551
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Phuong MA, Bi K, Moritz C. Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex. Mol Ecol 2017; 26:4743-4755. [PMID: 28734067 DOI: 10.1111/mec.14238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/15/2017] [Indexed: 01/06/2023]
Abstract
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture data set and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000 years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male-biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal-biased X-chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.
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Affiliation(s)
- Mark A Phuong
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Ke Bi
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Craig Moritz
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Acton, ACT, Australia
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552
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Battey C, Klicka J. Cryptic speciation and gene flow in a migratory songbird Species Complex: Insights from the Red-Eyed Vireo (Vireo olivaceus). Mol Phylogenet Evol 2017; 113:67-75. [DOI: 10.1016/j.ympev.2017.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/07/2017] [Accepted: 05/08/2017] [Indexed: 12/15/2022]
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553
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Uit de Weerd DR, Fernández Velázquez A. Pinning down Tenuistemma (Pulmonata: Urocoptidae): local evolution of an extreme shell type. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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554
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Signatures of mito-nuclear discordance in Schistosoma turkestanicum indicate a complex evolutionary history of emergence in Europe. Parasitology 2017; 144:1752-1762. [PMID: 28747240 DOI: 10.1017/s0031182017000920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
High levels of molecular diversity were identified in mitochondrial cytochrome c oxidase (cox1) gene sequences of Schistosoma turkestanicum from Hungary. These cox1 sequences were all specific to Hungary which contrasted with the low levels of diversity seen in the nuclear internal transcribed spacer region (ITS) sequences, the majority of which were shared between China and Iran isolates. Measures of within and between host molecular variation within S. turkestanicum showed there to be substantial differences in molecular diversity, with cox1 being significantly more diverse than the ITS. Measures of haplotype frequencies revealed that each host contained its own subpopulation of genetically unique parasites with significant levels of differentiation. Pairwise mismatch analysis of cox1 sequences indicated S. turkestanicum populations to have a bimodal pairwise difference distribution and to be stable unlike the ITS sequences, which appeared to have undergone a recent population expansion event. Positive selection was also detected in the cox1 sequences, and biochemical modelling of the resulting protein illustrated significant mutational events causing an alteration to the isoelectric point of the cox1 protein, potentially altering metabolism. The evolutionary signature from the cox1 indicates local adaptation and long establishment of S. turkestanicum in Hungary with continual introgression of nuclear genes from Asian isolates. These processes have led to the occurrence of mito-nuclear discordance in a schistosome population.
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555
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De Ré FC, Robe LJ, Wallau GL, Loreto ELS. Inferring the phylogenetic position of the Drosophila flavopilosa
group: Incongruence within and between mitochondrial and nuclear multilocus datasets. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Francine C. De Ré
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
| | - Lizandra J. Robe
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
- Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais; Universidade Federal do Rio Grande (FURG); Rio Grande Rio Grande do Sul Brazil
| | - Gabriel L. Wallau
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
- Departamento de Entomologia; Instituto Aggeu Magalhães - FIOCRUZ-IAM; Recife PE Brazil
| | - Elgion L. S. Loreto
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
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556
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Scicchitano V, Dedeine F, Bagnères AG, Luchetti A, Mantovani B. Genetic diversity and invasion history of the European subterranean termite Reticulitermes urbis (Blattodea, Termitoidae, Rhinotermitidae). Biol Invasions 2017. [DOI: 10.1007/s10530-017-1510-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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557
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Motochin R, Wang M, Ueshima R. Molecular phylogeny, frequent parallel evolution and new system of Japanese clausiliid land snails (Gastropoda: Stylommatophora). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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558
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Ortego J, Noguerales V, Cordero PJ. Geographical and Ecological Drivers of Mitonuclear Genetic Divergence in a Mediterranean Grasshopper. Evol Biol 2017. [DOI: 10.1007/s11692-017-9423-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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559
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Liu Y, Fend SV, Martinsson S, Luo X, Ohtaka A, Erséus C. Multi-locus phylogenetic analysis of the genus Limnodrilus (Annelida: Clitellata: Naididae). Mol Phylogenet Evol 2017; 112:244-257. [DOI: 10.1016/j.ympev.2017.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/24/2017] [Accepted: 04/20/2017] [Indexed: 12/14/2022]
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560
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Greve C, Haase M, Hutterer R, Rödder D, Ihlow F, Misof B. Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa. Ecol Evol 2017; 7:5524-5538. [PMID: 28770088 PMCID: PMC5528248 DOI: 10.1002/ece3.3138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 05/11/2017] [Accepted: 05/13/2017] [Indexed: 11/10/2022] Open
Abstract
The spatial subdivision of species often plays a pivotal role in speciation. Across their entire range, species are rarely panmictic and crucial consequences of spatial subdivision are (1) random genetic drift including historical factors, (2) uniform selection, and (3) divergent selection. Each of these consequences may result in geographic variation and eventually reproductive isolation, but their relative importance in speciation is still unclear. In this study, we used a combination of genetic, morphological, and climatic data to obtain a comprehensive picture of differentiation among three closely related, parapatrically distributed taxa of the land snail genus Theba occurring along the Atlantic coasts of South Morocco and Western Sahara. We conducted Mantel and partial Mantel tests to relate phenotypic and genotypic variation of these species to geography and/or climate. As null hypothesis for an evolutionary scenario, we assumed nonadaptive speciation and expected a pattern of isolation by distance among taxa. Rejection of the null hypothesis would indicate isolation by environment due to adaptation. Generally, genetic drift plays an important role but is rarely considered as sole driver of speciation. It is the combination of drift and selection that predominantly drives speciation. This study, however, provides a potential example, in which nonadaptive speciation, that is, genetic drift, is apparently the main driver of shaping the diversity of Theba in NW Africa. Restriction of gene flow between populations caused by geographic isolation probably has played an important role. Climate oscillations during the Plio- and Pleistocene may have led to repeated ecological changes in NW Africa and disruptions of habitats promoting differentiation by geographic isolation. The inferred evolutionary scenario, however, did not fully explain the incongruence between the AFLP- and mtDNA-tree topologies. This incongruence might indicate past hybridization among the studied Theba forms.
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Affiliation(s)
- Carola Greve
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Martin Haase
- Vogelwarte, Zoologisches Institut und MuseumErnst‐Moritz‐Arndt‐Universität GreifswaldGreifswaldGermany
| | - Rainer Hutterer
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Dennis Rödder
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Flora Ihlow
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Bernhard Misof
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
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561
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Boonkhaw P, Prayoon U, Kanchanasaka B, Hayashi F, Tamura N. Colour polymorphism and genetic relationships among twelve subspecies of Callosciurus finlaysonii in Thailand. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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562
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Caron Y, Celi-Erazo M, Hurtrez-Boussès S, Lounnas M, Pointier JP, Saegerman C, Losson B, Benítez-Ortíz W. Is Galba schirazensis (Mollusca, Gastropoda) an intermediate host of Fasciola hepatica (Trematoda, Digenea) in Ecuador? Parasite 2017; 24:24. [PMID: 28664841 PMCID: PMC5492793 DOI: 10.1051/parasite/2017026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/14/2017] [Indexed: 11/25/2022] Open
Abstract
Fasciolosis is a widely distributed disease in livestock in South America but knowledge about the epidemiology and the intermediate hosts is relatively scarce in Ecuador. For three months, lymnaeid snails were sampled (n = 1482) in Pichincha Province at two sites located in a highly endemic area. Snails were identified (based on morphology and ITS-2 sequences) and the infection status was established through microscopic dissection and a multiplex polymerase chain reaction (PCR)-based technique. Techniques based on morphology were not useful to accurately name the collected snail species. Comparison with available DNA sequences showed that a single snail species was collected, Galba schirazensis. Live rediae were observed in 1.75% (26/1482) and Fasciola sp. DNA was detected in 6% (89/1482) of collected snails. The COX-1 region permitted identification of the parasite as Fasciola hepatica. The relative sensitivity and specificity of the microscope study, compared to PCR results, were 25.84% and 99.78%, respectively. The mean size of the snails recorded positive for F. hepatica through crushing and microscopy was significantly higher than the mean size of negative snails, but there was no such difference in PCR-positive snails. The role of G. schirazensis as an intermediate host of F. hepatica in Ecuador is discussed and the hypothesis of an adaptation of the parasite to this invasive snail is proposed. For the first time, an epidemiological survey based on molecular biology-based techniques assessed the possible role of lymnaeid snails in the epidemiology of fasciolosis in Ecuador.
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Affiliation(s)
- Yannick Caron
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Parasitology and Pathology of Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège Quartier Vallée 2, 6 Avenue de Cureghem 4000
Liège Belgium
| | - Maritza Celi-Erazo
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International Center for Zoonosis, Day Hospital, Central University of Ecuador PO Box 17-03-100
Quito Ecuador
| | - Sylvie Hurtrez-Boussès
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MIVEGEC, UMR IRD 224-CNRS 5290-UM 911 Avenue Agropolis 34394
Montpellier France
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Department of Biology Ecology (Sciences Faculty), Montpellier University 2 Place Pierre Viala 34060
Montpellier France
| | - Mannon Lounnas
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MIVEGEC, UMR IRD 224-CNRS 5290-UM 911 Avenue Agropolis 34394
Montpellier France
| | - Jean-Pierre Pointier
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PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Perpignan University 58 Avenue Paul Alduy 66860
Perpignan France
| | - Claude Saegerman
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Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULg), Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège Quartier Vallée 2, 7A-7D Avenue de Cureghem 4000
Liège Belgium
| | - Bertrand Losson
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Parasitology and Pathology of Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège Quartier Vallée 2, 6 Avenue de Cureghem 4000
Liège Belgium
| | - Washington Benítez-Ortíz
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International Center for Zoonosis, Day Hospital, Central University of Ecuador PO Box 17-03-100
Quito Ecuador
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Veterinary Medicine and Zootechny Faculty, Avenida América, Central University of Ecuador PO Box 17-03-100
Quito Ecuador
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563
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Abstract
Human-mediated secondary contact of recently diverged taxa offers valuable opportunities for studying the evolutionary mechanisms involved in the establishment and maintenance of genetic boundaries between taxa. We used mitochondrial and microsatellite markers to examine a recently introduced population of the spur-thighed tortoise (Testudo graeca) of mixed origin in the Doñana National Park (SW Spain). The earliest records of tortoises in Doñana trace back to the 18th century, but several population reinforcements in the 20th century with animals from Morocco are well-documented. Consequently, different genetic lineages, which represent distinct subspecies, are thought to co-exist there. Our results confirmed the presence of distinct lineages by revealing that tortoises of the subspecies T. g. marokkensis were introduced into a local allochthonous T. g. graeca population. Unexpectedly, T. g. marokkensis haplotypes exclusively appeared in males, and admixture levels were statistically sex-biased toward males. The sex ratio of the population deviated from parity, with males being 2.36-fold more abundant than females. Our results indicated that population reinforcements had a strong effect on the genetic composition of this population and aggravated its sex ratio deviation. We predict that this sex-biased pattern of introgression is ephemeral and advocated to the near loss of T. g. marokkensis haplotypes.
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564
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Experimental Support That Natural Selection Has Shaped the Latitudinal Distribution of Mitochondrial Haplotypes in Australian Drosophila melanogaster. Mol Biol Evol 2017. [DOI: 10.1093/molbev/msx184] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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565
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Ribardière A, Daguin-Thiébaut C, Houbin C, Coudret J, Broudin C, Timsit O, Broquet T. Geographically distinct patterns of reproductive isolation and hybridization in two sympatric species of the Jaera albifrons complex (marine isopods). Ecol Evol 2017; 7:5352-5365. [PMID: 28770073 PMCID: PMC5528242 DOI: 10.1002/ece3.3106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 01/25/2023] Open
Abstract
Sympatric species that in some populations hybridize and in other populations remain reproductively isolated open interesting research possibilities for the study of hybridization and speciation. Here, we test for such a situation in two littoral isopods (Jaera albifrons and J. praehirsuta) that occur in mixed populations and where past morphological descriptions suggested that the two species are generally reproductively isolated except in rare populations where hybridization may be happening. Using field surveys and microsatellite genetic structure analyses in two regions from France (Normandy and Brittany), we confirmed that introgressive hybridization occurs in a subset of mixed J. albifrons/J. praehirsuta populations (region Normandy) where the two species are found in the same habitat (pebbles on the shore). Moreover, we found that introgression in these populations is differential, 21 of 23 microsatellite markers showing little genetic divergence between species (hierarchical analysis of molecular variance FCT = 0.017) while the remaining two loci were strongly differentiated (FCT = 0.428). By contrast, J. albifrons and J. praehirsuta in mixed populations from region Brittany occupied distinct habitats (pebbles and seaweeds, respectively) with little overlap and showed stronger genetic divergence (FCT = 0.132). In hybridizing populations, the majority of individuals show morphological traits that are characteristic of one or the other species. This raises the question of the forces that act to maintain this polymorphism, noting that hybridizing populations seem to be geographically isolated from potential source parental populations and show no detectable habitat divergence between species.
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Affiliation(s)
- Ambre Ribardière
- Centre National de la Recherche Scientifique Team Diversity and Connectivity of Coastal Marine Landscapes Roscoff France.,Sorbonne Universités UPMC Univ Paris 06 Roscoff France
| | - Claire Daguin-Thiébaut
- Centre National de la Recherche Scientifique Team Diversity and Connectivity of Coastal Marine Landscapes Roscoff France.,Sorbonne Universités UPMC Univ Paris 06 Roscoff France
| | - Céline Houbin
- Sorbonne Universités UPMC Univ Paris 06 Roscoff France.,Centre National de la Recherche Scientifique Roscoff France
| | - Jérôme Coudret
- Centre National de la Recherche Scientifique Team Diversity and Connectivity of Coastal Marine Landscapes Roscoff France.,Sorbonne Universités UPMC Univ Paris 06 Roscoff France
| | - Caroline Broudin
- Sorbonne Universités UPMC Univ Paris 06 Roscoff France.,Centre National de la Recherche Scientifique Roscoff France
| | - Olivier Timsit
- Groupe d'Etude des Milieux Estuariens et Littoraux de Normandie Centre Régional d'Etudes Côtières Luc-sur-Mer France
| | - Thomas Broquet
- Centre National de la Recherche Scientifique Team Diversity and Connectivity of Coastal Marine Landscapes Roscoff France.,Sorbonne Universités UPMC Univ Paris 06 Roscoff France
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566
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Quaternary history, population genetic structure and diversity of the cold-adapted Alpine newt Ichthyosaura alpestris in peninsular Italy. Sci Rep 2017; 7:2955. [PMID: 28592856 PMCID: PMC5462806 DOI: 10.1038/s41598-017-03116-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022] Open
Abstract
Mediterranean peninsulas are major biodiversity hotspots, and cold-adapted species are an important component of this biodiversity. However, cold-adapted species contributed surprisingly little to our knowledge of the intimate links between Quaternary environmental changes, species' responses to these changes, and current patterns of intraspecific biodiversity. Here, we investigated the genetic structure and evolutionary history of a cold-adapted amphibian, the Alpine newt Ichthyosaura alpestris, within the Italian peninsula. Nuclear and mitochondrial markers consistently identified three distinct genetic lineages, whose divergence dates to the Early Pleistocene (1.9 and 0.8 million years ago). Our results show that the Italian peninsula provided multiple Pleistocene refugia to this cold-adapted species, and suggest that allopatric fragmentation followed by secondary admixture have been key events in the formation of its current pattern of genetic diversity. Indeed, estimates of population genetic diversity clearly identified contact populations as those achieving the highest levels of diversity. Such concordance among cold-adapted and temperate species in terms of processes triggering the formation of regional patterns of genetic diversity provides strong support for the hypothesis that gene exchange between divergent lineages, rather than long-term stability of refugial populations, has been the main step toward the formation of hotspots of intraspecific biodiversity.
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567
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Kim JK, Bae SE, Lee SJ, Yoon MG. New insight into hybridization and unidirectional introgression between Ammodytes japonicus and Ammodytes heian (Trachiniformes, Ammodytidae). PLoS One 2017; 12:e0178001. [PMID: 28582394 PMCID: PMC5459329 DOI: 10.1371/journal.pone.0178001] [Citation(s) in RCA: 6] [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: 02/03/2017] [Accepted: 05/05/2017] [Indexed: 11/19/2022] Open
Abstract
Based on northern (NOL) and southern (SOL) mitochondrial lineages, recently, it proposed the new species Ammodytes heian and revived the species name Ammodytes japonicus to describe sand lances from the northwestern Pacific Ocean. This study used molecular methods to investigate genetic relationships between the two sand lance species in Korea and Japan. In total, 154 specimens were collected from four locations in Korea (Baengnyeongdo in the Yellow Sea, Tongyeong in the Korean Strait, and Jumunjin and Gijang in the East Sea), and 50 specimens were collected from a single location in Japan (Wakkanai in the Okhotsk Sea). Mitochondrial DNA analysis demonstrated that the individuals from Baengnyeongdo and Tongyeong all belonged to the SOL, whereas those from Gijang, Jumunjin, and Wakkanai included individuals from both the NOL and SOL (over 75% NOL). Population structure analyses were performed on the same individuals using seven microsatellite DNA markers. The population structure analysis based on 201 specimens identified two clusters (named as northern group and southern group), with the admixture proportion (q) of < 0.1 for the northern group in the Backyeongdo and Tongyeong sand lances and < 0.1 for the southern group in the Wakkanai sand lances. The high heterogeneity indicated that the former was probably A. japonicus and the latter probably A. heian. However, the admixture proportion in the Jumunjin and Gijang sand lances was 0.71–0.75 for the southern group, indicating that hybridization and unidirectional introgression from SOL to NOL occurs in southwestern margin of the East Sea. Our findings illustrate the speciation process based on different patterns of gene flow between Korean and Japanese sand lance, which is strongly influenced by both the paleo-climatic change and the contemporary local oceanic current pattern.
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Affiliation(s)
- Jin-Koo Kim
- Department of Marine Biology, Pukyong National University, Busan, Korea
- * E-mail:
| | - Seung Eun Bae
- Department of Marine Biology, Pukyong National University, Busan, Korea
| | - Soo Jeong Lee
- Department of Marine Biology, Pukyong National University, Busan, Korea
- Fisheries Resources and Environment Division, East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangnung, Korea
| | - Moon Geun Yoon
- Marine Biodiversity Institute of Korea, Seocheon-gun, Chungcheongnam-do, Korea
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568
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Mclean AJ, Joseph L, Toon A, Schmidt DJ, Drew A, Mason IJ, Hughes JM. Reassessment of a possible case of intraspecific gene flow across Australia’s Great Dividing Range in the variegated fairy wren, Malurus lamberti (Aves: Maluridae), and its systematic consequences. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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569
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Kuo HC, Soisook P, Ho YY, Csorba G, Wang CN, Rossiter SJ. A Taxonomic Revision of the Kerivoula hardwickii Complex (Chiroptera: Vespertilionidae) with the Description of a New Species. ACTA CHIROPTEROLOGICA 2017. [DOI: 10.3161/15081109acc2017.19.1.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Hao-Chih Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Ying-Yi Ho
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Gabor Csorba
- Department of Zoology, Hungarian Natural History Museum, Baross u. 13, H-1088 Budapest, Hungary
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
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570
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Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa. Mol Phylogenet Evol 2017; 111:132-148. [DOI: 10.1016/j.ympev.2017.03.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 03/26/2017] [Accepted: 03/26/2017] [Indexed: 11/18/2022]
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571
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Singhal S, Grundler M, Colli G, Rabosky DL. Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Mol Ecol Resour 2017; 17:e12-e24. [PMID: 28417603 DOI: 10.1111/1755-0998.12681] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/05/2017] [Accepted: 04/03/2017] [Indexed: 11/28/2022]
Abstract
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches-anchored hybrid enrichment (AHE) and ultraconserved elements (UCE)-and both approaches have proven useful for addressing questions in phylogenomics, phylogeography and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness and suggest areas for future improvement.
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Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Maggie Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Guarino Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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572
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Wielstra B, Burke T, Butlin RK, Avcı A, Üzüm N, Bozkurt E, Olgun K, Arntzen JW. A genomic footprint of hybrid zone movement in crested newts. Evol Lett 2017; 1:93-101. [PMID: 30283642 PMCID: PMC6121819 DOI: 10.1002/evl3.9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/04/2017] [Indexed: 01/18/2023] Open
Abstract
Speciation typically involves a stage in which species can still exchange genetic material. Interspecific gene flow is facilitated by the hybrid zones that such species establish upon secondary contact. If one member of a hybridizing species pair displaces the other, their hybrid zone would move across the landscape. Although theory predicts that moving hybrid zones quickly stagnate, hybrid zones tracked over one or a few decades do not always follow such a limitation. This suggests that hybrid zones have the potential to traverse considerable distances over extended periods of time. When hybrid zones move, introgression is predicted to result in biased gene flow of selectively neutral alleles, from the receding species into the advancing species. We test for such a genomic footprint of hybrid zone movement in a pair of crested newt species (genus Triturus) for which we have a priori support for westward hybrid zone movement. We perform a multilocus phylogeographical survey and conduct Bayesian clustering analysis, estimation of ancestry and heterozygosity, and geographical cline analysis. In a 600 km wide area east of the present day hybrid zone a genomic footprint constitutes empirical evidence consistent with westward hybrid zone movement. The crested newt case suggests that hybrid zone movement can occur over an extensive span of time and space. Inferring hybrid zone movement provides fundamental insight into historical biogeography and the speciation process, and we anticipate that hybrid zones will prove to be far more mobile than currently appreciated.
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Affiliation(s)
- Ben Wielstra
- Department of Animal and Plant Sciences University of Sheffield S10 2TN Sheffield United Kingdom.,Naturalis Biodiversity Center 2300 RA Leiden The Netherlands.,Department of Ecology and Evolutionary Biology University of California Los Angeles California 90095
| | - Terry Burke
- Department of Animal and Plant Sciences University of Sheffield S10 2TN Sheffield United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield S10 2TN Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg S 405 30 Gothenburg Sweden
| | - Aziz Avcı
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Nazan Üzüm
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Emin Bozkurt
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Kurtuluş Olgun
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Jan W Arntzen
- Naturalis Biodiversity Center 2300 RA Leiden The Netherlands
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573
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Janecka JE, Zhang Y, Li D, Munkhtsog B, Bayaraa M, Galsandorj N, Wangchuk TR, Karmacharya D, Li J, Lu Z, Uulu KZ, Gaur A, Kumar S, Kumar K, Hussain S, Muhammad G, Jevit M, Hacker C, Burger P, Wultsch C, Janecka MJ, Helgen K, Murphy WJ, Jackson R. Range-Wide Snow Leopard Phylogeography Supports Three Subspecies. J Hered 2017; 108:597-607. [DOI: 10.1093/jhered/esx044] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
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574
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Corrigan S, Maisano Delser P, Eddy C, Duffy C, Yang L, Li C, Bazinet AL, Mona S, Naylor GJ. Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks. Mol Phylogenet Evol 2017; 110:122-126. [DOI: 10.1016/j.ympev.2017.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 02/16/2017] [Accepted: 03/08/2017] [Indexed: 11/26/2022]
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575
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Peres EA, Silva MJ, Solferini VN. Phylogeography of the spider Araneus venatrix (Araneidae) suggests past connections between Amazon and Atlantic rainforests. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elen A. Peres
- Department of Genetics, Evolution and Bioagents, Institute of Biology, Rua Bertrand Russel s/n, University of Campinas, Campinas, 13083-970 São Paulo, Brazil
- Department of Zoology, Institute of Biosciences, Rua do Matão 101, travessa 14, University of São Paulo, São Paulo, 05508-090 São Paulo, Brazil
| | - Márcio J. Silva
- Centre for Molecular Biology and Genetic Engineering, Avenida Cândido Rondon 400, University of Campinas, Campinas, 13083-875 São Paulo, Brazil
| | - Vera N. Solferini
- Department of Genetics, Evolution and Bioagents, Institute of Biology, Rua Bertrand Russel s/n, University of Campinas, Campinas, 13083-970 São Paulo, Brazil
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576
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Anco C, Kolokotronis SO, Henschel P, Cunningham SW, Amato G, Hekkala E. Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:455-473. [PMID: 28423965 DOI: 10.1080/24701394.2017.1307973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.
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Affiliation(s)
- Corey Anco
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Sergios-Orestis Kolokotronis
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA.,c Department of Epidemiology and Biostatistics, School of Public Health , SUNY Downstate Medical Center , Brooklyn , USA
| | | | - Seth W Cunningham
- a Department of Biological Sciences , Fordham University , Bronx , USA
| | - George Amato
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Evon Hekkala
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
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577
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Morales HE, Sunnucks P, Joseph L, Pavlova A. Perpendicular axes of differentiation generated by mitochondrial introgression. Mol Ecol 2017; 26:3241-3255. [DOI: 10.1111/mec.14114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Hernán E. Morales
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
- Centre for Marine Evolutionary Biology Department of Marine Sciences University of GothenburgBox 461 SE 405 30 Göteborg Sweden
| | - Paul Sunnucks
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections AustraliaGPO Box 1700 Canberra ACT 2601 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
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578
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Wallis GP, Cameron-Christie SR, Kennedy HL, Palmer G, Sanders TR, Winter DJ. Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes. Mol Ecol 2017; 26:3116-3127. [DOI: 10.1111/mec.14096] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Graham P. Wallis
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Sophia R. Cameron-Christie
- Women's and Children's Health; Paediatrics & Child Health; Dunedin School of Medicine; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Hannah L. Kennedy
- Molecular Pathology Laboratory; Canterbury Health Laboratories; PO Box 151 Christchurch 8140 New Zealand
- Department of Pathology; University of Otago; Riccarton Avenue PO Box 4345 Christchurch 8140 New Zealand
| | - Gemma Palmer
- Melbourne IVF; Suite 10 320 Victoria Parade East Melbourne Vic. 3002 Australia
| | - Tessa R. Sanders
- National Institutes of Health; 9000 Rockville Pike Bethesda MD 20892 USA
| | - David J. Winter
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
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579
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Wang N, Hosner PA, Liang B, Braun EL, Kimball RT. Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data. Mol Phylogenet Evol 2017; 109:217-225. [DOI: 10.1016/j.ympev.2017.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 12/24/2016] [Accepted: 01/07/2017] [Indexed: 12/09/2022]
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580
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Sloan DB, Havird JC, Sharbrough J. The on-again, off-again relationship between mitochondrial genomes and species boundaries. Mol Ecol 2017; 26:2212-2236. [PMID: 27997046 PMCID: PMC6534505 DOI: 10.1111/mec.13959] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
The study of reproductive isolation and species barriers frequently focuses on mitochondrial genomes and has produced two alternative and almost diametrically opposed narratives. On one hand, mtDNA may be at the forefront of speciation events, with co-evolved mitonuclear interactions responsible for some of the earliest genetic incompatibilities arising among isolated populations. On the other hand, there are numerous cases of introgression of mtDNA across species boundaries even when nuclear gene flow is restricted. We argue that these seemingly contradictory patterns can result from a single underlying cause. Specifically, the accumulation of deleterious mutations in mtDNA creates a problem with two alternative evolutionary solutions. In some cases, compensatory or epistatic changes in the nuclear genome may ameliorate the effects of mitochondrial mutations, thereby establishing coadapted mitonuclear genotypes within populations and forming the basis of reproductive incompatibilities between populations. Alternatively, populations with high mitochondrial mutation loads may be rescued by replacement with a more fit, foreign mitochondrial haplotype. Coupled with many nonadaptive mechanisms of introgression that can preferentially affect cytoplasmic genomes, this form of adaptive introgression may contribute to the widespread discordance between mitochondrial and nuclear genealogies. Here, we review recent advances related to mitochondrial introgression and mitonuclear incompatibilities, including the potential for cointrogression of mtDNA and interacting nuclear genes. We also address an emerging controversy over the classic assumption that selection on mitochondrial genomes is inefficient and discuss the mechanisms that lead lineages down alternative evolutionary paths in response to mitochondrial mutation accumulation.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
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581
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Van Doren BM, Campagna L, Helm B, Illera JC, Lovette IJ, Liedvogel M. Correlated patterns of genetic diversity and differentiation across an avian family. Mol Ecol 2017; 26:3982-3997. [PMID: 28256062 DOI: 10.1111/mec.14083] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/19/2017] [Accepted: 02/22/2017] [Indexed: 01/01/2023]
Abstract
Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology and migratory behaviour, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from five taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked whether these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g. areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation.
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Affiliation(s)
- Benjamin M Van Doren
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Leonardo Campagna
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Barbara Helm
- Animal Health and Comparative Medicine, Institute of Biodiversity, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Campus of Mieres, Research Building, 5th Floor, c/ Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain
| | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Miriam Liedvogel
- Max Planck Institute for Evolutionary Biology, AG Behavioural Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany
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582
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Ely CR, Wilson RE, Talbot SL. Genetic structure among greater white-fronted goose populations of the Pacific Flyway. Ecol Evol 2017; 7:2956-2968. [PMID: 28479995 PMCID: PMC5415542 DOI: 10.1002/ece3.2934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/23/2017] [Accepted: 03/03/2017] [Indexed: 01/13/2023] Open
Abstract
An understanding of the genetic structure of populations in the wild is essential for long‐term conservation and stewardship in the face of environmental change. Knowledge of the present‐day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white‐fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine‐scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long‐lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population‐specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white‐fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.
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Affiliation(s)
- Craig R Ely
- U.S. Geological Survey Alaska Science Center Anchorage AK USA
| | - Robert E Wilson
- U.S. Geological Survey Alaska Science Center Anchorage AK USA
| | - Sandra L Talbot
- U.S. Geological Survey Alaska Science Center Anchorage AK USA
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583
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Bilton DT, Turner L, Foster GN. Frequent discordance between morphology and mitochondrial DNA in a species group of European water beetles (Coleoptera: Dytiscidae). PeerJ 2017; 5:e3076. [PMID: 28289570 PMCID: PMC5346281 DOI: 10.7717/peerj.3076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/07/2017] [Indexed: 11/20/2022] Open
Abstract
The Hydroporus memnonius species group includes both widespread and range restricted diving beetle taxa in the western Palaearctic, some of which have been divided into a number of geographical subspecies. Of these, Hydroporus necopinatus is distributed in the far west of Europe, from central Spain to southern Britain, and has been split into three subspecies, occurring in Iberia (necopinatus sst.), France (robertorum) and England (roni) respectively—the last of these being a rare example of an insect taxon apparently endemic to northern Europe. Here we explore inter-relationships between populations and subspecies of H. necopinatus and related members of the Hydroporus melanarius subgroup, using mitochondrial COI sequence data. We reveal widespread discordance between mitochondrial DNA sequence variation and morphology in areas where H. necopinatus and H. melanarius come into contact, consistent with historical introgressive hybridization between these taxa. In light of this discordance, the lack of clear genetic divergence between H. necopinatus subspecies, and the fact that both robertorum and roni are morphologically intermediate between H. necopinatus sstr. and H. melanarius, we suggest that these taxa may be of hybridogenic origin, rather than representing discrete evolutionary lineages.
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Affiliation(s)
- David T Bilton
- Marine Biology & Ecology Research Centre, University of Plymouth , Plymouth , United Kingdom
| | - Lucy Turner
- Marine Biology & Ecology Research Centre, University of Plymouth , Plymouth , United Kingdom
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584
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The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae). Mol Phylogenet Evol 2017; 110:50-59. [PMID: 28286101 DOI: 10.1016/j.ympev.2017.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/29/2016] [Accepted: 03/06/2017] [Indexed: 11/23/2022]
Abstract
The large number of endemic species in Middle America is frequently attributed to the interplay of geographical barriers and historical climatic changes in the region. This process promotes genetic divergence between populations, and given enough time, may yield new species. Animals that inhabit mid-elevation or highland habitats may be disproportionately affected in this way. Genetic analyses of animals in this region allow us to better understand how historical patterns of isolation have influenced the generation of new species in this biodiversity hotspot. We studied the biogeography and systematics of two closely related genera of sparrows (Passerellidae): Melozone and Aimophila. Collectively, this group is distributed from the southwestern United States and southward as far as central Costa Rica. We sampled 81 individuals of 8 Melozone and 2 Aimophila species, from 19 localities distributed throughout their ranges. We reconstructed phylogenetic relationships and time-calibrated species trees using multilocus sequence data comprised of one mitochondrial gene and five nuclear genes. We conducted an ancestral area reconstruction analysis to determine the probability of ancestral range at each divergent event. Despite analyzing six loci, we were unable to obtain a fully resolved phylogenetic tree. We recovered four main lineages: lineage 1 includes four Melozone species distributed north of Isthmus of Tehuantepec (M. albicollis, M. crissalis, M. aberti, M. fusca); lineage 2 includes three Melozone species distributed south of the Isthmus of Tehuantepec (M. biarcuata, M. cabanisi, M. leucotis); lineage 3 lineage consists of a single species endemic to the Pacific coast of Mexico (M. kieneri); and lineage 4 includes the more widely distributed sparrows in the genus Aimophila. Our analyses suggest that these genera probably originated during the late Miocene in the Madrean Highlands of southern Mexico. We identified dispersal as the prevalent cause of speciation in this clade with most lineages dispersing to their current distributions from southern Mexico either to the north following a developing and expanding Madro-Tertiary flora, or to the south across the Isthmus of Tehuantepec. A similar pattern of dispersal from this biogeographic region has been reported in other taxa including fishes, reptiles, and birds. Our results reveal that the four lineages identified represent geographically coherent and ecologically similar assemblages of taxa. Finally, when our genetic results are considered, along with apparent differences in morphology and song, the allopatric forms M. b. cabanisi and M. l. occipitalis warrant recognition as biological species.
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585
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Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C. Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Front Genet 2017; 8:25. [PMID: 28316610 PMCID: PMC5334354 DOI: 10.3389/fgene.2017.00025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes. In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it. We advocate that recent interdisciplinary advances assist in the consolidation of links between genotype and phenotype. For example, advances in genomics allow us to unravel signatures of selection in mitochondrial and nuclear OXPHOS genes at population-relevant scales, while newly published complete atomic-resolution structures of the OXPHOS machinery enable more robust predictions of how these genes interact epistatically and co-evolutionarily. We use three case studies to show how integrative approaches have improved the understanding of mitonuclear interactions in OXPHOS, namely those driving high-altitude adaptation in bar-headed geese, allopatric population divergence in Tigriopus californicus copepods, and the genome architecture of nuclear genes coding for mitochondrial functions in the eastern yellow robin.
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Affiliation(s)
- Paul Sunnucks
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Hernán E. Morales
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
- Department of Marine Sciences, University of GothenburgGothenburg, Sweden
| | - Annika M. Lamb
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
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586
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Salvi D, Pinho C, Harris DJ. Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta. BMC Evol Biol 2017; 17:63. [PMID: 28253846 PMCID: PMC5335832 DOI: 10.1186/s12862-017-0899-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity. RESULTS We analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured. CONCLUSIONS Our study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy. .,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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587
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Crawford JE, Alves JM, Palmer WJ, Day JP, Sylla M, Ramasamy R, Surendran SN, Black WC, Pain A, Jiggins FM. Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector. BMC Biol 2017; 15:16. [PMID: 28241828 PMCID: PMC5329927 DOI: 10.1186/s12915-017-0351-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/19/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The mosquito Aedes aegypti is the main vector of dengue, Zika, chikungunya and yellow fever viruses. This major disease vector is thought to have arisen when the African subspecies Ae. aegypti formosus evolved from being zoophilic and living in forest habitats into a form that specialises on humans and resides near human population centres. The resulting domestic subspecies, Ae. aegypti aegypti, is found throughout the tropics and largely blood-feeds on humans. RESULTS To understand this transition, we have sequenced the exomes of mosquitoes collected from five populations from around the world. We found that Ae. aegypti specimens from an urban population in Senegal in West Africa were more closely related to populations in Mexico and Sri Lanka than they were to a nearby forest population. We estimate that the populations in Senegal and Mexico split just a few hundred years ago, and we found no evidence of Ae. aegypti aegypti mosquitoes migrating back to Africa from elsewhere in the tropics. The out-of-Africa migration was accompanied by a dramatic reduction in effective population size, resulting in a loss of genetic diversity and rare genetic variants. CONCLUSIONS We conclude that a domestic population of Ae. aegypti in Senegal and domestic populations on other continents are more closely related to each other than to other African populations. This suggests that an ancestral population of Ae. aegypti evolved to become a human specialist in Africa, giving rise to the subspecies Ae. aegypti aegypti. The descendants of this population are still found in West Africa today, and the rest of the world was colonised when mosquitoes from this population migrated out of Africa. This is the first report of an African population of Ae. aegypti aegypti mosquitoes that is closely related to Asian and American populations. As the two subspecies differ in their ability to vector disease, their existence side by side in West Africa may have important implications for disease transmission.
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Affiliation(s)
- Jacob E Crawford
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
- Present Address: Verily Life Sciences, South San Francisco, CA, 94080, USA
| | - Joel M Alves
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - William J Palmer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Massamba Sylla
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Sinnathamby N Surendran
- ID-FISH Technology, Palo Alto, CA, 94303, USA
- Department of Zoology, University of Jaffna, Jaffna, Sri Lanka
| | - William C Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, KAUST, Thuwal, Kingdom of Saudi Arabia
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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588
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Wang C, Shikano T, Persat H, Merilä J. Phylogeography and historical introgression in smoothtail nine-spined sticklebacks, Pungitius laevis (Gasterosteiformes: Gasterosteidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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589
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Massey SE. Strong Amerindian Mitonuclear Discordance in Puerto Rican Genomes Suggests Amerindian Mitochondrial Benefit. Ann Hum Genet 2017; 81:59-77. [DOI: 10.1111/ahg.12185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/06/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Steven E. Massey
- Biology Department; University of Puerto Rico - Rio Piedras; PO Box 23360 San Juan Puerto Rico 00931
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590
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Tóth JP, Varga Z, Verovnik R, Wahlberg N, Váradi A, Bereczki J. Mito-nuclear discordance helps to reveal the phylogeographic patterns of Melitaea ornata (Lepidoptera: Nymphalidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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591
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Alter SE, Munshi-South J, Stiassny MLJ. Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River. Mol Ecol 2017; 26:1401-1419. [PMID: 28028845 DOI: 10.1111/mec.13973] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/13/2016] [Accepted: 11/21/2016] [Indexed: 12/20/2022]
Abstract
The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double-digest restriction-associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD-Seq data in understanding diversification processes operating both below and above the species level.
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Affiliation(s)
- S Elizabeth Alter
- Department of Biology, York College/The City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY, 11451, USA.,The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Jason Munshi-South
- Louis Calder Center-Biological Field Station, Fordham University, Armonk, NY, 10504, USA
| | - Melanie L J Stiassny
- The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
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592
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Ball SE, Bovero S, Sotgiu G, Tessa G, Angelini C, Bielby J, Durrant C, Favelli M, Gazzaniga E, Garner TWJ. Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus. Ecol Evol 2017; 7:1190-1211. [PMID: 28303189 PMCID: PMC5306002 DOI: 10.1002/ece3.2665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 12/04/2022] Open
Abstract
The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.
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Affiliation(s)
- Sarah E. Ball
- Institute of ZoologyThe Zoological Society of LondonLondonUK
| | - Stefano Bovero
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giuseppe Sotgiu
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giulia Tessa
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversita degli Studi di TorinoTorinoItaly
| | - Claudio Angelini
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Jon Bielby
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | | | - Marco Favelli
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Enrico Gazzaniga
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Trenton W. J. Garner
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
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593
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Barbosa S, Paupério J, Herman JS, Ferreira CM, Pita R, Vale-Gonçalves HM, Cabral JA, Garrido-García JA, Soriguer RC, Beja P, Mira A, Alves PC, Searle JB. Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole. Mol Ecol 2017; 26:951-967. [DOI: 10.1111/mec.13994] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 11/18/2016] [Accepted: 12/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- S. Barbosa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Ecology and Evolutionary Biology; Corson Hall, Cornell University; Ithaca NY 14853-2701 USA
| | - J. Paupério
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
| | - J. S. Herman
- Department of Natural Sciences; National Museums Scotland; Chambers Street Edinburgh EH1 1JF UK
| | - C. M. Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
| | - R. Pita
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade de Évora; 7000-890 Évora Portugal
| | - H. M. Vale-Gonçalves
- CITAB, Centro de Investigação e Tecnologias Agroambientais e Biológicas; Universidade de Trás-os-Montes e Alto Douro (UTAD); 5001-801 Vila Real Portugal
| | - J. A. Cabral
- CITAB, Centro de Investigação e Tecnologias Agroambientais e Biológicas; Universidade de Trás-os-Montes e Alto Douro (UTAD); 5001-801 Vila Real Portugal
| | - J. A. Garrido-García
- Estación Biológica de Doñana (CSIC); Avda Américo Vespucio s/n, Isla de la Cartuja 41092 Sevilla Spain
| | - R. C. Soriguer
- Estación Biológica de Doñana (CSIC); Avda Américo Vespucio s/n, Isla de la Cartuja 41092 Sevilla Spain
| | - P. Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - A. Mira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade de Évora; 7000-890 Évora Portugal
| | - P. C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM); 13005 Ciudad Real Spain
| | - J. B. Searle
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Ecology and Evolutionary Biology; Corson Hall, Cornell University; Ithaca NY 14853-2701 USA
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594
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Lumme J, Ziętara MS, Lebedeva D. Ancient and modern genome shuffling: Reticulate mito-nuclear phylogeny of four related allopatric species of Gyrodactylus von Nordmann, 1832 (Monogenea: Gyrodactylidae), ectoparasites on the Eurasian minnow Phoxinus phoxinus (L.) (Cyprinidae). Syst Parasitol 2017; 94:183-200. [PMID: 28130668 DOI: 10.1007/s11230-016-9696-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 12/07/2016] [Indexed: 11/26/2022]
Abstract
Phylogenetic analyses including four allopatric species of Gyrodactylus von Nordmann, 1832 on the Eurasian minnow Phoxinus phoxinus (L.) (Cyprinidae) revealed incongruence between the nuclear ITS1-5.8S-ITS2 and mitochondrial cox1 phylogenies due to ancient hybridisation. Gyrodactylus pannonicus Molnár, 1968 was sampled close to its type-locality, the upper reaches of River Tisza, tributary of Danube in the Black Sea Basin. Faunistic search detected three new related species with maximum composite likelihood distances in cox1 between 16.8-23.2% (tentatively 1.3 to 1.8 My of divergence). Gyrodactylus albolacustris n. sp. recorded in the White Sea Basin, eastern Baltic Basin and Mongolia was close to G. pannonicus in the nuclear ITS (divergence of 0.9%), but diverged in cox1 by 19.8%. The Mongolian isolate of G. albolacustris n. sp. diverged from the European isolates in cox1 by 8.9%, suggesting 0.7 My of isolation. The two other new species differed from G. pannonicus by >4% in ITS and some large indels in ITS1, and by >20% in cox1. Gyrodactylus danastriae n. sp. was found in River Strwiąż, a tributary of the River Dniester (Black Sea Basin) and was characterised by smaller size of anchors and by 29-41 bp dimorphic insertion in ITS1. Gyrodactylus botnicus n. sp. is considered endemic in the Baltic Basin, but was also found in the White Sea Basin as a postglacial immigrant, where it had hybridised with G. albolacustris n. sp. in spite of the high divergence in ITS (3.9%) and cox1 (22%). The discordant nuclear and mitochondrial phylogenies revealed an ancient mitochondrial introgression: G. albolacustris n. sp. was derived from a hybridisation combining proto-pannonicus ITS with proto-danastriae mitochondria, perhaps 1.3 My ago. The postglacial hybridisation of G. albolacustris n. sp. (as the donor of mtDNAalb and ITSalb) and G. botnicus n. sp. (donor of the ITSbot) offered a model of shuffling of the genomic components: the process of the homogenisation and stabilisation of nuclear ITS (concerted evolution) and the lineage sorting has hardly begun.
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Affiliation(s)
- Jaakko Lumme
- Department of Biology, University of Oulu, 90014, Oulu, Finland
| | - Marek S Ziętara
- Department of Molecular Evolution, University of Gdańsk, Wita Stwosza St., 59, 80-308, Gdańsk, Poland
| | - Dar'ya Lebedeva
- Institute of Biology of Karelian Research Center, Pushkinskaya St., 11, Petrozavodsk, Russian Federation, 185910.
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595
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Range expansion underlies historical introgressive hybridization in the Iberian hare. Sci Rep 2017; 7:40788. [PMID: 28120863 PMCID: PMC5264399 DOI: 10.1038/srep40788] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/09/2016] [Indexed: 12/27/2022] Open
Abstract
Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after the last glacial maximum. Here, we asked whether a south-north expansion wave of L. granatensis into L. timidus territory could underlie mtDNA introgression, and whether nuclear genes interacting with mitochondria (“mitonuc” genes) were affected. We extended previous RNA-sequencing and produced a comprehensive annotated transcriptome assembly for L. granatensis. We then genotyped 100 discovered nuclear SNPs in 317 specimens spanning the species range. The distribution of allele frequencies across populations suggests a northwards range expansion, particularly in the region of mtDNA introgression. We found no correlation between variants at 39 mitonuc genes and mtDNA introgression frequency. Whether the nuclear and mitochondrial genomes coevolved will need a thorough investigation of the hundreds of mitonuc genes, but range expansion and species replacement likely promoted massive mtDNA introgression.
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596
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Poorten TJ, Knapp RA, Rosenblum EB. Population genetic structure of the endangered Sierra Nevada yellow-legged frog (Rana sierrae) in Yosemite National Park based on multi-locus nuclear data from swab samples. CONSERV GENET 2017. [DOI: 10.1007/s10592-016-0923-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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597
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The genetic characterization of an isolated remnant population of an endangered rodent (Cricetus cricetus L.) using comparative data: implications for conservation. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0925-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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598
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Allendorf FW. Genetics and the conservation of natural populations: allozymes to genomes. Mol Ecol 2017; 26:420-430. [DOI: 10.1111/mec.13948] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/28/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Fred W. Allendorf
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
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599
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Breusing C, Vrijenhoek RC, Reusch TBH. Widespread introgression in deep-sea hydrothermal vent mussels. BMC Evol Biol 2017; 17:13. [PMID: 28086786 PMCID: PMC5237248 DOI: 10.1186/s12862-016-0862-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/21/2016] [Indexed: 11/29/2022] Open
Abstract
Background The analysis of hybrid zones is crucial for gaining a mechanistic understanding of the process of speciation and the maintenance of species boundaries. Hybrid zones have been studied intensively in terrestrial and shallow-water ecosystems, but very little is known about their occurrence in deep-sea environments. Here we used diagnostic, single nucleotide polymorphisms in combination with one mitochondrial gene to re-examine prior hypotheses about a contact zone involving deep-sea hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis, living along the Mid-Atlantic Ridge. Results Admixture was found to be asymmetric with respect to the parental species, while introgression was more widespread geographically than previously recognized. Admixed individuals with a majority of alleles from one of the parental species were most frequent in habitats corresponding to that species. Mussels found at a geographically intermediate vent field constituted a genetically mixed population that showed no evidence for hybrid incompatibilities, a finding that does not support a previously inferred tension zone model. Conclusions Our analyses indicate that B. azoricus and B. puteoserpentis hybridize introgressively across a large geographic area without evidence for general hybrid incompatibilities. While these findings shed new light onto the genetic structure of this hybrid zone, many aspects about its nature still remain obscure. Our study sets a baseline for further research that should primarily focus on the acquisition of additional mussel samples and environmental data, a detailed exploration of vent areas and hidden populations as well as genomic analyses in both mussel hosts and their bacterial symbionts. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0862-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Corinna Breusing
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany. .,Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA.
| | - Robert C Vrijenhoek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Thorsten B H Reusch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany
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600
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Gryseels S, Baird SJE, Borremans B, Makundi R, Leirs H, Goüy de Bellocq J. When Viruses Don't Go Viral: The Importance of Host Phylogeographic Structure in the Spatial Spread of Arenaviruses. PLoS Pathog 2017; 13:e1006073. [PMID: 28076397 PMCID: PMC5226678 DOI: 10.1371/journal.ppat.1006073] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/17/2016] [Indexed: 01/07/2023] Open
Abstract
Many emerging infections are RNA virus spillovers from animal reservoirs. Reservoir identification is necessary for predicting the geographic extent of infection risk, but rarely are taxonomic levels below the animal species considered as reservoir, and only key circumstances in nature and methodology allow intrinsic virus-host associations to be distinguished from simple geographic (co-)isolation. We sampled and genetically characterized in detail a contact zone of two subtaxa of the rodent Mastomys natalensis in Tanzania. We find two distinct arenaviruses, Gairo and Morogoro virus, each spatially confined to a single M. natalensis subtaxon, only co-occurring at the contact zone’s centre. Inter-subtaxon hybridization at this centre and a continuum of quality habitat for M. natalensis show that both viruses have the ecological opportunity to spread into the other substaxon’s range, but do not, strongly suggesting host-intrinsic barriers. Such barriers could explain why human cases of another M. natalensis-borne arenavirus, Lassa virus, are limited to West Africa. Reservoirs of zoonotic viruses are usually equated with a particular wildlife species. It is rarely assessed whether genetic groups below the species level may instead represent the actual reservoir, though this would have major implications on estimations of the zoonosis’ spatial distribution. Here we investigate whether geographically and genetically distinct subtaxa of the widespread African rodent Mastomys natalensis carry distinct arenaviruses, by sampling in detail across a contact zone of two of these subtaxa. Ongoing hybridization shows that individuals of the subtaxa are in direct physical contact, in principle allowing viral exchange, yet neither of the two arenaviruses -Gairo and Morogoro virus- were found to have crossed the zone. Such intraspecific genetic barriers to arenavirus spatial spread have important implications for our understanding of the related Lassa arenavirus, a pathogen potentially lethal to humans of which Mastomys natalensis is also the main reservoir. Although Lassa virus appears to infect several secondary hosts, its distribution is restricted to West Africa and matches that of another M. natalensis subtaxon. Our data thus indicates that it is because of M. natalensis intraspecific distinctions that the human Lassa fever endemic area has not expanded to the rest of sub-Saharan Africa.
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Affiliation(s)
- Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- * E-mail:
| | - Stuart J. E. Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Research Facility Studenec, Brno, Czech Republic
| | - Benny Borremans
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Rhodes Makundi
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Joëlle Goüy de Bellocq
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Research Facility Studenec, Brno, Czech Republic
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