We have recently published a paper in G3: Genes, Genomes, Genetics:

Diversifying Selection Between Pure-Breed and Free-Breeding Dogs Inferred from Genome-Wide SNP Analysis

Pilot M., Malewski T., Moura A.E., Grzybowski T., Olenski K., Kaminski S., Fadel F.R., Alagaili A., Mohammed O., Bogdanowicz W.

G3: Genes, Genomes, Genetics 6 (2016): 2285-2298

Domesticated species are often composed of distinct populations differing in the character and strength of artificial and natural selection pressures, providing a valuable model to study adaptation. In contrast to pure-breed dogs that constitute artificially maintained inbred lines, free-ranging dogs are typically free-breeding, i.e., unrestrained in mate choice. Many traits in free-breeding dogs (FBDs) may be under similar natural and sexual selection conditions to wild canids, while relaxation of sexual selection is expected in pure-breed dogs. We used a Bayesian approach with strict false-positive control criteria to identify F_ST-outlier SNPs between FBDs and either European or East Asian breeds, based on 167,989 autosomal SNPs. By identifying outlier SNPs located within coding genes, we found four candidate genes under diversifying selection shared by these two comparisons. Three of them are associated with the Hedgehog (HH) signaling pathway regulating vertebrate morphogenesis. A comparison between FBDs and East Asian breeds also revealed diversifying selection on the BBS6 gene, which was earlier shown to cause snout shortening and dental crowding via disrupted HH signaling. Our results suggest that relaxation of natural and sexual selection in pure-breed dogs as opposed to FBDs could have led to mild changes in regulation of the HH signaling pathway. HH inhibits adhesion and the migration of neural crest cells from the neural tube, and minor deficits of these cells during embryonic development have been proposed as the underlying cause of “domestication syndrome.” This suggests that the process of breed formation involved the same genetic and developmental pathways as the process of domestication.

The paper can be downloaded from here:

http://www.g3journal.org/content/6/8/2285.full.pdf+html

A new paper has been published in Scientific Reports:

Differences in Trait Impulsivity Indicate Diversification of Dog Breeds into Working and Show Lines

Fernanda Ruiz Fadel, Patricia Driscoll, Malgorzata Pilot, Hannah Wright, Helen Zulch & Daniel Mills

Impulsiveness describes the inability to inhibit behaviour in the presence of salient cues. Trait-level impulsivity exists on a continuum and individual differences can be adaptive in different contexts. While breed related differences in behavioural tendency in the domestic dog (Canis familiaris) are well established, the phenomenon within lines of a breed which have been selected more recently is not well studied, although it may challenge the popular notion of breed-typical behaviour. We describe differences in impulsivity between and within two dog breeds with working and show lines selected for different levels of impulsivity: Border Collies (herding work) and Labrador Retrievers (gun work). Recent show line selection might have lessened differences in impulsivity between breeds. We tested this hypothesis on a dataset of 1161 individuals assessed using a validated psychometric tool (Dog Impulsivity Assessment Scale – DIAS). Collies were more impulsive on average, consistent with the original purpose of breed selection. Regarding line, working Collies differed from working Labradors, but show lines from the two breeds were not significantly different. Altered or relaxed artificial selection for behavioural traits when appearance rather than behaviour become the primary focus for breeders may reduce average differences in impulsivity between breeds in show lines.

Fully funded PhD studentship in canine genetics: Linking phenotypes with genotypes for canine chemosensory perception

School of Life Sciences, University of Lincoln, UK

We are seeking to recruit a Science graduate with MSc or a good BSc degree (or equivalent) for a project on genetics of canine chemosensory perception, starting in October 2016. Experience in molecular genetics, bioinformatics and/or behavioural research methods will be seen as an advantage. This is a fully-funded position with a stipend of £14,124 per annum for three years for both home and international students. The project will be supervised by a team of researchers with complementary expertise in evolutionary genetics (Malgorzata Pilot, primary supervisor), veterinary behavioural medicine (Daniel Mills) and molecular neurobiology (Humberto Gutierrez).

This project will address a fundamental question in chemosensory system evolution concerning the trade-off between olfaction (sense of smell) and vomeronasal sensing (detection of emotionally salient chemosignals), and at the same time contribute to improving efficiency of selection of dogs for detection work (e.g. explosives, drugs). Olfactory receptors (OR) and vomeronasal receptors (V1R) provide systems to detect molecules of odorants and chemicals that mediate pheromone perception, respectively. There is growing evidence on functional and evolutionary interactions between these two systems, but this has not been assessed yet at an intra-specific level. The aim of this PhD project is to compare OR and V1R repertoires and chemosensory perception abilities in different groups of dogs, including breeds currently used for scent detection and breeds considered as poor sniffers, and in dogs’ wild ancestors, grey wolves. The project will involve the analysis of the complete set of OR and V1R genes using NGS methods, behavioural experiments to test odour and pheromone perception performance, and the analysis of genotype-phenotype interactions.

The student will be supervised by an interdisciplinary team with complementary expertise in evolutionary genetics and genomics, molecular neurobiology, neuronal cell signalling, olfaction and pheromone detection, veterinary behavioural medicine, and behaviour of domestic and wild canids. Therefore, the student will have an opportunity to obtain a broad range of research skills, and develop a unique interdisciplinary research profile. The student will be also given opportunities to attend external courses and workshops, and international conferences. The School of Life Sciences provides a great research environment and has a large international community of postgraduate students.

To apply, send a CV and cover letter to Malgorzata Pilot (mpilot@lincoln.ac.uk) by 17 April 2016, 11 pm of UK time. You may also contact Malgorzata Pilot for informal enquiries. Shortlisted applicants will be invited for interview.

A new paper has been published in the Proceedings of the Royal Society of London B:

On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

Authors: Małgorzata Pilot, Tadeusz Malewski, Andre E. Moura, Tomasz Grzybowski, Kamil Oleński, Anna Ruść, Stanisław Kamiński, Fernanda Ruiz Fadel, Daniel S. Mills, Abdulaziz N. Alagaili, Osama B. Mohammed, Grzegorz Kłys, Innokentiy M. Okhlopkov, Ewa Suchecka, Wiesław Bogdanowicz

Abstract

Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.

 

A new paper has been published in The Holocene:

An Arctic seal in temperate waters: History of the ringed seal (Pusa hispida) in the Baltic Sea and its adaptation to the changing environment

by Pirkko Ukkonen, Kim Aaris-Sørensen, Laura Arppe, Linas Daugnora, Antti Halkka, Lembi Lõugas, Markku Juhani Oinonen, Malgorzata Pilot and Jan Storå

Abstract
The ringed seal (Pusa hispida) is an early immigrant in the Baltic Basin and has since its arrival experienced substantial changes in the climate, salinity and productivity of the Basin. In this paper, we discuss the dispersal and distribution of the ringed seal during different stages of the Baltic Sea in relation to past and ongoing environmental changes. Subfossil ringed seal remains around the Baltic Sea and the Danish Straits were radiocarbon dated in order to map the distribution of the species in different time periods. The δ13C data were used in evaluating the changes in the marine character of the Baltic Basin.
The sequence of the dates indicates a continuous presence of the species in the Baltic Basin. The earliest ringed seal finds come from the Skagerrak/Kattegat area (Denmark, Swedish west coast) and date to the full glacial period and Baltic Ice Lake. In the Baltic Basin, the species appears in the subfossil record during the Ancylus period, but the main part of the remains date to the Littorina stage. During the Littorina stage, the distribution of the species was at least periodically wider than today, covering also southern parts of the Baltic. The presence of breeding populations in southern parts of the Baltic during the Holocene Thermal Maximum (HTM) indicates that the winters were at least periodically cold enough for winter ice. The changes in the marine influence in the Baltic Basin can be seen in the seal collagen δ13C values, which serve as a proxy for qualitative changes in water mass salinity.