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Since Darwin's era, speciation has been one of the most central issues in evolutionary biology studies. Understanding the processes of species origin is crucial in deepening our understanding of the formation of species biodiversity, which is essential for their protections. However, speciation research has been challenging due to the rather complex evolutionary histories of many extant species. In recent years, with the continuous advancements in genomic sequencing techniques, significant advances have been achieved in the field of speciation researches. In this review, we overview speciation study advances, especially in the concepts and latest developments in research methods for studying speciation in the genomic era, encompassing the major research aspects: species delimitation, bifurcating speciation, hybrid speciation, polyploid speciation, reproductive isolation genes and speciation genes. Furthermore, we discuss the limitations of these studies and methods. Finally, we provide the outlook on the future challenges and directions in speciation researches.

The northern part of Asia, including Siberia, the Mongolian Plateau, and northern China, is not only a crossroads for population exchange on the Eurasian continent but also an important bridge connecting the American continent. This region holds a unique and irreplaceable significance in exploring the origins of humanity, tracking human migration routes, and elucidating evolutionary mechanisms. Despite the limited number of samples unearthed, varying preservation conditions, and constraints of technical means, our understanding of the interactions among populations in northern Asia is still in its infancy. However, the development of high-throughput sequencing technology and its advancement in ancient DNA research have provided us with a new perspective for delving into the genetic history of ancient populations from a molecular level. In this review, we synthesize the changes in the genetic structure of ancient populations in different stages of northern Asia, aiming to reveal the patterns of interaction among ancient populations in this region, the evolutionary process of their genetic structure, and their genetic contributions to modern populations. It will also discuss the adaptive strategies of humans in response to extreme natural conditions. This will not only deepen our understanding of the origins and migration processes of humanity but also provide a solid foundation for studying the evolutionary mechanisms and adaptive strategies of humans under environmental selective pressures.

Over the past decade, the continuous development of ancient genomic technology and research has significantly advanced our understanding of human history. Since 2017, large-scale studies of ancient human genomes in East Asia, particularly in China, have emerged, resulting in a wealth of ancient genomic data from various time periods and locations, which has provided new insights into the genetic history of East Asian populations over tens of thousands of years. Especially since 2022, there emerged a series of new research progresses in the genetic histories of the northern and southern Chinese populations within the past 10,000 years. However, there is currently no systematic review focused on these recent ancient genomic studies in East Asia. Therefore, this article emphasizes the study of ancient human genomes in China and systematically reviews the genetic patterns and migration history of populations in East Asia since the Late Paleolithic. Existing research indicates that by at least 19,000 years ago, there was a north-south differentiation among ancient East Asian populations, leading to different genetic lineages divided by the Qinling-Huaihe line. Gene flow and interactions between northern and southern East Asians began in the Early Neolithic and were further strengthened from the Mid-Neolithic. By the historical period, northern East Asian ancestry played a profound role in the genetic components of southern populations, shaping the genetic structure of present-day Chinese populations. Throughout this process, ancient populations in northern and southern China also engaged in extensive interactions through coastal and inland routes with populations from surrounding regions, including Siberia, Japan, Korea, Southeast Asia, and Pacific islands, playing a crucial role in the formation of different linguistic groups. These studies have charted the evolutionary and interaction history of East Asian populations over tens of thousands of years; yet, many unresolved mysteries remain. Further exploration is needed through ancient genomic data from additional time periods and broader geographic areas to facilitate a more comprehensive and detailed investigation, thereby advancing related scientific questions.

Speciation research represents our thinking and exploration about how new species are generated and maintained, and it is one of the most important parts of evolutionary biology. Revealing new species formation modes, processes of reproductive isolation establishment and their intrinsic genetic mechanisms, are not only important issues and primary tasks in the field of speciation, but also the key clues for our understandings about the species diversity in nature. Here, by focusing on animal groups, we first introduced different definitions of species concept, and then summarized present research progress and important breakthroughs made in the speciation modes and molecular mechanism of reproductive isolation. We also pointed out some limitations in current studies. Finally, we discuss the potential opportunities and new breakthroughs that can be made in the future studies of animal speciation.

Due to the unique geographical features of large numbers, isolated by water and diverse formation histories, islands have become natural laboratories for ecological and evolutionary research. Islands have a high proportion of endemic species and disharmony in representing the species compared with that in the continent, which provides a good opportunity to explore the formation of island biodiversity. In this review, we focuse on island ecosystems and describes the progress of research in island biogeography in recent years from three aspects: formation, maintenance, and loss of island biodiversity. First, we take several representative island systems in the world as examples to introduce the formation mechanism of island biodiversity from species dispersal and immigration, population establishment and selection, species evolution and adaptive radiation. Based on the Equilibrium Theory of Island Biogeography, we then review the species-area relationship and species-isolation relationship and focus on the research progress in community assembly, including Diamond's rule, nestedness pattern, the framework of community structure of island biota, and species interactions on islands. We also discuss the high extinction risks of island species threatened from natural and human disturbances, especially from the impact of habitat loss and change, climate change, alien species invasion and the synergistic effect of these factors on the loss of island biodiversity. Finally, based on the status of island biodiversity, we summarized the current conservation practices for island biodiversity and possible research frontiers in island biogeographic studies.

It has been more than 40 years since the beginning of exploring the genetic composition of ancient organisms from the perspective of ancient DNA. In the recent 20 years, with the development and application of high-throughput sequencing technology platforms and the improved efficiency of retrieving highly fragmented DNA molecules, ancient DNA research moved forward to a brand-new era of deep-time paleogenomics. It not only solved many controversial phylogenetic problems, enriched the migration and evolution details of various organisms including humans, but also launched exploration of the molecular responses to climate changes in terms of "whole genomic-big data-multi-species" level. Moreover, it expanded the sample age from no more than 100,000 years to the Early Pleistocene, ~2 million years ago. Recently, Chinese scientists have made many influential breakthroughs in evolution and migration integration of East Asian populations and thus filled an important gap in the evolutionary process of modern human. Compared to the situation in human paleogenomic studies, less attention has been paid to the study of ancient DNA from vertebrates remains. In this review, we introduce a series of advances in ancient DNA investigations of large mammals in Late Quaternary in China, summarize the research breakthroughs in revealing the systematic evolutionary relationship between ancient and extant groups, gene flow, and molecular responses of mammalian populations to climate change, and explore the opportunities and key challenges in the field of mammalian paleogenomics.

Being the most magnificent plateau in elevation and size on Earth, the Qinghai-Tibet Plateau has a profound impact on biodiversity due to the unique geographic and climatic conditions. Here we review the speciation patterns and genetic diversity of the birds from the Qinghai-Tibet Plateau in relation to the geological history and climatic changes. First, the uplift of the Qinghai-Tibet Plateau forms a geographic barrier and promotes interspecific and intraspecific genetic differentiation. Second, the uplift of the Qinghai-Tibet Plateau has provided new ecological niches for many endemic birds and facilitated their speciation. Third, the emigration and immigration of bird species between the Qinghai-Tibet Plateau and adjacent zoological regions have promoted species divergence, colonization and dispersal. Furthermore, Pleistocene glaciations and associated climate change drive postglacial colonization and lead to secondary contact, which influenced the genetic divergence of the conspecific populations and sister species. The multi-omics approach has increasingly been used in the studies on the ecological adaptive evolution of birds in Qinghai-Tibet Plateau. Future studies should focus on the role of geological and climatic factors in species differentiation, develop integrative approach with multi-omics methods, and explore the ecological mechanisms of high-elevation adaptation of plateau species. As an important region for biodiversity conservation, more efforts should be implemented to maintain the stability and sustainability of the Qinghai-Tibet Plateau and its ecosystem in light of global change.

The Yugur people represent one of the ethnic groups residing within the Hexi Corridor, distinguishable by their small population size, linguistic diversity, intricate ancestral components, serving as a quintessential exemplar of the populations inhabiting this corridor. There are still many controversial issues in the academic community regarding the origin, migration, and formation process of the Yugur. In this study, we explored the formation process of the Yugur from the perspective of molecular anthropology, based on the paternal genetic characteristics of the Yugur people. And the study will synthesize multiple disciplines, encompassing ethnology, history and linguistics, in order to offer a thorough analysis. Within this research endeavor, a high-resolution kit comprising 35 Y-STRs was employed to examine 237 male specimens from the Yugur people in Gansu province. Y-SNP haplogroups were deduced through the utilization of Y-STR data. The paternal genetic data from diverse populations documented in published literature were merged to construct a 16 Y-STR dataset, a 25 Y-STR dataset, and a dataset detailing haplogroup frequencies. In this study, we employed haplotype network analysis, principal component analysis, multidimensional scaling analysis, phylogenetic tree construction, and genetic distance calculations to delve into the genetic structure, haplotype distribution, and genetic relationship with neighboring populations of the Yugur people. The findings of this study reveal that the Yugur people are a blend of ancestral lineages from both Eastern and Western Eurasian origins, with approximately 13% of their genetic component traced back to Western Eurasian populations. The Yugur people in Gansu province exhibits a more intimate genetic relationship with the Han, Tibetan, and Mongolian populations inhabiting nearby regions, while showing distinct genetic differences with Turkic-speaking groups like the Uyghur. Based on the merged data, we identified Q1b1a3-L330 and R1a1a-M17 shared with Turkic-speaking people, C2a1a1-F1756, C2a1a3-M504, C2a1a3a-F3796, C2a1a2-M48 and C2b1a1a1a-M407 shared with Mongolic-speaking people, D1a1a-M15 and D1a1b1-P47 shared with Tibetans, and multiple paternal lineages shared with Han people, which are the main paternal lineages of Yugur people, indicating multiple ancestral components and complex origins of Yugur. In this study, we provided a clearer genetic landscape which further supports the formation process and population characteristics of the Yugur people recorded in history, ethnology, and linguistics, and lays the foundation for more detailed studies on population genetics and forensic genetics in the future.

Solute carrier 25 member 21 (SLC25A21) serves as an oxodicarboxylate carrier, which mainly conveys 2-oxoadipate from the cytoplasm to the mitochondria via a reverse exchange mechanism. Previous studies have indicated that the capacity for glucose consumption is significantly enhanced in 3T3-L1 cells overexpressing SLC25A21. In this study, we upregulate SLC25A21 in 3T3-L1 cells to further probe into the downstream key metabolic genes of SLC25A21. Through high-throughput sequencing combined with bioinformatics analysis, differentially expressed genes are obtained, and the expression of key genes is verified by qRT-PCR. The results demonstrat that: (1) There are 26 up-regulated genes and 66 down-regulated genes in the adipocytes overexpressing SLC25A21; (2) GO (gene ontology) analysis indicates that the biological functions of differentially expressed genes are predominantly involved in lipid synthesis and metabolism, and KEGG (Kyoto encyclopedia of genes and genomes) and GSEA (gene set enrichment analysis) analyses reveal that differentially expressed genes are mainly concentrated in sphingolipid metabolism, secretion and synthesis of insulin and glucagon-like peptide 1; (3) By means of cytoHubba, 10 key genes with the highest scores, such as GRB2, SOS1, SHC1, CBL, HRAS, SOS2, EGFR, MET, PLCG2 and KRAS, were screened out and they are mainly involved in the sugar and lipid metabolism processes of cells; (4) SLC25A21 is overexpressed in adipocytes, and the qRT-PCR verification results show that the mRNA expression levels of other genes increased correspondingly, except for KRAS expression, which exhibits no significant change. These results provide a theoretical basis for further investigations on the role and mechanism of SLC25A21 in the process of glucose and lipid metabolism.

Eggshell colors have a significant effect on sale of eggs. The aim of this study is to identify sequence variants associated with color variation of chicken brown eggs in the ABCG2, a protoporphyrin transport-related gene. Three successive eggs were collected from each of 381 Lueyang black-boned hens at the 31 weeks old. Eggshell color was quantified via the L*a*b color space. g.18378442T>C (a non-synonymous mutation C21R), g.18383682A>G and g.18391548A>T were genotyped via the MassARRAY platform. The associations of genotypes with color indexes were tested by one-way ANOVA. The conservation of the C21R locus was analyzed by multiple alignment of 52 avian genomes from the UCSC database. We predicted 3D structures of ABCG2 with C²¹ and R²¹ by homology modelling using the MODELLER program to analyze effect of C21R on protein structures. Results showed that g.18378442T>C was significantly associated with L and b values. The L value (75.3±4.0) of CC was significantly lower than ones of CT (76.6±4.3) and TT (78.0±4.4) genotypes. The b value (16.2±3.5) of CC was significantly higher than ones of CT (15.7±3.6) and TT (15.7±3.6). g.18383682A>G was only associated with the L value (P<0.05). There was no any association between g.18391548A>T and three color indexes (P>0.05)。The C²¹ was completely conserved among 45 bird species. In contrast, the R²¹ was only present in two species of Psittaciformes. Structure comparisons showed that C21R potentially cause 468 structure alternations, of which 49.6% belong to hydrogen bond alternations, 38.8% for solvent accessible, 8.1% for positive φ angle and 3.5% for changes of secondary structures. In conclusion, this study identifies C21R as a molecular marker that is associated with color variation of chicken brown eggs and has a potential effect on protein structures. The CC genotype of C21R is associated with dark brown color and the TT for light brown.