Phylogenetic Principal Component Analysis Research Articles

BIOINFORMATICS AND MOLECULAR ANALYSES IDENTIFIED THE CONTROL REGION AS THE MOST POWERFUL MITOGENOMIC MARKER FOR DISTINGUISHING THE MAIN MATERNAL HAPLOGROUPS IN GOATS

Identification of genetic markers to distinguish animals within and between species demands extensive genomic and bioinformatics investigation. Previous studies have not carefully taken into consideration the effect of mitogenomic components on the genetic differentiation of the maternal lineages in goats. As a precaution, the complete goat mitogenome was downloaded from the NCBI database and used in the current study to assess the effects of the choice of mitogenomic fragments on phylogenetic studies and to identify any potential polymorphic region by which the main maternal haplogroups of goats can be classified. Phylogenetic results confirmed that all 13 individual mitochondrial protein-coding genes and 2 ribosomal genes are not applicable to differentiate the maternal lineages. Instead, a single novel polymorphic region with a length of 756 bp within the control region was successfully amplified by newly designed primers. Both phylogenetic analysis and principal components analysis of the sequenced mitogenomic region of the mtDNA control region efficiently differentiated the main maternal haplogroups in goats. Higher numbers of polymorphic sites were found in the control region and the mitogenomic marker region. Highly significant correlations were discovered between the polymorphic sites and the length of each individual mitogenomic component. Our results demonstrate useful guidance and cautionary notes for researchers who are interested in the investigation of genetic diversity in animal species using mtDNA sequences. The bioinformatics and molecular methods used herein can be powerful in selecting a minimum amount of data using PCR amplification when the entire sequences of the mitogenome are unavailable.

Gymnosperms demonstrate patterns of fine‐root trait coordination consistent with the global root economics space

Abstract Gymnosperms encompass a diverse group of mostly woody plants with high ecological and economic value, yet little is known about the scope and organization of fine‐root trait diversity among gymnosperms due to the undersampling of most gymnosperm families and the dominance of angiosperm groups in recent syntheses. New and existing data were compiled for morphological traits (root diameter, length, tissue density, specific root length [SRL] and specific root area [SRA]), the architectural trait branching ratio, root nitrogen content [N] and mycorrhizal colonization. We used phylogenetic least squares regression and principal component analysis to determine trait–trait relationships and coordination across 66 species, representing 11 of the 12 extant gymnosperm families from boreal, temperate, subtropical and tropical biomes. Finally, we compared the relationship between family divergence time and mean trait values to determine whether evolutionary history structured variation in fine‐root traits within the gymnosperm phylogeny. Wide variation in gymnosperm root traits could be largely captured by two primary axes of variation defined by SRL and diameter, and root tissue density and root nitrogen, respectively. However, individual root length and SRA each had significant correlations with traits defining both main axes of variation. Neither mycorrhizal colonization nor root branching ratio were closely related to other traits. We did not observe a directional evolution of mean trait values from older to more recently diverged gymnosperm families. Synthesis. Despite their unique evolutionary history, gymnosperms display a root economic space similar to that identified in angiosperms, likely reflecting common constraints on plants adapting to diverse environments in both groups. These findings provide greater confidence that patterns observed in broad syntheses justly capture patterns of trait diversity among multiple, distinct lineages. Additionally, independence between root architecture and other traits may support greater diversity in below‐ground resource acquisition strategies. Unlike angiosperms, there were no clear trends towards increasingly thin roots over evolutionary time, possibly because of lower diversification rates or unique biogeographic history among gymnosperms, though additional observations are needed to more richly test evolutionary trends among gymnosperms.

Forensic parameters and population analysis of 21 autosomal STR loci in the Wuhu Han population from Anhui Province, East China

Background At present, there are no available genetic data on the AGCU EX22 Kit from the Wuhu Han population. Aim This study investigates the applicability of the AGCU EX22 kit, designed for the Chinese population for forensic analysis and population genetics of the Wuhu Han population. Subjects and methods Bloodstains from 1565 unrelated healthy individuals in Wuhu city, Anhui Province, were collected for analysis. The AGCU EX22 kit was used for amplification, and capillary electrophoresis was used to separate the amplification products. Allele frequencies and forensic parameters were determined. The Wuhu Han population was compared to 10 reference populations through genetic distance, a phylogenetic neighbor-joining tree and principal component analysis. Results In total, 281 alleles and 1187 genotypes were observed. No significant deviations from Hardy-Weinberg equilibrium at any locus were found after Bonferroni’s correction. The 21 autosomal short tandem repeat (STR) genetic markers exhibited high informativeness and polymorphism. The cumulative power of discrimination and power of exclusion were 0.999999999999999999999999913380 and 0.999999996752339, respectively. Population comparisons revealed a genetic affinity between Wuhu Han and southern Han populations, except for the Guangdong Han population, which aligned with the traditional geographical division in China. Conclusion The AGCU EX22 Kit, containing 21 STR loci, is suitable for forensic application and population genetics studies in the Wuhu Han population.

Analytical advances alleviate model misspecification in non-Brownian multivariate comparative methods.

Adams and Collyer argue that contemporary multivariate (Gaussian) phylogenetic comparative methods are prone to favouring more complex models of evolution and sometimes rotation invariance can be an issue. Here we dissect the concept of rotation invariance and point out that, depending on the understanding, this can be an issue with any method that relies on numerical instead of analytical estimation approaches. We relate this to the ongoing discussion concerning phylogenetic principal component analysis. Contrary to what Adams and Collyer found, we do not observe a bias against the simpler Brownian motion process in simulations when we use the new, improved, likelihood evaluation algorithm employed by mvSLOUCH, which allows for studying much larger phylogenies and more complex model setups.

Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat.

Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.

Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability

Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and causes mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.

Population genetic structure and implication for adaptive differentiation of the snail (Gastropoda, Provannidae) in deep‐sea chemosynthetic ecosystems

AbstractThe snail Provanna glabra is a dominant species inhabiting both hydrothermal vents and cold seeps of the Northwest Pacific Ocean. The genetic diversity and population structure of the snail from the hydrothermal vents of Okinawa Trough and a methane seep in the South China Sea were investigated using mitochondrial cytochrome c oxidase subunit I (COI) and genome‐wide single nucleotide polymorphisms (SNPs). A total of 28,805 SNPs were screened based on 2b‐RAD sequencing. Substantial genetic differences between vent and seep populations were identified based on the two datasets with FST = 0.753 (COI) and FST = 0.109 (SNPs), respectively. The results of phylogenetic tree, ADMIXTURE and principal component analysis jointly supported the population differentiation. Outlier detection confirmed the local adaptation of P. glabras populations, and the annotation of these outliers revealed that they were closely associated with processes of signal transduction, immunity, DNA repair, transposable elements and biological development. The genetic divergence observed between hydrothermal vent and methane seep P. glabra populations might be induced by the geographic barrier, limited dispersal ability and natural selection imposed by local environmental pressures from different deep‐sea habitats, e.g. chemical composition, temperature and microbes. These results provide a genetic basis for the microevolution of snails inhabiting deep‐sea chemosynthetic ecosystems.

Development and application of Single Primer Enrichment Technology (SPET) SNP assay for population genomics analysis and candidate gene discovery in lettuce.

Single primer enrichment technology (SPET) is a novel high-throughput genotyping method based on short-read sequencing of specific genomic regions harboring polymorphisms. SPET provides an efficient and reproducible method for genotyping target loci, overcoming the limits associated with other reduced representation library sequencing methods that are based on a random sampling of genomic loci. The possibility to sequence regions surrounding a target SNP allows the discovery of thousands of closely linked, novel SNPs. In this work, we report the design and application of the first SPET panel in lettuce, consisting of 41,547 probes spanning the whole genome and designed to target both coding (~96%) and intergenic (~4%) regions. A total of 81,531 SNPs were surveyed in 160 lettuce accessions originating from a total of 10 countries in Europe, America, and Asia and representing 10 horticultural types. Model ancestry population structure clearly separated the cultivated accessions (Lactuca sativa) from accessions of its presumed wild progenitor (L. serriola), revealing a total of six genetic subgroups that reflected a differentiation based on cultivar typology. Phylogenetic relationships and principal component analysis revealed a clustering of butterhead types and a general differentiation between germplasm originating from Western and Eastern Europe. To determine the potentiality of SPET for gene discovery, we performed genome-wide association analysis for main agricultural traits in L. sativa using six models (GLM naive, MLM, MLMM, CMLM, FarmCPU, and BLINK) to compare their strength and power for association detection. Robust associations were detected for seed color on chromosome 7 at 50 Mbp. Colocalization of association signals was found for outer leaf color and leaf anthocyanin content on chromosome 9 at 152 Mbp and on chromosome 5 at 86 Mbp. The association for bolting time was detected with the GLM, BLINK, and FarmCPU models on chromosome 7 at 164 Mbp. Associations were detected in chromosomal regions previously reported to harbor candidate genes for these traits, thus confirming the effectiveness of SPET for GWAS. Our findings illustrated the strength of SPET for discovering thousands of variable sites toward the dissection of the genomic diversity of germplasm collections, thus allowing a better characterization of lettuce collections.

The mycoremediation potential of the armillarioids: a comparative genomics analysis.

Genes involved in mycoremediation were identified by comparative genomics analysis in 10 armillarioid species and selected groups of white-rot Basidiomycota (14) and soft-rot Ascomycota (12) species to confine the distinctive bioremediation capabilities of the armillarioids. The genomes were explored using phylogenetic principal component analysis (pPCA), searching for genes already documented in a biocatalysis/biodegradation database. The results underlined a distinct, increased potential of aromatics-degrading genes/enzymes in armillarioids, with particular emphasis on a high copy number and diverse spectrum of benzoate 4-monooxygenase [EC:1.14.14.92] homologs. In addition, other enzymes involved in the degradation of various monocyclic aromatics were more abundant in the armillarioids than in the other white-rot basidiomycetes, and enzymes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) were more prevailing in armillarioids and other white-rot species than in soft-rot Ascomycetes. Transcriptome profiling of A. ostoyae and A. borealis isolates confirmed that several genes involved in the degradation of benzoates and other monocyclic aromatics were distinctively expressed in the wood-invading fungal mycelia. Data were consistent with armillarioid species offering a more powerful potential in degrading aromatics. Our results provide a reliable, practical solution for screening the likely fungal candidates for their full biodegradation potential, applicability, and possible specialization based on their genomics data.

Population genetic assessment of Viburnum japonicum in China using ddRAD-seq.

Viburnum japonicum is a rare plant species and endemic to the coastal region of Eastern Asia with extremely small populations. Within mainland China, this species can be only found in narrow habitats of the northeast coastal islands of Zhejiang Province. However, there are scarce conservation genetic studies on V. japonicum, which has limited the effective conservation and management of this rare species. Here, 51 individuals in four natural populations covering the Chinese geographic range of the species were sampled to assess the genetic diversity and population structure. A total of 445,060 high-quality single nucleotide polymorphisms (SNPs) were identified using double digest restriction-site associated sequencing (ddRAD-seq). The overall average values of observed heterozygosity (Ho), expected heterozygosity (He), and average nucleotide diversity (π), were 0.2207, 0.2595, and 0.2741, respectively. The DFS-2 population exhibited the highest level of genetic diversity among all the populations. Genetic differentiation between populations was moderate (F ST = 0.1425), and there was selfing between populations (F IS = 0.1390, S = 24.52%). Of the total genetic variation, 52.9% was found among populations through AMOVA analysis. The Mantel test (r = 0.982, p = 0.030) combined with analyses of the Maximum Likelihood (ML) phylogenetic tree, ADMIXTURE, and principal component analysis (PCA), revealed that populations of V. japonicum were genetically segregated and significantly correlated with their geographical distribution. Our study demonstrated that V. japonicum maintained a medium level of genetic diversity and differentiation with a strong population structure, and the results were mainly affected by its island distribution pattern and self-crossing characteristics. These results provide insights into the genetic diversity and population history of V. japonicum, critical information for conserving and sustainably developing its genetic resources.

Molecular marker development and genetic diversity exploration in Medicago polymorpha.

Medicago polymorpha L. (bur clover), an invasive plant species of the genus Medicago, has been traditionally used in China as an edible vegetable crop because of its high nutritive value. However, few molecular markers for M. polymorpha have been identified. Using the recently published high-quality reference genome of M. polymorpha, we performed a specific-locus amplified fragment sequencing (SLAF-seq) analysis of 10 M. polymorpha accessions to identify molecular markers and explore genetic diversity. A total of 52,237 high-quality single nucleotide polymorphisms (SNPs) were developed. These SNPs were mostly distributed on pseudochromosome 3, least distributed on pseudochromosome 7, and relatively evenly distributed on five other pseudochromosomes of M. polymorpha. Phenotypic analysis showed that there was a great difference in phenotypic traits among different M. polymorpha accessions. Moreover, clustering all M. polymorpha accessions based on their phenotypic traits revealed three groups. Both phylogenetic analysis and principal component analysis (PCA) of all M. polymorpha accessions based on SNP markers consistently indicated that all M. polymorpha accessions could be divided into three distinct groups (I, II, and III). Subsequent genetic diversity analysis for the 10 M. polymorpha accessions validated the effectiveness of the M. polymorpha germplasm molecular markers in China. Additionally, SSR mining analysis was also performed to identify polymorphic SSR motifs, which could provide valuable candidate markers for the further breeding of M. polymorpha. Since M. polymorpha genetics have not been actively studied, the molecular markers generated from our research will be useful for further research on M. polymorpha resource utilization and marker-assisted breeding.

Population whole-genome resequencing reveals the phylogenetic relationships and population structure of four Hunan typical tea landraces

Hunan located at the evolutionary transitional zone edge of the Yunnan-Guizhou plateau, tea germplasms are abundant. At present, although morphological, enzymological and molecular markers have been used to study the genetic relationship of these tea germplasms. However, due to the complexity of the genetic background of tea germplasm resources, the evolution history and taxonomy of Hunan tea germplasm is still unclear. In this study, four Hunan tea landraces from the evolutionary transitional zone were collected, including 9 'Chengbu Dongcha' (CBDC), 8 'Jianghua Kucha' (JHKC), 11 'Rucheng Baimao' (RCBM) and 8 'Anhua Yuntai' (AHYT). We used whole-genome re-sequencing to identify genetic variation, phylogenetic placement, and population structure among the four tea landraces and then scanned the genome for regions related to population potential selective. Across the samples, we identified an average of 1.38 million (M) SNPs and 6.82 × 10³ INDELs. Based on the high-quality SNPs, we performed neighbor-joining phylogenetic tree, population structure, and principal component analysis, all of which supported that the 36 tea germplasms could been divided into two groups, CBDC and AHYT were clustered into a group, and RCBM and JHKC were clustered into another group. With CBDC, JHKC, and RCBM as control, 407, 380, and 147 selected genes were identified in AHYT, respectively, were in the top 5% of F_ST and Log₂^Ratioθπ scores. The identified genes are mainly involved in stress tolerance, biosynthesis of important secondary metabolites, adaptability, and yield. These results will be helpful in the classification of tea germplasms and investigating selection–related genes.

SLAF-Seq Technology-Based Genome-Wide Association and Population Structure Analyses of Ancient Camellia sinensis (L.) Kuntze in Sandu County, China

Guizhou is one of the centers of origin for the tea plant (Camellia sinensis (L.) Kuntze). The location contains highly diverse ancient tea plant germplasms in its Sandu Aquarium Autonomous County. After a prolonged course of continuous evolution, these ancient plants have gained a wealth of genetic diversity. Their resources could be harnessed for the selection and breeding of fine varieties of tea plant, as well as for the effective utilization and protection of germplasm resources. In this study, the specific locus-amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) for the three traits of 125 ancient tea plants in the Sandu County of Guizhou province, China. A total of 807,743 SLAF tags and 9,428,309 population single-nucleotide polymorphism (SNP) tags were obtained. The results of the phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 125 germplasms were clustered into four groups, and the heterozygosity rates for groups I, II, III, and IV, were 0.211, 0.504, 0.144, and 0.192, respectively. Additionally, GWAS analysis suggested that seven candidate genes were related to altitude at the origin of the plants, eight were related to tree shape, and three were associated with leaf color. In this study, we clarified genetic relationships between four ancient tea plant-producing areas in Sandu County and obtained candidate genes related to their development associated with altitude, tree shape, and leaf color. The study provides useful information for tea plant-breeding development and molecular identification.

Morphometric analysis of the elasmobranch olfactory rosette.

The olfactory rosettes of elasmobranchs vary in shape and structure among species, but the functional consequences of this diversity are unresolved. Our goal was to quantify rosette morphology on dissected as well as diffusible iodine-based contrast-enhanced computed tomography (diceCT)-imaged specimens to analyze the drivers of observed trends in a phylogenetic context and compare the methodologies. We hypothesized that lamellar count and rosette shape (fineness ratio) would not scale with animal size, but other rosette size variables would scale positively. We dissected rosettes from 14 elasmobranch species and collected morphometric data (fineness ratio, lamellar count, interlamellar distance, lamellar thickness, and raphe width). A subset of rosettes (five species) wasused to analyze the effects of body size, while all 14 species were used for a phylogenetic principal component analysis (pPCA). We found that fineness ratio and lamellar counts varied significantly among species, and were positively correlated. The first two principal components of the pPCA explained 82% of the variation, with fineness ratio and lamellar count contributing most to the loadings, respectively.DiceCTwas used for in situ imaging of four species of Carcharhiniformes. There were no significant differences between rosette structure or volume when comparing values from dissected specimens to values from in situ specimens obtained using diceCT. We also quantified the volume of the excurrent channel in the olfactory capsule. These data add to our understanding of how olfactory organ shape varies among species and can be used to create three-dimensional models for future olfactory hydrodynamic studies.

Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count.

Simple SummaryChinese Holstein cows, crossbred cattle in China, have abundant genetic diversity due to the fact that Holstein cows were crossbred with various local breeds. Therefore, to reveal their genetic diversity, we sequenced the complete mitochondrial DNA (mtDNA) D-loop region of 501 Chinese Holstein cows and found abundant genetic resources (including 219 haplotypes, polymorphisms of 260 SNPs, and 32 indels) and two haplogroups in the study population. Meanwhile, the two haplogroups had different maternal origins and corresponding distinguished mutations. Furthermore, the association between haplogroups and antral follicle count was found, and the mtDNA haplogroup HG1 with Bos indicus maternal origin had more antral follicles (diameter ≥ 8 mm), implying that these individuals of HG1 had higher reproductive potential. Finally, these distinguished mutations between two haplogroups could be considered as important genetic markers for cattle breeding.Maternal origins based on the bovine mitochondrial D-loop region are proven to have two main origins: Bos taurus and Bos indicus. To examine the association between the maternal origins of bovine and reproductive traits, the complete mitochondrial D-loop region sequences from 501 Chinese Holstein cows and 94 individuals of other breeds were analyzed. Based on the results obtained from the haplotype analysis, 260 SNPs (single nucleotide polymorphism), 32 indels (insertion/deletion), and 219 haplotypes were identified. Moreover, the nucleotide diversity (π) and haplotype diversity (Hd) were 0.024 ± 0.001 and 0.9794 ± 0.003, respectively, indicating the abundance of genetic resources in Chinese Holstein cows. The results of the median-joining network analysis showed two haplogroups (HG, including HG1 and HG2) that diverged in genetic distance. Furthermore, the two haplogroups were significantly (p < 0.05) correlated with the antral follicle (diameter ≥ 8 mm) count, and HG1 individuals had more antral follicles than HG2 individuals, suggesting that these different genetic variants between HG1 and HG2 correlate with reproductive traits. The construction of a neighbor-joining phylogenetic tree and principal component analysis also revealed two main clades (HG1 and HG2) with different maternal origins: Bos indicus and Bos taurus, respectively. Therefore, HG1 originating from the maternal ancestors of Bos indicus may have a greater reproductive performance, and potential genetic variants discovered may promote the breeding process in the cattle industry.

Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae).

Species of Osmanthus are economically important ornamental trees, yet information regarding their plastid genomes (plastomes) have rarely been reported, thus hindering taxonomic and evolutionary studies of this small but enigmatic genus. Here, we performed comparative genomics and evolutionary analyses on plastomes of 16 of the 28 currently accepted species, with 11 plastomes newly sequenced. Phylogenetic studies identified four main lineages within the genus that are here designated the: “Caucasian Osmanthus” (corresponding to O. decorus), “Siphosmanthus” (corresponding to O. sect. Siphosmanthus), “O. serrulatus + O. yunnanensis,” and “Core Osmanthus: (corresponding to O. sect. Osmanthus + O. sect. Linocieroides). Molecular clock analysis suggested that Osmanthus split from its sister clade c. 15.83 Ma. The estimated crown ages of the lineages were the following: genus Osmanthus at 12.66 Ma; “Siphosmanthus” clade at 5.85 Ma; “O. serrulatus + O. yunnanensis” at 4.89 Ma; and “Core Osmanthus: clade at 6.2 Ma. Ancestral state reconstructions and trait mapping showed that ancestors of Osmanthus were spring flowering and originated at lower elevations. Phylogenetic principal component analysis clearly distinguished spring‐flowering species from autumn‐flowering species, suggesting that flowering time differentiation is related to the difference in ecological niches. Nucleotide substitution rates of 80 common genes showed slow evolutionary pace and low nucleotide variations, all genes being subjected to purifying selection.

Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds

This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, F ST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.

Evidence of Differences in Covariation Among Root Traits Across Plant Growth Forms, Mycorrhizal Types, and Biomes.

Fine roots play an important role in plant ecological strategies, adaptation to environmental constraints, and ecosystem functions. Covariation among root traits influence the physiological and ecological processes of plants and ecosystems. Root trait covariation in multiple dimensions at the global scale has been broadly discussed. How fine-root traits covary at the regional scale and whether the covariation is generalizable across plant growth forms, mycorrhizal types, and biomes are largely unknown. Here, we collected six key traits – namely root diameter (RD), specific root length (SRL), root tissue density (RTD), root C content (RCC), root N content (RNC), and root C:N ratio (RCN) – of first- and second-order roots of 306 species from 94 sampling sites across China. We examined the covariation in root traits among different plant growth forms, mycorrhizal types, and biomes using the phylogenetic principal component analysis (pPCA). Three independent dimensions of the covariation in root traits were identified, accounting for 39.0, 26.1, and 20.2% of the total variation, respectively. The first dimension was represented by SRL, RNC, RTD, and RCN, which was in line with the root economics spectrum (RES). The second dimension described a negative relationship between RD and SRL, and the third dimension was represented by RCC. These three main principal components were mainly influenced by biome and mycorrhizal type. Herbaceous and ectomycorrhizal species showed a more consistent pattern with the RES, in which RD, RTD, and RCN were negatively correlated with SRL and RNC within the first axis compared with woody and arbuscular mycorrhizal species, respectively. Our results highlight the roles of plant growth form, mycorrhizal type, and biome in shaping root trait covariation, suggesting that root trait relationships in specific regions may not be generalized from global-scale analyses.

Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) Kuntze) Germplasm in Qiannan, China, Based on SLAF-Seq Technology

Duyun Maojian tea is a famous tea in China. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of 2 leaf traits of 123 tea plants in Qiannan, China. A total of 462,019 SLAF tags and 11,362,041 single-nucleotide polymorphism (SNP) loci were obtained. The results of phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 123 tea germplasms were clustered into three groups, and the heterozygosity rates for Groups I, II, and II were 0.206, 0.224, and 0.34, respectively. Generally, tea germplasms in a production area are clustered in a group, indicating that tea germplasms in different production areas have certain genetic diversity. The traditional Duyun Maojian tea core production areas, TS and DC-SJ, are clustered into Group I and Group II respectively, while the ZY production area is relatively independent in Group III. Furthermore, based on GWAS analysis, 11 candidate genes related to leaf apex and 7 candidate genes related to leaf shape were obtained. This study clarified the genetic relationship among eight Duyun Maojian tea production areas and obtained candidate genes related to leaf apex and leaf shape development. The results showed that population structure and candidate genes are an effective basis for the breeding of Duyun Maojian tea germplasm.

Endoparasite community structure of an anuran assemblage in the Caatinga, Northeastern Neotropical Region.

Amphibians are a widespread Chordata taxon and are important for maintaining the balance of both terrestrial and aquatic ecosystems. Brazil has a rich amphibian fauna; however, little is known about the role of their ecology and phylogenetic relationships during the assembly processes of associated endoparasite communities. Herein, we describe an endoparasite community in an anuran assemblage in the Caatinga, a unique biome of dry forests in north-eastern Brazil. We studied endoparasite diversity, as well as the effects of body length, body mass, body volume and sex on parasite abundance. We also investigated the influence of ecological and historical factors and anuran microhabitat use on endoparasite composition. We analysed individuals from 13 anuran species distributed across five families: Odontophrynidae (Proceratophrys cristiceps); Leptodactylidae (Leptodactylus fuscus, Leptodactylus vastus, Leptodactylus macrosternum, Leptodactylus troglodytes and Physalaemus cuvieri); Hylidae (Pithecopus gonzagai, Scinax x-signatus, Boana raniceps and Dendropsophus nanus); Bufonidae (Rhinella diptycha and Rhinella granulosa); and Microhylidae (Dermatonotus muelleri). We found nine species of endoparasites, including seven nematodes (Aplectana membranosa, Cosmocerca sp., Oswaldocruzia mazzai, Raillietnema spectans, Rhabdias fuelleborni, Schrankiana sp. and Physaloptera sp.), one species of Trematoda (Glypthelmins pseudium) and one non-identified cestode. There was no significant relationship between endoparasite abundance and host body length, body mass, body volume and sex. A phylogenetic principal component analysis showed that ecological factors had a greater influence on endoparasite assemblage than historical factors. Similarly, our results showed that ecological factors had a greater influence on anuran microhabitat use compared to historical factors, which contributed to the generalist characteristics presented by most of the sampled endoparasite species.