Drought responses and population differentiation of Calohypnum plumiforme inferred from comparative transcriptome analysis

Bryophytes, known as poikilohydric plants, possess vegetative desiccation-tolerant (DT) ability to withstand water deficit stress. Consequently, they offer valuable genetic resources for enhancing resistance to water scarcity stress. In this research, we examined the physiological, phytohormonal, and transcriptomic changes in DT mosses Calohypnum plumiforme from two populations, with and without desiccation treatment. Comparative analysis revealed population differentiation at physiological, gene sequence, and expression levels. Under desiccation stress, the activities of superoxide dismutase (SOD) and peroxidase (POD) showed significant increases, along with elevation of soluble sugars and proteins, consistent with the transcriptome changes. Notable activation of the bypass pathway of JA biosynthesis suggested their roles in compensating for JA accumulation. Furthermore, our analysis revealed significant correlations among phytohormones and DEGs in their respective signaling pathway, indicating potential complex interplays of hormones in C plumiforme. Protein phosphatase 2C (PP2C) in the abscisic acid signaling pathway emerged as the pivotal hub in the phytohormone crosstalk regulation network. Overall, this study was one of the first comprehensive transcriptome analyses of moss C. plumiforme under slow desiccation rates, expanding our knowledge of bryophyte transcriptomes and shedding light on the gene regulatory network involved in response to desiccation, as well as the evolutionary processes of local adaptation across moss populations.

A comprehensive analysis of copy number variations in diverse apple populations

BACKGROUND

As an important source of genetic variation, copy number variation (CNV) can alter the dosage of DNA segments, which in turn may affect gene expression level and phenotype. However, our knowledge of CNV in apple is still limited. Here, we obtained high-confidence CNVs and investigated their functional impact based on genome resequencing data of two apple populations, cultivars and wild relatives.

RESULTS

In this study, we identified 914,610 CNVs comprising 14,839 CNV regions (CNVRs) from 346 apple accessions, including 289 cultivars and 57 wild relatives. CNVRs summed to 71.19 Mb, accounting for 10.03% of the apple genome. Under the low linkage disequilibrium (LD) with nearby SNPs, they could also accurately reflect the population structure of apple independent of SNPs. Furthermore, A total of 3,621 genes were covered by CNVRs and functionally involved in biological processes such as defense response, reproduction and metabolic processes. In addition, the population differentiation index ([Formula: see text]) analysis between cultivars and wild relatives revealed 127 CN-differentiated genes, which may contribute to trait differences in these two populations.

CONCLUSIONS

This study was based on identification of CNVs from 346 diverse apple accessions, which to our knowledge was the largest dataset for CNV analysis in apple. Our work presented the first comprehensive CNV map and provided valuable resources for understanding genomic variations in apple.

Analyzing Autopolyploid Genetic Data Using GenoDive

Analyzing autopolyploid genetic data still presents numerous challenges due to, e.g., missing dosage information of genotypes and the presence of multiple ploidy levels within species or populations, but also because the choice of software is limited when compared to what is available for diploid data. However, over the last years, the number of software programs that can deal with polyploid data is slowly increasing. The software GENODIVE is one of the most widely used programs for the analysis of polyploid genetic data, presenting a wide array of different methods. In this chapter, I outline several frequently used types of population genetic analyses and explain how these apply to polyploid data, including possible pitfalls and biases. I then explain how GENODIVE approaches these analyses and whether and how it can overcome possible biases. Specifically, I focus on analyses of genetic diversity, Hardy-Weinberg equilibrium, quantifying population differentiation, clustering, and calculation of genetic distances. GENODIVE can be downloaded freely from http://www.patrickmeirmans.com/software .

Population Genomic Analysis of Diploid-Autopolyploid Species

This chapter outlines an empirical analysis of genome-wide single-nucleotide polymorphism (SNP) variation and its underlying drivers among multiple natural populations within a diploid-autopolyploid species. The aim is to reconstruct the genetic structure among natural populations of varying ploidy and infer footprints of selection in these populations, framed around specific questions that are typically encountered when analyzing a mixed-ploidy data set,e.g., addressing the relevance of natural whole-genome duplication for speciation and adaptation. We briefly review the options for the analysis of polyploid population genomic data involving variant calling, population structure, demographic history inference, and selection scanning approaches. Further, we provide suggestions for methods and associated software, possible caveats, and examples of their application to mixed-ploidy and autopolyploid data sets.

Genetic diversity of Plasmodium vivax populations from the China-Myanmar border identified by genotyping merozoite surface protein markers

BACKGROUND

Parasite diversity and population structure influence malaria control measures. Malaria transmission at international borders affects indigenous residents and migrants, defying management efforts and resulting in malaria re-introduction. Here we aimed to determine the extent and distribution of genetic variations in Plasmodium vivax populations and the complexity of infections along the China-Myanmar border.

METHODS

We collected clinical P. vivax samples from local and migrant malaria patients from Laiza and Myitsone, Kachin State, Myanmar, respectively. We characterized the polymorphisms in two P. vivax merozoite surface protein markers, Pvmsp-3α and Pvmsp-3β, by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. We sought to determine whether these genetic markers could differentiate these two neighboring parasite populations.

RESULTS

PCR revealed three major size variants for Pvmsp-3α and four for Pvmsp-3β among the 370 and 378 samples, respectively. PCR-RFLP resolved 26 fragment-size alleles by digesting Pvmsp-3α with Alu I and Hha I and 28 alleles by digesting Pvmsp-3β with Pst I. PCR-RFLP analysis of Pvmsp-3α found that infections in migrant laborers from Myitsone bore more alleles than did infections in residents of Laiza, while such difference was not evident from genotyping Pvmsp-3β. Infections originating from these two places contained distinct but overlapping subpopulations of P. vivax. Infections from Myitsone had a higher multiplicity of infection as judged by the size of the Pvmsp-3α amplicons and alleles after Alu I/Hha I digestion.

CONCLUSIONS

Migrant laborers from Myitsone and indigenous residents from Laiza harbored overlapping but genetically distinct P. vivax parasite populations. The results suggested a more diverse P. vivax population in Myitsone than in the border town of Laiza. PCR-RFLP of Pvmsp-3α offers a convenient method to determine the complexity of P. vivax infections and differentiate parasite populations.

Genetic variation of Cerastium alpinum L. from Babia Góra, a critically endangered species in Poland

Babia Góra massif is the only site of occurrence of the Cerastium alpinum L. in Poland, an arctic-alpine perennial plant with a wide distribution in North America, northwestern Asia, and Europe. To determine whether the isolated Polish populations are genetically distinct, we have performed an evaluation of C. alpinum from Babia Góra with the use of iPBS markers. A total number of 133 individuals of C. alpinum from seven populations representing four localizations of the species were analyzed, i.e., from Babia Góra (Poland), Alps (Switzerland), Nuolja massif (Sweden), and Kaffiøyra (Svalbard, Norway). Genetic analysis of all C. alpinum samples using eight PBS primers identified 262 bands, 79.4% of which were polymorphic. iPBS markers revealed low genetic diversity (average H_e = 0.085) and high population differentiation (F_ST = 0.617). AMOVA results confirmed that the majority of the genetic variation (62%) was recorded among populations. The grouping revealed by PCoA showed that C. alpinum from Svalbard is the most diverged population, C. alpinum from Switzerland and Sweden form a pair of similar populations, whereas C. alpinum from the Babia Góra form a heterogeneous group of four populations. Results of isolation by distance analysis suggested that the spatial distance is the most probable cause of the observed differentiation among populations. Although significant traces of a bottleneck effect were noted for all populations of C. alpinum from Babia Góra, the populations still maintain a low but significant level of genetic polymorphism. These results are of great importance for developing conservation strategies for this species in Poland.

More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China

BACKGROUND

The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown.

RESULTS

Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes.

CONCLUSIONS

The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.

Geological and climatic influences on population differentiation of the Phrynocephalus vlangalii species complex (Sauria: Agamidae) in the northern Qinghai-Tibet Plateau

Extremely heterogeneous topography and complex paleoclimate history of the Qinghai-Tibet Plateau (QTP) have a key role in promoting genetic divergence and lineage/species formation. Here, we sequenced one nuclear and three mitochondrial markers of 532 individuals from the entire range of the Phrynocephalus vlangalii species complex including two species, P. putjatai and P. vlangalii, endemic to the northern QTP. We integrated multilocus phylogeny, demographic analysis and geographic barrier detection to evaluate the population structure and dynamics. We found a new mitochondrial clade (PV-I) in the Gonghe County population of P. vlangalii, partial mitochondrial DNA replacement within P. vlangalii and complete mitochondrial DNA replacement between P. putjatai and P. vlangalii. Neutrality test, mismatch distribution analysis and Extended Bayesian Skyline Plot (EBSP) analysis all supported a significant expansion of the Qaidam Basin population of P. vlangalii (PV-II-2) from 0.091 to 0.026 Ma after Penultimate Glaciation. The uplift of the Arjin and Anyemanqen Mountains during the Kunhuang Movement (∼1.2 Ma) split populations of P. vlangalii in Akesai, Qaidam Basin and source of the Yellow River. The uplift of the Elashan Mountains during the second phase of the Qingzang Movement (∼2.5 Ma) contributed to the divergence of the Gonghe County population of P. vlangalii from other conspecific populations. The third phase of the Qingzang Movement (∼1.7 Ma) contributed to the divergence of the Xinghai population of P. vlangalii from P. putjatai and to the divergence of the northern populations of P. putjatai from the southern conspecific populations. Our data support the idea that the geological and climatic changes following the orogeny of the QTP may have promoted population differentiation and shaped the current population patterns of the P. vlangalii species complex in the northeastern QTP.

Seed and seedling diversity delimitation and differentiation of Indian populations of Melia dubia cav

Melia dubia is one of the most important industrial tree species in the South East Asia. In last few decades, the populations of M. dubia has rapidly expanded in the Indian sub-continents, leading to an increase in the genetic diversity of species. However, very less information is available on intra-specific variation in Melia under the Indian subcontinent. Therefore, a present investigation was undertaken, to assess the level of diversity in seed and saplings of the Melia populations (ecotypes) collected from three agro-ecological regions of India. Results revealed that the seed and saplings of all the ecotypes are significantly different for all the traits, except for number of branches per plant, and the maximum variability was recorded in germination percentage, seed weight, internodal length, and sapling height of the species. The high heritability for seed weight (0.99), length (0.99), and width (0.97), and germination percentage (0.99) indicated that selection and genetic gain for these traits would be effective during the commencement of improvement program. Trait association analysis explained that higher seed weight significantly reduced sapling height, collar diameter, number of leaves per plant, internodal length, petiole length, and germination percentage (r = −0.86; p < 0.001) that ultimately reduced the seedling vigor in Melia dubia. Interestingly, the number of branches per plant were not associated with any of the morphological traits. The first principal component explained 50.09% of the entire variation and all the traits contributed greatly to the variation for this principal component, except for number of branches, leaf width and seed length. The clustering approach assorted geographic variation of M. dubia populations into three main sub-clusters i.e. South, North, and North East populations each consisting of five, seven and one populations (including cultivar), respectively. Among different ecotypes, Bahumukhi, Varsha and US Nagar seed sources outperformed all others in seedling vigour (sapling height) and rest of the growth parameters. Overall, findings explained that considerable scope exists for the development of superior planting material of M. dubia through exploration of seeds and selection at the early seedling stage.

Prioritising positively selected variants in whole-genome sequencing data using FineMAV

Background

In population genomics, polymorphisms that are highly differentiated between geographically separated populations are often suggestive of Darwinian positive selection. Genomic scans have highlighted several such regions in African and non-African populations, but only a handful of these have functional data that clearly associates candidate variations driving the selection process. Fine-Mapping of Adaptive Variation (FineMAV) was developed to address this in a high-throughput manner using population based whole-genome sequences generated by the 1000 Genomes Project. It pinpoints positively selected genetic variants in sequencing data by prioritizing high frequency, population-specific and functional derived alleles.

Results

We developed a stand-alone software that implements the FineMAV statistic. To graphically visualise the FineMAV scores, it outputs the statistics as bigWig files, which is a common file format supported by many genome browsers. It is available as a command-line and graphical user interface. The software was tested by replicating the FineMAV scores obtained using 1000 Genomes Project African, European, East and South Asian populations and subsequently applied to whole-genome sequencing datasets from Singapore and China to highlight population specific variants that can be subsequently modelled. The software tool is publicly available at https://github.com/fadilla-wahyudi/finemav.

Conclusions

The software tool described here determines genome-wide FineMAV scores, using low or high-coverage whole-genome sequencing datasets, that can be used to prioritize a list of population specific, highly differentiated candidate variants for in vitro or in vivo functional screens. The tool displays these scores on the human genome browsers for easy visualisation, annotation and comparison between different genomic regions in worldwide human populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04506-9.

Urbanization processes drive divergence at the major histocompatibility complex in a common waterbird

Urban sprawl is one of the most common landscape alterations occurring worldwide, and there is a growing list of species that are recognised to have adapted to urban life. To be successful, processes of urban colonization by wildlife require a broad spectrum of phenotypic (e.g., behavioural or physiological) adjustments, but evidence for genetic adaptations is much scarcer. One hypothesis proposes that different pathogen-driven selective pressures between urban and non-urban landscapes leads to adaptations in host immune genes. Here, we examined urbanization-related differentiation at the key pathogen-recognition genes of vertebrate adaptive immunity-the major histocompatibility complex (MHC)-in a common waterbird, the Eurasian coot (Fulica atra). Samples were collected from an old urban population (established before the 1950s), a new urban population (established in the 2000s), and two rural populations from central Poland. We found strong significant divergence (as measured with Jost's D) at the MHC class II between the old urban population and the remaining (new urban and rural) populations. Also, there was a moderate, but significant divergence at the MHC between the new urban population and two rural populations, while no divergence was found between the two rural populations. The total number of MHC alleles and the number of private (population-specific) MHC alleles was lower in old urban populations, as compared to the rural ones. These patterns of differentiation at the MHC were not consistent with patterns found for neutral genetic markers (microsatellites), which showed few differences between the populations. Our results indicate that MHC allele composition depended on the level of anthropogenic disturbance and the time which passed since urban colonization, possibly due to the processes of genotype sorting and local adaptation. As such, our study contributes to the understanding of genetic mechanisms associated with urbanization processes in wildlife.

Moderate Population Structure in Drosophila sturtevanti from the South American Atlantic Forest Biome

Drosophila sturtevanti is a widely distributed Neotropical species. In South America, it is abundant and adapted to different phytophysiognomies of the Atlantic Forest biome. Reproductive, chromosomal and enzymatic studies have indicated the existence of a differentiation among D. sturtevanti populations. In this work, the level of genetic diversity and the population genetic structure were analyzed using four population groupings. One hundred and twenty-six D. sturtevanti males collected from nine forest fragments were analyzed for 11 species-specific microsatellite loci. A total of 109 alleles, ranging from 2 to 16 alleles per locus, were detected. The highest mean observed heterozygosity -H _O was estimated in samples from the largest collection areas, and the lowest H _O was from a population where fire events are common. A low molecular variation, around 3% among populations and negative among groups, an absence of genetic and geographic correlations and a moderate genetic differentiation -F _ST = 0.0663 -indicated that D. sturtevanti is not strongly structured. Besides no overall genetic and geographic distance correlation, the pair of closest geographically populations Matão and Nova Granada showed the lower differentiation through F _ST, DC and a Neighbor Joining tree. Ribeirão da Ilha -RDI, an isolated insular population, was the most differentiated according to F _ST, DC and a cluster-based Bayesian analysis. The isolation of RDI that resulted in significant divergence could be ancient, because of sea level regressions/transgressions, or more recently via founder effect/genetic drift by anthropic action carrying D. sturtevanti hosts from continent to island. This work is important for understanding the genetic variability distribution of a Neotropical forest-dwelling Drosophila species using for the first time, a wide population distribution approach.

Molecular genetic diversity and population structure analyses of rutabaga accessions from Nordic countries as revealed by single nucleotide polymorphism markers

Background

Rutabaga or swede (Brassica napus ssp. napobrassica (L.) Hanelt) varies in root and leaf shape and colour, flesh colour, foliage growth habits, maturity date, seed quality parameters, disease resistance and other traits. Despite these morphological differences, no in-depth molecular analyses of genetic diversity have been conducted in this crop. Understanding this diversity is important for conservation and broadening the use of this resource.

Results

This study investigated the genetic diversity within and among 124 rutabaga accessions from five Nordic countries (Norway, Sweden, Finland, Denmark and Iceland) using a 15 K single nucleotide polymorphism (SNP) Brassica array. After excluding markers that did not amplify genomic DNA, monomorphic and low coverage site markers, the accessions were analyzedwith 6861 SNP markers. Allelic frequency statistics, including polymorphism information content (PIC), minor allele frequency (MAF) and mean expected heterozygosity (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \overline{H} $$\end{document}H¯e) and population differentiation statistics such as Wright’s F-statistics (F_ST) and analysis of molecular variance (AMOVA) indicated that the rutabaga accessions from Norway, Sweden, Finland and Denmark were not genetically different from each other. In contrast, accessions from these countries were significantly different from the accessions from Iceland (P < 0.05). Bayesian analysis with the software STRUCTURE placed 66.9% of the rutabaga accessions into three to four clusters, while the remaining 33.1% constituted admixtures. Three multivariate analyses: principal coordinate analysis (PCoA), the unweighted pair group method with arithmetic mean (UPGMA) and neighbour-joining (NJ) clustering methods grouped the 124 accessions into four to six subgroups.

Conclusion

Overall, the correlation of the accessions with their geographic origin was very low, except for the accessions from Iceland. Thus, Icelandic rutabaga accessions can offer valuable germplasm for crop improvement.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07762-4.

Identification of putative key genes for thermal adaptation in the Japanese mantis shrimp (Oratosquilla oratoria) through population genomic analysis

Little is known about the mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different habitat temperature. Here, the genome-wide genetic information of three O. oratoria populations were obtained by IIB restriction site-associated DNA (2b-RAD) sequencing and 2403 single-nucleotide polymorphisms (SNPs) were identified. Based on the 2403 SNPs, we found a remarkable genetic differentiation between the Yellow Sea and the East China Sea groups of O. oratoria. Furthermore, 63 SNPs are thought to be associated with different sea temperatures. Based on the 63 SNPs, it is hypothesised that the long-term temperature differences may contribute to the variation of genes associated with multiple biological functions, such as material metabolism, cytoskeleton, cellular processes, inflammatory response and hormonal regulation. This study provides new information for elucidating the molecular mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different temperature.

Evaluation of the genetic diversity of wild Salvadora persica 'Arak' from Saudi Arabia

Assessment of genetic diversity is crucial for efficient selection genotypes in plant breeding and improvement programs. Studies of genetic diversity of S. persica are rare relative to the large species diversity in Saudi Arabia, despite its valuable importance as one of the most popular medicinal plants. We investigate the genetic variability and genetic differentiation among and within wild Salvadora persica populations distributed in four regions of Saudi Arabia. Twelve sequence-related amplified polymorphism (SRAP) primers combination generated 326 alleles, with an average of 27.2 alleles per primer. All primers showed 100 polymorphism percentage, and higher PIC values exceeded 0.90. Jaccard similarity values varied between 0.04 to 0.43, with an average of 0.31, which showed a weak relationship among the accessions and their origin. Based on UGPMA and principal coordinate analysis, accessions collected from the same region showed less aggregation. Genetic diversity parameters showed that both Aflaj and Joodah populations recorded the highest mean values for the effective number of alleles (1.26 and 1.24). Shannon index and genetic heterozygosity (0.23 and 0.15 for both populations), and percent of polymorphism 45.45% for Aflaj and 43.87 for Joodah population. Most of the genetic variation was because of differences within populations (77%) and 23% among populations. SRAP markers explored the genetic diversity among and within S. persica populations. In this work, genetic diversity within populations was high, and the population structure was weak. We detected no specific geographic structure, which may reveal an active movement of plants among populations.

Improved reference genome of the arboviral vector Aedes albopictus

BACKGROUND

The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.

RESULTS

We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.

CONCLUSION

The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Identification of a new Indian camel germplasm by microsatellite markers based genetic diversity and population structure of three camel populations

Camel invokes fascinating chapter of Indian desert history and is integral component of its ecosystem. Camel population has reached a crisis point after three decades of decline (75%) causing major concern to the policy makers. >28% of Indian camel is not yet characterized. It is imperative to describe country’s camel germplasm and its existing diversity for designing conservation plan. One such population is Sindhi, distributed along border with Pakistan. Twenty five microsatellite markers being valuable tool for estimating genetic diversity were selected to elucidate genetic variability and relationship of Sindhi with two registered camel breeds of India- Marwari and Kharai. The standard metrics of genomic diversity detected moderate variability in all the three populations. A total of 303 alleles with a mean of 8.116 ± 0.587 alleles per locus were found in total of 143 animals. Sindhi population had intermediate allelic diversity with 8.522 ± 1.063 alleles per locus. Corresponding values in Marwari and Kharai were 8.783 ± 0.962 and 7.043 ± 1.030, respectively. Genetic variability within the breeds was moderate as evidenced by the mean observed heterozygosity of 0.556 ± 0.025. Sindhi camel population harbors higher genetic variability (Ho = 0.594) as compared to the two registered camel breeds (Marwari, 0.543 and Kharai, 0.531). Mean expected heterozygosity under Hardy-Weinberg equilibrium was higher than the observed values across the three camel groups, indicating deviations from assumptions of this model. In fact, average positive F value of 0.084 to 0.206 reflected heterozygote deficiency in these populations. These Indian camel populations have not experienced serious demographic bottlenecks in the recent past. Differences among populations were medium and accounted for 7.3% of total genetic variability. Distinctness of three camel populations was supported by all the approaches utilized to study genetic relationships such as genetic distances, phylogenetic relationship, correspondence analysis, clustering method based on Bayesian approach and individual assignment. Sindhi camel population was clearly separated from two registered breeds of Indian camel. Results conclude Sindhi to be a separate genepool. Moderate genetic diversity provides an optimistic viewpoint for the survival of severely declining indigenous camel populations with appropriate planning strategies for conserving the existing genetic variation and to avoid any escalation of inbreeding.

Mitochondrial DNA (hypervariable region I) diversity in Basrah population - Iraq

In attempt to investigate the origin of Basrah, we examined the mitochondrial DNA(mt-DNA) variations by hypervariable segment 1(HVS1) Sequencing and determination of specific site haplogroups. In Basrah, no significant differences diversity among Iraqis' HVS1 compared with other countries. The values were within the range of gene diversity across the Middle East and exhibited the unimodal pattern of differences in the pairwise sequence. Given the small genetic differences between people living in this area, phylogenetic analysis showed a large variability of the communities of Basrah; they didn't cluster on the phylogenetic tree.

The ghost of temperature past: interactive effects of previous and current thermal conditions on gene expression in Manduca sexta

High temperatures can negatively impact the performance and survival of organisms, particularly ectotherms. While an organism's response to high temperature stress clearly depends on current thermal conditions, its response may also be affected by the temporal pattern and duration of past temperature exposures. We used RNA sequencing of Manduca sexta larvae fat body tissue to evaluate how diurnal temperature fluctuations during development affected gene expression both independently and in conjunction with subsequent heat stress. Additionally, we compared gene expression between two M. sexta populations, a lab colony and a genetically related field population that have been separated for >300 generations and differ in their thermal sensitivities. Lab-adapted larvae were predicted to show increased expression responses to both single and repeated thermal stress, whereas recurrent exposure could decrease later stress responses for field individuals. We found large differences in overall gene expression patterns between the two populations across all treatments, as well as population-specific transcriptomic responses to temperature; more differentially expressed genes were upregulated in the field compared with lab larvae. Developmental temperature fluctuations alone had minimal effects on long-term gene expression patterns, with the exception of a somewhat elevated stress response in the lab population. Fluctuating rearing conditions did alter gene expression during exposure to later heat stress, but this effect depended on both the population and the particular temperature conditions. This study contributes to increased knowledge of molecular mechanisms underlying physiological responses of organisms to temperature fluctuations, which is needed for the development of more accurate thermal performance models.

Selected neuropeptide genes show genetic differentiation between Africans and non-Africans

Background

Publicly available genome data provides valuable information on the genetic variation patterns across different modern human populations. Neuropeptide genes are crucial to the nervous, immune, endocrine system, and physiological homeostasis as they play an essential role in communicating information in neuronal functions. It remains unclear how evolutionary forces, such as natural selection and random genetic drift, have affected neuropeptide genes among human populations. To date, there are over 100 known human neuropeptides from the over 1000 predicted peptides encoded in the genome. The purpose of this study is to analyze and explore the genetic variation in continental human populations across all known neuropeptide genes by examining highly differentiated SNPs between African and non-African populations.

Results

We identified a total of 644,225 SNPs in 131 neuropeptide genes in 6 worldwide population groups from a public database. Of these, 5163 SNPs that had ΔDAF |(African - non-African)| ≥ 0.20 were identified and fully annotated. A total of 20 outlier SNPs that included 19 missense SNPs with a moderate impact and one stop lost SNP with high impact, were identified in 16 neuropeptide genes. Our results indicate that an overall strong population differentiation was observed in the non-African populations that had a higher derived allele frequency for 15/20 of those SNPs. Highly differentiated SNPs in four genes were particularly striking: NPPA (rs5065) with high impact stop lost variant; CHGB (rs6085324, rs236150, rs236152, rs742710 and rs742711) with multiple moderate impact missense variants; IGF2 (rs10770125) and INS (rs3842753) with moderate impact missense variants that are in linkage disequilibrium. Phenotype and disease associations of these differentiated SNPs indicated their association with hypertension and diabetes and highlighted the pleiotropic effects of these neuropeptides and their role in maintaining physiological homeostasis in humans.

Conclusions

We compiled a list of 131 human neuropeptide genes from multiple databases and literature survey. We detect significant population differentiation in the derived allele frequencies of variants in several neuropeptide genes in African and non-African populations. The results highlights SNPs in these genes that may also contribute to population disparities in prevalence of diseases such as hypertension and diabetes.

Genetic differentiation and population structure of Anopheles funestus from Uganda and the southern African countries of Malawi, Mozambique, Zambia and Zimbabwe

Background

Anopheles funestus (s.s.) is a primary vector of the malaria parasite Plasmodium falciparum in Africa, a human pathogen that causes almost half a million deaths each year. The population structure of An. funestus was examined in samples from Uganda and the southern African countries of Malawi, Mozambique, Zambia and Zimbabwe.

Methods

Twelve microsatellites were used to estimate the genetic diversity and differentiation of An. funestus from 13 representative locations across five countries. These were comprised of four sites from Uganda, three from Malawi and two each from Mozambique, Zambia and Zimbabwe.

Results

All loci were highly polymorphic across the populations with high allelic richness and heterozygosity. A high genetic diversity was observed with 2–19 alleles per locus and an average number of seven alleles. Overall, expected heterozygosity (H_e) ranged from 0.65 to 0.79. When samples were pooled three of the 12 microsatellite loci showed Hardy–Weinberg equilibrium. Unsupervised Bayesian clustering analysis of microsatellite data revealed two clusters with An. funestus samples from Mozambique, Uganda and Zambia falling into one group and Malawi and Zimbabwe into another. The overall genetic differentiation between the populations was moderate (F_ST = 0.116). Pairwise differentiation between the pairs was low but significant. A weak but significant correlation was established between genetic and geographical distance for most populations.

Conclusions

High genetic diversity revealed by the loci with low to moderate differentiation, identified two clusters among the An. funestus populations. Further research on the population dynamics of An. funestus in east and southern Africa is essential to understand the implications of this structuring and what effect it may have on the efficient implementation of mosquito vector control strategies.

Life history of Macrocheles muscaedomesticae (Parasitiformes: Macrochelidae): new insights on life history and evidence of facultative parasitism on Drosophila

Macrocheles muscaedomesticae is a cosmopolitan macrochelid mite whose populations have likely diverged considering the many locations they inhabit, but most of the work published on this mite species has been on the basis of their association with the house fly, Musca domestica. Here, we studied several aspects of the biology of M. muscaedomesticae associated with drosophilid flies collected in Alberta, Canada. We assessed the degree of divergence of our populations from others, compared their life history to other published populations and experimentally tested whether M. muscaedomesticae feeds on Drosophila hydei hosts by comparing the body mass of mites that attached to hosts to those that did not. There was no strong phylogenetic differentiation among any of the M. muscaedomesticae specimens, suggesting multiple recent introductions of this species to Canada. Compared to other populations, our mites exhibited lower fecundity, which may have been a result of the temperature or nematode-only diet in which they were maintained. Finally, mites that attached to hosts for 4 h weighed significantly more than those that did not. Without direct evidence for host tissue transfer to the mites, it is difficult to determine whether the mites are indeed feeding on their hosts while attached. However, the existing evidence for the costs fly hosts endure at the expense of these mites makes this relationship antagonistic.

New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa

Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.

Genetic diversity and population structure analysis of synthetic and bread wheat accessions in Western Siberia

Recurrent selection and intercrossing between best of the best parents in each generation of breeding cycle resulted in a narrower genetic diversity in elite wheat (Triticum aestivum L.) germplasm. Therefore, we investigated diverse source of 143 synthetic and bread wheat accessions for identifying potentially rich genetic resources for improving the genetic diversity in wheat. This study identified 47,526 genotyping-by-sequencing-derived SNP markers that were nearly evenly distributed across three genomes of wheat. The population structure analysis identified three distinct clusters (Japan synthetics, CIMMYT synthetics, and bread wheat) of wheat genotypes on the basis of type and geographical origin of wheat accessions. Population differentiation using analysis of molecular variance indicated 21% of the total genetic variance among subgroups and the remainder within subgroups. This study also identified that the Japan synthetic group was the most divergent group compared with other subgroups. The genetic diversity comparisons between synthetic and bread wheat lines showed that the gene diversity of synthetic wheat was 33% higher than bread wheat accessions, indicating the potential use of these lines for broadening the genetic diversity of modern wheat cultivars. The results from this study will be helpful in further understanding genomic features of wheat and facilitate their use in wheat breeding programs.

From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

Background

Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAMtools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes.

Results

Although we identified orders of magnitude fewer SNPs in our devil dataset than for goose, we found remarkable symmetry between the two species in our assessment of software performance. For both datasets, all three methods were able to delineate population structure, even with varying numbers of loci. For both species, population structure inferences were influenced by the percent of missing data.

Conclusions

For studies of non-model species with a reference genome, we recommend combining Stacks output with further filtering (as included in our R pipeline) for population genetic studies, paying particular attention to potential impact of missing data thresholds. We recognise SAMtools as a viable alternative for researchers more familiar with this software. We caution against the use of GATK in studies with limited computational resources or time.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5806-y) contains supplementary material, which is available to authorized users.

Conservation implications of population genetic structure in a threatened orchid Cypripedium tibeticum

Cypripedium tibeticum is a threatened orchid which efficient conservation requires knowledge of its extent and structure of genetic variation. Using two chloroplast DNA fragments (rps16 and trnL-F), we analyzed 157 individuals from 9 populations representing the species range in China. Seven haplotypes were identified. C. tibeticum had high total genetic diversity (H T = 0.80) with major contribution to this diversity made by among-population component (G ST  = 0.64, Φ ST  = 0.86). However, despite high population differentiation there was no clear phylogeographic structure. The populations CY and DC made the greatest contribution to the total gene diversity as well as allelic richness. The possible mechanisms and implications of these findings for conservation of the species are discussed.

Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation?

Background

Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals.

Results

The results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations.

Conclusions

Geographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1317-8) contains supplementary material, which is available to authorized users.

Delineating species along shifting shorelines: Tropheus (Teleostei, Cichlidae) from the southern subbasin of Lake Tanganyika

BACKGROUND

Species delineation is particularly challenging in taxa with substantial intra-specific variation. In systematic studies of fishes, meristics and linear measurements that describe shape are often used to delineate species. Yet, little is known about the taxonomic value of these two types of morphological characteristics. Here, we used Tropheus (Teleostei, Cichlidae) from the southern subbasin of Lake Tanganyika to test which of these types of characters best matched genetic lineages that could represent species in this group of stenotypic rock-dwelling cichlids. We further investigated intra-population variation in morphology. By linking this to a proxy of a population's age, we could assess the evolutionary stability of different kinds of morphological markers.

RESULTS

Morphological data was collected from 570 specimens originating from 86 localities. An AFLP approach revealed the presence of five lineages in the southern subbasin: T. moorii, T. brichardi, T. sp. 'maculatus', T. sp. 'Mpimbwe' and T. sp. 'red', which we consider to represent distinct species. Although both types of morphological data supported this classification, a comparison of PST-values that describe inter-population morphological differentiation, revealed a better correspondence between the taxon delineation based on AFLP data and the patterns revealed by an analysis of meristics than between the AFLP-based taxon delineation and the patterns revealed by an analysis of shape. However, classifying southern populations of Tropheus was inherently difficult as they contained a large amount of clinal variation, both in genetic and in morphological data, and both within and among species. A scenario is put forward to explain the current-day distribution of the species and colour varieties and the observed clinal variation across the subbasin's shoreline. Additionally, we observed that variation in shape was larger in populations from shallow shores whereas populations from steep shores were more variable in meristics. This difference is explained in terms of the different timescales at which small and large scale lake level fluctuations affected populations of littoral cichlids at steep and shallow shores.

CONCLUSIONS

Our results showed meristics to be more evolutionary stable, and of higher taxonomic value for species delimitation in Tropheus, than linear measurements that describe shape. These results should be taken into account when interpreting morphological differences between populations of highly stenotypic species, such as littoral cichlids from the Great East African Lakes.

Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny

Genetic structure was evaluated among wild Alpinia nigra (Gaertn.) B.L. Burtt, populations. The information of genetic relatedness was developed using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and barcoding loci (plastid and mitochondrial). The order (high to low) of Shannon's information index (I) and Nei's gene diversity (h) from the populations was: "IIT Guwahati" > "Amingaon" > "Saraighat". Genetic diversity decreased and genetic differentiation increased among the three populations. We observed no isolation by distance thus lower amount of gene flow was observed. Narrow range of genetic distance among the three populations and appearance of two distinct clusters strengthened the geographical isolation in dendrogram and principal component analysis. No mutation among the three populations was observed for seven plastid loci and two mitochondrial tested suggesting the taxonomic homogeneity. The phylogeny based on nine barcoding loci supported our observation that individuals of IIT Guwahati were partially isolated from the outside populations. Our study will provide a backbone for developing strategies to resist habitat fragmentation of Zingiberaceous plants.

Genetic resolution of applied biosystems™ precision ID Ancestry panel for seven Asian populations

Massively parallel sequencing (MPS) offers additional information in cases that lack reference samples for comparison. The HID-Ion AmpliSeq Ancestry Panel is a forensic multiplex platform consisting of 165 autosomal markers designed to provide biogeographic ancestry information. We analyzed seven different population groups from Asia to assess the accuracy and reliability of analysis, using this panel. In this study, we have designated 750 unrelated Asians, from southern China (n = 99), Beijing (n = 100), Japan (n = 101), Korea (n = 100), Vietnam (n = 100), Nepal (n = 100), India (n = 51), and Pakistan (n = 99). The likelihood ratios of 750 Asians were calculated, using the Torrent Server and the HID SNP Genotyper Plugin Version 4.3.2. The results reveal that all Northeast Asians (China, Japan, and Korea), and Vietnamese, were predicted as East Asians with the highest ethnicity likelihood values from reference data. Although the samples from Nepal, India and Pakistan (Southwest Asians), were predominantly predicted as South Asians, there were seven cases of which results revealed as Europeans, with similar likelihood patterns. Population structure analysis indicated that Southwest Asians have a genetic profile that is distinguishable from those of other Asian populations. This panel was validated for potential usefulness in forensic analysis and the findings could be used as a basis for building additional Asian specific reference databases. Nevertheless, additional analyses comprising larger sample sizes will be necessary, especially Southeast Asians, to fully understand the Asian population structure, and to discriminate them with further details.

Complex signatures of genomic variation of two non-model marine species in a homogeneous environment

BACKGROUND

Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist.

RESULTS

Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region.

CONCLUSIONS

Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.

Pleistocene land bridges act as semipermeable agents of avian gene flow in Wallacea

Cyclical periods of global cooling have been important drivers of biotic differentiation throughout the Quaternary. Ice age-induced sea level fluctuations can lead to changing patterns of land connections, both facilitating and disrupting gene flow. In this study, we test if species with differing life histories are differentially affected by Quaternary land connections. We used genome-wide SNPs in combination with mitochondrial gene sequences to analyse levels of divergence and gene flow between two songbird complexes across two Wallacean islands that have been repeatedly connected during glaciations. Although the two bird complexes are similar in ecological attributes, the forest and edge-inhabiting golden whistler Pachycephala pectoralis is comparatively flexible in its diet and niche requirements as compared to the henna-tailed jungle-flycatcher Cyornis colonus, which is largely restricted to the forest interior. Using population-genomic and coalescent approaches, we estimated levels of gene flow, population differentiation and divergence time between the two island populations. We observed higher levels of differentiation, an approximately two to four times deeper divergence time and near-zero levels of gene flow between the two island populations of the more forest-dependent henna-tailed jungle-flycatcher as compared to the more generalist golden whistler. Our results suggest that Quaternary land bridges act as semipermeable agents of gene flow in Wallacea, allowing only certain taxa to connect between islands while others remain isolated. Quaternary land bridges do not accommodate all terrestrial species equally, differing in suitability according to life history and species biology. More generalist species are likely to use Quaternary land connections as a conduit for gene flow between islands whereas island populations of more specialist species may continue to be reproductively isolated even during periods of Quaternary land bridges.

Genetic structure and polymorphism analysis of Xinjiang Hui ethnic minority based on 21 STRs

In the present study, we calculated the allelic frequencies and forensic descriptive parameters of Hui ethnic minority on the basis of 21 short tandem repeat (STR) loci aiming at understanding population structure better and enriching population genetic database. Bloodstain samples of 506 unrelated healthy Hui individuals in Xinjiang Uygur Autonomous Region were collected. Altogether 268 alleles were observed and the allelic frequencies ranged from 0.0010 to 0.5306. The combined power of discrimination and the cumulative probability of exclusion of the 21 STR loci in Hui ethnic minority were 0.9999999999999999999999998697 and 0.9999999968, respectively. Population data obtained manifested that the panel of 21 STR loci could provide robust genetic information for individual identification and paternity testing involved in forensic applications for Huis of Xinjiang Region. Furthermore, the present results of interpopulation differentiations, phylogenetic trees and principal component analysis which were conducted based on the overlapping 16 STR loci revealed that Hui group was genetically close to Xibe ethnic group and Han populations from different regions.

Population differentiation in allele frequencies of obesity-associated SNPs

BACKGROUND

Obesity is emerging as a global health problem, with more than one-third of the world's adult population being overweight or obese. In this study, we investigated worldwide population differentiation in allele frequencies of obesity-associated SNPs (single nucleotide polymorphisms).

RESULTS

We collected a total of 225 obesity-associated SNPs from a public database. Their population-level allele frequencies were derived based on the genotype data from 1000 Genomes Project (phase 3). We used hypergeometric model to assess whether the effect allele at a given SNP is significantly enriched or depleted in each of the 26 populations surveyed in the 1000 Genomes Project with respect to the overall pooled population. Our results indicate that 195 out of 225 SNPs (86.7%) possess effect alleles significantly enriched or depleted in at least one of the 26 populations. Populations within the same continental group exhibit similar allele enrichment/depletion patterns whereas inter-continental populations show distinct patterns. Among the 225 SNPs, 15 SNPs cluster in the first intron region of the FTO gene, which is a major gene associated with body-mass index (BMI) and fat mass. African populations exhibit much smaller blocks of LD (linkage disequilibrium) among these15 SNPs while European and Asian populations have larger blocks. To estimate the cumulative effect of all variants associated with obesity, we developed the personal composite genetic risk score for obesity. Our results indicate that the East Asian populations have the lowest averages of the composite risk scores, whereas three European populations have the highest averages. In addition, the population-level average of composite genetic risk scores is significantly correlated (R2 = 0.35, P = 0.0060) with obesity prevalence.

CONCLUSIONS

We have detected substantial population differentiation in allele frequencies of obesity-associated SNPs. The results will help elucidate the genetic basis which may contribute to population disparities in obesity prevalence.

Patrilineal background of the She minority population from Chaoshan Fenghuang Mountain, an isolated mountain region, in China

The She ethnic minority population is distributed in southern China. The origin of the She population has been controversial. The purpose of this work was to investigate the genomic diversity of She. The Chaoshan She population living in the Chaoshan Fenghuang mountain is a relatively isolated population. We detected 14 Y chromosome biallelic markers (Y-SNPs) and 6 Y chromosome short tandem repeat (Y-STR) loci in Chaoshan She people. Y-SNP analysis showed the Chaoshan She was closely related to the Chaoshan Hakka, Chaoshanese, Tujia and Gaoshan national minority. Compared with the Fujian She, the Chaoshan She maintained a more southern native genetic structure. Y-STR analysis revealed the Chaoshan She population was more closely related to the Hakka population than the other Hans. We concluded the Chaoshan She population had a closer genetic relationship with the southern national minority and Hakka Han and it may be representative of She ancestors' patrilineal genetic structure.

Genetic structure of a regionally endangered orchid, the dark red helleborine (Epipactis atrorubens) at the edge of its distribution

The genetic structure and diversity of species is determined by both current population dynamics and historical processes. Population genetic structure at the edge of the distribution is often expected to differ substantially from populations at the centre, as these edge populations are often small and fragmented. In addition, populations located in regions that have experienced repeated glaciations throughout the Pleistocene, may still carry imprints from the genetic consequences of frequent distribution shifts. Using chloroplast DNA sequences and nuclear microsatellite markers we studied the genetic structure of Epipactis atrorubens at the northern edge of its distribution. Contrary to populations in the centre of the distribution, populations at the northern range are regionally endangered as they are small and disjunct. Sequence data of 2 chloroplast loci and allelic data from 6 nuclear microsatellite markers were obtained from 297 samples from Finland, Estonia and Russia. We sought for genetic indicators of past population processes, such as post-glacial colonisation history of E. atrorubens. As expected, we observed low genetic variation, in terms of numbers of substitutions, haplotypes and alleles, and significant levels of differentiation, especially pronounced in the chloroplast DNA. These features suggest that the edge populations could be prone to extinction.

Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers

Small giant clam, Tridacna maxima, widely distributed from French Polynesia to East Africa, has faced population declines due to over-exploitation. Comoros islands are an important biogeographic region due to potential richness of marine species, but no relevant information is available. In order to facilitate devising effective conservation management plan for T. maxima, nine microsatellite markers were used to survey genetic diversity and population differentiation of 72 specimens collected from three Comoros islands, Grande Comore, Moheli and Anjouan. A total of 51 alleles were detected ranged from 2 to 8 per locus. Observed and expected heterozygosity varied from 0.260 to 0.790 and from 0.542 to 0.830, respectively. All populations have high genetic diversity, especially the population in Moheli, a protected area, has higher genetic diversity than the others. Significant heterozygote deficiencies were recorded, and null alleles were probably the main factor leading to these deficits. F_ST value indicated medium genetic differentiation among the populations. Although significant, AMOVA revealed 48.9 % of genetic variation within individuals and only a small variation of 8.9 % was found between populations. Gene flow was high (Nm = 12.40) between Grande Comore and Moheli, while lower (Nm = 1.80) between Grande Comore and Anjouan, explaining geographic barriers to genetic exchanges might exist in these two islands. Global gene flow analysis (Nm = 5.50) showed that larval dispersal is enough to move between the islands. The high genetic diversity and medium population differentiation revealed in the present study offer useful information on genetic conservation of small giant clams.

Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species

BACKGROUND

Loss of genetic variability due to environmental changes, limitation of gene flow between pools of individuals or putative selective pressure at specific markers, were previously documented for Antarctic notothenioid fish species. However, so far no studies were performed for the Gaudy notothen Lepidonotothen nudifrons. Starting from a species-specific spleen transcriptome library, we aimed at isolating polymorphic microsatellites (Type I; i.e. derived from coding sequences) suitable to quantify the genetic variability in this species, and additionally to assess the population genetic structure and demography in nototheniids.

RESULTS

We selected 43,269 transcripts resulting from a MiSeq sequencer run, out of which we developed 19 primer pairs for sequences containing microsatellite repeats. Sixteen loci were successfully amplified in L. nudifrons. Eleven microsatellites were polymorphic and allele numbers per locus ranged from 2 to 17. In addition, we amplified loci identified from L. nudifrons in two other congeneric species (L. squamifrons and L. larseni). Thirteen loci were highly transferable to the two congeneric species. Differences in polymorphism among species were detected.

CONCLUSIONS

Starting from a transcriptome of a non-model organism, we were able to identify promising polymorphic nuclear markers that are easily transferable to other closely related species. These markers can be a key instrument to monitor the genetic structure of the three Lepidonotothen species if genotyped in larger population samples. When compared with anonymous loci isolated in other notothenioids, i.e. Type II (isolated from genomic libraries), they offer the possibility to test how the effects of occurring environmental change influence the population genetic structure in each species and subsequently the composition of the entire ecosystem.

Evolutionary triangulation: informing genetic association studies with evolutionary evidence

Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with diseases appropriately distributed among populations. Our results indicate that ET can filter association results to improve our ability to discover disease loci.

Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

Single nucleotide polymorphism (SNP) is a powerful molecular marker technique that has been widely used in population genetics and molecular mapping studies for various organisms. However, the technique has not been used for studying Puccinia striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen. In this study, we developed over a hundred secreted protein gene-derived SNP (SP-SNP) markers and used 92 markers to study the population structure of Pst. From 352 isolates collected in the United States, we identified 242 multi-locus genotypes. The SP-SNP genotypes had a moderate, but significant correlation with the virulence phenotype data. Clustering of the multi-locus genotypes was consistent by various analyses, revealing distinct genetic groups. Analysis of molecular variance detected significant differences between the eastern and western US Pst populations. High heterozygosity was found in the US population with significant differences identified among epidemiological regions. Analysis of population differentiation revealed that populations between the eastern and western US were highly differentiated while moderate differentiation was found in populations within the western or eastern US. Isolates from the western US were more diverse than isolates from the eastern US. The information is useful for guiding the disease management in different epidemiological regions.

Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid

We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An = 4.0, Ho = 0.436, He = 0.448) and cpDNA microsatellites (average An = 1.57, Nh = 1.57 and H = 0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst = 0.075; ϕPT = 0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2) = 0.209, P = 0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species.

24 Y-chromosomal STR haplotypic polymorphisms for Chinese Uygur ethnic group and its phylogenic analysis with other Chinese groups

The Uygur ethnic minority is the largest ethnic group in the Xinjiang Uygur Autonomous Region of China, and is a precious resource for the study of ethnogeny and forensic biology. Previous studies have focused on the genetic background of the Uygur group, however, the patrilineal descent of the group is still unclear. In this study, we investigated the genetic diversity of 24 Y-STR loci in the Uygur group and analyzed the population differentiations as well as the genetic relationships between the Uygur group and other previously reported populations using 17 Y-filer loci. According to haplotypic analysis of the 24 Y-STR loci in 109 Uygur individuals, 104 different haplotypes were obtained, 99 of which were unique. The haplotypic diversity and discrimination capacity of these 24 Y-STR loci in Uygur group were 0.9992 and 0.9541, respectively. An additional 7 loci (DYS388, DYS444, DYS447, DYS449, DYS522, and DYS527a,b) showed high genetic diversity and improved the overall discrimination capacity of the 24 Y-STR system. Pairwise Fst and neighbor-joining analysis showed that the Uygur group was genetically close to the Han populations from different regions.

Transcriptome analyses of Anguillicola crassus from native and novel hosts

Anguillicola crassus is a swim bladder nematode of eels. The parasite is native to the Asian eel Anguilla japonica, but was introduced to Europe and the European eel Anguilla anguilla in the early 1980s. A Taiwanese source has been proposed for this introduction. In the new host in the recipient area, the parasite appears to be more pathogenic. As a reason for these differences, genetically fixed differences in infectivity and development between Taiwanese and European A.crassus have been described and disentangled from plasticity induced by different host environments. To explore whether transcriptional regulation is involved in these lifecycle differences, we have analysed a “common garden”, cross infection experiment, using deep-sequencing transcriptomics. Surprisingly, in the face of clear phenotypic differences in life history traits, we identified no significant differences in gene expression between parasite populations or between experimental host species. From 120,000 SNPs identified in the transcriptome data we found that European A. crassus were not a genetic subset of the Taiwanese nematodes sampled. The loci that have the major contribution to the European-Taiwanese population differentiation show an enrichment of synonymous and non-coding polymorphism. This argues against positive selection in population differentiation. However, genes involved in protein processing in the endoplasmatic reticulum membrane and genes bearing secretion signal sequences were enriched in the set of genes most differentiated between European and Taiwanese A. crassus. These genes could be a source for the phenotypically visible genetically fixed differences between European and Taiwanese A. crassus.

Intensive sampling identifies previously unknown chemotypes, population divergence and biosynthetic connections among terpenoids in Eucalyptus tricarpa

Australian members of the Myrtaceae produce large quantities of ecologically and economically important terpenes and display abundant diversity in both yield and composition of their oils. In a survey of the concentrations of leaf terpenes in Eucalyptus tricarpa (L.A.S. Johnson) L.A.S. Johnson & K.D. Hill, which were previously known from few samples, exceptional variability was found in composition. The aim was to characterize the patterns of variation and covariation among terpene components in this species and to use this information to enhance our understanding of their biosynthesis. There were marked discontinuities in the distributions of numerous compounds, including the overall proportions of mono- and sesquiterpenes, leading us to delineate three distinct chemotypes. Overall, positive covariation predominated, but negative covariation suggested competitive interactions involved in monoterpene synthesis. Two groups of covarying monoterpenes were found, each of which was positively correlated with a group of sesquiterpenes and negatively correlated with the alternate sesquiterpene group. These results imply substantial cross-talk between mono- and sesquiterpene biosynthesis pathways. However, only those compounds hypothesized to share final carbocation intermediates or post-processing steps were strongly positively correlated within chemotypes. This suggests that the broader patterns of covariation among groups of compounds may result from co-regulation of multiple biosynthetic genes, controlling the complex terpene profiles of the chemotypes of Eucalyptus.

Genetic and morphological population differentiation in the rock-dwelling and specialized shrimp-feeding cichlid fish species Altolamprologus compressiceps from Lake Tanganyika, East Africa

With about 250 endemic species, Lake Tanganyika contains an extraordinarily diverse cichlid fish fauna, and thus represents an ideal model system for the study of pathways and processes of speciation. The Lamprologini form the most species-rich tribe in Lake Tanganyika comprising about 100 species in seven genera, most of which are endemic to the lake. They are territorial substrate-breeders and represent a monophyletic tribe. By combined analysis of population genetics and geometric morphometric markers, we assessed gene flow among three populations of the highly specialized shrimp-feeding rock-dweller Altolamprologus compressiceps, separated by geographic distance and ecological barriers. Five highly polymorphic microsatellite markers were analyzed in conjunction with 17 landmarks in order to compare genetic differences to body shape differences among populations. Both genetic and morphological analyses revealed significant differentiation among the three studied populations. A significant, but overall relatively low degree of genetic differentiation supports a very recent divergence. Phenotypic differentiation was primarily found in the head region of A. compressiceps. In agreement with findings in other cichlid species, similar adaptations to specialized feeding mechanisms can consequently lead to marginal shape changes in the trophic apparatus.

Population differentiation of migratory directions in birds: comparison between ringing results and orientation behaviour of hand-raised migrants

Blackcaps (Sylvia atricapilla) from five areas in Central Europe were hand-raised. Their autumn migratory orientation was tested in funnel-shaped cages. Their directional choices were compared to recoveries of conspecifics ringed during the breeding season in the same areas, which are situated on a transect across a migratory divide between southeastward and southwestward migrating populations. Results from ringing and orientation tests were in good agreement with respect to mean direction and dispersion of flight directions. An exception is the area around Linz (NW Austria), right on the migratory divide, where ringing yielded a strong scatter, but hand-raised birds chose westerly directions. The recent establishment of a novel migration route toward the British Isles was reflected in both data sets: in southern Germany the percentage of northwestward migrants is 6.8% according to orientation tests and 11.8% according to ringing recoveries. Testing the orientation of young passerines in captivity can yield valuable information about population differentiation of migratory behaviour. It is more efficient than ringing in this respect, because it circumvents the low recovery rates and is free of biases affecting ringing data. In the blackcap, geographic differentiation of migratory directions occurs on a finer scale than previously recognized and can change significantly within 2-3 decades.