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Garrido-Bautista J, Comas M, Jowers MJ, Smith S, Penn DJ, Bakkali M, Moreno-Rueda G. Fine-scale genetic structure and phenotypic divergence of a passerine bird population inhabiting a continuous Mediterranean woodland. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240601. [PMID: 39253402 PMCID: PMC11382889 DOI: 10.1098/rsos.240601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 09/11/2024]
Abstract
Genetic differentiation between populations inhabiting ecologically different habitats might appear because of limited dispersal and gene flow, which may lead to patterns of phenotypic divergence and local adaptation. In this study, we use dispersal, genotypic (24 microsatellite loci) and phenotypic (body size and clutch size) data to analyse patterns of genetic structuring and phenotypic divergence in a blue tit (Cyanistes caeruleus) population inhabiting a continuous and heterogeneous woodland along a valley. The two slopes of the valley differ in their forest formations and environmental conditions. Findings showed that most blue tits reproduced within their natal slope. Accordingly, microsatellite analyses revealed that populations of blue tits established in the two slopes show subtle genetic differentiation. The two genetic populations diverged in clutch size, exceeding the level of differentiation expected based on genetic drift, hence suggesting divergent selection (or other processes promoting divergence) on this life-history trait. Our findings reveal that restricted dispersal and spatial heterogeneity may lead to genetic differentiation among bird populations at a surprisingly small scale. In this respect, it is worth highlighting that such differentiation occurs for an organism with high dispersal capacity and within a continuous woodland. Moreover, we show that small-scale ecological differences, together with limited gene flow, can result in selection favouring different phenotypes even within the same continuum population.
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Affiliation(s)
| | - Mar Comas
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Michael J Jowers
- Department of Zoology, University of Granada, Granada 18071, Spain
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Dustin J Penn
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Mohammed Bakkali
- Department of Genetics, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - Gregorio Moreno-Rueda
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
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2
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Joshi BD, Kumar V, De R, Sharma R, Bhattacharya A, Dolker S, Pal R, Kumar VP, Sathyakumar S, Adhikari BS, Habib B, Goyal SP. Mitochondrial cytochrome b indicates the presence of two paraphyletic diverged lineages of the blue sheep Pseudois nayaur across the Indian Himalaya: conservation implications. Mol Biol Rep 2022; 49:11177-11186. [PMID: 36097126 DOI: 10.1007/s11033-022-07832-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Populations exhibit signatures of local adaptive traits due to spatial and environmental heterogeneity resulting in microevolution. The blue sheep is widely distributed across the high Asian mountains and are the snow leopard's principal prey species. These mountains differ in their evolutionary history due to differential glaciation and deglaciation periods, orography, and rainfall patterns, and such factors causes diversification in species. METHODS AND RESULTS Therefore, we assess the phylogeographic status of blue sheep using the mitochondrial cytochrome b gene (220 bp) across the Indian Himalayan region (IHR) and its relationship with other populations. Of the observed five haplotypes, two and three were from the western Himalayas (WH) and eastern Himalayas (EH) respectively. One of the haplotypes from WH was shared with the population of Pamir plateau, suggesting historical maternal connectivity between these areas. The phylogenetic analyses split the blue sheep into two paraphyletic clades, and western and eastern populations of IHR were within the Pamir and Tibetan plateau clades, respectively. We observed a relatively higher mean sequence divergence in the EH population than in the WH. CONCLUSION We propose five 'Evolutionary Significant Units' across the blue sheep distribution range based on observed variation in the species' ecological requirements, orography, climatic conditions, and maternal lineages, viz.; Western Himalaya-Pamir plateau (WHPP); Eastern Himalaya-Tibetan plateau (EHTP); Qilian mountains; Helan mountains and Hengduan mountains population. Despite the small sample size, population divergence was observed across the IHR, therefore, we suggest a transboundary, collaborative study on comparative morphology, anatomy, ecology, behaviour, and population genetics using harmonized different genetic markers for identifying the overall taxonomic status of the blue sheep across its range for planning effective conservation strategies.
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Affiliation(s)
- Bheem Dutt Joshi
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India.,Zoological Survey of India, 700020, Kolkata, India.,ENPROTEC INDIA FOUNDATION, 222161, Lucknow, Uttar Pradesh, India
| | - Vinay Kumar
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | - Rahul De
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | - Reeta Sharma
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | | | | | - Ranjana Pal
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | | | | | | | - Bilal Habib
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India.
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3
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Sylvain FÉ, Normandeau E, Holland A, Luis Val A, Derome N. Genomics of Serrasalmidae teleosts through the lens of microbiome fingerprinting. Mol Ecol 2022; 31:4656-4671. [PMID: 35729748 DOI: 10.1111/mec.16574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Associations between host genotype and host-associated microbiomes have been shown in a variety of animal clades, but studies on teleosts mostly show weak associations. Our study aimed to explore these relationships in four sympatric Serrasalmidae (i.e. piranha) teleosts from an Amazonian lake, using datasets from the hosts genomes (SNPs from GBS), skin and gut microbiomes (16S rRNA gene metataxonomics), and diets (COI metabarcoding) from the same fish individuals. Firstly, we investigated whether there were significant covariations of microbiome and fish genotypes at the inter and intraspecific levels. We also assessed the extent of co-variation between Serrasalmidae diet and microbiome, to isolate genotypic from dietary effects on community structure. We observed a significant covariation of skin microbiomes and host genotypes at interspecific (R2 =24.4%) and intraspecific (R2 =6.2%) levels, whereas gut microbiomes correlated poorly with host genotypes. Serrasalmidae diet composition was significantly correlated to fish genotype only at the interspecific level (R2 =5.4%), but did not covary with gut microbiome composition (mantel R=-0.04). Secondly, we investigated whether the study of interspecific differentiation could benefit from considering host associated microbial communities in addition to host genotypes. By using a NMDS ordination-based approach, we observed that ordinations from skin and gut species-specific bacterial biomarkers identified through a random forest algorithm, could significantly increase the average interspecific differentiation detected through host genotype data alone. Although future studies encompassing additional species and environments are needed, our results suggest Serrasalmidae microbiomes could constitute an insightful trait to be considered when studying the interspecific differences between members of this clade.
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Affiliation(s)
- François-Étienne Sylvain
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Albury/Wodonga Campus, Vic, Australia
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, AM, 69067-375, Brazil
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
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Onley IR, Moseby KE, Austin JJ, Sherratt E. Morphological variation in skull shape and size across extinct and extant populations of the greater stick-nest rat (Leporillus conditor): implications for translocation. AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am21047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Jabłońska A, Navarro N, Laffont R, Wattier R, Pešić V, Zawal A, Vukić J, Grabowski M. An integrative approach challenges species hypotheses and provides hints for evolutionary history of two Mediterranean freshwater palaemonid shrimps (Decapoda: Caridea). THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1953624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- A. Jabłońska
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - N. Navarro
- EPHE, PSL University, Paris, France
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - R. Laffont
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - R. Wattier
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - V. Pešić
- Department of Biology, University of Montenegro, Podgorica, Montenegro
| | - A. Zawal
- Department of Invertebrate Zoology and Limnology, Center of Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland
| | - J. Vukić
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - M. Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
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Perrin A, Khimoun A, Faivre B, Ollivier A, de Pracontal N, Théron F, Loubon M, Leblond G, Duron O, Garnier S. Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species. Heredity (Edinb) 2021; 126:148-162. [PMID: 32934360 PMCID: PMC7853120 DOI: 10.1038/s41437-020-00366-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 01/11/2023] Open
Abstract
Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.
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Affiliation(s)
- Antoine Perrin
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France.
| | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Nyls de Pracontal
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Franck Théron
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Maxime Loubon
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Gilles Leblond
- SARL BIOS, Route de Davidon, Duzer, 97115, Sainte-Rose, France
| | - Olivier Duron
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
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Engler JO, Sacher T, Coppack T, Bairlein F. Assortative mating frames establishment in a young island bird population. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190050. [PMID: 31598228 PMCID: PMC6731715 DOI: 10.1098/rsos.190050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Successful island colonizations are key events to understand range dynamic processes, but studying a young population right after it reaches establishment is a rare opportunity in natural systems. The genetic structure of a recently established population may offer unique insights into its colonization history and demographic processes that are important for a successful colonization. Here, we studied the population genetics of a recently established island population of Eurasian blackbirds (Aves: Turdus merula) located on the island of Heligoland in the German North Sea. Using microsatellites, we genotyped the majority of the island population, including the nestlings, over a 4-year period between 2004 and 2007. We also genotyped high numbers of migrants on stopover and mainland individuals, as they are potential founders of the island population. We identified two genetic clusters that comply with the migrating and mainland birds. While most of the island birds belong to the mainland cluster, some breeding individuals and a low fraction of the offspring belong to the genetic cluster found in migrating individuals with almost no admixture between the two, pointing to assortative mating acting on the island population. We did not find any evidence for founder events and detected deviations from the Hardy-Weinberg equilibrium that disappeared in cohorts of older age that coincide with a lower number of siblings in older cohorts. The observed genetic patterns unravel a complex colonization history to which migratory and mainland birds have contributed and which is characterized by assortative mating. Further research will be directed towards habitat selection and phenotypic differences as potential drivers of assortative mating in this island population.
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Affiliation(s)
- Jan O. Engler
- Department of Biology, Terrestrial Ecology Unit, Ghent University, 9000 Ghent, Belgium
| | - Thomas Sacher
- Institute of Avian Research, Vogelwarte Helgoland, 26386 Wilhelmshaven, Germany
| | - Timothy Coppack
- Institute of Avian Research, Vogelwarte Helgoland, 26386 Wilhelmshaven, Germany
| | - Franz Bairlein
- Institute of Avian Research, Vogelwarte Helgoland, 26386 Wilhelmshaven, Germany
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8
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Basiita RK, Zenger KR, Mwanja MT, Jerry DR. Gene flow and genetic structure in Nile perch, Lates niloticus, from African freshwater rivers and lakes. PLoS One 2018; 13:e0200001. [PMID: 29995906 PMCID: PMC6040733 DOI: 10.1371/journal.pone.0200001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/18/2018] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Geological evolution of the African continent has been subject to complex processes including uplift, volcanism, desert formation and tectonic rifting. This complex geology has created substantial biogeographical barriers, and coupled with anthropogenic introductions of freshwater fishes, has influenced the genetic diversity, connectivity and sub-structuring of the teleost fauna. Nile perch, Lates niloticus, is an iconic fish in Africa and is of high commercial importance, both in the species' native range and where it has been translocated. However, the species is in decline and there is a need to understand its population genetic structure to facilitate sustainable management of the fishery and aquaculture development. METHODOLOGY Nile perch tissue samples were acquired from two West and four East (Lakes; Albert, Kyoga, Victoria and Turkana) African locations. Nineteen polymorphic microsatellite loci were used to study the genetic variation among populations across regions (West and East Africa), as well as between native and introduced environments within East Africa. PRINCIPAL FINDINGS AND THEIR SIGNIFICANCE Results revealed strong and significant genetic structuring among populations across the sampled distribution (divergence across regions, FCT = 0.26, P = 0.000). STRUCTURE analysis at a broad scale revealed K = 2 clusters, the West African individuals were assigned to one cluster, while all individuals from the East African region, regardless of whether native or introduced, were assigned to another cluster. The distinct genetic clusters identified in the current study between the West and East African Nile perch, appear to have been maintained by presence of biogeographic barriers and restricted gene flow between the two regions. Therefore, any translocations of Nile perch should be carefully considered across the regions of West and East Africa. Further analysis at a regional scale revealed further structuring of up to K = 3 genetic clusters in East African Nile perch. Significantly (P < 0.05) lower genetic diversity based on analysis of allelic richness (AR) was obtained for the two translocated populations of Lake Kyoga (AR = 3.61) and Lake Victoria (AR = 3.52), compared to Nile perch populations from their putative origins of Lakes Albert (AR = 4.12) and Turkana (AR = 4.43). The lower genetic diversity in the translocated populations may be an indication of previous bottlenecks and may also indicate a difficulty for these populations to persist and adapt to climatic changes and anthropogenic pressures that are currently present in the East African region.
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Affiliation(s)
- Rose K. Basiita
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- National Agricultural Research Organization, National Fisheries Resources Research Institute, Aquaculture Research and Development Center Kajjansi, Kampala, Uganda
- WorldFish Zambia Office, Ridgeway Lusaka, Zambia
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Matthew T Mwanja
- National Agricultural Research Organization, National Fisheries Resources Research Institute, Aquaculture Research and Development Center Kajjansi, Kampala, Uganda
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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Kristensen NP, Johansson J, Chisholm RA, Smith HG, Kokko H. Carryover effects from natal habitat type upon competitive ability lead to trait divergence or source-sink dynamics. Ecol Lett 2018; 21:1341-1352. [PMID: 29938889 DOI: 10.1111/ele.13100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/27/2018] [Accepted: 05/16/2018] [Indexed: 01/26/2023]
Abstract
Local adaptation to rare habitats is difficult due to gene flow, but can occur if the habitat has higher productivity. Differences in offspring phenotypes have attracted little attention in this context. We model a scenario where the rarer habitat improves offspring's later competitive ability - a carryover effect that operates on top of local adaptation to one or the other habitat type. Assuming localised dispersal, so the offspring tend to settle in similar habitat to the natal type, the superior competitive ability of offspring remaining in the rarer habitat hampers immigration from the majority habitat. This initiates a positive feedback between local adaptation and trait divergence, which can thereafter be reinforced by coevolution with dispersal traits that match ecotype to habitat type. Rarity strengthens selection on dispersal traits and promotes linkage disequilibrium between locally adapted traits and ecotype-habitat matching dispersal. We propose that carryover effects may initiate isolation by ecology.
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Affiliation(s)
| | | | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
| | - Henrik G Smith
- Department of Biology, Lund University, Lund, Sweden.,Centre of Environmental and Climate Research, Lund University, Lund, Sweden
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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10
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Dohms KM, Graham BA, Burg TM. Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine ( Perisoreus canadensis). Ecol Evol 2017; 7:9869-9889. [PMID: 29238522 PMCID: PMC5723591 DOI: 10.1002/ece3.3478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/08/2017] [Accepted: 08/19/2017] [Indexed: 11/29/2022] Open
Abstract
An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.
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Affiliation(s)
- Kimberly M Dohms
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada.,Present address: Canadian Wildlife Service, Environment and Climate Change Canada Delta BC Canada
| | - Brendan A Graham
- Department of Biological Sciences University of Windsor Windsor ON Canada
| | - Theresa M Burg
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada
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Khimoun A, Peterman W, Eraud C, Faivre B, Navarro N, Garnier S. Landscape genetic analyses reveal fine-scale effects of forest fragmentation in an insular tropical bird. Mol Ecol 2017; 26:4906-4919. [DOI: 10.1111/mec.14233] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Aurélie Khimoun
- CNRS; Biogéosciences UMR6282; Université Bourgogne Franche-Comté; Dijon France
| | - William Peterman
- School of Environment and Natural Resources; The Ohio State University; Columbus OH USA
| | - Cyril Eraud
- CNERA Avifaune Migratrice; Office National de la Chasse et de la Faune Sauvage; Villiers en Bois France
| | - Bruno Faivre
- CNRS; Biogéosciences UMR6282; Université Bourgogne Franche-Comté; Dijon France
| | - Nicolas Navarro
- CNRS; Biogéosciences UMR6282; Université Bourgogne Franche-Comté; Dijon France
- EPHE; PSL Research University Paris; Dijon France
| | - Stéphane Garnier
- CNRS; Biogéosciences UMR6282; Université Bourgogne Franche-Comté; Dijon France
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12
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Khimoun A, Ollivier A, Faivre B, Garnier S. Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs. Mol Ecol Resour 2017; 17:893-903. [PMID: 27978606 DOI: 10.1111/1755-0998.12642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/26/2016] [Accepted: 12/06/2016] [Indexed: 12/12/2022]
Abstract
Microsatellites, also called simple sequence repeats (SSRs), are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers, and highly conserved SSRs have recently been developed from expressed sequence tags (EST) to improve SSR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multispecies approach on passerine birds. We tested whether patterns and levels of genetic diversity within and between populations assessed from EST- and from genomic SSRs are congruent, and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.
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Affiliation(s)
- Aurélie Khimoun
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Stéphane Garnier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
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Khimoun A, Eraud C, Ollivier A, Arnoux E, Rocheteau V, Bely M, Lefol E, Delpuech M, Carpentier ML, Leblond G, Levesque A, Charbonnel A, Faivre B, Garnier S. Habitat specialization predicts genetic response to fragmentation in tropical birds. Mol Ecol 2016; 25:3831-44. [PMID: 27314987 DOI: 10.1111/mec.13733] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 01/19/2023]
Abstract
Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species-specific population structure are rare. Here, we used a comparative approach on eight bird species, co-occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology.
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Affiliation(s)
- Aurélie Khimoun
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Cyril Eraud
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Anthony Ollivier
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Emilie Arnoux
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Vincent Rocheteau
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Marine Bely
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Emilie Lefol
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Martin Delpuech
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Marie-Laure Carpentier
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Gilles Leblond
- SARL BIOS, 168 rue de Brindeau, 97190, Le Gosier, France
| | - Anthony Levesque
- Office National de la Chasse et de la Faune Sauvage, Cellule Technique des Antilles Françaises, Chemin de Boyer, Section Boisbert, 97129, Le Lamentin, France
| | - Anaïs Charbonnel
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Bruno Faivre
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Stéphane Garnier
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
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14
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Camacho C, Sáez P, Sánchez S, Palacios S, Molina C, Potti J. The road to opportunities: landscape change promotes body-size divergence in a highly mobile species. Curr Zool 2016; 62:7-14. [PMID: 29491885 PMCID: PMC5804134 DOI: 10.1093/cz/zov008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/23/2015] [Indexed: 11/16/2022] Open
Abstract
Landscape change provides a suitable framework for investigating population-level responses to novel ecological pressures. However, relatively little attention has been paid to examine the potential influence of landscape change on the geographic scale of population differentiation. Here, we tested for morphological differentiation of red-necked nightjars Caprimulgus ruficollis breeding in a managed property and a natural reserve situated less than 10 km apart. At both sites, we also estimated site fidelity over 5 years and quantified the potential foraging opportunities for nightjars. Breeding birds in the managed habitat were significantly larger in size—as indexed by keel length—than those in the natural one. However, there were no significant differences in wing or tail length. Immigration from neighboring areas was almost negligible and, furthermore, no individual (out of 1130 captures overall) exchanged habitats between years, indicating strong site fidelity. Food supply for nightjars was equally abundant in both habitats, but the availability of foraging sites was remarkably higher in the managed property. As a result, nightjars—particularly fledglings—in the latter habitat benefited from increased foraging opportunities in relation to those in the natural site. It seems likely that the fine-scale variation in nightjar morphology reflects a phenotypic response to unequal local conditions, since non-random dispersal or differential mortality had been determined not to be influential. High site fidelity appears to contribute to the maintenance of body-size differences between the two habitats. Results from this nightjar population highlight the potential of human-induced landscape change to promote population-level responses at exceedingly small geographic scales.
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Affiliation(s)
- Carlos Camacho
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain
| | - Pedro Sáez
- Department of Environmental Biology and Public Health. University of Huelva. Av. Andalucía, 21071 Huelva, Spain
| | - Sonia Sánchez
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain
| | - Sebastián Palacios
- Department of Conservation Biology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain, and
| | - Carlos Molina
- Sociedad Española de Ornitología. Centro Ornitológico Francisco Bernis. Paseo Marismeño sn, 21750 Huelva, Spain
| | - Jaime Potti
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain
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15
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Khimoun A, Arnoux E, Martel G, Pot A, Eraud C, Condé B, Loubon M, Théron F, Covas R, Faivre B, Garnier S. Contrasted patterns of genetic differentiation across eight bird species in the Lesser Antilles. Genetica 2016; 144:125-38. [PMID: 26797853 DOI: 10.1007/s10709-016-9883-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 11/26/2022]
Abstract
Archipelagoes are considered as "natural laboratories" for studying processes that shape the distribution of diversity. The Lesser Antilles provide a favorable geographical context for divergence to occur. However, although morphological subspecies have been described across this archipelago in numerous avian species, the potential for the Lesser Antilles in driving intra-specific genetic divergence in highly mobile organisms such as birds remains understudied. Here, we assessed level of intra-specific genetic diversity and differentiation between three islands of the Lesser Antilles (Guadeloupe, Dominica and Martinique) using a multi-species approach on eight bird species. For each species, we built a set of microsatellite markers from cross-species amplifications. Significant patterns of inter-island and/or within-island genetic differentiation were detected in all species. However, levels of intra-specific genetic differentiation among the eight bird species were not always consistent with the boundaries of subspecies previously described in the sampled islands. These results suggest different histories of colonization/expansion and/or different species-specific ecological traits affecting gene flow, advocating for multi-species studies of historical and contemporary factors shaping the distribution of diversity on islands.
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Affiliation(s)
- Aurélie Khimoun
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France.
| | - Emilie Arnoux
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Guillaume Martel
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Alexandre Pot
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Cyril Eraud
- CNERA Avifaune migratrice, Office National de la Chasse et de la Faune Sauvage, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Béatriz Condé
- Cellule Technique des Antilles Françaises, Office National de la Chasse et de la Faune Sauvage, 5 rue de la Dorade, 79229, Les Trois-Ilets, Martinique, France
| | - Maxime Loubon
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Franck Théron
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Rita Covas
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Bruno Faivre
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Stéphane Garnier
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
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16
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Price MR, Person C, Hayes WK. Geographic variation and genetic structure in the Bahama Oriole (Icterus northropi), a critically endangered synanthropic species. PeerJ 2015; 3:e1421. [PMID: 26644974 PMCID: PMC4671193 DOI: 10.7717/peerj.1421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/02/2015] [Indexed: 11/20/2022] Open
Abstract
Bird species may exhibit unexpected population structuring over small distances, with gene flow restricted by geographic features such as water or mountains. The Bahama Oriole (Icterus northropi) is a critically endangered, synanthropic island endemic with a declining population of fewer than 300 individuals. It now remains only on Andros Island (The Bahamas), which is riddled with waterways that past studies assumed did not hinder gene flow. We examined 1,858 base pairs of mitochondrial DNA sequenced from four gene regions in 14 birds (roughly 5% of the remaining population) found on the largest land masses of Andros Island (North Andros and Mangrove Cay/South Andros). We sought to discern genetic structuring between the remaining subpopulations and its relationship to current conservation concerns. Four unique haplotypes were identified, with only one shared between the two subpopulations. Nucleotide and haplotype diversity were higher for the North Andros subpopulation than for the Mangrove Cay/South Andros subpopulation. Analysis of molecular variance (AMOVA) yielded a Wright's fixation index (F st) of 0.60 (P Fst = 0.016), with 40.2% of the molecular variation explained by within-population differences and 59.8% by among-population differences. Based on the mitochondrial regions examined in this study, we suggest the extant subpopulations of Bahama Oriole exhibit significant population structuring over short distances, consistent with some other non-migratory tropical songbird species.
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Affiliation(s)
- Melissa R. Price
- Department of Natural Resources and Environmental Management, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Carl Person
- Department of Earth and Biological Sciences, Loma Linda University, Loma Linda, CA, United States
| | - William K. Hayes
- Department of Earth and Biological Sciences, Loma Linda University, Loma Linda, CA, United States
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Langin KM, Sillett TS, Funk WC, Morrison SA, Desrosiers MA, Ghalambor CK. Islands within an island: repeated adaptive divergence in a single population. Evolution 2015; 69:653-65. [PMID: 25645813 DOI: 10.1111/evo.12610] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/19/2015] [Indexed: 01/27/2023]
Abstract
Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially replicated patterns of phenotypic divergence within a bird species endemic to 250 km(2) Santa Cruz Island, California, USA. Island scrub-jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species' mainland congener. Variation in both bill measurements was heritable, and island scrub-jays mated nonrandomly with respect to bill morphology. The population was not panmictic; instead, we found a continuous pattern of isolation by distance across the east-west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. The ecological factors that appear to have facilitated adaptive differentiation at such a fine scale--environmental heterogeneity and localized dispersal--are ubiquitous in nature. These findings support recent arguments that microgeographic patterns of adaptive divergence may be more common than currently appreciated, even in mobile taxonomic groups like birds.
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Affiliation(s)
- Kathryn M Langin
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523; Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523; Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, 80526.
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