Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska

Phylogeography of introgression: Spatial and temporal analyses identify two introgression events between brown and American black bears

Brown bears (Ursus arctos) colonized North America from Eurasia in two distinct and temporally separated waves. Once in North America they encountered endemic American black bears (U. americanus) during range expansions from eastern Beringia southwards into the interior of the continent. The establishment of sympatry between these species provided the opportunity for hybridization and introgression, which was previously identified at the species level using D-statistics. Both species have broad spatial ranges that should limit the extent of introgression, such that it is found primarily between sympatric populations. Here, we used range-wide sampling and whole genome sequencing of both bear species to test for spatial variability in introgression. We identified two pulses of introgression between brown and American black bears, and demonstrate the introgressed segments occur across spatially structured lineages in both species. The first pulse occurred 270-120 kya, near the initiation of intraspecific divergence, approximately 99-93 kya, within each species. This pulse occurred as sympatry was established in western North America. The second pulse occurred between western American black bears and North American brown bears and lasted to 9 kya. Introgression was bidirectional and sympatric lineages had more introgressed tracts and a larger proportion of the genome introgressed from the other species. This study advances our phylogeographic understanding of both iconic bear species through investigating the timing of divergence and gene flow as bears expanded and contracted their ranges across North America.

Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones

A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation.

Relationships of Late Pleistocene giant deer as revealed by Sinomegaceros mitogenomes from East Asia

The giant deer, widespread in northern Eurasia during the Late Pleistocene, have been classified as western Megaloceros and eastern Sinomegaceros through morphological studies. While Megaloceros's evolutionary history has been unveiled through mitogenomes, Sinomegaceros remains molecularly unexplored. Herein, we generated mitogenomes of giant deer from East Asia. We find that, in contrast to the morphological differences between Megaloceros and Sinomegaceros, they are mixed in the mitochondrial phylogeny, and Siberian specimens suggest a range contact or overlap between these two groups. Meanwhile, one deep divergent clade and another surviving until 20.1 thousand years ago (ka) were detected in northeastern China, the latter implying this area as a potential refugium during the Last Glacial Maximum (LGM). Moreover, stable isotope analyses indicate correlations between climate-introduced vegetation changes and giant deer extinction. Our study demonstrates the genetic relationship between eastern and western giant deer and explores the promoters of their extirpation in northern East Asia.