Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids.
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ABSTRACT:
SUBMITTER: Pilot M
PROVIDER: S-EPMC5978975 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Introgressive hybridization between domestic animals and their wild relatives is an indirect form of human-induced evolution, altering gene pools and phenotypic traits of wild and domestic populations. Although this process is well documented in many taxa, its evolutionary consequences are poorly understood. In this study, we assess introgression patterns in admixed populations of Eurasian wolves and free-ranging domestic dogs (FRDs), identifying chromosomal regions with significantly overrepresented hybrid ancestry and assessing whether genes located within these regions show signatures of selection. Although the dog admixture proportion in West Eurasian wolves (2.7%) was greater than the wolf admixture proportion in FRDs (0.75%), the number and average length of chromosomal blocks showing significant overrepresentation of hybrid ancestry were smaller in wolves than FRDs. In wolves, 6% of genes located within these blocks showed signatures of positive selection compared to 23% in FRDs. We found that introgression from wolves may provide a considerable adaptive advantage to FRDs, counterbalancing some of the negative effects of domestication, which can include reduced genetic diversity and excessive tameness. In wolves, introgression from FRDs is mostly driven by drift, with a small number of positively selected genes associated with brain function and behaviour. The predominance of drift may be the consequence of small effective size of wolf populations, which reduces efficiency of selection for weakly advantageous or against weakly disadvantageous introgressed variants. Small wolf population sizes result largely from human-induced habitat loss and hunting, thus linking introgression rates to anthropogenic processes. Our results imply that maintenance of large population sizes should be an important element of wolf management strategies aimed at reducing introgression rates of dog-derived variants.
| S-EPMC8549620 | biostudies-literature
Project description:Understanding how closely related wildlife species and their domesticated counterparts exchange or share parasites, or replace each other in parasite life cycles, is of great interest to veterinary and human public health, and wildlife ecology. Grey wolves (Canis lupus) host and spread endoparasites that can either directly infect canid conspecifics or their prey serving as intermediate hosts of indirectly transmitted species. The wolf recolonization of Central Europe represents an opportunity to study parasite transmission dynamics between wildlife and domestic species for cases when a definitive host returns after local extinction - a situation equivalent to a 'removal experiment'. Here we investigate whether the re-appearance of wolves has increased parasite pressure on hunting dogs - a group of companion animals of particular interest as they have a similar diet to wolves and flush wolf habitats when hunting. We compared prevalence (P) and species richness (SR) of helminths and the protozoan Sarcocystis to determine whether they were higher in hunting dogs from wolf areas (ndogs = 49) than a control area (ndogs = 29) without wolves. Of particular interest were S. grueneri and S. taeniata, known as 'wolf specialists'. Five helminth and 11 Sarcocystis species were identified, of which all helminths and eight Sarcocystis species were shared between dogs and wolves. Overall prevalence and species richness of helminths (P:38.5% vs. 24.1%; SRmean:0.4 vs. 0.3 species) and Sarcocystis (P:63.3% vs. 65.5%, SRmean:2.1 vs. 1.8 species) did not differ between study sites. However, hunting dogs were significantly more likely to be infected with S. grueneri in wolf areas (P:45.2% vs. 10.5%; p = 0.035). The findings suggest that wolves indirectly increase S. grueneri infection risk for hunting dogs since cervids are intermediate hosts and occasionally fed to dogs. Furthermore, a periodic anthelminthic treatment of hunting dogs may be an effective measure to control helminth infections regardless of wolf presence.
| S-EPMC5605491 | biostudies-literature
Project description:The evolutionary relationships between extinct and extant lineages provide important insight into species' response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period's profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves' evolutionary history, and could have facilitated their adaptation to environmental change.
| S-EPMC6874602 | biostudies-literature
Project description:Adaptation during the domestication from wolves (Canis lupus) to dogs (Canis lupus familiaris) is a debated ecological topic. Changes in food and environment are major divergences in the domestication of dogs. Gut microbes play an important role in animal adaptation to the food and environmental changes. In this study, shotgun sequencing was performed to compare the species diversity and functional diversity of gut microbes in wild wolves (group CLW, n = 3), captive wolves (group CLC, n = 4), and domestic dogs (group CLF, n = 4). The results found that Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and Bacteroides, Fusobacterium, Prevotella, Megamonas, Paraprevotella, Faecalibacterium, Clostridium were the most abundant genera in the gut of wolves and dogs. Groups CLW, CLC and CLF have shown significant difference in gut microbial species diversity and functional diversity. Bacteroides, Fusobacterium and Faecalibacterium were most abundant genera in groups CLW, CLC and CLF, respectively. Their abundance varied significantly among groups. Compared to the wild wolves, the intestinal microbiol genes of domestic dogs were significantly enriched in the carbohydrate metabolism pathway of KEGG database. One hundred and seventy-seven enzymes were detected with significantly higher abundance in group CLF than that in group CLW, and 49 enzymes showed extremely significant higher abundance in group CLF than that in group CLW (q < 0.01) base on the function abundance annotated in CAZy database. It is noteworthy that there were also significant differences in the abundance of 140 enzymes between groups CLC and CLW (q < 0.05). Clustering analysis based on both the species and the function abundance of intestinal microbiota all found that groups CLC and CLF clustered into one branch, while samples from group CLW clustered into the other branch. This result suggests that captive wolves are more similar to domestic dogs than wild wolves in both species composition and function composition of intestinal microbiota.
| S-EPMC9663663 | biostudies-literature
Project description:The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.
| S-EPMC4849173 | biostudies-literature
Project description:BACKGROUND:While it is generally accepted that patterns of intra-specific genetic differentiation are substantially affected by glacial history, population genetic processes occurring during Pleistocene glaciations are still poorly understood. In this study, we address the question of the genetic consequences of Pleistocene glaciations for European grey wolves. Combining our data with data from published studies, we analysed phylogenetic relationships and geographic distribution of mitochondrial DNA haplotypes for 947 contemporary European wolves. We also compared the contemporary wolf sequences with published sequences of 24 ancient European wolves. RESULTS:We found that haplotypes representing two haplogroups, 1 and 2, overlap geographically, but substantially differ in frequency between populations from south-western and eastern Europe. A comparison between haplotypes from Europe and other continents showed that both haplogroups are spread throughout Eurasia, while only haplogroup 1 occurs in contemporary North American wolves. All ancient wolf samples from western Europe that dated from between 44,000 and 1,200 years B.P. belonged to haplogroup 2, suggesting the long-term predominance of this haplogroup in this region. Moreover, a comparison of current and past frequencies and distributions of the two haplogroups in Europe suggested that haplogroup 2 became outnumbered by haplogroup 1 during the last several thousand years. CONCLUSIONS:Parallel haplogroup replacement, with haplogroup 2 being totally replaced by haplogroup 1, has been reported for North American grey wolves. Taking into account the similarity of diets reported for the late Pleistocene wolves from Europe and North America, the correspondence between these haplogroup frequency changes may suggest that they were associated with ecological changes occurring after the Last Glacial Maximum.
| S-EPMC2873414 | biostudies-literature
Project description:The indigenous populations of inner Eurasia-a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra-harbour tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine and Uzbekistan. We furthermore report additional damage-reduced genome-wide data of two previously published individuals from the Eneolithic Botai culture in Kazakhstan (~5,400 BP). We find that present-day inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries, mirroring geography. The Botai and more recent ancient genomes from Siberia show a decrease in contributions from so-called 'ancient North Eurasian' ancestry over time, which is detectable only in the northern-most 'forest-tundra' cline. The intermediate 'steppe-forest' cline descends from the Late Bronze Age steppe ancestries, while the 'southern steppe' cline further to the south shows a strong West/South Asian influence. Ancient genomes suggest a northward spread of the southern steppe cline in Central Asia during the first millennium BC. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.
| S-EPMC6542712 | biostudies-literature
Project description:Domestic dogs have been recognized for their social sensitivity and aptitude in human-guided tasks. For example, prior studies have demonstrated that dogs look to humans when confronted with an unsolvable task; an action often interpreted as soliciting necessary help. Conversely, wolves persist on such tasks. While dogs' 'looking back' behaviour has been used as an example of socio-cognitive advancement, an alternative explanation is that pet dogs show less persistence on independent tasks more generally. In this study, pet dogs, shelter dogs and wolves were given up to three opportunities to open a solvable puzzle box: when subjects were with a neutral human caretaker, alone and when encouraged by the human. Wolves were more persistent and more successful on this task than dogs, with 80% average success rate for wolves versus a 5% average success rate for dogs in both the human-in and alone conditions. Dogs showed increased contact with the puzzle box during the encouragement condition, but only a moderate increase in problem-solving success. Social sensitivity appears to play an important role in pet and shelter dogs' willingness to engage in problem-solving behaviour, which could suggest generalized dependence on, or deference to, human action.
| S-EPMC4614426 | biostudies-literature
Project description:BackgroundHybridization is an evolutionary event present in the natural world. Several studies suggest that natural hybridization is an important process in plant evolution, creating new genetic combinations which can play a vital role in speciation (Soltis and Soltis 2009, Soltis 2013, Neri et al. 2017, Taylor and Larson 2019). Therefore, it is important to understand and protect naturally occurring hybrids, conserving their ecological novelties and new traits, such as the ability to explore new niches, different from those of the parental species (Soltis 2013, Supple and Shapiro 2018).The British Virgin Islands (BVI) is a UK Overseas Territory situated in the Caribbean biodiversity hotspot (Myers et al. 2000). To date, three natural hybrids are known to occur within this territory: Tillandsia × lineatispica Mez, Anthurium × selloanum K.Koch and Coccoloba krugii × C. uvifera R.A.Howard (Howard 1957, Acevedo-Rodriguez and Strong 2005, Acevedo-Rodriguez and Strong 2012).Tillandsia × lineatispica is endemic to the Puerto Rican Bank, occurring in Puerto Rico, the US Virgin Islands (USVI) and the British Virgin Islands with an extent of occurrence estimated to be 3,390 km2 and a limited number of locations. The suitable habitat for this hybrid is declining mainly due to the negative impacts of feral ungulates, development for tourism and residential infrastructure and the impact of human-induced wildfires. In addition, it is suspected that the global population does not exceed 10,000 individuals with the largest subpopulation on Beef Island in the BVI thought to have no more than 1,000 mature individuals. This hybrid is therefore evaluated as Vulnerable, based on IUCN Red List Criteria, B1a(iii)+2b(iii) + C2a(i).Anthurium × selloanum is an endemic hybrid to BVI and USVI with a very restricted extent of occurrence which was estimated to range between 103 km2 and 207 km2 and an area of occupancy which was estimated to range between 56 km2 and 188 km2 and a limited number of locations. The suitable habitat of this species is declining mainly due to the negative impacts of feral ungulates, development for tourism and residential infrastructure and the negative impact of recreation activities in protected areas. This species is therefore evaluated as Endangered, based on IUCN Red List Criteria B1a+ b(iii) + B2a+b(iii).Coccoloba krugii × C. uvifera is native to the BVI, USVI, Puerto Rico, Dominican Republic, Haiti and Anguilla. It is estimated to have an extent of occurrence of 89,412 km2. This value exceeds the threshold for any threatened category. Despite an observed continuing decline of suitable habitat for this species, which is being degraded mainly through ongoing development pressures, this species occurs in more than 10 locations. It is therefore assessed as Least Concern (LC).New informationIn this paper, we discuss the conservation status of all the known, naturally occurring, native hybrids in the the British Virgin Islands and we provide distribution data, including new records, from across these hybrid species ranges. Although conservation assessments of hybrids are out of the scope of the published IUCN Red List of Threatened Species (IUCN Standards and Petitions Committee 2019), we use the IUCN Red List Criteria and Categories (version 3.1) to establish an equivalent conservation status of these hybrids and discuss conservation action due to the potential evolutionary importance of these naturally occurring hybrids. These assessments provide the necessary baseline information for prioritising species conservation and making informed management decisions, such as establishing the BVI's Tropical Important Plant Areas (TIPAS) network (Sanchez et al. 2019).
| S-EPMC7987705 | biostudies-literature
Project description:Although domestic dogs play many important roles in rural households, they can also be an important threat to the conservation of wild vertebrates due to predation, competition and transmission of infectious diseases. An increasing number of studies have addressed the impact of dogs on wildlife but have tended to ignore the motivations and attitudes of the humans who keep these dogs and how the function of dogs might influence dog-wildlife interactions. To determine whether the function of domestic dogs in rural communities influences their interactions with wildlife, we conducted surveys in rural areas surrounding protected lands in the Valdivian Temperate Forests of Chile. Sixty percent of farm animal owners reported the use of dogs as one of the primary means of protecting livestock from predators. The probability of dog-wild carnivore interactions was significantly associated with the raising of poultry. In contrast, dog-wild prey interactions were not associated with livestock presence but had a significant association with poor quality diet as observed in previous studies. Dog owners reported that they actively encouraged the dogs to chase off predators, accounting for 25-75% of the dog-wild carnivore interactions observed, depending on the predator species. Humans controlled the dog population by killing pups and unwanted individuals resulting in few additions to the dog population through breeding; the importation of predominantly male dogs from urban areas resulted in a sex ratios highly dominated by males. These results indicate that dog interactions with wildlife are related to the role of the dog in the household and are directly influenced by their owners. To avoid conflict with local communities in conservation areas, it is important to develop strategies for managing dogs that balance conservation needs with the roles that dogs play in these rural households.
| S-EPMC3896434 | biostudies-literature