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Mitogenomes are valuable data sources for phylogeographic and evolutionary studies of relatively closely related organisms. Here we describe eight complete sequences of moose mitogenomes belonging to the three clades of the European lineage and compare them with those of the Asian lineage. Mitochondrial genomes of moose and other cervids were used to infer highly resolved phylogenetic relationships and estimate divergence times. The analyses clearly distinguished two mtDNA lineages of moose and supported the division of the European lineage into three clades: East, West, and Central. The divergence of the European and Asian mtDNA lineages occurred in the Middle Pleistocene (ca. 443 kya), which significantly exceeds the fossil records of modern Alces alces dated to 100-200 kya. It indicates that the evolutionary history of the moose is more complex and could encompass inheritance of the ancestral variation. Our estimates also showed rapid diversification of present-day clades of the European lineage, which coincided with the transition from the Penultimate Glacial Period (MIS 6) and the Eemian interglacial (MIS 5) approximately 100 kya. Despite the strong division of the nucleotide sequences, we detected no evidence for the divergence ofamino acid sequences between Clade Central and Clade East. The recent diversification of A. alces clades, incombinationwiththeirevidentreciprocal monophyly, could be a result of low effective population size over its evolutionary history, augmented by severe bottlenecks during the Last Glacial Period. Our results are in agreement with the presence of different glacial refugia recently proposed for three identified clades of the European lineage and suggested the relict character of the Scandinavian (from Clade West) and the Biebrza moose population in northeastern Poland (belonging to Clade Central). [ABSTRACT FROM AUTHOR]

Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness-related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer ( Capreolus capreolus) in Poland from mitochondrial ( CR and cyt b) and sex-linked markers ( ZFX, SRY, DBY4 and DBY8). Analyses of CR mt DNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer ( C. pygargus) mt DNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mt DNA results, sex-specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8-10.0 ka BP). Initially, introgressed mt DNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human-mediated introductions of C. pygargus had minimal effect on the extent of mt DNA introgression. [ABSTRACT FROM AUTHOR]