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Reyes JA, Espinosa de los Monteros A, Santiago-Jiménez QJ. Phylogeography of Falagonia mexicana Sharp, 1883 (Coleoptera, Staphylinidae, Aleocharinae). Zookeys 2023; 1156:107-131. [DOI: 10.3897/zookeys.1156.84943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Falagonia mexicana is an aleocharine distributed from northern Mexico to Guatemala and El Salvador. It is associated with Atta mexicana ants and lives within their piles of waste or external debris. The phylogeography and historical demography of 18 populations from Mexico, Guatemala, and El Salvador were studied. The data set encompasses a 472 bp fragment of the COI. Results suggest that F. mexicana was originated during Middle Pliocene (ca. 0.5 Mya), starting its diversification at the Upper Pleistocene and Holocene. Populations were recovered forming at least four main lineages, with a significant phylogeographic structure. Evidence of contemporary restricted gene flow was found among populations. The historical demography suggests that the geographic structure is due to recent physical barriers (e.g., Isthmus of Tehuantepec) rather than ancient geological events. Also, recent geological and volcanic events in the east of the Trans-Mexican Volcanic Belt and the Sierra Madre Oriental might be responsible for the restricted gene flow among populations. Skyline-plot analyses suggested that a demographic expansion event took place at the end of the Late Quaternary glacial-interglacial cycles.
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2
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Ortego J, Knowles LL. Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization. Mol Ecol 2021; 31:296-312. [PMID: 34651368 DOI: 10.1111/mec.16225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/21/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
Alpine biotas are paradigmatic of the countervailing roles of geographical isolation and dispersal during diversification. In temperate regions, repeated distributional shifts driven by Pleistocene climatic oscillations produced both recurrent pulses of population fragmentation and opportunities for gene flow during range expansions. Here, we test whether a model of divergence in isolation vs. with gene flow is more likely in the diversification of flightless alpine grasshoppers of the genus Podisma from the Iberian Peninsula. The answer to this question can also provide key insights about the pace of evolution. Specifically, if the data fit a divergence in isolation model, this suggests rapid evolution of reproductive isolation. Genomic data confirm a Pleistocene origin of the species complex, and multiple analytical approaches revealed limited asymmetric historical hybridization between two taxa. Genomic-based demographic reconstructions, spatial patterns of genetic structure and range shifts inferred from palaeodistribution modelling suggest severe range contraction accompanied by declines in effective population sizes during interglacials (i.e., contemporary populations confined to sky islands are relicts) and expansions during the coldest stages of the Pleistocene in each taxon. Although limited hybridization during secondary contact leads to phylogenetic uncertainty if gene flow is not accommodated when estimating evolutionary relationships, all species exhibit strong genetic cohesiveness. Our study lends support to the notion that the accumulation of incipient differences during periods of isolation were sufficient to lead to lineage persistence, but also that the demographic changes, dispersal constraints and spatial distribution of the sky islands themselves mediated species diversification in temperate alpine biotas.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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3
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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4
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Thomaz AT, Knowles LL. Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo‐landscape sieves structure a coastal riverine fish community. Mol Ecol 2020; 29:783-796. [DOI: 10.1111/mec.15357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Andréa T. Thomaz
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
- Biodiversity Research Centre and Department of Zoology University of British Columbia Vancouver BC Canada
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
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Ouyang F, Hu J, Wang J, Ling J, Wang Z, Wang N, Ma J, Zhang H, Mao JF, Wang J. Complete plastome sequences of Picea asperata and P. crassifolia and comparative analyses with P. abies and P. morrisonicola. Genome 2019; 62:317-328. [PMID: 30998854 DOI: 10.1139/gen-2018-0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (psbJ-petA, trnT-psaM, trnS-trnD, trnL-rps4, psaC-ccsA, and rps7-trnL) and one gene (ycf1). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of Picea as well as Pinaceae in general.
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Affiliation(s)
- Fangqun Ouyang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Jiwen Hu
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Junchen Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China.,b Northwest Agriculture & Forestry University, Xi'an, P.R. China
| | - Juanjuan Ling
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Zhi Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Nan Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Jianwei Ma
- c Research Institute of Forestry of Xiaolong Mountain, Gansu Provincial Key Laboratory of Secondary Forest Cultivation, Gansu, P.R. China
| | - Hanguo Zhang
- d State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, P.R. China
| | - Jian-Feng Mao
- e National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plant of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Junhui Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
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6
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Gradish A, Keyghobadi N, Sperling F, Otis G. Population genetic structure and assessment of allochronic divergence in the Macoun’s Arctic (Oeneis macounii) butterfly. CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Patterns in the genetic variation of species can be used to infer their specific demographic and evolutionary history and provide insight into the general mechanisms underlying population divergence and speciation. The Macoun’s Arctic (Oeneis macounii (W.H. Edwards, 1885); MA) butterfly occurs across Canada and parts of the northern United States in association with jack pine (Pinus banksiana Lamb.) and lodgepole pine (Pinus contorta Douglas ex Loudon). MA’s current distribution is highly fragmented, and the extent of reproductive isolation among allopatric populations is unknown. Furthermore, although MA is biennial, adults emerge every year in some populations. These populations presumably consist of two alternate-year cohorts, providing the opportunity for sympatric divergence via allochronic isolation. Using mitochondrial DNA (mtDNA) and amplified fragment length polymorphism (AFLP) markers, we analyzed MA’s genetic structure to determine the current and historical role of allopatric and allochronic isolation in MA population divergence. Both markers revealed high diversity and a low, but significant, degree of spatial structure and pattern of isolation by distance. Phylogeographic structure was generally absent, with low divergence among mtDNA haplotypes. MA likely exhibits low dispersal and gene flow among most allopatric populations; however, there was no evidence of differentiation resulting from allochronic isolation for sympatric cohorts.
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Affiliation(s)
- A.E. Gradish
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - N. Keyghobadi
- Department of Biology, Western University, London, ON N6A 3K7, Canada
| | - F.A.H. Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - G.W. Otis
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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7
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Chan KO, Alexander AM, Grismer LL, Su YC, Grismer JL, Quah ESH, Brown RM. Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs. Mol Ecol 2017; 26:5435-5450. [DOI: 10.1111/mec.14296] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - Alana M. Alexander
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology; Kaohsiung Medical University; Kaohsiung City Taiwan
| | - Jesse L. Grismer
- Department of Biological Sciences; Auburn University; Auburn AL USA
- La Kretz Center for Californian Conservation Science; Institute of the Environment and Sustainability; University of California Los Angeles; Los Angeles CA USA
| | - Evan S. H. Quah
- School of Biological Sciences; Universiti Sains Malaysia; Penang Malaysia
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
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8
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A complex history of introgression and vicariance in a threatened montane skink (Pseudemoia cryodroma) across an Australian sky island system. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0945-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Abstract
The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent. We show that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries. Because of the misidentification of population structure as putative species, our work raises questions about the practice of genome-based species discovery, with cascading consequences in other fields. Specifically, all fields that rely on species as units of analysis, from conservation biology to studies of macroevolutionary dynamics, will be impacted by inflated estimates of the number of species, especially as genomic resources provide unprecedented power for detecting increasingly finer-scaled genetic structure under the multispecies coalescent. As such, our work also represents a general call for systematic study to reconsider a reliance on genomic data alone. Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.
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Affiliation(s)
- Jeet Sukumaran
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor MI 48109-1079
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor MI 48109-1079
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10
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Hague MTJ, Avila LA, Hanifin CT, Snedden WA, Stokes AN, Brodie ED, Brodie ED. Toxicity and population structure of the Rough-Skinned Newt (Taricha granulosa) outside the range of an arms race with resistant predators. Ecol Evol 2016; 6:2714-24. [PMID: 27066249 PMCID: PMC4798830 DOI: 10.1002/ece3.2068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 01/07/2023] Open
Abstract
Species interactions, and their fitness consequences, vary across the geographic range of a coevolutionary relationship. This spatial heterogeneity in reciprocal selection is predicted to generate a geographic mosaic of local adaptation, wherein coevolutionary traits are phenotypically variable from one location to the next. Under this framework, allopatric populations should lack variation in coevolutionary traits due to the absence of reciprocal selection. We examine phenotypic variation in tetrodotoxin (TTX) toxicity of the Rough-Skinned Newt (Taricha granulosa) in regions of allopatry with its TTX-resistant predator, the Common Garter Snake (Thamnophis sirtalis). In sympatry, geographic patterns of phenotypic exaggeration in toxicity and toxin-resistance are closely correlated in prey and predator, implying that reciprocal selection drives phenotypic variation in coevolutionary traits. Therefore, in allopatry with TTX-resistant predators, we expect to find uniformly low levels of newt toxicity. We characterized TTX toxicity in northwestern North America, including the Alaskan panhandle where Ta. granulosa occur in allopatry with Th. sirtalis. First, we used microsatellite markers to estimate population genetic structure and determine if any phenotypic variation in toxicity might be explained by historical divergence. We found northern populations of Ta. granulosa generally lacked population structure in a pattern consistent with northern range expansion after the Pleistocene. Next, we chose a cluster of sites in Alaska, which uniformly lacked genetic divergence, to test for phenotypic divergence in toxicity. As predicted, overall levels of newt toxicity were low; however, we also detected unexpected among- and within-population variation in toxicity. Most notably, a small number of individuals contained large doses of TTX that rival means of toxic populations in sympatry with Th. sirtalis. Phenotypic variation in toxicity, despite limited neutral genetic divergence, suggests that factors other than reciprocal selection with Th. sirtalis likely contribute to geographic patterns of toxicity in Ta. granulosa.
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Affiliation(s)
- Michael T J Hague
- Department of Biology University of Virginia Charlottesville Virginia
| | - Leleña A Avila
- Museum of Vertebrate Zoology University of California Berkeley California
| | - Charles T Hanifin
- Department of Biology Utah State University, Uintah Basin Campus Vernal Utah
| | | | - Amber N Stokes
- Department of Biology California State University Bakersfield California
| | | | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia
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11
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Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9785-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Alda F, Doadrio I. Spatial genetic structure across a hybrid zone between European rabbit subspecies. PeerJ 2014; 2:e582. [PMID: 25289181 PMCID: PMC4183957 DOI: 10.7717/peerj.582] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 08/28/2014] [Indexed: 11/20/2022] Open
Abstract
The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose we obtained multilocus genotypes and mitochondrial DNA data from 771 rabbits across most of the distribution range of the European rabbit in Spain. Based on the nuclear markers we observed a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus), which were subsequently subdivided into seven genetic groups. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Additionally, the significantly positive spatial correlation up to a distance of only 100 km supported the idea that differentiation at a local level is of greater importance when considering the species overall genetic structure. When looking at the subspecies, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus. This could be due to local geographic barriers, limited resources, soil type and/or social behavior limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioral differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioral and molecular, that hierarchically interact through time and space.
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Affiliation(s)
- Fernando Alda
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC) , Madrid , Spain
| | - Ignacio Doadrio
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC) , Madrid , Spain
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Ponce de León JL, León G, Rodríguez R, Metcalfe CJ, Hernández D, Casane D, García-Machado E. Phylogeography of Cuban Rivulus: evidence for allopatric speciation and secondary dispersal across a marine barrier. Mol Phylogenet Evol 2014; 79:404-14. [PMID: 25050928 DOI: 10.1016/j.ympev.2014.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/18/2022]
Abstract
The genus Rivulus is currently comprised of two species, R. cylindraceus and R. insulaepinorum, which are endemic to Cuba. However, the taxonomic status of the latter species remains dubious because of the poor quality of the original description. In addition, a recent barcoding survey suggests that the two species may be conspecific. The aim of this study was to test the hypothesis that the two species represent a single evolutionary clade. To delimit the species and their evolutionary history, we used a combination of molecular phylogenetic analyses, with both mitochondrial and nuclear sequences, tests of phylogeographic hypotheses, combined with morphological measurements and information on known dispersal barriers and species distribution. None of the data sets support R. insulaepinorum and R. cylindraceus as separate taxa. However, a new species, restricted to the northwestern part of the main island, was identified by phylogenetic analyses, body colour pattern and geographical distribution. The evolutionary distance between the two lineages (cytb, d=15%; CAM-4, d=2.5%) indicates a long period of divergence. Phylogeographic analyses shed light on the dispersal history of R. cylindraceus, which probably originated on the Isla de la Juventud. They also suggest that each lineage had contrasting histories; Rivulus sp. is restricted to a relatively small geographic area whereas R. cylindraceus has dispersed considerably and more than once from its centre of origin, probably facilitated by sea level fluctuations. These results strengthen previous findings, i.e. that the diversity of Cuban freshwater fishes is far from well-known and deserves more in-depth studies, and that vicariance and dispersal events have resulted in a complex biogeographical landscape which has had a significant impact on the freshwater fishes of the Caribbean islands.
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Affiliation(s)
- José Luis Ponce de León
- Facultad de Biología, Universidad de La Habana, Calle 25, No. 455 entre J e I, Vedado, Ciudad Habana 10400, Cuba.
| | - Gunnary León
- Facultad de Biología, Universidad de La Habana, Calle 25, No. 455 entre J e I, Vedado, Ciudad Habana 10400, Cuba.
| | - Rodet Rodríguez
- Facultad de Biología, Universidad de La Habana, Calle 25, No. 455 entre J e I, Vedado, Ciudad Habana 10400, Cuba.
| | - Cushla J Metcalfe
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária, São Paulo, 05508-090 SP, Brazil.
| | - Damir Hernández
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 entre 1ra y 3ra, Miramar, Playa, La Habana 11300, Cuba.
| | - Didier Casane
- Laboratoire Evolution Génomes et Spéciation, UPR9034 CNRS, 1 avenue de la terrasse, 91198 Gif-sur-Yvette, France; Université Paris Diderot, Sorbonne Paris Cité, 5 rue Thomas-Mann, 75205 Paris, France.
| | - Erik García-Machado
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 entre 1ra y 3ra, Miramar, Playa, La Habana 11300, Cuba.
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14
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Dupas S, le Ru B, Branca A, Faure N, Gigot G, Campagne P, Sezonlin M, Ndemah R, Ong'amo G, Calatayud PA, Silvain JF. Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation inBusseola fusca(Lepidoptera: Noctuidae). Mol Ecol 2014; 23:2313-25. [DOI: 10.1111/mec.12730] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 03/05/2014] [Accepted: 03/13/2014] [Indexed: 11/27/2022]
Affiliation(s)
- S. Dupas
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
| | - B. le Ru
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
| | - A. Branca
- Ecologie, Systématique et Evolution, Bâtiment 360; Université Paris-Sud; F-91405 Orsay France
| | - N. Faure
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - G. Gigot
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - P. Campagne
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - M. Sezonlin
- Département de Zoologie et de Génétique; Faculté des Sciences et Techniques; Université d'Abomey - Calavi; 01 BP 526 Cotonou Bénin
| | - R. Ndemah
- International Institute of Tropical Agriculture; PO Box 2008 Messa Yaoundé Cameroon
| | - G. Ong'amo
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
- School of Biological Sciences; University of Nairobi; PO Box 30197 Nairobi Kenya
| | - P.-A. Calatayud
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
| | - J.-F. Silvain
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
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15
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Bagley JC, Johnson JB. Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas. Biol Rev Camb Philos Soc 2014; 89:767-90. [PMID: 24495219 DOI: 10.1111/brv.12076] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 11/29/2013] [Accepted: 12/03/2013] [Indexed: 01/06/2023]
Abstract
Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene-Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.
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Affiliation(s)
- Justin C Bagley
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, 401 WIDB (Widtsoe Building), Provo, UT, 84602, U.S.A
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Tollis M, Boissinot S. Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the quaternary. Genetica 2013; 142:59-72. [PMID: 24379168 DOI: 10.1007/s10709-013-9754-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/23/2013] [Indexed: 11/27/2022]
Abstract
The green anole lizard (Anolis carolinensis) is a model organism for behavior and genomics that is native to the southeastern United States. It is currently thought that the ancestors of modern green anoles dispersed to peninsular Florida from Cuba. However, the climatic changes and geological features responsible for the early diversification of A. carolinensis in North America have remained largely unexplored. This is because previous studies (1) differ in their estimates of the divergence times of populations, (2) are based on a single genetic locus or (3) did not test specific hypotheses regarding the geologic and topographic history of Florida. Here we provide a multi-locus study of green anole genetic diversity and find that the Florida peninsula contains a larger number of genetically distinct populations that are more diverse than those on the continental mainland. As a test of the island refugia hypothesis in Pleistocene Florida, we use a coalescent approach to estimate the divergence times of modern green anole lineages. We find that all demographic events occurred during or after the Upper Pliocene and suggest that green anole diversification was driven by population divergence on interglacial island refugia in Florida during the Lower Pleistocene, while the region was often separated from continental North America. When Florida reconnected to the mainland, two separate dispersal events led to the expansion of green anole populations across the Atlantic Seaboard and Gulf Coastal Plain.
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Affiliation(s)
- Marc Tollis
- Biology Department, Queens College, City University of New York (CUNY), 65-30 Kissena Boulevard, Flushing, New York, NY, USA,
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Markolf M, Kappeler PM. Phylogeographic analysis of the true lemurs (genus Eulemur) underlines the role of river catchments for the evolution of micro-endemism in Madagascar. Front Zool 2013; 10:70. [PMID: 24228694 PMCID: PMC3835867 DOI: 10.1186/1742-9994-10-70] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/28/2013] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Due to its remarkable species diversity and micro-endemism, Madagascar has recently been suggested to serve as a biogeographic model region. However, hypothesis-based tests of various diversification mechanisms that have been proposed for the evolution of the island's micro-endemic lineages are still limited. Here, we test the fit of several diversification hypotheses with new data on the broadly distributed genus Eulemur using coalescent-based phylogeographic analyses. RESULTS Time-calibrated species tree analyses and population genetic clustering resolved the previously polytomic species relationships among eulemurs. The most recent common ancestor of eulemurs was estimated to have lived about 4.45 million years ago (mya). Divergence date estimates furthermore suggested a very recent diversification among the members of the "brown lemur complex", i.e. former subspecies of E. fulvus, during the Pleistocene (0.33-1.43 mya). Phylogeographic model comparisons of past migration rates showed significant levels of gene flow between lineages of neighboring river catchments as well as between eastern and western populations of the redfronted lemur (E. rufifrons). CONCLUSIONS Together, our results are concordant with the centers of endemism hypothesis (Wilmé et al. 2006, Science 312:1063-1065), highlight the importance of river catchments for the evolution of Madagascar's micro-endemic biota, and they underline the usefulness of testing diversification mechanisms using coalescent-based phylogeographic methods.
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Affiliation(s)
- Matthias Markolf
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, Göttingen 37077, Germany.
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Malaney JL, Conroy CJ, Moffitt LA, Spoonhunter HD, Patton JL, Cook JA. Phylogeography of the western jumping mouse (Zapus princeps) detects deep and persistent allopatry with expansion. J Mammal 2013. [DOI: 10.1644/12-mamm-a-006.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Bagley JC, Sandel M, Travis J, Lozano-Vilano MDL, Johnson JB. Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota. BMC Evol Biol 2013; 13:223. [PMID: 24107245 PMCID: PMC3851817 DOI: 10.1186/1471-2148-13-223] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 09/13/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Climatic and sea-level fluctuations throughout the last Pleistocene glacial cycle (~130-0 ka) profoundly influenced present-day distributions and genetic diversity of Northern Hemisphere biotas by forcing range contractions in many species during the glacial advance and allowing expansion following glacial retreat ('expansion-contraction' model). Evidence for such range dynamics and refugia in the unglaciated Gulf-Atlantic Coastal Plain stems largely from terrestrial species, and aquatic species Pleistocene responses remain relatively uninvestigated. Heterandria formosa, a wide-ranging regional endemic, presents an ideal system to test the expansion-contraction model within this biota. By integrating ecological niche modeling and phylogeography, we infer the Pleistocene history of this livebearing fish (Poeciliidae) and test for several predicted distributional and genetic effects of the last glaciation. RESULTS Paleoclimatic models predicted range contraction to a single southwest Florida peninsula refugium during the Last Glacial Maximum, followed by northward expansion. We inferred spatial-population subdivision into four groups that reflect genetic barriers outside this refuge. Several other features of the genetic data were consistent with predictions derived from an expansion-contraction model: limited intraspecific divergence (e.g. mean mtDNA p-distance = 0.66%); a pattern of mtDNA diversity (mean Hd = 0.934; mean π = 0.007) consistent with rapid, recent population expansion; a lack of mtDNA isolation-by-distance; and clinal variation in allozyme diversity with higher diversity at lower latitudes near the predicted refugium. Statistical tests of mismatch distributions and coalescent simulations of the gene tree lent greater support to a scenario of post-glacial expansion and diversification from a single refugium than to any other model examined (e.g. multiple-refugia scenarios). CONCLUSIONS Congruent results from diverse data indicate H. formosa fits the classic Pleistocene expansion-contraction model, even as the genetic data suggest additional ecological influences on population structure. While evidence for Plio-Pleistocene Gulf Coast vicariance is well described for many freshwater species presently codistributed with H. formosa, this species demography and diversification departs notably from this pattern. Species-specific expansion-contraction dynamics may therefore have figured more prominently in shaping Coastal Plain evolutionary history than previously thought. Our findings bolster growing appreciation for the complexity of phylogeographical structuring within North America's southern refugia, including responses of Coastal Plain freshwater biota to Pleistocene climatic fluctuations.
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Affiliation(s)
- Justin C Bagley
- Department of Biology, Brigham Young University, 401 WIDB, Provo, UT 84602, USA
| | - Michael Sandel
- Department of Biological Science, Biodiversity & Systematics, The University of Alabama, Box 870345, Tuscaloosa, AL 35487, USA
| | - Joseph Travis
- Department of Biological Science, The Florida State University, Tallahassee, FL 32306, USA
| | - María de Lourdes Lozano-Vilano
- Laboratorio de Ictiología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Jerald B Johnson
- Department of Biology, Brigham Young University, 401 WIDB, Provo, UT 84602, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
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Roy T, Chang TH, Lan T, Lindqvist C. Phylogeny and biogeography of New World Stachydeae (Lamiaceae) with emphasis on the origin and diversification of Hawaiian and South American taxa. Mol Phylogenet Evol 2013; 69:218-38. [DOI: 10.1016/j.ympev.2013.05.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/25/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022]
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Malaney JL, Cook JA. Using biogeographical history to inform conservation: the case of Preble's meadow jumping mouse. Mol Ecol 2013; 22:6000-17. [DOI: 10.1111/mec.12476] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Jason L. Malaney
- Museum of Southwestern Biology; Department of Biology; University of New Mexico; Albuquerque NM 87131 USA
| | - Joseph A. Cook
- Museum of Southwestern Biology; Department of Biology; University of New Mexico; Albuquerque NM 87131 USA
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Ohtsuki T, Ikeda H, Setoguchi H. Recent colonization by a coastal plant of inland habitats at an ancient freshwater lake, Lake Biwa: multilocus sequencing and a demographic history of Lathyrus japonicus(Fabaceae). Ecol Evol 2013. [DOI: 10.1002/ece3.654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Tatsuo Ohtsuki
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho; Sakyo-ku; Kyoto; 606-8501; Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources; Okayama University; Kurashiki-shi; Okayama; 710-0046; Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho; Sakyo-ku; Kyoto; 606-8501; Japan
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He Q, Edwards DL, Knowles LL. INTEGRATIVE TESTING OF HOW ENVIRONMENTS FROM THE PAST TO THE PRESENT SHAPE GENETIC STRUCTURE ACROSS LANDSCAPES. Evolution 2013; 67:3386-402. [DOI: 10.1111/evo.12159] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 04/26/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Qixin He
- Department of Ecology & Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
| | - Danielle L. Edwards
- Department of Ecology and Evolutionary Biology; Yale University; New Haven Connecticut 06520
| | - L. Lacey Knowles
- Department of Ecology & Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
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Ren QP, Fan Z, Zhou XM, Jiang GF, Wang YT, Liu YX. Identification and characterization of anonymous nuclear markers for the double-striped cockroach, Blattella bisignata. BULLETIN OF ENTOMOLOGICAL RESEARCH 2013; 103:29-35. [PMID: 22697889 DOI: 10.1017/s0007485312000375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
During the last decade, multilocus analysis has gradually become a powerful tool for the studies of population genetics and phylogeography. The double-striped cockroach, Blattella bisignata, is endemic to southeast Asia, and there is currently little genetic information available for the species. We chose it as the target species to investigate a biodiversity hotspot in southwest China. Here, we report the identification and characterization of 11 single-copy anonymous nuclear markers with an average length of 378bp. These loci, isolated from a genomic library of B. bisignata, can amplify in two additional Blattella species (B. germanica and B. lituricollis). While testing these markers in representative species of Blattellidae, Blattidae and Epilampridae, some of them can cross-amplify successfully. After sequencing 30 individuals collected from southern China per locus, we found relatively high variability (approximately 3.6 SNPs per 100bp). Finally, a small-scale study was also performed to show that these markers do indeed fulfill the expectations as phylogeographic markers.
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Affiliation(s)
- Q-P Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Reid NM, Carstens BC. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol Biol 2012; 12:196. [PMID: 23031350 PMCID: PMC3503838 DOI: 10.1186/1471-2148-12-196] [Citation(s) in RCA: 329] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 09/19/2012] [Indexed: 11/10/2022] Open
Abstract
Background Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating species boundaries for further analysis. Several methods have been proposed to accomplish this. Here we present a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC). Our implementation integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo (MCMC) simulation in order to produce marginal probabilities of species identities. Results We conducted simulations testing the effects of species evolutionary history, levels of intraspecific sampling and number of nucleotides sequenced. We also re-analyze the dataset used to introduce the original GMYC model. We found that the model results are improved with addition of DNA sequence and increased sampling, although these improvements have limits. The most important factor in the success of the model is the underlying phylogenetic history of the species under consideration. Recent and rapid divergences result in higher amounts of uncertainty in the model and eventually cause the model to fail to accurately assess uncertainty in species limits. Conclusion Our results suggest that the GMYC model can be useful under a wide variety of circumstances, particularly in cases where divergences are deeper, or taxon sampling is incomplete, as in many studies of ecological communities, but that, in accordance with expectations from coalescent theory, rapid, recent radiations may yield inaccurate results. Our implementation differs from existing ones in two ways: it allows for the accounting for important sources of uncertainty in the model (phylogenetic and in parameters specific to the model) and in the specification of informative prior distributions that can increase the precision of the model. We have incorporated this model into a user-friendly R package available on the authors’ websites.
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Affiliation(s)
- Noah M Reid
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA.
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Wachter GA, Arthofer W, Dejaco T, Rinnhofer LJ, Steiner FM, Schlick-Steiner BC. Pleistocene survival on central Alpine nunataks: genetic evidence from the jumping bristletail Machilis pallida. Mol Ecol 2012; 21:4983-95. [PMID: 22994297 DOI: 10.1111/j.1365-294x.2012.05758.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 06/23/2012] [Accepted: 07/05/2012] [Indexed: 11/30/2022]
Abstract
Mechanisms of survival during the Pleistocene glaciation periods have been studied for more than a century. Until now, molecular studies that confirmed animal survival on Alpine nunataks, that is, ice-free summits surrounded by glaciers, were restricted to peripheral areas. Here, we search for molecular signatures of inner-Alpine survival of the narrow endemic and putatively parthenogenetic Alpine jumping bristletail Machilis pallida combining mitochondrial and AFLP data from its three known populations. The mitochondrial data indicate survival on both peripheral and central nunataks, the latter suggesting that refugia in the centre of the Alpine main ridge were more widespread than previously recognized. Incongruences between mitochondrial and AFLP patterns suggest a complex evolutionary history of the species and may be explained via parallel fixation of parthenogenesis of different origins during the last glacial maximum. We suggest that the inferred parthenogenesis may have been essential for central nunatak survival, but may pose a serious threat for M. pallida in consideration of the present climatic changes.
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Affiliation(s)
- Gregor A Wachter
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
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Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT. Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions. BMC Evol Biol 2012; 12:176. [PMID: 22963132 PMCID: PMC3499221 DOI: 10.1186/1471-2148-12-176] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/30/2012] [Indexed: 01/22/2023] Open
Abstract
Background Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescent-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. Results We found that divergence estimates, from both concatenated gene tree and coalescent-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. Conclusions Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.
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FERNÁNDEZ MARIAJIMENAGÓMEZ, GAGGIOTTI OSCARE, MIROL PATRICIA. The evolution of a highly speciose group in a changing environment: are we witnessing speciation in the Iberá wetlands? Mol Ecol 2012; 21:3266-82. [DOI: 10.1111/j.1365-294x.2012.05598.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Molecular phylogeny of African bush-shrikes and allies: tracing the biogeographic history of an explosive radiation of corvoid birds. Mol Phylogenet Evol 2012; 64:93-105. [PMID: 22475817 DOI: 10.1016/j.ympev.2012.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 03/09/2012] [Accepted: 03/13/2012] [Indexed: 11/23/2022]
Abstract
The Malaconotidea (e.g., butcherbirds, bush-shrikes, batises, vangas) represent an Old World assemblage of corvoid passerines that encompass many different foraging techniques (e.g., typical flycatchers, flycatcher-shrikes, canopy creepers, undergrowth skulkers). At present, relationships among the primary Malaconotidea clades are poorly resolved, a result that could either be attributed to a rapid accumulation of lineages over a short period of time (hard polytomy) or to an insufficient amount of data having been brought to bear on the problem (soft polytomy). Our objective was to resolve the phylogenetic relationships and biogeographic history of the Malaconotidea using DNA sequences gathered from 10 loci with different evolutionary properties. Given the range of substitution rates of molecular markers we sequenced (mitochondrial, sex-linked, autosomal), we also sought to explore the effect of altering the branch-length prior in Bayesian tree estimation analyses. We found that changing the branch-length priors had no major effect on topology, but clearly improved mixing of the chains for some loci. Our phylogenetic analyses clarified the relationships of several genera (e.g., Pityriasis, Machaerirhynchus) and provide for the first time strong support for a sister-group relationship between core platysteirids and core vangids. Our biogeographic reconstruction somewhat unexpectedly suggests that the large African radiation of malaconotids originated after a single over-water dispersal from Australasia around 45-33.7 mya, shedding new light on the origins of the Afrotropical avifauna.
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Phylogeography of Saproxylic and Forest Floor Invertebrates from Tallaganda, South-eastern Australia. INSECTS 2012; 3:270-94. [PMID: 26467960 PMCID: PMC4553628 DOI: 10.3390/insects3010270] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/21/2012] [Accepted: 02/22/2012] [Indexed: 12/02/2022]
Abstract
The interaction between physiogeographic landscape context and certain life history characteristics, particularly dispersal ability, can generate predictable outcomes for how species responded to Pleistocene (and earlier) climatic changes. Furthermore, the extent to which impacts of past landscape-level changes ‘scale-up’ to whole communities has begun to be addressed via comparative phylogeographic analyses of co-distributed species. Here we present an overview of a body of research on flightless low-mobility forest invertebrates, focusing on two springtails and two terrestrial flatworms, from Tallaganda on the Great Dividing Range of south-eastern Australia. These species are distantly-related, and represent contrasting trophic levels (i.e., slime-mold-grazers vs. higher-level predators). However, they share an association with the dead wood (saproxylic) habitat. Spatial patterns of intraspecific genetic diversity partly conform to topography-based divisions that circumscribe five ‘microgeographic regions’ at Tallaganda. In synthesizing population processes and past events that generated contemporary spatial patterns of genetic diversity in these forest floor invertebrates, we highlight cases of phylogeographic congruence, pseudo-congruence, and incongruence. Finally, we propose conservation-oriented recommendations for the prioritisation of areas for protection.
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Mardulyn P, Othmezouri N, Mikhailov YE, Pasteels JM. Conflicting mitochondrial and nuclear phylogeographic signals and evolution of host-plant shifts in the boreo-montane leaf beetle Chrysomela lapponica. Mol Phylogenet Evol 2011; 61:686-96. [DOI: 10.1016/j.ympev.2011.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 10/17/2022]
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Olave M, Martinez LE, Avila LJ, Sites JW, Morando M. Evidence of hybridization in the Argentinean lizards Liolaemus gracilis and Liolaemus bibronii (IGUANIA: LIOLAEMINI): An integrative approach based on genes and morphology. Mol Phylogenet Evol 2011; 61:381-91. [DOI: 10.1016/j.ympev.2011.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 06/09/2011] [Accepted: 07/05/2011] [Indexed: 11/26/2022]
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Neiswenter SA, Riddle BR. Landscape and climatic effects on the evolutionary diversification of the Perognathus fasciatus species group. J Mammal 2011. [DOI: 10.1644/11-mamm-a-037.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Emerson BC, Cicconardi F, Fanciulli PP, Shaw PJA. Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities. Philos Trans R Soc Lond B Biol Sci 2011; 366:2391-402. [PMID: 21768154 PMCID: PMC3130430 DOI: 10.1098/rstb.2011.0057] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages.
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Affiliation(s)
- Brent C Emerson
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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SÉRSIC ALICIAN, COSACOV ANDREA, COCUCCI ANDREAA, JOHNSON LEIGHA, POZNER RAÚL, AVILA LUCIANOJ, SITES Jr. JACKW, MORANDO MARIANA. Emerging phylogeographical patterns of plants and terrestrial vertebrates from Patagonia. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01656.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Stone GN, Nee S, Felsenstein J. Controlling for non-independence in comparative analysis of patterns across populations within species. Philos Trans R Soc Lond B Biol Sci 2011; 366:1410-24. [PMID: 21444315 PMCID: PMC3081573 DOI: 10.1098/rstb.2010.0311] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of 'mixed models' in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.
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Affiliation(s)
- Graham N Stone
- Institute of Evolutionary Biology, The King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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Hird S, Kubatko L, Carstens B. Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling. Mol Phylogenet Evol 2010; 57:888-98. [DOI: 10.1016/j.ympev.2010.08.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/05/2010] [Accepted: 08/10/2010] [Indexed: 01/24/2023]
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LACEY KNOWLES L, ALVARADO-SERRANO DIEGOF. Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic and genetic models in montane grasshoppers. Mol Ecol 2010; 19:3727-45. [DOI: 10.1111/j.1365-294x.2010.04702.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL. CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS. Evolution 2010; 65:184-202. [DOI: 10.1111/j.1558-5646.2010.01097.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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40
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CAMARGO ARLEY, SINERVO BARRY, SITES JACKW. Lizards as model organisms for linking phylogeographic and speciation studies. Mol Ecol 2010; 19:3250-70. [DOI: 10.1111/j.1365-294x.2010.04722.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Neiswenter SA, Riddle BR. Diversification of the Perognathus flavus species group in emerging arid grasslands of western North America. J Mammal 2010. [DOI: 10.1644/09-mamm-a-102.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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42
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The scale of population structure in Arabidopsis thaliana. PLoS Genet 2010; 6:e1000843. [PMID: 20169178 PMCID: PMC2820523 DOI: 10.1371/journal.pgen.1000843] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 01/12/2010] [Indexed: 12/04/2022] Open
Abstract
The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales. Much of the modern field of population genetics is premised on particular models of what an organism's population structure is and how it behaves. The classic models generally start with the idea of a single randomly mating population that has reached an evolutionary equilibrium. Many models relax some of these assumptions, allowing for phenomena such as assortative mating, discrete sub-populations with migration, self-fertilization, and sex-ratio distortion. Virtually all models, however, have as their core premise the notion that there exist classes of exchangeable individuals each of which represents an identical, independent sample from that class' distribution. For certain organisms, such as Drosophila melanogaster, these models do an excellent job of describing how populations work. For other organisms, such as humans, these models can be reasonable approximations but require a great deal of care in assembling samples and can begin to break down as sampling becomes locally dense. For the vast majority of organisms the applicability of these models has never been investigated.
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Drotz MK, Brodin T, Nilsson AN. Multiple origins of elytral reticulation modifications in the west palearctic Agabus bipustulatus complex (coleoptera, dytiscidae). PLoS One 2010; 5:e9034. [PMID: 20140264 PMCID: PMC2815794 DOI: 10.1371/journal.pone.0009034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 12/29/2009] [Indexed: 11/18/2022] Open
Abstract
The Agabus bipustulatus complex includes one of Europe's most widely distributed and common diving beetles. This complex, which is known for its large morphological variation, has a complex demographic and altitudinal variation in elytral reticulation. The various depth of the reticulation imprint, both in smaller and larger meshes, results in both mat and shiny individuals, as well as intermediate forms. The West Palearctic lowland is inhabited by a sexually dimorphic form, with shiny males and mat females. In mountain regions, shiny individuals of both sexes are found intermixed with mat individuals or in pure populations in central and southern areas, whereas pure populations of mat individuals are exclusively found in the northern region at high altitude. Sexual selection is proposed as a driving force in shaping this variation. However, the occurrence of different types of reticulation in both sexes and disjunct geographical distribution patterns suggest an additional function of the reticulation. Here we investigate the phylogeographical history, genetic structure and reticulation variation of several named forms within the Agabus bipustulatus complex including A. nevadensis. The molecular analyses recognised several well-supported clades within the complex. Several of the named forms had two or more independent origins. Few south European populations were uniform in reticulation patterns, and the males were found to display large variation. Reticulation diversity and population genetic variability were clearly correlated to altitude, but no genetic differences were detected among populations with mixed or homogenous forms. Observed reduction in secondary reticulation in female and increased variance in male at high altitude in South Europe may be explained by the occurrence of an additional selective force, beside sexual selection. The combined effect of these selective processes is here demonstrated in an extreme case to generate isolation barriers between populations at high altitudes. Here we discuss this selective force in relation to thermal selection.
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Affiliation(s)
- Marcus K Drotz
- Lake Vänern Museum of Natural and Cultural History, Lidköping, Sweden.
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Vigilant L. Elucidating population histories using genomic DNA sequences. CURRENT ANTHROPOLOGY 2009; 50:201-12. [PMID: 19817223 DOI: 10.1086/592025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In 1993, Cliff Jolly suggested that rather than debating species definitions and classifications, energy would be better spent investigating multidimensional patterns of variation and gene flow among populations. Until now, however, genetic studies of wild primate populations have been limited to very small portions of the genome. Access to complete genome sequences of humans, chimpanzees, macaques, and other primates makes it possible to design studies surveying substantial amounts of DNA sequence variation at multiple genetic loci in representatives of closely related but distinct wild primate populations. Such data can be analyzed with new approaches that estimate not only when populations diverged but also the relative amounts and directions of subsequent gene flow. These analyses will reemphasize the difficulty of achieving consistent species and subspecies definitions by revealing the extent of variation in the amount and duration of gene flow accompanying population divergences.
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Affiliation(s)
- Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
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45
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Huang H, Knowles LL. What Is the Danger of the Anomaly Zone for Empirical Phylogenetics? Syst Biol 2009; 58:527-36. [DOI: 10.1093/sysbio/syp047] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Huateng Huang
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA; E-mail:
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA; E-mail:
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McCormack JE, Huang H, Knowles LL. Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design. Syst Biol 2009; 58:501-8. [DOI: 10.1093/sysbio/syp045] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- John E. McCormack
- Department of Ecology and Evolutionary Biology, and the Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - Huateng Huang
- Department of Ecology and Evolutionary Biology, and the Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, and the Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
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Keever CC, Sunday J, Puritz JB, Addison JA, Toonen RJ, Grosberg RK, Hart MW. Discordant distribution of populations and genetic variation in a sea star with high dispersal potential. Evolution 2009; 63:3214-27. [PMID: 19663996 DOI: 10.1111/j.1558-5646.2009.00801.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Patiria miniata, a broadcast-spawning sea star species with high dispersal potential, has a geographic range in the intertidal zone of the northeast Pacific Ocean from Alaska to California that is characterized by a large range gap in Washington and Oregon. We analyzed spatial genetic variation across the P. miniata range using multilocus sequence data (mtDNA, nuclear introns) and multilocus genotype data (microsatellites). We found a strong phylogeographic break at Queen Charlotte Sound in British Columbia that was not in the location predicted by the geographical distribution of the populations. However, this population genetic discontinuity does correspond to previously described phylogeographic breaks in other species. Northern populations from Alaska and Haida Gwaii were strongly differentiated from all southern populations from Vancouver Island and California. Populations from Vancouver Island and California were undifferentiated with evidence of high gene flow or very recent separation across the range disjunction between them. The surprising and discordant spatial distribution of populations and alleles suggests that historical vicariance (possibly caused by glaciations) and contemporary dispersal barriers (possibly caused by oceanographic conditions) both shape population genetic structure in this species.
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Affiliation(s)
- Carson C Keever
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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SCHOVILLE SEAND, RODERICK GEORGEK. Alpine biogeography of Parnassian butterflies during Quaternary climate cycles in North America. Mol Ecol 2009; 18:3471-85. [DOI: 10.1111/j.1365-294x.2009.04287.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Mardulyn P, Mikhailov YE, Pasteels JM. Testing phylogeographic hypotheses in a Euro-Siberian cold-adapted leaf beetle with coalescent simulations. Evolution 2009; 63:2717-29. [PMID: 19545269 DOI: 10.1111/j.1558-5646.2009.00755.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Few studies to date have investigated the impact of Pleistocene climatic oscillations on the genetic diversity of cold-adapted species. We focus on the geographic distribution of genetic diversity in a Euro-Siberian boreo-montane leaf beetle, Gonioctena pallida. We present the molecular variation from three independent gene fragments over the entire geographic range of this insect. The observed sequence variation identifies a genetic diversity hot spot in the Carpathian Mountains, in central Europe, which reveals the presence of (1) an ancestral refuge population or (2) a secondary contact zone in this area. Modeling of population evolution in a coalescent framework allowed us to favor the ancestral refuge hypothesis. These analyses suggest that the Carpathian Mountains served as a refuge for G. pallida, whereas the rest of the species distribution, that spans a large portion of Europe and Asia, experienced a dramatic reduction in genetic variation probably associated to bottlenecks and/or founder events. We estimated the time of isolation of the ancestral refuge population, using an approximate Bayesian method, to be larger than 90,000 years. If true, the current pattern of genetic variation in this cold-adapted organism was shaped by a climatic event predating by far the end of the last ice age.
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Affiliation(s)
- Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, 1050 Brussels, Belgium.
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