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O'Neill DG, Williams A, Brodbelt DC, Church DB, Hedley J. Conformation-associated health in pet rabbits in the UK: A VetCompass cohort study. Vet Rec 2024:e4396. [PMID: 38978404 DOI: 10.1002/vetr.4396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 07/10/2024]
Abstract
BACKGROUND Domestic rabbit breeds vary substantially from the wild rabbit body type. However, little is known about how the conformation of pet rabbits influences their health. METHODS Data were extracted from VetCompass anonymised clinical records of rabbits under UK primary veterinary care during 2019. RESULTS The study included 162,107 rabbits. Based on 88,693 rabbits with relevant breed information recorded, skull shape was classified as brachycephalic (79.69%), mesaticephalic (16.80%) and dolichocephalic (3.51%). Based on 83,821 rabbits with relevant breed information recorded, ear carriage was classified as lop-eared (57.05%) and erect-eared (42.95%). From a random sample of 3933 rabbits, the most prevalent disorders recorded overall were overgrown nail(s) (28.19%), overgrown molar(s) (14.90%) and obesity (8.82%). Compared to those with a mesaticephalic skull shape, brachycephalic rabbits had lower odds of obesity, anorexia and gastrointestinal stasis and higher odds of perineal faecal impaction, tear duct abnormality and haircoat disorder. Compared to erect-eared rabbits, lop-eared rabbits had higher odds of perineal faecal impaction and tear duct abnormality. LIMITATION A large proportion of records with incomplete breed information hindered full analysis for breed-related and conformation-related attributes. CONCLUSION Limited evidence for major links between skull shape or ear carriage conformations and overall disorder risk suggests that factors such as husbandry or even just living life as a domesticated species may be bigger drivers of common health issues in pet rabbits in the UK.
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Affiliation(s)
- Dan G O'Neill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Abbie Williams
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Dave C Brodbelt
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - David B Church
- Department of Clinical Science and Services, Royal Veterinary College, Hatfield, UK
| | - Joanna Hedley
- Department of Clinical Science and Services, Royal Veterinary College, Hatfield, UK
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2
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Martin CA, Sheppard EC, Ali HAA, Illera JC, Suh A, Spurgin LG, Richardson DS. Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci? Mol Ecol 2024; 33:e17365. [PMID: 38733214 DOI: 10.1111/mec.17365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/01/2024] [Indexed: 05/13/2024]
Abstract
When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | | | - Hisham A A Ali
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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3
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Wersebe MJ, Sherman RE, Jeyasingh PD, Weider LJ. The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex. Mol Ecol 2023; 32:1478-1496. [PMID: 35119153 DOI: 10.1111/mec.16383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/16/2022] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.
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Affiliation(s)
- Matthew J Wersebe
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Ryan E Sherman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
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4
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Talbert P, Henikoff S. Centromere drive: chromatin conflict in meiosis. Curr Opin Genet Dev 2022; 77:102005. [PMID: 36372007 DOI: 10.1016/j.gde.2022.102005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/08/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022]
Abstract
Centromeres are essential loci in eukaryotes that are necessary for the faithful segregation of chromosomes in mitosis and meiosis. Centromeres organize the kinetochore, the protein machine that attaches sister chromatids or homologous chromosomes to spindle microtubules and regulates their disjunction. Centromeres have both genetic and epigenetic determinants, which can come into conflict in asymmetric female meiosis in seed plants and animals. The centromere drive model was proposed to describe this conflict and explain how it leads to the rapid evolution of both centromeres and kinetochores. Recent studies confirm key aspects of the centromere drive model, clarify its mechanisms, and implicate rapid centromere/kinetochore evolution in hybrid inviability between species.
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Affiliation(s)
- Paul Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.
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5
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Kretschmer R, Goes CAG, Bertollo LAC, Ezaz T, Porto-Foresti F, Toma GA, Utsunomia R, de Bello Cioffi M. Satellitome analysis illuminates the evolution of ZW sex chromosomes of Triportheidae fishes (Teleostei: Characiformes). Chromosoma 2022; 131:29-45. [PMID: 35099570 DOI: 10.1007/s00412-022-00768-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 12/14/2022]
Abstract
Satellites are an abundant source of repetitive DNAs that play an essential role in the chromosomal organization and are tightly linked with the evolution of sex chromosomes. Among fishes, Triportheidae stands out as the only family where almost all species have a homeologous ZZ/ZW sex chromosomes system. While the Z chromosome is typically conserved, the W is always smaller, with variations in size and morphology between species. Here, we report an analysis of the satellitome of Triportheus auritus (TauSat) by integrating genomic and chromosomal data, with a special focus on the highly abundant and female-biased satDNAs. In addition, we investigated the evolutionary trajectories of the ZW sex chromosomes in the Triportheidae family by mapping satDNAs in selected representative species of this family. The satellitome of T. auritus comprised 53 satDNA families of which 24 were also hybridized by FISH. Most satDNAs differed significantly between sexes, with 19 out of 24 being enriched on the W chromosome of T. auritus. The number of satDNAs hybridized into the W chromosomes of T. signatus and T. albus decreased to six and four, respectively, in accordance with the size of their W chromosomes. No TauSat probes produced FISH signals on the chromosomes of Agoniates halecinus. Despite its apparent conservation, our results indicate that each species differs in the satDNA accumulation on the Z chromosome. Minimum spanning trees (MSTs), generated for three satDNA families with different patterns of FISH mapping data, revealed different homogenization rates between the Z and W chromosomes. These results were linked to different levels of recombination between them. The most abundant satDNA family (TauSat01) was exclusively hybridized in the centromeres of all 52 chromosomes of T. auritus, and its putative role in the centromere evolution was also highlighted. Our results identified a high differentiation of both ZW chromosomes regarding satellites composition, highlighting their dynamic role in the sex chromosomes evolution.
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Affiliation(s)
- Rafael Kretschmer
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | | | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Ricardo Utsunomia
- Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
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6
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Banker SE, Bonhomme F, Nachman MW. Bidirectional introgression between Mus musculus domesticus and Mus spretus. Genome Biol Evol 2022; 14:6509516. [PMID: 35038727 PMCID: PMC8784167 DOI: 10.1093/gbe/evab288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles—including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
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Affiliation(s)
- Sarah E Banker
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - François Bonhomme
- Institut des Sciences de l'Evolution, Université de Montpellier, Montpellier, France
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
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7
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Yang N, Zhao B, Chen Y, D'Alessandro E, Chen C, Ji T, Wu X, Song C. Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). Genome Biol Evol 2021; 13:6322960. [PMID: 34270728 PMCID: PMC8346653 DOI: 10.1093/gbe/evab168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Although the rabbit genome has already been annotated, it is mobilome remains largely unknown. Here, multiple pipelines were used to de novo mine and annotate the mobilome in rabbit. Four families and 19 subfamilies of LINE1s, two families and nine subfamilies of SINEs, and 12 ERV families were defined in rabbit based on sequence identity, structural organization, and phylogenetic tree. The analysis of insertion age and polymerase chain reaction suggests that a number of families are very young and may remain active, such as L1B, L1D, OcuSINEA, and OcuERV1. RepeatMasker annotation revealed a distinct transposable element landscape within the genome, with approximately two million copies of SINEs, representing the greatest proportion of the genome (19.61%), followed by LINEs (15.44%), and LTRs (4.11%), respectively, considerably different from most other mammal mobilomes except hedgehog and tree shrew, in which LINEs have the highest proportion. Furthermore, a very high rate of insertion polymorphisms (>85%) for the youngest subfamily (OcuSINEA1) was identified by polymerase chain reaction. The majority of retrotransposon insertions overlapped with protein-coding regions (>80%) and lncRNA (90%) genes. Genomic distribution bias was observed for retrotransposons, with those immediately upstream (-1 kb) and downstream (1 kb) of genes significantly depleted. Local GC content in 50-kb widows had significantly negative correlations with LINE (rs=-0.996) and LTR (rs=-0.829) insertions. The current study revealed a distinct mobilome landscape in rabbit, which will assist in the elucidation of the evolution of the genome of lagomorphs, and even other mammals.
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Affiliation(s)
- Naisu Yang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Bohao Zhao
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Yang Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | | | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Ting Ji
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Xinsheng Wu
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
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8
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Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evol Lett 2021; 5:196-213. [PMID: 34136269 PMCID: PMC8190449 DOI: 10.1002/evl3.227] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 01/11/2023] Open
Abstract
Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.
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Affiliation(s)
- Eva L Koch
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Hernán E Morales
- Evolutionary Genetics Section Globe Institute University of Copenhagen Copenhagen Denmark.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Jenny Larsson
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Anja M Westram
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,IST Austria Klosterneuburg Austria
| | - Rui Faria
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida FL 32306-4120
| | - E Moriarty Lemmon
- Department of Biological Science Florida State University Tallahassee Florida FL 32306-4295
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
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9
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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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10
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The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes ( Zosterops lateralis). G3-GENES GENOMES GENETICS 2020; 10:3147-3163. [PMID: 32660974 PMCID: PMC7466963 DOI: 10.1534/g3.120.401352] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.
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11
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Sousa M, Silva V, Silva A, Silva N, Ribeiro J, Tejedor-Junco MT, Capita R, Chenouf NS, Alonso-Calleja C, Rodrigues TM, LeitÃo M, GonÇalves D, CaniÇa M, Torres C, Igrejas G, Poeta P. Staphylococci among Wild European Rabbits from the Azores: A Potential Zoonotic Issue? J Food Prot 2020; 83:1110-1114. [PMID: 32572496 DOI: 10.4315/0362-028x.jfp-19-423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/11/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT The prevalence and diversity of Staphylococcus species from wild European rabbits (Oryctolagus cuniculus) in the Azores were investigated, and the antibiotic resistance phenotype and genotype of the isolates were determined. Nasal samples from 77 wild European rabbits from São Jorge and São Miguel islands in Azores were examined. Antibiotic susceptibility of the isolates was determined using the Kirby-Bauer disk diffusion method, and the presence of antimicrobial resistance genes and virulence factors was determined by PCR. The genetic lineages of S. aureus isolates were characterized by spa typing and multilocus sequence typing. A total of 49 staphylococci were obtained from 35 of the 77 wild rabbits. Both coagulase-positive (8.2%) and coagulase-negative (91.8%) staphylococci were detected: 4 S. aureus, 17 S. fleurettii, 13 S. sciuri, 7 S. xylosus, 4 S. epidermidis, and 1 each of S. simulans, S. saprophyticus, S. succinus, and S. equorum. The four S. aureus isolates showed methicillin susceptibility and were characterized as spa type t272/CC121, Panton-Valentine leukocidin negative, and hlB positive. Most of the coagulase-negative staphylococci showed resistance to fusidic acid and beta-lactams, and multidrug resistance was identified especially among S. epidermidis isolates. The mecA gene was detected in 20 isolates of the species S. fleurettii and S. epidermidis, associated with the blaZ gene in one S. epidermidis isolate. Five antimicrobial resistance genes were detected in one S. epidermidis isolate (mecA,dfrA,dfrG,aac6'-aph2'', and ant4). Our results highlight that wild rabbits are reservoirs or "temporary hosts" of Staphylococcus species with zoonotic potential, some of them carrying relevant antimicrobial resistances. HIGHLIGHTS
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Affiliation(s)
- Margarida Sousa
- Veterinary and Animal Science Research Center (CECAV), University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, National Institute of Health Dr. Ricardo Jorge (NIH), Avenida Padre Cruz, 1600-560, Lisboa, Portugal.,Department of Agriculture and Food, Area of Biochemistry and Molecular Biology, University of La Rioja (UR), 26006 Logroño, Spain.,Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, 2829-516 Caparica, Portugal
| | - Adriana Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, 2829-516 Caparica, Portugal
| | - Nuno Silva
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, Scotland, UK
| | - Jessica Ribeiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal
| | - MarÍa Teresa Tejedor-Junco
- Research Institute of Biomedical and Health Sciences, University of Las Palmas de Gran Canaria, 35001 Canary Islands, Spain
| | - Rosa Capita
- Department of Food Hygiene and Technology, Veterinary Faculty, University of León, 24071 León, Spain.,Institute of Food Science and Technology, University of León, 24071 León, Spain
| | - Nadia Safia Chenouf
- Department of Agriculture and Food, Area of Biochemistry and Molecular Biology, University of La Rioja (UR), 26006 Logroño, Spain
| | - Carlos Alonso-Calleja
- Department of Food Hygiene and Technology, Veterinary Faculty, University of León, 24071 León, Spain.,Institute of Food Science and Technology, University of León, 24071 León, Spain
| | - Tiago M Rodrigues
- DRRF, Direção Regional dos Recursos Florestais, Rua do Contador, 9500-050 Ponta Delgada, Azores, Portugal
| | - Manuel LeitÃo
- DRRF, Direção Regional dos Recursos Florestais, Rua do Contador, 9500-050 Ponta Delgada, Azores, Portugal
| | - David GonÇalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4099-002 Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Manuela CaniÇa
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, National Institute of Health Dr. Ricardo Jorge (NIH), Avenida Padre Cruz, 1600-560, Lisboa, Portugal.,Centre for the Study of Animal Sciences (CECA/ICETA), Universidade do Porto, 4099-002 Porto, Portugal
| | - Carmen Torres
- Department of Agriculture and Food, Area of Biochemistry and Molecular Biology, University of La Rioja (UR), 26006 Logroño, Spain
| | - Gilberto Igrejas
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, 2829-516 Caparica, Portugal
| | - PatrÍcia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Quinta de Prados 500-801, Vila Real, Portugal.,Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, 2829-516 Caparica, Portugal
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12
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Moutinho AF, Serén N, Paupério J, Silva TL, Martínez-Freiría F, Sotelo G, Faria R, Mappes T, Alves PC, Brito JC, Boratyński Z. Evolutionary history of two cryptic species of northern African jerboas. BMC Evol Biol 2020; 20:26. [PMID: 32054437 PMCID: PMC7020373 DOI: 10.1186/s12862-020-1592-z] [Citation(s) in RCA: 8] [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: 07/30/2019] [Accepted: 02/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Climatic variation and geologic change both play significant roles in shaping species distributions, thus affecting their evolutionary history. In Sahara-Sahel, climatic oscillations shifted the desert extent during the Pliocene-Pleistocene interval, triggering the diversification of several species. Here, we investigated how these biogeographical and ecological events have shaped patterns of genetic diversity and divergence in African Jerboas, desert specialist rodents. We focused on two sister and cryptic species, Jaculus jaculus and J. hirtipes, where we (1) evaluated their genetic differentiation, (2) reconstructed their evolutionary and demographic history; (3) tested the level of gene flow between them, and (4) assessed their ecological niche divergence. RESULTS The analyses based on 231 individuals sampled throughout North Africa, 8 sequence fragments (one mitochondrial and seven single copy nuclear DNA, including two candidate genes for fur coloration: MC1R and Agouti), 6 microsatellite markers and ecological modelling revealed: (1) two distinct genetic lineages with overlapping distributions, in agreement with their classification as different species, J. jaculus and J. hirtipes, with (2) low levels of gene flow and strong species divergence, (3) high haplotypic diversity without evident geographic structure within species, and (4) a low level of large-scale ecological divergence between the two taxa, suggesting species micro-habitat specialization. CONCLUSIONS Overall, our results suggest a speciation event that occurred during the Pliocene-Pleistocene transition. The contemporary distribution of genetic variation suggests ongoing population expansions. Despite the largely overlapping distributions at a macrogeographic scale, our genetic results suggest that the two species remain reproductively isolated, as only negligible levels of gene flow were observed. The overlapping ecological preferences at a macro-geographic scale and the ecological divergence at the micro-habitat scale suggest that local adaptation may have played a crucial role in the speciation process of these species.
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Affiliation(s)
- Ana Filipa Moutinho
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal.
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal.
| | - Nina Serén
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Joana Paupério
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Teresa Luísa Silva
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Fernando Martínez-Freiría
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Graciela Sotelo
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Rui Faria
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Tapio Mappes
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Paulo Célio Alves
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - José Carlos Brito
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal.
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13
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Talbert PB, Henikoff S. What makes a centromere? Exp Cell Res 2020; 389:111895. [PMID: 32035948 DOI: 10.1016/j.yexcr.2020.111895] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/26/2022]
Abstract
Centromeres are the eukaryotic chromosomal sites at which the kinetochore forms and attaches to spindle microtubules to orchestrate chromosomal segregation in mitosis and meiosis. Although centromeres are essential for cell division, their sequences are not conserved and evolve rapidly. Centromeres vary dramatically in size and organization. Here we categorize their diversity and explore the evolutionary forces shaping them. Nearly all centromeres favor AT-rich DNA that is gene-free and transcribed at a very low level. Repair of frequent centromere-proximal breaks probably contributes to their rapid sequence evolution. Point centromeres are only ~125 bp and are specified by common protein-binding motifs, whereas short regional centromeres are 1-5 kb, typically have unique sequences, and may have pericentromeric repeats adapted to facilitate centromere clustering. Transposon-rich centromeres are often ~100-300 kb and are favored by RNAi machinery that silences transposons, by suppression of meiotic crossovers at centromeres, and by the ability of some transposons to target centromeres. Megabase-length satellite centromeres arise in plants and animals with asymmetric female meiosis that creates centromere competition, and favors satellite monomers one or two nucleosomes in length that position and stabilize centromeric nucleosomes. Holocentromeres encompass the length of a chromosome and may differ dramatically between mitosis and meiosis. We propose a model in which low level transcription of centromeres facilitates the formation of non-B DNA that specifies centromeres and promotes loading of centromeric nucleosomes.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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14
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Abstract
The increasing amount of available biological information on the markers can be used to inform the models applied for genomic selection to improve predictions. The objective of this study was to propose a general model for genomic selection using a link function approach within the hierarchical generalized linear model framework (hglm) that can include external information on the markers. These models can be fitted using the well-established hglm package in R. We also present an R package (CodataGS) to fit these models, which is significantly faster than the hglm package. Simulated data were used to validate the proposed model. We tested categorical, continuous and combination models where the external information on the markers was related to 1) the location of the QTL on the genome with varying degree of uncertainty, 2) the relationship of the markers with the QTL calculated as the LD between them, and 3) a combination of both. The proposed models showed improved accuracies from 3.8% up to 23.2% compared to the SNP-BLUP method in a simulated population derived from a base population with 100 individuals. Moreover, the proposed categorical model was tested on a dairy cattle dataset for two traits (Milk Yield and Fat Percentage). These results also showed improved accuracy compared to SNP-BLUP, especially for the Fat% trait. The performance of the proposed models depended on the genetic architecture of the trait, as traits that deviate from the infinitesimal model benefited more from the external information. Also, the gain in accuracy depended on the degree of uncertainty of the external information provided to the model. The usefulness of these type of models is expected to increase with time as more accurate information on the markers becomes available.
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15
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Nelson TC, Crandall JG, Ituarte CM, Catchen JM, Cresko WA. Selection, Linkage, and Population Structure Interact To Shape Genetic Variation Among Threespine Stickleback Genomes. Genetics 2019; 212:1367-1382. [PMID: 31213503 PMCID: PMC6707445 DOI: 10.1534/genetics.119.302261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/11/2019] [Indexed: 11/18/2022] Open
Abstract
The outcome of selection on genetic variation depends on the geographic organization of individuals and populations as well as the organization of loci within the genome. Spatially variable selection between marine and freshwater habitats has had a significant and heterogeneous impact on patterns of genetic variation across the genome of threespine stickleback fish. When marine stickleback invade freshwater habitats, more than a quarter of the genome can respond to divergent selection, even in as little as 50 years. This process largely uses standing genetic variation that can be found ubiquitously at low frequency in marine populations, can be millions of years old, and is likely maintained by significant bidirectional gene flow. Here, we combine population genomic data of marine and freshwater stickleback from Cook Inlet, Alaska, with genetic maps of stickleback fish derived from those same populations to examine how linkage to loci under selection affects genetic variation across the stickleback genome. Divergent selection has had opposing effects on linked genetic variation on chromosomes from marine and freshwater stickleback populations: near loci under selection, marine chromosomes are depauperate of variation, while these same regions among freshwater genomes are the most genetically diverse. Forward genetic simulations recapitulate this pattern when different selective environments also differ in population structure. Lastly, dense genetic maps demonstrate that the interaction between selection and population structure may impact large stretches of the stickleback genome. These findings advance our understanding of how the structuring of populations across geography influences the outcomes of selection, and how the recombination landscape broadens the genomic reach of selection.
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Affiliation(s)
- Thomas C Nelson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | | | - Catherine M Ituarte
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Julian M Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Illinois 61801
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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16
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Alves JM, Carneiro M, Cheng JY, Lemos de Matos A, Rahman MM, Loog L, Campos PF, Wales N, Eriksson A, Manica A, Strive T, Graham SC, Afonso S, Bell DJ, Belmont L, Day JP, Fuller SJ, Marchandeau S, Palmer WJ, Queney G, Surridge AK, Vieira FG, McFadden G, Nielsen R, Gilbert MTP, Esteves PJ, Ferrand N, Jiggins FM. Parallel adaptation of rabbit populations to myxoma virus. Science 2019; 363:1319-1326. [PMID: 30765607 DOI: 10.1126/science.aau7285] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/10/2018] [Accepted: 02/01/2019] [Indexed: 12/18/2022]
Abstract
In the 1950s the myxoma virus was released into European rabbit populations in Australia and Europe, decimating populations and resulting in the rapid evolution of resistance. We investigated the genetic basis of resistance by comparing the exomes of rabbits collected before and after the pandemic. We found a strong pattern of parallel evolution, with selection on standing genetic variation favoring the same alleles in Australia, France, and the United Kingdom. Many of these changes occurred in immunity-related genes, supporting a polygenic basis of resistance. We experimentally validated the role of several genes in viral replication and showed that selection acting on an interferon protein has increased the protein's antiviral effect.
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Affiliation(s)
- Joel M Alves
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK. .,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Miguel Carneiro
- 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, 4169-007 Porto, Portugal
| | - Jade Y Cheng
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ana Lemos de Matos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Masmudur M Rahman
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Liisa Loog
- Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK.,Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA.,Department of Archaeology, University of York, King's Manor, York YO1 7EP, UK
| | - Anders Eriksson
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Tanja Strive
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.,Centre for Invasive Species Solutions, University of Canberra, Bruce, ACT 2601, Australia
| | - Stephen C Graham
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Diana J Bell
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Laura Belmont
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Susan J Fuller
- School of Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | | | - William J Palmer
- The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Guillaume Queney
- ANTAGENE, Wildlife Genetics Laboratory, La Tour de Salvagny (Lyon), France
| | - Alison K Surridge
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Grant McFadden
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Nuno Ferrand
- 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, 4169-007 Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park 2006, South Africa
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
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17
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Pereira AG, Schrago CG. Incomplete lineage sorting impacts the inference of macroevolutionary regimes from molecular phylogenies when concatenation is employed: An analysis based on Cetacea. Ecol Evol 2018; 8:6965-6971. [PMID: 30073059 PMCID: PMC6065336 DOI: 10.1002/ece3.4212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 11/27/2022] Open
Abstract
Interest in methods that estimate speciation and extinction rates from molecular phylogenies has increased over the last decade. The application of such methods requires reliable estimates of tree topology and node ages, which are frequently obtained using standard phylogenetic inference combining concatenated loci and molecular dating. However, this practice disregards population-level processes that generate gene tree/species tree discordance. We evaluated the impact of employing concatenation and coalescent-based phylogeny inference in recovering the correct macroevolutionary regime using simulated data based on the well-established diversification rate shift of delphinids in Cetacea. We found that under scenarios of strong incomplete lineage sorting, macroevolutionary analysis of phylogenies inferred by concatenating loci failed to recover the delphinid diversification shift, while the coalescent-based tree consistently retrieved the correct rate regime. We suggest that ignoring microevolutionary processes reduces the power of methods that estimate macroevolutionary regimes from molecular data.
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Affiliation(s)
- Anieli G. Pereira
- Department of GeneticsFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Carlos G. Schrago
- Department of GeneticsFederal University of Rio de JaneiroRio de JaneiroBrazil
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18
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Campbell CR, Poelstra JW, Yoder AD. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly063] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - J W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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19
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Schumer M, Xu C, Powell DL, Durvasula A, Skov L, Holland C, Blazier JC, Sankararaman S, Andolfatto P, Rosenthal GG, Przeworski M. Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science 2018; 360:656-660. [PMID: 29674434 PMCID: PMC6069607 DOI: 10.1126/science.aar3684] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/23/2018] [Indexed: 12/29/2022]
Abstract
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the "minor" parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on swordtail hybrids stems predominantly from deleterious combinations of epistatically interacting alleles.
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Affiliation(s)
- Molly Schumer
- Howard Hughes Medical Institute (HHMI), Boston, MA, USA.
- Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
| | - Chenling Xu
- Center for Computational Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Daniel L Powell
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Chris Holland
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - John C Blazier
- Department of Biology, Texas A&M University, College Station, TX, USA
- Texas A&M Institute for Genome Sciences and Society, College Station, TX, USA
| | - Sriram Sankararaman
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA
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20
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Mořkovský L, Janoušek V, Reif J, Rídl J, Pačes J, Choleva L, Janko K, Nachman MW, Reifová R. Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility. Mol Ecol 2018; 27:949-958. [PMID: 29319911 DOI: 10.1111/mec.14479] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 12/24/2022]
Abstract
Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule, it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species, we identified genomic islands of high differentiation (FST ) and of high divergence (Dxy ), and we analysed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females.
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Affiliation(s)
- Libor Mořkovský
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Václav Janoušek
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Jakub Rídl
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague 4, Czech Republic
| | - Jan Pačes
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague 4, Czech Republic
| | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic
| | - Michael W Nachman
- Museum of Comparative Zoology and Integrative Biology, University of California, Berkeley, CA, USA
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
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21
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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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22
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Makino T, Rubin CJ, Carneiro M, Axelsson E, Andersson L, Webster MT. Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants. Genome Biol Evol 2018; 10:276-290. [PMID: 29325102 PMCID: PMC5786255 DOI: 10.1093/gbe/evy004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here, we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken, and silkworm) and two domestic plant species (rice and soybean) compared with their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more single nucleotide polymorphisms in highly conserved elements in domestic species and a tendency for domestic species to harbor a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.
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Affiliation(s)
- Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - 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, Portugal
| | - Erik Axelsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
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23
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Reeve J, Ortiz-Barrientos D, Engelstädter J. The evolution of recombination rates in finite populations during ecological speciation. Proc Biol Sci 2017; 283:rspb.2016.1243. [PMID: 27798297 DOI: 10.1098/rspb.2016.1243] [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] [Received: 06/05/2016] [Accepted: 10/04/2016] [Indexed: 11/12/2022] Open
Abstract
Recombination can impede ecological speciation with gene flow by mixing locally adapted genotypes with maladapted migrant genotypes from a divergent population. In such a scenario, suppression of recombination can be selectively favoured. However, in finite populations evolving under the influence of random genetic drift, recombination can also facilitate adaptation by reducing Hill-Robertson interference between loci under selection. In this case, increased recombination rates can be favoured. Although these two major effects on recombination have been studied individually, their joint effect on ecological speciation with gene flow remains unexplored. Using a mathematical model, we investigated the evolution of recombination rates in two finite populations that exchange migrants while adapting to contrasting environments. Our results indicate a two-step dynamic where increased recombination is first favoured (in response to the Hill-Robertson effect), and then disfavoured, as the cost of recombining locally with maladapted migrant genotypes increases over time (the maladaptive gene flow effect). In larger populations, a stronger initial benefit for recombination was observed, whereas high migration rates intensify the long-term cost of recombination. These dynamics may have important implications for our understanding of the conditions that facilitate incipient speciation with gene flow and the evolution of recombination in finite populations.
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Affiliation(s)
- James Reeve
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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24
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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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25
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Britton-Davidian J, Caminade P, Davidian E, Pagès M. Does chromosomal change restrict gene flow between house mouse populations (Mus musculus domesticus)? Evidence from microsatellite polymorphisms. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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26
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Kindler C, Chèvre M, Ursenbacher S, Böhme W, Hille A, Jablonski D, Vamberger M, Fritz U. Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species. Sci Rep 2017; 7:7378. [PMID: 28785033 PMCID: PMC5547120 DOI: 10.1038/s41598-017-07847-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022] Open
Abstract
Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.
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Affiliation(s)
- Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Maxime Chèvre
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, 4056, Basel, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, 4056, Basel, Switzerland.,Karch, Passage Maximilien-de-Meuron 6, 2000, Neuchâtel, Switzerland
| | - Wolfgang Böhme
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Axel Hille
- Rosengarten 21, 33605, Bielefeld, Germany
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Melita Vamberger
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany.
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27
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Vijay N, Weissensteiner M, Burri R, Kawakami T, Ellegren H, Wolf JBW. Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa. Mol Ecol 2017; 26:4284-4295. [PMID: 28570015 DOI: 10.1111/mec.14195] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 12/15/2022]
Abstract
Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in Ne . Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in Ne would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (FST , PBS, dxy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.
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Affiliation(s)
- Nagarjun Vijay
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Lab of Molecular and Genomic Evolution, Department of Ecology and Evolutionary Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Weissensteiner
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Reto Burri
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Takeshi Kawakami
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Hans Ellegren
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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28
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Weissensteiner MH, Pang AWC, Bunikis I, Höijer I, Vinnere-Petterson O, Suh A, Wolf JBW. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Res 2017; 27:697-708. [PMID: 28360231 PMCID: PMC5411765 DOI: 10.1101/gr.215095.116] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/10/2017] [Indexed: 12/27/2022]
Abstract
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.
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Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| | | | - Ignas Bunikis
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | - Ida Höijer
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | | | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
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29
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Knief U, Forstmeier W. Mapping centromeres of microchromosomes in the zebra finch (Taeniopygia guttata) using half-tetrad analysis. Chromosoma 2016; 125:757-68. [PMID: 26667931 PMCID: PMC5023761 DOI: 10.1007/s00412-015-0560-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 12/24/2022]
Abstract
Centromeres usually consist of hundreds of kilobases of repetitive sequence which renders them difficult to assemble. As a consequence, centromeres are often missing from assembled genomes and their locations on physical chromosome maps have to be inferred from flanking sequences via fluorescence in situ hybridization (FISH). Alternatively, centromere positions can be mapped using linkage analyses in accidentally triploid individuals formed by half-tetrads (resulting from the inheritance of two chromatids from a single meiosis). The current genome assembly of the zebra finch (Taeniopygia guttata) comprises 32 chromosomes, but only for the ten largest chromosomes centromere positions have been mapped using FISH. We here map the positions of most of the remaining centromeres using half-tetrad analyses. For this purpose, we genotyped 37 zebra finches that were triploid or tetraploid due to inheritance errors (and mostly died as embryos) together with their parents at 64 microsatellite markers (at least two per chromosome). Using the information on centromere positions on the ten largest chromosomes, we were able to identify 12 cases of non-disjunction in maternal meiosis I and 10 cases of non-disjunction in maternal meiosis II. These 22 informative cases allowed us to infer centromere positions on additional 19 microchromosomes in reference to the current genome assembly. This knowledge will be valuable for studies of chromosome evolution, meiotic drive and species divergence in the avian lineage.
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Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
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30
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Kenney AM, Sweigart AL. Reproductive isolation and introgression between sympatric
Mimulus
species. Mol Ecol 2016; 25:2499-517. [DOI: 10.1111/mec.13630] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Amanda M. Kenney
- Department of Genetics University of Georgia Athens GA 30602 USA
- Department of Biological Sciences St. Edward's University Austin TX 78704 USA
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31
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Kim KW, Griffith SC, Burke T. Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae). Heredity (Edinb) 2016; 116:409-16. [PMID: 26786066 PMCID: PMC4806697 DOI: 10.1038/hdy.2015.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/25/2015] [Accepted: 12/11/2015] [Indexed: 01/04/2023] Open
Abstract
Colour polymorphism is known to facilitate speciation but the genetic basis of animal pigmentation and how colour polymorphisms contribute to speciation is poorly understood. Restricted recombination may promote linkage disequilibrium between the colour locus and incompatibility genes. Genomic rearrangement and the position of relevant loci within a chromosome are important factors that influence the frequency of recombination. Therefore, it is important to know the position of the colour locus, gene order and recombination landscape of the chromosome to understand the mechanism that generates incompatibilities between morphs. Recent studies showed remarkable pre- and postzygotic incompatibilities between sympatric colour morphs of the Gouldian finch (Erythrura gouldiae), in which head feather colour is genetically determined by a single sex-linked locus, Red. We constructed a genetic map for the Z chromosome of the Gouldian finch (male-specific map distance=131 cM), using 618 captive-bred birds and 34 microsatellite markers, to investigate the extent of inter- and intraspecific genomic rearrangements and variation in recombination rate within the Z chromosome. We refined the location of the Red locus to a ~7.2-cM interval in a region with a moderate recombination rate but outside the least-recombining, putative centromeric region. There was no evidence of chromosome-wide genomic rearrangements between the chromosomes carrying the red or black alleles with the current marker resolution. This work will contribute to identifying the causal gene, which will in turn enable alternative explanations for the association between incompatibility and colouration, such as fine-scale linkage disequilibrium, genomic rearrangements and pleiotropy, to be tested.
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Affiliation(s)
- K-W Kim
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - S C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - T Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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32
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Schneider KL, Xie Z, Wolfgruber TK, Presting GG. Inbreeding drives maize centromere evolution. Proc Natl Acad Sci U S A 2016. [PMID: 26858403 DOI: 10.1073/pnas.1522008113113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Functional centromeres, the chromosomal sites of spindle attachment during cell division, are marked epigenetically by the centromere-specific histone H3 variant cenH3 and typically contain long stretches of centromere-specific tandem DNA repeats (∼1.8 Mb in maize). In 23 inbreds of domesticated maize chosen to represent the genetic diversity of maize germplasm, partial or nearly complete loss of the tandem DNA repeat CentC precedes 57 independent cenH3 relocation events that result in neocentromere formation. Chromosomal regions with newly acquired cenH3 are colonized by the centromere-specific retrotransposon CR2 at a rate that would result in centromere-sized CR2 clusters in 20,000-95,000 y. Three lines of evidence indicate that CentC loss is linked to inbreeding, including (i) CEN10 of temperate lineages, presumed to have experienced a genetic bottleneck, contain less CentC than their tropical relatives; (ii) strong selection for centromere-linked genes in domesticated maize reduced diversity at seven of the ten maize centromeres to only one or two postdomestication haplotypes; and (iii) the centromere with the largest number of haplotypes in domesticated maize (CEN7) has the highest CentC levels in nearly all domesticated lines. Rare recombinations introduced one (CEN2) or more (CEN5) alternate CEN haplotypes while retaining a single haplotype at domestication loci linked to these centromeres. Taken together, this evidence strongly suggests that inbreeding, favored by postdomestication selection for centromere-linked genes affecting key domestication or agricultural traits, drives replacement of the tandem centromere repeats in maize and other crop plants. Similar forces may act during speciation in natural systems.
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Affiliation(s)
- Kevin L Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822
| | - Zidian Xie
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822
| | - Thomas K Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822
| | - Gernot G Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822
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33
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Abstract
Functional centromeres, the chromosomal sites of spindle attachment during cell division, are marked epigenetically by the centromere-specific histone H3 variant cenH3 and typically contain long stretches of centromere-specific tandem DNA repeats (∼1.8 Mb in maize). In 23 inbreds of domesticated maize chosen to represent the genetic diversity of maize germplasm, partial or nearly complete loss of the tandem DNA repeat CentC precedes 57 independent cenH3 relocation events that result in neocentromere formation. Chromosomal regions with newly acquired cenH3 are colonized by the centromere-specific retrotransposon CR2 at a rate that would result in centromere-sized CR2 clusters in 20,000-95,000 y. Three lines of evidence indicate that CentC loss is linked to inbreeding, including (i) CEN10 of temperate lineages, presumed to have experienced a genetic bottleneck, contain less CentC than their tropical relatives; (ii) strong selection for centromere-linked genes in domesticated maize reduced diversity at seven of the ten maize centromeres to only one or two postdomestication haplotypes; and (iii) the centromere with the largest number of haplotypes in domesticated maize (CEN7) has the highest CentC levels in nearly all domesticated lines. Rare recombinations introduced one (CEN2) or more (CEN5) alternate CEN haplotypes while retaining a single haplotype at domestication loci linked to these centromeres. Taken together, this evidence strongly suggests that inbreeding, favored by postdomestication selection for centromere-linked genes affecting key domestication or agricultural traits, drives replacement of the tandem centromere repeats in maize and other crop plants. Similar forces may act during speciation in natural systems.
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34
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Limborg MT, McKinney GJ, Seeb LW, Seeb JE. Recombination patterns reveal information about centromere location on linkage maps. Mol Ecol Resour 2015; 16:655-61. [PMID: 26561199 DOI: 10.1111/1755-0998.12484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/29/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022]
Abstract
Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres - an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half-tetrad analyses. We validate the method on a linkage map for sockeye salmon (Oncorhynchus nerka) with known centromeric regions. Further tests suggest that the method will work well in other salmonids and other eukaryotes. However, the method performed weakly when applied to a male linkage map (rainbow trout; O. mykiss) characterized by low and unevenly distributed recombination - a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations, our method should work well for high-density maps in species with strong recombination interference and will enrich many existing and future mapping resources.
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Affiliation(s)
- Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA.,National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
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35
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Gante HF, Doadrio I, Alves MJ, Dowling TE. Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae). BMC Evol Biol 2015; 15:111. [PMID: 26066794 PMCID: PMC4465174 DOI: 10.1186/s12862-015-0392-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/28/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes. RESULTS Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs. CONCLUSIONS We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.
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Affiliation(s)
- Hugo F Gante
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
- Current address: Zoological Institute, University of Basel, 4051, Basel, Switzerland.
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| | - Maria Judite Alves
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
| | - Thomas E Dowling
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Current address: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, 48202, Detroit, MI, USA.
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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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Vamberger M, Stuckas H, Sacco F, D'Angelo S, Arculeo M, Cheylan M, Corti C, Lo Valvo M, Marrone F, Wink M, Fritz U. Differences in gene flow in a twofold secondary contact zone of pond turtles in southern Italy (Testudines: Emydidae:Emys orbicularis galloitalica,E. o. hellenica,E. trinacris). ZOOL SCR 2015. [DOI: 10.1111/zsc.12102] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Melita Vamberger
- Museum of Zoology (Museum für Tierkunde); Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - Heiko Stuckas
- Museum of Zoology (Museum für Tierkunde); Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - Francesco Sacco
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche (STEBICEF); Università di Palermo; Via Archirafi 18 90123 Palermo Italy
| | - Stefania D'Angelo
- WWF Nature Reserve ‘Lago Preola e Gorghi Tondi’; Via G. Lozano 29 91026 Mazara del Vallo Italy
| | - Marco Arculeo
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche (STEBICEF); Università di Palermo; Via Archirafi 18 90123 Palermo Italy
| | - Marc Cheylan
- Biogéographie et Ecologie des Vertébrés (E.P.H.E.); Centre d'Ecologie Fonctionnelle & Evolutive (CNRS); UMR 5175; campus CNRS, 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Claudia Corti
- Museo di Storia Naturale dell'Università di Firenze; Sezione di Zoologia ‘La Specola’; Via Romana, 17 50125 Firenze Italy
| | - Mario Lo Valvo
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche (STEBICEF); Università di Palermo; Via Archirafi 18 90123 Palermo Italy
| | - Federico Marrone
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche (STEBICEF); Università di Palermo; Via Archirafi 18 90123 Palermo Italy
| | - Michael Wink
- Universität Heidelberg; Institut für Pharmazie & Molekulare Biotechnologie (IPMB); Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde); Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
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38
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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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39
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Kessler MD, Dean MD. Effective population size does not predict codon usage bias in mammals. Ecol Evol 2014; 4:3887-900. [PMID: 25505518 PMCID: PMC4242573 DOI: 10.1002/ece3.1249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022] Open
Abstract
Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (Ne), with selection on CUB operating less efficiently in species with small Ne. Here, we specifically ask whether variation in Ne predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of Ne (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X-linked genes, and high-recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in Ne predicts variation in CUB. Second, across six mammalian species with genetic estimates of Ne (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), Ne and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in Ne does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between Ne and CUB.
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Affiliation(s)
- Michael D Kessler
- Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California, 90089
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California, 90089
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40
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Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 2014; 345:1074-1079. [PMID: 25170157 PMCID: PMC5421586 DOI: 10.1126/science.1253714] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
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MESH Headings
- Animals
- Animals, Domestic/anatomy & histology
- Animals, Domestic/genetics
- Animals, Domestic/psychology
- Animals, Wild/anatomy & histology
- Animals, Wild/genetics
- Animals, Wild/psychology
- Base Sequence
- Behavior, Animal
- Breeding
- Evolution, Molecular
- Gene Frequency
- Genetic Loci
- Genome/genetics
- Molecular Sequence Data
- Phenotype
- Polymorphism, Single Nucleotide
- Rabbits/anatomy & histology
- Rabbits/genetics
- Rabbits/psychology
- Selection, Genetic
- Sequence Analysis, DNA
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Affiliation(s)
- Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Carl-Johan Rubin
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Federica Di Palma
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
- Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK
| | - Frank W Albert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jessica Alföldi
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Alvaro Martinez Barrio
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gerli Pielberg
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nima Rafati
- Science of 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
| | - Jason Turner-Maier
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Shady Younis
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Production, Ain Shams University, Shoubra El-Kheima, Cairo, Egypt
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joel M Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard Bolet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France
| | | | - Hernán A Burbano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rita Campos
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Jean L Chang
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Veronique Duranthon
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna Italy
| | - Hervé Garreau
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France
| | - David Heiman
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jeremy Johnson
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rose G Mage
- Laboratory of Immunology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Ze Peng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | | | - Claire Rogel-Gaillard
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, F- 78350, Jouy-en-Josas, France
| | - Magali Ruffier
- Wellcome Trust Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Rafael Villafuerte
- Instituto de Estudios Sociales Avanzados, (IESA-CSIC) Campo Santo de los Mártires 7, Córdoba Spain
| | - Anqi Xiong
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarah Young
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Karin Forsberg-Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jeffrey M Good
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Eric S Lander
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n. 4169-007 Porto, Portugal
| | - Kerstin Lindblad-Toh
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Leif Andersson
- Science of 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, USA
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41
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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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Zhou L, Bawa R, Holliday JA. Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa). Mol Ecol 2014; 23:2486-99. [PMID: 24750333 DOI: 10.1111/mec.12752] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022]
Abstract
Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. FST outlier analysis revealed that promoter, 5'-UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within-population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.
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Affiliation(s)
- L Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
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43
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Convergent evolution of IL-6 in two leporids (Oryctolagus and Pentalagus) originated an extended protein. Immunogenetics 2014; 66:589-95. [DOI: 10.1007/s00251-014-0787-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
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Ruegg K, Anderson EC, Boone J, Pouls J, Smith TB. A role for migration-linked genes and genomic islands in divergence of a songbird. Mol Ecol 2014; 23:4757-69. [PMID: 24954641 DOI: 10.1111/mec.12842] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/13/2014] [Accepted: 06/18/2014] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently, there has been a debate around the role of 'genomic islands of divergence' (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson's thrush, Catharus ustulatus, is a migratory songbird with two genetically distinct subspecies that differ in a number of traits known to be involved in reproductive isolation in birds (plumage coloration, song and migratory behaviour), despite contemporary gene flow along a secondary contact zone. Here, we use RAD-PE sequencing to test emerging hypotheses about the process of divergence at the level of the genome and identify genes and gene regions involved in differentiation in this migratory songbird. Our analyses revealed distinct genomic islands on 15 of the 23 chromosomes and an accelerated rate of divergence on the Z chromosome, one of the avian sex chromosomes. Further, an analysis of loci linked to traits known to be involved in reproductive isolation in songbirds showed that genes linked to migration are significantly more differentiated than expected by chance, but that these genes lie primarily outside the genomic islands. Overall, our analysis supports the idea that genes linked to migration play an important role in divergence in migratory songbirds, but we find no compelling evidence that the observed genomic islands are facilitating adaptive divergence in migratory behaviour.
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Affiliation(s)
- Kristen Ruegg
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, La Kretz Hall, Suite 300, 619 Charles E. Young Dr. East, Los Angeles, CA, 90095, USA; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, 95060, USA
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45
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Clarkson CS, Weetman D, Essandoh J, Yawson AE, Maslen G, Manske M, Field SG, Webster M, Antão T, MacInnis B, Kwiatkowski D, Donnelly MJ. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation. Nat Commun 2014; 5:4248. [PMID: 24963649 PMCID: PMC4086683 DOI: 10.1038/ncomms5248] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 05/28/2014] [Indexed: 11/16/2022] Open
Abstract
Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary
responses, though it may be counterbalanced by potential for detrimental disruption of the
recipient genomic background. We examine the extent and impact of recent introgression of a
strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of
two exceptionally large genomic islands of divergence separating the Anopheles
gambiae species pair. Here we show that transfer of the Vgsc mutation results
in homogenization of the entire genomic island region (~1.5% of the genome) between
species. Despite this massive disruption, introgression is clearly adaptive with a dramatic
rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive
isolation between species. Our results show (1) how resilience of genomes to massive
introgression can permit rapid adaptive response to anthropogenic selection and (2) that
even extreme prominence of genomic islands of divergence can be an unreliable indicator of
importance in speciation. Highly divergent genomic islands segregate between a species pair of the
mosquito, Anopheles gambiae. Here Clarkson et al. show that loss of one of the
largest islands, driven by adaptive introgression of an insecticide-resistance mutation, had
no impact on reproductive isolation.
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Affiliation(s)
- Chris S Clarkson
- 1] Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK [2]
| | - David Weetman
- 1] Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK [2]
| | - John Essandoh
- 1] Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK [2] Cape Coast Department of Entomology and Wildlife, School of Biological Science, University of Cape Coast, Cape Coast, Ghana
| | - Alexander E Yawson
- 1] Cape Coast Department of Entomology and Wildlife, School of Biological Science, University of Cape Coast, Cape Coast, Ghana [2] Biotechnology and Nuclear Agriculture Research Institute, Ghana Atomic Energy Commission, PO Box LG 80, Legon, Accra, Ghana
| | - Gareth Maslen
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Magnus Manske
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Stuart G Field
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | | | - Tiago Antão
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Bronwyn MacInnis
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Dominic Kwiatkowski
- 1] Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Martin J Donnelly
- 1] Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK [2] Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
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Cruickshank TE, Hahn MW. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 2014; 23:3133-57. [DOI: 10.1111/mec.12796] [Citation(s) in RCA: 764] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 12/18/2022]
Affiliation(s)
| | - Matthew W. Hahn
- Department of Biology; Indiana University; Bloomington IN 47405 USA
- School of Informatics and Computing; Indiana University; Bloomington IN 47405 USA
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47
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Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL. Speciation and introgression between Mimulus nasutus and Mimulus guttatus. PLoS Genet 2014; 10:e1004410. [PMID: 24967630 PMCID: PMC4072524 DOI: 10.1371/journal.pgen.1004410] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 04/11/2014] [Indexed: 12/30/2022] Open
Abstract
Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a population genomic data set which shows that M. nasutus budded from a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the M. nasutus genome has accrued genomic signatures of the transition to predominant selfing, including an elevated proportion of nonsynonymous variants, an accumulation of premature stop codons, and extended levels of linkage disequilibrium. Despite clear biological differentiation, we document genomic signatures of ongoing, bidirectional introgression. We observe a negative relationship between the recombination rate and divergence between M. nasutus and sympatric M. guttatus samples, suggesting that selection acts against M. nasutus ancestry in M. guttatus.
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Affiliation(s)
- Yaniv Brandvain
- Department of Evolution and Ecology & Center for Population Biology, University of California - Davis, Davis, California, United States of America
- Department of Plant Biology, University of Minnesota – Twin Cities. St. Paul, Minnesota, United States of America
| | - Amanda M. Kenney
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Lex Flagel
- Monsanto Company, Chesterfield, Missouri, United States of America
| | - Graham Coop
- Department of Evolution and Ecology & Center for Population Biology, University of California - Davis, Davis, California, United States of America
| | - Andrea L. Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
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48
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Rincent R, Moreau L, Monod H, Kuhn E, Melchinger AE, Malvar RA, Moreno-Gonzalez J, Nicolas S, Madur D, Combes V, Dumas F, Altmann T, Brunel D, Ouzunova M, Flament P, Dubreuil P, Charcosset A, Mary-Huard T. Recovering power in association mapping panels with variable levels of linkage disequilibrium. Genetics 2014; 197:375-87. [PMID: 24532779 PMCID: PMC4012494 DOI: 10.1534/genetics.113.159731] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/09/2014] [Indexed: 11/18/2022] Open
Abstract
Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We analytically studied power in association studies by computing noncentrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high linkage disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimating the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers that are not located on the same chromosome than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and were more powerful than classical models.
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Affiliation(s)
- Renaud Rincent
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
- Biogemma, Genetics and Genomics in Cereals, 63720 Chappes, France
- Kleinwanzlebener Saatzucht Saat AG, 37555 Einbeck, Germany
- Limagrain, site d’Ulice, BP173, 63204 Riom Cedex, France
| | - Laurence Moreau
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Hervé Monod
- Institut National de la Recherche Agronomique, Unité de Mathématique et Informatique Appliquées, 78352 Jouy-en-Josas, France
| | - Estelle Kuhn
- Institut National de la Recherche Agronomique, Unité de Mathématique et Informatique Appliquées, 78352 Jouy-en-Josas, France
| | - Albrecht E. Melchinger
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Rosa A. Malvar
- Misión Biológica de Galicia, Spanish National Research Council, 36080 Pontevedra, Spain
| | | | - Stéphane Nicolas
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Delphine Madur
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Valérie Combes
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Fabrice Dumas
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Thomas Altmann
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm and Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Dominique Brunel
- Institut National de la Recherche Agronomique, Etude du Polymorphisme des Génomes Végétaux, Commissariat à l'Energie Atomique Institut de Génomique, Centre National de Génotypage, 91057 Evry, France
| | | | - Pascal Flament
- Limagrain, site d’Ulice, BP173, 63204 Riom Cedex, France
| | - Pierre Dubreuil
- Biogemma, Genetics and Genomics in Cereals, 63720 Chappes, France
| | - Alain Charcosset
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
- Institut National de la Recherche Agronomique/AgroParisTech, Unité Mixte de Recherche 518, 75231, Paris, France
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Morán T, Fontdevila A. Genome-wide dissection of hybrid sterility in Drosophila confirms a polygenic threshold architecture. J Hered 2014; 105:381-96. [PMID: 24489077 DOI: 10.1093/jhered/esu003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To date, different studies about the genetic basis of hybrid male sterility (HMS), a postzygotic reproductive barrier thoroughly investigated using Drosophila species, have demonstrated that no single major gene can produce hybrid sterility without the cooperation of several genetic factors. Early work using hybrids between Drosophila koepferae (Dk) and Drosophila buzzatii (Db) was consistent with the idea that HMS requires the cooperation of several genetic factors, supporting a polygenic threshold (PT) model. Here we present a genome-wide mapping strategy to test the PT model, analyzing serially backcrossed fertile and sterile males in which the Dk genome was introgressed into the Db background. We identified 32 Dk-specific markers significantly associated with hybrid sterility. Our results demonstrate 1) a strong correlation between the number of segregated sterility markers and males' degree of sterility, 2) the exchangeability among markers, 3) their tendency to cluster into low-recombining chromosomal regions, and 4) the requirement for a minimum number (threshold) of markers to elicit sterility. Although our findings do not contradict a role for occasional major hybrid-sterility genes, they conform more to the view that HMS primarily evolves by the cumulative action of many interacting genes of minor effect in a complex PT architecture.
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Affiliation(s)
- Tomás Morán
- the Grup de Biologia Evolutiva, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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50
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Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory. Mol Phylogenet Evol 2013; 69:1172-85. [DOI: 10.1016/j.ympev.2013.06.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 06/06/2013] [Accepted: 06/12/2013] [Indexed: 11/22/2022]
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