Knut H. Røed

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr bp). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr bp), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5 million years before present (Myr bp), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72 kyr bp, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences.

Abstract The glacial‐interglacial cycles of the upper Pleistocene have had a major impact on the recent evolutionary history of Arctic species. To assess the effects of these large‐scale climatic fluctuations to a large, migratory Arctic mammal, we assessed the phylogeography of reindeer (Rangifer tarandus) as inferred from mitochondrial DNA (mtDNA) sequence variation in the control region. Phylogenetic relationships among haplotypes seem to reflect historical patterns of fragmentation and colonization rather than clear‐cut relationships among extant populations and subspecies. Three major haplogroups were detected, presumably representing three separate populations during the last glacial. The most influential one has contributed to the gene pool of all extant subspecies and seems to represent a large and continuous glacial population extending from Beringia and far into Eurasia. A smaller, more localized refugium was most likely isolated in connection with ice expansion in western Eurasia. A third glacial refugium was presumably located south of the ice sheet in North America, possibly comprising several separate refugial populations. Significant demographic population expansion was detected for the two haplogroups representing the western Eurasian and Beringian glacial populations. The former apparently expanded when the ice cap retreated by the end of the last glacial. The large continuous one, in contrast, seems to have expanded by the end of the last interglacial, indicating that the warm interglacial climate accompanied by marine transgression and forest expansion significantly confined population size on the continental mainland. Our data demonstrate that the current subspecies designation does not reflect the mtDNA phylogeography of the species, which in turn may indicate that morphological differences among subspecies have evolved as adaptive responses to postglacial environmental change.

A high density SNP array for the domestic horse and extant Perissodactyla: Utility for association mapping, genetic diversity, and phylogeny studies

An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalskis Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

Monomorphism and polymorphism at Mhc DRB loci in domestic and wild ruminants

Summary: Genetic polymorphism at Mhc class II DRB loci was investigated in samples of musk‐ox from Canada and Greenland; moose from Sweden, Norway, Canada, and Alaska, roe deer from Norway and Sweden; reindeer from Svalbard and Norway; fallow deer from Norway and Sweden; and red deer from Norway. The results were compared with published data on cattle, bison, goal, sheep, and red deer. Cattle‐specific primers amplified a single DRB locus in all species except fallow deer and red deer, in which two loci were found. Single strand conformation polymorphism analysis and DNA sequence analysis were employed to detect genetic polymorphism. Complete monomorphism was found in musk‐ox and fallow deer. Limited polymorphism was found in the moose, roe deer, and reindeer from Svalbard, whereas intermediate to extensive DRB diversity was present in reindeer from Norway and in bison, sheep, goat, cattle, and red deer. The restricted Mhc diversity in moose, roe deer, and fallow deer is notable in relation to the dramatic population expansion of moose and roe deer in Sweden during this century and since fallow deer is used for meat and game production with good results and without any marked disease problems. The results question the view that species or populations with restricted Mhc diversity have poor resistance to infectious diseases. A phylogenelic tree analysis revealed a clustering of DRB sequences within species rather than within allelic lineages across species. The results suggest trans‐species persistence of polymorphic sequence motifs rather than of allelic lineages.

Selection response of cortisol and lysozyme in rainbow trout and correlation to growth

Abstract Progeny groups of rainbow trout ( Oncorhynchus mykiss Walbaum) selected for high or low post-stress levels of plasma cortisol, or similarly for high or low post-stress lysozyme activity, have been tested for their response to the selection. In four of the four stress exposures, individuals from the line selected for high cortisol responsiveness displayed significantly higher levels of post-stress cortisol than individuals of the low responding line. Phenotypic correlations of cortisol response between samplings, irrespective of line, were highly significant. The realised heritability of cortisol was 0.50, which is very similar to the estimated h 2 based on the parental generation. Only in the last two of the four stress experiments did the high lysozyme selected line exhibit significantly higher lysozyme activity than the low lysozyme line. The timing of vaccination may cause this, since the vaccine is known to affect lysozyme activity. Breeding values of parents were based on vaccinated fish only. The phenotypic correlations between samplings of lysozyme response were weaker than for cortisol, though still significant. The realised heritability of lysozyme was 0.32, which is also in agreement with the previously estimated h 2 . The phenotypic correlations between cortisol and lysozyme in individual samplings were in cases of significance negative. There is qualified support for better growth performance in the low cortisol responding line as compared to the high responding line. The data are not conclusive as to establishing whether selection for altered post-stress lysozyme activity affects growth. In conclusion, the present data confirm that the progeny inherit stress-related traits identified in the parents; the response to selection for both cortisol and lysozyme is encouraging. The practical implications or gain of selecting for either trait under aquacultural conditions is still being resolved.

Genetic relationships in the peregrine falcon (Falco peregrinus) analysed by microsatellite DNA markers.

Microsatellite DNA markers were developed from a peregrine falcon (Falco peregrinus) and genetic relationships among peregrine falcons in southern Norway were analysed using the markers. The genomic DNA library was screened for the presence of dinucleotide microsatellite repeats. Twelve loci revealed polymorphism through the initial analysis of 24 unrelated peregrine falcons, and Mendelian inheritance was confirmed in two peregrine falcon families bred in captivity. The estimated mean probability of identical genotypes in two unrelated individuals was 3 × 10−8, and the combined exclusion probability for parentage testing was 0.99 and 0.94 for one or both parents unknown, respectively. The markers were used to investigate the parentage of peregrine broods from the same nest site from different breeding seasons, and subsequently the nest‐site fidelity of the breeding peregrines. High nest‐site fidelity was found by studying pairwise comparisons of relatedness (rxy) estimates among chicks at six nest sites from three different breeding seasons. Cross‐species amplifications showed that most loci also appeared to amplify polymorphic products in the gyrfalcon (F. rusticolus), merlin (F. columbarius), hobby (F. subbuteo) and kestrel (F. tinnunculus), demonstrating that the loci will provide powerful genetic markers in these falcons too.

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Effects of age, density and sex ratio on reproductive effort in male reindeer (Rangifer tarandus)

In sexually dimorphic ungulates, male reproductive success depends on fighting with other males for access to females during a brief rutting season. Large body size is necessary for success in intrasexual competition, and af ew large-sized males are often able to monopolize access to female groups. Earlier studies have reported that reproductive effort increases with age until prime-age is reached, and one study that population density lowered effort in (older) males. No study has directly assessed whether there is within-age-class variation in effort resulting from varying levels of intra-male competition. It is reported here the weight loss during the rutting season of 54 individual male reindeer Rangifer tarandus coming from eight herds with varying density (3.3–6.0 deer/km 2 ) and sex ratio (4–28% males). In agreement with earlier studies, reproductive effort was lower for young (1- to 2-year-old) than for prime-aged (3- to 5-year-old) males both on an absolute and relative scale. Among 1-year-old males (n = 33), effort was lower as sex ratio became closer to even, but density during the rutting season had no effect. This suggests that yearling males take a more active role when prime-aged males are absent. In addition to the insight into male ungulate life history, understanding male rutting behaviour may also have implications for population dynamics.

Transport of Ticks by Migratory Passerine Birds to Norway

Abstract Ticks can be transported over large distances and across geographical barriers by avian hosts. During the spring migrations of 2003 to 2005, 9,768 passerine birds from 4 bird observatories along the southern coastline of Norway were examined for ticks. Altogether, 713 birds carried a total of 517 larvae and 1,440 nymphs. The highest prevalence of tick infestation was observed in thrushes and dunnock (Prunella modularis). The degree of tick infestation varied during each season, between localities, and from year to year. Blackbirds (Turdus merula) caught in localities with many ticks had greater infestation than those from localities with few or no ticks, suggesting local tick recruitment. A similar study performed during 1965–1970 involving 2 of the bird observatories in the present study found ticks on 4.2% of birds, while we found infestation of 6.9% at the same localities (P < 0.001). With the exception of 10 nymphs and 1 larva, the predominant tick was Ixodes ricinus. Seven nymphs of Hyalomma rufipes and 1 larva of Dermacentor sp. were also found. No species of Dermacentor had previously been found in Norway.