Population Cluster Analysis Research Articles

Long-lived marine species may be resilient to environmental variability through a temporal portfolio effect.

Maintenance of genetic variation may provide resilience of populations to natural environmental variability. We used Pacific ocean perch (POP; Sebastes alutus) to test for the maintenance of adaptive variation across overlapping generations. POP are a long‐lived species characterized by widespread larval dispersal in their first year and a longevity of over 100 years. In order to understand how early marine dispersal affects POP survival and population structure, we used restriction site‐associated DNA sequencing (RADseq) to obtain 11,146 single‐nucleotide polymorphisms (SNPs) from 401 young‐of‐the‐year (YOY) POP collected during surveys conducted in 2014 (19 stations) and 2015 (4 stations) in the eastern Gulf of Alaska. Population clustering analysis showed that the POP samples represented four distinct ancestral populations mixed throughout the sampling area. Based on prior work on larval dispersal of POP, these larvae are most likely from distinct parturition locations that are mixing during their pelagic dispersal life stage. Latent factor mixed models revealed that POP larvae face significant selection during their first year at sea, which is specific to the year of their birth. Thus each adult cohort's genetic composition is heavily influenced by the environmental conditions experienced during their first year at sea. Long‐lived species relying on broadcast spawning strategies may therefore be uniquely resilient to environmental variability by maintaining a portfolio of cohort‐specific adaptive genotypes, and age truncation due to overfishing of older cohorts may have detrimental effect on the population viability.

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

BackgroundThe United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response.ResultsWe identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions.ConclusionsThe NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.

Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates.

A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.

SNP Mining by Genome Resequencing of 30 Apple Varieties in Shandong Province

In this article, we carried out genome resequencing and SNP mining for cultivated apples in Shandong Province for the sake of the rapid identification of apple varieties, germplasm evaluation, and utilization. Genomic DNA was extracted immediately from leaves of each sample, and Paired-end Illumina genomic libraries were prepared and sequenced on an Illumina Hiseq 4 000 platform following the manufacturer's instructions. Resequencing of the 31 apple genomes generated a total of 363 Gb high-quality cleaned sequences, with an average of 12.5 Gb per accession that represented approximately 15.9x coverage of the apple genome. The data volume fully meets the needs of downstream analysis and SNP mining. When we used the nucleotide mismatch parameter from 1~12, the mapping rate gradually increased to saturation. There was a highly significant correlation ( p <0.0001) between the total mapping rate, mapping rate of pair-end data, and mismatch parameter. Univariate fourth-order equation (regression coefficient  r >0.99) were predicted. As the mismatch rate increases, the accuracy of mapping decreases; the genome coverage gradually increases, and heterozygous sites' accuracy gradually increases. In this study, two algorithms were used in SNP mining. The intersection was further taken based on the 'chromosome+site information' as the eigenvalues to obtain a highly reliable single nucleotide variant dataset. A total of 374 404 SNP locus were detected. On average, one variation can be identified from 1 896 bp. The accuracy of the Sanger verification test is as high as 98.1%. Annotation analysis shows that among the 373 763 SNPs, 25 047 (6.7%) are located in the gene coding region, 143 269 (38.27%) are located in the intergenic region, and 179 426 (47.92%) are located in the 2 kb region upstream or downstream of the corresponding genes. Among the coding region SNPs, 13 422 are non-synonymous, while 11 625 are synonymous variations. The ratio of non-synonymous to synonymous SNP is 1.15: 1. Using the filtered 4DTV sites, population clustering analysis results constructed using neighbor-joining algorithms are in line with the trend of the classification of cultivated apples in Shandong province.

Multiallelic and multilocus simple sequence repeats (SSRs) to assess the genetic diversity of a Salix spp. germplasm collection

Salix L. (willow) is the largest genus of the family Salicaceae and plays an important role in riparian habitats, wetlands and in shrub tundra. Due to the different implications for the species belonging to this family, it is fundamental to identify molecular tools characterizing relevant clones. A set of six multilocus and multiallelic simple sequence repeat (SSRs) markers are presented, leading to 390 polymorphic fragments considered as single dominant markers and able to discriminate successfully 92 S. alba L. from 24 Salix spp. The polymorphic fragments have been used to perform genetic diversity studies, and to investigate population structures and cluster analysis in a germplasm collection. The results highlight the capability of the six SSRs to be powerful genetic resources in applied forestry research, both to distinguish S. alba clones from Salix spp. and to perform genetic population studies for breeding programs.

Development, Characterization, and Cross Species/Genera Transferability of Novel EST-SSR Markers in Lentil, with Their Molecular Applications

Lentil is nutritionally important crop for human diet and enriched with quality protein, complex carbohydrates, fibers, essential minerals, and vitamins. However, genetic improvement of lentil is hampered largely due to unattributed and unexploited genetic and genomic resources. To administer genomic resources in lentil, we have identified 9949 EST-SSR loci from lentil RNA Seq data and validated 50 of them using 234 genotypes representing various Lens species and 34 accessions of 12 different legumes. Out of 50 EST-SSRs, 46 were polymorphic with polymorphic information content (PIC) ranging from 0.16–0.74. The transferability of these markers exhibited varied levels from 45.1 to 71.3% across the cultivated/wild species of lentil and from 10.8 to 54.3% across the twelve legume genera. On the basis of total identified EST-SSRs, mononucleotide (51%) repeat proportion was high followed by trinucleotide (30%) and dinucleotide (14%) repeat. Population structure and cluster analysis classified all the studied genotypes into 4 groups. However, principal coordinate analysis (PCA) was able to group genotypes based on their area of collection. Annotation of all the 46 polymorphic marker sequences revealed that most of the markers linked to genes involved in metabolism of plants. Further, polymorphic markers were also used for linkage mapping in F3 population where 4 markers were found to be linked with a map distance of 72.5 cM. The newly developed markers represent an impressive tool for characterization of germplasm, genetic linkage mapping, phylogenetic studies, as well as to determine disparity in taxonomic status of subspecies of the genus Lens.

Biogeographic origin prediction of three continental populations through 42 ancestry informative SNPs.

A biogeographic estimate of a certain population can not only discern population substructure in the whole genome association study, but also provide informative clues for forensic investigations when obtained DNA genotypes do not find a match in the available forensic DNA database. In this study, 100 ancestry informative single nucleotide polymorphisms (AISNPs) were first presented to differentiate three continental ancestries (African, East Asian and European). Ultimately, forty-two AISNPs were chosen from the 100 AISNPs. Distinguishing power of the 100 and 42 AISNPs for differentiating continental populations was further evaluated with population cluster analyses. Results indicated both of AISNP sets could efficiently differentiate 11 training populations from the three continents. Further validation of 42 AISNPs in testing population set indicated these 42 AISNPs performed well for ancestry inferences of these testing individuals. Ancestry components of Uyghur group were assessed by comparing with different continental populations based on these 42 AISNPs. Results revealed that East Asian populations contributed more ancestry components to the studied Uyghur group than European populations. In conclusion, our study is expected to provide more AISNP markers and enrich extant reference database.

Genomic Analysis Confirms Population Structure and Identifies Inter-Lineage Hybrids in Aegilops tauschii.

Aegilops tauschii, the D-genome donor of bread wheat, Triticum aestivum, is a storehouse of genetic diversity, and an important resource for future wheat improvement. Genomic and population analysis of 549 Ae. tauschii and 103 wheat accessions was performed by using 13,135 high quality SNPs. Population structure, principal component, and cluster analysis confirmed the differentiation of Ae. tauschii into two lineages; lineage 1 (L1) and lineage 2 (L2), the latter being the wheat D-genome donor. Lineage L1 contributes only 2.7% of the total introgression from Ae. tauschii for a set of United States winter wheat lines, confirming the great amount of untapped genetic diversity in L1. Lineage L2 accessions had overall greater allelic diversity and wheat accessions had the least allelic diversity. Both lineages also showed intra-lineage differentiation with L1 being driven by longitudinal gradient and L2 differentiated by altitude. There has previously been little reported on natural hybridization between L1 and L2. We found nine putative inter-lineage hybrids in the population structure analysis, each containing numerous lineage-specific private alleles from both lineages. One hybrid was confirmed as a recombinant inbred between the two lineages, likely artificially post collection. Of the remaining eight putative hybrids, a group of seven from Georgia carry 713 SNPs with private alleles, which points to the possibility of a novel L1–L2 hybrid lineage. To facilitate the use of Ae. tauschii in wheat improvement, a MiniCore consisting of 29 L1 and 11 L2 accessions, has been developed based on genotypic, phenotypic and geographical data. MiniCore reduces the collection size by over 10-fold and captures 84% of the total allelic diversity in the whole collection.

Persistence of remnant patches and genetic loss at the distribution periphery in island and mainland populations of the quokka

Understanding the spatial structure of populations is important in developing effective management options for threatened species, and for managing habitat connectivity for metapopulation function, and for demographic and genetic heterogeneity. We used genetic information to investigate the structure of populations of the quokka, Setonix brachyurus, in south-west Western Australia. We hypothesised that movement between known populations would be relatively rare and result in significant genetic structuring. Genetic analyses from 412 adult individuals at 14 nuclear markers (microsatellite) from 33 sampling locations identified structure, diversity and spatial separation of quokkas across their mainland distribution and on two islands. We identified nine inferred (K = 9) populations of quokka that would be otherwise difficult to define with standard ecological techniques. The highest genetic diversity was evident in a large central population of quokka in the southern forest area and genetic diversity was lower at the peripheries of the distribution. The Rottnest Island population contained 70% of the genetic diversity of the mainland populations but the genetic diversity of animals on Bald Island was markedly lower. Populations of quokka in the northern jarrah forest were the only ones to show evidence of recent or long-term population bottlenecking. Of particular interest was the recently identified population at the Muddy Lakes area (the only remaining locality on the Swan Coastal Plain), which was identified as being genetically associated with the southern forest population. Overall, spatial and population cluster analysis showed small insular populations in the northern jarrah forest area, but in the southern forests there appears to be a large panmictic population.

Landscape and population genetics reveal long distance sharp-tailed grouse (Tympanuchus phasianellus) movements and a recent bottleneck in Minnesota

Sharp-tailed grouse (Tympanuchus phasianellus) are an area-sensitive species that relies on open landscapes of grass and brush. These areas have become highly fragmented in the Great Lakes Region by succession to forest, agriculture, and other human land uses. We used microsatellites in a landscape-genetic approach to identify landscape features that influence movement and connectivity for sharp-tailed grouse in Minnesota, where they have a regional stronghold. Feathers from leks and hunter wing submissions resulted in 367 individuals from the northwest (NW) and 84 from the east-central (EC) management regions. Both the NW and EC regions were genetically diverse and distinct, with high connectivity between them, although it is unclear whether this connection is contemporary or historical. Our analysis indicated that sharp-tailed grouse were structured across regions by land cover or by the amount of agriculture, grasslands, shrublands, and wet meadows on the larger landscape. Numerous long distance dispersal events were detected. Population clustering analysis indicated greatest support for two genetic clusters in the NW and three clusters in the EC region; however, mapping sample locations of individuals by assigned cluster revealed panmixia of clusters in the EC region. High genetic diversity, a low inbreeding coefficient, and significant excess in heterozygosity are consistent with a recent demographic compression or bottleneck in the EC region, and also consistent with surveys indicating a recent decline there. Sustained low population size or further declines would be expected to reduce genetic diversity. We recommend increasing grassland and shrubland quantity and quality to increase population size in the EC region soon.

Distance based parameter adaptation for Success-History based Differential Evolution

Abstract This paper proposes a simple, yet effective, modification to scaling factor and crossover rate adaptation in Success-History based Adaptive Differential Evolution (SHADE), which can be used as a framework to all SHADE-based algorithms. The performance impact of the proposed method is shown on the real-parameter single objective optimization (CEC2015 and CEC2017) benchmark sets in 10, 30, 50, and 100 dimensions for all SHADE, L-SHADE (SHADE with linear decrease of population size), and jSO algorithms. The proposed distance based parameter adaptation is designed to address the premature convergence of SHADE–based algorithms in higher dimensional search spaces to maintain a longer exploration phase. This design effectiveness is supported by presenting a population clustering analysis, along with a population diversity measure. Also, the new distance based algorithm versions (Db_SHADE, DbL_SHADE, and DISH) have obtained significantly better optimization results than their canonical counterparts (SHADE, L_SHADE, and jSO) in 30, 50, and 100 dimensional functions.

Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed.

In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate, and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8550 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96 × 10-11 and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the DA distance and Fst values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group, and several Han populations.

Population structure of the NPGS Senegalese sorghum collection and its evaluation to identify new disease resistant genes.

Sorghum germplasm from West and Central Africa is cultivated in rainy and high humidity regions and is an important source of resistance genes to fungal diseases. Mold and anthracnose are two important biotic constraints to sorghum production in wet areas worldwide. Here, 158 National Plant Germplasm System (NPGS) accessions from Senegal were evaluated for agronomic traits, anthracnose, and grain mold resistance at two locations, and genetically characterized according to 20 simple sequence repeat markers. A total of 221 alleles were amplified with an average of 11 alleles per locus. Each accession had a unique genetic profile (i.e., no duplicates), and the average genetic distance between accessions was 0.42. Population structure and cluster analysis separated the collection into four populations with pairwise FST values >0.15. Three of the populations were composed of Guinea-race sorghum germplasm, and one included multiple races. Anthracnose resistant accessions were present at high frequency and evenly distributed among the three Guinea-race populations. Fourteen accessions showed resistance to grain mold, and eight were resistant to both diseases. These results indicated that the NPGS of Senegal is a genetically diverse collection with a high frequency of disease resistant accessions. Nevertheless, its population structure suggests the presence of few sources of resistance to both grain mold and anthracnose, which are fixed in the germplasm. The phenotypic and genotypic information for these accessions provides a valuable resource for its correct use to broaden the genetic base of breeding programs.

Effect of multiple allelic combinations of genes on regulating grain size in rice.

The grain size is one of the complex trait of rice yield controlled by a plethora of interaction of several genes in different pathways. The present study was undertaken to investigate the influence of seven known grain size regulating genes: DEP1, GS7, GS3, GW8, GL7, GS5 and GW2. A wide phenotypic variation for grain length, grain width and grain length-width ratio were observed in 89 germplasm. The correlation analysis showed a strong association among these three grain traits viz. GL, GW, GLWR and TGW which play important roles in determining the final rice grain size. Except for GW2, all six genes showed strong association with grain size traits. A total of 21 alleles were identified with an average of 2.1 allele/locus in 89 germplasm of which seven alleles were found to be favourable alleles for improving the grain size with the frequency range of 24 (26.97%) to 82 (92.13%); the largest was found in GS5 followed by GW8, GL7, DEP1, GS3 and GS7 genes. Through ANOVA, four markers (GS3-PstI, S9, GID76 and GID711) of three genes (GS3, DEP1 and GL7) were found significantly associated with all the three traits (GL, GLWR and TGW). Concurrent results of significant associations of grain size traits with other markers were observed in both analysis of variance and genetic association through the general linear model. Besides, the population structure analysis, cluster analysis and PCoA divided the entire germplasm into three sub-groups with the clear-cut demarcation of long and medium grain types. The present results would help in formulating strategies by selecting suitable candidate markers/genes for obtaining preferred grain shape/size and improving grain yield through marker-assisted breeding.

A Global Perspective on the Population Structure and Reproductive System of Phyllosticta citricarpa.

The citrus pathogen Phyllosticta citricarpa was first described 117 years ago in Australia; subsequently, from the summer rainfall citrus-growing regions in China, Africa, and South America; and, recently, the United States. Limited information is available on the pathogen's population structure, mode of reproduction, and introduction pathways, which were investigated by genotyping 383 isolates representing 12 populations from South Africa, the United States, Australia, China, and Brazil. Populations were genotyped using seven published and eight newly developed polymorphic simple-sequence repeat markers. The Chinese and Australian populations had the highest genetic diversities, whereas populations from Brazil, the United States, and South Africa exhibited characteristics of founder populations. The U.S. population was clonal. Based on principal coordinate and minimum spanning network analyses, the Chinese populations were distinct from the other populations. Population differentiation and clustering analyses revealed high connectivity and possibly linked introduction pathways between South Africa, Australia, and Brazil. With the exception of the clonal U.S. populations that only contained one mating type, all the other populations contained both mating types in a ratio that did not deviate significantly from 1:1. Although most populations exhibited sexual reproduction, linkage disequilibrium analyses indicated that asexual reproduction is important in the pathogen's life cycle.

Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement

BackgroundThe USDA Agriculture Research Service National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world, which includes 7,217 accessions from the center of diversity in Ethiopia. The characterization of this exotic germplasm at a genome-wide scale will improve conservation efforts and its utilization in research and breeding programs. Therefore, we phenotyped a representative core set of 374 Ethiopian accessions at two locations for agronomic traits and characterized the genomes.ResultsUsing genotyping-by-sequencing, we identified 148,476 single-nucleotide polymorphism (SNP) markers distributed across the entire genome. Over half of the alleles were rare (frequency < 0.05). The genetic profile of each accession was unique (i.e., no duplicates), and the average genetic distance among accessions was 0.70. Based on population structure and cluster analyses, we separated the collection into 11 populations with pairwise FST values ranging from 0.11 to 0.47. In total, 198 accessions (53%) were assigned to one of these populations with an ancestry membership coefficient of larger than 0.60; these covered 90% of the total genomic variation. We characterized these populations based on agronomic and seed compositional traits. We performed a cluster analysis with the sorghum association panel based on 26,026 SNPs and determined that nine of the Ethiopian populations expanded the genetic diversity in the panel. Genome-wide association analysis demonstrated that these low-coverage data and the observed population structure could be employed for the genomic dissection of important phenotypes in this core set of Ethiopian sorghum germplasm.ConclusionsThe NPGS Ethiopian sorghum germplasm is a genetically and phenotypically diverse collection comprising 11 populations with high levels of admixture. Genetic associations with agronomic traits can be used to improve the screening of exotic germplasm for selection of specific populations. We detected many rare alleles, suggesting that this germplasm contains potentially useful undiscovered alleles, but their discovery and characterization will require extensive effort. The genotypic data available for these accessions provide a valuable resource for sorghum breeders and geneticists to effectively improve crops.

High genetic diversity and connectivity in Colossoma macropomum in the Amazon basin revealed by microsatellite markers.

Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations.

Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.).

BackgroundDuring the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today’s diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum.ResultsA population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west.ConclusionsOur results contribute to awareness of increased population sizes, following significant contractions, as having been important in shaping diversity in Australian arid and semi-arid zones. Further, we improve knowledge of the role of Pleistocene climatic shifts in areas of the planet that were not glaciated at that time but which still experienced that period’s cyclical climatic fluctuations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0798-6) contains supplementary material, which is available to authorized users.

Marker-Trait Association for Biomass Yield of Potential Bio-fuel Feedstock Miscanthus sinensis from Southwest China.

As a great potential bio-fuel feedstock, the genus Miscanthus has been widely studied around the world, especially Miscanthus × giganteus owing to its high biomass yield in Europe and North America. However, the narrow genetic basis and sterile characteristics of M. × giganteus have become a limitation for utilization and adaptation to extreme climate conditions. In this study, we focused on one of the progenitors of M. × giganteus, Miscanthus sinensis, which was originally distributed in East Asia with abundant genetic resources and comparable biomass yield potential to M. × giganteus in some areas. A collection of 138 individuals was selected for conducting a 3-year trial of biomass production and analyzed by using 104 pairs of SRAP, ISAP, and SSR primers for genetic diversity as well as marker-trait association. Significant differences in biomass yield and related traits were observed among individuals. Tiller number, fresh biomass yield per plant and dry biomass yield per plant had a high level of phenotypic variation among individuals and the coefficient of variation were all above 40% in 2011, 2012, and 2013. The majority of the traits had a significant correlation with the biomass yield except for the length and width of flag leaves. Plant height was a highly stable trait correlated with biomass yield. A total of 1059 discernible loci were detected by markers across individuals. The population structure (Q) and cluster analyses identified three subpopulations in the collection and family relative kinship (K) represented high gene flow among M. sinensis populations from Southwest China. Model testing identified that Q+K was the best model for describing the associations between the markers and traits, compared to the simple linear, Q or K model. Using the Q+K model, 12 significant associations (P < 0.001) were identified including four markers with plant height and one with biomass yield. Such associations would serve an efficient tool for an early selection of M. sinensis and facilitate a genetic improvement of biomass yield for this species.

Genetic Diversity and Divergence in Populations of the Threatened Grassland Perennial Vincetoxicum atratum (Apocynaceae-Asclepiadoideae) in Japan.

We examined the genetic diversity and structure in populations of the endangered grassland herb Vincetoxicum atratum using 11 polymorphic microsatellite loci. Although the populations were small and disconnected, our molecular data indicated that the species maintains relatively high levels of genetic diversity and connectivity among populations. Population clustering analyses detected 2 to 3 clusters and most of the populations of V. atratum comprised admixture of these genetic clusters. These admixtures likely formed during the process of colonizing habitats that had been disturbed by human activities. However, STRUCTURE clustering detected low-admixtures in populations occurring in rocky maritime sites, which may not be suitable for agriculture/rangeland activities. High genetic diversity and population connectivity suggested that loss of the remaining populations by grassland reduction might be an immediate threat for this species. Small grasslands populations managed by local farmers need appropriate conservation practices. Although our results showed genetic diversity and gene flow among populations of V. atratum were high, it is possible that this resulted from the historical continuous distribution of the species. To examine this hypothesis, further periodical monitoring of the genetic diversity and the genetic differentiation for the species is needed for a conservation action of the species.