House sparrows () are a hugely successful anthrodependent species; occurring on nearly every continent. Yet, despite their ubiquity and familiarity to humans, surprisingly little is known about their origins. We sought to investigate the evolutionary history of the house sparrow and identify the processes involved in its transition to a human-commensal niche. We used a whole genome resequencing dataset of 120 individuals from three Eurasian species, including three populations of Bactrianus sparrows, a non-commensal, divergent house sparrow lineage occurring in the Near East. Coalescent modelling supports a split between house and Bactrianus sparrow 11 Kya and an expansion in the house sparrow at 6 Kya, consistent with the spread of agriculture following the Neolithic revolution. Commensal house sparrows therefore likely moved into Europe with the spread of agriculture following this period. Using the Bactrianus sparrow as a proxy for a pre-commensal, ancestral house population, we performed a comparative genome scan to identify genes potentially involved with adaptation to an anthropogenic niche. We identified potential signatures of recent, positive selection in the genome of the commensal house sparrow that are absent in Bactrianus populations. The strongest selected region encompasses two major candidate genes; -which regulates craniofacial and skull development and, part of the amylase gene family which has previously been linked to adaptation to high-starch diets in humans and dogs. Our work examines human-commensalism in an evolutionary framework, identifies genomic regions likely involved in rapid adaptation to this new niche and ties the evolution of this species to the development of modern human civilization.

BackgroundDNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene (cox1 or COI) has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric species or of hybridising sister species.Methodology/Principal FindingsIn this study we extend the sample size of prior studies in birds for cox1 (2776 sequences, 756 species) and target especially species that are known to occur parapatrically, and/or are known to hybridise, on a Holarctic scale. In order to obtain a larger set of taxa (altogether 2719 species), we include also DNA sequences of two other mitochondrial genes: cytochrome b (cob) (4614 sequences, 2087 species) and 16S (708 sequences, 498 species). Our results confirm the existence of a wide gap between intra- and interspecies divergences for both cox1 and cob, and indicate that distance-based DNA barcoding provides sufficient information to identify and delineate bird species in 98% of all possible pairwise comparisons. This DNA barcoding gap was not statistically influenced by the number of individuals sequenced per species. However, most of the hybridising parapatric species pairs have average divergences intermediate between intraspecific and interspecific distances for both cox1 and cob.Conclusions/SignificanceDNA barcoding, if used as a tool for species discovery, would thus fail to identify hybridising parapatric species pairs. However, most of them can probably still assigned to known species by character-based approaches, although development of complementary nuclear markers will be necessary to account for mitochondrial introgression in hybridising species.

We used measurements of museum skins to assess morphological differences between the 22 currently recognized species of wheatear and to identify correlations between morphological features, behavioural traits and degrees of sympatry between species. Ground‐dwelling species of steppe‐like habitats have long tarsi, long claws and short tails; some are migratory and have long pointed wings and non‐emarginated primaries (O. isabellina and O. oenanthe), while others are sedentary and have more rounded and slotted wings (O. bottae, O. heuglini and O. pileata). Vegetation‐tolerant species (O. pleschanka, O. hispanica, O. cypriaca and O. deserti) have relatively long tails, short tarsi, long middle toes and long claws. The rock‐dwelling species have short tarsi, long toes and short claws; they can be either relatively heavy (O. leucura and O. monticola) or light, like the wheatears inhabiting the most arid areas (O. monacha, O. leucopyga and O. alboniger). Although sedentary, the latter show intermediate characteristics between sedentary and migratory species, having relatively pointed wings with non‐emarginated primaries. Together with their low wing‐loadings, these traits may be related to the scarcity of resources in their habitats, which obliges them to make frequent and long flights. The clear morphological differentiation between wheatear species appears to be mainly related to their migratory and foraging habits, but seems to bear no relation to their degree of sympatry.