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Hans Ellegren

Publications and source records attributed to Hans Ellegren.

At least 19 recordsLinked to original sources
PubMed2005

Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe.

Domesticated cattle were one of the cornerstones of European Neolithisation and are thought to have been introduced to Europe from areas of aurochs domestication in the Near East. This is consistent with mitochondrial DNA (mtDNA) data, where a clear separation exists between modern European cattle and ancient specimens of British aurochsen. However, we show that Y chromosome haplotypes of north European cattle breeds are more similar to haplotypes from ancient specimens of European aurochsen, than to contemporary cattle breeds from southern Europe and the Near East. There is a sharp north-south gradient across Europe among modern cattle breeds in the frequencies of two distinct Y chromosome haplotypes; the northern haplotype is found in 20 out of 21 European aurochsen or early domestic cattle dated 9500-1000 BC. This indicates that local hybridization with male aurochsen has left a paternal imprint on the genetic composition of modern central and north European breeds. Surreptitious mating between aurochs bulls and domestic cows may have been hard to avoid, or may have occurred intentionally to improve the breeding stock. Rather than originating from a few geographical areas only, as indicated by mtDNA, our data suggest that the origin of domestic cattle may be far more complex than previously thought.

Animals↗
PubMed2005

Gene conversion drives the evolution of HINTW, an ampliconic gene on the female-specific avian W chromosome.

The HINTW gene on the female-specific W chromosome of chicken and other birds is amplified and present in numerous copies. Moreover, as HINTW is distinctly different from its homolog on the Z chromosome (HINTZ), is a candidate gene in avian sex determination, and evolves rapidly under positive selection, it shows several common features to ampliconic and testis-specific genes on the mammalian Y chromosome. A phylogenetic analysis within galliform birds (chicken, turkey, quail, and pheasant) shows that individual HINTW copies within each species are more similar to each other than to gene copies of related species. Such convergent evolution is most easily explained by recurrent events of gene conversion, the rate of which we estimated at 10(-6)-10(-5) per site and generation. A significantly higher GC content of HINTW than of other W-linked genes is consistent with biased gene conversion increasing the fixation probability of mutations involving G and C nucleotides. Furthermore, and as a likely consequence, the neutral substitution rate is almost twice as high in HINTW as in other W-linked genes. The region on W encompassing the HINTW gene cluster is not covered in the initial assembly of the chicken genome, but analysis of raw sequence reads indicates that gene copy number is significantly higher than a previous estimate of 40. While sexual selection is one of several factors that potentially affect the evolution of ampliconic, male-specific genes on the mammalian Y chromosome, data from HINTW provide evidence that gene amplification followed by gene conversion can evolve in female-specific chromosomes in the absence of sexual selection. The presence of multiple and highly similar copies of HINTW may be related to protein function, but, more generally, amplification and conversion offers a means to the avoidance of accumulation of deleterious mutations in nonrecombining chromosomes.

Animals↗
PubMed2005

Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle.

The geographic situation of the Iberian Peninsula makes it a natural link between Europe and North Africa. However, it is a matter of debate to what extent African influences via the Straits Gibraltar have affected Iberia's prehistoric development. Because early African pastoralist communities were dedicated to cattle breeding, a possible means to detect prehistoric African-Iberian contacts might be to analyze the origin of cattle breeds on the Iberian Peninsula. Some contemporary Iberian cattle breeds show a mtDNA haplotype, T1, that is characteristic to African breeds, generally explained as being the result of the Muslim expansion of the 8th century A.D., and of modern imports. To test a possible earlier African influence, we analyzed mtDNA of Bronze Age cattle from the Portalón cave at the Atapuerca site in northern Spain. Although the majority of samples showed the haplotype T3 that dominates among European breeds of today, the T1 haplotype was found in one specimen radiocarbon dated 1800 calibrated years B.C. Accepting T1 as being of African origin, this result indicates prehistoric African-Iberian contacts and lends support to archaeological finds linking early African and Iberian cultures. We also found a wild ox haplotype in the Iberian Bronze Age sample, reflecting local hybridization or backcrossing or that aurochs were hunted by these farming cultures.

Africa, Northern↗
PubMed2005

Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.

Regional biases in substitution pattern are likely to be responsible for the large-scale variation in base composition observed in vertebrate genomes. However, the evolutionary forces responsible for these biases are still not clearly defined. In order to study the processes of mutation and fixation across the entire human genome, we analyzed patterns of substitution in Alu repeats since their insertion. We also studied patterns of human polymorphism within the repeats. There is a highly significant effect of recombination rate on the pattern of substitution, whereas no such effect is seen on the pattern of polymorphism. These results suggest that regional biases in substitution are caused by biased gene conversion, a process that increases the probability of fixation of mutations that increase GC content. Furthermore, the strongest correlate of substitution patterns is found to be male recombination rates rather than female or sex-averaged recombination rates. This indicates that in addition to sexual dimorphism in recombination rates, the sexes also differ in the relative rates of crossover and gene conversion.

Alu Elements↗
PubMed2005

Microsatellite genotyping of DNA isolated from claws left on tanned carnivore hides.

Tanned hides, a common form of preservation of mammalian specimens, are usually resistant to DNA analysis. However, we show that DNA isolated from the pulp of claws of tanned hides amplifies well for microsatellite markers. For eight wolverine and eight lynx hides tanned 5-20 years ago, 93-98% of replicate amplifications gave distinct PCR products. Genotypes obtained in analysis of tissue samples of the same individuals were in all cases in agreement with those obtained by analysis of claws. We thus conclude that the use of claws from tanned hides offers new possibilities to genetic studies of preserved mammalian specimens, for instance, in the monitoring of illegal trade.

Animals↗
PubMed2005

Genes of domestic mammals augmented by backcrossing with wild ancestors.

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 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.

Alleles↗
PubMed2004

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.

Alleles↗
PubMed2004

Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes.

A distinctive feature of the avian genome is the large heterogeneity in the size of chromosomes, which are usually classified into a small number of macrochromosomes and numerous microchromosomes. These chromosome classes show characteristic differences in a number of interrelated features that could potentially affect the rate of sequence evolution, such as GC content, gene density, and recombination rate. We studied the effects of these factors by analyzing patterns of nucleotide substitution in two sets of chicken-turkey sequence alignments. First, in a set of 67 orthologous introns, divergence was significantly higher in microchromosomes (chromosomes 11-38; 11.7% divergence) than in both macrochromosomes (chromosomes 1-5; 9.9% divergence; P = 0.016) and intermediate-sized chromosomes (chromosomes 6-10; 9.5% divergence; P = 0.026). At least part of this difference was due to the higher incidence of CpG sites on microchromosomes. Second, using 155 orthologous coding sequences we noted a similar pattern, in which synonymous substitution rates on microchromosomes (13.1%) were significantly higher than were rates on macrochromosomes (10.3%; P = 0.024). Broadly assuming neutrality of introns and synonymous sites, or constraints on such sequences do not differ between chromosomal classes, these observations imply that microchromosomal genes are exposed to more germ line mutations than those on other chromosomes. We also find that dN/dS ratios for genes located on microchromosomes (average, 0.094) are significantly lower than those of macrochromosomes (average, 0.185; P = 0.025), suggesting that the proteins of genes on microchromosomes are under greater evolutionary constraint.

Animals↗
PubMed2004

Chicken W: a genetically uniform chromosome in a highly variable genome.

The Y chromosome of organisms with male heterogamety is expected to show reduced levels of genetic diversity, because the effective population size is one-fourth that of autosomes. However, studies in mammals, flies, and plants show that Y chromosome diversity is lower than expected even when differences in effective population size are taken into account. This may be explained by skewed reproductive success among males, leading to low male effective population size, or by a strong role of selection in shaping levels of nucleotide diversity in nonrecombining chromosomes. We tested these hypotheses in a system with female heterogamety by estimating nucleotide diversity in the female-specific W chromosome of the domestic chicken by resequencing of 7,643 base pairs in 47 birds from 10 highly divergent breeds. The screening revealed only one single segregating site, which is in sharp contrast to our previous observation, using a similar panel of birds of, on average, one segregating site every 39 base pairs in autosomal sequence. When taking sex-specific mutation rates and differences in effective population size into account, the observed degree of W chromosome polymorphism is 28-fold lower than expected for the frequency of segregating sites and 13-fold lower than expected for estimates of nucleotide diversity (autosomes, 6.5 x 10(-3); W, 7.0 x 10(-5)). We note that selection is the only factor that can explain the reduced diversity in the sex-limited chromosome irrespective of mode of reproduction or whether there is male or female heterogamety. Reduced variability in female-specific W chromosomes is not easily explained by sexual selection.

Animals↗
PubMed2004

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

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 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.

Animals↗
PubMed2004

Gene expression, synteny, and local similarity in human noncoding mutation rates.

The human genome is organized with regard to many features such as isochores, Giemsa bands, clusters of genes with similar expression patterns, and contiguous regions with shared evolutionary histories (synteny blocks). In addition to these genomic features, it is clear that mutation rates also vary across the human genome. To address how mutation rates and genomic features are related, we analyzed substitution rates at three classes of putatively neutral noncoding sites (nongenic, intronic, and ancestral repeats) in approximately 14 Mb of human-chimpanzee alignments covering human chromosome 7. Patterns of mutation rate variation inferred from substitution rate variation differ among the three site classes. In particular, we find that intronic mutation rates are strongly affected by the breadth of expression of the genes in which they reside, with broadly expressed genes exhibiting low mutation rates, probably as a consequence of the transcription-coupled repair process acting in the germ line. All site classes show significant local similarities in mutation rate at the megabase scale, and regional similarities in nongenic mutation rate covary with blocks of synteny between the human and mouse genomes, indicating that the evolutionary history of a genomic region is an important determinant of mutation rate.

Animals↗
PubMed2004

Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and Turkey.

To investigate mutation-rate variation between autosomes and sex chromosomes in the avian genome, we have analyzed divergence between chicken (Gallus gallus) and turkey (Meleagris galopavo) sequences from 33 autosomal, 28 Z-linked, and 14 W-linked introns with a total ungapped alignment length of approximately 43,000 bp. There are pronounced differences in the mean divergence among autosomes and sex chromosomes (autosomes [A] = 10.08%, Z chromosome = 10.99%, and W chromosome = 5.74%), and we use these data to estimate the male-to-female mutation-rate ratio (alpha(m)) from Z/A, Z/W, and A/W comparisons at 1.71, 2.37, and 2.52, respectively. Because the alpha(m) estimates of the three comparisons do not differ significantly, we find no statistical support for a specific reduction in the Z chromosome mutation rate (Z reduction estimated at 4.89%, P = 0.286). The idea of mutation-rate reduction in the sex chromosome hemizygous in one sex (i.e., X in mammals, Z in birds) has been suggested on the basis of theory on adaptive mutation-rate evolution. If it exists in birds, the effect would, thus, seem to be weak; a preliminary power analysis suggests that it is significantly less than 18%. Because divergence may vary within chromosomal classes as a result of variation in mutation and/or selection, we developed a novel double-bootstrapping method, bootstrapping both by introns and sites from concatenated alignments, to estimate confidence intervals for chromosomal class rates and for alpha(m). The narrowest interval for the alpha(m) estimate is 1.88 to 2.97 from the Z/W comparison. We also estimated alpha(m) using maximum likelihood on data from all three chromosome classes; this method yielded alpha(m) = 2.47 and approximate 95% confidence intervals of 2.27 to 2.68. Our data are broadly consistent with the idea that mutation-rate differences between chromosomal classes can be explained by the male mutation bias alone.

Animals↗
PubMed2004

Limited number of patrilines in horse domestication.

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 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.

Animals↗
PubMed2004

Individual variation in microsatellite mutation rate in barn swallows.

The hypermutable nature of some microsatellite loci implies realistic possibilities for the large-scale detection of germline mutations by pedigree analysis. We have developed a model system for mutation analysis by the characterisation of patterns of mutation at three hypervariable microsatellites (two tetranucleotide and one pentanucleotide repeat loci) in barn swallows, all three markers having mutation rates at the percentage level. Here, we study how the mutation rate varies between individual birds of a Spanish population of barn swallows. A total of 53 mutations were identified from 2920 germline transmissions in 90 families with a total of 694 offspring. Mutations were not randomly distributed among individuals (P = 0.020). Attempts to correlate mutation rate with allele size, degree of inbreeding, immunocompetence and male age only revealed a strong effect of allele size. The mean mutation rate differed between colonies of breeding swallows which was probably due to a corresponding variation in allele size between colonies. There was no difference in the mean mutation rate between the Spanish and an Italian population. These results corroborate earlier findings, at the population level, of an allele size effect on the microsatellite mutation rate.

Animals↗
PubMed2004

Do avian mitochondria recombine?

The dogma of strict maternal inheritance of mitochondria is now being tested with population genetics methods on sequence data from many species. In this study we investigated whether recombination occurs in the mitochondria of the blue tit ( Parus caeruleus) by studying polymorphisms in the mitochondrial control region and in a recently identified (A)(n) microsatellite on the W chromosome. The female heterogamety of avian sex chromosomes allows a test of whether mitochondrial recombination affects genealogical inference by comparison of mitochondrial and W-linked sequence variation. There is no discrepancy between mitochondrial and W-linked genealogies in blue tits, consistent with no recombination. We also analyzed mitochondrial sequence variation in both blue tits and peregrine falcons ( Falco peregrinus) using a coalescent-based approach which accounts for recurrent mutation; in neither bird species did we find evidence of recombination. We conclude that it is unlikely that mitochondrial recombination has large effects on mitochondrial genetic variability in birds.

Animals↗
PubMed2004

Evidence for turnover of functional noncoding DNA in mammalian genome evolution.

The vast majority of the mammalian genome does not code for proteins, and a fundamental question in genomics is: What proportion of the noncoding mammalian genome is functional? Most attempts to address this issue use sequence comparisons between highly diverged mammals such as human and mouse to identify conservation due to negative selection. But such comparisons will underestimate the true proportion of functional noncoding DNA if there is turnover, if patterns of negative selection change over time. Here we test whether the inferred level of negative selection differs between different pairwise species comparisons. Using a multiple alignment of more than a megabase of contiguous sequence from eight mammalian species, we find a strong negative relationship between inferred levels of negative selection and pairwise divergence using 21 pairwise comparisons. This result suggests that there is a high rate of turnover of functional noncoding elements in the mammalian genome, so measures of functional constraint based on human-mouse comparisons may seriously underestimate the true value.

Animals↗
PubMed2004

Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution.

The human X chromosome exhibits four "evolutionary strata," interpreted to represent distinct steps in the process whereby recombination became arrested between the proto X and proto Y. To test if this is a general feature of sex chromosome evolution, we studied the Z-W sex chromosomes of birds, which have female rather than male heterogamety and evolved from a different autosome pair than the mammalian X and Y. Here we analyze all five known gametologous Z-W gene pairs to investigate the "strata" hypothesis in birds. Comparisons of the rates of synonymous substitution and intronic divergence between Z and W gametologs reveal the presence of at least two evolutionary strata spread over the p and q arms of the chicken Z chromosome. A phylogenetic analysis of intronic sequence data from different avian lineages indicates that Z-W recombination ceased in the oldest stratum (on Zq; CHD1Z, HINTZ, and SPINZ) 102-170 million years ago (MYA), before the split of the Neoaves and Eoaves. However, recombination continued in the second stratum (on Zp; UBAP2Z and ATP5A1Z) until after the divergence of extant avian orders, with Z and W diverging 58-85 MYA. Our data suggest that progressive and stepwise cessation of recombination is a general feature behind sex chromosome evolution.

Animals↗