Yanhua Qu

• PhD
• Professor at Institute of Zoology, Chinese Academy of Sciences

The study of mutational processes in somatic genomes has gained recent momentum, uncovering a wide array of endogenous and exogenous factors associated with somatic changes. However, the overall landscape of mutational processes in germline mutations across the tree of life and associated evolutionary driving forces are rather unclear. In this stud...

Horseshoe crabs are unique living fossils that have remained almost unaltered through 400 million years of global change. They face rapid worldwide declines under increasing anthropogenic pressure. Using comprehensive geographic and genomic sampling combined with approaches that integrate DNA with environmental and climatic datasets, we assessed th...

While Epstein-Barr virus (EBV) infection is ubiquitous globally, a high-risk EBV subtype associated with the extremely high incidence of nasopharyngeal carcinoma (NPC) was found in southern China, but the evolution history of EBV in humans and the origin of this high-risk subtype remains enigmatic. By obtaining one of the largest datasets of EBV ge...

The use of genetic data to reconstruct systematic relationships has revolutionized our understanding of avian evolution. Morphology-based classifications were often in conflict because of different opinions among scholars about the relative importance of certain phenotypes. The considerable morphological variation observed among birds was codified...

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called ‘plasticity first.’ Herein, we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimen...

Background Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene–Pleistocene boundary. Results Here we investigate the phylogenetic relationships of all species of Prunellidae usin...

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We...

Conservation planning in areas prone to human–wildlife interactions requires strong integration between biodiversity protection and other human society needs. Livestock depredation by felids is one of the most reported human–wildlife conflicts in Tibet, reinforced by expanding rangeland and rebounding of wildlife populations. Tibet harbors the rich...

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species...

Understanding the determinants of the range expansion of invasive alien species is crucial for developing effective prevention and control strategies. Nevertheless, we still lack a global picture of the potential factors influencing the invaded range expansion across taxonomic groups, especially for the world's worst invaders with high ecological a...

Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae...

Climate adaptation and dispersal can determine a species’ response to climate change. However, quantifying how they can mitigate climate change risks remains a challenge. Here we combine ecological genomic, niche modelling and landscape genetic approaches to reveal similar population-level vulnerability for a keystone species and its two beneficiar...

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called “plasticity first”. Herein we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experiment...

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called “plasticity first”. Herein we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experiment...

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called “plasticity followed by genetic change”. Herein we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestr...

Early events in the evolution of an ancestral lineage can shape the adaptive patterns of descendant species, but the evolutionary mechanisms driving initial adaptation from an ancestor remain largely unexplored. High-altitude adaptations have been extensively explored from the viewpoint of protein-coding genes; however, the contribution of noncodin...

Speciation is fundamental for building and maintaining biodiversity. The formation of the highly differentiated genomic regions between diverging taxa has been interpreted as a result of divergence with gene flow, linked selection, and reduction in recombination. It is challenging to unravel these nonexclusive processes in shaping genomic divergenc...

Over the past 40 years, the climate has been changing and human disturbance has increased in the vast Qinghai–Tibet Plateau (QTP). These 2 factors are expected to affect the distribution of a large number of endemic vertebrate species. However, quantitative relationships between range shifts and climate change and human disturbance of these species...

Environmentally heterogeneous mountains provide opportunities for rapid diversification and speciation. The family Prunellidae (accentors) is a group of birds comprising primarily mountain specialists that have recently radiated across the Palearctic region. This rapid diversification poses challenges to resolving their phylogeny. Herein we sequenc...

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called "plasticity followed by genetic change". Herein we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestr...

Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or from genetic swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai-Tibetan P...

Given the current era of rapid biodiversity loss, there is an urgent need to understand the mechanisms driving the biodiversity dynamics in biodiversity hotspots because these results could guide make conservation actions to protect species under threat from rapid environmental changes and extensive human impacts. To achieve this goal, we have orga...

The seasonal migration of birds is a fascinating natural wonder. Avian migratory behavior changes are common and are likely a polygenic process, as avian migration is governed by multiple correlated components with a variable genetic basis. However, the genetic and phenotypic changes involving migration changes are poorly studied. Using one annotat...

The rate of mutation accumulation in germline cells can be affected by cell replication and/or DNA damage, which are further related to life history traits such as generation time and body mass. Leveraging the existing datasets of 233 neoavian bird species, here, we investigated whether generation time and body mass contribute to the interspecific...

The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor,...

Global warming is increasingly exacerbating biodiversity loss. Populations locally adapted to spatially heterogeneous environments may respond differentially to climate change, but this intraspecific variation has only recently been considered when modelling vulnerability under climate change. Here, we incorporate intraspecific variation in genomic...

Aim To investigate how and when allopatric populations of a widely spread mountain bird in New Guinea, Amblyornis macgregoriae, have diversified, how they differ genetically, and how they may respond to future climate conditions. Location New Guinea. Methods Using whole‐genome resequencing data for 26 individuals of A. macgregoriae, we studied ho...

The phenotypic plasticity in responses to short-term stress can provide clues for understanding the adaptive fixation mechanism of genetic variation during long-term exposure to extreme environments. However, few studies have compared short-term stress responses with long-term evolutionary patterns, in particular no interactions between the two pro...

Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively sma...

Significance A reduction in heterozygosity may limit the opportunity for species facing the same selective pressures to evolve parallel adaptation. Examining 19 East Asian tits’ genomes, we find a pattern of lower heterozygosity in western endemics compared with that found in both eastern endemics and widespread taxa, consistent with expectations o...

Aim Species living in a shared environment face similar selective pressures and often evolve adaptive divergence to avoid competition. Quantifying phenotypic divergence and its genetic parallelism among sympatric species is important for understanding of ecologically moderated biodiversity. Here, we integrate ecologic, phenotypic and genomic datase...

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study a...

Genetic diversity is an essential component of biodiversity. Developing robust quantification methods is critically important in depicting the genetic diversity underlying the geographical distributions of species, especially for the sequence data with unequal lengths. Traditional calculation of genetic diversity depends on sequences of equal lengt...

Corticosteroid-binding globulin (CBG) is a high-affinity plasma protein that binds glucocorticoids (GCs) and regulates their biological activities. The structural and functional properties of CBG are crucial to understanding the biological actions of GCs in mediating stress responses and the underlying mechanisms. In response to stress, avian CBGs...

Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships wit...

Significance Harsh conditions in high elevations present strong stresses for organisms. Previous studies targeting phylogenetically distinct species revealed cases of diversified adaptations, but it remains largely unknown how common ancestry contributes to evolution of similar adaptations. Our study based on a species complex (snowfinches) living...

The difficulty of effectively monitoring and managing the environment to achieve conservation of biodiversity is as yet an unsolved conundrum. A project of the Chinese Academy of Sciences has concluded that progress can be made through the use of flagship species for special attention, these being selected using criteria drawn both from conservatio...

Skeletal muscle plays a central role in regulating glucose uptake and body metabolism; however, highland hypoxia is a severe challenge to aerobic metabolism in small endotherms. Therefore, understanding the physiological and genetic convergence of muscle hypoxia tolerance has a potential broad range of medical implications. Here we report and exper...

Strong correlations between species diversity and climate have been widely observed, but the mechanism underlying this relationship is unclear. Here, we explored the causes of the richness-climate relationships among passerine birds in China by integrating tropical conservatism and diversification rate hypotheses using path models. We found that as...

The Ground Tit (Pseudopodoces humilis) has lived on the Qinghai-Tibet Plateau for ∼5.7 million years and has the highest altitudinal distribution among all parids. This species has evolved an elongated beak in response to long-term selection imposed by ground-foraging and cavity-nesting habits, yet the genetic basis for beak elongation remains unkn...

The Ground Tit (Pseudopodoces humilis) has lived on the Qinghai-Tibet Plateau for ~5.7 million years and has the highest altitudinal distribution among all parids. This species has evolved an elongated beak in response to long-term selection imposed by ground-foraging and cavity-nesting habits, yet the genetic basis for beak elongation remains unkn...

The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bo...

Aim The Pleistocene glacial cycles play a prominent role in shaping phylogeographical patterns of organisms, while few studies have focused on the regional difference of glacial effects. By acquiring comprehensive knowledge of the origin, diversification and historical demography of an intensively studied passerine species complex, Great Tit, we ai...

Aim Variation in species diversity among different geographical areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions, and a long time available for the...

Functional traits are the essential phenotypes that underlie an organism's life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals’ ecology, studies of functional variation are often restricted to species‐level comparisons, ignoring critical variation within species. In birds, i...

Background Pectoralis phenotypic variation plays a fundamental role in locomotion and thermogenesis in highland birds. However, its regulatory and metabolic mechanisms remain enigmatic to date. Here, we integrated phenomic, transcriptomic and metabolomic approaches to determine muscle variation and its underpinning mechanisms across altitudinal son...

Background Pectoralis phenotypic variation plays a fundamental role in locomotion and thermogenesis in highland birds. However, its regulatory and metabolic mechanisms remain enigmatic to date. Here, we integrated phenomic, transcriptomic and metabolomic approaches to determine muscle variation and its underpinning mechanisms across altitudinal son...

Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial p...

Background: Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced ge...

In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by 'speciation reversal' or by mitochondrial capture through genet...

High-altitude environments present strong stresses for living organisms, which have driven striking phenotypic and genetic adaptations. While previous studies have revealed multiple genetic adaptations in high-altitude species, how evolutionary history (i.e., phylogenetic background) contributes to similarity in genetic adaptations to high-altitude...

Adaptive convergent evolution, which refers to the same or similar phenotypes produced by species from independent lineages under similar selective pressures, has been widely examined for a long time. Accumulating studies on the adaptive convergent evolution have been reported from many different perspectives (cellular, anatomical, morphological, p...

Complex geological environments and Pleistocene glaciations contribute to speciation. For example, the unique geomorphological configuration and distinct geological evolution of the Qinghai–Tibet Plateau has led to the evolution of many endemic species adapted to a life at the plateau. Most of these endemic birds show no genetic divergence between...

Pleistocene climatic oscillations have played an important role in shaping many species’ current distributions. In recent years, there has been increasing interest in studying the effects of glacial periods on East Asian birds. Integrated approaches allow us to study past distribution range changes due to Pleistocene glaciation, and how these chang...

Background: Feathers with complex and fine structure are hallmark avian integument appendages, which have contributed significantly to the survival and breeding for birds. Here, we aimed to explore the differentiation, morphogenesis and development of diverse feathers in the domestic duck. Results: Transcriptome profiles of skin owing feather fo...

The rollers (Coraciidae) constitute a relative small avian family with ca. 12 species distributed in Africa, western and southern Eurasia, and eastern Australia. In this study we examine the phylogenetic relationships of all species currently recognized in the family, including two taxa whose taxonomic status is currently contested. By using shotgu...

Background/aims: Genomic adaptations to high altitudes have been well studied in the last several years; however, the roles of microRNAs (miRNAs), which are essential modulators of a variety of genes and key cellular processes, have rarely been explored. Here, we explored the interactions between miRNAs and their target genes as an adaptation to h...

When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to...

Background Beak morphology exhibits considerable adaptive plasticity in birds, which results in highly varied or specialized forms in response to variations in ecology and life history. As the only parid species endemic to the Qinghai-Tibet Plateau, the Ground Tit (Parus humilis) has evolved a distinctly long and curved beak from other parids. An i...

The first molecular phylogenetic hypothesis for the possibly extinct pink-headed duck Rhodonessa caryophyllacea unambiguously shows that it belongs to the pochard radiation that also includes the genera Aythya and Netta. It is the sister to all modern-day pochards and belongs to a lineage that branched off from the others more than 2.8 million year...

Previous studies have suggested that bird populations in East Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitoc...

Aim The Sino‐Himalayas have higher species richness than adjacent regions, making them a global biodiversity hotspot. Various mechanisms, including ecological constraints, energetic constraints, diversification rate (DivRate) variation, time‐for‐speciation effect and multiple colonizations, have been posited to explain this pattern. We used pheasan...

Significance We produced a genome-scale dataset from representatives of all placental mammal orders to infer diversification timing relative to the Cretaceous–Paleogene (KPg) boundary. Our sensitivity analyses show that divergence time estimates within placentals are considerably biased by the specific way in which a given dataset is processed. We...

Gene flow and demographic history can play important roles in the adaptive genetic differentiation of species, which is rarely understood in the high-altitude adaptive evolution of birds. To elucidate genetic divergence of populations in the great tit complex (Parus major, P. minor and P. cinereus) at different elevations, we compared the genetic s...

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based...