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Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison with the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping‐by‐sequencing of high‐quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low‐quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based on Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation‐related studies of genetic variation may benefit from the two‐step approach we employed that first surveys genomic variation using high‐quality samples and then genotypes low‐quality samples at particularly informative loci.

Biological invasions are accelerating, and invasive species can have large economic impacts as well as severe consequences for biodiversity. During invasions, species can interact, potentially resulting in hybridization. Here, we examined two Cakile species, C. edentula and C. maritima (Brassicaceae), that co-occur and may hybridize during range expansion in separate regions of the globe. Cakile edentula invaded each location first, while C. maritima established later, apparently replacing the former. We assessed the evidence for hybridization in western North America and Australia, where both species have been introduced, and identified source populations with 4561 SNPs using Genotype-by-Sequencing. Our results indicate that C. edentula in Australia originated from one region of eastern North America while in western North America it is probably from multiple sources. Cakile maritima in Australia is derived from at least two different parts of Europe while the introduction in western North America is from one. Although morphological evidence of hybridization is generally limited to mixed species populations in Australia and virtually absent elsewhere, our genetic analysis revealed relatively high levels of hybridization in Australia (58% hybrids using Admixture) and supported the presence of hybrids in western North America (16% hybrids using Admixture) and New Zealand. Hybrids might be commonly overlooked in invaders, as identification based solely on morphological traits may represent only the tip of the iceberg. Our study reveals a repeated pattern of invasion, hybridization and apparent replacement of one species by another, which offers an opportunity to investigate the role of hybridization and introgression during invasion.

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. In the western Canadian province of British Columbia, a subspecies of the northern goshawk (Accipiter gentilis laingi) is designated as Threatened under the Canadian Species at Risk Act. Historically, the range of this bird of prey has been ambiguous and its genetic distinctness from the other North American subspecies (Accipiter gentilis atricapillus) has not been well established. Given the uncertainty in using morphological traits to assign individual goshawks to these two subspecies, we analyzed genomic relationships in tens of thousands of single nucleotide polymorphisms identified using genotyping-bysequencing of high-quality genetic samples. This genome-wide analysis revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle genetic structuring among the remainder of our sampling sites within North America. Following from this analysis, we developed targeted genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing the addition of hundreds of low-quality samples to our analysis. This additional information confirmed that the distinct genetic cluster on Haida Gwaii is restricted to that archipelago. As the laingi form was originally described as being based in Haida Gwaii, where the type specimen of that form is from, further study (especially of morphological traits) may indicate a need to restrict this name to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, our finding of a distinct Haida Gwaii genetic cluster along with the small and historically declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. We anticipate that these results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.

International audience; Understanding the genetic structure of domestic species provides a window into the process of domestication and motivates the design of studies aimed at making links between genotype and phenotype. Rabbits exhibit exceptional phenotypic diversity, are of great commercial value, and serve as important animal models in biomedical research. Here, we provide the first comprehensive survey of nucleotide polymorphism and linkage disequilibrium (LD) within and among rabbit breeds. We resequenced 16 genomic regions in population samples of both wild and domestic rabbits and additional 35 fragments in 150 rabbits representing six commonly used breeds. Patterns of genetic variation suggest a single origin of domestication in wild populations from France, supporting historical records that place rabbit domestication in French monasteries. Levels of nucleotide diversity both within and among breeds were ;0.2%, but only 60% of the diversity present in wild populations from France was captured by domestic rabbits. Despite the recent origin of most breeds, levels of population differentiation were high (FST 5 17.9%), but the majority of polymorphisms were shared and thus transferable among breeds. Coalescent simulations suggest that domestication began with a small founding population of less than 1,200 individuals. Taking into account the complex demographic history of domestication with two successive bottlenecks, two loci showed deviations that were consistent with artificial selection, including GPC4, which is known to be associated with growth rates in humans. Levels of diversity were not significantly different between autosomal and X-linked loci, providing no evidence for differential contributions of males and females to the domesticated gene pool. The structure of LD differed substantially within and among breeds. Within breeds, LD extends over large genomic distances. Markers separated by 400 kb typically showed r2 higher than 0.2, and some LD extended up to 3,200 kb. Much less LD was found among breeds. This advantageous LD structure holds great promise for reducing the interval of association in future mapping studies.

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of ‘turnover’ of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6–7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.

Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N50 = 694 kb, including contigs with N50 = 20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43 384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (Ks) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species. © 2012 Blackwell Publishing Ltd.

Summary We have sequenced 2388 bp of the European rabbit sex determining region Y (SRY) gene. These data provide a 10-fold increase in the coverage of the Y chromosome in this species, including the entire open reading frame of the SRY, the polyadenylation signal, and two repetitive sequences in the 5¢ -region. A survey of 2021 bp of this gene in eight domestic breeds and four wild individuals revealed a total of nine single nucleotide polymorphisms and one indel, defining two deeply divergent lineages. The resulting estimation of nucleotide diversity (p ¼ 1.34 · 10 )3 ) is very high when compared with other species, but no variability was detected among the domestic breeds. This study represents a first step in the characterization of the European rabbit Y chromosome and its variability. These sequences can be used in additional phylogeographical analyses of the European rabbit and other Leporid species, as well as in evolutionary studies of sex determination and the Y chromosome in wild species.

In this work we report the genetic polymorphism of a 7-bp insertion in the 3' untranslated region of the rabbit SRY gene. The polymorphic GAATTAA motif was found exclusively in one of the two divergent rabbit Y-chromosomal lineages, suggesting that its origin is more recent than the separation of the O. c. algirus and O. c. cuniculus Y-chromosomes. In addition, the remarkable observation of haplotypes exhibiting 0, 1 and 2 7-bp inserts in essentially all algirus populations suggests that the rabbit SRY gene is duplicated and evolving under concerted evolution., This work was partly supported by Fundação para a Ciência e a Tecnologia (SFRH/BD/4621/2001 Ph.D. grant to Armando Geraldes and Research Project POCTI/BSE/40280/2001).