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Zhang H, Lundberg M, Tarka M, Hasselquist D, Hansson B. Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird. Genome Biol Evol 2023; 15:evad180. [PMID: 37793164 PMCID: PMC10627410 DOI: 10.1093/gbe/evad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.
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Affiliation(s)
- Hongkai Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | - Maja Tarka
- Department of Biology, Lund University, Lund, Sweden
| | | | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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2
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Hoffmann G, Mátrai N, Bakonyi G, Vili N, Gyurácz J, Lenczl M, Kisfali P, Stranczinger S, Magonyi NM, Mátics E, Mátics R. Contrasting mtDNA and microsatellite data of great reed warbler Acrocephalus arundinaceus breeding populations on a small geographic scale. Biol Futur 2022; 73:445-453. [PMID: 35904714 DOI: 10.1007/s42977-022-00127-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/11/2022] [Indexed: 01/10/2023]
Abstract
The great reed warbler has two genetically distinguishable haplogroups: "Clade A" occurs in higher proportions in Western Europe and Kazakhstan, and colonised Europe and Asia from a refugium in South-West Europe; and "Clade B", which is more common in Eastern Europe, and colonised parts of Europe from a refugium in the Middle East. Our aims were (i) to analyse the rate of differentiation in Hungarian breeding populations in order to see whether European-scale pattern is visible or not on as a small scale as the territory of Hungary and (ii) to compare the results obtained with mtDNA sequencing and microsatellite markers. To analyse the genetic differentiation, the mtDNA control region II was sequenced in 68 adult breeding birds, and 51 were fingerprinted at 11 microsatellite loci, while both analyses were performed on 36 birds (a total of 83 birds). The microsatellite data gave a better resolution and represented the fine-scale pattern of the suspected recolonisation. The lack of genetic differentiation among the breeding populations based on mitochondrial data seems to support this finding, because the admixture of the clades in this particular geographic region obliterates differentiation. Accordingly, the Fst values from different branches are significantly based on microsatellite data only. The mtDNA methods only give reliable results when a geographic and ecological factor plays a role in the population subdivision, but in the case of an intermixing population larger-scale studies are needed.
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Affiliation(s)
- Gyula Hoffmann
- Department of General Zoology and Developmental Biology, University of Pécs, Ifjúság u. 6, Hungary, 7601, Pécs
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
| | - Norbert Mátrai
- Department of Genetics, Hungarian Institute for Forensic Sciences, Mosonyi str. 9, Hungary, 1087, Budapest.
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka.
- Department of Zoology and Ecology, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Hungary, 2100, Gödöllő.
| | - Gábor Bakonyi
- Department of Zoology and Ecology, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Hungary, 2100, Gödöllő
| | - Nóra Vili
- Molecular Ecology Research Group, University of Veterinary Medicine, István str. 2, 1078, Budapest, Hungary
| | - József Gyurácz
- Department of Biology, Eötvös Loránd University, Savaria Campus, POB 170, Hungary, 9701, Szombathely
| | - Mihály Lenczl
- Institute of Isotopes CO., LTD, Konkoly Thege Miklós Rd. 29-33, Hungary, 1121, Budapest
| | - Péter Kisfali
- Department of Medical Genetics, University of Pécs, Szigeti Rd. 12, Hungary, 7624, Pécs
| | - Szilvia Stranczinger
- Department of Plant Biology, University of Pécs, Ifjúság Rd. 6, Hungary, 7624, Pécs
| | - Nóra Mária Magonyi
- Doctoral School of Biology and Sportbiology, University of Pécs, Ifjúság Rd. 6, Hungary, 7624, Pécs
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
| | - Erika Mátics
- Doctoral School of Biology and Sportbiology, University of Pécs, Ifjúság Rd. 6, Hungary, 7624, Pécs
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
| | - Róbert Mátics
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
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3
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Lombardo G, Migliore NR, Colombo G, Capodiferro MR, Formenti G, Caprioli M, Moroni E, Caporali L, Lancioni H, Secomandi S, Gallo GR, Costanzo A, Romano A, Garofalo M, Cereda C, Carelli V, Gillespie L, Liu Y, Kiat Y, Marzal A, López-Calderón C, Balbontín J, Mousseau TA, Matyjasiak P, Møller AP, Semino O, Ambrosini R, Alquati AB, Rubolini D, Ferretti L, Achilli A, Gianfranceschi L, Olivieri A, Torroni A. The Mitogenome Relationships and Phylogeography of Barn Swallows (Hirundo rustica). Mol Biol Evol 2022; 39:6591937. [PMID: 35617136 PMCID: PMC9174979 DOI: 10.1093/molbev/msac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The barn swallow (Hirundo rustica) poses a number of fascinating scientific questions, including the taxonomic status of postulated subspecies. Here we obtained and assessed the sequence variation of 411 complete mitogenomes, mainly from the European H. r. rustica, but other subspecies as well. In almost every case, we observed subspecies-specific haplogroups, which we employed together with estimated radiation times to postulate a model for the geographical and temporal worldwide spread of the species. The female barn swallow carrying the Hirundo rustica ancestral mitogenome left Africa (or its vicinity) around 280 thousand years ago (kya), and her descendants expanded first into Eurasia and then, at least 51 kya, into the Americas, from where a relatively recent (< 20 kya) back migration to Asia took place. The exception to the haplogroup subspecies specificity is represented by the sedentary Levantine H. r. transitiva that extensively shares haplogroup A with the migratory European H. r. rustica and, to a lesser extent, haplogroup B with the Egyptian H. r. savignii. Our data indicate that rustica and transitiva most likely derive from a sedentary Levantine population source that split at the end of the Younger Dryas (11.7 kya). Since then, however, transitiva received genetic inputs from and admixed with both the closely related rustica and the adjacent savignii. Demographic analyses confirm this species' strong link with climate fluctuations and human activities making it an excellent indicator for monitoring and assessing the impact of current global changes on wildlife.
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Affiliation(s)
- Gianluca Lombardo
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
| | - Manuela Caprioli
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Elisabetta Moroni
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Simona Secomandi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Guido Roberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alessandra Costanzo
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Romano
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Maria Garofalo
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy.,Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40139 Bologna, Italy
| | - Lauren Gillespie
- Department of Academic Education, Central Community College, Columbus, NE 68601, USA
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yosef Kiat
- Israeli Bird Ringing Center (IBRC), Israel Ornithological Center, Tel Aviv, Israel
| | - Alfonso Marzal
- Department of Zoology, University of Extremadura, 06071 Badajoz, Spain
| | - Cosme López-Calderón
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, 41092 Seville, Spain
| | - Javier Balbontín
- Department of Zoology, University of Seville, 41012 Seville, Spain
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Piotr Matyjasiak
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland
| | - Anders Pape Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Bonisoli Alquati
- Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA 91767, USA
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
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4
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Eberle J, Husemann M, Doerfler I, Ulrich W, Müller J, Bouget C, Brin A, Gossner MM, Heilmann-Clausen J, Isacsson G, Krištín A, Lachat T, Larrieu L, Rigling A, Schmidl J, Seibold S, Vandekerkhove K, Habel JC. Molecular biogeography of the fungus-dwelling saproxylic beetle Bolitophagus reticulatus indicates rapid expansion from glacial refugia. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The geographical distributions of species associated with European temperate broadleaf forests have been significantly influenced by glacial–interglacial cycles. During glacial periods, these species persisted in Mediterranean and extra-Mediterranean refugia and later, during interglacial periods, expanded northwards. The widespread saproxylic beetle Bolitophagus reticulatus depends closely on European temperate broadleaf forests. It usually develops in the tinder fungus Fomes fomentarius, a major decomposer of broadleaf-wood. We sampled B. reticulatus in sporocarps from European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis) across Europe and the Caucasus region. We analysed mitochondrial gene sequences (cox1, cox2, cob) and 17 microsatellites to reconstruct the geographical distribution of glacial refugia and postglacial recolonization pathways. We found only marginal genetic differentiation of B. reticulatus, except for a significant split between populations of the Caucasus region and Europe. This indicates the existence of past refugia south of the Great Caucasus, and a contact zone with European populations in the Crimean region. Further potential refugia might have been located at the foothills of the Pyrenees and in the Balkan region. Our genetic data suggest a phalanx-wise recolonization of Europe, a reflection of the high mobility of B. reticulatus.
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Affiliation(s)
- Jonas Eberle
- Evolutionary Zoology, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Martin Husemann
- Center of Natural History, University of Hamburg, Hamburg, Germany
| | - Inken Doerfler
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Germany
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, Technical University of Munich, Freising, Germany
| | - Werner Ulrich
- Department of Ecology and Biogeography, Nicolaus Copernicus University, Toruń, Poland
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Rauhenebrach, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - Christophe Bouget
- INRAE, ‘Forest Ecosystems’ Research Unit, Nogent-sur-Vernisson, France
| | - Antoine Brin
- Engineering School of PURPAN, UMR 1201 Dynafor INRAE-INPT, University of Toulouse, Toulouse, France
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Thibault Lachat
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Laurent Larrieu
- University of Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, France
- CNPF-CRPF Occitanie, Tarbes, France
| | - Andreas Rigling
- Forest Dynamics, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Jürgen Schmidl
- Ecology Group, Department Biology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Sebastian Seibold
- Ecosystem Dynamics and Forest Management, Technical University of Munich, Freising, Germany
- Berchtesgaden National Park, Berchtesgaden, Germany
| | | | - Jan Christian Habel
- Evolutionary Zoology, Department of Biosciences, University of Salzburg, Salzburg, Austria
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5
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Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
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Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
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6
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Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards. Mol Phylogenet Evol 2019; 134:269-281. [PMID: 30763758 DOI: 10.1016/j.ympev.2019.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 11/20/2022]
Abstract
Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.
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7
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Friis G, Fandos G, Zellmer AJ, McCormack JE, Faircloth BC, Milá B. Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird. Mol Ecol 2018; 27:5137-5153. [PMID: 30451354 DOI: 10.1111/mec.14946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/26/2018] [Accepted: 10/15/2018] [Indexed: 12/25/2022]
Abstract
The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.
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Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Guillermo Fandos
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Amanda J Zellmer
- Department of Biology, Occidental College, Los Angeles, California
| | - John E McCormack
- Department of Biology, Occidental College, Los Angeles, California.,Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, California
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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8
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Hansson B, Sigeman H, Stervander M, Tarka M, Ponnikas S, Strandh M, Westerdahl H, Hasselquist D. Contrasting results from GWAS and QTL mapping on wing length in great reed warblers. Mol Ecol Resour 2018; 18:867-876. [DOI: 10.1111/1755-0998.12785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Martin Stervander
- Department of Biology Lund University Lund Sweden
- Institute of Ecology and Evolution University of Oregon Eugene Oregon
| | - Maja Tarka
- Department of Biology Lund University Lund Sweden
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9
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Alaei Kakhki N, Aliabadian M, Förschler MI, Ghasempouri SM, Kiabi BH, Verde Arregoitia LD, Schweizer M. Phylogeography of theOenanthe hispanica-pleschanka-cypriacacomplex (Aves, Muscicapidae: Saxicolinae): Diversification history of open-habitat specialists based on climate niche models, genetic data, and morphometric data. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Niloofar Alaei Kakhki
- Department of Biology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad Iran
| | - Mansour Aliabadian
- Department of Biology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad Iran
- Research Department of Zoological Innovations; Institute of Applied Zoology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad Iran
| | - Marc I. Förschler
- Department of Ecosystem Monitoring, Research and Conservation; Black Forest National Park; Freudenstadt Germany
| | - Seyed Mahmoud Ghasempouri
- Department of Environmental Science; Faculty of Natural Resources and Marine Sciences; Tarbiat Modares University (TMU); Noor Iran
| | - Bahram H. Kiabi
- Department of zoology; Faculty of Biological Sciences; Shahid Beheshti University; Tehran Iran
| | - Luis D. Verde Arregoitia
- Museo de Zoología “Alfonso L. Herrera”; Facultad de Ciencias; Universidad Nacional Autónoma de México; Ciudad Universitaria; Coyoacán CDMX Mexico
| | - Manuel Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern; Bern Switzerland
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10
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Friis G, Aleixandre P, Rodríguez-Estrella R, Navarro-Sigüenza AG, Milá B. Rapid postglacial diversification and long-term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence. Mol Ecol 2016; 25:6175-6195. [PMID: 27862578 DOI: 10.1111/mec.13911] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/01/2016] [Accepted: 11/02/2016] [Indexed: 01/04/2023]
Abstract
Natural systems composed of closely related taxa that vary in the degree of phenotypic divergence and geographic isolation provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and colour, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence. Here, we quantify patterns of phenotypic divergence in morphology and plumage colour and use mitochondrial DNA genes, a nuclear intron, and genomewide SNPs to reconstruct the demographic and evolutionary history of the genus to infer relative rates of evolutionary divergence among lineages. We found that geographically isolated populations have evolved independently for hundreds of thousands of years despite little differentiation in phenotype, in sharp contrast to phenotypically diverse northern forms, which have diversified within the last few thousand years as a result of the rapid postglacial recolonization of North America. SNP data resolved young northern lineages into reciprocally monophyletic lineages, indicating low rates of gene flow even among closely related parapatric forms, and suggesting a role for strong genetic drift or multifarious selection acting on multiple loci in driving lineage divergence. Juncos represent a compelling example of speciation in action, where the combined effects of historical and selective factors have produced one of the fastest cases of speciation known in vertebrates.
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Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Pau Aleixandre
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | | | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, 28006, Spain
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11
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Impacts of forest fragmentation and post-glacial colonization on the distribution of genetic diversity in the Polish population of the hazel grouse Terastes bonasia. EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-1002-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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El-Arabany N, Sorensen M, Hansson B. Inferring the links between breeding and wintering grounds in a Palearctic– African migratory bird, the Great Reed Warbler, using mitochondrial DNA data. AFRICAN ZOOLOGY 2015. [DOI: 10.1080/15627020.2015.1055301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Abalaka J, Hudin NS, Ottosson U, Bloomer P, Hansson B. Genetic diversity and population structure of the range restricted rock firefinch Lagonosticta sanguinodorsalis. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0667-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Mitochondrial evidence for genetic diversity and low phylogeographic differentiation in the Marsh Warbler Acrocephalus palustris (Aves: Acrocephalidae). ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0177-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Malpica A, Ornelas JF. Postglacial northward expansion and genetic differentiation between migratory and sedentary populations of the broad-tailed hummingbird (Selasphorus platycercus). Mol Ecol 2014; 23:435-52. [DOI: 10.1111/mec.12614] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 11/13/2013] [Accepted: 11/15/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Andreia Malpica
- Departamento de Biología Evolutiva; Instituto de Ecología, AC; Carretera antigua a Coatepec No. 351, El Haya Xalapa Veracruz 91070 México
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva; Instituto de Ecología, AC; Carretera antigua a Coatepec No. 351, El Haya Xalapa Veracruz 91070 México
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16
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Tarka M, Akesson M, Hasselquist D, Hansson B. Intralocus sexual conflict over wing length in a wild migratory bird. Am Nat 2013; 183:62-73. [PMID: 24334736 DOI: 10.1086/674072] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Intralocus sexual conflict (ISC) occurs when males and females have different adaptive peaks but are constrained from evolving sexual dimorphism because of shared genes. Implications of this conflict on evolutionary dynamics in wild populations have not been investigated in detail. In comprehensive analyses of selection, heritability, and genetic correlations, we found evidence for an ISC over wing length, a key trait for flight performance and migration, in a long-term study of wild great reed warblers (Acrocephalus arundinaceus). We found moderate sexual dimorphism, high heritability, moderate sexually antagonistic selection, and strong positive cross-sex genetic correlation in wing length, together supporting the presence of ISC. A negative genetic correlation between male wing length and female fitness indicated that females inheriting alleles for longer wings from their male relatives also inherited lower fitness. Moreover, cross-sex genetic correlations imposed constraint on the predicted microevolutionary trajectory of wing length (based on selection gradients), especially in females where the predicted response was reversed. The degree of sexual dimorphism in wing length did not change over time, suggesting no sign of conflict resolution. Our study provides novel insight into how an ISC over a fitness trait can affect microevolution in a wild population under natural selection.
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Affiliation(s)
- Maja Tarka
- Department of Biology, Lund University, SE-223 62 Lund, Sweden
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17
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García-Fernández A, Iriondo JM, Escudero A, Aguilar JF, Feliner GN. Genetic patterns of habitat fragmentation and past climate-change effects in the Mediterranean high-mountain plant Armeria caespitosa (Plumbaginaceae). AMERICAN JOURNAL OF BOTANY 2013; 100:1641-1650. [PMID: 23857736 DOI: 10.3732/ajb.1200653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Mountain plants are among the species most vulnerable to global warming, because of their isolation, narrow geographic distribution, and limited geographic range shifts. Stochastic and selective processes can act on the genome, modulating genetic structure and diversity. Fragmentation and historical processes also have a great influence on current genetic patterns, but the spatial and temporal contexts of these processes are poorly known. We aimed to evaluate the microevolutionary processes that may have taken place in Mediterranean high-mountain plants in response to changing historical environmental conditions. METHODS Genetic structure, diversity, and loci under selection were analyzed using AFLP markers in 17 populations distributed over the whole geographic range of Armeria caespitosa, an endemic plant that inhabits isolated mountains (Sierra de Guadarrama, Spain). Differences in altitude, geographic location, and climate conditions were considered in the analyses, because they may play an important role in selective and stochastic processes. KEY RESULTS Bayesian clustering approaches identified nine genetic groups, although some discrepancies in assignment were found between alternative analyses. Spatially explicit analyses showed a weak relationship between genetic parameters and spatial or environmental distances. However, a large proportion of outlier loci were detected, and some outliers were related to environmental variables. CONCLUSIONS A. caespitosa populations exhibit spatial patterns of genetic structure that cannot be explained by the isolation-by-distance model. Shifts along the altitude gradient in response to Pleistocene climatic oscillations and environmentally mediated selective forces might explain the resulting structure and genetic diversity values found.
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Truong C, Divakar PK, Yahr R, Crespo A, Clerc P. Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 2013; 68:357-72. [DOI: 10.1016/j.ympev.2013.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 02/01/2013] [Accepted: 04/02/2013] [Indexed: 12/31/2022]
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19
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Neto JM, Arroyo JL, Bargain B, Monrós JS, Mátrai N, Procházka P, Zehtindjiev P. Phylogeography of a habitat specialist with high dispersal capability: the Savi's Warbler Locustella luscinioides. PLoS One 2012; 7:e38497. [PMID: 22701653 PMCID: PMC3372518 DOI: 10.1371/journal.pone.0038497] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 05/09/2012] [Indexed: 11/18/2022] Open
Abstract
In order to describe the influence of Pleistocene glaciations on the genetic structure and demography of a highly mobile, but specialized, passerine, the Savi’s Warbler (Locustella luscinioides), mitochondrial DNA sequences (ND2) and microsatellites were analysed in c.330 individuals of 17 breeding and two wintering populations. Phylogenetic, population genetics and coalescent methods were used to describe the genetic structure, determine the timing of the major splits and model the demography of populations. Savi’s Warblers split from its sister species c.8 million years ago and have two major haplotype groups that diverged in the early/middle Pleistocene. One of these clades originated in the Balkans and is currently widespread, showing strong evidence for population expansion; whereas the other is restricted to Iberia and remained stable. Microsatellites agreed with a genetic break around the Pyrenees, but showed considerable introgression and a weaker genetic structure. Both genetic markers showed an isolation-by-distance pattern associated with the population expansion of the eastern clade. Breeding populations seem to be segregated at the wintering sites, but results on migratory connectivity are preliminary. Savi’s Warbler is the only known migratory bird species in which Iberian birds did not expand beyond the Pyrenees after the last glaciation. Despite the long period of independent evolution of western and eastern populations, complete introgression occurred when these groups met in Iberia. Mitochondrial sequences indicated the existence of refugia-within-refugia in the Iberian Peninsula during the last glacial period, which is surprising given the high dispersal capacity of this species. Plumage differences of eastern subspecies seemed to have evolved recently through natural selection, in agreement with the glacial expansion hypothesis. This study supports the great importance of the Iberian Peninsula and its role for the conservation of genetic variation.
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Affiliation(s)
- Júlio M Neto
- Department of Biology, University of Lund, Ecology Building, Lund, Sweden.
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20
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Sonsthagen SA, McClaren EL, Doyle FI, Titus K, Sage GK, Wilson RE, Gust JR, Talbot SL. Identification of metapopulation dynamics among Northern Goshawks of the Alexander Archipelago, Alaska, and Coastal British Columbia. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0352-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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ILLERA JUANCARLOS, KOIVULA KARI, BROGGI JULI, PÄCKERT MARTIN, MARTENS JOCHEN, KVIST LAURA. A multi-gene approach reveals a complex evolutionary history in the Cyanistes species group. Mol Ecol 2011; 20:4123-39. [DOI: 10.1111/j.1365-294x.2011.05259.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Lim HC, Sheldon FH. Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia. Mol Ecol 2011; 20:3414-38. [PMID: 21777318 DOI: 10.1111/j.1365-294x.2011.05190.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Sundaland has a dynamic geographic history because its landmasses were periodically interconnected when sea levels fell during glacial periods. Superimposed on this geographic dynamism were environmental changes related to climatic oscillations. To investigate how tropical taxa responded to such changes, we studied the divergence and demographic history of two co-distributed rainforest passerine species, Arachnothera longirostra and Malacocincla malaccensis. We sampled birds primarily from Borneo and the Malay Peninsula, which straddle the now-submerged Sunda shelf, and analysed multilocus DNA data with a variety of coalescent and gene genealogy methods. Cross-shelf divergence in both species occurred well before the last glacial maximum, i.e., before the most recent land connection. However, post-divergence gene flow occurred, and it was more pronounced in A. longirostra (a highly vagile nectarivore/insectivore) than in M. malaccensis (an understory insectivore). Despite current habitat continuity on Borneo, the population of M. malaccensis in northeastern Borneo is substantially divergent from that on the rest of the island. The NE population experienced dramatic demographic fluctuations, probably because of competition with the other population, which expanded from western Borneo after the mid-Pleistocene. In contrast, the Borneo population of A. longirostra has little structure and appears to have experienced demographic expansion 16 kya, long after it had diverged from the Malay Peninsula population (630-690 kya). Malay Peninsula populations of both species have remained relatively stable. Overall, the most recent glacial period was not the chief determinant of the evolutionary dynamics of our study species, and in this respect, they are different from temperate species.
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Affiliation(s)
- Haw Chuan Lim
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
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Wellenreuther M, Sánchez-Guillén RA, Cordero-Rivera A, Svensson EI, Hansson B. Environmental and climatic determinants of molecular diversity and genetic population structure in a coenagrionid damselfly. PLoS One 2011; 6:e20440. [PMID: 21655216 PMCID: PMC3105071 DOI: 10.1371/journal.pone.0020440] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 05/03/2011] [Indexed: 11/19/2022] Open
Abstract
Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed damselfly Ischnuraelegans, which has been the target of many ecological and evolutionary studies. We addressed the following questions: (i) Is the population structure affected by longitudinal or latitudinal gradients?; (ii) Do geographic boundaries limit gene flow?; (iii) Does geographic distance affect connectivity and is there a signature of past bottlenecks?; (iv) Is there evidence of a recent range expansion and (vi) what is the effect of geography and climatic factors on population structure? We found low to moderate genetic sub-structuring between populations (mean F(ST) = 0.06, D(est) = 0.12), and an effect of longitude, but not latitude, on genetic diversity. No significant effects of geographic boundaries (e.g. water bodies) were found. F(ST)-and D(est)-values increased with geographic distance; however, there was no evidence for recent bottlenecks. Finally, we did not detect any molecular signatures of range expansions or an effect of geographic suitability, although local precipitation had a strong effect on genetic differentiation. The population structure of this small insect has probably been shaped by ecological factors that are correlated with longitudinal gradients, geographic distances, and local precipitation. The relatively weak global population structure and high degree of genetic variation within populations suggest that I. elegans has high dispersal ability, which is consistent with this species being an effective and early coloniser of new habitats.
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Abstract
How does genome evolution affect the rate of diversification of biological lineages? Recent studies have suggested that the overall rate of genome evolution is correlated with the rate of diversification. If true, this claim has important consequences for understanding the process of diversification, and implications for the use of DNA sequence data to reconstruct evolutionary history. However, the generality and cause of this relationship have not been established. Here, we test the relationship between the rate of molecular evolution and net diversification with a 19-gene, 17-kb DNA sequence dataset from 64 families of birds. We show that rates of molecular evolution are positively correlated to net diversification in birds. Using a 7.6-kb dataset of protein-coding DNA, we show that the synonymous substitution rate, and therefore the mutation rate, is correlated to net diversification. Further analysis shows that the link between mutation rates and net diversification is unlikely to be the indirect result of correlations with life-history variables that may influence both quantities, suggesting that there might be a causal link between mutation rates and net diversification.
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Cibois A, Thibault JC, Pasquet E. Influence of quaternary sea-level variations on a land bird endemic to Pacific atolls. Proc Biol Sci 2010; 277:3445-51. [PMID: 20554555 DOI: 10.1098/rspb.2010.0846] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little is known about the effect of quaternary climate variations on organisms that inhabited carbonate islands of the Pacific Ocean, although it has been suggested that one or several uplifted islands provided shelter for terrestrial birds when sea-level reached its highest. To test this hypothesis, we investigated the history of colonization of the Tuamotu reed-warbler (Acrocephalus atyphus) in southeastern Polynesia, and found high genetic structure between the populations of three elevated carbonate islands. Estimates of time since divergence support the hypothesis that these islands acted as refugia during the last interglacial maximum. These findings are particularly important for defining conservation priorities on atolls that endure the current trend of sea-level rise owing to global warming.
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Affiliation(s)
- Alice Cibois
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, 1211 Geneva 6, Switzerland.
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Mona S, Catalano G, Lari M, Larson G, Boscato P, Casoli A, Sineo L, Di Patti C, Pecchioli E, Caramelli D, Bertorelle G. Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion. BMC Evol Biol 2010; 10:83. [PMID: 20346116 PMCID: PMC2858146 DOI: 10.1186/1471-2148-10-83] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/26/2010] [Indexed: 11/17/2022] Open
Abstract
Background The aurochs (Bos primigenius) was a large bovine that ranged over almost the entirety of the Eurasian continent and North Africa. It is the wild ancestor of the modern cattle (Bos taurus), and went extinct in 1627 probably as a consequence of human hunting and the progressive reduction of its habitat. To investigate in detail the genetic history of this species and to compare the population dynamics in different European areas, we analysed Bos primigenius remains from various sites across Italy. Results Fourteen samples provided ancient DNA fragments from the mitochondrial hypervariable region. Our data, jointly analysed with previously published sequences, support the view that Italian aurochsen were genetically similar to modern bovine breeds, but very different from northern/central European aurochsen. Bayesian analyses and coalescent simulations indicate that the genetic variation pattern in both Italian and northern/central European aurochsen is compatible with demographic stability after the last glaciation. We provide evidence that signatures of population expansion can erroneously arise in stable aurochsen populations when the different ages of the samples are not taken into account. Conclusions Distinct groups of aurochsen probably inhabited Italy and northern/central Europe after the last glaciation, respectively. On the contrary, Italian and Fertile Crescent aurochsen likely shared several mtDNA sequences, now common in modern breeds. We argue that a certain level of genetic homogeneity characterized aurochs populations in Southern Europe and the Middle East, and also that post-glacial recolonization of northern and central Europe advanced, without major demographic expansions, from eastern, and not southern, refugia.
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Affiliation(s)
- Stefano Mona
- Dipartimento di Biologia ed Evoluzione, Università di Ferrara, Ferrara, Italy
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Tarka M, Akesson M, Beraldi D, Hernández-Sánchez J, Hasselquist D, Bensch S, Hansson B. A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers. Proc Biol Sci 2010; 277:2361-9. [PMID: 20335216 DOI: 10.1098/rspb.2010.0033] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Wing length is a key character for essential behaviours related to bird flight such as migration and foraging. In the present study, we initiate the search for the genes underlying wing length in birds by studying a long-distance migrant, the great reed warbler (Acrocephalus arundinaceus). In this species wing length is an evolutionary interesting trait with pronounced latitudinal gradient and sex-specific selection regimes in local populations. We performed a quantitative trait locus (QTL) scan for wing length in great reed warblers using phenotypic, genotypic, pedigree and linkage map data from our long-term study population in Sweden. We applied the linkage analysis mapping method implemented in GridQTL (a new web-based software) and detected a genome-wide significant QTL for wing length on chromosome 2, to our knowledge, the first detected QTL in wild birds. The QTL extended over 25 cM and accounted for a substantial part (37%) of the phenotypic variance of the trait. A genome scan for tarsus length (a body-size-related trait) did not show any signal, implying that the wing-length QTL on chromosome 2 was not associated with body size. Our results provide a first important step into understanding the genetic architecture of avian wing length, and give opportunities to study the evolutionary dynamics of wing length at the locus level.
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Affiliation(s)
- Maja Tarka
- Section for Animal Ecology, Department of Biology, Lund University, 223 62 Lund, Sweden
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WILLIS SC, NUNES M, MONTAÑA CG, FARIAS IP, ORTÍ G, LOVEJOY NR. The Casiquiare river acts as a corridor between the Amazonas and Orinoco river basins: biogeographic analysis of the genusCichla. Mol Ecol 2010; 19:1014-30. [DOI: 10.1111/j.1365-294x.2010.04540.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Anderson MG, Moskát C, Bán M, Grim T, Cassey P, Hauber ME. Egg eviction imposes a recoverable cost of virulence in chicks of a brood parasite. PLoS One 2009; 4:e7725. [PMID: 19907639 PMCID: PMC2768821 DOI: 10.1371/journal.pone.0007725] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 10/12/2009] [Indexed: 12/04/2022] Open
Abstract
Background Chicks of virulent brood parasitic birds eliminate their nestmates and avoid costly competition for foster parental care. Yet, efforts to evict nest contents by the blind and naked common cuckoo Cuculus canorus hatchling are counterintuitive as both adult parasites and large older cuckoo chicks appear to be better suited to tossing the eggs and young of the foster parents. Methodology/Principal Findings Here we show experimentally that egg tossing imposed a recoverable growth cost of mass gain in common cuckoo chicks during the nestling period in nests of great reed warbler Acrocephalus arundinaceus hosts. Growth rates of skeletal traits and morphological variables involved in the solicitation of foster parental care remained similar between evictor and non-evictor chicks throughout development. We also detected no increase in predation rates for evicting nests, suggesting that egg tossing behavior by common cuckoo hatchlings does not increase the conspicuousness of nests. Conclusion The temporary growth cost of egg eviction by common cuckoo hatchlings is the result of constraints imposed by rejecter host adults and competitive nestmates on the timing and mechanism of parasite virulence.
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Affiliation(s)
- Michael G. Anderson
- Ecology and Conservation Group, Institute of Natural Science, Massey University, Albany Campus, Auckland, New Zealand
| | - Csaba Moskát
- Animal Ecology Research Group of the Hungarian Academy of Sciences, Hungarian Natural History Museum, Budapest, Hungary
| | - Miklós Bán
- Behavioural Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, Hungary
| | - Tomáš Grim
- Department of Zoology and Laboratory of Ornithology, Palacky University, Olomouc, Czech Republic
| | - Phillip Cassey
- Centre for Ornithology, School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Mark E. Hauber
- Department of Psychology, Hunter College, City University of New York, New York, United States of America
- * E-mail:
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Calvignac S, Hughes S, Hänni C. Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa. DIVERS DISTRIB 2009. [DOI: 10.1111/j.1472-4642.2009.00586.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Hansson B, Ljungqvist M, Dawson DA, Mueller JC, Olano-Marin J, Ellegren H, Nilsson JÅ. Avian genome evolution: insights from a linkage map of the blue tit (Cyanistes caeruleus). Heredity (Edinb) 2009; 104:67-78. [DOI: 10.1038/hdy.2009.107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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BARROWCLOUGH GEORGEF, ZINK ROBERTM. Funds enough, and time: mtDNA, nuDNA and the discovery of divergence. Mol Ecol 2009. [DOI: 10.1111/j.1365-294x.2009.04271.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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