A5018190918- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Aquatic Ecosystems and Phytoplankton Dynamics
- Protist diversity and phylogeny
- Aquatic Invertebrate Ecology and Behavior
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Corporate Finance and Governance
- Microbial Community Ecology and Physiology
- Methane Hydrates and Related Phenomena
- Banking stability, regulation, efficiency
- Plant and animal studies
- Fish Ecology and Management Studies
- Metabolomics and Mass Spectrometry Studies
- Decision-Making and Behavioral Economics
- Genetic Mapping and Diversity in Plants and Animals
- Microfinance and Financial Inclusion
- International Business and FDI
- Ecology and Vegetation Dynamics Studies
- Economic Growth and Development
- Cancer, Hypoxia, and Metabolism
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Aquatic Ecosystems and Biodiversity
- Identification and Quantification in Food
- Actinomycetales infections and treatment
Central China Normal University
2023-2025
Arizona State University
2019-2023
East China University of Science and Technology
2013-2022
Indiana University Bloomington
2015-2017
Kunming Institute of Zoology
2011-2012
Chinese Academy of Sciences
2011-2012
Jianquan Liu and colleagues report the draft genome sequence of domestic yak, Bos grunniens. Their comparative analyses with low-altitude cattle provide insights into high-altitude adaptation in yak. Domestic yaks (Bos grunniens) meat other necessities for Tibetans living at high altitude on Qinghai-Tibetan Plateau adjacent regions. Comparison between yak closely related taurus) is informative studying animal to altitude. Here, we present a female generated using Illumina-based technology...
Although it is well known that microbial populations can respond adaptively to challenges from antibiotics, empirical difficulties in distinguishing the roles of de novo mutation and natural selection have left several issues unresolved. Here, we explore mutational properties Escherichia coli exposed long-term sublethal levels antibiotic norfloxacin, using a accumulation design combined with whole-genome sequencing replicate lines. The genome-wide rate significantly increases norfloxacin...
Despite evolutionary biology’s obsession with natural selection, few studies have evaluated multigenerational series of patterns selection on a genome-wide scale in populations. Here, we report 10-y population-genomic survey the microcrustacean Daphnia pulex. The genome sequences <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"> <mml:mo>></mml:mo> </mml:math> 800 isolates provide insights into that cannot be obtained from long-term...
Abstract Background Lactic acid bacteria (LAB) are important in the food industry for production of fermented products and human health as commensals gut. However, phylogenetic relationships among LAB species remain under intensive debate owing to disagreements different data sets. Results We performed a analysis based on 232 genes from 28 genome sequences. Regardless tree-building methods used, combined analyses yielded an identical, well-resolved tree topology with strong supports all...
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact effective population size on genome evolution. For this purpose, we present a high quality assembly Daphnia pulex (PA42), and compare first sequenced species (TCO), which was derived an isolate >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at gene level, average amino acid sequence identity 98.8 >60% orthologous proteins identical....
Using data from 83 isolates a single population, the population genomics of microcrustacean Daphnia pulex are described and compared to current knowledge for only other well-studied invertebrate, Drosophila melanogaster These two species quite similar with respect effective sizes mutation rates, although some features recombination appear be different, linkage disequilibrium being elevated at short ([Formula: see text] bp) distances in D. long The study adheres closely expectations under...
Hybridization plays a potentially important role in the origin of obligate parthenogenesis (OP) many organisms. However, it remains controversial whether hybridization directly triggers transition from sexual reproduction to asexuality or hybrid genetic background enables asexual species persist. Furthermore, we know little about specific elements divergent, yet still hybridizing lineages responsible for this and how these are further spread create other OP lineages. In study, address...
Daphnia normally reproduce by cyclical parthenogenesis, with offspring sex being determined environmental cues. However, some females have lost the ability to produce males. Our results demonstrate that this loss of male-producing is controlled a dominant allele at single locus. We identified locus comparing whole-genome sequences 67 nonmale-producing (NMP) and 100 (MP) clones from 5 pulex populations, revealing 132 NMP-linked SNPs 59 indels within 1.1-Mb nonrecombining region on chromosome...
Nonindigenous members of the
The ways in which genetic variation is distributed within and among populations a key determinant of the evolutionary features species. However, most comprehensive studies these have been restricted to subdivision settings known driven by local adaptation, leaving our understanding natural dispersion allelic less than ideal. Here, we present geographic population-genomic analysis 10 freshwater microcrustacean Daphnia pulex, an emerging model system genomics. These exhibit pattern moderate...
Microorganisms play a central role in sustaining soil ecosystems and agriculture, these functions are usually associated with their complex life history. Yet, the regulation evolution of history have remained enigmatic poorly understood, especially protozoa, third most abundant group organisms soil. Here, we explore cosmopolitan species-
Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play crucial role nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces China to preliminarily investigate biodiversity genetic structure Streptomyces soils different dimensions, using recently developed cost-efficient amplicon whole-genome library preparation methods. Amplicon analysis showed that...
Whole-genome sequencing provides lists of genes putative relevance to organismal biology. However, in all metazoans, a large fraction inferred has no known functions, some cases with orthologs related species, and even orthology at the DNA-sequence level often not providing indisputable evidence gene function. A first step towards resolving functional features encyclopedias multicellular species is evaluate tissues which individual are expressed. Here, we report on assays expression for full...
Abstract Despite evolutionary biology’s obsession with natural selection, few studies have evaluated multi-generational series of patterns selection on a genome-wide scale in populations. Here, we report nine-year population-genomic survey the microcrustacean Daphnia pulex. The genome-sequences > 800 isolates provide insights into that cannot be obtained from long-term molecular-evolution studies, including pervasiveness near quasi-neutrality across genome (mean net coefficients zero, but...
Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular evolutionary processes. However, owing to paucity genome-wide data within-individual levels, broad patterns these two forms variation remain poorly understood. Here, we analyze 1,804 complete genome sequences from Daphnia pulex, pulicaria, obtusa. Extensive heteroplasmy is observed D. obtusa, where high level intraclonal divergence...
Colpoda , one of the most widespread ciliated protozoa in soil, are poorly understood regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by loss events, potentially leading streamlining mitogenomes. Surprisingly, while interspecific abound, our population-level mitogenomic study a conserved order within species, offering potential new identification criterion. Phylogenomic analysis traced lineage over 326 million years, revealing...
Phenotypic plasticity, which involves phenotypic transformation in the absence of genetic change, may serve as a strategy for organisms to survive complex and highly fluctuating environments. However, its reaction norm, molecular basis, evolution remain unclear most organisms, especially microbial eukaryotes. In this study, we explored these questions by investigating regulation, plasticity cosmopolitan marine free-living ciliates Glauconema spp., undergo significant changes response food...
Abstract Despite increasing empirical evidence that chromosomal rearrangements may play an important role in adaptive divergence and speciation, the degree to which divergent genomic regions are associated with remains unclear. In this study, we provide first whole-genome analyses of ecological speciation evolution a Daphnia species complex, using chromosome-scale assemblies natural-population sequencing recently diverged pair, pulicaria pulex , occupy distinct yet overlapping habitats North...
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well genomic deterioration. Daphnia pulex serves useful model for studying TE dynamics potential cause and/or consequence asexuality. We analyzed insertion polymorphisms TEs 20 sexual asexual isolates D. across North American from their available whole-genome sequencing data. Our results show that the total fraction derived sequences is not...
Abstract By revealing the influence of recombinational activity beyond what can be achieved with controlled crosses, measures linkage disequilibrium (LD) in natural populations provide a powerful means defining landscape within which genes evolve. In one most comprehensive studies this sort ever performed, involving whole-genome analyses on nearly 1,000 individuals cyclically parthenogenetic microcrustacean Daphnia pulex, data suggest relatively uniform pattern recombination across genome....
Abstract Although obligately asexual lineages are thought to experience selective disadvantages associated with reduced efficiency of fixing beneficial mutations and purging deleterious mutations, such phylogenetically geographically widespread. However, despite several genome-wide association studies, little is known about the genetic elements underlying origin obligate asexuality how they spread. Because many have hybrid origins, it has been suggested that caused by unbalanced expression...
Abstract The field of genomics has ushered in new methods for studying molecular-genetic variation natural populations. However, most population-genomic studies still rely on small sample sizes (typically, &lt;100 individuals) from single time points, leaving considerable uncertainties with respect to the behavior relatively young (and rare) alleles and, owing large sampling variance measures variation, specific gene targets unusually strong selection. Genomic sequences ∼1,700 haplotypes...