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Díaz‐Ruiz F, Vaquerizas PH, Márquez AL, Delibes‐Mateos M, Piorno V, Castro F, Ramírez E, Farfán MÁ, Olivero J, Real R, Villafuerte R. Unravelling the historical biogeography of the European rabbit subspecies in the Iberian Peninsula. Mamm Rev 2022. [DOI: 10.1111/mam.12306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Francisco Díaz‐Ruiz
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
| | - Patricia H. Vaquerizas
- Instituto de Estudios Sociales Avanzados (IESA‐CSIC) Campo Santo de los Mártires 7 14004 Córdoba Spain
| | - Ana Luz Márquez
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
| | - Miguel Delibes‐Mateos
- Instituto de Estudios Sociales Avanzados (IESA‐CSIC) Campo Santo de los Mártires 7 14004 Córdoba Spain
| | - Vicente Piorno
- Parque Nacional de las Islas Atlánticas de Galicia. Consellería de Medio Ambiente Territorio e Vivenda. Xunta de Galicia Rúa Oliva 3 36202 Vigo Pontevedra Spain
| | - Francisca Castro
- Departamento de Didácticas Específicas, Avda. San Alberto Magno, Universidad de Córdoba, “Sociedad, Ecología y Gestión del Medio Ambiente, UCO‐IESA” Unidad Asociada al CSIC 14004 Córdoba Spain
| | - Esther Ramírez
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ronda de Toledo n° 12 13071 Ciudad Real Spain
| | - Miguel Ángel Farfán
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
| | - Jesús Olivero
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
- Instituto IBYDA Centro de Experimentación Grice‐Hutchinson Loma de San Julián 2, Barriada de San Julián 29004 Málaga Spain
| | - Raimundo Real
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
- Instituto IBYDA Centro de Experimentación Grice‐Hutchinson Loma de San Julián 2, Barriada de San Julián 29004 Málaga Spain
| | - Rafael Villafuerte
- Instituto de Estudios Sociales Avanzados (IESA‐CSIC) Campo Santo de los Mártires 7 14004 Córdoba Spain
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2
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Keeping an eye on the use of eye-lens weight as a universal indicator of age for European wild rabbits. Sci Rep 2021; 11:8711. [PMID: 33888785 PMCID: PMC8062486 DOI: 10.1038/s41598-021-88087-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/08/2021] [Indexed: 11/09/2022] Open
Abstract
Accurate methods for age determination are critical to the knowledge of wildlife populations' age structure and, therefore, to their successful management. The reliability of age estimation may have profound economic and ecological consequences on the management of the European wild rabbits, Oryctolagus cuniculus, in its native and introduced range, where it is a keystone species and a major pest, respectively. As in other mammal species, European rabbits' age is often estimated using the Gompertz relationship between age and lens' weight. The growth rate formula has been developed based on data collected from European rabbits introduced in Australia, where a single subspecies (O. cuniculus cuniculus, Occ) is present. However, this curve has never been validated in the species native range, the Iberian Peninsula, where two subspecies (Occ, and O. c. algirus, Oca) coexist naturally. In this study, we tested the relationship between age and lens' weight using 173 Occ and 112 Oca wild rabbits that were surveyed in two experimental facilities in Spain. Our findings show that, in the native range, the published growth curve formula fits well Occ but not Oca data. Therefore, we recommend using the formula reported in this study to estimate the age of Oca (Lens dry weight = 240 × 10(-64.9/(Age+32))). This study supports Oca rabbits' distinctiveness revealed by previous studies, which suggests that management interventions should be applied to protect this subspecies whose distribution range is very narrow and whose populations seem to be declining. More broadly, our findings point to the importance of testing the suitability of growth curves defined for other species with different genetic forms as occurs in the European wild rabbit case.
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3
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Funosas G, Triadó-Margarit X, Castro F, Villafuerte R, Delibes-Mateos M, Rouco C, Casamayor EO. Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus). Sci Rep 2021; 11:766. [PMID: 33436896 PMCID: PMC7804928 DOI: 10.1038/s41598-020-80782-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.
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Affiliation(s)
- Gerard Funosas
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Francisca Castro
- Departamento de Didácticas Específicas, Universidad de Córdoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14004, Córdoba, Spain
| | - Rafael Villafuerte
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Miguel Delibes-Mateos
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Carlos Rouco
- Ecology Area, Faculty of Science, University of Cordoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14071, Córdoba, Spain
| | - Emilio O Casamayor
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain.
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4
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Vaquerizas PH, Delibes-Mateos M, Piorno V, Arroyo B, Castro F, Villafuerte R. The paradox of endangered European rabbits regarded as pests on the Iberian Peninsula: trends in subspecies matter. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The European rabbit Oryctolagus cuniculus faces a paradoxical situation in its native range on the Iberian Peninsula. While many populations have declined sharply due to a new variant of the rabbit haemorrhagic disease virus (RHDV-b), others remain healthy. The latter populations, which flourish mostly on farmland, cause significant crop damage. We explored if this difference could be related to the existence of the 2 rabbit subspecies (O. c. algirus and O. c. cuniculus) that coexist allopatrically on the Iberian Peninsula. Potential differences in population trends between rabbit subspecies may also be relevant in assisting the conservation of endangered rabbit-dependent predators which mainly occur in the distribution area of O. c. algirus. To test this, we assessed rabbit trends after the outbreak of RHDV-b by an online questionnaire to the senior administrative officers of all provincial official game departments throughout peninsular Spain (n = 47). A generalized negative trend was reported by officers in the distribution area of O. c. algirus, while a more stable or even positive trend was reported in the distribution area of O. c. cuniculus. We point to the need for establishing a long-term rabbit population monitoring programme on the Iberian Peninsula to further confirm the observed patterns, but also to contribute to evidence-based management decision-making. Our results suggest a need to apply different management systems for each rabbit subspecies.
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Affiliation(s)
- PH Vaquerizas
- Instituto de Estudios Sociales Avanzados (IESA-CSIC), 14004 Córdoba, Spain
| | - M Delibes-Mateos
- Instituto de Estudios Sociales Avanzados (IESA-CSIC), 14004 Córdoba, Spain
| | - V Piorno
- Parque Nacional de las Islas Atlánticas de Galicia, Consellería de Medio Ambiente, Territorio e Vivienda - Xunta de Galicia, 36202 Vigo, Spain
| | - B Arroyo
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), 13005 Ciudad Real, Spain
| | - F Castro
- Departamento de Didácticas Específicas, Universidad de Córdoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14071 Córdoba, Spain
| | - R Villafuerte
- Instituto de Estudios Sociales Avanzados (IESA-CSIC), 14004 Córdoba, Spain
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5
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Martincová I, Ďureje Ľ, Kreisinger J, Macholán M, Piálek J. Phenotypic effects of the Y chromosome are variable and structured in hybrids among house mouse recombinant lines. Ecol Evol 2019; 9:6124-6137. [PMID: 31161024 PMCID: PMC6540687 DOI: 10.1002/ece3.5196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/03/2019] [Indexed: 12/12/2022] Open
Abstract
Hybrid zones between divergent populations sieve genomes into blocks that introgress across the zone, and blocks that do not, depending on selection between interacting genes. Consistent with Haldane's rule, the Y chromosome has been considered counterselected and hence not to introgress across the European house mouse hybrid zone. However, recent studies detected massive invasion of M. m. musculus Y chromosomes into M. m. domesticus territory. To understand mechanisms facilitating Y spread, we created 31 recombinant lines from eight wild-derived strains representing four localities within the two mouse subspecies. These lines were reciprocally crossed and resulting F1 hybrid males scored for five phenotypic traits associated with male fitness. Molecular analyses of 51 Y-linked SNPs attributed ~50% of genetic variation to differences between the subspecies and 8% to differentiation within both taxa. A striking proportion, 21% (frequencies of sperm head abnormalities) and 42% (frequencies of sperm tail dissociations), of phenotypic variation was explained by geographic Y chromosome variants. Our crossing design allowed this explanatory power to be examined across a hierarchical scale from subspecific to local intrastrain effects. We found that divergence and variation were expressed diversely in different phenotypic traits and varied across the whole hierarchical scale. This finding adds another dimension of complexity to studies of Y introgression not only across the house mouse hybrid zone but potentially also in other contact zones.
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Affiliation(s)
- Iva Martincová
- Research Facility Studenec, Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
- Department of Botany and Zoology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Ľudovít Ďureje
- Research Facility Studenec, Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of ScienceCharles University in PraguePragueCzech Republic
| | - Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
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6
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Sciuchetti L, Dufresnes C, Cavoto E, Brelsford A, Perrin N. Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: A simulation study. Evolution 2018; 72:1350-1361. [PMID: 29806172 DOI: 10.1111/evo.13510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/08/2018] [Indexed: 11/28/2022]
Abstract
Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane's rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin's corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex-linked markers. From our simulations, X-Y incompatibilities generate steep clines for both X-linked and Y-linked markers; random effects may produce strong noise in cline center positions when migration is high relative to fitness costs, but X- and Y-centers always coincide strictly. X-autosome and Y-autosome incompatibilities also generate steep clines, but systematic shifts in cline centers occur when migration is high relative to selection, as a result of a dominance drive linked to Darwin's corollary. Interestingly, sex-linked genes always show farther introgression than the associated autosomal genes. We discuss ways of disentangling the potentially confounding effects of sex biases in migration, we compare our results to those of a few documented contact zones, and we stress the need to study independent replicates of the same contact zone.
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Affiliation(s)
- Luca Sciuchetti
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Department of Animal & Plant Sciences, University of Sheffield, Alfred Denny building, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Elisa Cavoto
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Alan Brelsford
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Biology Department, University of California, Riverside, CA, 92521
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
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7
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Rafati N, Blanco-Aguiar JA, Rubin CJ, Sayyab S, Sabatino SJ, Afonso S, Feng C, Alves PC, Villafuerte R, Ferrand N, Andersson L, Carneiro M. A genomic map of clinal variation across the European rabbit hybrid zone. Mol Ecol 2018; 27:1457-1478. [PMID: 29359877 DOI: 10.1111/mec.14494] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023]
Abstract
Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we studied patterns of allele frequency change across their hybrid zone using whole-genome sequencing. To connect levels and patterns of genetic differentiation with phenotypic manifestations of subfertility in hybrid rabbits, we further investigated patterns of gene expression in testis. Geographic cline analysis revealed 253 regions characterized by steep changes in allele frequency across their natural region of contact. This catalog of regions is likely to be enriched for loci implicated in reproductive barriers and yielded several insights into the evolution of hybrid dysfunction in rabbits: (i) incomplete reproductive isolation is likely governed by the effects of many loci, (ii) protein-protein interaction analysis suggest that genes within these loci interact more than expected by chance, (iii) regulatory variation is likely the primary driver of incompatibilities, and (iv) large chromosomal rearrangements appear not to be a major mechanism underlying incompatibilities or promoting isolation in the face of gene flow. We detected extensive misregulation of gene expression in testis of hybrid males, but not a statistical overrepresentation of differentially expressed genes in candidate regions. Our results also did not support an X chromosome-wide disruption of expression as observed in mice and cats, suggesting variation in the mechanistic basis of hybrid male reduced fertility among mammals.
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Affiliation(s)
- Nima Rafati
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - José A Blanco-Aguiar
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Instituto de Investigacion en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Carl J Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Stephen J Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Chungang Feng
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | | | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland, South Africa
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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8
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Delibes-Mateos M, Castro F, Piorno V, Ramírez E, Blanco-Aguiar JA, Aparicio F, Mínguez LE, Ferreira CC, Rouco C, Ríos-Saldaña CA, Recuerda P, Villafuerte R. First assessment of the potential introduction by hunters of eastern cottontail rabbits (Sylvilagus floridanus) in Spain. WILDLIFE RESEARCH 2018. [DOI: 10.1071/wr17185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Humans have introduced lagomorph species in areas outside their native ranges for their meat, fur or value as game species. Assessing the rate of success of lagomorph introductions is vital to address the ecological damage they may cause. Cases of failed lagomorph introductions in apparently suitable areas may also shed light on mechanisms that may deter invasion, which are useful in developing strategies for population control. In Spain, it has been suggested that hunters introduced the non-native eastern cottontail (Sylvilagus floridanus) to compensate for the recent drastic declines of the native European rabbit (Oryctolagus cuniculus).
Aims
Our main goals were to investigate (1) whether Sylvilagus rabbits have indeed been introduced by hunters across Spain, and (2) whether the species has become established in Spanish ecosystems.
Methods
We interviewed 311 hunters or naturalists across Spain. The questionnaires inquired about the characteristics of game management in each locality, including the frequency of rabbit restocking, and particularly whether Sylvilagus rabbits had been released in the surveyed localities. In addition, we sampled 192 rabbit populations (n=3974 individuals) across Spain by using molecular analysis to determine whether Sylvilagus rabbits were present in these areas.
Key results
Our interview results suggest that Sylvilagus rabbits may have been released in 6% of the 311 localities surveyed. However, molecular analyses failed to confirm their persistence, because all samples belonged to O. cuniculus.
Conclusions
We infer that Sylvilagus rabbits failed to establish themselves in Spain, although interviewees reported their introduction. Several reasons may explain the unsuccessful establishment of this species, such as a low propagule pressure, competition with native species, predation, inability to cope with local pathogens and unsuitable climatic conditions.
Implications
The risk of future introductions of non-native game species can be reduced through the implementation of stricter regulations of animal releases into the wild. Long-term monitoring networks should be developed to help identify non-native game species before they become established and spread to neighbouring areas, thereby preventing any ecological or economic impacts these species may cause.
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9
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Dowle EJ, Bracewell RR, Pfrender ME, Mock KE, Bentz BJ, Ragland GJ. Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae). Mol Ecol 2017; 26:6071-6084. [PMID: 29116665 DOI: 10.1111/mec.14342] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 05/12/2017] [Accepted: 08/05/2017] [Indexed: 12/23/2022]
Abstract
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo-Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.
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Affiliation(s)
- Eddy J Dowle
- Department of Entomology, Kansas State University, Manhattan, KS, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Ryan R Bracewell
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Karen E Mock
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Barbara J Bentz
- Department of Wildland Resources, Utah State University, Logan, UT, USA.,USDA Forest Service, Rocky Mountain Research Station, Logan, UT, USA
| | - Gregory J Ragland
- Department of Entomology, Kansas State University, Manhattan, KS, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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10
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Bernardini F, Galizi R, Wunderlich M, Taxiarchi C, Kranjc N, Kyrou K, Hammond A, Nolan T, Lawniczak MNK, Papathanos PA, Crisanti A, Windbichler N. Cross-Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex. Genetics 2017; 207:729-740. [PMID: 28860320 PMCID: PMC5629335 DOI: 10.1534/genetics.117.300221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/21/2017] [Indexed: 02/03/2023] Open
Abstract
Y chromosome function, structure and evolution is poorly understood in many species, including the Anopheles genus of mosquitoes-an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility. Here, we used an F1 × F0 crossing scheme to overcome a severe bottleneck of male hybrid incompatibilities that enabled us to experimentally purify a genetically labeled A. gambiae Y chromosome in an A. arabiensis background. Whole genome sequencing (WGS) confirmed that the A. gambiae Y retained its original sequence content in the A. arabiensis genomic background. In contrast to comparable experiments in Drosophila, we find that the presence of a heterospecific Y chromosome has no significant effect on the expression of A. arabiensis genes, and transcriptional differences can be explained almost exclusively as a direct consequence of transcripts arising from sequence elements present on the A. gambiae Y chromosome itself. We find that Y hybrids show no obvious fertility defects, and no substantial reduction in male competitiveness. Our results demonstrate that, despite their radically different structure, Y chromosomes of these two species of the gambiae complex that diverged an estimated 1.85 MYA function interchangeably, thus indicating that the Y chromosome does not harbor loci contributing to hybrid incompatibility. Therefore, Y chromosome gene flow between members of the gambiae complex is possible even at their current level of divergence. Importantly, this also suggests that malaria control interventions based on sex-distorting Y drive would be transferable, whether intentionally or contingent, between the major malaria vector species.
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Affiliation(s)
- Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Mariana Wunderlich
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Chrysanthi Taxiarchi
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Mara N K Lawniczak
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, United Kingdom
| | - Philippos Aris Papathanos
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132, Italy
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
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11
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Villafuerte R, Castro F, Ramírez E, Cotilla I, Parra F, Delibes-Mateos M, Recuerda P, Rouco C. Large-scale assessment of myxomatosis prevalence in European wild rabbits (Oryctolagus cuniculus) 60 years after first outbreak in Spain. Res Vet Sci 2017; 114:281-286. [DOI: 10.1016/j.rvsc.2017.05.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 05/06/2017] [Accepted: 05/10/2017] [Indexed: 11/24/2022]
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12
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LO VALVO M, RUSSO R, MANCUSO FP, PALLA F. mtDNA diversity in a rabbit population from Sicily (Italy). TURK J ZOOL 2017. [DOI: 10.3906/zoo-1511-53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Chávez-Galarza J, Henriques D, Johnston JS, Carneiro M, Rufino J, Patton JC, Pinto MA. Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia. Mol Ecol 2015; 24:2973-92. [PMID: 25930679 DOI: 10.1111/mec.13223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 12/30/2022]
Abstract
Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity.
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Affiliation(s)
- Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.,Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.,Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - José Rufino
- Polytechnic Institute of Bragança, 5301-857, Bragança, Portugal
| | - John C Patton
- Department of Forestry and Natural Resources, Purdue University, 715 W State St., West Lafayette, IN, 4797-2061, USA
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal
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14
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Ferreira CC, Castro F, Piorno V, Barrio IC, Delibes-Mateos M, Rouco C, Mínguez LE, Aparicio F, Blanco-Aguiar JA, Ramírez E, Iriarte C, Ríos-Saldaña CA, Cañadilla J, Arias de Reyna L, Ferreras P, Alves PC, Villafuerte R. Biometrical analysis reveals major differences between the two subspecies of the European rabbit. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catarina Campos Ferreira
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Department of Biology; Trent University; Peterborough ON K9J 7B8 Canada
| | - Francisca Castro
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
| | - Vicente Piorno
- Parque Nacional de las Islas Atlánticas de Galicia; Calle Oliva, 3 36202 Vigo Spain
| | - Isabel Catalán Barrio
- Department of Biological Sciences; University of Alberta; Biological Sciences Building CW-405 Edmonton AB T6G2E9 Canada
- Pyrenean Institute of Ecology (CSIC); Avda. Nuestra Señora de la Victoria 22700 Jaca Spain
| | - Miguel Delibes-Mateos
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
| | - Carlos Rouco
- Landcare Research; PO Box 1930 9054 Dunedin New Zealand
| | - Luis E. Mínguez
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Fernando Aparicio
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
| | - José A. Blanco-Aguiar
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Esther Ramírez
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Candelaria Iriarte
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Carlos A. Ríos-Saldaña
- BioCórima A. C.; Blvd. Dr. Jesús Valdés Sánchez km 10 Col. Presa de las Casas Arteaga Coahuila 25350 México
| | - Jesús Cañadilla
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Luis Arias de Reyna
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Paulo C. Alves
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre, s/n Edifício FC4 4169-007 Porto Portugal
- Wildlife Biology Program; College of Forestry and Conservation; University of Montana; Missoula MT USA
| | - Rafael Villafuerte
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
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15
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Alda F, Doadrio I. Spatial genetic structure across a hybrid zone between European rabbit subspecies. PeerJ 2014; 2:e582. [PMID: 25289181 PMCID: PMC4183957 DOI: 10.7717/peerj.582] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 08/28/2014] [Indexed: 11/20/2022] Open
Abstract
The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose we obtained multilocus genotypes and mitochondrial DNA data from 771 rabbits across most of the distribution range of the European rabbit in Spain. Based on the nuclear markers we observed a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus), which were subsequently subdivided into seven genetic groups. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Additionally, the significantly positive spatial correlation up to a distance of only 100 km supported the idea that differentiation at a local level is of greater importance when considering the species overall genetic structure. When looking at the subspecies, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus. This could be due to local geographic barriers, limited resources, soil type and/or social behavior limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioral differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioral and molecular, that hierarchically interact through time and space.
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Affiliation(s)
- Fernando Alda
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC) , Madrid , Spain
| | - Ignacio Doadrio
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC) , Madrid , Spain
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16
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Carneiro M, Albert FW, Afonso S, Pereira RJ, Burbano H, Campos R, Melo-Ferreira J, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Good JM, Ferrand N. The genomic architecture of population divergence between subspecies of the European rabbit. PLoS Genet 2014; 10:e1003519. [PMID: 25166595 PMCID: PMC4148185 DOI: 10.1371/journal.pgen.1003519] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 04/06/2013] [Indexed: 11/18/2022] Open
Abstract
The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In this study, we used next-generation sequencing to study genome-wide patterns of genetic differentiation between two hybridizing subspecies of rabbits (Oryctolagus cuniculus algirus and O. c. cuniculus) that are known to undergo high rates of gene exchange. Our primary objective was to identify specific genes or genomic regions that have resisted introgression and are likely to confer reproductive barriers in natural conditions. On the basis of 326,000 polymorphisms, we found low to moderate overall levels of differentiation between subspecies, and fewer than 200 genomic regions dispersed throughout the genome showing high differentiation consistent with a signature of reduced gene flow. Most differentiated regions were smaller than 200 Kb and contained very few genes. Remarkably, 30 regions were each found to contain a single gene, facilitating the identification of candidate genes underlying reproductive isolation. This gene-level resolution yielded several insights into the genetic basis and architecture of reproductive isolation in rabbits. Regions of high differentiation were enriched on the X-chromosome and near centromeres. Genes lying within differentiated regions were often associated with transcription and epigenetic activities, including chromatin organization, regulation of transcription, and DNA binding. Overall, our results from a naturally hybridizing system share important commonalities with hybrid incompatibility genes identified using laboratory crosses in mice and flies, highlighting general mechanisms underlying the maintenance of reproductive barriers.
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Affiliation(s)
- Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências Universidade do Porto, Porto, Portugal
- * E-mail:
| | - Frank W. Albert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Princeton University, Lewis Sigler Institute for Integrative Genomics, Princeton, New Jersey, United States of America
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
| | - Ricardo J. Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Hernan Burbano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Rita Campos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
| | - Jose A. Blanco-Aguiar
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Rafael Villafuerte
- Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Departamento de Zoología, Universidad de Córdoba, Córdoba, Spain
| | - Michael W. Nachman
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey M. Good
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Division of Biological Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências Universidade do Porto, Porto, Portugal
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17
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Roux C, Fraïsse C, Castric V, Vekemans X, Pogson GH, Bierne N. Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone. J Evol Biol 2014; 27:1662-75. [PMID: 24913446 DOI: 10.1111/jeb.12425] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/25/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
Abstract
The use of molecular data to reconstruct the history of divergence and gene flow between populations of closely related taxa represents a challenging problem. It has been proposed that the long-standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (Nm) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels, Mytilus edulis and M. galloprovincialis, across a well-studied mosaic hybrid zone in Europe and evaluated various scenarios of speciation, with or without variation in introgression rates, using an Approximate Bayesian Computation (ABC) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best-supported scenario was a long period of allopatric isolation during the first three-quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European Mytilus hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.
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Affiliation(s)
- C Roux
- Université Montpellier 2, Montpellier, France; CNRS-UMR5554 Institut des Sciences de l'Evolution, Station Méditerranéenne de l'Environnement Littoral, Sète, France; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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18
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Bidon T, Janke A, Fain SR, Eiken HG, Hagen SB, Saarma U, Hallström BM, Lecomte N, Hailer F. Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages. Mol Biol Evol 2014; 31:1353-63. [PMID: 24667925 DOI: 10.1093/molbev/msu109] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms.
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Affiliation(s)
- Tobias Bidon
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyGoethe University Frankfurt, Institute for Ecology, Evolution & Diversity, Frankfurt am Main, Germany
| | - Steven R Fain
- National Fish and Wildlife Forensic Laboratory, Ashland, OR
| | - Hans Geir Eiken
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Svanvik, Norway
| | - Snorre B Hagen
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Svanvik, Norway
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Björn M Hallström
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyScience for Life Laboratory, School of Biotechnology, KTH, Stockholm, Sweden
| | - Nicolas Lecomte
- Canada Research Chair in Polar and Boreal Ecology, Department of Biology, University of Moncton, Moncton, Canada
| | - Frank Hailer
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
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19
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Herrig DK, Modrick AJ, Brud E, Llopart A. Introgression in the Drosophila subobscura--D. Madeirensis sister species: evidence of gene flow in nuclear genes despite mitochondrial differentiation. Evolution 2013; 68:705-19. [PMID: 24152112 PMCID: PMC4255303 DOI: 10.1111/evo.12295] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 10/15/2013] [Indexed: 12/19/2022]
Abstract
Species hybridization, and thus the potential for gene flow, was once viewed as reproductive mistake. However, recent analysis based on large datasets and newly developed models suggest that gene exchange is not as rare as originally suspected. To investigate the history and speciation of the closely related species Drosophila subobscura, D. madeirensis, and D. guanche, we obtained polymorphism and divergence data for 26 regions throughout the genome, including the Y chromosome and mitochondrial DNA. We found that the D. subobscura X/autosome ratio of silent nucleotide diversity is significantly smaller than the 0.75 expected under neutrality. This pattern, if held genomewide, may reflect a faster accumulation of beneficial mutations on the X chromosome than on autosomes. We also detected evidence of gene flow in autosomal regions, while sex chromosomes remain distinct. This is consistent with the large X effect on hybrid male sterility seen in this system and the presence of two X chromosome inversions fixed between species. Overall, our data conform to chromosomal speciation models in which rearrangements are proposed to serve as gene flow barriers. Contrary to other observations in Drosophila, the mitochondrial genome appears resilient to gene flow in the presence of nuclear exchange.
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Affiliation(s)
- Danielle K Herrig
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242
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20
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Andrews KR, Perrin WF, Oremus M, Karczmarski L, Bowen BW, Puritz JB, Toonen RJ. The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers. Mol Ecol 2013; 22:2408-23. [DOI: 10.1111/mec.12193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 11/30/2012] [Accepted: 12/04/2012] [Indexed: 11/26/2022]
Affiliation(s)
| | - William F. Perrin
- Southwest Fisheries Science Center, National Marine Fisheries Service; NOAA; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Marc Oremus
- Opération Cétacés; 16 rue Henri Niautou 98800 Nouméa New Caledonia
| | - Leszek Karczmarski
- The Swire Institute of Marine Science; School of Biological Sciences; The University of Hong Kong; Cape d'Aguilar Shek O Hong Kong
| | - Brian W. Bowen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
| | | | - Robert J. Toonen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
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21
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Carneiro M, Baird SJE, Afonso S, Ramirez E, Tarroso P, Teotónio H, Villafuerte R, Nachman MW, Ferrand N. Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit. Mol Ecol 2013; 22:2511-25. [PMID: 23530594 DOI: 10.1111/mec.12272] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 11/27/2022]
Abstract
Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromosome and mtDNA in 1078 individuals sampled across the hybrid zone. While some loci revealed extremely wide clines (w ≥ 300 km) relative to an estimated dispersal of 1.95-4.22 km/generation, others showed abrupt transitions (w ≈ 10 km), indicating localized genomic regions of strong selection against introgression. The subset of loci showing steep clines had largely coincident centers and stepped changes in allele frequency that did not co-localize with any physical barrier or ecotone, suggesting that the rabbit hybrid zone is a tension zone. The steepest clines were for X- and Y-chromosome markers. Our results are consistent with previous inference based on DNA sequence variation of individuals sampled in allopatry in suggesting that a large proportion of each genome has escaped the overall barrier to gene flow in the middle of the hybrid zone. These results imply an old history of hybridization and high effective gene flow and anticipate that isolation factors should often localize to small genomic regions.
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Affiliation(s)
- Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.
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22
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Abstract
When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).
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Chan YC, Roos C, Inoue-Murayama M, Inoue E, Shih CC, Vigilant L. A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons. BMC Evol Biol 2012; 12:150. [PMID: 22909292 PMCID: PMC3444420 DOI: 10.1186/1471-2148-12-150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/15/2012] [Indexed: 01/06/2023] Open
Abstract
Background The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs). Results To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are monophyletic in the mtgenome phylogeny, respectively, but a H. pileatus individual falls into the H. lar Y chromosome clade. Conclusions Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance.
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Affiliation(s)
- Yi-Chiao Chan
- Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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Campbell P, Good JM, Dean MD, Tucker PK, Nachman MW. The contribution of the Y chromosome to hybrid male sterility in house mice. Genetics 2012; 191:1271-81. [PMID: 22595240 PMCID: PMC3416006 DOI: 10.1534/genetics.112.141804] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 05/10/2012] [Indexed: 12/18/2022] Open
Abstract
Hybrid sterility in the heterogametic sex is a common feature of speciation in animals. In house mice, the contribution of the Mus musculus musculus X chromosome to hybrid male sterility is large. It is not known, however, whether F1 male sterility is caused by X-Y or X-autosome incompatibilities or a combination of both. We investigated the contribution of the M. musculus domesticus Y chromosome to hybrid male sterility in a cross between wild-derived strains in which males with a M. m. musculus X chromosome and M. m. domesticus Y chromosome are partially sterile, while males from the reciprocal cross are reproductively normal. We used eight X introgression lines to combine different X chromosome genotypes with different Y chromosomes on an F1 autosomal background, and we measured a suite of male reproductive traits. Reproductive deficits were observed in most F1 males, regardless of Y chromosome genotype. Nonetheless, we found evidence for a negative interaction between the M. m. domesticus Y and an interval on the M. m. musculus X that resulted in abnormal sperm morphology. Therefore, although F1 male sterility appears to be caused mainly by X-autosome incompatibilities, X-Y incompatibilities contribute to some aspects of sterility.
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Affiliation(s)
- Polly Campbell
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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25
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Nachman MW, Payseur BA. Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice. Philos Trans R Soc Lond B Biol Sci 2012; 367:409-21. [PMID: 22201170 DOI: 10.1098/rstb.2011.0249] [Citation(s) in RCA: 254] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently diverged taxa may continue to exchange genes. A number of models of speciation with gene flow propose that the frequency of gene exchange will be lower in genomic regions of low recombination and that these regions will therefore be more differentiated. However, several population-genetic models that focus on selection at linked sites also predict greater differentiation in regions of low recombination simply as a result of faster sorting of ancestral alleles even in the absence of gene flow. Moreover, identifying the actual amount of gene flow from patterns of genetic variation is tricky, because both ancestral polymorphism and migration lead to shared variation between recently diverged taxa. New analytic methods have been developed to help distinguish ancestral polymorphism from migration. Along with a growing number of datasets of multi-locus DNA sequence variation, these methods have spawned a renewed interest in speciation models with gene flow. Here, we review both speciation and population-genetic models that make explicit predictions about how the rate of recombination influences patterns of genetic variation within and between species. We then compare those predictions with empirical data of DNA sequence variation in rabbits and mice. We find strong support for the prediction that genomic regions experiencing low levels of recombination are more differentiated. In most cases, reduced gene flow appears to contribute to the pattern, although disentangling the relative contribution of reduced gene flow and selection at linked sites remains a challenge. We suggest fruitful areas of research that might help distinguish between different models.
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Affiliation(s)
- Michael W Nachman
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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26
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Carneiro M, Albert FW, Melo-Ferreira J, Galtier N, Gayral P, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Ferrand N. Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome. Mol Biol Evol 2012; 29:1837-49. [PMID: 22319161 DOI: 10.1093/molbev/mss025] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The nearly neutral theory of molecular evolution predicts that the efficacy of both positive and purifying selection is a function of the long-term effective population size (N(e)) of a species. Under this theory, the efficacy of natural selection should increase with N(e). Here, we tested this simple prediction by surveying ~1.5 to 1.8 Mb of protein coding sequence in the two subspecies of the European rabbit (Oryctolagus cuniculus algirus and O. c. cuniculus), a mammal species characterized by high levels of nucleotide diversity and N(e) estimates for each subspecies on the order of 1 × 10(6). When the segregation of slightly deleterious mutations and demographic effects were taken into account, we inferred that >60% of amino acid substitutions on the autosomes were driven to fixation by positive selection. Moreover, we inferred that a small fraction of new amino acid mutations (<4%) are effectively neutral (defined as 0 < N(e)s < 1) and that this fraction was negatively correlated with a gene's expression level. Consistent with models of recurrent adaptive evolution, we detected a negative correlation between levels of synonymous site polymorphism and the rate of protein evolution, although the correlation was weak and nonsignificant. No systematic X chromosome-autosome difference was found in the efficacy of selection. For example, the proportion of adaptive substitutions was significantly higher on the X chromosome compared with the autosomes in O. c. algirus but not in O. c. cuniculus. Our findings support widespread positive and purifying selection in rabbits and add to a growing list of examples suggesting that differences in N(e) among taxa play a substantial role in determining rates and patterns of protein evolution.
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Affiliation(s)
- Miguel Carneiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal.
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27
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Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus). Heredity (Edinb) 2011; 108:531-6. [PMID: 22146981 DOI: 10.1038/hdy.2011.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Comparative genomic studies have revealed that mammals typically possess two or more tandemly duplicated copies of the α-globin (HBA) gene. The domestic rabbit represents an exception to this general rule, as this species was found to possess a single HBA gene. Previous electrophoretic surveys of HBA polymorphism in natural populations of the European rabbit (Oryctolagus cuniculus) revealed extensive geographic variation in the frequencies of three main electromorphs. The variation in frequency of two electromorphs is mainly partitioned between two distinct subspecies of European rabbit, and a third is restricted to the hybrid zone between the two rabbit subspecies in Iberia. Here we report the results of a survey of nucleotide polymorphism, which revealed HBA copy number polymorphism in Iberian populations of the European rabbit. By characterizing patterns of HBA polymorphism in populations from the native range of the European rabbit, we were able to identify the specific amino-acid substitutions that distinguish the previously characterized electromorphs. Within the hybrid zone, we observed the existence of a second HBA gene duplicate, named HBA2, that mostly represents a novel sequence haplotype, which occurs in higher frequency within the hybrid zone, and thus appears to have arisen in hybrids of the two distinct subspecies. Although this novel gene is also present in other wild Iberian populations, it is almost absent from French populations, which suggest a recent ancestry, associated with the establishment of the post-Pleistocene contact zone between the two European rabbit subspecies.
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Geraldes A, Basset P, Smith KL, Nachman MW. Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination. Mol Ecol 2011; 20:4722-36. [PMID: 22004102 DOI: 10.1111/j.1365-294x.2011.05285.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the early stages of reproductive isolation, genomic regions of reduced recombination are expected to show greater levels of differentiation, either because gene flow between species is reduced in these regions or because the effects of selection at linked sites within species are enhanced in these regions. Here, we study the patterns of DNA sequence variation at 27 autosomal loci among populations of Mus musculus musculus, M. m. domesticus, and M. m. castaneus, three subspecies of house mice with collinear genomes. We found that some loci exhibit considerable shared variation among subspecies, while others exhibit fixed differences. We used an isolation-with-gene-flow model to estimate divergence times and effective population sizes (N(e) ) and to disentangle ancestral variation from gene flow. Estimates of divergence time indicate that all three subspecies diverged from one another within a very short period of time approximately 350,000 years ago. Overall, N(e) for each subspecies was associated with the degree of genetic differentiation: M. m. musculus had the smallest N(e) and the greatest proportion of monophyletic gene genealogies, while M. m. castaneus had the largest N(e) and the smallest proportion of monophyletic gene genealogies. M. m. domesticus and M. m. musculus were more differentiated from each other than either were from M. m. castaneus, consistent with greater reproductive isolation between M. m. domesticus and M. m. musculus. F(ST) was significantly greater at loci experiencing low recombination rates compared to loci experiencing high recombination rates in comparisons between M. m. castaneus and M. m. musculus or M. m. domesticus. These results provide evidence that genomic regions with less recombination show greater differentiation, even in the absence of chromosomal rearrangements.
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Affiliation(s)
- A Geraldes
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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29
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Wu Y, Xia L, Zhang Q, Yang Q, Meng X. Bidirectional introgressive hybridization between Lepus capensis and Lepus yarkandensis. Mol Phylogenet Evol 2011; 59:545-55. [DOI: 10.1016/j.ympev.2011.03.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 03/10/2011] [Accepted: 03/24/2011] [Indexed: 11/29/2022]
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30
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Carneiro M, Blanco-Aguiar JA, Villafuerte R, Ferrand N, Nachman MW. Speciation in the European rabbit (Oryctolagus cuniculus): islands of differentiation on the X chromosome and autosomes. Evolution 2011; 64:3443-60. [PMID: 20666840 DOI: 10.1111/j.1558-5646.2010.01092.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Studies of gene flow between closely related taxa can provide insight into the genetic basis of speciation. To evaluate the importance of the X chromosome in reproductive isolation between subspecies of the European rabbit and to study the genomic scale over which islands of differentiation extend, we resequenced a total of 34 loci distributed along the X chromosome and chromosome 14. Previous studies based on few markers suggested that loci in centromeric regions were highly differentiated between rabbit subspecies, whereas loci in telomeric regions were less differentiated. Here, we confirmed this finding but also discovered remarkable variation in levels of differentiation among loci, with F(ST) values from nearly 0 to 1. Analyses using isolation-with-migration models suggest that this range appears to be largely explained by differential levels of gene flow among loci. The X chromosome was significantly more differentiated than the autosomes. On chromosome 14, differentiation decayed very rapidly at increasing distances from the centromere, but on the X chromosome distinct islands of differentiation encompassing several megabases were observed both at the centromeric region and along the chromosome arms. These findings support the idea that the X chromosome plays an important role in reproductive isolation between rabbit subspecies. These results also demonstrate the mosaic nature of the genome at species boundaries.
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Affiliation(s)
- Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
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31
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32
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Márquez FJ. Molecular detection of Bartonella alsatica in European wild rabbits (Oryctolagus cuniculus) in Andalusia (Spain). Vector Borne Zoonotic Dis 2010; 10:731-4. [PMID: 20059317 DOI: 10.1089/vbz.2009.0135] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A sample of 279 European wild rabbits, Oryctolagus cuniculus (141 males, 138 females), captured alive in Andalusia (Spain) and belonging to the two haplotype classes previously described for this species (230 and 49 corresponding with haplotypes A and B, respectively), were tested for the presence of Bartonella alsatica DNA. Two species-specific nested polymerase chain reaction assays targeting for 16S-23S rRNA intergenic spacer region and RNA polymerase β subunit genes have been developed. Forty-eight (17.20%) rabbits were infected with B. alsatica. Two-way contingency table analyses and the calculation of Cramer's V statistic showed no differences in infection rate, considering haplotype lineage or sex. The risk of infection of human population, especially for hunters in close contact with this demonstrated human pathogen, should be considered.
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Affiliation(s)
- Francisco J Márquez
- Department of Animal Biology, Vegetal Biology and Ecology, University of Jaen, Jaen, Spain.
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33
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Simple Y-autosomal incompatibilities cause hybrid male sterility in reciprocal crosses between Drosophila virilis and D. americana. Genetics 2010; 184:779-87. [PMID: 20048051 DOI: 10.1534/genetics.109.112896] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Postzygotic reproductive isolation evolves when hybrid incompatibilities accumulate between diverging populations. Here, I examine the genetic basis of hybrid male sterility between two species of Drosophila, Drosophila virilis and D. americana. From these analyses, I reach several conclusions. First, neither species carries any autosomal dominant hybrid male sterility alleles: reciprocal F(1) hybrid males are perfectly fertile. Second, later generation (backcross and F(2)) hybrid male sterility between D. virilis and D. americana is not polygenic. In fact, I identified only three genetically independent incompatibilities that cause hybrid male sterility. Remarkably, each of these incompatibilities involves the Y chromosome. In one direction of the cross, the D. americana Y is incompatible with recessive D. virilis alleles at loci on chromosomes 2 and 5. In the other direction, the D. virilis Y chromosome causes hybrid male sterility in combination with recessive D. americana alleles at a single QTL on chromosome 5. Finally, in contrast with findings from other Drosophila species pairs, the X chromosome has only a modest effect on hybrid male sterility between D. virilis and D. americana.
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Abstract
Data analysis in phylogeographic investigations is typically conducted in either a qualitative manner, or alternatively via the testing of null hypotheses. The former, where inferences about population processes are derived from geographical patterns of genetic variation, may be subject to confirmation bias and prone to overinterpretation. Testing the predictions of null hypotheses is arguably less prone to bias than qualitative approaches, but only if the tested hypotheses are biologically meaningful. As it is difficult to know a priori if this is the case, there is the general need for additional methodological approaches in phylogeographic research. Here, we explore an alternative method for analysing phylogeographic data that utilizes information theory to quantify the probability of multiple hypotheses given the data. We accomplish this by augmenting the model-selection procedure implemented in ima with calculations of Akaike Information Criterion scores and model probabilities. We generate a ranking of 17 models each representing a set of historical evolutionary processes that may have contributed to the evolution of Plethodon idahoensis, and then quantify the relative strength of support for each hypothesis given the data using metrics borrowed from information theory. Our results suggest that two models have high probability given the data. Each of these models includes population divergence and estimates of ancestral theta that differ from estimates of descendent theta, inferences consistent with prior work in this system. However, the models disagree in that one includes migration as a parameter and one does not, suggesting that there are two regions of parameter space that produce model likelihoods that are similar in magnitude given our data. Results of a simulation study suggest that when data are simulated with migration, most of the optimal models include migration as a parameter, and further that when all of the shared polymorphism results from incomplete lineage sorting, most of the optimal models do not. The results could also indicate a lack of precision, which may be a product of the amount of data that we have collected. In any case, the information-theoretic metrics that we have applied to the analysis of our data are statistically rigorous, as are hypothesis-testing approaches, but move beyond the 'reject/fail to reject' dichotomy of conventional hypothesis testing in a manner that provides considerably more flexibility to researchers.
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Affiliation(s)
- Bryan C Carstens
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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35
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Petit RJ, Excoffier L. Gene flow and species delimitation. Trends Ecol Evol 2009; 24:386-93. [PMID: 19409650 DOI: 10.1016/j.tree.2009.02.011] [Citation(s) in RCA: 473] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/19/2009] [Accepted: 02/23/2009] [Indexed: 10/20/2022]
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MELO-FERREIRA J, ALVES PC, FREITAS H, FERRAND N, BOURSOT P. The genomic legacy from the extinctLepus timidusto the three hare species of Iberia: contrast between mtDNA, sex chromosomes and autosomes. Mol Ecol 2009; 18:2643-58. [DOI: 10.1111/j.1365-294x.2009.04221.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Carneiro M, Ferrand N, Nachman MW. Recombination and speciation: loci near centromeres are more differentiated than loci near telomeres between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics 2009; 181:593-606. [PMID: 19015539 PMCID: PMC2644949 DOI: 10.1534/genetics.108.096826] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 11/10/2008] [Indexed: 11/18/2022] Open
Abstract
Recent empirical and theoretical studies suggest that regions of restricted recombination play an important role in the formation of new species. To test this idea, we studied nucleotide variation in two parapatric subspecies of the European rabbit (Oryctolagus cuniculus). We surveyed five loci near centromeres, where recombination is expected to be suppressed, and five loci near telomeres, where recombination is expected to be higher. We analyzed this multilocus data set using a divergence-with-gene flow framework and we report three main findings. First, we estimated that these subspecies diverged approximately 1.8 MYA and maintained large effective population sizes (O. c. algirus N(e) approximately 1,600,000 and O. c. cuniculus N(e) approximately 780,000). Second, we rejected a strict allopatric model of divergence without gene flow; instead, high rates of gene flow were inferred in both directions. Third, we found different patterns between loci near centromeres and loci near telomeres. Loci near centromeres exhibited higher levels of linkage disequilibrium than loci near telomeres. In addition, while all loci near telomeres showed little differentiation between subspecies, three of five loci near centromeres showed strong differentiation. These results support a view of speciation in which regions of low recombination can facilitate species divergence in the presence of gene flow.
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Affiliation(s)
- Miguel Carneiro
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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38
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Abstract
Hybridization between genetically divergent populations is common in nature. By comparing the rate of gene flow throughout the genome, loci that impede genetic mixing, and therefore underlie reproductive isolation, can be identified, providing key insights into the process of speciation. In a previous issue of Molecular Ecology, Geraldes et al. (2008) report the geographical distribution of Y chromosome lineages in wild populations of rabbits from across the Iberian Peninsula and southern France. Y chromosomes showed a high level of differentiation between rabbit subspecies on either side of a hybrid zone, despite clear evidence for gene flow at other loci. This provocative result suggests a role for the Y chromosome in reproductive isolation, and adds to a growing list of nascent species with mosaic patterns of differentiation across their genomes.
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Affiliation(s)
- Bret A Payseur
- Laboratory of Genetics, 2428 Genetics/Biotechnology, University of Wisconsin, Madison, WI 53706, USA.
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