Molecular population genetics

Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae)

Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.

A neutral model for the loss of recombination on sex chromosomes

The loss of recombination between sex chromosomes has occurred repeatedly throughout nature, with important implications for their subsequent evolution. Explanations for this remarkable convergence have generally invoked only adaptive processes (e.g. sexually antagonistic selection); however, there is still little evidence for these hypotheses. Here we propose a model in which recombination on sex chromosomes is lost due to the neutral accumulation of sequence divergence adjacent to (and thus, in linkage disequilibrium with) the sex determiner. Importantly, we include in our model the fact that sequence divergence, in any form, reduces the probability of recombination between any two sequences. Using simulations, we show that, under certain conditions, a region of suppressed recombination arises and expands outwards from the sex-determining locus, under purely neutral processes. Further, we show that the rate and pattern of recombination loss are sensitive to the pre-existing recombination landscape of the genome and to sex differences in recombination rates, with patterns consistent with evolutionary strata emerging under some conditions. We discuss the applicability of these results to natural systems. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.

Late Miocene lineage divergence and ecological differentiation of rare endemic Juniperus blancoi: clues for the diversification of North American conifers

Western North America and Mexico contain a large number of conifer species. This diversity could be the product of orographic and climate changes of the late Tertiary and Quaternary. In this study, we focus on the evolutionary history of Juniperus blancoi, in order to determine the impact of climate change and environmental heterogeneity on population differentiation. We estimated the population structure, phylogenetic relationships and historical demography of J. blancoi populations using nuclear genes. We correlated genetic structure with ecological differentiation, divergence times and changes in population size. Populations of J. blancoi are differentiated into three lineages that correspond to low-, mid- and high-altitude populations. The three groups diversified in the late Miocene, early Pliocene, with only a few events of gene flow since then. Two lineages in the north exhibited a pattern of population growth during the Pleistocene that could be linked to climate changes. Populations of J. blancoi experienced significant ecological differentiation and early divergence events, which correspond to periods of global cooling and mountain uplift during the Miocene. This suggests that mountain ranges in tropical and subtropical latitudes play an important role in the speciation and persistence of conifer taxa in diversity hotspots, by providing diverse environmental conditions.

Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice

qLTG3-1 is a major quantitative trait locus (QTL) controlling tolerance to low-temperature at the seed germination stage (termed low-temperature germinability) in rice using a population derived from the cross between Italica Livorno from Italy and Hayamasari from Japan. Map-based cloning identified that qLTG3-1 encodes a protein of unknown function. The molecular identification of this major QTL could make it possible to identify allelic variation and favorable alleles for rice breeding programs. The present study examined the identification of qLTG3-1 alleles and their distribution among 62 landraces of Asian cultivated rice (Oryza sativa L.) collected from 19 different countries, termed the rice core collection. In the coding region, a single non-synonymous substitution and 3 in-frame insertion/deletion polymorphisms (indels) were detected. The almost completely conserved protein alignment of qLTG3-1 was also identified among 5 Oryza species, suggesting that the function of qLTG3-1 is critical for seed germination or for rice growth by pleiotropic effects of the gene. The functional nucleotide polymorphisms (FNPs), a 71-bp deletion found in Hayamasari and an amino acid substitution found in Nipponbare, was identified in varieties from Japan. These alleles with FNPs might be adapted to rice cultivation in specific local conditions. The present results may contribute to the utilization of favorable alleles of qLTG3-1 for the improvement of low-temperature germinability in rice breeding programs.

Population genetics of foxtail millet and its wild ancestor

Background

Foxtail millet (Setaria italica (L.) P. Beauv.), one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD) is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L.) P. Beauv.). Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication.

Results

In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059), θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027) when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively). The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice.

Conclusions

The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population based studies in foxtail millet.

Comparative phylogeny and historical perspectives on population genetics of the Pacific hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas), inferred from feeding populations in the Yaeyama Islands, Japan

Mitochondrial DNA sequence polymorphisms and patterns of genetic diversity represent the genealogy and relative impacts of historical, geographic, and demographic events on populations. In this study, historical patterns of population dynamics and differentiation in hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas) in the Pacific were estimated from feeding populations in the Yaeyama Islands, Japan. Phylogenetic relationships of the haplotypes indicated that hawksbill and green turtles in the Pacific probably underwent very similar patterns and processes of population dynamics over the last million years, with population subdivision during the early Pleistocene and population expansion after the last glacial maximum. These significant contemporary historical events were suggested to have been caused by climatic and sea-level fluctuations. On the other hand, comparing our results to long-term population dynamics in the Atlantic, population subdivisions during the early Pleistocene were specific to Pacific hawksbill and green turtles. Therefore, regional differences in historical population dynamics are suggested. Despite limited sampling locations, these results are the first step in estimating the historical trends in Pacific sea turtles by using phylogenetics and population genetics.

DNA sequence polymorphism analysis using DnaSP

The analysis of DNA sequence polymorphisms and SNPs (single nucleotide polymorphisms) can provide insights into the evolutionary forces acting on populations and species. Available population-genetic methods, and particularly those based on the coalescent theory, have become the primary framework to analyze such DNA polymorphism data. Here, I explain some essential analytical methods for interpreting DNA polymorphism data and also describe the basic functionalities of the DnaSP software. DnaSP is a multi-propose program that allows conducting exhaustive DNA polymorphism analysis using a graphical user-friendly interface.

Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis

Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in approximately 10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have approximately 45% higher recombination per kilobase than outcrossing A. lyrata.

Molecular evolution of the Pi-ta gene resistant to rice blast in wild rice (Oryza rufipogon)

Rice blast disease resistance to the fungal pathogen Magnaporthe grisea is triggered by a physical interaction between the protein products of the host R (resistance) gene, Pi-ta, and the pathogen Avr (avirulence) gene, AVR-pita. The genotype variation and resistant/susceptible phenotype at the Pi-ta locus of wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the Pi-ta gene. The low nucleotide polymorphism of the Pi-ta gene of O. rufipogon was similar to that of O. sativa, but greatly differed from what has been reported for other O. rufipogon genes. The haplotypes can be subdivided into two divergent haplogroups named H1 and H2. H1 is derived from H2, with nearly no variation and at a low frequency. H2 is common and is the ancestral form. The leucine-rich repeat (LRR) domain has a high pi(non)/pi(syn) ratio, and the low polymorphism of the Pi-ta gene might have primarily been caused by recurrent selective sweep and constraint by other putative physiological functions. Meanwhile, we provide data to show that the amino acid Ala-918 of H1 in the LRR domain has a close relationship with the resistant phenotype. H1 might have recently arisen during rice domestication and may be associated with the scenario of a blast pathogen-host shift from Italian millet to rice.

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice

Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation ((sil) = 0.0077 approximately 0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as (sil) = 0.0024 and even lower ((sil) = 0.0021 for indica and 0.0011 for japonica), if we consider the 2 subspecies separately. Overall, only 20-10% of the diversity in the wild species was retained in 2 subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all 10 loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as 2 ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r(2) value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( approximately 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.

The molecular population genetics of shoot development in Arabidopsis thaliana

Studies in Arabidopsis thaliana have provided us with a wealth of information about the genetic pathways that regulate plant morphogenesis. This developmental genetic treasure trove represents a fantastic resource for researchers interested in the microevolution of development. Several laboratories have begun using molecular population genetic analyses to investigate the evolutionary forces that act upon loci that regulate shoot morphogenesis. Much of this work has focused on coding sequence variation in transcription factors; however, recent studies have explored sequence variation in other types of proteins and in promoter regions. Several genes that regulate shoot development contain signatures of selective sweeps associated with positive selection or harbor putative balanced polymorphisms in coding and noncoding sequences. Other regulatory genes appear to be evolving neutrally, but have accumulated potentially deleterious replacement polymorphisms.

Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae)

Besides showing an extraordinary degree of phenotypic variability, Capsella bursa-pastoris (Brassicaceae) is also one of the world's most common plant species and a serious weed in many countries. We have employed a coalescent-based Bayesian analysis of chloroplast microsatellite data to infer demographic and evolutionary parameters of this species. Two different demographic models applied to data from seven chloroplast microsatellite loci among 59 accessions show that the effective population size of C. bursa-pastoris is very small indicating a rapid expansion of the species, a result that is in accordance with fossil and historical data. Against this background, analysis of flowering time variation among accessions suggests that ecotypic differentiation in flowering time has occurred recently in the species' history. Finally, our results also indicate that mononucleotide repeat loci in the chloroplast genome can deteriorate in relatively short periods of evolutionary time.

Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir

Nuclear sequence variation and linkage disequilibrium (LD) were studied in 15 cold-hardiness- and 3 wood quality-related candidate genes in Douglas fir [Pseudotsuga menziesii (Mirb.) Franco]. This set of genes was selected on the basis of its function in other plants and collocation with cold-hardiness-related quantitative trait loci (QTL). The single-nucleotide polymorphism (SNP) discovery panel represented 24 different trees from six regions in Washington and Oregon plus parents of a segregating population used in the QTL study. The frequency of SNPs was one SNP per 46 bp across coding and noncoding regions on average. Haplotype and nucleotide diversities were also moderately high with H(d) = 0.827 +/- 0.043 and pi = 0.00655 +/- 0.00082 on average, respectively. The nonsynonymous (replacement) nucleotide substitutions were almost five times less frequent than synonymous ones and substitutions in noncoding regions. LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress.

Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum

Sorghum halepense L. (johnsongrass) is one of the world's most noxious weeds, and a paradigm for the potential dangers of crop-weed hybridization. Introduced into the southeastern United States about 200 years ago, S. halepense is a close relative of cultivated sorghum (Sorghum bicolor). Both artificial crossing and experimental field studies have demonstrated the potential for S. halepensex S. bicolor hybrid formation, but no prior study has addressed the long-term persistence of sorghum genes in johnsongrass populations. We surveyed 283 loci (on all 10 sorghum linkage groups) to identify 77 alleles at 69 loci that are found in US sorghum cultivars but are absent from a worldwide sampling of johnsongrass genotypes. These putatively cultivar-specific alleles were present in up to 32.3% of individuals in johnsongrass populations adjacent to long-term sorghum production fields in Texas and Nebraska. Lower frequencies of cultivar-specific alleles at smaller numbers of loci are found in johnsongrass populations from New Jersey and Georgia with no recent exposure to cultivated sorghum, suggesting that introgressed sorghum alleles may be dispersed across long distances. The number of cultivar-specific alleles and extensive multilocus patterns of cultivar-specific allelic composition observed at both linked and unlinked loci in the johnsongrass populations, are inconsistent with alternatives to introgression such as convergence, or joint retention of ancestral polymorphisms. Naturalized johnsongrass populations appear to provide a conduit by which transgenes from sorghum could become widely disseminated.

The glucosinolate-myrosinase system in an ecological and evolutionary context

Functional analysis of natural variation in the model species Arabidopsis thaliana has enabled the cloning of many glucosinolate biosynthesis and hydrolysis genes. Variation in these genes is central to understanding the ecological role of the glucosinolate-myrosinase defense system, and allows us to dissect the evolutionary and ecological forces that shape polymorphism at underlying loci. These same genes are also variable in other crucifer species, suggesting the presence of recurring selection, possibly mediated by insects. By utilizing the genomic tools available in A. thaliana to investigate these loci fully, it might be possible to generate detailed evolutionary or ecological models to apply to other species.

Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium

Resistance (R) genes of plants are responsible for pathogen recognition and encode proteins that trigger a cascade of responses when a pathogen invades a plant. R genes are assumed to be under strong selection, but there is limited knowledge of the processes affecting R gene diversity in the wild. In this study, DNA sequence variation of Cf-2 homologs was surveyed in populations of Solanum pimpinellifolium, a wild relative of the cultivated tomato. The Cf-2 locus is involved in resistance to strains of the fungus Cladosporium fulvum. At least 26 different Cf-2 homologs were detected in natural populations of S. pimpinellifolium. These homologs differ by single base pair substitutions as well as indels in regions coding for leucine-rich repeats. Molecular population genetic analyses suggest that natural selection has acted heterogeneously on Cf-2 homologs, with selection against amino acid substitutions occurring in the 5' portion of the genes, and possible restricted positive selection in the 3' end. Balancing selection may have maintained haplotypes at the 5' end of the genes. Limited sequence exchange between genes has also contributed to sequence variation. S. pimpinellifolium individuals differ in the number of Cf-2 homologs they contain, obscuring the relationships of orthology and paralogy. This survey of Cf-2 variation in S. pimpinellifolium illustrates the wealth of R gene diversity that exists in wild plant populations, as well as the complexity of interacting genetic and evolutionary processes that generate such diversity.

Genomic approaches to analyzing natural variation in Arabidopsis thaliana

The genomics tools available for studying Arabidopsis thaliana are a great resource for researchers trying to characterize and understand the genetic basis of natural variation. Abundant polymorphic markers aid quantitative trait locus (QTL) mapping, the fully sequenced genome provides rapid identification of candidate loci, and extensive knockout collections allow those candidate loci to be tested. Combining QTL mapping of classic phenotypic traits with biochemical or expression analysis is providing mechanistic insight into the traits of interest. Conversely, natural variation studies are now being done on genomic traits such as methylation or chiasma frequency.

Evolution of plant resistance at the molecular level: ecological context of species interactions

Molecular data regarding the diversity of plant loci involved in resistance to herbivores or pathogens are becoming increasingly available. These genes demonstrate variable patterns of diversity, suggesting that they differ in their evolutionary history. In parallel, the study of natural variation for resistance, generally conducted at the phenotypic level, has shown that resistance does not evolve solely under selection pressures exerted by enemies. Metapopulation dynamics and other ecological characteristics of interacting species also appear to have a large impact on resistance evolution. Until now, studies of resistance at the molecular level have been conducted separately from ecological studies in extant populations. Future progress requires an evolutionary approach integrating both molecular and ecological aspects of resistance evolution. Such an approach will contribute greatly to our understanding of the evolution of molecular diversity at loci involved in biotic stress.

Distinguishing the Hitchhiking and Background Selection Models

A simple method to distinguish hitchhiking and background selection is proposed. It is based on the observation that these models make different predictions about the average level of nucleotide diversity in regions of low recombination. The method is applied to data from Drosophila melanogaster and two highly selfing tomato species.

Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus

Glucosinolate profiles differ among Arabidopsis thaliana ecotypes, caused by the composition of alleles at several glucosinolate biosynthetic loci. One of these, GS-Elong, harbors a family of methylthioalkylmalate synthase (MAM) genes that determine the side chain length of aliphatic glucosinolate structures. Fine mapping reveals that GS-Elong constitutes an insect resistance quantitative trait locus, caused by variation in glucosinolate profiles conferred by polymorphism of MAM alleles in this region. A sequence survey of randomly chosen ecotypes indicates that GS-Elong is highly variable among A. thaliana ecotypes: indel polymorphisms are frequent, as well as gene conversion events between gene copies arranged in tandem. Furthermore, statistical methods of molecular population genetics suggest that one of the genes, MAM2, is subject to balancing selection. This may be caused by ecological tradeoffs, i.e., by contrasting physiological effects of glucosinolates on generalist vs. specialist insects.

Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation

Phylogeographical and mismatch analysis of chloroplast DNA (cpDNA) variation were used to infer the temporal dynamics of distributional and demographic history of Taiwan fir (Cunninghamia konishii). We examined 64 and 52 trees from 17 populations of C. konishii and 14 provenances of C. lanceolata, respectively, by sequencing three intergenic spacers and one intron using cpDNA universal primers. Of the aligned 1888 base pairs (bp) sequence, 30 varied among 28 haplotypes, which consisted of three transitions, 14 transversions and 13 indels. One ancestral haplotype was found in 86 individuals across the surveyed range of both species, C. konishii and C. lanceolata, which was distributed in all populations and provenances. The 28 haplotypes also included 15 C. konishii specific and 12 C. lanceolata-specific haplotypes. Ancestral haplotype was found fixed in five populations of C. konishii and five provenances of C. lanceolata. Other haplotypes occurred mainly as singletons. The levels of population differentiation studied are relatively low in both Cunninghamia species. The nucleotide diversity (theta) of chloroplast DNA sequences within C. konishii was slightly higher than that of C. lanceolata. Excess in singletons as well as star-like phylogeny of haplotypes suggested no clearcut migration patterns of C. konishii after glacial maximum. One probable demographic history of C. konishii is the postglacial population growth of C. konishii after a glacial bottleneck event. This inference is supported by the combined results of fossil pollen record, low nucleotide diversity, significant Tajima's d-value, phylogeographical analysis and unimodal mismatch distribution. Similarities and discrepancies between our results and those of Lu et al. (2001) are discussed.

Effects of inbreeding on the genetic diversity of populations

The study of variability within species is important to all biologists who use genetic markers. Since the discovery of molecular variability among normal individuals, data have been collected from a wide range of organisms, and it is important to understand the major factors affecting diversity levels and patterns. Comparisons of inbreeding and outcrossing populations can contribute to this understanding, and therefore studying plant populations is important, because related species often have different breeding systems. DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions.