Ceiridwen J. Edwards

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

BACKGROUNDnPolar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U.xa0arctos) or their response to previous environmental change.nnnRESULTSnWe used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.nnnCONCLUSIONSnThe reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.

Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation.

Background Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. Methodology and Principal Findings Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. Conclusions We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.

Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories

Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the worlds most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y‐chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long‐term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva.

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

Early diffusion of domestic bovids in Europe: An indicator for human contacts, exchanges and migrations?

Cattle, sheep and goat were domesticated in the Near-East during the 9th millennium BC. From there, sheep and goat, which had no wild ancestors in Europe, were introduced to this continent at the beginning of the 7th millennium B.C. and diffused following two main flows: a southern route along the northern coastline of the Mediterranean, and a northern route across central Europe following the Danubian corridor. Possible scenarios of migration have been complicated to investigate regarding cattle, as the species had a possible wild ancestor in Europe: the local aurochs, whose disappearance only occurred at the end of the 17th century A.D. and whose remains are hardly distinguishable from those of the early domestic forms on the basis of classical osteometry. A tight cooperation between Archaeozoology and Genetics has provided, in the frame of several publicly funded projects (among which the OMLL scheme), substantial new data allowing refinement of historical scenarios to a degree never achieved thus far. We were able to demonstrate that local aurochs did not contribute, or contributed to a very limited extent, to the constitution of European domestic cattle herds, whose origin can be clearly traced back to the Near East. Thus, from this point of view, domestic cattle biogeographical history is very similar to sheep and goat, and their appearance in Europe probably owes more to farming pioneers than to local hunter-gatherers. Analyses of goat aDNA revealed the preservation of an important genetic diversity very far from the diffusion centre. This is suggestive of the persistence of gene flow between domestic herds across the dispersion area along the different diffusion routes, which prevented the occurrence of severe bottleneck effects. This diversity also indicates that the existence of contacts between farming groups encompassed very large areas. It is very interesting to note that recent works published on domestication and diffusion of pig in Neolithic Europe have proposed very different scenarios. This highlights the specificity of domestic bovids as tracers of human contacts, exchanges and displacements during the Neolithicisation of Europe.

Himalayan ‘yeti’ DNA: polar bear or DNA degradation? A comment on ‘Genetic analysis of hair samples attributed to yeti’ by Sykes et al. (2014)

Based on 104 base pairs of the mitochondrial 12S ribosomal RNA gene, Sykes et al . [[1][1]] identified two Himalayan samples of hair, from Ladakh (India) and Bhutan, respectively, as belonging to the species Ursus maritimus (polar bear). The authors claim that these samples have the closest genetic

Letter to the editor: Apple down 152 putative syphilis: Pre-colombian date confirmed

In our article (Cole and Waldron, 2011), we described a case of treponemal disease, distinguished by the presence of caries sicca, widespread bilateral symmetrical periosteal new bone, and skeletal lesions consistent with gummatous activity. This skeleton came from Apple Down, a large, well preserved, isolated, undisturbed rural cemetery, excavated in the 1980s by Down and Welch (1990). An Anglo-Saxon date for the cemetery was clearly indicated by the presence of wellknown Anglo-Saxon grave goods, and several grave goods were radiocarbon dated to the Anglo-Saxon period. The excavators dated burial 152 to the sixth century based on grave goods found with the body. Given the extensive corpus of radiocarbon dated AngloSaxon grave goods at the site, the museum curator responsible for the material felt there was no ethical justification for destructive testing to confirm the preColombian date in relation to our work. In a subsequent comprehensive review, Harper and coworkers (2011) cast doubt on both our diagnosis and the pre-Colombian date. In our response (Cole and Waldron, 2012), we reiterated that the differential diagnosis reduced to a single condition, treponemal disease. We also pointed out the well-defined narrow temporal range for Anglo-Saxon grave goods. One of us (CJE) is undertaking research on material from the Apple Down cemetery, looking at potential differences between those individuals accompanied by pagan Anglo-Saxon grave goods and those without. Radiocarbon dating is thus justified and essential given the presence of unaccompanied burials in this data set, and a uniform sampling methodology has been applied to both groups. Burial 152 was radiocarbon dated as part of this study to 1513 6 25 uncalibrated BP (OxA28869). This date was calibrated using OxCal (ver. 4.2; Bronk Ramsey 2009) and the most recent calibration curve, IntCal13 (Reimer et al., 2013). The calibrated date was AD 427–634 at three sigma (99.7%) probability. The mean date was AD 547, the median date was AD 558, and the most probable calibrated date was AD 560. There was no evidence to suggest consumption of a marine diet at Apple Down. Indeed, when the dietary stable isotopes of burial 152 were tested, he was found to have eaten a terrestrial diet, with a d13C value of 220.54 and a d15N value of 9.4. Therefore, we did not calculate a marine-corrected date. The spread of dates (AD 427–634) is consistent with the pagan Anglo-Saxon period, the end of which was marked by the conversion to Christianity in the eighth century AD, and further confirms the validity of dating using Anglo-Saxon grave goods. In our article (Cole and Waldron, 2011), we proposed that the pathological evidence from burial 152 suggests a possible case of venereal syphilis rather than one of the endemic forms of treponemal disease. The factors taken into account in this decision, made on the basis of probabilities, include the geographical pathogen range, the apparent low prevalence of the disease at this large cemetery, the high social status of the individual, the presence of social upheaval at the time, and the early age of death of the individual. These factors should be considered in their totality. Based on our analyses of burial 152 from the Anglo-Saxon cemetery site of Apple Down, we have solid evidence that venereal syphilis existed in pre-Columbian Europe, thus supporting an Old World, or a dual origin, for the disease.