Genetic studies facilitated management decisions on the invasion of the ruddy duck in Europe

The ruddy duck (Oxyura jamaicensis), a stifftail native to the Americas, was introduced to the UK in the 1950s and has since been recorded in 22 western Palearctic countries. By 2000, the UK popu- lation peaked at nearly 6,000 individuals. In 1991, hybridisation with the native and globally threatened (IUCN Endangered) white-headed duck (Oxyura leu- cocephala), a stifftail restricted to the Mediterranean and Asia, was recorded in Spain and culling of hybrids and ruddy ducks began. Here we report on a series of genetic studies that have enabled and supported management decisions to the benefit of the white- headed duck. First, genetic data confirmed that these are two distinct species, each of which is more closely related to other stifftail species. Second, molecular studies indicated that ruddy ducks in Spain, Iceland and elsewhere in Europe were of captive origin and not descendants from vagrants from their native North America. Third, genetic methods were used to distin- guish among different hybrid generations in Spain and detected no ruddy duck introgression in birds identi- fied morphologically as white-headed ducks. Collec- tively, these results supported management decisions to eradicate ruddy ducks from Europe. Subsequently, a control programme reduced the UK population by over 95 % by 2010, and the arrival of ruddy ducks to Spain decreased from 21 birds in 2003 to two sightings in 2010–2011. However, increased efforts to control small ruddy duck populations elsewhere in Europe and Morocco are still required to ensure conservation of the white-headed duck. This case of invasion by hybridization demonstrates that successful control is feasible given early detection followed by a rapid response plan; it also shows the contribution of research to management and that to guarantee the conservation of an endangered native species action may be required in countries outside its distribution range.Peer reviewe

The genetic legacy of extirpation and re-colonization in Vancouver Island wolves

Hybridization between wild and domestic species is of conservation concern because it can result in the loss of adaptations and/or disappearance of a distinct taxon. Wolves from Vancouver Island, British Columbia (Canada), have been subject to several eradication campaigns during the twentieth century and were considered virtually extirpated between 1950 and 1970. In this study, we use control region mitochondrial DNA sequences and 13 autosomal microsatellite loci to characterize Vancouver Island wolves as well as dogs from British Columbia. We observe a turnover in the haplotypes of wolves sampled before and after the 1950-1970 period, when there was no permanent wolf population on the island, supporting the probable local extinction of wolves on Vancouver Island during this time, followed by re-colonization of the island by wolves from mainland British Columbia. In addition, we report the presence of a domestic dog mtDNA haplotype in three individuals eliminated in 1986 that were morphologically identified as wolves. Here we show that Vancouver Island wolves were also identified as wolves based on autosomal microsatellite data. We attribute the hybridization event to the episodically small size of this population during the re-colonization event. Our results demonstrate that at least one female hybrid offspring, resulting from a cross of a male wolf and a female dog or a female hybrid pet with dog mtDNA, successfully introgressed into the wolf population. No dog mtDNA has been previously reported in a population of wild wolves. Genetic data show that Vancouver Island wolves are distinct from dogs and thus should be recognized as a population of wild wolves. We suggest that the introgression took place due to the Allee effect, specifically a lack of mates when population size was low. Our findings exemplify how small populations are at risk of hybridization. © 2009 Springer Science+Business Media B.V.Peer Reviewe

Hybridization between white-headed ducks and introduced ruddy ducks in Spain

The ruddy duck, Oxyura jamaicensis , was introduced to Great Britain in the mid-20th century and has recently spread to other Western European countries. In Spain, ruddy ducks hybridize with the globally endangered white-headed duck, Oxyura leucocephala . We assessed the effects of hybridization on the Spanish white-headed ducks, which constitute 25% of the global population of this species, using a panel of eight nuclear intron markers, 10 microsatellite loci, and mtDNA control region sequences. These data allowed parental individuals, F 1 hybrids, and the progeny of backcrossing to be reliably distinguished. We show that hybrids between the two species are fertile and produce viable offspring in backcrosses with both parental species. To date, however, we found no extensive introgression of ruddy duck genes into the Spanish white-headed duck population, probably due to the early implementation of an effective ruddy duck and hybrid control programme. We also show that genetic diversity in the expanding European ruddy duck population, which was founded by just seven individuals, exceeds that of the native Spanish white-headed duck population, which recently recovered from a severe bottleneck. Unless effective control of ruddy ducks is continued, genetic introgression will compromise the unique behavioural and ecological adaptations of white-headed ducks and consequently their survival as a genetically and evolutionary distinct species.Peer reviewe

Identification of Parelaphostrongylus odocoilei (Nematoda: Protostrongylidae) First-Stage Larvae in the Feces of Gray Wolves (Canis lupus) by Molecular Methods

First-stage nematode larvae with a dorsal-spine (DSL) were detected in five of 1,565 fecal samples from gray wolves (Canis lupus) collected in British Columbia, Canada, between 2005 and 2008. Molecular techniques were used to identify the DSL because it was not possible to determine their species identity using morphologic characters. The DSL were identified as Parelaphostrongylus odocoilei based on the results of single-strand conformation polymorphism (SSCP) analyses and DNA sequencing of the ribosomal DNA first and second internal transcribed spacers. Finding DSL of P. odocoilei in the feces of gray wolves was unexpected because P. odocoilei adults are parasites of cervids and bovids. The most likely explanation for the presence of DSL in wolf feces is that they were ingested along with the viscera of recently consumed prey. This was probably black-tailed deer (Odocoileus hemionus columbianus), which are known in the sampling area to be hosts of P. odocoilei. The present study demonstrates the use of SSCP and DNA sequencing for the identification, to the species level, of parasitic nematode larvae in feces

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation.

The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied

Mendelian gene identification through mouse embryo viability screening.

BACKGROUND: The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful. A full spectrum of intolerance to loss-of-function variation has been previously described, providing evidence that gene essentiality should not be considered as a simple and fixed binary property. METHODS: Here we further dissected this spectrum by assessing the embryonic stage at which homozygous loss-of-function results in lethality in mice from the International Mouse Phenotyping Consortium, classifying the set of lethal genes into one of three windows of lethality: early, mid, or late gestation lethal. We studied the correlation between these windows of lethality and various gene features including expression across development, paralogy and constraint metrics together with human disease phenotypes. We explored a gene similarity approach for novel gene discovery and investigated unsolved cases from the 100,000 Genomes Project. RESULTS: We found that genes in the early gestation lethal category have distinct characteristics and are enriched for genes linked with recessive forms of inherited metabolic disease. We identified several genes sharing multiple features with known biallelic forms of inborn errors of the metabolism and found signs of enrichment of biallelic predicted pathogenic variants among early gestation lethal genes in patients recruited under this disease category. We highlight two novel gene candidates with phenotypic overlap between the patients and the mouse knockouts. CONCLUSIONS: Information on the developmental period at which embryonic lethality occurs in the knockout mouse may be used for novel disease gene discovery that helps to prioritise variants in unsolved rare disease cases

Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental chang

Human and mouse essentiality screens as a resource for disease gene discovery.

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery