Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the<scp>E</scp>uropean rabbit

Carneiro, Miguel; Baird, Stuart J. E.; Afonso, Sandra; Ramírez, Esther; Tarroso, Pedro; Teotónio, Henrique; Villafuerte, Rafael; Nachman, Michael W.; Ferrand, Nuno

doi:10.1111/mec.12272

Cited by 47 publications

(74 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…same group. Geographical isolation was found for wild rabbits (Fuller et al, 1997;Carneiro et al, 2013;Alda and Doadrio, 2014). In this study, we confirmed the spatial representation of the genetic inter-individual distances using the FCA analysis (Figure 3).…”

Section: Discussionsupporting

confidence: 71%

See 1 more Smart Citation

Diversity assessment among native Middle Egypt rabbit populations in North Upper-Egypt province by microsatellite polymorphism

Emam¹,

Azoz²,

Mehaisen

et al. 2017

World Rabbit Sci.

View full text Add to dashboard Cite

Safeguarding biodiversity is an important goal for animal production in developed countries. This study investigated genetic diversity among native Middle-Egypt rabbit (NMER) populations in North UpperEgypt province by using microsatellite polymorphism. Nineteen microsatellite loci were used in the study and an area of 231 km was surveyed, as native rabbits covered 14 points belonging to four Northern Upper Egypt governorates (South Giza, Fayoum, Beni Suef and Minya). Standard statistical parameters of genetic variability within and between populations confirmed that the highest genetic diversity was found towards the south. Among NMER populations, the mean number of alleles per locus was lowest in South Giza (5.32), while it was highest in Minya (6.00). This study found that NMER featured a high number of private alleles ranging between 7 and 11 (mean value was 10.5). Results also showed a high genetic diversity in NMER populations and that heterozygosity ranged between 0.384 and 0.445, strongly indicating extensive genetic variation in the NMER populations. The mean values of observed and expected heterozygosity were 0.405 and 0.612, respectively. Factorial correspondence analysis and neighbour joining trees (NJ) showed 2 main NMER rabbit groups: the Northern group (South Giza and Fayoum) and the Southern group (Beni Suef and Minya). All populations showed a high percentage of assignment in this study (0.913 to 0.946). The structure analysis showed that each population existed in separate clusters. This research provides an overview of genetic diversity of NMER populations in the Northern Upper Egypt province for the first time. In conclusion, results of this study could be used to designate priorities for conservation of NMER populations.

show abstract

Section: Discussionsupporting

confidence: 71%

“…They reported a lower MNA and PVT (ranging from 3.65 to 3.94 and 1 to 8) than those observed in our study in Table 2. These variations might be due to a genetic bottleneck position in other Egyptian local rabbit breeds (Emam et al, 2016). Positive values F IS.…”

Section: Discussionmentioning

confidence: 99%

Diversity assessment among native Middle Egypt rabbit populations in North Upper-Egypt province by microsatellite polymorphism

Emam¹,

Azoz²,

Mehaisen

et al. 2017

World Rabbit Sci.

View full text Add to dashboard Cite

show abstract

“…This dataset was obtained in rabbits sampled at some distance from the primary contact zone (Figure S1), but in geographic regions that nonetheless show high levels of introgression [21], [24]–[27] (see Figure S2). …”

Section: Resultsmentioning

confidence: 99%

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

et al. 2014

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…, ; Carneiro et al . , ). Cruickshank & Hahn () provide several explanations for the apparent inconsistency.…”

Section: Heterogeneous Gene Flow Vs Heterogeneous Selectionmentioning

confidence: 99%

Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones

2016

View full text Add to dashboard Cite

Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genome-wide scale, and recent genome scans have focused on the presence of “islands” of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness, and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the “same” species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.

show abstract

Steep clines within a highly permeable genome across a hybrid zone between two subspecies of theEuropean rabbit

Cited by 47 publications

References 77 publications

Diversity assessment among native Middle Egypt rabbit populations in North Upper-Egypt province by microsatellite polymorphism

Diversity assessment among native Middle Egypt rabbit populations in North Upper-Egypt province by microsatellite polymorphism

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones

Contact Info

Product

Resources

About