601
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Brown RP, Paterson S, Risse J. Genomic Signatures of Historical Allopatry and Ecological Divergence in an Island Lizard. Genome Biol Evol 2016; 8:3618-3626. [PMID: 28040775 PMCID: PMC5203796 DOI: 10.1093/gbe/evw268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Geographical variation among contiguous populations is frequently attributed to ecological divergence or historical isolation followed by secondary contact. Distinguishing between these effects is key to studies of incipient speciation and could be revealed by different genomic signatures. We used RAD-seq analyses to examine morphologically divergent populations of the endemic lizard (Gallotia galloti) from the volcanic island of Tenerife. Previous analyses have suggested ecological and historical causes to explain the morphological diversity. Analyses of 276,483 single nucleotide polymorphisms (SNPs) from >20 Mbp of the genome revealed one genetically divergent population from Anaga, a region associated with divergent mtDNA lineages in other Tenerife endemics. This population also has a high number of private alleles, and its divergence can be explained by historical isolation. Bayesian outlier analyses identified a small proportion of SNPs as candidates for selection (0.04%) which were strongly differentiated between xeric and mesic habitat types. Individual testing for specific xeric–mesic selection using an alternative approach also supported ecological divergence in a similarly small proportion of SNPs. The study indicates the roles of both historical isolation and ecological divergence in shaping genomic diversity in G. galloti. However, north–south morphological divergence appears solely associated with the latter and likely involves a relatively small proportion of the genome.
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Affiliation(s)
- Richard P Brown
- School of Natural Sciences & Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Steve Paterson
- Department of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Judith Risse
- Department of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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602
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Bernal MA, Gaither MR, Simison WB, Rocha LA. Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon). Mol Ecol 2016; 26:639-652. [PMID: 27873385 DOI: 10.1111/mec.13937] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/18/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
Abstract
Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263 Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.
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Affiliation(s)
- Moisés A Bernal
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia.,Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Michelle R Gaither
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA.,School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Luiz A Rocha
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
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603
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Haenel GJ. Introgression of mtDNA inUrosauruslizards: historical and ecological processes. Mol Ecol 2016; 26:606-623. [DOI: 10.1111/mec.13930] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/01/2016] [Indexed: 01/09/2023]
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604
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Hung CM, Drovetski SV, Zink RM. Matching loci surveyed to questions asked in phylogeography. Proc Biol Sci 2016; 283:20152340. [PMID: 26962145 DOI: 10.1098/rspb.2015.2340] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.
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Affiliation(s)
- Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sergei V Drovetski
- Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC 20004, USA
| | - Robert M Zink
- Bell Museum and Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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605
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Porretta D, Latrofa MS, Dantas-Torres F, Mastrantonio V, Iatta R, Otranto D, Urbanelli S. Exon-intron structure and sequence variation of the calreticulin gene among Rhipicephalus sanguineus group ticks. Parasit Vectors 2016; 9:640. [PMID: 27955695 PMCID: PMC5154033 DOI: 10.1186/s13071-016-1909-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/23/2016] [Indexed: 11/12/2022] Open
Abstract
Background Calreticulin proteins (CRTs) are important components of tick saliva, which is involved in the blood meal success, pathogen transmission and host allergic responses. The characterization of the genes encoding for salivary proteins, such as CRTs, is pivotal to understand the mechanisms of tick-host interaction during blood meal and to develop tick control strategies based on their inhibition. In hard ticks, crt genes were shown to have only one intron with conserved position among species. In this study we investigated the exon-intron structure and variation of the crt gene in Rhipicephalus spp. ticks in order to assess the crt exon-intron structure and the potential utility of crt gene as a molecular marker. Methods We sequenced the exon-intron region of crt gene in ticks belonging to so-called tropical and temperate lineages of Rhipicephalus sanguineus (sensu lato), Rhipicephalus sp. I, Rhipicephalus sp. III, Rhipicephalus sp. IV, R. guilhoni, R. muhsamae and R. turanicus. Genetic divergence and phylogenetic relationships between the sequences obtained were estimated. Results All individuals belonging to the tropical lineage of R. sanguineus (s.l.), R. guilhoni, R. muhsamae, R. turanicus, Rhipicephalus sp. III and Rhipicephalus sp. IV analysed showed crt intron-present alleles. However, both crt intron-present and intron-absent alleles were found in Rhipicephalus sp. I and the temperate lineage of R. sanguineus (s.l.), showing the occurrence of an intraspecific intron presence-absence polymorphism. Phylogenetic relationships among the crt intron-present sequences showed distinct lineages for all taxa, with the tropical and temperate lineages of R. sanguineus (s.l.) being more closely related to each other. Conclusions We expanded previous studies about the characterization of crt gene in hard ticks. Our results highlighted a previously overlooked variation in the crt structure among Rhipicephalus spp., and among hard ticks in general. Notably, the intron presence/absence polymorphism observed herein can be a candidate study-system to investigate the early stages of intron gain/loss before fixation at species level and some debated questions about intron evolution. Finally, the sequence variation observed supports the suitability of the crt gene for molecular recognition of Rhipicephalus spp. and for phylogenetic studies in association with other markers. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1909-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniele Porretta
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | | | - Filipe Dantas-Torres
- Department of Veterinary Medicine, University of Bari, 70010, Valenzano, Bari, Italy.,Department of Immunology, Aggeu Magalhães Research Centre, Oswaldo Cruz Foundation, 50740465, Recife, PE, Brazil
| | | | - Roberta Iatta
- Department of Veterinary Medicine, University of Bari, 70010, Valenzano, Bari, Italy
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, 70010, Valenzano, Bari, Italy.
| | - Sandra Urbanelli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
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606
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Hawlitschek O, Morinière J, Lehmann GUC, Lehmann AW, Kropf M, Dunz A, Glaw F, Detcharoen M, Schmidt S, Hausmann A, Szucsich NU, Caetano-Wyler SA, Haszprunar G. DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland. Mol Ecol Resour 2016; 17:1037-1053. [PMID: 27863033 DOI: 10.1111/1755-0998.12638] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 12/21/2022]
Abstract
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.
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Affiliation(s)
- O Hawlitschek
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37, 08003, Barcelona, Spain
| | - J Morinière
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - G U C Lehmann
- Department of Biology, Behavioural Physiology, Humboldt University Berlin, Invalidenstr. 43, 10115, Berlin, Germany
| | - A W Lehmann
- Orthoptera Working Group Brandenburg and Berlin, Friedensallee 37, 14532, Stahnsdorf, Germany
| | - M Kropf
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Gregor Mendel-Str. 33, 1180, Vienna, Austria
| | - A Dunz
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - F Glaw
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - M Detcharoen
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - S Schmidt
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - A Hausmann
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - N U Szucsich
- 3rd Zoological Dep., Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - S A Caetano-Wyler
- Université de Genève, Département de Génétique et Evolution, Quai Ernest Ansermet 30, 1211, Geneva 4, Switzerland
| | - G Haszprunar
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Department Biology II and GeoBio-Center of Ludwig-Maximilians-Universität München, Groβhaderner Str. 2, 82152, Planegg-Martinsried, Germany
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607
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Stewart KA, Hudson CM, Lougheed SC. Can alternative mating tactics facilitate introgression across a hybrid zone by circumventing female choice? J Evol Biol 2016; 30:412-421. [DOI: 10.1111/jeb.13017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 01/30/2023]
Affiliation(s)
- K. A. Stewart
- College of Environmental Science and Engineering; Tongji University; Shanghai China
| | - C. M. Hudson
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW Australia
| | - S. C. Lougheed
- Department of Biology; Queen's University; Kingston ON Canada
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608
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Ersmark E, Klütsch CFC, Chan YL, Sinding MHS, Fain SR, Illarionova NA, Oskarsson M, Uhlén M, Zhang YP, Dalén L, Savolainen P. From the Past to the Present: Wolf Phylogeography and Demographic History Based on the Mitochondrial Control Region. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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609
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Perea S, Vukić J, Šanda R, Doadrio I. Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece. PLoS One 2016; 11:e0166292. [PMID: 27906993 PMCID: PMC5132402 DOI: 10.1371/journal.pone.0166292] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022] Open
Abstract
Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data. We found evidence of complete mitochondrial introgression of Squalius keadicus into two populations recognized as Squalius peloponensis from the Miras and Pamissos River basins and a divergence of mitochondrial genomes of S. keadicus from the Evrotas basin from that of the introgressed populations dating from the Pleistocene. Secondary contact among basins is a possible factor in connection of the species and the introgression event. Morphological analyses support the hypothesis of mitochondrial introgression, as S. keadicus was different from the other three populations recognized as S. peloponensis, although significant differences were found among the four populations. Isolation by geographical barriers arose during Pleistocene in the western Peloponnese were the source of the evolution of the two reciprocally monophyletic subclades found in the S. keadicus mitochondrial clade, and the morphological differences found among the four populations. Along with the lack of structure in the nuclear genome in the three populations ascribed to S. peloponensis, this suggests an incipient speciation process occurring in these Squalius species in the western Peloponnese.
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Affiliation(s)
- Silvia Perea
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal, Madrid, Spain
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Václavské nám, Prague, Czech Republic
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal, Madrid, Spain
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610
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Wang C, Agrawal S, Laudien J, Häussermann V, Held C. Discrete phenotypes are not underpinned by genome-wide genetic differentiation in the squat lobster Munida gregaria (Crustacea: Decapoda: Munididae): a multi-marker study covering the Patagonian shelf. BMC Evol Biol 2016; 16:258. [PMID: 27903261 PMCID: PMC5131467 DOI: 10.1186/s12862-016-0836-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/21/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers. The widespread squat lobster Munida gregaria comprises two discrete ecotypes, gregaria s. str. and subrugosa, which were long regarded as different species due to marked differences in morphological, ecological and behavioral traits. We studied the morphometry and genetics of M. gregaria s. l. and tested (1) whether the phenotypic differences remain stable after continental-scale sampling and inclusion of different life stages, (2) and whether each phenotype is underpinned by a specific genotype. RESULTS A total number of 219 gregaria s. str. and subrugosa individuals from 25 stations encompassing almost entire range in South America were included in morphological and genetic analyses using nine unlinked hypervariable microsatellites and new COI sequences. Results from the PCA and using discriminant functions demonstrated that the morphology of the two forms remains discrete. The mitochondrial data showed a shallow, star-like haplotype network and complete overlap of genetic distances within and among ecotypes. Coalescent-based species delimitation methods, PTP and GMYC, coherently suggested that haplotypes of both ecotypes forms a single species. Although all microsatellite markers possess sufficient genetic variation, AMOVA, PCoA and Bayesian clustering approaches revealed no genetic clusters corresponding to ecotypes or geographic units across the entire South-American distribution. No evidence of isolation-by-distance could be detected for this species in South America. CONCLUSIONS Despite their pronounced bimodal morphologies and different lifestyles, the gregaria s. str. and subrugosa ecotypes form a single, dimorphic species M. gregaria s. l.. Based on adequate geographic coverage and multiple independent polymorphic loci, there is no indication that each phenotype may have a unique genetic basis, leaving phenotypic plasticity or localized genomic islands of speciation as possible explanations.
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Affiliation(s)
- Chen Wang
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Shobhit Agrawal
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Jürgen Laudien
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Vreni Häussermann
- Universidad Católica de Valparaíso, Facultad de Recursos Naturales, Escuela de Ciencias del Mar, Avda. Brasil 2950, Valparaíso, Chile
- Huinay Scientific Field Station, Huinay, Los Lagos Chile
| | - Christoph Held
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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611
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Choi YJ, Tyagi R, McNulty SN, Rosa BA, Ozersky P, Mafrtin J, Hallsworth-Pepin K, Unnasch TR, Norice CT, Nutman TB, Weil GJ, Fischer PU, Mitreva M. Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont. Nat Microbiol 2016; 2:16207. [PMID: 27869792 PMCID: PMC5512550 DOI: 10.1038/nmicrobiol.2016.207] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/19/2016] [Indexed: 01/03/2023]
Abstract
Ongoing elimination efforts have altered the global distribution of Onchocerca volvulus, the agent of river blindness, and further population restructuring is expected as efforts continue. Therefore, a better understanding of population genetic processes and their effect on biogeography is needed to support elimination goals. We describe O. volvulus genome variation in 27 isolates from the early 1990s (before widespread mass treatment) from four distinct locales: Ecuador, Uganda, the West African forest and the West African savanna. We observed genetic substructuring between Ecuador and West Africa and between the West African forest and savanna bioclimes, with evidence of unidirectional gene flow from savanna to forest strains. We identified forest:savanna-discriminatory genomic regions and report a set of ancestry informative loci that can be used to differentiate between forest, savanna and admixed isolates, which has not previously been possible. We observed mito-nuclear discordance possibly stemming from incomplete lineage sorting. The catalogue of the nuclear, mitochondrial and endosymbiont DNA variants generated in this study will support future basic and translational onchocerciasis research, with particular relevance for ongoing control programmes, and boost efforts to characterize drug, vaccine and diagnostic targets.
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Affiliation(s)
- Young-Jun Choi
- McDonnell Genome Institute, Washington University in St. Louis, MO, USA
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University in St. Louis, MO, USA
| | | | - Bruce A. Rosa
- McDonnell Genome Institute, Washington University in St. Louis, MO, USA
| | - Philip Ozersky
- McDonnell Genome Institute, Washington University in St. Louis, MO, USA
| | - John Mafrtin
- McDonnell Genome Institute, Washington University in St. Louis, MO, USA
| | | | - Thomas R. Unnasch
- Global Health Infectious Disease Research Program, Department of Global Health, University of South Florida, Tampa, FL, USA
| | - Carmelle T. Norice
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Thomas B. Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Gary J. Weil
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter U. Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in St. Louis, MO, USA
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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612
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Li X, Lin L, Cui A, Bai J, Wang X, Xin C, Zhang Z, Yang C, Gao R, Huang Y, Lei F. Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments. Mol Phylogenet Evol 2016; 104:14-20. [DOI: 10.1016/j.ympev.2016.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/20/2016] [Accepted: 07/18/2016] [Indexed: 11/24/2022]
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613
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Molecular phylogeny and patterns of diversification in syngnathid fishes. Mol Phylogenet Evol 2016; 107:388-403. [PMID: 27989632 DOI: 10.1016/j.ympev.2016.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 08/19/2016] [Accepted: 10/06/2016] [Indexed: 11/22/2022]
Abstract
The family Syngnathidae is a large and diverse clade of morphologically unique bony fishes, with 57 genera and 300 described species of seahorses, pipefishes, pipehorses, and seadragons. They primarily inhabit shallow coastal waters in temperate and tropical oceans, and are characterized by a fused jaw, male brooding, and extraordinary crypsis. Phylogenetic relationships within the Syngnathidae remain poorly resolved due to lack of generic taxon sampling, few diagnostic morphological characters, and limited molecular data. The phylogenetic placement of the threatened, commercially exploited seahorses remains a topic of intense interest, with conflicting topologies based on morphology and predominantly mitochondrial genetic data. In this study, we integrate eight nuclear and mitochondrial markers and 17 morphological characters to investigate the phylogenetic structure of the family Syngnathidae at the generic level. We include 91 syngnathid species representing 48 of the 57 recognized genera, all major ocean basins, and a broad array of temperate and tropical habitats including rocky and coral reefs, sand and silt, mangroves, seagrass beds, estuaries, and rivers. Maximum likelihood and Bayesian analyses of 5160bp from eight loci produced high congruence among alternate topologies, defining well-supported and sometimes novel clades. We present a hypothesis that confirms a deep phylogenetic split between lineages with trunk- or tail-brood pouch placement, and provides significant new insights into the morphological evolution and biogeography of this highly derived fish clade. Based on the fundamental division between lineages - the tail brooding "Urophori" and the trunk brooding "Gastrophori" - we propose a revision of Syngnathidae classification into only two subfamilies: the Nerophinae and the Syngnathinae. We find support for distinct principal clades within the trunk-brooders and tail-brooders, the latter of which include seahorses, seadragons, independent lineages of pipehorses, and clades that originated in southern Australia and the Western Atlantic. We suggest the seahorse genus Hippocampus is of Indo-Pacific origin and its sister clade is an unexpected grouping of several morphologically disparate Indo-Pacific genera, including the Pacific pygmy pipehorses. Taxonomic revision is required for multiple genera, particularly to reflect deep evolutionary splits in nominal lineages from the Atlantic versus the Indo-Pacific.
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614
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Jang SJ, Park E, Lee WK, Johnson SB, Vrijenhoek RC, Won YJ. Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries. BMC Evol Biol 2016; 16:235. [PMID: 27793079 PMCID: PMC5084463 DOI: 10.1186/s12862-016-0807-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/14/2016] [Indexed: 11/29/2022] Open
Abstract
Background The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinella pompejana. DNA sequences from one mitochondrial and eleven nuclear genes were examined in samples collected from ten vent localities that comprise the species’ known range from 23°N latitude on the East Pacific Rise to 38°S latitude on the Pacific Antarctic Ridge. Results Multi-locus genotypes inferred from these sequences clustered the individual worms into three metapopulation segments — the northern East Pacific Rise (NEPR), southern East Pacific Rise (SEPR), and northeastern Pacific Antarctic Ridge (PAR) — separated by the Equator and Easter Microplate boundaries. Genetic diversity estimators were negatively correlated with tectonic spreading rates. Application of the isolation-with-migration (IMa2) model provided information about divergence times and demographic parameters. The PAR and NEPR metapopulation segments were estimated to have split roughly 4.20 million years ago (Mya) (2.42–33.42 Mya, 95 % highest posterior density, (HPD)), followed by splitting of the SEPR and NEPR segments about 0.79 Mya (0.07–6.67 Mya, 95 % HPD). Estimates of gene flow between the neighboring regions were mostly low (2 Nm < 1). Estimates of effective population size decreased with southern latitudes: NEPR > SEPR > PAR. Conclusions Highly effective dispersal capabilities allow A. pompejana to overcome the temporal instability and intermittent distribution of active hydrothermal vents in the eastern Pacific Ocean. Consequently, the species exhibits very high levels of genetic diversity compared with many co-distributed vent annelids and mollusks. Nonetheless, its levels of genetic diversity in partially isolated populations are inversely correlated with tectonic spreading rates. As for many other vent taxa, this pioneering colonizer is similarly affected by local rates of habitat turnover and by major dispersal filters associated with the Equator and the Easter Microplate region. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0807-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sook-Jin Jang
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, South Korea
| | - Eunji Park
- Division of Ecoscience, Ewha Womans University, Seoul, South Korea
| | - Won-Kyung Lee
- Division of Ecoscience, Ewha Womans University, Seoul, South Korea
| | - Shannon B Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039-9644, USA
| | | | - Yong-Jin Won
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, South Korea. .,Division of Ecoscience, Ewha Womans University, Seoul, South Korea.
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615
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Sawyer YE, Cook JA. Phylogeographic structure in long-tailed voles (Rodentia: Arvicolinae) belies the complex Pleistocene history of isolation, divergence, and recolonization of Northwest North America's fauna. Ecol Evol 2016; 6:6633-6647. [PMID: 27777736 PMCID: PMC5058534 DOI: 10.1002/ece3.2393] [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: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/24/2022] Open
Abstract
Quaternary climate fluctuations restructured biodiversity across North American high latitudes through repeated episodes of range contraction, population isolation and divergence, and subsequent expansion. Identifying how species responded to changing environmental conditions not only allows us to explore the mode and tempo of evolution in northern taxa, but also provides a basis for forecasting future biotic response across the highly variable topography of western North America. Using a multilocus approach under a Bayesian coalescent framework, we investigated the phylogeography of a wide‐ranging mammal, the long‐tailed vole, Microtus longicaudus. We focused on populations along the North Pacific Coast to refine our understanding of diversification by exploring the potentially compounding roles of multiple glacial refugia and more recent fragmentation of an extensive coastal archipelago. Through a combination of genetic data and species distribution models (SDMs), we found that historical climate variability influenced contemporary genetic structure, with multiple isolated locations of persistence (refugia) producing multiple divergent lineages (Beringian or northern, southeast Alaska or coastal, and southern or continental) during glacial advances. These vole lineages all occur along the North Pacific Coast where the confluence of numerous independent lineages in other species has produced overlapping zones of secondary contact, collectively a suture zone. Finally, we detected high levels of neoendemism due to complex island geography that developed in the last 10,000 years with the rising sea levels of the Holocene.
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Affiliation(s)
- Yadéeh E Sawyer
- Department of Biology and Museum of Southwestern Biology University of New Mexico MSC03 2020 Albuquerque New Mexico 87131-0001
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico MSC03 2020 Albuquerque New Mexico 87131-0001
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616
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Manthey JD, Tollis M, Lemmon AR, Moriarty Lemmon E, Boissinot S. Diversification in wild populations of the model organism Anolis carolinensis: A genome-wide phylogeographic investigation. Ecol Evol 2016; 6:8115-8125. [PMID: 27891220 PMCID: PMC5108263 DOI: 10.1002/ece3.2547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 01/14/2023] Open
Abstract
The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.
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Affiliation(s)
| | - Marc Tollis
- Biodesign Institute Arizona State University Tempe AZ USA
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee FL USA
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617
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Sun K, Kimball RT, Liu T, Wei X, Jin L, Jiang T, Lin A, Feng J. The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data. Sci Rep 2016; 6:35417. [PMID: 27748429 PMCID: PMC5066199 DOI: 10.1038/srep35417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/27/2016] [Indexed: 12/21/2022] Open
Abstract
Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization.
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Affiliation(s)
- Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Xuewen Wei
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
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618
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Multilocus approach reveals an incipient differentiation process in the Stone-curlew, Burhinus oedicnemus around the Mediterranean basin. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0894-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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619
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Hamilton CA, Lemmon AR, Lemmon EM, Bond JE. Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life. BMC Evol Biol 2016; 16:212. [PMID: 27733110 PMCID: PMC5062932 DOI: 10.1186/s12862-016-0769-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 09/28/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. RESULTS Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. CONCLUSIONS The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
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Affiliation(s)
- Chris A. Hamilton
- Department of Biological Sciences, Auburn University & Auburn University Museum of Natural History, Auburn, AL USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL USA
| | | | - Jason E. Bond
- Department of Biological Sciences, Auburn University & Auburn University Museum of Natural History, Auburn, AL USA
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620
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Lee YS, Markov N, Argunov A, Voloshina I, Bayarlkhagva D, Kim B, Min M, Lee H, Kim KS. Genetic diversity and phylogeography of Siberian roe deer, Caproulus pygargus, in central and peripheral populations. Ecol Evol 2016; 6:7286-7297. [PMID: 28725397 PMCID: PMC5513270 DOI: 10.1002/ece3.2458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 11/10/2022] Open
Abstract
Current understanding of phylogeographical structure and genetic diversity of Siberian roe deer remains limited mainly due to small sample size and/or low geographical coverage in previous studies. Published data suggest at least two phylogroups: western (Ural Mountains and Western Siberia) and eastern (east from lake Baikal, including the Korean peninsula), but their phylogenetic relationship remains unclear. Combined sequences of cytochrome b (1140 bp) and the mtDNA control region (963 bp) were analyzed from 219 Siberian roe deer from 12 locations in Russia, Mongolia, and South Korea, which cover a large part of its range, to assess genetic diversity and phylogeographical status. Special emphasis was placed on the demographic history and genetic features of central, peripheral, and isolated populations. Results of median-joining network and phylogenetic tree analyses indicate that Siberian roe deer from the Urals to the Pacific Ocean are genetically diverse and that geographical distribution and composition of haplogroups coincide with previously described ranges of the subspecies Capreolus pygargus pygargus and Capreolus pygargus tianschanicus. We found that peripheral populations in the northwestern parts of the species range (Urals), as well as the isolated population from Jeju Island, are genetically distinct from those in the core part of the range, both in terms of genetic diversity and quantitative composition of haplogroups. We also found that northwestern (Urals) and northern (Yakutia) peripheral populations share the same haplogroup and fall into the same phylogenetic clade with the isolated population from Jeju Island. This finding sheds light on the taxonomic status of the Jeju Island population and leads to hypotheses about the discordance of morphological and genetic evolution in isolated populations and specific genetic features of peripheral populations.
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Affiliation(s)
- Yun Sun Lee
- Conservation Genome Resource Bank for Korean WildlifeCollege of Veterinary Medicine and Research Institute for Veterinary ScienceSeoul National UniversitySeoulKorea
| | - Nickolay Markov
- Institute of Plant and Animal Ecology Urals Branch of Russian Academy of SciencesYekaterinburgRussia
| | - Alexander Argunov
- Institute for Biological Problems of Cryolihtozone Siberian Branch of Russian Academy of SciencesYakutskRussia
| | | | - Damdingiin Bayarlkhagva
- Department of Molecular Biology and GeneticsNational University of MongoliaUlaanbaatarMongolia
| | - Baek‐Jun Kim
- Department of Climate and EcologyNational Institute of EcologyMaseo‐myeonSeocheon‐gunChungcheongnam‐doKorea
| | - Mi‐Sook Min
- Conservation Genome Resource Bank for Korean WildlifeCollege of Veterinary Medicine and Research Institute for Veterinary ScienceSeoul National UniversitySeoulKorea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean WildlifeCollege of Veterinary Medicine and Research Institute for Veterinary ScienceSeoul National UniversitySeoulKorea
| | - Kyung Seok Kim
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIAUSA
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621
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Guillemin ML, Valero M, Morales Collio K, Pinochet Sanchez R, Henríquez Espinosa M, Silva AX. Microsatellite markers and cytoplasmic sequences reveal contrasting pattern of spatial genetic structure in the red algae species complex Mazzaella laminarioides. JOURNAL OF PHYCOLOGY 2016; 52:806-816. [PMID: 27317474 DOI: 10.1111/jpy.12440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/04/2016] [Indexed: 06/06/2023]
Abstract
Mazzaella laminarioides is a common haploid-diploid red alga that forms dense beds. This alga has a wide distributional range, covering 3,500 km of the Chilean coast, but is restricted to high rocky intertidal zones. Recently, the existence of three highly divergent genetic lineages was demonstrated for this taxon, and two cytoplasmic markers were used to determine that these lineages are distributed in strict parapatry. Here, using 454 next-generation sequencing, we developed polymorphic microsatellite loci that cross amplify in all three cytoplasmic lineages. Six sites (i.e., two sites within each lineage) were analyzed using nine microsatellite loci. Our work shows that, although substantial cytoplasmic differentiation occurs within M. laminarioides, the microsatellite loci did not retrieve three nuclear genetic clusters as expected. Indeed, while the northernmost and southernmost cytoplasmic lineages form two strongly divergent nuclear groups characterized by diagnostic alleles, the third cytoplasmic lineage did not form a third nuclear independent group. It is possible that inter-lineage gene exchange has occurred, particularly at sites along the contact zone between the different cytoplasmic lineages. This nuclear-cytoplasmic incongruence in M. laminarioides could be explained by incomplete lineage sorting of the nuclear genes or asymmetric introgressive hybridization between the lineages. Finally, highly significant heterozygote deficiencies (suggesting occurrence of intergametophytic selfing) were observed in the three small northernmost sites while the large southernmost sites generally approached panmixia.
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Affiliation(s)
- Marie-Laure Guillemin
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
- CNRS, Sorbonne Universités, UPMC University Paris VI, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888, Roscoff, France
| | - Myriam Valero
- CNRS, Sorbonne Universités, UPMC University Paris VI, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888, Roscoff, France
| | - Kennia Morales Collio
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Ramona Pinochet Sanchez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Miguel Henríquez Espinosa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Andrea X Silva
- AUSTRAL-omics, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
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622
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Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity (Edinb) 2016; 118:211-220. [PMID: 27649619 PMCID: PMC5315522 DOI: 10.1038/hdy.2016.72] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 06/24/2016] [Accepted: 06/29/2016] [Indexed: 02/01/2023] Open
Abstract
Genetic variation shared between closely related species may be due to retention of ancestral polymorphisms because of incomplete lineage sorting (ILS) and/or introgression following secondary contact. It is challenging to distinguish ILS and introgression because they generate similar patterns of shared genetic diversity, but this is nonetheless essential for inferring accurately the history of species with overlapping distributions. To address this issue, we sequenced 33 independent intron loci across the genome of two closely related pine species (Pinus massoniana Lamb. and Pinus hwangshanensis Hisa) from Southeast China. Population structure analyses revealed that the species showed slightly more admixture in parapatric populations than in allopatric populations. Levels of interspecific differentiation were lower in parapatry than in allopatry. Approximate Bayesian computation suggested that the most likely speciation scenario explaining this pattern was a long period of isolation followed by a secondary contact. Ecological niche modeling suggested that a gradual range expansion of P. hwangshanensis during the Pleistocene climatic oscillations could have been the cause of the overlap. Our study therefore suggests that secondary introgression, rather than ILS, explains most of the shared nuclear genomic variation between these two species and demonstrates the complementarity of population genetics and ecological niche modeling in understanding gene flow history. Finally, we discuss the importance of contrasting results from markers with different dynamics of migration, namely nuclear, chloroplast and mitochondrial DNA.
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623
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Edgington HA, Ingram CM, Taylor DR. Cyto-nuclear discordance suggests complex evolutionary history in the cave-dwelling salamander, Eurycea lucifuga. Ecol Evol 2016; 6:6121-38. [PMID: 27648230 PMCID: PMC5016636 DOI: 10.1002/ece3.2212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/28/2016] [Accepted: 05/02/2016] [Indexed: 11/12/2022] Open
Abstract
Our understanding of the evolutionary history and ecology of cave‐associated species has been driven historically by studies of morphologically adapted cave‐restricted species. Our understanding of the evolutionary history and ecology of nonrestricted cave species, troglophiles, is limited to a few studies, which present differing accounts of troglophiles’ relationship with the cave habitat, and its impact on population dynamics. Here, we used phylogenetics, demographic statistics, and population genetic methods to study lineage divergence, dates of divergence, and population structure in the Cave Salamander, Eurycea lucifuga, across its range. In order to perform these analyses, we sampled 233 individuals from 49 populations, using sequence data from three gene loci as well as genotyping data from 19 newly designed microsatellite markers. We find, as in many other species studied in a phylogeographic context, discordance between patterns inferred from mitochondrial relationships and those inferred by nuclear markers indicating a complicated evolutionary history in this species. Our results suggest Pleistocene‐based divergence among three main lineages within E. lucifuga corresponding to the western, central, and eastern regions of the range, similar to patterns seen in species separated in multiple refugia during climatic shifts. The conflict between mitochondrial and nuclear patterns is consistent with what we would expect from secondary contact between regional populations following expansion from multiple refugia.
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Affiliation(s)
- Hilary A Edgington
- Ontario Institute for Cancer Research Toronto ON Canada; Department of Biology University of Virginia Charlottesville Virginia
| | - Colleen M Ingram
- Department of Biology University of Virginia Charlottesville Virginia; Division of Vertebrate Biology American Museum of Natural History New York City New York
| | - Douglas R Taylor
- Department of Biology University of Virginia Charlottesville Virginia
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624
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Zarza E, Faircloth BC, Tsai WL, Bryson RW, Klicka J, McCormack JE. Hidden histories of gene flow in highland birds revealed with genomic markers. Mol Ecol 2016; 25:5144-5157. [DOI: 10.1111/mec.13813] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/10/2016] [Accepted: 08/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Eugenia Zarza
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
| | - Whitney L.E. Tsai
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Robert W. Bryson
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John Klicka
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John E. McCormack
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
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625
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Eyer PA, Leniaud L, Tinaut A, Aron S. Combined hybridization and mitochondrial capture shape complex phylogeographic patterns in hybridogenetic Cataglyphis desert ants. Mol Phylogenet Evol 2016; 105:251-262. [PMID: 27591172 DOI: 10.1016/j.ympev.2016.08.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022]
Abstract
Some species of Cataglyphis desert ants have evolved a hybridogenetic mode of reproduction at the social scale. In hybridogenetic populations, two distinct genetic lineages coexist. Non-reproductive offspring (workers) are hybrids of the two lineages, whereas sexual offspring (males and new queens) are produced by parthenogenesis and belong to the mother queen lineage. How this unusual reproductive system affects phylogeographic patterns and speciation processes remains completely unknown to date. Using one mitochondrial and four nuclear genes, we examined the phylogenetic relationships between three species of Cataglyphis (C. hispanica, C. humeya and C. velox) where complex DNA inheritance through social hybridogenesis may challenge phylogenetic inference. Our results bring two important insights. First, our data confirm a hybridogenetic mode of reproduction across the whole distribution range of the species C. hispanica. In contrast, they do not provide support for hybridogenesis in the populations sampled of C. humeya and C. velox. This suggests that these populations are not hybridogenetic, or that hybridogenesis is too recent to result in reciprocally monophyletic lineages on nuclear genes. Second, due to mitochondrial introgression between lineages (Darras and Aron, 2015), the faster-evolving COI marker is not lineage specific, hence, unsuitable to further investigate the segregation of lineages in the species studied. Different mitochondrial haplotypes occur in each locality sampled, resulting in strongly structured populations. This micro-allopatric structure leads to over-splitting species delimitation on mitochondrial gene, as every locality could potentially be considered a putative species; haploweb analyses of nuclear markers, however, yield species delimitations that are consistent with morphology. Overall, this study highlights how social hybridogenesis varies across species and shapes complex phylogeographic patterns.
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Affiliation(s)
- P A Eyer
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium.
| | - L Leniaud
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium
| | - A Tinaut
- Department of Animal Biology, Faculty of Sciences, University of Granada, E-18071 Granada, Spain
| | - S Aron
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium
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626
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McLean BS, Jackson DJ, Cook JA. Rapid divergence and gene flow at high latitudes shape the history of Holarctic ground squirrels (Urocitellus). Mol Phylogenet Evol 2016; 102:174-88. [DOI: 10.1016/j.ympev.2016.05.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
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627
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Winker K. An examination of species limits in the Aulacorhynchus "prasinus" toucanet complex (Aves: Ramphastidae). PeerJ 2016; 4:e2381. [PMID: 27635345 PMCID: PMC5012271 DOI: 10.7717/peerj.2381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/30/2016] [Indexed: 11/20/2022] Open
Abstract
The number of species recognized in Aulacorhynchus toucanets has varied tremendously over the past century. Revisors seem to disagree on whether head and bill coloration are useful indicators of species limits, especially in the A. "prasinus" complex. Using morphometrics, I tested the hypothesis that the major color-based subspecific groups of A. "prasinus" sensu lato are simply "cookie-cutter" (i.e., morphologically nearly identical) toucanets with different head and bill colorations. Univariate and multivariate analyses show that they are not simply morphological replicates of different colors: a complex array of morphometric similarities and dissimilarities occur between the major subspecific groups, and these variations differ between the sexes. Latitude and longitude had a small but significant association with female (but not male) PC1 and PC2. Hybridization and intergradation were also considered using plumage and bill characters as a surrogate to infer gene flow. Hybridization as indicated by phenotype appears to be substantial between A. "p." cyanolaemus and A. "p." atrogularis and nonexistent between other major groups, although from genetic evidence it is likely rare between A. "p." albivitta and A. "p." cyanolaemus. The congruence and complexities of the morphological and color changes occurring among these groups suggest that ecological adaptation (through natural selection) and social selection have co-occurred among these groups and that species limits are involved. Further, hybridization is not evident at key places, despite in many cases (hypothetical) opportunity for gene flow. Consequently, I recommend that this complex be recognized as comprising five biological species: A. wagleri, prasinus, caeruleogularis, albivitta, and atrogularis. Four of these also have valid subspecies within them, and additional work may eventually support elevation of some of these subspecies to full species. Species limits in South America especially need more study.
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Affiliation(s)
- Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks
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628
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Bertola LD, Jongbloed H, van der Gaag KJ, de Knijff P, Yamaguchi N, Hooghiemstra H, Bauer H, Henschel P, White PA, Driscoll CA, Tende T, Ottosson U, Saidu Y, Vrieling K, de Iongh HH. Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo). Sci Rep 2016; 6:30807. [PMID: 27488946 PMCID: PMC4973251 DOI: 10.1038/srep30807] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.
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Affiliation(s)
- L D Bertola
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H Jongbloed
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - K J van der Gaag
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - P de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - N Yamaguchi
- Qatar University, Department of Biological and Environmental Sciences, College of Arts and Sciences, PO Box 2713, Doha, Qatar
| | - H Hooghiemstra
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - H Bauer
- WildCRU, Recanati-Kaplan Centre, University of Oxford. Tubney House, Abingdon Road, OX13 5QL, UK
| | - P Henschel
- Panthera, 8 West 40th Street, 18th Floor, New York, NY 10018, USA
| | - P A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - C A Driscoll
- Wildlife Institute of India, Dehradun 248001, Uttarakhand, India
| | - T Tende
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - U Ottosson
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - Y Saidu
- Nigeria National Park Service, PMB 0258 Garki-Abuja, Nigeria
| | - K Vrieling
- Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H H de Iongh
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,University of Antwerp, Department Biology, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
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629
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Ottenburghs J, Megens HJ, Kraus RH, Madsen O, van Hooft P, van Wieren SE, Crooijmans RP, Ydenberg RC, Groenen MA, Prins HH. A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese. Mol Phylogenet Evol 2016; 101:303-313. [DOI: 10.1016/j.ympev.2016.05.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 11/26/2022]
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630
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Piwczyński M, Pabijan M, Grzywacz A, Glinkowski W, Bereś PK, Buszko J. High regional genetic diversity and lack of host-specificity in Ostrinia nubilalis (Lepidoptera: Crambidae) as revealed by mtDNA variation. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:512-521. [PMID: 27019346 DOI: 10.1017/s0007485316000195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The European corn borer (Ostrinia nubilalis) infests a wide array of host plants and is considered one of the most serious pests of maize in Europe. Recent studies suggest that individuals feeding on maize in Europe should be referred to O. nubilalis (sensu nov.), while those infesting dicots as Ostrinia scapulalis (sensu nov.). We test if the clear genetic distinctiveness among individuals of O. nubilalis living on maize vs. dicots is tracked by mitochondrial DNA (mtDNA). We used fragments of COI and COII genes of 32 individuals traditionally recognized as O. nubilalis collected on three host plants, maize, mugwort and hop, growing in different parts of Poland. In addition, we reconstructed the mtDNA phylogeny of Ostrinia species based on our data and sequences retrieved from GenBank to assess host and/or biogeographic patterns. We also compared haplotype variation found in Poland (east-central Europe) with other regions (Anatolia, Eastern Europe, Balkans, Far East, North America). Our study showed high mtDNA diversity of O. nubilalis in Poland in comparison with other regions and revealed rare haplotypes likely of Asian origin. We did not find distinct mtDNA haplotypes in larvae feeding on maize vs. dicotyledonous plants. Phylogenetic analyses showed an apparent lack of mtDNA divergence among putatively distinct lineages belonging to the O. nubilalis group as identical haplotypes are shared by Asian and European individuals. We argue that human-mediated dispersal, hybridization and sporadic host jumps are likely responsible for the lack of a geographic pattern in mtDNA variation.
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Affiliation(s)
- M Piwczyński
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
| | - M Pabijan
- Department of Comparative Anatomy,Institute of Zoology,Jagiellonian University,Gronostajowa 9,30-387 Kraków,Poland
| | - A Grzywacz
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
| | - W Glinkowski
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
| | - P K Bereś
- Institute of Plant Protection - National Research Institute,Regional Experimental Station,Langiewicza 28,35-101 Rzeszów,Poland
| | - J Buszko
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
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631
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Ortiz D, Francke OF. Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae). Mol Phylogenet Evol 2016; 101:176-193. [DOI: 10.1016/j.ympev.2016.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/07/2016] [Accepted: 05/01/2016] [Indexed: 12/13/2022]
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632
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Hill GE. Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap. Ecol Evol 2016; 6:5831-42. [PMID: 27547358 PMCID: PMC4983595 DOI: 10.1002/ece3.2338] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.
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Affiliation(s)
- Geoffrey E. Hill
- Department Biological ScienceAuburn University331 Funchess HallAuburnAlabama36849‐5414
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633
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Mastrantonio V, Porretta D, Urbanelli S, Crasta G, Nascetti G. Dynamics of mtDNA introgression during species range expansion: insights from an experimental longitudinal study. Sci Rep 2016; 6:30355. [PMID: 27460445 PMCID: PMC4962091 DOI: 10.1038/srep30355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/30/2016] [Indexed: 11/23/2022] Open
Abstract
Introgressive hybridization represents one of the long-lasting debated genetic consequences of species range expansion. Mitochondrial DNA has been shown to heavily introgress between interbreeding animal species that meet in new sympatric areas and, often, asymmetric introgression from local to the colonizing populations has been observed. Disentangling among the evolutionary and ecological processes that might shape this pattern remains difficult, because they continuously act across time and space. In this context, long-term studies can be of paramount importance. Here, we investigated the dynamics of mitochondrial introgression between two mosquito species (Aedes mariae and Ae. zammitii ) during a colonization event that started in 1986 after a translocation experiment. By analyzing 1,659 individuals across 25 years, we showed that introgression occurred earlier and at a higher frequency in the introduced than in the local species, showing a pattern of asymmetric introgression. Throughout time, introgression increased slowly in the local species, becoming reciprocal at most sites. The rare opportunity to investigate the pattern of introgression across time during a range expansion along with the characteristics of our study-system allowed us to support a role of demographic dynamics in determining the observed introgression pattern.
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Affiliation(s)
- V Mastrantonio
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - D Porretta
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - S Urbanelli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - G Crasta
- Department of Mathematics, Sapienza University of Rome, Rome, Italy
| | - G Nascetti
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy
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634
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Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization. Heredity (Edinb) 2016; 117:358-366. [PMID: 27460499 DOI: 10.1038/hdy.2016.56] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 12/26/2022] Open
Abstract
Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern Massasauga Rattlesnake (Sistrurus catenatus). We then use coalescent-based modeling techniques to identify the evolutionary mechanisms responsible for the origin of the lineages in this species. We find equivocal evidence for distinct phylogenetic lineages within S. catenatus east of the Mississippi River, but strong support for a previously unrecognized lineage on the western edge of the range of this snake, represented by populations from Iowa, USA. Snakes from these populations show patterns of genetic admixture with a nearby non-threatened sister species (Sistrurus tergeminus). Tests of historical demographic models support the hypothesis that the genetic distinctiveness of Iowa snakes is due to a combination of isolation and historical introgression between S. catenatus and S. tergeminus. Our work provides an example of how model-based analysis of genomic-scale data can help identify conservation units in rare species.
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635
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Campbell KK, Braile T, Winker K. Integration of Genetic and Phenotypic Data in 48 Lineages of Philippine Birds Shows Heterogeneous Divergence Processes and Numerous Cryptic Species. PLoS One 2016; 11:e0159325. [PMID: 27442510 PMCID: PMC4956044 DOI: 10.1371/journal.pone.0159325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/30/2016] [Indexed: 12/19/2022] Open
Abstract
The Philippine Islands are one of the most biologically diverse archipelagoes in the world. Current taxonomy, however, may underestimate levels of avian diversity and endemism in these islands. Although species limits can be difficult to determine among allopatric populations, quantitative methods for comparing phenotypic and genotypic data can provide useful metrics of divergence among populations and identify those that merit consideration for elevation to full species status. Using a conceptual approach that integrates genetic and phenotypic data, we compared populations among 48 species, estimating genetic divergence (p-distance) using the mtDNA marker ND2 and comparing plumage and morphometrics of museum study skins. Using conservative speciation thresholds, pairwise comparisons of genetic and phenotypic divergence suggested possible species-level divergences in more than half of the species studied (25 out of 48). In speciation process space, divergence routes were heterogeneous among taxa. Nearly all populations that surpassed high genotypic divergence thresholds were Passeriformes, and non-Passeriformes populations surpassed high phenotypic divergence thresholds more commonly than expected by chance. Overall, there was an apparent logarithmic increase in phenotypic divergence with respect to genetic divergence, suggesting the possibility that divergence among these lineages may initially be driven by divergent selection in this allopatric system. Also, genetic endemism was high among sampled islands. Higher taxonomy affected divergence in genotype and phenotype. Although broader lineage, genetic, phenotypic, and numeric sampling is needed to further explore heterogeneity among divergence processes and to accurately assess species-level diversity in these taxa, our results support the need for substantial taxonomic revisions among Philippine birds. The conservation implications are profound.
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Affiliation(s)
- Kyle K. Campbell
- University of Alaska Museum and Department of Biology and Wildlife, Fairbanks, Alaska, United States of America
| | - Thomas Braile
- University of Alaska Museum and Department of Biology and Wildlife, Fairbanks, Alaska, United States of America
| | - Kevin Winker
- University of Alaska Museum and Department of Biology and Wildlife, Fairbanks, Alaska, United States of America
- * E-mail:
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636
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Mende MB, Bartel M, Hundsdoerfer AK. A comprehensive phylogeography of the Hyles euphorbiae complex (Lepidoptera: Sphingidae) indicates a 'glacial refuge belt'. Sci Rep 2016; 6:29527. [PMID: 27439775 PMCID: PMC4954964 DOI: 10.1038/srep29527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
We test the morphology based hypothesis that the Western Palaearctic spurge hawkmoths represent two species, the Eurasian H. euphorbiae and Afro-Macaronesian H. tithymali. It has been suggested that these species merged into several hybrid swarm populations, although a mitochondrial phylogeography revealed substructure with local differentiation. We analysed a three-gene mt-dataset (889 individuals) and 12 microsatellite loci (892 individuals). Microsatellite analyses revealed an overall weak differentiation and corroborated the superordinate division into two clusters. The data indicate that the populations studied belong to only one species according to the biological species concept, refuting the opening hypothesis. A future taxonomic revision appears necessary to reflect the division into two subgroups. Ancestral mitochondrial polymorphisms are retained in H. euphorbiae, indicating gene flow within a broad 'glacial refuge belt' and ongoing postglacial gene flow. Diverse patterns of extensive mito-nuclear discordance in the Mediterranean and the Middle East presumably evolved by more recent processes. This discordance indicates introgression of H. tithymali-related mitochondrial haplogroups, accompanied (to a lesser degree) by nuclear alleles, into Italian and Aegean H. euphorbiae populations as recently as the late Holocene. The complex mosaic of divergence and reintegration is assumed to have been influenced by locally differing environmental barriers to gene flow.
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Affiliation(s)
- Michael B Mende
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Morphologie, Systematik und Evolutionsbiologie, Berliner Str. 28, D-37073 Göttingen, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Manuela Bartel
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany
| | - Anna K Hundsdoerfer
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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637
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Phylogeography and population genetics of Schizothorax o'connori: strong subdivision in the Yarlung Tsangpo River inferred from mtDNA and microsatellite markers. Sci Rep 2016; 6:29821. [PMID: 27425185 PMCID: PMC4947931 DOI: 10.1038/srep29821] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 06/27/2016] [Indexed: 11/08/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) is a biodiversity hotspot, resulting from its geological history, contemporary environment and isolation. Uplift of the QTP and Quaternary climatic oscillations are hypothesised to have influenced the genetic diversity, population structure and dynamics of all QTP endemic species. In this study, we tested this hypothesis by assaying variation at two mitochondrial DNA regions (cytochrome b and control region) and at 12 microsatellite loci of seven populations of the endemic fish, Schizothorax o'connori from the Yarlung Tsangpo River (YLTR) on the QTP. Analyses revealed one group of six populations to the west, above the Yarlung Tsangpo Grand Canyon (YTGC), and a second group to the east below the YTGC. Estimates of the timing of this east-west split indicate that these groups represent evolutionarily significant units that have evolved separately and rapidly in the middle Pleistocene, at the time of the Kunlun-Huanghe Movement A Phase and the Naynayxungla glaciation. Population dynamic analyses indicate that S. o'connori experienced a pronounced late Pleistocene expansion during the last interglacial period. The results of this study support the hypotheses that the QTP uplift and Quaternary climatic oscillations have played important roles in shaping the population genetics and dynamics of this endemic fish.
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638
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639
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Jelić M, Klobučar GIV, Grandjean F, Puillandre N, Franjević D, Futo M, Amouret J, Maguire I. Insights into the molecular phylogeny and historical biogeography of the white-clawed crayfish (Decapoda, Astacidae). Mol Phylogenet Evol 2016; 103:26-40. [PMID: 27404041 DOI: 10.1016/j.ympev.2016.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/04/2023]
Abstract
In this study, the evolutionary history of the white-clawed crayfish (WCC) was evaluated using large-scale datasets comprising >1350 specimens from the entire distribution range. Using species delimitation methods on mitochondrial DNA (mtDNA) sequences, we propose four primary species hypotheses for WCC. Sequences for several nuclear regions were screened but none showed significant variation within WCC. This result favours a single secondary species hypothesis and indicates the existence of a mito-nuclear discordance in WCC. Therefore, mtDNA groups were considered only as genetic units that carry information about ancient divergences within WCC and not as taxonomic units. The reconstruction of ancestral ranges and divergence time estimates were used to link the current genetic structure with paleogeographic processes. These results showed that the emergence of mtDNA groups in WCC could be related to the Messinian Salinity Crisis, the climate cooling during the Pliocene and Pleistocene, and (paleo)shifting of the Adriatic Sea coastline in the Padanovenezian Plain. The most recent common ancestor of the mtDNA groups most likely originated from Dalmatia (eastern Adriatic coast) as indicated by the reconstruction of ancestral ranges. This ecoregion, along with the Gulf of Venice Drainages, harbours a high genetic diversity and should be emphasised as an area of the highest conservation priority.
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Affiliation(s)
- Mišel Jelić
- University of Zagreb, Faculty of Science, Department of Biology, Division of Zoology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Göran I V Klobučar
- University of Zagreb, Faculty of Science, Department of Biology, Division of Zoology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Frédéric Grandjean
- Université de Poitiers, UMR CNRS 7267, Laboratoire "Ecologie et Biologie des Interactions", équipe "Ecologie, Evolution, Symbiose", 6 rue Michel Brunet, F-86073 Poitiers, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE Muséum national d'Histoire naturelle, Sorbonne Universités, 43 rue Cuvier, CP26 F-75005 Paris, France
| | - Damjan Franjević
- University of Zagreb, Faculty of Science, Department of Biology, Division of Zoology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Momir Futo
- University of Münster, Institute for Evolution and Biodiversity, Animal Evolutionary Ecology Group, Hüfferstrasse 1, D-48149 Münster, Germany
| | - Julien Amouret
- University of Iceland, Department of Life and Environmental Sciences, Sturlugötu 7, 101 Reykjavík, Iceland
| | - Ivana Maguire
- University of Zagreb, Faculty of Science, Department of Biology, Division of Zoology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia.
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640
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Fratini S, Ragionieri L, Cannicci S. Demographic History and Reproductive Output Correlates with Intraspecific Genetic Variation in Seven Species of Indo-Pacific Mangrove Crabs. PLoS One 2016; 11:e0158582. [PMID: 27379532 PMCID: PMC4933389 DOI: 10.1371/journal.pone.0158582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/17/2016] [Indexed: 11/18/2022] Open
Abstract
The spatial distribution and the amount of intraspecific genetic variation of marine organisms are strongly influenced by many biotic and abiotic factors. Comparing biological and genetic data characterizing species living in the same habitat can help to elucidate the processes driving these variation patterns. Here, we present a comparative multispecies population genetic study on seven mangrove crabs co-occurring in the West Indian Ocean characterized by planktotrophic larvae with similar pelagic larval duration. Our main aim was to investigate whether a suite of biological, behavioural and ecological traits could affect genetic diversities of the study species in combination with historical demographic parameters. As possible current explanatory factors, we used the intertidal micro-habitat colonised by adult populations, various parameters of individual and population fecundity, and the timing of larval release. As the genetic marker, we used partial sequences of cytochrome oxidase subunit I gene. Genetic and ecological data were collected by the authors and/or gathered from primary literature. Permutational multiple regression models and ANOVA tests showed that species density and their reproductive output in combination with historical demographic parameters could explain the intraspecific genetic variation indexes across the seven species. In particular, species producing consistently less eggs per spawning event showed higher values of haplotype diversity. Moreover, Tajima's D parameters well explained the recorded values for haplotype diversity and average γst. We concluded that current intraspecific gene diversities in crabs inhabiting mangrove forests were affected by population fecundity as well as past demographic history. The results were also discussed in terms of management and conservation of fauna in the Western Indian Ocean mangroves.
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Affiliation(s)
- Sara Fratini
- Department of Biology, University of Florence, Firenze, Italy
| | - Lapo Ragionieri
- Institute for Zoology, Functional Peptidomics, University of Cologne, Cologne, Germany
| | - Stefano Cannicci
- Department of Biology, University of Florence, Firenze, Italy
- The Swire Institute of Marine Science and the School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
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641
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Dufresnes C, Litvinchuk SN, Leuenberger J, Ghali K, Zinenko O, Stöck M, Perrin N. Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis). Mol Ecol 2016; 25:4285-300. [PMID: 27220555 DOI: 10.1111/mec.13706] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/26/2016] [Accepted: 05/11/2016] [Indexed: 11/30/2022]
Abstract
Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg, 194064, Russia
| | - Julien Leuenberger
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Karim Ghali
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Oleksandr Zinenko
- The Museum of Nature, V. N. Karazin Kharkiv National University, Trinkler st. 8, Kharkiv, 61058, Ukraine
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, Berlin, D-12587, Germany
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
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642
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El Mokhefi M, Kerdelhué C, Burban C, Battisti A, Chakali G, Simonato M. Genetic differentiation of the pine processionary moth at the southern edge of its range: contrasting patterns between mitochondrial and nuclear markers. Ecol Evol 2016; 6:4274-88. [PMID: 27386074 PMCID: PMC4884675 DOI: 10.1002/ece3.2194] [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: 01/19/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 01/27/2023] Open
Abstract
The pine processionary moth (Thaumetopoea pityocampa) is an important pest of coniferous forests at the southern edge of its range in Maghreb. Based on mitochondrial markers, a strong genetic differentiation was previously found in this species between western (pityocampa clade) and eastern Maghreb populations (ENA clade), with the contact zone between the clades located in Algeria. We focused on the moth range in Algeria, using both mitochondrial (a 648 bp fragment of the tRNA-cox2) and nuclear (11 microsatellite loci) markers. A further analysis using a shorter mtDNA fragment and the same microsatellite loci was carried out on a transect in the contact zone between the mitochondrial clades. Mitochondrial diversity showed a strong geographical structure and a well-defined contact zone between the two clades. In particular, in the pityocampa clade, two inner subclades were found whereas ENA did not show any further structure. Microsatellite analysis outlined a different pattern of differentiation, with two main groups not overlapping with the mitochondrial clades. The inconsistency between mitochondrial and nuclear markers is probably explained by sex-biased dispersal and recent afforestation efforts that have bridged isolated populations.
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Affiliation(s)
- M'hamed El Mokhefi
- Département de Zoologie Agricole et ForestièreEcole Nationale Supérieure AgronomiqueEl‐Harrach16200AlgiersAlgeria
| | | | | | - Andrea Battisti
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE)University of PaduaViale dell'Università 1635020Legnaro (PD)Italy
| | - Gahdab Chakali
- Département de Zoologie Agricole et ForestièreEcole Nationale Supérieure AgronomiqueEl‐Harrach16200AlgiersAlgeria
| | - Mauro Simonato
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE)University of PaduaViale dell'Università 1635020Legnaro (PD)Italy
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643
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Verovnik R, Wiemers M. Species delimitation in the Grayling genus Pseudochazara (Lepidoptera, Nymphalidae, Satyrinae) supported by DNA barcodes. Zookeys 2016; 600:131-54. [PMID: 27408604 PMCID: PMC4926685 DOI: 10.3897/zookeys.600.7798] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/09/2016] [Indexed: 11/12/2022] Open
Abstract
The Palaearctic Grayling genus Pseudochazara encompasses a number of petrophilous butterfly species, most of which are local endemics especially in their centre of radiation in SW Asia and the Balkans. Due to a lack of consistent morphological characters, coupled with habitat induced variability, their taxonomy is poorly understood and species delimitation is hampered. We employed a DNA barcoding approach to address the question of separate species status for several European taxa and provide first insight into the phylogeny of the genus. Unexpectedly we found conflicting patterns with deep divergences between presumably conspecific taxa and lack of divergence among well-defined species. We propose separate species status for Pseudochazara tisiphone, Pseudochazara amalthea, Pseudochazara amymone, and Pseudochazara kermana all of which have separate well supported clades, with the majority of them becoming local endemics. Lack of resolution in the 'Mamurra' species group with well-defined species (in terms of wing pattern and coloration) such as Pseudochazara geyeri, Pseudochazara daghestana and Pseudochazara alpina should be further explored using nuclear molecular markers with higher genetic resolution.
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Affiliation(s)
- Rudi Verovnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjev 101, Ljubljana, Slovenia
| | - Martin Wiemers
- UFZ – Helmholtz-Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120 Halle, Germany
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644
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Streicher JW, McEntee JP, Drzich LC, Card DC, Schield DR, Smart U, Parkinson CL, Jezkova T, Smith EN, Castoe TA. Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes. Evolution 2016; 70:1435-49. [DOI: 10.1111/evo.12967] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 04/30/2016] [Accepted: 05/16/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Jeffrey W. Streicher
- Department of Life Sciences The Natural History Museum London United Kingdom
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Jay P. McEntee
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
- Department of Biology University of Florida Gainesville Florida
| | - Laura C. Drzich
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Daren C. Card
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Drew R. Schield
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Utpal Smart
- Department of Biology University of Texas at Arlington Arlington Texas
| | | | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
| | - Eric N. Smith
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Todd A. Castoe
- Department of Biology University of Texas at Arlington Arlington Texas
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645
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Egizi A, Kiser J, Abadam C, Fonseca DM. The hitchhiker's guide to becoming invasive: exotic mosquitoes spread across a US state by human transport not autonomous flight. Mol Ecol 2016; 25:3033-47. [PMID: 27087539 DOI: 10.1111/mec.13653] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/10/2016] [Accepted: 03/31/2016] [Indexed: 02/03/2023]
Abstract
Not all exotic species establish and expand aggressively (i.e. become invasive). As potential vectors of disease agents, invasive mosquitoes can have considerable impact on public health, livestock and wildlife; therefore, understanding the species characteristics and ecological circumstances promoting their invasiveness is important. The mosquito Aedes japonicus japonicus, originally from north-east Asia, was introduced at least two separate times to the north-eastern USA, as surmised from the initial existence of two populations with distinct nuclear and mitochondrial genetic signatures that later intermixed. Since these original introductions in the late 1990s, Ae. j. japonicus has expanded across 31 US states, two Canadian provinces and five European countries. Although some of the expanded range was due to other independent introductions, to understand what drove the postintroduction expansion of Ae. j. japonicus within the north-eastern USA, we performed a high-resolution landscape genetic analysis of 461 specimens collected across Virginia, a state south of the original introductions. All specimens were genotyped at seven pre-optimized microsatellite loci, and a subsample was sequenced at one mitochondrial locus. We concluded that throughout Virginia this species has primarily expanded in association with humans: genetic distance and distance along roads remained correlated after controlling for geographic distance, and proximity to I-95, a major interstate highway, strongly predicted nuclear ancestry. In contrast, there was very limited evidence of diffusion even at distances potentially suitable for autonomous mosquito flight. This implies that its association with humans (rather than innate species characteristics) is the single most important determinant of invasiveness in this mosquito.
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Affiliation(s)
- Andrea Egizi
- Department of Entomology, Rutgers University, 180 Jones Ave, New Brunswick, NJ, 08901, USA.,Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ, USA
| | - Jay Kiser
- City of Suffolk Mosquito Control, 866 Carolina Rd., Suffolk, VA, 23434, USA
| | - Charles Abadam
- City of Suffolk Mosquito Control, 866 Carolina Rd., Suffolk, VA, 23434, USA
| | - Dina M Fonseca
- Department of Entomology, Rutgers University, 180 Jones Ave, New Brunswick, NJ, 08901, USA.,Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ, USA
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646
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Menezes L, Canedo C, Batalha-Filho H, Garda AA, Gehara M, Napoli MF. Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest. PLoS One 2016; 11:e0154626. [PMID: 27248688 PMCID: PMC4889069 DOI: 10.1371/journal.pone.0154626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/16/2016] [Indexed: 11/21/2022] Open
Abstract
We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.
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Affiliation(s)
- Lucas Menezes
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Clarissa Canedo
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Henrique Batalha-Filho
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Adrian Antonio Garda
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Botânica, Ecologia e Zoologia, Laboratório de Anfíbios e Répteis-LAR, Campus Universitário, Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Gehara
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Felgueiras Napoli
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
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647
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Card DC, Schield DR, Adams RH, Corbin AB, Perry BW, Andrew AL, Pasquesi GIM, Smith EN, Jezkova T, Boback SM, Booth W, Castoe TA. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism. Mol Phylogenet Evol 2016; 102:104-16. [PMID: 27241629 DOI: 10.1016/j.ympev.2016.05.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 05/05/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras.
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Affiliation(s)
- Daren C Card
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Drew R Schield
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Richard H Adams
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Andrew B Corbin
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Blair W Perry
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Audra L Andrew
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Giulia I M Pasquesi
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Eric N Smith
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Tereza Jezkova
- Department of Ecology & Evolutionary Biology, University of Arizona, P.O. Box 210088, Tucson, AZ 85721, USA
| | - Scott M Boback
- Department of Biology, P.O. Box 1773, Dickinson College, Carlisle, PA 17013, USA
| | - Warren Booth
- Department of Biological Science, 800 South Tucker Drive, University of Tulsa, Tulsa, OK 74104, USA
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA.
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648
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Testing heterogeneous base composition as potential cause for conflicting phylogenetic signal between mitochondrial and nuclear DNA in the land snail genus Theba Risso 1826 (Gastropoda: Stylommatophora: Helicoidea). ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0288-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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649
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Yassin A. Unresolved questions in genitalia coevolution: bridging taxonomy, speciation, and developmental genetics. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0286-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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650
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Wang N, Liang B, Wang J, Yeh CF, Liu Y, Liu Y, Liang W, Yao CT, Li SH. Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves). Mol Phylogenet Evol 2016; 102:62-73. [PMID: 27233437 DOI: 10.1016/j.ympev.2016.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 04/26/2016] [Accepted: 05/20/2016] [Indexed: 01/11/2023]
Abstract
Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process.
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Affiliation(s)
- Ning Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Bin Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jichao Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yang Liu
- State Key Laboratory of BioControl, College of Ecology and Evolution/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanlin Liu
- Institute of Forestry Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Cheng-Te Yao
- High-Altitude Experimental Station, Taiwan Endemic Species Research Institute, Chi-chi 55244, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan.
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