Dynamic evolution of transposable elements,demographic history,and gene content of paleognathous birds

Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.

Genetic structure and recent population demographic history of Taihangshan macaque(Macaca mulatta tcheliensis),North China

Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will benefit the understand-ing of the long-term survival of a species.The Taihangshan macaque(Macaca mulatta tcheliensis),a subspecies of rhesus macaque(Macaca mulatta),is endemic to China and currently restricted to southern Mt.Taihangshan area.Herein,we evaluated the genetic diversity,population structure,and demographic history of this subspecies using mitochondrial(Cytb and high variable region I:HVR I)and nuclear markers(microsatellite loci)of 131 in-dividuals collected from 9 localities covering the distribution range of this subspecies.Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades,THS-east and THS-west.Low genetic diversity(π:0.00266±0.00016)but high haplotype diversity(Hd:0.80352±0.015)were detected in the Taihangshan macaques,particularly in THS-east.Analyses of demographic history suggested that the Taihangshan macaques experiencedfirst a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years.We suggest that bridging the neighbor populations(i.e.setting corridors)would facilitate the male-mediated geneflow and subsequently increase the genetic diversity of the Taihangshan macaque populations.

Senome-scale analysis of demographic history and adaptive selection

One of the main topics in population genetics is identi- fication of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and exclude it in selection identification. With the rapid progress in genomics in the past decade, vast genome- scale variations are available for population genetic analysis, which however requires more sophisticated models to infer species＇ demographic history and robust methods to detect local adaptation. Here we aim to review what have been achieved in the fields of demographic modeling and selection detection. We summarize their rationales, implementations, and some classical applications. We also propose that some widely-used methods can be improved in both theoreti- cal and practical aspects in near future.

Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation

Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat.Uncovering the landscape of genetic variations in T.urartu will help us understand the evolutionary and polyploid characteristics of wheat.Here,we investigated the population genomics of T.urartu by genome-wide sequencing of 59 representative accessions collected around the world.A total of 42.2 million highquality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome.The ancient T.urartu population experienced a significant reduction in effective population size(Ne)from3000000 to140000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period.A map of allelic drift paths displayed splits and mixtures between different geographic groups,and a strong genetic drift towards hexaploid wheat was also observed,indicating that the direct donor of the A subgenome originated from northwestern Syria.Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses.A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T.urartu ecotype groups.Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomicsenabled improvements in wheat breeding.

Wind-dispersed seeds blur phylogeographic breaks:The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin

The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits.Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants.Here,we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa,a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China.We sequenced and analyzed three plastid DNA fragments(ptDNA) and eight nuclear microsatellites(nSSRs) of 265 individuals of P.lasiocarpa from 21 populations spanning the entire distribution range.Distribution patterns based on nSSR data revealed that there are three genetic groups in P.lasiocarpa.This is consistent with the three phylogeographic breaks(Sichuan Basin,the Kaiyong Line and the 105°E line),where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups.However,the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks,and wind-dispersed seeds may be one of the main contributing factors.Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial.A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages.These results indicate that biological traits are likely to affect the evolutionary history of plants,and that nuclear molecular markers,which experience higher levels of gene flow,might be better indicators of phylogeographic breaks.

Insights into genetic variation and demographic history of sharpnose rays:examinations of three species of Telatrygon(Elasmobranchii,Dasyatidae)from the Indo-West Pacific

Coastal and demersal chondrichthyans(sharks,rays,and skates)are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology.Population genetic studies investigating the extent to which demographic history shapes the genetic structure of thesefishes are rare.Here,we combined mitochondrial DNA(Cytb and ND2)and 8 nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the 3 Indo-West Pacific species of sharpnose rays(Telatrygon zugei,Telatrygon biasa,and Trygon crozieri).High levels of genetic variation both within and between species were identified.Phylogenetic analysis partitioned haplotypes into 2 lineages supporting divergence of T.zugei from T.crozieri and T.biasa during the Pleistocene.Furthermore,microsatellite-based clustering analyses identified 4 genetic groups(i.e.T.zugei from Japan,T.zugei from coastal China,T.biasa from Gulf of Thailand,and T.crozieri from the Andaman Sea).Measurements of genetic differentiation also support these 4 groups.Additionally,Pleistocene demographic expansions were examined in all genetic groups.The climate oscillations and current hydrologic cycles in the Indo-West Pacific appear to coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays.Considering the species group has,until recently,been thought to be one species,these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity.

Genetic diversity,population structure and demographic history of Dugesia japonica in Taihang Mountains

The freshwater planarian Dugesia japonica has become a model organism in regeneration biology and toxicology due to its powerful regeneration capability and highly chemical sensitivity.Nonetheless,little is known about its evolutionary history and demographics.Taihang Mountains is the natural boundary between the Loess Plateau and the North China Plain,and is considered as one of the important priority areas for biodiversity conservation in China.In order to figure out the genetic diversity,population structure and demographic history of D.japonica in Taihang Mountains,a study based on the mitochondrial COI from 116 individuals sampled across 20 populations has been conducted.The results showed that the 116 COI sequences yielded 32 haplotypes,including 8 shared haplotypes and 24 private ones.The overall haplotype diversity(Hd)and nucleotide diversity(π)were 0.920 and 0.083,respectively.Even though the AMOVA results suggested that the genetic variation among populations was significant(FST=0.480,P<0.01),the phylogeny and haplotype network analysis based on 32 haplotypes revealed no obvious phylogeographic pattern.Furthermore,the significantly positive values of neutrality test(Tajima’s D=2.596,P<0.05;Fu’s Fs=2.769,P<0.01)together with the multimodal arrangement of mismatch distribution indicated that D.japonica in Taihang Mountains would have been undergoing population decline.We hope these findings will arouse conservation and management strategy regarding freshwater planarians and contribute to the biodiversity in the long run.

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.

Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load

Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.

Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses

Although domestic ducks have been important poultry species throughout human history,their origin remains enigmatic,with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s)of domestic ducks.Here,we analyzed 118 whole genomes from mallard,Chinese spotbilled,and domestic ducks to reconstruct their evolutionary history.We found pervasive introgression patterns among these duck populations.Furthermore,we showed that domestic ducks separated from mallard and Chinese spotbilled ducks nearly 38 thousand years ago(kya)and 54 kya,respectively,which is considerably outside the time period of presumed duck domestication.Thus,our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled,rather than from present-day mallard and/or Chinese spot-billed ducks,as previously thought.Overall,this study provides new insight into the complex evolution of ducks.

Population genetic variation and historical dynamics of the natural enemy insect Propylea japonica(Coleoptera: Coccinellidae) in China

Propylea japonica(Coleoptera:Coccinellidae)is a natural enemy insect with a wide range of predation in Chinese mainland and is commonly used in pest management.However,its genetic pattern(i.e.,genetic variation,genetic structure,and historical population dynamics)is still unclear,impeding the development of biological control of insect pests.Population genetic research has the potential to optimize strategies at different stages of the biological control processes.This study used 23 nuclear microsatellite sites and mitochondrial COI genes to investigate the population genetics of Propylea japonica based on 462 specimens collected from 30 sampling sites in China.The microsatellite dataset showed a moderate level of genetic diversity,but the mitochondrial genes showed a high level of genetic diversity.Populations from the Yellow River basin were more genetically diverse than those in the Yangtze River basin.Propylea japonica has not yet formed a significant genealogical structure in China,but there was a population structure signal to some extent,which may be caused by frequent gene flow between populations.The species has experienced population expansion after a bottleneck,potentially thanks to the tri-trophic plant–insect–natural enemy relationship.Knowledge of population genetics is of importance in using predators to control pests.Our study complements existing knowledge of an important natural predator in agroecosystems through estimating its genetic diversity and population differentiation and speculating about historical dynamics.

First genetic assessment of brackish water polychaete Tylorrhynchus heterochaetus: mitochondrial CO/sequences reveal strong genetic differentiation and population expansion in samples collected from southeast China and north Vietnam

Tylorrhynchus heterochaetus is a widespread benthic polychaete worm found in coastal brackish waters of the west Pacific.It has high ecological and economic value as a biomarker of water quality and as a high-quality feed in aquaculture and fisheries and is considered a delicacy in some areas of Asia.However,it has experienced a marked reduction in recent years due to overexploitation as well as changes in the environment and climate.Here,to comprehensively understand its genetic background and thus provide insights for better conservation and utilization of this species,we assessed the genetic variability and demographic history of T.heterochaetus individuals sampled from eight locations along the coasts of southeast China and north Vietnam based on mitochondrial cytochrome c oxidase I(COI)sequences.We observed high haplotype diversity(Hd),with an average of 0.926,but relatively low nucleotide diversity(π),with a mean of 0.032 across all samples.A total of 94 polymorphic sites and 85 haplotypes were identified among 320 individuals.The pairwise genetic distances among haplotypes ranged from 0.001 to 0.067,with the high intraspecific divergence possibly reflecting geographic isolation and gene pool fragmentation.Significant genetic structures were revealed among the studied locations;specifically,the eight locations could be treated as six genetically different populations based on pairwiseΦST results(0.026–0.951,P<0.01).A significant pattern of isolation-by-distance was detected between the genetic and geographic distances(r=0.873,P=0.001).Three geographic lineages were defined based on phylogenetic tree and network analyses of COI haplotypes.AMOVA results indicated that genetic variations mainly occurred among the three lineages(89.96%).Tests of neutrality and mismatch distribution suggested that T.heterochaetus underwent recent population expansion.These results provide the first report on the genetic status of T.heterochaetus and will be valuable for the management of genetic resources and better understanding of the ecology and evolution in this species.

Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques(genus Macaca)

The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification(about five million years ago)and rapid radiation of constituent species.To understand evolutionary gene flow in macaques,we sequenced four whole genomes(two M.arctoides and two M.thibetana)and combined them with publicly available macaque genome data for genome-wide analyses.We analyzed 14 individuals from nine Macaca species covering all Asian macaque species groups and detected extensive gene flow signals,with the strongest signals between the fascicularis and silenus species groups.Notably,we detected bidirectional gene flow between M.fascicularis and M.nemestrina.The estimated proportion of the genome inherited via gene flow between the two species was 6.19%.However,the introgression signals found among studied island species,such as Sulawesi macaques and M.fuscata,and other species were largely attributed to the genomic similarity of closely related species or ancestral introgression.Furthermore,gene flow signals varied in individuals of the same species(M.arctoides,M.fascicularis,M.mulatta,M.nemestrina and M.thibetana),suggesting very recent gene flow after the populations split.Pairwise sequentially Markovian coalescence(PSMC)analysis showed all macaques experienced a bottleneck five million years ago,after which different species exhibited different fluctuations in demographic history trajectories,implying they have experienced complicated environmental variation and climate change.These results should help improve our understanding of the complicated evolutionary history of macaques,particularly introgressive gene flow.

Comparative population genomics reveals glacial cycles to drive diversifications in tropical montane birds(Aves,Timaliidae)

Many bird species are specialized to live in the broadleaved,evergreen forests in the mountain regions in Southeast Asia.These mountain habitats are not continuously distributed as the different mountain areas are separated by lowlands,which has restricted gene flow and thus contributed to the high biological diversity in this region.The degree of connectivity between mountain areas has fluctuated with the Pleistocene glacial cycles,being largest during the glaciations when the mountain forests spread to lower elevations.Here we study how the intermittent periods of restricted gene flow and connectivity between the populations of five montane species of babblers(Aves,Timaliidae)in Vietnam may be traced in their genomes.The results suggest that the babbler species in the Central Highlands have been isolated from their sister-populations in northern Vietnam for between ca.585 and 380 ky.For two species with populations in both the Central Highlands and the Da Lat region,we found that these split at more or less the same time(440–340 kya).We also found a significant statistical correlation between the time of the splits of these populations and the lowest altitude at which they are known to occur(no similar correlation was found with the geographic distances between populations).The populations in northern Vietnam show higher genetic variation than their counterparts in South-Central Vietnam,supporting the postulate that smaller populations may have lower genetic variation than larger.In accordance with this,we found the lowest genetic variation in the two species with the smallest populations in the Central Highlands.These two populations also show low levels of genomic heterozygosity.Our results show that the south-central populations of the studied babbler species are genetically distinct from their sister-populations in northern Vietnam,providing additional argument for the long-term protection of the evergreen mountain forests in Southeast Asia.

Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau

Most species have clearly defined distribution ranges and ecological niches.The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are,however,less clearly defined.This study investigated the genetic structure and clines in Pinus densata,a pine of hybrid origin on the southeastern Tibetan Plateau,to gain an understanding of the contemporary dynamics of species barriers.We analyzed genetic diversity in a range-wide collection of P.densata and representative populations of its progenitors,Pinus tabuliformis and Pinus yunnanensis,using exome capture sequencing.We detected four distinct genetic groups within P.densata that reflect its migration history and major gene-flow barriers across the landscape.The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories.Interestingly,population sizes rebounded rapidly during interglacial periods,suggesting persistence and resilience of the species during the Quaternary ice age.In the contact zone between P.densata and P.yunnanensis,3.36%of the analyzed loci(57849)showed exceptional patterns of introgression,suggesting their potential roles in either adaptive introgression or reproductive isolation.These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation.This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition.Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.

An instantaneous coalescent method insensitive to population structure

Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates.To develop a coalescent method unhampered by population structure,we perform two analyses.First,we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure.Second,motivated by this finding,we propose a new coalescent method:i-coalescent analysis.The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles.Using simulated data,we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations,although we find this method often requires larger sample sizes for structured populations than for panmictic populations.Overall,our results indicate i-coalescent analysis to be a useful tool,especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.

Models, methods and tools for ancestry inference and admixture analysis

Background： Genetic admixture refers to the process or consequence of interbreeding between two or more previously isolated populations within a species. Compared to many other evolutionary driving forces such as mutations, genetic drift, and natural selection, genetic admixture is a quick mechanism for shaping population genomie diversity. In particular, admixture results in ＂recombination＂ of genetic variants that have been fixed in different populations, which has many evolutionary and medical implications. Results： However, it is challenging to accurately reconstruct population admixture history and to understand of population admixture dynamics. In this review, we provide an overview of models, methods, and tools for ancestry inference and admixture analysis. Conclusions： Many methods and tools used for admixture analysis were originally developed to analyze human data, but these methods can also be directly applied and/or slightly modified to study non-human species as well.