Carles Vilà

Publications of Carles Vilà

• Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

  Authors: Amaury Vaysse, Abhirami Ratnakumar, Thomas Derrien, Erik Axelsson, Gerli Rosengren Pielberg, Snaevar Sigurdsson, Tove Fall, Eija H Seppälä, Mark S T Hansen, Cindy T Lawley [......] Carles Vilà, Hannes Lohi, Francis Galibert, Merete Fredholm, Jens Häggström, Ake Hedhammar, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Matthew T Webster

  PLoS genetics. 10/2011; 7(10):e1002316.

  The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysisThe extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.

• Vanishing native American dog lineages.

  Authors: Santiago Castroviejo-Fisher, Pontus Skoglund, Raúl Valadez, Carles Vilà, Jennifer A Leonard

  BMC evolutionary biology. 03/2011; 11:73.

  Dogs were an important element in many native American cultures at the time Europeans arrived. Although previous ancient DNA studies revealed the existence of unique native American mitochondrialDogs were an important element in many native American cultures at the time Europeans arrived. Although previous ancient DNA studies revealed the existence of unique native American mitochondrial sequences, these have not been found in modern dogs, mainly purebred, studied so far. We identified many previously undescribed mitochondrial control region sequences in 400 dogs from rural and isolated areas as well as street dogs from across the Americas. However, sequences of native American origin proved to be exceedingly rare, and we estimate that the native population contributed only a minor fraction of the gene pool that constitutes the modern population. The high number of previously unidentified haplotypes in our sample suggests that a lot of unsampled genetic variation exists in non-breed dogs. Our results also suggest that the arrival of European colonists to the Americas may have led to an extensive replacement of the native American dog population by the dogs of the invaders.

• Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes.

  Authors: Violeta Muñoz-Fuentes, Anna Di Rienzo, Carles Vilà

  PloS one. 01/2011; 6(11):e25498.

  Meiotic recombination is a fundamental process needed for the correct segregation of chromosomes during meiosis in sexually reproducing organisms. In humans, 80% of crossovers are estimated to occurMeiotic recombination is a fundamental process needed for the correct segregation of chromosomes during meiosis in sexually reproducing organisms. In humans, 80% of crossovers are estimated to occur at specific areas of the genome called recombination hotspots. Recently, a protein called PRDM9 was identified as a major player in determining the location of genome-wide meiotic recombination hotspots in humans and mice. The origin of this protein seems to be ancient in evolutionary time, as reflected by its fairly conserved structure in lineages that diverged over 700 million years ago. Despite its important role, there are many animal groups in which Prdm9 is absent (e.g. birds, reptiles, amphibians, diptera) and it has been suggested to have disruptive mutations and thus to be a pseudogene in dogs. Because of the dog's history through domestication and artificial selection, we wanted to confirm the presence of a disrupted Prdm9 gene in dogs and determine whether this was exclusive of this species or whether it also occurred in its wild ancestor, the wolf, and in a close relative, the coyote. We sequenced the region in the dog genome that aligned to the last exon of the human Prdm9, containing the entire zinc finger domain, in 4 dogs, 17 wolves and 2 coyotes. Our results show that the three canid species possess mutations that likely make this gene non functional. Because these mutations are shared across the three species, they must have appeared prior to the split of the wolf and the coyote, millions of years ago, and are not related to domestication. In addition, our results suggest that in these three canid species recombination does not occur at hotspots or hotspot location is controlled through a mechanism yet to be determined.

• Genetic analyses reveal independent domestication origins of Eurasian reindeer.

  Authors: Knut H Røed, Oystein Flagstad, Mauri Nieminen, Oystein Holand, Mark J Dwyer, Nils Røv, Carles Vilà

  Proceedings. Biological sciences / The Royal Society. 09/2008; 275(1645):1849-55.

  Although there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largelyAlthough there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largely unresolved for many species. Reindeer are considered to be in the early phase of domestication with wild and domestic herds still coexisting widely across Eurasia. This provides a unique model system for understanding how the early domestication process may have taken place. We analysed mitochondrial sequences and nuclear microsatellites in domestic and wild herds throughout Eurasia to address the origin of reindeer herding and domestication history. Our data demonstrate independent origins of domestic reindeer in Russia and Fennoscandia. This implies that the Saami people of Fennoscandia domesticated their own reindeer independently of the indigenous cultures in western Russia. We also found that augmentation of local reindeer herds by crossing with wild animals has been common. However, some wild reindeer populations have not contributed to the domestic gene pool, suggesting variation in domestication potential among populations. These differences may explain why geographically isolated indigenous groups have been able to make the technological shift from mobile hunting to large-scale reindeer pastoralism independently.

• The legacy of domestication: Accumulation of deleterious mutations in the dog genome.

  Authors: Fernando Cruz, Carles Vilà, Matthew T Webster

  Molecular biology and evolution. 09/2008;

  Dogs exhibit more phenotypic variation than any other mammal and are affected by a wide variety of genetic diseases. However, the origin and genetic basis of this variation is still poorlyDogs exhibit more phenotypic variation than any other mammal and are affected by a wide variety of genetic diseases. However, the origin and genetic basis of this variation is still poorly understood. We examined the effect of domestication on the dog genome by comparison with its wild ancestor, the grey wolf. We compared variation in dog and wolf genes using whole genome SNP data. The d(N)/d(S) ratio (omega) was around 50% greater for SNPs found in dogs than in wolves, indicating that a higher proportion of nonsynonymous alleles segregate in dogs compared with non-functional genetic variation. We suggest that the majority of these alleles are slightly deleterious and that two main factors may have contributed to their increase. The first is a relaxation of selective constraint due to a population bottleneck and altered breeding patterns accompanying domestication. The second is a reduction of effective population size at loci linked to those under positive selection due to Hill-Robertson interference. An increase in slightly deleterious genetic variation could contribute to the prevalence of disease in modern dog breeds.

• Assortative mating and fragmentation within dog breeds.

  Authors: Susanne Björnerfeldt, Frank Hailer, Maria Nord, Carles Vilà

  BMC evolutionary biology. 02/2008; 8:28.

  BACKGROUND: There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groupsBACKGROUND: There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. RESULTS: Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. CONCLUSION: The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored.In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds.

• Barking up the wrong tree: modern northern European dogs fail to explain their origin.

  Authors: Helena Malmström, Carles Vilà, M Thomas P Gilbert, Jan Storå, Eske Willerslev, Gunilla Holmlund, Anders Götherström

  BMC evolutionary biology. 02/2008; 8:71.

  BACKGROUND: Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption isBACKGROUND: Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption is that phylogeographic patterns among domesticates were established during, or shortly after the domestication. Human activities are assumed not to have altered the haplogroup frequencies to any great extent. We studied this hypothesis by analyzing 24 mtDNA sequences in ancient Scandinavian dogs. Breeds originating in northern Europe are characterized by having a high frequency of mtDNA sequences belonging to a haplogroup rare in other populations (HgD). This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe. RESULTS: The sequences observed in the ancient samples do not include the haplogroup indicative for northern European breeds (HgD). Instead, several of them correspond to haplogroups that are uncommon in the region today and that are supposed to have Asian origin. CONCLUSION: We find no evidence for local domestication. We conclude that interpretation of the processes responsible for current domestic haplogroup frequencies should be carried out with caution if based only on contemporary data. They do not only tell their own story, but also that of humans.

• Barking up the wrong tree: Modern northern European dogs fail to explain their origin

  Authors: Helena Malmström, Carles Vilà, M Gilbert, Jan Storå, Eske Willerslev, Gunilla Holmlund, Anders Götherström

  BMC Evolutionary Biology. 01/2008;

  Abstract Background Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlyingAbstract Background Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption is that phylogeographic patterns among domesticates were established during, or shortly after the domestication. Human activities are assumed not to have altered the haplogroup frequencies to any great extent. We studied this hypothesis by analyzing 24 mtDNA sequences in ancient Scandinavian dogs. Breeds originating in northern Europe are characterized by having a high frequency of mtDNA sequences belonging to a haplogroup rare in other populations (HgD). This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe. Results The sequences observed in the ancient samples do not include the haplogroup indicative for northern European breeds (HgD). Instead, several of them correspond to haplogroups that are uncommon in the region today and that are supposed to have Asian origin. Conclusion We find no evidence for local domestication. We conclude that interpretation of the processes responsible for current domestic haplogroup frequencies should be carried out with caution if based only on contemporary data. They do not only tell their own story, but also that of humans.

• Differentiation of tundra/taiga and boreal coniferous forest wolves: genetics, coat colour and association with migratory caribou.

  Authors: Marco Musiani, Jennifer A Leonard, H Dean Cluff, C Cormack Gates, Stefano Mariani, Paul C Paquet, Carles Vilà, Robert K Wayne

  Molecular ecology. 10/2007; 16(19):4149-70.

  The grey wolf has one of the largest historic distributions of any terrestrial mammal and can disperse over great distances across imposing topographic barriers. As a result, geographical distanceThe grey wolf has one of the largest historic distributions of any terrestrial mammal and can disperse over great distances across imposing topographic barriers. As a result, geographical distance and physical obstacles to dispersal may not be consequential factors in the evolutionary divergence of wolf populations. However, recent studies suggest ecological features can constrain gene flow. We tested whether wolf-prey associations in uninterrupted tundra and forested regions of Canada explained differences in migratory behaviour, genetics, and coat colour of wolves. Satellite-telemetry data demonstrated that tundra wolves (n = 19) migrate annually with caribou (n = 19) from denning areas in the tundra to wintering areas south of the treeline. In contrast, nearby boreal coniferous forest wolves are territorial and associated year round with resident prey. Spatially explicit analysis of 14 autosomal microsatellite loci (n = 404 individuals) found two genetic clusters corresponding to tundra vs. boreal coniferous forest wolves. A sex bias in gene flow was inferred based on higher levels of mtDNA divergence (F(ST) = 0.282, 0.028 and 0.033; P < 0.0001 for mitochondrial, nuclear autosomal and Y-chromosome markers, respectively). Phenotypic differentiation was substantial as 93% of wolves from tundra populations exhibited light colouration whereas only 38% of boreal coniferous forest wolves did (chi(2) = 64.52, P < 0.0001). The sharp boundary representing this discontinuity was the southern limit of the caribou migration. These findings show that substantial genetic and phenotypic differentiation in highly mobile mammals can be caused by prey-habitat specialization rather than distance or topographic barriers. The presence of a distinct wolf ecotype in the tundra of North America highlights the need to preserve migratory populations.

• Megafaunal extinctions and the disappearance of a specialized wolf ecomorph.

  Authors: Jennifer A Leonard, Carles Vilà, Kena Fox-Dobbs, Paul L Koch, Robert K Wayne, Blaire Van Valkenburgh

  Current biology : CB. 08/2007; 17(13):1146-50.

  The gray wolf (Canis lupus) is one of the few large predators to survive the Late Pleistocene megafaunal extinctions [1]. Nevertheless, wolves disappeared from northern North America in the LateThe gray wolf (Canis lupus) is one of the few large predators to survive the Late Pleistocene megafaunal extinctions [1]. Nevertheless, wolves disappeared from northern North America in the Late Pleistocene, suggesting they were affected by factors that eliminated other species. Using skeletal material collected from Pleistocene permafrost deposits of eastern Beringia, we present a comprehensive analysis of an extinct vertebrate by exploring genetic (mtDNA), morphologic, and isotopic (delta(13)C, delta(15)N) data to reveal the evolutionary relationships, as well as diet and feeding behavior, of ancient wolves. Remarkably, the Late Pleistocene wolves are genetically unique and morphologically distinct. None of the 16 mtDNA haplotypes recovered from a sample of 20 Pleistocene eastern-Beringian wolves was shared with any modern wolf, and instead they appear most closely related to Late Pleistocene wolves of Eurasia. Moreover, skull shape, tooth wear, and isotopic data suggest that eastern-Beringian wolves were specialized hunters and scavengers of extinct megafauna. Thus, a previously unrecognized, uniquely adapted, and genetically distinct wolf ecomorph suffered extinction in the Late Pleistocene, along with other megafauna. Consequently, the survival of the species in North America depended on the presence of more generalized forms elsewhere.

• Selection for tameness modulates the expression of heme related genes in silver foxes.

  Authors: Julia Lindberg, Susanne Björnerfeldt, Morten Bakken, Carles Vilà, Elena Jazin, Peter Saetre

  Behavioral and brain functions : BBF. 02/2007; 3:18.

  BACKGROUND: The genetic and molecular mechanisms of tameness are largely unknown. A line of silver foxes (Vulpes vulpes) selected for non-aggressive behavior has been used in Russia since the 1960'sBACKGROUND: The genetic and molecular mechanisms of tameness are largely unknown. A line of silver foxes (Vulpes vulpes) selected for non-aggressive behavior has been used in Russia since the 1960's to study the effect of domestication. We have previously compared descendants of these selected (S) animals with a group of non-selected (NS) silver foxes kept under identical conditions, and showed that changes in the brain transcriptome between the two groups are small. Unexpectedly, many of the genes showing evidence of differential expression between groups were related to hemoproteins. RESULTS: In this study, we use quantitative RT-PCR to demonstrate that the activity of heme related genes differ between S and NS foxes in three regions of the brain. Furthermore, our analyses also indicate that changes in mRNA levels of heme related genes can be well described by an additive polygenic effect. We also show that the difference in genetic background between the two lines of foxes is limited, as estimated by mitochondrial DNA divergence. CONCLUSION: Our results indicate that selection for tameness can modify the expression of heme related genes in canid brain regions known to modulate emotions and behavior. The possible involvement of heme related genes in behavior is surprising. It is possible that hemoglobin modulates the behavior of canids by interaction with CO and NO signaling. Another possibility is that hemorphins, known to be produced after enzymatic cleavage of hemoglobin, are responsible for behavioral alterations. Thus, we hypothesize that hemoglobin metabolism can be a functionally relevant aspect of the domestic phenotype in foxes selected for tameness.

• Relaxation of selective constraint on dog mitochondrial DNA following domestication.

  Authors: Susanne Björnerfeldt, Matthew T Webster, Carles Vilà

  Genome research. 09/2006; 16(8):990-4.

  The domestication of dogs caused a dramatic change in their way of life compared with that of their ancestor, the gray wolf. We hypothesize that this new life style changed the selective forces thatThe domestication of dogs caused a dramatic change in their way of life compared with that of their ancestor, the gray wolf. We hypothesize that this new life style changed the selective forces that acted upon the species, which in turn had an effect on the dog's genome. We sequenced the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes. Here we show that dogs have accumulated nonsynonymous changes in mitochondrial genes at a faster rate than wolves, leading to elevated levels of variation in their proteins. This suggests that a major consequence of domestication in dogs was a general relaxation of selective constraint on their mitochondrial genome. If this change also affected other parts of the dog genome, it could have facilitated the generation of novel functional genetic diversity. This diversity could thus have contributed raw material upon which artificial selection has shaped modern breeds and may therefore be an important source of the extreme phenotypic variation present in modern-day dogs.

• Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline.

  Authors: Frank Hailer, Björn Helander, Alv O Folkestad, Sergei A Ganusevich, Steinar Garstad, Peter Hauff, Christian Koren, Torgeir Nygård, Veljo Volke, Carles Vilà, Hans Ellegren

  Biology letters. 07/2006; 2(2):316-9.

  Most of the white-tailed eagle (Haliaeetus albicilla) populations in Europe experienced dramatic declines during the twentieth century. However, owing to intense conservation actions and the ban ofMost of the white-tailed eagle (Haliaeetus albicilla) populations in Europe experienced dramatic declines during the twentieth century. However, owing to intense conservation actions and the ban of DDT and other persistent pollutants, populations are currently recovering. We show that despite passing through demographic bottlenecks, white-tailed eagle populations have retained significant levels of genetic diversity. Both genetic and ringing data indicate that migration between populations has not been a major factor for the maintenance of genetic variability. We argue that the long generation time of eagles has acted as an intrinsic buffer against loss of genetic diversity, leading to a shorter effective time of the experienced bottleneck. Notably, conservation actions taken in several small sub-populations have ensured the preservation of a larger proportion of the total genetic diversity than if conservation had focused on the population stronghold in Norway. For conservation programmes targeting other endangered, long-lived species, our results highlight the possibility for local retention of high genetic diversity in isolated remnant populations.

• The ruddy duck Oxyura jamaicensis in Europe: natural colonization or human introduction?

  Authors: Violeta Muñoz-Fuentes, Andy J Green, Michael D Sorenson, Juan J Negro, Carles Vilà

  Molecular ecology. 06/2006; 15(6):1441-53.

  Native to North America, ruddy ducks Oxyura jamaicensis now occur in 21 countries in the western Palaearctic (including Iceland) and their expanding population threatens the native white-headed duck,Native to North America, ruddy ducks Oxyura jamaicensis now occur in 21 countries in the western Palaearctic (including Iceland) and their expanding population threatens the native white-headed duck, Oxyura leucocephala, through hybridization and possibly competition for food and nest sites. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the European ruddy duck population is descended solely from the captive population in the UK, which traces to seven individuals imported from the USA in 1948, or, alternatively, has been augmented by natural dispersal of birds from North America. Limited genetic diversity in the European population is consistent with a founder population as small as seven birds. In addition, shifts in allele frequencies at several loci, presumably due to genetic drift in the founding population, result in significant differentiation between the European and North American populations. Despite the recent separation of these populations, almost all individuals could be unambiguously assigned based on their composite genotypes, to one of two distinct populations, one comprising all of the European ruddy ducks we sampled (including those from Iceland and captive birds in the UK) and the other comprising all North American samples. Our results confirm that the European ruddy duck population is likely to derive solely from the captive population in the UK and we find no evidence of recent arrivals from North America or of admixture between ruddy ducks from Europe and North America.

• Selection for tameness has changed brain gene expression in silver foxes.

  Authors: Julia Lindberg, Susanne Björnerfeldt, Peter Saetre, Kenth Svartberg, Birgitte Seehuus, Morten Bakken, Carles Vilà, Elena Jazin

  Current biology : CB. 12/2005; 15(22):R915-6.

• Genes of domestic mammals augmented by backcrossing with wild ancestors.

  Authors: Carles Vilà, Jennifer Seddon, Hans Ellegren

  Trends in genetics : TIG. 05/2005; 21(4):214-8.

  Both archaeological data and the presence of few mitochondrial DNA lineages suggest that most widespread domestic mammals (cattle, sheep, goats, pigs and dogs) derive from only a handful ofBoth archaeological data and the presence of few mitochondrial DNA lineages suggest that most widespread domestic mammals (cattle, sheep, goats, pigs and dogs) derive from only a handful of domestication events. However, each of these species shows a high level of diversity at the nuclear genes of the major histocompatibility complex (MHC). Through simulations incorporating various degrees of population subdivision, growth rate and selection, we demonstrate that the numerous MHC DRB alleles that are present in modern domestic mammals implies that substantial backcrossing with wild ancestors, either accidental or intentional, has been important in shaping the genetic diversity of our domesticates. These results support the view that, contrary to common assumption, domestic and wild lineages might not have been clearly separated throughout their history.

• Legacy lost: genetic variability and population size of extirpated US grey wolves (Canis lupus).

  Authors: Jennifer A Leonard, Carles Vilà, Robert K Wayne

  Molecular ecology. 02/2005; 14(1):9-17.

  By the mid 20th century, the grey wolf (Canis lupus) was exterminated from most of the conterminous United States (cUS) and Mexico. However, because wolves disperse over long distances, extantBy the mid 20th century, the grey wolf (Canis lupus) was exterminated from most of the conterminous United States (cUS) and Mexico. However, because wolves disperse over long distances, extant populations in Canada and Alaska might have retained a substantial proportion of the genetic diversity once found in the cUS. We analysed mitochondrial DNA sequences of 34 pre-extermination wolves and found that they had more than twice the diversity of their modern conspecifics, implying a historic population size of several hundred thousand wolves in the western cUS and Mexico. Further, two-thirds of the haplotypes found in the historic sample are unique. Sequences from Mexican grey wolves (C. l. baileyi) and some historic grey wolves defined a unique southern clade supporting a much wider geographical mandate for the reintroduction of Mexican wolves than currently planned. Our results highlight the genetic consequences of population extinction within Ice Age refugia and imply that restoration goals for grey wolves in the western cUS include far less area and target vastly lower population sizes than existed historically.

• From wild wolf to domestic dog: gene expression changes in the brain.

  Authors: Peter Saetre, Julia Lindberg, Jennifer A Leonard, Kerstin Olsson, Ulf Pettersson, Hans Ellegren, Tomas F Bergström, Carles Vilà, Elena Jazin

  Brain research. Molecular brain research. 08/2004; 126(2):198-206.

  Despite the relatively recent divergence time between domestic dogs (Canis familiaris) and gray wolves (Canis lupus), the two species show remarkable behavioral differences. Since dogs and wolves areDespite the relatively recent divergence time between domestic dogs (Canis familiaris) and gray wolves (Canis lupus), the two species show remarkable behavioral differences. Since dogs and wolves are nearly identical at the level of DNA sequence, we hypothesize that the two species may differ in patterns of gene expression. We compare gene expression patterns in dogs, wolves and a close relative, the coyote (Canis latrans), in three parts of the brain: hypothalamus, amygdala and frontal cortex, with microarray technology. Additionally, we identify genes with region-specific expression patterns in all three species. Among the wild canids, the hypothalamus has a highly conserved expression profile. This contrasts with a marked divergence in domestic dogs. Real-time PCR experiments confirm the altered expression of two neuropeptides, CALCB and NPY. Our results suggest that strong selection on dogs for behavior during domestication may have resulted in modifications of mRNA expression patterns in a few hypothalamic genes with multiple functions. This study indicates that rapid changes in brain gene expression may not be exclusive to the development of human brains. Instead, they may provide a common mechanism for rapid adaptive changes during speciation, particularly in cases that present strong selective pressures on behavioral characters.

• Limited number of patrilines in horse domestication.

  Authors: Gabriella Lindgren, Niclas Backström, June Swinburne, Linda Hellborg, Annika Einarsson, Kaj Sandberg, Gus Cothran, Carles Vilà, Matthew Binns, Hans Ellegren

  Nature genetics. 05/2004; 36(4):335-6.

  Genetic studies using mitochondrial DNA (mtDNA) have identified extensive matrilinear diversity among domestic horses. Here, we show that this high degree of polymorphism is not matched by aGenetic studies using mitochondrial DNA (mtDNA) have identified extensive matrilinear diversity among domestic horses. Here, we show that this high degree of polymorphism is not matched by a corresponding patrilinear diversity of the male-specific Y chromosome. In fact, a screening for single-nucleotide polymorphisms (SNPs) in 14.3 kb of noncoding Y chromosome sequence among 52 male horses of 15 different breeds did not identify a single segregation site. These observations are consistent with a strong sex-bias in the domestication process, with few stallions contributing genetically to the domestic horse.

• Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant.

  Authors: Carles Vilà, Anna-Karin Sundqvist, Øystein Flagstad, Jennifer Seddon, Susanne Björnerfeldt, Ilpo Kojola, Adriano Casulli, Håkan Sand, Petter Wabakken, Hans Ellegren

  Proceedings. Biological sciences / The Royal Society. 02/2003; 270(1510):91-7.

  The fragmentation of populations is an increasingly important problem in the conservation of endangered species. Under these conditions, rare migration events may have important effects for theThe fragmentation of populations is an increasingly important problem in the conservation of endangered species. Under these conditions, rare migration events may have important effects for the rescue of small and inbred populations. However, the relevance of such migration events to genetically depauperate natural populations is not supported by empirical data. We show here that the genetic diversity of the severely bottlenecked and geographically isolated Scandinavian population of grey wolves (Canis lupus), founded by only two individuals, was recovered by the arrival of a single immigrant. Before the arrival of this immigrant, for several generations the population comprised only a single breeding pack, necessarily involving matings between close relatives and resulting in a subsequent decline in individual heterozygosity. With the arrival of just a single immigrant, there is evidence of increased heterozygosity, significant outbreeding (inbreeding avoidance), a rapid spread of new alleles and exponential population growth. Our results imply that even rare interpopulation migration can lead to the rescue and recovery of isolated and endangered natural populations.