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Chen S, Juan C, Rossiter SJ, Kinjo T, Fukui D, Kawai K, Tsang SM, Veluz MJ, Sakurai H, Lin H, Jang‐Liaw N, Osawa K, Ko W, Izawa M. Population genetic structure of the insular Ryukyu flying fox
Pteropus dasymallus. Biotropica 2021. [DOI: 10.1111/btp.12897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shiang‐Fan Chen
- Center for General Education National Taipei University New Taipei City Taiwan
| | - Chung‐Hao Juan
- Center for General Education National Taipei University New Taipei City Taiwan
| | | | | | - Dai Fukui
- The University of Tokyo Hokkaido Forest The University of Tokyo Hokkaido Japan
| | - Kuniko Kawai
- Department of Biology Tokai University Hokkaido Japan
| | - Susan M. Tsang
- Department of Mammalogy American Museum of Natural History New York NY USA
- Mammalogy Section National Museum of Natural History Manila Philippines
| | | | | | - Hua‐Ching Lin
- Forestry Bureau Council of Agriculture Taipei Taiwan
| | | | | | - Wen‐Ya Ko
- Department of Life Sciences and Institute of Genome Sciences National Yang‐Ming University Taipei Taiwan
| | - Masako Izawa
- Biology Program Faculty of Science University of the Ryukyus Okinawa Japan
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Bachorec E, Horáček I, Hulva P, Konečný A, Lučan RK, Jedlička P, Shohdi WM, Řeřucha Š, Abi‐Said M, Bartonička T. Egyptian fruit bats do not preferentially roost with their relatives. J Zool (1987) 2020. [DOI: 10.1111/jzo.12816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. Bachorec
- Department of Botany and Zoology Masaryk University Brno Czech Republic
| | - I. Horáček
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - P. Hulva
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - A. Konečný
- Department of Botany and Zoology Masaryk University Brno Czech Republic
| | - R. K. Lučan
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - P. Jedlička
- Institute of Scientific Instruments of the Czech Academy of Sciences (ISI) Brno Czech Republic
| | | | - Š. Řeřucha
- Institute of Scientific Instruments of the Czech Academy of Sciences (ISI) Brno Czech Republic
| | - M. Abi‐Said
- Department of Earth and Life Sciences Faculty of Sciences II Lebanese University JdeidehFanar Lebanon
| | - T. Bartonička
- Department of Botany and Zoology Masaryk University Brno Czech Republic
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Chakravarty R, Chattopadhyay B, Ramakrishnan U, Sivasundar A. Comparative Population Structure in Species of Bats Differing in Ecology and Morphology in the Andaman Islands, India. ACTA CHIROPTEROLOGICA 2018. [DOI: 10.3161/15081109acc2018.20.1.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rohit Chakravarty
- Post-Graduate Program in Wildlife Biology and Conservation, Wildlife Conservation Society-India, Bangalore 560097, India and National Centre for Biological Sciences, Bangalore 560065, India
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Arjun Sivasundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
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Krehenwinkel H, Wolf M, Lim JY, Rominger AJ, Simison WB, Gillespie RG. Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding. Sci Rep 2017; 7:17668. [PMID: 29247210 PMCID: PMC5732254 DOI: 10.1038/s41598-017-17333-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.
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Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA.
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive, San Francisco, California, USA.
| | - Madeline Wolf
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Jun Ying Lim
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Andrew J Rominger
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Warren B Simison
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive, San Francisco, California, USA
| | - Rosemary G Gillespie
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
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Flanders J, Inoue-Murayama M, Rossiter SJ, Hill DA. Female philopatry and limited male-biased dispersal in the Ussuri tube-nosed bat, Murina ussuriensis. J Mammal 2016. [DOI: 10.1093/jmammal/gyv200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractMale-biased dispersal and female philopatry are common traits among social mammals, often leading to elevated relatedness within social groups. However, exceptions do occur, with documented cases of female-biased dispersal, dispersal by both sexes, and philopatry of both sexes. In this study, we examined levels of dispersal and relatedness based on analyses of the mitochondrial D-loop and 12 nuclear microsatellite markers in the woodland specialist Ussuri tube-nosed bat ( Murina ussuriensis ), a relatively widespread, yet locally rare species that is thought to be threatened by loss of its forest habitats across its range. A total of 85 individuals were captured in lowland temperate forest on the island of Yakushima and 28 individuals in montane forest in Hokkaido, Japan. In the former, haplotypes showed extreme spatial clustering among females consistent with strong philopatry, but spatial mixing among males suggesting dispersal over short distances. These findings were broadly supported by microsatellite analyses, which indicated considerable genealogical structure within sampling locations but a lack of spatial structure, again indicating that some gene flow does occur in one or both sexes. The Hokkaido data, although limited, did not show these patterns and instead suggest that differences in environmental and behavioral variables may influence movement ecology of individuals at these 2 sites and consequently fine-scale genetic structure within this species.
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Burns LE, Frasier TR, Broders HG. Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus). Ecol Evol 2014; 4:4130-49. [PMID: 25505539 PMCID: PMC4242565 DOI: 10.1002/ece3.1266] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 08/29/2014] [Accepted: 09/03/2014] [Indexed: 01/29/2023] Open
Abstract
Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of F ST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global F ST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation.
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Affiliation(s)
- Lynne E Burns
- Department of Biology, Dalhousie University, Life Sciences Centre 1355 Oxford Street, Halifax, Nova Scotia, B3H 4J1, Canada
| | - Timothy R Frasier
- Department of Biology, Saint Mary's University 923 Robie Street, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Hugh G Broders
- Department of Biology, Saint Mary's University 923 Robie Street, Halifax, Nova Scotia, B3H 3C3, Canada
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Dong J, Mao X, Sun H, Irwin DM, Zhang S, Hua P. Introgression of mitochondrial DNA promoted by natural selection in the Japanese pipistrelle bat (Pipistrellus abramus). Genetica 2014; 142:483-94. [DOI: 10.1007/s10709-014-9794-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
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Odendaal LJ, Jacobs DS, Bishop JM. Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity. BMC Evol Biol 2014; 14:60. [PMID: 24674227 PMCID: PMC3986686 DOI: 10.1186/1471-2148-14-60] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/20/2014] [Indexed: 02/04/2023] Open
Abstract
Background Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of ‘adaptive differentiation with minimal gene flow’ in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats. Results Our analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations. Conclusions Our study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments.
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Affiliation(s)
- Lizelle J Odendaal
- Department of Biological Sciences, University of Cape Town, 7701 Cape Town, South Africa.
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Lu G, Lin A, Luo J, Blondel DV, Meiklejohn KA, Sun K, Feng J. Phylogeography of the Rickett's big-footed bat, Myotis pilosus (Chiroptera: Vespertilionidae): a novel pattern of genetic structure of bats in China. BMC Evol Biol 2013; 13:241. [PMID: 24188176 PMCID: PMC4228257 DOI: 10.1186/1471-2148-13-241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 10/29/2013] [Indexed: 12/03/2022] Open
Abstract
Background China is characterized by complex topographic structure and dramatic palaeoclimatic changes, making species biogeography studies particularly interesting. Previous researchers have also demonstrated multiple species experienced complex population histories, meanwhile multiple shelters existed in Chinese mainland. Despite this, species phylogeography is still largely unexplored. In the present study, we used a combination of microsatellites and mitochondrial DNA (mtDNA) to investigate the phylogeography of the east Asian fish-eating bat (Myotis pilosus). Results Phylogenetic analyses showed that M. pilosus comprised three main lineages: A, B and C, which corresponded to distinct geographic populations of the Yangtze Plain (YTP), Sichuan Basin (SCB) and North and South of China (NSC), respectively. The most recent common ancestor of M. pilosus was dated as 0.25 million years before present (BP). Population expansion events were inferred for populations of Clade C, North China Plain region, Clade B and YunGui Plateau region at 38,700, 15,900, 4,520 and 4,520 years BP, respectively. Conflicting results were obtained from mtDNA and microsatellite analyses; strong population genetic structure was obtained from mtDNA data but not microsatellite data. The microsatellite data indicated that genetic subdivision fits an isolation-by-distance (IBD) model, but the mtDNA data failed to support this model. Conclusions Our results suggested that Pleistocene climatic oscillations might have had a profound influence on the demographic history of M. pilosus. Spatial genetic structures of maternal lineages that are different from those observed in other sympatric bats species may be as a result of interactions among special population history and local environmental factors. There are at least three possible refugia for M. pilosus during glacial episodes. Apparently contradictory genetic structure patterns of mtDNA and microsatellite could be explained by male-mediated gene flow among populations. This study also provides insights on the necessity of conservation of M. pilosus populations to conserve this genetic biodiversity, especially in the areas of YTP, SCB and NSC regions.
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Affiliation(s)
| | | | | | | | | | - Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China.
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Mondol S, Bruford MW, Ramakrishnan U. Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc Biol Sci 2013; 280:20130496. [PMID: 23677341 PMCID: PMC3673047 DOI: 10.1098/rspb.2013.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/23/2013] [Indexed: 11/12/2022] Open
Abstract
India is home to approximately 60 per cent of the world's remaining wild tigers, a species that has declined in the last few centuries to occupy less than 7 per cent of its former geographical range. While Indian tiger numbers have somewhat stabilized in recent years, they remain low and populations are highly fragmented. Therefore, the application of evidence-based demographic and genetic management to enhance the remaining populations is a priority. In this context, and using genetic data from historical and modern tigers, we investigated anthropogenic impacts on genetic variation in Indian tigers using mitochondrial and nuclear genetic markers. We found a very high number of historical mitochondrial DNA variants, 93 per cent of which are not detected in modern populations. Population differentiation was higher in modern tigers. Simulations incorporating historical data support population decline, and suggest high population structure in extant populations. Decreased connectivity and habitat loss as a result of ongoing fragmentation in the Indian subcontinent has therefore resulted in a loss of genetic variants and increased genetic differentiation among tiger populations. These results highlight that anthropogenic fragmentation and species-specific demographic processes can interact to alter the partitioning of genetic variation over very short time scales. We conclude that ongoing strategies to maximize the size of some tiger populations, at the expense of losing others, is an inadequate conservation strategy, as it could result in a loss of genetic diversity that may be of adaptive significance for this emblematic species.
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Affiliation(s)
- Samrat Mondol
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | | | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
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Hua P, Zhang L, Guo T, Flanders J, Zhang S. Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats. PLoS One 2013; 8:e54428. [PMID: 23349888 PMCID: PMC3548791 DOI: 10.1371/journal.pone.0054428] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/11/2012] [Indexed: 11/28/2022] Open
Abstract
Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus) is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST) estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST) values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.
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Affiliation(s)
- Panyu Hua
- Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, China
| | - Libiao Zhang
- Guangdong Entomological Institute, Guangzhou, China
| | - Tingting Guo
- Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Jon Flanders
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Shuyi Zhang
- Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
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Moussy C, Hosken D, Mathews F, Smith G, Aegerter J, Bearhop S. Migration and dispersal patterns of bats and their influence on genetic structure. Mamm Rev 2012. [DOI: 10.1111/j.1365-2907.2012.00218.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline Moussy
- Centre for Ecology and Conservation; University of Exeter; Tremough Campus, Penryn; Cornwall; TR10 9EZ; UK
| | - D.J. Hosken
- Centre for Ecology and Conservation; University of Exeter; Tremough Campus, Penryn; Cornwall; TR10 9EZ; UK
| | - F. Mathews
- University of Exeter, Hatherly Laboratories; Prince of Wales Road; Exeter; EX4 4PS; UK
| | - G.C. Smith
- The Food and Environment Research Agency; Sand Hutton; York; YO41 1LZ; UK
| | - J.N. Aegerter
- The Food and Environment Research Agency; Sand Hutton; York; YO41 1LZ; UK
| | - S. Bearhop
- Centre for Ecology and Conservation; University of Exeter; Tremough Campus, Penryn; Cornwall; TR10 9EZ; UK
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Mitochondrial DNA paradox: sex-specific genetic structure in a marine mussel--despite maternal inheritance and passive dispersal. BMC Genet 2012; 13:45. [PMID: 22694765 PMCID: PMC3465189 DOI: 10.1186/1471-2156-13-45] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/13/2012] [Indexed: 12/29/2022] Open
Abstract
Background When genetic structure is identified using mitochondrial DNA (mtDNA), but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. Results We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species) and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. Conclusions This is the first study to report sex-specific differences in genetic structure based on matrilineally-inherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single generation.
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Sun YH, Monagin C, Liu XS, Chen JP. A Test for Sex-Biased Dispersal inCynopterus sphinx: Inferences from Microsatellite Markers and Mitochondrial DNA. ACTA CHIROPTEROLOGICA 2012. [DOI: 10.3161/150811012x654240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yannic G, Basset P, Büchi L, Hausser J, Broquet T. SCALE-SPECIFIC SEX-BIASED DISPERSAL IN THE VALAIS SHREW UNVEILED BY GENETIC VARIATION ON THE Y CHROMOSOME, AUTOSOMES, AND MITOCHONDRIAL DNA. Evolution 2012; 66:1737-50. [DOI: 10.1111/j.1558-5646.2011.01554.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dixon MD. Population genetic structure and natal philopatry in the widespread North American batMyotis lucifugus. J Mammal 2011. [DOI: 10.1644/10-mamm-a-426.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Turmelle AS, Kunz TH, Sorenson MD. A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat. Mol Ecol 2010; 20:357-75. [PMID: 21143331 DOI: 10.1111/j.1365-294x.2010.04947.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
One of the most widely distributed bats in the New World, the big brown bat (Eptesicus fuscus) exhibits well-documented geographic variation in morphology and life history traits, suggesting the potential for significant phylogeographic structure as well as adaptive differentiation among populations. In a pattern broadly consistent with morphologically defined subspecies, we found deeply divergent mitochondrial lineages restricted to different geographic regions. In contrast, sequence data from two nuclear loci suggest a general lack of regional genetic structure except for peripheral populations in the Caribbean and Mexico/South America. Coalescent analyses suggest that the striking difference in population structure between genomes cannot be attributed solely to different rates of lineage sorting, but is likely due to male-mediated gene flow homogenizing nuclear genetic diversity across most of the continental range. Despite this ongoing gene flow, selection has apparently been effective in producing and maintaining adaptive differentiation among populations, while strong female site fidelity, maintained over the course of millions of years, has produced remarkably deep divergence among geographically isolated matrilines. Our results highlight the importance of evaluating multiple genetic markers for a more complete understanding of population structure and history.
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Affiliation(s)
- Amy S Turmelle
- Department of Biology, Boston University, Boston, MA 02215, USA.
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Mukherjee S, Krishnan A, Tamma K, Home C, Navya R, Joseph S, Das A, Ramakrishnan U. Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India. PLoS One 2010; 5:e13724. [PMID: 21060831 PMCID: PMC2966403 DOI: 10.1371/journal.pone.0013724] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 09/28/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. METHODOLOGY/PRINCIPAL FINDINGS We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F(ST) of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. CONCLUSIONS/SIGNIFICANCE Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.
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Affiliation(s)
- Shomita Mukherjee
- National Centre for Biological Sciences, Bangalore, Karnataka, India.
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WEI LI, FLANDERS JONR, ROSSITER STEPHENJ, MILLER-BUTTERWORTH CASSANDRAM, ZHANG LIB, ZHANG SHUYIY. Phylogeography of the Japanese pipistrelle bat, Pipistrellus abramus, in China: the impact of ancient and recent events on population genetic structure. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01387.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chen SF, Jones G, Rossiter SJ. Determinants of echolocation call frequency variation in the Formosan lesser horseshoe bat (Rhinolophus monoceros). Proc Biol Sci 2009; 276:3901-9. [PMID: 19692399 PMCID: PMC2817295 DOI: 10.1098/rspb.2009.1185] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 07/29/2009] [Indexed: 11/12/2022] Open
Abstract
The origin and maintenance of intraspecific variation in vocal signals is important for population divergence and speciation. Where vocalizations are transmitted by vertical cultural inheritance, similarity will reflect co-ancestry, and thus vocal divergence should reflect genetic structure. Horseshoe bats are characterized by echolocation calls dominated by a constant frequency component that is partly determined by maternal imprinting. Although previous studies showed that constant frequency calls are also influenced by some non-genetic factors, it is not known how frequency relates to genetic structure. To test this, we related constant frequency variation to genetic and non-genetic variables in the Formosan lesser horseshoe bat (Rhinolophus monoceros). Recordings of bats from across Taiwan revealed that females called at higher frequencies than males; however, we found no effect of environmental or morphological factors on call frequency. By comparison, variation showed clear population structure, with frequencies lower in the centre and east, and higher in the north and south. Within these regions, frequency divergence was directional and correlated with geographical distance, suggesting that call frequencies are subject to cultural drift. However, microsatellite clustering analysis showed that broad differences in constant frequency among populations corresponded to discontinuities in allele frequencies resulting from vicariant events. Our results provide evidence that the processes shaping genetic subdivision have concomitant consequences for divergence in echolocation call frequency.
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Affiliation(s)
- Shiang-Fan Chen
- School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
- Conservation and Research Center, Taipei Zoo, Taipei 11656, Taiwan, Republic of China
| | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
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Why the Indian subcontinent holds the key to global tiger recovery. PLoS Genet 2009; 5:e1000585. [PMID: 19680439 PMCID: PMC2716534 DOI: 10.1371/journal.pgen.1000585] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 07/02/2009] [Indexed: 11/29/2022] Open
Abstract
With only ∼3,000 wild individuals surviving restricted to just 7% of their historical range, tigers are now a globally threatened species. Therefore, conservation efforts must prioritize regions that harbor more tigers, as well try to capture most of the remaining genetic variation and habitat diversity. Only such prioritization based on demographic, genetic, and ecological considerations can ensure species recovery and retention of evolutionary flexibility in the face of ongoing global changes. Although scientific understanding of ecological and demographic aspects of extant wild tiger populations has improved recently, little is known about their genetic composition and variability. We sampled 73 individual tigers from 28 reserves spread across a diversity of habitats in the Indian subcontinent to obtain 1,263 bp of mitochondrial DNA and 10 microsatellite loci. Our analyses reveals that Indian tigers retain more than half of the extant genetic diversity in the species. Coalescent simulations attribute this high genetic diversity to a historically large population size of about 58,200 tigers for peninsular India south of the Gangetic plains. Furthermore, our analyses indicate a precipitous, possibly human-induced population crash ∼200 years ago in India, which is in concordance with historical records. Our results suggest that only 1.7% (with an upper limit of 13% and a lower limit of 0.2%) of tiger numbers in historical times remain now. In the global conservation context our results suggest that, based on genetic, demographic, and ecological considerations, the Indian subcontinent holds the key to global survival and recovery of wild tigers. Tiger range and numbers have collapsed globally despite substantial conservation efforts. Genetic data quantifying variation from 73 wild tigers in 28 reserves in the Indian subcontinent suggests historically high numbers for tigers, and simulations reveal a signature of a 200-year-old, possibly human-induced decline. Simulations suggest that only 1.7% of historical tiger numbers now persist in peninsular Indian. Our data also reveal that tigers of the Indian subcontinent retain most of the species' genetic diversity, besides this region harbouring maximum diversity of tiger habitats. Overall, the Indian subcontinent appears to be a global hotspot holding the key to any future recovery of wild tigers from both an ecological and genetic perspective.
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Herreman JK, Blundell GM, McDonald DB, Ben-David M. Asymmetrical male-mediated gene flow between harbor seal (Phoca vitulina) populations in Alaska. CAN J ZOOL 2009. [DOI: 10.1139/z09-033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Harbor seals ( Phoca vitulina richardii (Gray, 1864)) in Alaska are currently treated as three distinct management stocks. Previous genetic analyses using mitochondrial DNA suggested that these stocks are differentiated genetically. We studied populations in Glacier Bay (GB; Southeast Alaska Stock), where harbor seals are declining, and Prince William Sound (PWS; Gulf of Alaska Stock), where the population has recently stabilized. Using six pairs of hypervariable microsatellite primers, we determined that these populations are a single panmictic unit with estimated migration rates of 22 animals/generation (PWS to GB) and 63 animals/generation (GB to PWS). The asymmetrical gene flow between GB and PWS is likely driven in part by a recent increase in competitors and predators of seals in GB. In contrast with males, emigration of females from PWS to GB (8.3 seals/generation) is higher than emigration of females from GB to PWS (3.3 seals/generation), likely because females use glacial ice as pupping habitat. Despite the high gene flow, the number of migrants per year (0.02% of the Gulf of Alaska population) is likely too low to influence the demographics of harbor seals in PWS, and the two populations may best be managed as separate stocks.
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Affiliation(s)
- J. K. Herreman
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
| | - G. M. Blundell
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
| | - D. B. McDonald
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
| | - M. Ben-David
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
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Floyd CH, Flores-Martínez JJ, Herrera M. LG, Mejía O, May B. Conserving the endangered Mexican fishing bat (Myotis vivesi): genetic variation indicates extensive gene flow among islands in the Gulf of California. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9902-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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