[show abstract][hide abstract] ABSTRACT: Noninvasive genetic monitoring has the potential to estimate vital rates essential for conservation and management of many species. In a long-term genetic capture-mark-recapture study using scats we evaluated temporal variation in adult survival in a wolverine (Gulo gulo) population in southern Norway. In contrast to most previous studies of large mammals we found evidence for negative density dependence in adult survival in this large carnivore. Both sexes showed the same pattern of density dependence, with higher annual survival rates in adult females than males. In addition, we also found an additive mortality effect of harvesting in the population, resulting in the lowest adult survival rates at a combination of high population density and high harvest rate. The additive effects of density and harvest on adult survival of wolverines have relevance to the conservation and management of solitary carnivores with strong intrasexual territoriality, especially for species where combats among conspecifics can cause serious injury or even mortality. (C) 2009 Elsevier Ltd. All rights reserved.
[show abstract][hide abstract] ABSTRACT: Local variation in neutral substitution rate across mammalian genomes is governed by several factors, including sequence context variables and structural variables. In addition, the interplay of replication and transcription, known to induce a strand bias in mutation rate, gives rise to variation in substitutional strand asymmetries. Here, we address the conservation of variation in mutation rate and substitutional strand asymmetries using primate- and rodent-specific repeat elements located within the introns of protein-coding genes. We find significant but weak conservation of local mutation rates between human and mouse orthologs. Likewise, substitutional strand asymmetries are conserved between human and mouse, where substitution rate asymmetries show a higher degree of conservation than mutation rate. Moreover, we provide evidence that replication and transcription are correlated to the strength of substitutional asymmetries. The effect of transcription is particularly visible for genes with highly conserved gene expression. In comparison with replication and transcription, mutation rate influences the strength of substitutional asymmetries only marginally.
Genome Biology and Evolution 01/2010; 2:19-28. · 4.76 Impact Factor
[show abstract][hide abstract] ABSTRACT: Recent reports have suggested that birds lack a mechanism of wholesale dosage compensation for the Z sex chromosome. This discovery was rather unexpected, as all other animals investigated with chromosomal mechanisms of sex determination have some method to counteract the effects of gene dosage of the dominant sex chromosome in males and females. Despite the lack of a global mechanism of avian dosage compensation, the pattern of gene expression difference between males and females varies a great deal for individual Z-linked genes. This suggests that some genes may be individually dosage compensated, and that some less-than-global pattern of dosage compensation, such as local or temporal, exists on the avian Z chromosome. We used global gene expression profiling in males and females for both somatic and gonadal tissue at several time points in the life cycle of the chicken to assess the pattern of sex-biased gene expression on the Z chromosome. Average fold-change between males and females varied somewhat among tissue time-point combinations, with embryonic brain samples having the smallest gene dosage effects, and adult gonadal tissue having the largest degree of male bias. Overall, there were no neighborhoods of overall dosage compensation along the Z. Taken together, this suggests that dosage compensation is regulated on the Z chromosome entirely on a gene-by-gene level, and can vary during the life cycle and by tissue type. This regulation may be an indication of how critical a given gene's functionality is, as the expression level for essential genes will be tightly regulated in order to avoid perturbing important pathways and networks with differential expression levels in males and females.
[show abstract][hide abstract] ABSTRACT: We report an attempt to induce extrapair copulations and fertilizations in a species with a low intensity of sperm competition, the pied flycatcher Ficedula hypoleuca. Shortly after pair formation males were made less attractive to females by removing certain wing and tail feathers. Earlier research has shown that this manipulation reduces a male's pairing success. The idea was to test whether females mated to such males (N= 9) were more likely to obtain extrapair fertilizations than females mated to unmanipulated controls (N= 9). Paternity testing was carried out on all 98 young in the 18 broods, using a set of six microsatellite markers isolated from the species. Extrapair fertilizations were revealed in only three (17%) broods; two broods of handicapped males and one of a control male. A total of seven (7%) offspring were not genetically related to their putative father, a level which agrees well with results of other studies of this and other populations. We conclude that there was no evidence to suggest that the fertilization pattern was altered by the experimental manipulation. One reason for the lack of response could be that female mate choice in this species is based on male phenotypic, and not genotypic, quality.
[show abstract][hide abstract] ABSTRACT: Insight into the molecular evolution of birds has been offered by the steady accumulation of avian DNA sequence data, recently culminating in the first draft sequence of an avian genome, that of chicken. By studying avian molecular evolution we can learn about adaptations and phenotypic evolution in birds, and also gain an understanding of the similarities and differences between mammalian and avian genomes. In both these lineages, there is pronounced isochore structure with highly variable GC content. However, while mammalian isochores are decaying, they are maintained in the chicken lineage, which is consistent with a biased gene conversion model where the high and variable recombination rate of birds reinforces heterogeneity in GC. In Galliformes, GC is positively correlated with the rate of nucleotide substitution; the mean neutral mutation rate is 0.12-0.15% at each site per million years but this estimate comes with significant local variation in the rate of mutation. Comparative genomics reveals lower d(N)/d(S) ratios on micro- compared to macrochromosomes, possibly due to population genetic effects or a non-random distribution of genes with respect to chromosome size. A non-random genomic distribution is shown by genes with sex-biased expression, with male-biased genes over-represented and female-biased genes under-represented on the Z chromosome. A strong effect of selection is evident on the non-recombining W chromosome with high d(N)/d(S) ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4-5 x 10(-3) which might be seen as surprisingly high given presumed bottlenecks during domestication, but is lower than that recently observed in several natural populations of other species. Several important aspects of the molecular evolutionary process of birds remain to be understood and it can be anticipated that the upcoming genome sequence of a second bird species, the zebra finch, as well as the integration of data on gene expression, shall further advance our knowledge of avian evolution.
Cytogenetic and Genome Research 02/2007; 117(1-4):120-30. · 1.84 Impact Factor
[show abstract][hide abstract] ABSTRACT: Dogs (Canis familiaris) were domesticated from the gray wolf (Canis lupus) at least 14,000 years ago, and there is evidence of dogs with phenotypes similar to those in modern breeds 4000 years ago. However, recent genetic analyses have suggested that modern dog breeds have a much more recent origin, probably <200 years ago. To study the origin of contemporaneous breeds we combined the analysis of paternally inherited Y chromosome markers with maternally inherited mitochondrial DNA and biparentally inherited autosomal microsatellite markers in both domestic dogs and their wild ancestor, the gray wolf. Our results show a sex bias in the origin of breeds, with fewer males than females contributing genetically, which clearly differs from the breeding patterns in wild gray wolf populations where both sexes have similar contributions. Furthermore, a comparison of mitochondrial DNA and Y chromosome diversity in dog groups recognized by the World Canine Organization, as well as in groups defined by the breeds' genetic composition, shows that paternal lineages are more differentiated among groups than maternal lineages. This demonstrates a lower exchange of males than of females between breeds belonging to different groups, which illustrates how breed founders may have been chosen.
[show abstract][hide abstract] ABSTRACT: Continued gene flow is fundamental to the survival of small, isolated populations. However, geography and human intervention
can often act contrary to this requirement. The Scandinavian wolf population is threatened with a loss of genetic variation
yet limited in the accessibility to new immigrants by the geographical distance of this peninsular population from its nearest
neighbouring population and by human reluctance to allow wolves in the northern reindeer-breeding areas. In this study, we
describe the identification of immigrants into this population using autosomal microsatellites, and maternally inherited mtDNA.
Samples of 14 wolves collected in the “dispersal corridor” in northern Sweden in 2002–2005 were compared with 185 resident
Scandinavian wolves and 79 wolves from the neighbouring Finnish population. We identified four immigrant wolves, suggesting
some westward migration, although only one of these is likely to still survive. The integration of such immigrants into the
breeding population is necessary to assure the long-term survival of this isolated and inbred population and highlights the
importance of genetics techniques to the management of threatened populations.
[show abstract][hide abstract] ABSTRACT: The genome of the European hedgehog, Erinaceus concolor and E. europaeus, shows a strong signal of cycles of restriction to glacial refugia and postglacial expansion. Patterns of expansion, however, differ for mitochondrial DNA (mtDNA) and preliminary analysis of nuclear markers. In this study, we determine phylogeographic patterns in the hedgehog using two loci of the major histocompatibility complex (MHC), isolated for the first time in hedgehogs. These genes show long persistence times and high polymorphism in many species because of the actions of balancing selection. Among 84 individuals screened for variation, only two DQA alleles were identified in each species, but 10 DQB alleles were found in E. concolor and six in E. europaeus. A strong effect of demography on patterns of DQB variability is observed, with only weak evidence of balancing selection. While data from mtDNA clearly subdivide both species into monophyletic subgroups, the MHC data delineate only E. concolor into distinct subgroups, supporting the preliminary findings of other nuclear markers. Together with differences in variability, this suggests that the refugia history and/or expansion patterns of E. concolor and E. europaeus differ.
[show abstract][hide abstract] ABSTRACT: Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.
[show abstract][hide abstract] ABSTRACT: The major histocompatibility complex (MHC) has an integral role in the immune system, and hence diversity at its genes may be of particular importance for the health of populations. In large populations, balancing selection maintains diversity in MHC genes, but theoretical expectations indicate that this form of selection is absent or inefficient in small populations. We examine the level of diversity at three MHC class II loci in the wolf population of Scandinavia, a population naturally recolonized with a genetic contribution from as few as three founders, and in four neighbouring wolf populations. In the Scandinavian wolf population, two alleles were found for each locus and the distribution of alleles is compatible with their linkage into two haplotypes. Changes in the level of heterozygosity over time since recolonization demonstrate the effects of the proposed arrival of an immigrant wolf. The maintenance of diversity is shown to be compatible with a neutral, random allocation of alleles, in conjunction with crossing between packs. A total of 15 DRB1, seven DQA and 10 DQB1 alleles are found in four neighbouring wolf populations, with substantial sharing across populations. Even in these larger populations, bottlenecks and fragmentation with consequent genetic drift are likely to have resulted in few indicators for balancing selection and significant differentiation of populations.
Proceedings of the Royal Society B: Biological Sciences 11/2004; 271(1554):2283-91. · 5.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: Natural selection may act in different directions during different life-history stages, or in different directions on different classes of individuals. Antagonistic selection of this kind may be an important mechanism by which additive genetic variation for quantitative traits is maintained, and can prevent populations or species reaching local adaptive peaks. This paper reports the results of a study of viability selection on morphological traits of nestling collared flycatchers Ficedula albicollis. Analyses performed without knowledge of the sex of nestlings suggested that no selection was occurring on these traits. However, using molecular sex identification with the avian CHD gene, it is shown that selection acts in different directions on male and female body size from fledging to breeding, apparently favouring relatively small males and large females. The results suggest that differential selection on male and female nestlings may contribute to purely phenotypic sexual size dimorphism in this species. These findings highlight the potential of newly developed molecular sexing techniques to reveal the consequences of an individual's gender for many aspects of its life history in taxa where gender cannot be determined on the basis of external appearance.
[show abstract][hide abstract] ABSTRACT: Sex allocation theory predicts that parents should adjust investment in sons and daughters according to relative fitness of differently sexed offspring. In species with female preference for highly ornamented males, one advantage potentially accruing to parents from investing more in sons of the most ornamented males is that male offspring will inherit characters ensuring sexual attractiveness or high-quality genes, if ornaments honestly reveal male genetic quality. Furthermore, in species where extra-pair fertilizations occur, offspring sired by an extra-pair male are expected to more frequently be male than those of the legitimate male if the latter is of lower quality than the extra-pair male. We investigated adjustment of sex ratio of offspring in relation to ornamentation of the extra-pair and the social mate of females by direct manipulation of tails of male barn swallows Hirundo rustica. Molecular sexing of the offspring was performed using the W chromosome-linked avian chromo-helicase-DNA-binding protein (CHD) gene while paternity assessment was conducted by typing of hypervariable microsatellite loci. Extra-pair offspring sex ratio was not affected by ornamentation of their biological fathers relative to the experimental ornamentation of the parental male. Experimental ornamentation of the parental males did not affect the sex ratio of nestlings in their broods. Female barn swallows might be unable to bias offspring sex ratio at hatching according to the quality of the biological father. Alternatively, fitness benefits in terms of sexual attractiveness of sons might be balanced by the cost of compensating for little parental care provided by highly ornamented parental males, if sons are more costly to rear than daughters, or the advantage of producing more daughters, if males with large ornaments contribute differentially more to the viability of daughters than sons.
[show abstract][hide abstract] ABSTRACT: The grey wolf (Canis lupus) was numerous on the Scandinavian peninsula in the early 19th century. However, as a result of intense persecution, the population declined dramatically and was virtually extinct from the peninsula by the 1960s. We examined historical patterns of genetic variability throughout the period of decline, from 1829 to 1979. Contemporary Finnish wolves, considered to be representative of a large eastern wolf population, were used for comparison. Mitochondrial DNA (mtDNA) variability among historical Scandinavian wolves was significantly lower than in Finland while Y chromosome variability was comparable between the two populations. This may suggest that long-distance migration from the east has been male-biased. Importantly though, as the historical population was significantly differentiated from contemporary Finnish wolves, the overall immigration rate to the Scandinavian peninsula appears to have been low. Levels of variability at autosomal microsatellite loci were high by the early 1800s but declined considerably towards the mid-20th century. At this time, approximately 40% of the allelic diversity and 30% of the heterozygosity had been lost. After 1940, however, there is evidence of several immigration events, coinciding with episodes of marked population increase in Russian Karelia and subsequent westwards migration.
[show abstract][hide abstract] ABSTRACT: The identification of hybrids is often a subject of primary concern for the development of conservation and management strategies, but can be difficult when the hybridizing species are closely related and do not possess diagnostic genetic markers. However, the combined use of mitochondrial DNA (mtDNA), autosomal and Y chromosome genetic markers may allow the identification of hybrids and of the direction of hybridization. We used these three types of markers to genetically characterize one possible wolf-dog hybrid in the endangered Scandinavian wolf population. We first characterized the variability of mtDNA and Y chromosome markers in Scandinavian wolves as well as in neighboring wolf populations and in dogs. While the mtDNA data suggested that the target sample could correspond to a wolf, its Y chromosome type had not been observed before in Scandinavian wolves. We compared the genotype of the target sample at 18 autosomal microsatellite markers with those expected in pure specimens and in hybrids using assignment tests. The combined results led to the conclusion that the animal was a hybrid between a Scandinavian female wolf and a male dog. This finding confirms that inter-specific hybridization between wolves and dogs can occur in natural wolf populations. A possible correlation between hybridization and wolf population density and disturbance deserves further research.
[show abstract][hide abstract] ABSTRACT: Sex chromosomes may provide a context for studying the local effects of mutation rate on molecular evolution, since the two types of sex chromosomes are generally exposed to different mutational environments in male and female germ lines. Importantly, recent studies of some vertebrates have provided evidence for a higher mutation rate among males than among females. Thus, in birds, the Z chromosome, which spends two thirds of its time in the male germ line, is exposed to more mutations than the female-specific W chromosome. We show here that levels of nucleotide diversity are drastically higher on the avian Z chromosome than in paralogous sequences on the W chromosome. In fact, no intraspecific polymorphism whatsoever was seen in about 3.4 kb of CHD1W intron sequence from a total of >150 W chromosome copies of seven different bird species. In contrast, the amount of genetic variability in paralogous sequences on the Z chromosome was significant, with an average pairwise nucleotide diversity (d) of 0.0020 between CHD1Z introns and with 37 segregating sites in a total of 3.8 kb of Z sequence. The contrasting levels of genetic variability on the avian sex chromosomes are thus in a direction predicted from a male-biased mutation rate. However, although a low gene number, as well as some other factors, argues against background selection and/or selective sweeps shaping the genetic variability of the avian W chromosome, we cannot completely exclude selection as a contributor to the low levels of variation on the W chromosome.
Molecular Biology and Evolution 11/2001; 18(11):2010-6. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: We have taken a new approach to test the commonly accepted, but recently questioned, principle of clonal inheritance of vertebrate mitochondrial DNA (mtDNA) by relating its inheritance to a female-specific marker of nuclear DNA. Whereas this is impossible in organisms with male heterogamy (such as mammals), we show here that genealogies of mtDNA and the female-specific W chromosome of a bird species are completely concordant. Our results indicate that inheritance of mtDNA is free of detectable recombination effects over an evolutionary timescale.