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Red deer (Cervus elaphus/hanglu/canadensis) are a group of closely-related species that survived through the Last Glacial period in Eurasia and expanded into North America. The evolutionary modes of red deer in Europe through glacial and interglacial cycles have been established relatively well based on both modern and ancient genomes, while the evolutionary and migratory history of red deer in Asia are not so clear. Northern China, as the southern border of their current distribution, is a significant area for exploring the evolution of wapitoids (Cervus canadensis). Here, we constructed six mitochondrial genomes (lengths of 13,282–16,306 bp) from Late Pleistocene fossil cervid materials in Northeastern China, and four modern complete mitochondrial DNA sequences (16,798–16943 bp) from Northern China. Phylogenetic analyses suggest four clades in wapitoids, with our new individuals clustered into three out of the four clades. BEAST analysis indicates that the divergence between elaphoids (including Cervus elaphus and Cervus hanglu) and the complex of 'wapitoids + sika deer (Cervus nippon)' occurred at approximately 1.37 million years ago (Ma, 95%Cl: 1.64–1.15 Ma). Bayesian skyline plots (BSPs) show that the effective maternal population size of wapitoids had a slight and stable expansion between Marine isotope stages (MIS) 7–3, and then shrank from the beginning of the Last Glacial Maximum (LGM). Combined with the divergence dates, population dynamics, and fossil findings in Northern China, we infer that after wapitoids migrated eastward from Central Asia to Northeastern Asia, they had multiple migrations southward into Northern China. The current distribution of wapitoids in Northern China was likely shaped by these migrations as well as habitat fragmentation. Meanwhile, the radiocarbon dates of ancient individuals indicate that the Northeast China Plain, located at the same latitude as European refugia, may have provided a refugium for megafaunal species such as red deer to survive the LGM. • First combined sampling of both ancient and extant mitogenomes of wapitoids in China. • Demonstrating habitat fragmentation or multiple migratory events of wapitoids in Northern China. • Indicating a possible refuge for megafauna species in Northeastern China in LGM. [ABSTRACT FROM AUTHOR]

• In this study, we identified the genetic diversity and phylogenetic relationships of sika deer. • Based on CYTB gene, the sika deer was divided into four lineages. • Our research would provide scientific data for the evaluation, protection, and utilization of sika deer resources. The genetic diversity and phylogenetic relationships of sika deer of different subspecies are uncertain. In order to explore the phylogenetic relationship of different sika deer subspecies, this study used a wider sample collection to analyze mitochondrial sequences and nuclear microsatellites of sika deer. The full lengths of cytochrome-b gene of 134 sika deer were sequenced, and 16 haplotypes were obtained. Based on phylogenetic and haplotype networks analysis, the sika deer was not clustered according to subspecies but was divided into four lineages. Lineage I includes individuals from C.n.kopschi, C.n.sichuanicus , and C.n.hortulorum subspecies; Lineage II includes individuals from C.n.hortulorum subspecies; Lineage III includes individuals from C.n.centralis , C.n.yakushime , C.n.mageshimae , and C.n.keramae subspecies, namely southern Japanese population; Lineage IV includes individuals from C.n.centralis and C.n.yesoensis subspecies, namely northern Japanese population. The microsatellite analysis showed that the sika deer in China and Japan originated independently. The three subspecies of China have significant genetic differentiation, while the three subspecies of Japan have no significant differentiation. This study provides reference for the research of genetic diversity and phylogenetic relationship of sika deer, and also provides scientific data for the evaluation, protection, and utilization of sika deer resources. [ABSTRACT FROM AUTHOR]