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Banerjee AK, Feng H, Guo W, Harms NE, Xie H, Liang X, Xing F, Lin Y, Shao H, Guo Z, Ng WL, Huang Y. Glacial vicariance and oceanic circulation shape population structure of the coastal legume Derris trifoliata in the Indo-West Pacific. AMERICAN JOURNAL OF BOTANY 2022; 109:1016-1034. [PMID: 35419829 DOI: 10.1002/ajb2.1851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
PREMISE The phylogeography of coastal plant species is shaped by contemporary and historical biogeographic processes. In this study, we aim to decipher the phylogeography of Derris trifoliata, a woody legume of relatively recent origin and wide distribution, in coastal areas in the Indo-West Pacific (IWP) region. METHODS Genetic diversity and population structure were assessed by analyzing six nuclear and three chloroplast DNA sequences from 30 populations across the species' range. Phylogeography was inferred by estimating gene flow, divergence time, historical population size changes, and historical habitat suitability using paleoclimatic niche modeling. RESULTS High genetic diversity was observed at the species level. The populations of three oceanic regions included in this study (i.e., Indian Ocean, South China Sea, and Pacific Ocean) formed distinct clades and likely diverged during the late Pleistocene. Potential barriers to gene flow were identified, including the Sunda and Sahul shelves, geographic distance, and current patterns of oceanic circulation. Analysis of changes in population size supported the bottleneck model, which was strengthened by estimates of habitat suitability across paleoclimatic conditions. CONCLUSIONS The once widespread distribution of D. trifoliata was fragmented by changes in climatic suitability and biogeographic barriers that arose following sea-level changes during the Pleistocene. In addition, contemporary patterns of oceanic circulation and geographic distance between populations appear to maintain genetic differentiation across its distribution in the IWP.
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Affiliation(s)
- Achyut Kumar Banerjee
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Hui Feng
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wuxia Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
- Department of Bioengineering, Zunyi Medical University, Zhuhai, 519041 Guangdong, China
| | - Nathan E Harms
- US Army Engineer Research and Development Center, Lewisville, TX 75057, USA
| | - Hongxian Xie
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Xinru Liang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Fen Xing
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Yuting Lin
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Huiyu Shao
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Zixiao Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University, Malaysia, 43900 Sepang, Selangor, Malaysia
| | - Yelin Huang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
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Wham BE, Rahman SR, Martinez‐Correa M, Hines HM. Mito-nuclear discordance at a mimicry color transition zone in bumble bee Bombus melanopygus. Ecol Evol 2021; 11:18151-18168. [PMID: 35003664 PMCID: PMC8717287 DOI: 10.1002/ece3.8412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
As hybrid zones exhibit selective patterns of gene flow between otherwise distinct lineages, they can be especially valuable for informing processes of microevolution and speciation. The bumble bee, Bombus melanopygus, displays two distinct color forms generated by Müllerian mimicry: a northern "Rocky Mountain'' color form with ferruginous mid-abdominal segments (B. m. melanopygus) and a southern "Pacific'' form with black mid-abdominal segments (B. m. edwardsii). These morphs meet in a mimetic transition zone in northern California and southern Oregon that is more narrow and transitions further west than comimetic bumble bee species. To understand the historical formation of this mimicry zone, we assessed color distribution data for B. melanopygus from the last 100 years. We then examined gene flow among the color forms in the transition zone by comparing sequences from mitochondrial COI barcode sequences, color-controlling loci, and the rest of the nuclear genome. These data support two geographically distinct mitochondrial haplogroups aligned to the ancestrally ferruginous and black forms that meet within the color transition zone. This clustering is also supported by the nuclear genome, which, while showing strong admixture across individuals, distinguishes individuals most by their mitochondrial haplotype, followed by geography. These data suggest the two lineages most likely were historically isolated, acquired fixed color differences, and then came into secondary contact with ongoing gene flow. The transition zone, however, exhibits asymmetries: mitochondrial haplotypes transition further south than color pattern, and both transition over shorter distances in the south. This system thus demonstrates alternative patterns of gene flow that occur in contact zones, presenting another example of mito-nuclear discordance. Discordant gene flow is inferred to most likely be driven by a combination of mimetic selection, dominance effects, and assortative mating.
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Affiliation(s)
- Briana E. Wham
- Department of EntomologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- The Pennsylvania State University LibrariesUniversity ParkPennsylvaniaUSA
| | - Sarthok Rasique Rahman
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabamaUSA
| | | | - Heather M. Hines
- Department of EntomologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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McDonough MM, Ferguson AW, Dowler RC, Gompper ME, Maldonado JE. Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification. Mol Phylogenet Evol 2021; 167:107266. [PMID: 34302947 DOI: 10.1016/j.ympev.2021.107266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/28/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Four species of spotted skunks (Carnivora, Mephitidae, Spilogale) are currently recognized: Spilogale angustifrons, S. gracilis, S. putorius, and S. pygmaea. Understanding species boundaries within this group is critical for effective conservation given that regional populations or subspecies (e.g., S. p. interrupta) have experienced significant population declines. Further, there may be currently unrecognized diversity within this genus as some taxa (e.g., S. angustifrons) and geographic regions (e.g., Central America) never have been assessed using DNA sequence data. We analyzed species limits and diversification patterns in spotted skunks using multilocus nuclear (ultraconserved elements) and mitochondrial (whole mitogenomes and single gene analysis) data sets from broad geographic sampling representing all currently recognized species and subspecies. We found a high degree of genetic divergence among Spilogale that reflects seven distinct species and eight unique mitochondrial lineages. Initial divergence between S. pygmaea and all other Spilogale occurred in the Early Pliocene (∼ 5.0 million years ago). Subsequent diversification of the remaining Spilogale into an "eastern" and a "western" lineage occurred during the Early Pleistocene (∼1.5 million years ago). These two lineages experienced temporally coincident patterns of diversification at ∼0.66 and ∼0.35 million years ago into two and ultimately three distinct evolutionary units, respectively. Diversification was confined almost entirely within the Pleistocene during a timeframe characterized by alternating glacial-interglacial cycles, with the origin of this diversity occurring in northeastern Mexico and the southwestern United States of America. Mitochondrial-nuclear discordance was recovered across three lineages in geographic regions consistent with secondary contact, including a distinct mitochondrial lineage confined to the Sonoran Desert. Our results have direct consequences for conservation of threatened populations, or species, as well as for our understanding of the evolution of delayed implantation in this enigmatic group of small carnivores.
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Affiliation(s)
- Molly M McDonough
- Chicago State University Department of Biological Sciences 9501 S. King Drive, WSC 290 Chicago, IL 60628-1598.
| | - Adam W Ferguson
- Gantz Family Collection Center Field Museum 1400 South Lake Shore Drive Chicago, IL 60605
| | - Robert C Dowler
- Department of Biology Angelo State University ASU Station 10890 San Angelo, TX 76909
| | - Matthew E Gompper
- Department of Fish, Wildlife, and Conservation Ecology New Mexico State University Las Cruces, NM 88003
| | - Jesús E Maldonado
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park PO Box 37012 MRC 5503 Washington, DC 20013
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Gürün K, Furman A, Juste J, Ramos Pereira MJ, Palmeirim JM, Puechmaille SJ, Hulva P, Presetnik P, Hamidovic D, Ibáñez C, Karataş A, Allegrini B, Georgiakakis P, Scaravelli D, Uhrin M, Nicolaou H, Abi-Said MR, Nagy ZL, Gazaryan S, Bilgin R. A continent-scale study of the social structure and phylogeography of the bent-wing bat, Miniopterus schreibersii (Mammalia: Chiroptera), using new microsatellite data. J Mammal 2019. [DOI: 10.1093/jmammal/gyz153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractMiniopterus schreibersii is a cave-dwelling bat species with a wide distribution in the western Palearctic spanning southern and central Europe, North Africa, Anatolia, the Middle East, and the Caucasus. We investigated the social structure and its effects on the genetic makeup of this species, using 10 nuclear microsatellite markers and a partial fragment of the mitochondrial cytochrome b gene. Samples were examined from the species' entire circum-Mediterranean range. Local structuring that was previously detected among populations of M. schreibersii using mitochondrial markers was not observed for microsatellite markers, indicating male-biased dispersal for the species. Some support was found for postglacial expansions in Europe, with Anatolia potentially acting as the primary refugium during the Last Glacial Maximum (LGM). However, support for this hypothesis is not as strong as that previously detected using mitochondrial DNA markers. This is likely due to the diminishing effect of male-mediated dispersal, replenishing the nuclear diversity faster than the mitochondrial diversity in regions that are relatively far from the glacial refugia.
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Affiliation(s)
- Kanat Gürün
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Andrzej Furman
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Maria J Ramos Pereira
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain
- Department of Zoology, Institute of Biosciences, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91540-000, Brazil
- Centre for Environmental and Marine Studies, Wildlife Research Unit, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jorge M Palmeirim
- Center for Ecology, Evolution and Environmental Change, Dept. Biologia Animal, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sebastien J Puechmaille
- University College Dublin, School of Biological and Environmental Sciences, Belfield, Dublin 4, Ireland
- Zoology Institute, University of Greifswald, 17489 Greifswald, Germany
- Chauves-souris Aveyron (CSA), 12310, Vimenet, France
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, CZ-128 44 Praha 2, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Primoz Presetnik
- Centre for Cartography of Fauna and Flora, Ljubljana Office, Klunova 3, SI-1000, Ljubljana, Slovenia
| | - Daniela Hamidovic
- Croatian Biospeleological Society, Zagreb, Demetrova 1, 10000 Zagreb, Croatia
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Ahmet Karataş
- Department of Biology, Niğde University, Niğde 51100, Turkey
| | | | - Panagiotis Georgiakakis
- Natural History Museum of Crete, University of Crete, Knossos Ave., P.O. Box: 2208, GR71 409 Irakleion, Crete, Greece
| | - Dino Scaravelli
- Department Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano dell'Emilia (BO), Italy
| | - Marcel Uhrin
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, SK-040 01 Košice, Slovakia
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycká 1176, 165 21 Praha 6, Czech Republic
| | - Haris Nicolaou
- Parks and Environment Sector, Forestry Department, Ministry of Agriculture, Natural Resources and Environment, 1414 Nicosia, Cyprus
| | - Mounir R Abi-Said
- Animal Encounter, Aley, Lebanon
- Faculty of Sciences II, Lebanese University, Al Fanar, 90656 Jdeidet, Lebanon
| | | | - Suren Gazaryan
- Institute of Ecology of Mountain Territories RAS, Armand 37A360000, Nalchik, Russia
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
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Bernardo PH, Sánchez-Ramírez S, Sánchez-Pacheco SJ, Álvarez-Castañeda ST, Aguilera-Miller EF, Mendez-de la Cruz FR, Murphy RW. Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate. Heredity (Edinb) 2019; 123:359-370. [PMID: 30833746 PMCID: PMC6781153 DOI: 10.1038/s41437-019-0204-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.
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Affiliation(s)
- Pedro Henrique Bernardo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada. .,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Santiago J Sánchez-Pacheco
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | | | | | | | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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Bennett KL, Kaddumukasa M, Shija F, Djouaka R, Misinzo G, Lutwama J, Linton YM, Walton C. Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa. Ecol Evol 2018; 8:3019-3036. [PMID: 29531714 PMCID: PMC5838080 DOI: 10.1002/ece3.3668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon-primed intron-crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate-driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.
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Affiliation(s)
- Kelly Louise Bennett
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
| | - Martha Kaddumukasa
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
- WITS Institute for Malaria ResearchSchool of Pathology Faculty of Health SciencesUniversity of WitwatersrandParktownJohannesburg
| | - Fortunate Shija
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
- Department of Veterinary Microbiology and ParasitologySokoine University of AgricultureMorogoroTanzania
| | - Rousseau Djouaka
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Gerald Misinzo
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
| | - Yvonne Marie Linton
- Department of EntomologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Walter Reed Biosystematics UnitSmithsonian Institution Museum Support CenterSuitlandMDUSA
- Walter Reed Army Institute of ResearchSilver SpringMDUSA
- Uniformed Services University of Health SciencesBethesdaMDUSA
| | - Catherine Walton
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
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Conservation genomics of desert dwelling California voles (Microtus californicus) and implications for management of endangered Amargosa voles (Microtus californicus scirpensis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1010-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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da Silva JM, Feldheim KA, Measey GJ, Doucette-Riise S, Daniels RJ, Chauke LF, Tolley KA. Genetic diversity and differentiation of the Western Leopard Toad (Sclerophrys pantherina) based on mitochondrial and microsatellite markers. AFR J HERPETOL 2017. [DOI: 10.1080/21564574.2017.1294115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jessica M. da Silva
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - G. John Measey
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Natural Sciences Building, Matieland, Stellenbosch, South Africa
| | - Stephen Doucette-Riise
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 770, Cape Town, South Africa
| | - Ryan J. Daniels
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
| | - Lucas F. Chauke
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
| | - Krystal A. Tolley
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
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Howell PE, Delgado ML, Scribner KT. Landscape genetic analysis of co-distributed white-footed mice (Peromyscus leucopus) and prairie deer mice (Peromyscus maniculatus bairdii) in an agroecosystem. J Mammal 2017. [DOI: 10.1093/jmammal/gyx042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Kingsley EP, Kozak KM, Pfeifer SP, Yang DS, Hoekstra HE. The ultimate and proximate mechanisms driving the evolution of long tails in forest deer mice. Evolution 2016; 71:261-273. [PMID: 27958661 PMCID: PMC5324611 DOI: 10.1111/evo.13150] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 11/15/2016] [Accepted: 12/02/2016] [Indexed: 12/21/2022]
Abstract
Understanding both the role of selection in driving phenotypic change and its underlying genetic basis remain major challenges in evolutionary biology. Here, we use modern tools to revisit a classic system of local adaptation in the North American deer mouse, Peromyscus maniculatus, which occupies two main habitat types: prairie and forest. Using historical collections, we find that forest‐dwelling mice have longer tails than those from nonforested habitat, even when we account for individual and population relatedness. Using genome‐wide SNP data, we show that mice from forested habitats in the eastern and western parts of their range form separate clades, suggesting that increased tail length evolved independently. We find that forest mice in the east and west have both more and longer caudal vertebrae, but not trunk vertebrae, than nearby prairie forms. By intercrossing prairie and forest mice, we show that the number and length of caudal vertebrae are not correlated in this recombinant population, indicating that variation in these traits is controlled by separate genetic loci. Together, these results demonstrate convergent evolution of the long‐tailed forest phenotype through two distinct genetic mechanisms, affecting number and length of vertebrae, and suggest that these morphological changes—either independently or together—are adaptive.
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Affiliation(s)
- Evan P Kingsley
- Howard Hughes Medical Institute, Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138
| | - Krzysztof M Kozak
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom.,Current Address: Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá
| | - Susanne P Pfeifer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland and School of Life Sciences, Arizona State University, Tempe, Arizona, 85287
| | - Dou-Shuan Yang
- Burke Museum and Department of Biology, University of Washington, Seattle, Washington, 98195.,Current Address: US Fish and Wildlife Service, Ventura Field Office, 2493 Portola Road #B, Ventura, California, 93003
| | - Hopi E Hoekstra
- Howard Hughes Medical Institute, Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138
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12
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Carranza J, Salinas M, de Andrés D, Pérez‐González J. Iberian red deer: paraphyletic nature at mtDNA but nuclear markers support its genetic identity. Ecol Evol 2016; 6:905-22. [PMID: 26843924 PMCID: PMC4729781 DOI: 10.1002/ece3.1836] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 10/07/2015] [Accepted: 10/21/2015] [Indexed: 01/15/2023] Open
Abstract
Red deer populations in the Iberian glacial refugium were the main source for postglacial recolonization and subspecific radiation in north-western Europe. However, the phylogenetic history of Iberian red deer (Cervus elaphus hispanicus) and its relationships with northern European populations remain uncertain. Here, we study DNA sequences at the mitochondrial control region along with STR markers for over 680 specimens from all the main red deer populations in Spain and other west European areas. Our results from mitochondrial and genomic DNA show contrasting patterns, likely related to the nature of these types of DNA markers and their specific processes of change over time. The results, taken together, bring support to two distinct, cryptic maternal lineages for Iberian red deer that predated the last glacial maximum and that have maintained geographically well differentiated until present. Haplotype relationships show that only one of them contributed to the northern postglacial recolonization. However, allele frequencies of nuclear markers evidenced one main differentiation between Iberian and northern European subspecies although also supported the structure of both matrilines within Iberia. Thus, our findings reveal a paraphyletic nature for Iberian red deer but also its genetic identity and differentiation with respect to northern subspecies. Finally, we suggest that maintaining the singularity of Iberian red deer requires preventing not only restocking practices with red deer specimens belonging to other European populations but also translocations between both Iberian lineages.
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Affiliation(s)
- Juan Carranza
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - María Salinas
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - Damián de Andrés
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
- Instituto de AgrobiotecnologíaCSIC‐UPNA‐Gobierno de Navarra31192MutilvaNavarraSpain
| | - Javier Pérez‐González
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
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13
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Fang F, Ji Y, Zhao Q, Wang Y, Gao W, Chu K, Sun H. Phylogeography of the Chinese endemic freshwater crabSinopotamon acutum(Brachyura, Potamidae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fang Fang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yongkun Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Qiang Zhao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yujuan Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Wei Gao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Kelin Chu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
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14
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Abstract
In North America, Lyme disease (LD) is a tick-borne zoonosis caused by the spirochete bacterium Borrelia burgdorferi sensu stricto, which is maintained by wildlife. Tick vectors and bacteria are currently spreading into Canada and causing increasing numbers of cases of LD in humans and raising a pressing need for public health responses. There is no vaccine, and LD prevention depends on knowing who is at risk and informing them how to protect themselves from infection. Recently, it was found in the United States that some strains of B. burgdorferi sensu stricto cause severe disease, whereas others cause mild, self-limiting disease. While many strains occurring in the United States also occur in Canada, strains in some parts of Canada are different from those in the United States. We therefore recognize a need to identify which strains specific to Canada can cause severe disease and to characterize their geographic distribution to determine which Canadians are particularly at risk. In this review, we summarize the history of emergence of LD in North America, our current knowledge of B. burgdorferi sensu stricto diversity, its intriguing origins in the ecology and evolution of the bacterium, and its importance for the epidemiology and clinical and laboratory diagnosis of LD. We propose methods for investigating associations between B. burgdorferi sensu stricto diversity, ecology, and pathogenicity and for developing predictive tools to guide public health interventions. We also highlight the emergence of B. burgdorferi sensu stricto in Canada as a unique opportunity for exploring the evolutionary aspects of tick-borne pathogen emergence.
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15
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Harris SE, Munshi-South J, Obergfell C, O’Neill R. Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PLoS One 2013; 8:e74938. [PMID: 24015321 PMCID: PMC3756007 DOI: 10.1371/journal.pone.0074938] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/06/2013] [Indexed: 12/16/2022] Open
Abstract
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscusleucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar "urban adapter." We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.
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Affiliation(s)
- Stephen E. Harris
- Program in Ecology, Evolutionary Biology, & Behavior, The Graduate Center, City University of New York (CUNY), New York, New York, United States of America
| | - Jason Munshi-South
- Louis Calder Center, Fordham University, Armonk, New York, United States of America
| | - Craig Obergfell
- Molecular & Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Rachel O’Neill
- Molecular & Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
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16
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Andersen JJ, Portnoy DS, Hafner JC, Light JE. Populations at risk: conservation genetics of kangaroo mice (Microdipodops) of the Great Basin Desert. Ecol Evol 2013; 3:2497-513. [PMID: 24567823 PMCID: PMC3930042 DOI: 10.1002/ece3.637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/10/2013] [Accepted: 05/14/2013] [Indexed: 11/07/2022] Open
Abstract
The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mice are ecological specialists found within the Great Basin Desert and are potentially ideal organisms for assessing ecosystem health and inferring the biogeographic history of this vulnerable region. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of kangaroo mice and to evaluate gene flow, demographic trends, and genetic integrity. Results confirm that there are at least three genetically distinct units within M. megacephalus and two such units within M. pallidus. The three units of M. megacephalus appear to have different demographic histories, with effectively no gene flow among them since their divergence. Similarly, the two units of M. pallidus also appear to have experienced different demographic histories, with effectively no gene exchange. Contemporary effective population sizes of all groups within Microdipodops appear to be low (<500), suggesting that each genetic lineage may have difficulty coping with changing environmental pressures and hence may be at risk of extirpation. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem. The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of the dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mouse, and to evaluate gene flow, demographic trends, and genetic integrity. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem (photo credit J. C. Hafner).
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Affiliation(s)
- John J Andersen
- Department of Wildlife and Fisheries Sciences, Texas A&M University 210 Nagle Hall, College Station, Texas, 77843-2258 ; Department of Biological Sciences, Louisiana State University 202 Life Sciences Building, Baton Rouge, Louisiana, 70808
| | - David S Portnoy
- Department of Wildlife and Fisheries Sciences, Texas A&M University 210 Nagle Hall, College Station, Texas, 77843-2258
| | - John C Hafner
- Moore Laboratory of Zoology and Department of Biology, Occidental College Los Angeles, California, 90041
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences, Texas A&M University 210 Nagle Hall, College Station, Texas, 77843-2258
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17
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Lopes CM, Ximenes SSF, Gava A, de Freitas TRO. The role of chromosomal rearrangements and geographical barriers in the divergence of lineages in a South American subterranean rodent (Rodentia: Ctenomyidae: Ctenomys minutus). Heredity (Edinb) 2013; 111:293-305. [PMID: 23759727 DOI: 10.1038/hdy.2013.49] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/19/2013] [Accepted: 04/03/2013] [Indexed: 11/09/2022] Open
Abstract
Identifying factors and the extent of their roles in the differentiation of populations is of great importance for understanding the evolutionary process in which a species is involved. Ctenomys minutus is a highly karyotype-polymorphic subterranean rodent, with diploid numbers ranging from 42 to 50 and autosomal arm numbers (ANs) ranging from 68 to 80, comprising a total of 45 karyotypes described so far. This species inhabits the southern Brazilian coastal plain, which has a complex geological history, with several potential geographical barriers acting on different time scales. We assessed the geographical genetic structure of C. minutus, examining 340 individuals over the entire distributional range and using information from chromosomal rearrangements, mitochondrial DNA (mtDNA) sequences and 14 microsatellite loci. The mtDNA results revealed seven main haplogroups, with the most recent common ancestors dating from the Pleistocene, whereas clustering methods defined 12 populations. Some boundaries of mtDNA haplogroups and population clusters can be associated with potential geographical barriers to gene flow. The isolation-by-distance pattern also has an important role in fine-scale genetic differentiation, which is strengthened by the narrowness of the coastal plain and by common features of subterranean rodents (that is, small fragmented populations and low dispersal rates), which limit gene flow among populations. A step-by-step mechanism of chromosomal evolution can be suggested for this species, mainly associated with the metapopulation structure, genetic drift and the geographical features of the southern Brazilian coastal plain. However, chromosomal variations have no or very little role in the diversification of C. minutus populations.
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Affiliation(s)
- C M Lopes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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18
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Sauer J, Oldeland J, Hausdorf B. Continuing fragmentation of a widespread species by geographical barriers as initial step in a land snail radiation on crete. PLoS One 2013; 8:e62569. [PMID: 23658748 PMCID: PMC3641037 DOI: 10.1371/journal.pone.0062569] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/23/2013] [Indexed: 11/18/2022] Open
Abstract
The phylogeographic structure of the land snail Xerocrassa mesostena on Crete inferred from AFLP markers and mitochondrial cox1 sequences can be explained by three mechanisms: gene flow restriction, population expansion and leptokurtic dispersal. Gene flow restriction by geographic barriers caused subdivision of the gene pool into distinct clusters. Population expansion was probably facilitated by deforestation of Crete in the postglacial. Newly available areas were colonized by leptokurtic dispersal, i.e. slow active expansion resulting in isolation by distance within the clusters and occasional long distance dispersal events that resulted in departures from the isolation by distance model. Less than one percent of the AFLP markers show correlations with environmental variables. Random phylogeographic breaks in the distribution of the mitochondrial haplotype groups indicate that single locus markers, especially mitochondrial DNA, might result in a misleading picture of the phylogeographic structure of a species. Restriction of gene flow between metapopulations caused by geographical barriers can interact with sexual selection resulting in the differentiation of these metapopulations into separate species without noticeable ecological differentiation. Evidence for gene flow between parapatrically distributed evolutionary units representing different stages of the speciation process suggests that the ongoing process of fragmentation of the X. mesostena complex might be an example for parapatric speciation. The lack of ecological differentiation between these units confirms theoretical predictions that divergent selection for local adaptation is not required for rapid speciation.
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Affiliation(s)
- Jan Sauer
- Department of Chemical Ecology, University of Bielefeld, Bielefeld, Germany
- Zoological Museum, University of Hamburg, Hamburg, Germany
| | - Jens Oldeland
- Biodiversity, Evolution and Ecology of Plants, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
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19
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Tucker JM, Schwartz MK, Truex RL, Pilgrim KL, Allendorf FW. Historical and contemporary DNA indicate fisher decline and isolation occurred prior to the European settlement of California. PLoS One 2012; 7:e52803. [PMID: 23300783 PMCID: PMC3530519 DOI: 10.1371/journal.pone.0052803] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 11/21/2012] [Indexed: 11/30/2022] Open
Abstract
Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennanti) in California occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatellite loci from 275 contemporary and 21 historical fisher samples (1880-1920) to evaluate the demographic history of fisher in California. We did not find any evidence of a recent (post-European) bottleneck in the northwestern population. In the southern Sierra Nevada, genetic subdivision within the population strongly influenced bottleneck tests. After accounting for genetic subdivision, we found a bottleneck signal only in the northern and central portions of the southern Sierra Nevada, indicating that the southernmost tip of these mountains may have acted as a refugium for fisher during the anthropogenic changes of the late 19(th) and early 20(th) centuries. Using a coalescent-based Bayesian analysis, we detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. We hypothesize that fisher distribution in California contracted to the two current population areas pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement.
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Affiliation(s)
- Jody M Tucker
- Sequoia National Forest, United States Department of Agriculture Forest Service, Porterville, California, United States of America.
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20
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O’Donnell RP, Mock KE. Two frog species or one? A multi-marker approach to assessing the distinctiveness of genetic lineages in the Northern Leopard Frog, Rana pipiens. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0384-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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JACKSON NATHAND, AUSTIN CHRISTOPHERC. Inferring the evolutionary history of divergence despite gene flow in a lizard species, Scincella lateralis (Scincidae), composed of cryptic lineages. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01929.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Barton HD, Wisely SM. Phylogeography of striped skunks (Mephitis mephitis) in North America: Pleistocene dispersal and contemporary population structure. J Mammal 2012. [DOI: 10.1644/10-mamm-a-270.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Taylor ZS, Hoffman SMG. Microsatellite genetic structure and cytonuclear discordance in naturally fragmented populations of deer mice (Peromyscus maniculatus). J Hered 2011; 103:71-9. [PMID: 21976772 DOI: 10.1093/jhered/esr100] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Great Lakes impose high levels of natural fragmentation on local populations of terrestrial animals in a way rarely found within continental ecosystems. Although separated by major water barriers, woodland deer mouse (Peromyscus maniculatus gracilis) populations on the islands and on the Upper Peninsula (UP) and Lower Peninsula (LP) of Michigan have previously been shown to have a mitochondrial DNA contact zone that is incongruent with the regional landscape. We analyzed 11 microsatellite loci for 16 populations of P. m. gracilis distributed across 2 peninsulas and 6 islands in northern Michigan to address the relative importance of geographical structure and inferred postglacial colonization patterns in determining the nuclear genetic structure of this species. Results showed relatively high levels of genetic structure for this species and a significant correlation between interpopulation differentiation and separation by water but little genetic structure and no isolation-by-distance within each of the 2 peninsulas. Genetic diversity was generally high on both peninsulas but lower and correlated to island size in the Beaver Island Archipelago. These results are consistent with the genetic and demographic isolation of Lower Peninsula populations, which is a matter of concern given the dramatic decline in P. m. gracilis abundance on the Lower Peninsula in recent years.
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24
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Yang DS, Kenagy G. Population delimitation across contrasting evolutionary clines in deer mice (Peromyscus maniculatus). Ecol Evol 2011; 1:26-36. [PMID: 22393480 PMCID: PMC3287378 DOI: 10.1002/ece3.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 05/15/2011] [Accepted: 05/18/2011] [Indexed: 11/11/2022] Open
Abstract
Despite current interest in population genetics, a concrete definition of a "population" remains elusive. Multiple ecologically and evolutionarily based definitions of population are in current use, which focus, respectively, on demographic and genetic interactions. Accurate population delimitation is crucial for not only evolutionary and ecological population biology, but also for conservation of threatened populations. Along the Pacific Coast of North America, two contrasting patterns of geographic variation in deer mice (Peromyscus maniculatus) converge within the state of Oregon. Populations of these mice diverge morphologically across an east-west axis, and they diverge in mitochondrial DNA haplotypes across a north-south axis. In this study, we investigate these geographically contrasting patterns of differentiation in the context of ecological and evolutionary definitions (paradigms) of populations. We investigate these patterns using a new and geographically expansive sample that integrates data on morphology, mitochondrial DNA, and nuclear DNA. We found no evidence of nuclear genetic differentiation between the morphologically and mitochondrially distinct populations, thus indicating the occurrence of gene flow across Oregon. Under the evolutionary paradigm, Oregon populations can be considered a single population, whereas morphological and mitochondrial differentiations do not indicate distinct populations. In contrast, under the ecological paradigm morphological differentiation indicates distinct populations based on the low likelihood of demographic interactions between geographically distant individuals. The two sympatric but mitochondrially distinct haplogroups form a single population under the ecological paradigm. Hence, we find that the difference between evolutionary and ecological paradigms is the time-scale of interest, and we believe that the more chronologically inclusive evolutionary paradigm may be preferable except in cases where only a single generation is of interest.
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Affiliation(s)
- D-S Yang
- Burke Museum and Department of Biology, Box 351800, University of Washington Seattle, Washington 98195, USA
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25
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Ozer F, Gellerman H, Ashley MV. Genetic impacts of Anacapa deer mice reintroductions following rat eradication. Mol Ecol 2011; 20:3525-39. [PMID: 21711403 DOI: 10.1111/j.1365-294x.2011.05165.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Anacapa deer mouse is an endemic subspecies that inhabits Anacapa Island, part of Channel Islands National Park, California. We used mitochondrial DNA cytochrome c oxidase subunit II gene (COII) and 10 microsatellite loci to evaluate the levels of genetic differentiation and variation in ~1400 Anacapa deer mice sampled before and for 4 years after a black rat (Rattus rattus) eradication campaign that included trapping, captive holding and reintroduction of deer mice. Both mitochondrial and microsatellite analyses indicated significant differentiation between Anacapa deer mice and mainland mice, and genetic variability of mainland mice was significantly higher than Anacapa mice even prior to reintroduction. Bayesian cluster analysis and Principal Coordinates Analysis indicated that East, Middle and West Anacapa mice were genetically differentiated from each other, but translocation of mice among islands resulted in the East population becoming less distinct as a result of management. Levels of heterozygosity were similar before and after management. However, numerous private alleles in the founder populations were not observed after reintroduction and shifts in allele frequencies occurred, indicating that the reintroduced populations experienced substantial genetic drift. Surprisingly, two mitochondrial haplotypes observed in an earlier study of Anacapa deer mice were lost in the 20 years prior to the rat eradication program, leaving only a single haplotype in Anacapa deer mice. This study demonstrates how genetic monitoring can help to understand the re-establishment of endemic species after the eradication of invasive species and to evaluate the effectiveness of the management strategies employed.
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Affiliation(s)
- Fusun Ozer
- Sustainable Environment and Energy Systems Graduate Program, Middle East Technical University Northern Cyprus Campus, TRNC via Mersin 10, Turkey
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26
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Oomen RA, Reudink MW, Nocera JJ, Somers CM, Green MC, Kyle CJ. Mitochondrial evidence for panmixia despite perceived barriers to gene flow in a widely distributed waterbird. ACTA ACUST UNITED AC 2011; 102:584-92. [PMID: 21705489 DOI: 10.1093/jhered/esr055] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We examined the mitochondrial genetic structure of American white pelicans (Pelecanus erythrorhynchos) to: 1) verify or refute whether American white pelicans are panmictic and 2) understand if any lack of genetic structure is the result of contemporary processes or historical phenomena. Sequence analysis of mitochondrial DNA control region haplotypes of 367 individuals from 19 colonies located across their North American range revealed a lack of population genetic or phylogeographic structure. This lack of structure was unexpected because: 1) Major geographic barriers such as the North American Continental Divide are thought to limit dispersal; 2) Differences in migratory behavior are expected to promote population differentiation; and 3) Many widespread North American migratory bird species show historic patterns of differentiation resulting from having inhabited multiple glacial refugia. Further, high haplotype diversity and many rare haplotypes are maintained across the species' distribution, despite frequent local extinctions and recolonizations that are expected to decrease diversity. Our findings suggest that American white pelicans have a high effective population size and low natal philopatry. We suggest that the rangewide panmixia we observed in American white pelicans is due to high historical and contemporary gene flow, enabled by high mobility and a lack of effective physical or behavioral barriers.
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Affiliation(s)
- Rebekah A Oomen
- Forensic Science Department, Trent University, Peterborough, Ontario, Canada.
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27
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Chiesa S, Scalici M, Negrini R, Gibertini G, Nonnis Marzano F. Fine-scale genetic structure, phylogeny and systematics of threatened crayfish species complex. Mol Phylogenet Evol 2011; 61:1-11. [PMID: 21524706 DOI: 10.1016/j.ympev.2011.03.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 03/15/2011] [Accepted: 03/30/2011] [Indexed: 10/18/2022]
Abstract
Systematic uncertainties in the crayfish Austropotamobius pallipes are well grounded by the number of species and subspecies described using different approaches, causing scientists to define this taxon as "complex". However, a key task that conservation programmes are facing regarding the recent and drastic decline of European populations, is the coherent systematic classification of this threatened species. Here we present results obtained by coupling mtDNA and genome analysis suggestive of a novel evolutionary framework to explain the relationships among phylogenetic lineages of A. pallipes. The direct sequencing of mtDNA COI gene fragment revealed a strong geographic structure with four distinct haplogroups separated by a range of 5-25 mutations. However, mitochondrial data were not supported by genomic fingerprinting based on 535 AFLP polymorphisms. Nuclear markers showed an unexpected moderate level of genetic differentiation and the absence of any geographic structure. Consequently, this study proposes that the taxonomic hypothesis of a single species of A. pallipes settling the Italian continental waters, is affected by complex evolutionary events. To solve the paradox, we hypothesized an evolutive scenario in which the separation of ancient mtDNA lineages likely occurred before the latest glacial periods. However, the speciation process remained incomplete due to secondary intensive postglacial contacts that forced the mingling of the genomes, and confounds the phylogeographic signature still detectable within mtDNA. Postglacial dispersion and the following demographic events, such as founder effects, drift and bottlenecks, abruptly depleted the local mtDNA variation, and shaped the current genetic population structure of white-clawed crayfish.
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Affiliation(s)
- S Chiesa
- Department of Biology, University of Roma Tre, V G Marconi 446, 00146 Rome, Italy.
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28
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COLBECK GABRIELJ, TURGEON JULIE, SIROIS PASCAL, DODSON JULIANJ. Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus). Mol Ecol 2011; 20:1976-87. [DOI: 10.1111/j.1365-294x.2011.05069.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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29
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Humphries EM, Winker K. Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds. Mol Ecol 2010; 20:573-83. [PMID: 21199027 DOI: 10.1111/j.1365-294x.2010.04965.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.
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Affiliation(s)
- Elizabeth M Humphries
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA
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30
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Ohshima I, Tanikawa-Dodo Y, Saigusa T, Nishiyama T, Kitani M, Hasebe M, Mohri H. Phylogeny, biogeography, and host–plant association in the subfamily Apaturinae (Insecta: Lepidoptera: Nymphalidae) inferred from eight nuclear and seven mitochondrial genes. Mol Phylogenet Evol 2010; 57:1026-36. [DOI: 10.1016/j.ympev.2010.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Revised: 09/20/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
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31
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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MUNSHI-SOUTH JASON, KHARCHENKO KATERINA. Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City. Mol Ecol 2010; 19:4242-54. [DOI: 10.1111/j.1365-294x.2010.04816.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Chavez AS, Kenagy GJ. Historical biogeography of western heather voles (Phenacomys intermedius) in montane systems of the Pacific Northwest. J Mammal 2010. [DOI: 10.1644/09-mamm-a-303.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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