.2011.01260.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank T Burbrink
- Department of Biology, The College of Staten Island, The City University of New York, Staten Island, New York 10314, USA
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38
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Comparison of phylogeographic structure and population history of two Phrynocephalus species in the Tarim Basin and adjacent areas. Mol Phylogenet Evol 2010; 57:1091-104. [DOI: 10.1016/j.ympev.2010.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 09/30/2010] [Accepted: 10/04/2010] [Indexed: 11/23/2022]
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39
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WILSON JOSEPHS, PITTS JAMESP. Phylogeographic analysis of the nocturnal velvet ant genus Dilophotopsis (Hymenoptera: Mutillidae) provides insights into diversification in the Nearctic deserts. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01526.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Phylogeography of supralittoral rocky intertidal Ligia isopods in the pacific region from central California to central Mexico. PLoS One 2010; 5:e11633. [PMID: 20657776 PMCID: PMC2908127 DOI: 10.1371/journal.pone.0011633] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 06/03/2010] [Indexed: 11/24/2022] Open
Abstract
Background Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region. Methodology/Principal Findings We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland. Conclusions/Significance Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region.
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LEACHÉ ADAMD, HELMER DERSHING, MORITZ CRAIG. Phenotypic evolution in high-elevation populations of western fence lizards (Sceloporus occidentalis) in the Sierra Nevada Mountains. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01462.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Marshall DC. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst Biol 2009; 59:108-17. [PMID: 20525623 DOI: 10.1093/sysbio/syp080] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Partitioned Bayesian phylogenetic analyses of routine genetic data sets, constructed using MrBayes (Ronquist and Huelsenbeck 2003), can become trapped in regions of parameter space characterized by unrealistically long trees and distorted partition rate multipliers. Such analyses commonly fail to reach stationarity during hundreds of millions of generations of sampling-many times longer than most published analyses. Some data sets are so prone to this problem that paired MrBayes runs begun from different starting trees repeatedly find the same incorrect long-tree solutions and consequently pass the most commonly employed tests of stationarity, including the average standard deviation of split frequencies (ASDSF) and the potential scale reduction factor (PSRF) statistics offered by MrBayes (Gelman and Rubin 1992). In these situations, failure to reach stationarity is recognizable only in light of prior knowledge of model parameters, such as the expectation that third-codon-position sites usually evolve fastest in protein-coding genes. The conditions that lead to the long-tree problem are frequently encountered in phylogenetic studies today, and I present 6 demonstration examples from the literature. Although the effects on tree length (TL) are often dramatic, effects on topology appear to be subtle. Susceptibility to the problem is sometimes predicted by the difference between the true TL and the starting TL. In some cases, the problems described here can be avoided or reduced by manipulation of the starting TL and/or by adjustments to the prior on branch lengths. In more difficult situations, accurate branch length estimation may not be possible with Bayesian methods because of dependence of the solution on the branch length prior.
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Affiliation(s)
- David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269, USA.
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Delimiting species boundaries within the Neotropical bamboo Otatea (Poaceae: Bambusoideae) using molecular, morphological and ecological data. Mol Phylogenet Evol 2009; 54:344-56. [PMID: 19897047 DOI: 10.1016/j.ympev.2009.10.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 10/28/2009] [Accepted: 10/30/2009] [Indexed: 11/22/2022]
Abstract
Species delimitation is a task that has engaged taxonomists for more than two centuries. Recently, it has been demonstrated that molecular data and ecological niche modeling are useful in species delimitation. In this paper multiple data sets (molecular, morphological, ecological) were utilized to set limits for the species belonging to the Neotropical bamboo Otatea, because there is disagreement about species circumscriptions and also because the genus has an interesting distribution, with most of its populations in Mexico and a single disjunct population in Colombia. Molecular and morphological phylogenetic analyses recovered trees with conflicting topologies. Tree-based morphological and character-based analyses recognized the same entities. Ecological niche models and PCA/MANOVAS agreed with the recognition of the same entities that resulted from the morphological analyses. Morphological analyses retrieved clades supported by diagnostic characters and coherent geographical distributions. Based on these results seven entities should be recognized in Otatea, instead of the three previously described species.
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ALEXANDER PYRON R, BURBRINK FRANKT. Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake,Lampropeltis getula. Mol Ecol 2009; 18:3443-57. [DOI: 10.1111/j.1365-294x.2009.04292.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Harding LE, Smith FA. Mustela or Vison? Evidence for the taxonomic status of the American mink and a distinct biogeographic radiation of American weasels. Mol Phylogenet Evol 2009; 52:632-42. [PMID: 19501660 DOI: 10.1016/j.ympev.2009.05.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 05/15/2009] [Accepted: 05/28/2009] [Indexed: 10/20/2022]
Abstract
The American mink's relationship to the weasels in Mustela has been uncertain. Karyological, morphological, and phylogenetic comparisons to Eurasian Mustela support placing the mink outside the genus as Neovison vison. However, genetic comparisons that incorporate other endemic American Mustela suggest the interpretation of N. vison's position to Mustela has been handicapped by biased geographic sampling. Here, we analyzed mitochondrial cytochrome-b from all weasels endemic to the Americas, including two poorly known South American species (M. felipei, M. africana), weasels native to North America (M. vison, M. frenata, M. nigripes), Mustela migrant to North America (M. erminea, M. nivalis), palearctic Mustela, and other American members of Mustelidae. Bayesian and likelihood inference methods were used to construct a phylogeny of Mustela, and relaxed Bayesian phylogenetic techniques estimated ages of divergence within the genus using priors calibrated by fossil ages. Our analyses show that the American mink and the smaller Mustela endemic to the Americas represent a distinct phylogenetic heritage apart from their Eurasian cousins, and biogeographic barriers like the Bering and Panamanian land bridges have influenced the evolutionary history of Mustela in the Americas.
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Affiliation(s)
- Larisa E Harding
- Department of Biology MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA.
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Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular Deserts. Mol Phylogenet Evol 2009; 50:326-35. [DOI: 10.1016/j.ympev.2008.11.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 11/13/2008] [Accepted: 11/13/2008] [Indexed: 11/18/2022]
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Light JE, Reed DL. Multigene analysis of phylogenetic relationships and divergence times of primate sucking lice (Phthiraptera: Anoplura). Mol Phylogenet Evol 2008; 50:376-90. [PMID: 19027083 DOI: 10.1016/j.ympev.2008.10.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Cospeciation between hosts and parasites offers a unique opportunity to use information from parasites to infer events in host evolutionary history. Although lice (Insecta: Phthiraptera) are known to cospeciate with their hosts and have frequently served as important markers to infer host evolutionary history, most molecular studies are based on only one or two markers. Resulting phylogenies may, therefore, represent gene histories (rather than species histories), and analyses of multiple molecular markers are needed to increase confidence in the results of phylogenetic analyses. Herein, we phylogenetically examine nine molecular markers in primate sucking lice (Phthiraptera: Anoplura) and we use these markers to estimate divergence times among louse lineages. Individual and combined analyses of these nine markers are, for the most part, congruent, supporting relationships hypothesized in previous studies. Only one marker, the nuclear protein-coding gene Histone 3, has a significantly different tree topology compared to the other markers. The disparate evolutionary history of this marker, however, has no significant effect on topology or nodal support in the combined phylogenetic analyses. Therefore, phylogenetic results from the combined data set likely represent a solid hypothesis of species relationships. Additionally, we find that simultaneous use of multiple markers and calibration points provides the most reliable estimates of louse divergence times, in agreement with previous studies estimating divergences among species. Estimates of phylogenies and divergence times also allow us to verify the results of [Reed, D.L., Light, J.E., Allen, J.M., Kirchman, J.J., 2007. Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biol. 5, 7.]; there was probable contact between gorilla and archaic hominids roughly 3 Ma resulting in a host switch of Pthirus lice from gorillas to archaic hominids. Thus, these results provide further evidence that data from cospeciating organisms can yield important information about the evolutionary history of their hosts.
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Affiliation(s)
- Jessica E Light
- Florida Museum of Natural History, University of Florida, Dickinson Hall, P.O. Box 117800, Gainesville, FL 32611-7800, USA.
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Byrne M, Yeates DK, Joseph L, Kearney M, Bowler J, Williams MAJ, Cooper S, Donnellan SC, Keogh JS, Leys R, Melville J, Murphy DJ, Porch N, Wyrwoll KH. Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Mol Ecol 2008; 17:4398-417. [PMID: 18761619 DOI: 10.1111/j.1365-294x.2008.03899.x] [Citation(s) in RCA: 321] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.
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Affiliation(s)
- M Byrne
- Science Division, Department of Environment and Conservation, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
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Parham JF, Papenfuss TJ. High genetic diversity among fossorial lizard populations (Anniella pulchra) in a rapidly developing landscape (Central California). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9544-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Phylogeography and species boundaries of the western North American Nightsnake (Hypsiglena torquata): Revisiting the subspecies concept. Mol Phylogenet Evol 2008; 46:1095-115. [DOI: 10.1016/j.ympev.2007.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 11/26/2007] [Accepted: 12/04/2007] [Indexed: 11/21/2022]
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