Estimates Of Nucleotide Diversity Research Articles

Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection.

In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.

Kernel density estimation of allele frequency including undetected alleles.

Whereas undetected species contribute to estimation of species diversity, undetected alleles have not been used to estimated genetic diversity. Although random sampling guarantees unbiased estimation of allele frequency and genetic diversity measures, using undetected alleles may provide biased but more precise estimators useful for conservation. We newly devised kernel density estimation (KDE) for allele frequency including undetected alleles and tested it in estimation of allele frequency and nucleotide diversity using population generated by coalescent simulation as well as well as real population data. Contrary to expectations, nucleotide diversity estimated by KDE had worse bias and accuracy. Allele frequency estimated by KDE was also worse except when the sample size was small. These might be due to finity of population and/or the curse of dimensionality. In conclusion, KDE of allele frequency does not contribute to genetic diversity estimation.

Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.

Genetic diversity refers to the variety of genetic traits within a population or a species. It is an essential aspect of both plant ecology and plant breeding because it contributes to the adaptability, survival, and resilience of populations in changing environments. This chapter outlines a pipeline for estimating genetic diversity statistics from reduced representation or whole genome sequencing data. The pipeline involves obtaining DNA sequence reads, mapping the corresponding reads to a reference genome, calling variants from the alignments, and generating an unbiased estimation of nucleotide diversity and divergence between populations. The pipeline is suitable for single-end Illumina reads and can be adjusted for paired-end reads. The resulting pipeline provides a comprehensive approach for aligning and analyzing sequencing data to estimate genetic diversity.

Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses.

The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues. The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases. The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens. The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed. The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.

A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference.

Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.

Multiple founding paternal lineages inferred from the newly-developed 639-plex Y-SNP panel suggested the complex admixture and migration history of Chinese people

BackgroundNon-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity.ResultsHere, we developed one highest-resolution Y-chromosome single nucleotide polymorphism (Y-SNP) panel targeted for uniparental genealogy reconstruction and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs. We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 256 terminal Y-chromosomal lineages with frequency ranging from 0.0010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517, and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian, and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history.ConclusionsOur findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the promotion of Y-chromosome-based forensic applications.

Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms.

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.

Average weighted nucleotide diversity is more precise than pixy in estimating the true value of π from sequence sets containing missing data.

Nucleotide diversity remains an important statistic in population genetic/genomic studies. Although recent advances in massive sequencing make generating sequence data sets cheaper and faster, currently used technologies often introduce substantial amounts of missing nucleotides in their output. A novel method of estimating π from data sets containing missing data - pixy - has also recently been proposed. In this study, the pixy estimator, πpixy , was compared to average weighted nucleotide diversity, πW . The estimators were tested both on sequences simulated in fastsimcoal and real sequence sets. Both sets were modified by random insertion of missing nucleotides. Weighted nucleotide diversity performed better in all pairwise comparisons. It was characterized by a smaller error and a narrower distribution of the results. πpixy tends to overestimate the nucleotide diversity when both the proportion of missing data and the level of variation is low. Of the two estimators, only πW estimated the true nucleotide diversity in a part of the simulations. A simple formula for estimating πW allows for easy integration of the estimator in packages such as pixy, which would allow obtaining more precise estimates of nucleotide diversity either in a sliding window or for discrete genomic regions.

Genetic Variations and Expansion of the Blue Swimmer Crab (Portunus pelagicus) in Southeast Asia

Blue swimmer crabs (Portunus pelagicus) primarily inhabit the coastal regions of Southeast Asia. This study aimed to examine their population genetic structure, phylogeography, and historical demography by applying partial sequences to the control region in the mitochondrial DNA. The analysis focused on 6 populations comprising 166 individual samples collected from Taiwan (Kezailiao Kaohsiung (KK) and Penghu (PH)), mainland China (Xiamen (XM) and Hong Kong (HK)), Vietnam (Hanoi (VN)), and Singapore (SGP). The estimated nucleotide diversity (π) for all of the samples was 0.062, with values ranging between 0.018 (PH) and 0.045 (HK). Our study collected 116 haplotypes and classified them into lineages A and B. The XM, HK, VN, and SGP populations made up lineage A, and the PH and KK populations comprised lineage B. For each lineage, the results highlighted indications of demographic expansion. Lineage A can be traced back to the second-to-last interglacial period, while lineage B possibly originated in the last glacial period. There were significant differences in the FST values among the six populations, except for the pairs HK–XM and PH–KK. In conclusion, the phylogeography and genetic structure of P. pelagicus in Southeast Asia were potentially affected by the Pleistocene glacial cycles and human introduction. These findings further highlight the possible dispersal routes of P. pelagicus throughout Southeast Asia.

Parthenogenesis doubles the rate of amino acid substitution in whiptail mitochondria.

Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the dN/dS ratios in asexual vertebrate lineages in the genus Aspidoscelis using whole mitochondrial genomes from seven asexual and five sexual species. We found higher dN/dS ratios in asexual Aspidoscelis species, indicating that asexual whiptails accumulate nonsynonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provide empirical evidence to corroborate the connection between asexuality and increased amino acid substitutions in asexual vertebrate lineages.

Molecular ecology of a shallow water shrimp, Acetes sibogae sibogae Hansen 1919: Evidence for strongly limited gene flow across the western Pacific

AbstractThe shallow water shrimp Acetes sibogae sibogae is an ecological and economically important organism in the Asian region. We assessed the genetic diversity and population structure of this species based on samples obtained from eight sites in Japan, the Philippines and Indonesia. Nucleotide sequence analyses were performed based on PCR‐amplified mitochondrial DNA fragments comprising the control region and part of the 12S rRNA gene. In total, 656 bp nucleotide sequences were obtained from 377 individuals. The results show a low haplotype diversity value in shrimp from the Kokuba‐gawa River (0.5) in Japan and intermediate values (0.79–0.99) in other populations. While nucleotide diversity estimates in all sampled localities were lower (0.17%–0.86%) than those reported in other crustaceans, analysis of molecular variance revealed significant genetic differentiation (p < .001) among all sites. Furthermore, the mean fixation index estimate was very high (FST: 0.27), indicating that dispersal potential among sites was low and gene flow, therefore, was restricted. The mismatch distribution of pairwise differences between haplotypes indicated that A. s. sibogae did not fit a sudden population expansion model. Overall, the present study indicates that wild stocks of A. s. sibogae on Okinawa‐jima Island and the Philippine and Indonesian Archipelagos should be assigned high importance for conservation management of this species because adapted genotypes have significant evolutionary potential during environmental changes.[Correction added on 5th February 2022, after first online publication: Values have been corrected in the Abstract section.]

Hierarchical genetic structure and implications for conservation of the world\u2019s largest salmonid, Hucho taimen

Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.

Pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data.

Population genetic analyses often use summary statistics to describe patterns of genetic variation and provide insight into evolutionary processes. Among the most fundamental of these summary statistics are π and dXY , which are used to describe genetic diversity within and between populations, respectively. Here, we address a widespread issue in π and dXY calculation: systematic bias generated by missing data of various types. Many popular methods for calculating π and dXY operate on data encoded in the variant call format (VCF), which condenses genetic data by omitting invariant sites. When calculating π and dXY using a VCF, it is often implicitly assumed that missing genotypes (including those at sites not represented in the VCF) are homozygous for the reference allele. Here, we show how this assumption can result in substantial downward bias in estimates of π and dXY that is directly proportional to the amount of missing data. We discuss the pervasive nature and importance of this problem in population genetics, and introduce a user-friendly UNIX command line utility, pixy, that solves this problem via an algorithm that generates unbiased estimates of π and dXY in the face of missing data. We compare pixy to existing methods using both simulated and empirical data, and show that pixy alone produces unbiased estimates of π and dXY regardless of the form or amount of missing data. In summary, our software solves a long-standing problem in applied population genetics and highlights the importance of properly accounting for missing data in population genetic analyses.

Gene Genealogies Reveal High Nucleotide Diversity and Admixture Haplotypes Within Three Alternaria Species Associated with Tomato and Potato.

Early blight (EB) and leaf blight are two destructive diseases of tomato in North Carolina (NC), caused by Alternaria linariae and A. alternata, respectively. During the last decade, EB caused by A. solani has increased in potato-producing areas in Wisconsin (WI). We collected 152 isolates of three Alternaria spp. associated with tomato and potato in NC and WI and used the gene genealogical approach to compare the genetic relationships among them. Two nuclear genes: the glyceraldehyde-3-phosphate dehydrogenase (GPDH), RNA polymerase second largest subunit (RPB2), and the rDNA internal transcribed spacer (ITS) region of these isolates were sequenced. Besides, sequences of the GPDH locus from international isolates described in previous studies were included for comparison purposes. A set of single nucleotide polymorphisms was assembled to identify locus-specific and species-specific haplotypes. Nucleotide diversity varied among gene sequences and species analyzed. For example, the estimates of nucleotide diversity and Watterson's theta were higher in A. alternata than in A. linariae and A. solani. There was little or no polymorphisms in the ITS sequences and thus restricted haplotype placement. The RPB2 sequences were less informative to detect haplotype diversity in A. linariae and A. solani, yet six haplotypes were detected in A. alternata. The GPDH sequences enabled strongly supported phylogenetic inferences with the highest haplotype diversity and belonged to five haplotypes (AaH1 to AaH5), which consisted of only A. alternata from NC. However, 13 haplotypes were identified within and among A. linariae and A. solani sequences. Among them, six (AsAlH1 to AsAlH6) were identical to previously reported haplotypes in global samples and the remaining were new haplotypes. The most divergent haplotypes were AaH1, AsAlH2/AsAlH3, and AsAlH4 and consisted exclusively of A. alternata, A. linariae, and A. solani, respectively. Neutrality tests suggested an excess of mutations and population expansion, and selection may play an important role in nucleotide diversity of Alternaria spp.

Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication.

Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with regard to the processes producing observed levels of standing genetic variation. Here, we analyzed sequence diversity in cultivated sunflower (Helianthus annuus L.) and its wild progenitor (common sunflower, also H. annuus) to reconstruct phylogeographic relationships and population genetic/demographic patterns across sunflower. In common sunflower, south-north patterns in the distribution of nucleotide diversity and lineage splitting indicate a history of rapid postglacial range expansion from southern refugia. Cultivated sunflower accessions formed a clade, nested among wild populations from the Great Plains, confirming a single domestication event in central North America. Furthermore, cultivated accessions sorted by market type (i.e., oilseed vs. confectionery) rather than breeding pool, recapitulating the secondary development of oil-rich cultivars during its breeding history. Across sunflower, estimates of nucleotide diversity and effective population sizes suggest that cultivated sunflower underwent significant population bottlenecks following its establishment ~5000 years ago. The patterns inferred here corroborate those from previous studies of sunflower domestication, and provide a comprehensive overview of its evolutionary history.

Genetic variation in morphologically divergent mainland and island populations of Soemmerring’s gazelles (Nanger soemmerringii)

This study focuses on the taxonomic, evolutionary and conservation implications of a striking reduction in body size previously observed in an island population of gazelles by comparing the genetic structure of island and mainland populations. Mitochondrial sequence diversity of the mainland population was found to be comparable to that of other true gazelles of East Africa. We discuss this in the context of the prolonged armed conflict in our study region. In contrast, the gazelles on Dahlak Kebir, one of the over 200 islands and islets of the Dahlak archipelago on the Red Sea, were found to be genetically depauperate. Nucleotide and haplotype diversity estimates were a sixth and a third of that of the mainland population respectively. Using estimates of Tajima’s D statistic, we inferred that the Dahlak population has undergone expansion after a recent bottleneck. A minimum spanning genealogical network of mitochondrial control region sequences produced testable hypotheses on the route and timing of the colonization of Dahlak Kebir by gazelles from the mainland. Our mitochondrial DNA dataset has resolved the taxonomic ambiguity of the island gazelles. Their genetic distinctiveness and, their striking conformity to the Island Rule that was highlighted in a previous study, are discussed from evolutionary and conservation perspectives.

Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool‐seq data to generate a de novo genome assembly for mining exons, upon which Pool‐seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual‐based single nucleotide polymorphisms [SNPs]) and from mapping the Pool‐seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (π¯ ≈ 0.002 and π¯ ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high‐quality reference assembly from a divergent species. We conclude that the Pool‐seq‐only approach can be suitable for detecting and quantifying genome‐wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

Purifying selection does not drive signatures of convergent local adaptation of lodgepole pine and interior spruce

BackgroundLodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported.ResultsWe analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima’s D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization.ConclusionsThe results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.

Patterns of nucleotide diversity for different domains of centromeric histone H3 (CENH3) gene in Secale L.

Rye (Secale) is among staple cereals along with other members of the Triticeae tribe: wheat and barley. The genus Secale includes perennial and annual, cross-pollinating and self-pollinating species, and they can be donors of valuable genes in wheat and rye breeding programs. Studies of the structure of the gene for centromeric histone H3 (CENH3), essential for centromere functions, are relevant to the breeding of agronomically important crops. We have investigated the nucleotide diversity of sequences of two variants of the rye CENH3 gene inside the N-terminal tail (NTT) and the conservative HFD (histone fold domain) domain in the genus Secale. The mean values of nucleotide diversity in the NTT and HFD of wild cross- and self-pollinating taxa are close in αCENH3: πtot = 0.0176–0.0090 and 0.0136–0. 0052, respectively. In the case of βCENH3, the mean values for NTT (πtot = 0.0168–0.0062) are lower than for HFD (πtot = 0.0259–0.084). The estimates of nucleotide and haplotype diversity per site for the CENH3 domains are considerably lower in taxa with narrow geographic ranges: S. cereale subsp. dighoricum and S. strictum subsp. kuprijanovii. Commercial breeding reduces the nucleotide sequence variability in αCENH3 and βCENH3. Cultivated rye varieties have π values within 0.0122–0.0014. The nucleotide and haplotype diversity values in αCENH3 and βCENH3 are close in S. sylvestre, which is believed to be the oldest rye species. The results of this study prove that the frequency of single nucleotide polymorphisms and nucleotide diversity of sequences in genes for CENH3 in Secale species are influenced by numerous factors, including reproduction habits, the geographic isolation of taxa, breeding, and the evolutionary age of species.

Genome sequencing and conservation genomics in the Scandinavian wolverine population.

Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42Gb draft sequence representing >85% of the genome and including >21,000protein-coding genes. We then performed whole-genome resequencing of 10Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.