Machine learning identifies specific habitats associated with genetic connectivity in Hyla squirella

The goal of this study was to identify and differentiate the influence of multiple habitat types that span a spectrum of suitability for Hyla squirella, a widespread frog species that occurs in a broad range of habitat types. We collected microsatellite data from 675 samples representing 20 localities from the southeastern USA and used machine‐learning methodologies to identify significant habitat features associated with genetic structure. In simulation, we confirm that our machine‐learning algorithm can successfully identify landscape features responsible for generating between‐population genetic differentiation, suggesting that it can be a useful hypothesis‐generating tool for landscape genetics. In our study system, we found that H. squirella were spatially structured and models including specific habitat types (i.e. upland oak forest and urbanization) consistently explained more variation in genetic distance (median pR² = 47.78) than spatial distance alone (median pR² = 23.81). Moreover, we estimate the relative importance that spatial distance, upland oak and urbanized habitat have in explaining genetic structure of H. squirella. We discuss how these habitat types may mechanistically facilitate dispersal in H. squirella. This study provides empirical support for the hypothesis that habitat‐use can be an informative correlate of genetic differentiation, even for species that occur in a wide range of habitats.     

In the intimacy of the darkness: Genetic polyandry in deep-sea luminescent lanternsharks Etmopterus spinax and Etmopterus molleri (Squaliformes,Etmopteridae)

Multiple paternity seems common within elasmobranchs. Focusing on two deep-sea shark species, the velvet belly lanternshark (Etmopterus spinax) and the slendertail lanternshark (Etmopterus molleri) we inferred the paternity in 31 E. spinax litters from Norway (three to 18 embryos per litter) and six E. molleri litters from Japan (three to six embryos), using 21 and 10 specific microsatellites, respectively. At least two E. spinax litters were sired from multiple fathers each, with highly variable paternal skew (1:1 to 9:1). Conversely, no clear signal of genetic polyandry was found in E. molleri.     

Genetic differentiation in populations of the yellow-necked mouse,Apodemus flavicollis,harbouring B chromosomes in different frequencies

Two alternative models are used to explain maintenance of polymorphism of B chromosomes (Bs) in populations of a great number of species. The parasitic model suggests deleterious effects of Bs on fitness of carriers, while the heterotic model assumes that, in the absence of drive, equilibrium is produced by beneficial effects of Bs at low numbers. In order to determine the potential contribution of Bs to genetic differentiation and diversity, four populations of Apodemus flavicollis, differing in frequency of Bs (from 0.23 to 0.38) and settled in ecologically different habitats, were analyzed by 471 AFLP markers. Although numerous loci were demonstrated to be population specific, none of them was associated with individuals with Bs. AMOVA showed that the presence of Bs does not affect population differentiation, pointing to greater genetic similarity of Bs to A chromosomes. The greatest genetic diversity (0.241) was found in the population settled in optimal conditions for this species featured by the lowest frequency of animals with Bs (0.23). We found that the majority of loci marked as loci under directional selection, are characteristic of either a population with lower or one with a higher frequency of Bs. Several loci detected as outliers were associated with environmental variables that could directly and/or indirectly influence population dynamics of A. flavicollis. Thus, we suggest that the different frequency of Bs carriers in populations is related to adaptive differentiation to diverse habitats, which is in accordance with the heterotic model of Bs maintenance.     

SSRs transferability and genetic diversity of Tunisian Festuca arundinacea and Lolium perenne

SSR primers specific to Lolium perenne generated a total of 96 alleles and 124 genotypes within Festuca arundinacea and Lolium perenne accessions. Their highly transferability (100 %) across genera was evidenced. Six alleles specific to loci H01F02, H02C11 and K01A03 and only 5/96 common alleles between both species (60, 140, 144, 190 and 192) expressed the differentiation between species. Besides, based on the Wrights fixation indices, the genetic variation within each species was attributable to differences within populations with a significant deficiency of heterozygous. The unweighted pair group method with arithmetic averaging dendrogram based on the Nei’s distances and the principal coordinate analysis based on Jaccard coefficient similarity distinguished each genus independently of the geographical origin. However, typically continuous genetic diversity and a low level of gene flow (N_m: 0.29–2.47) expressed the relatively closely relationships of both genera and suggest a possible hybridization in nature.     

Genetic structure of Helianthus occidentalis (Asteraceae) in a preserve withfragmented habitat

We examined the spatial genetic structure of Helianthus occidentalis Riddell ssp. occidentalis Riddell (western sunflower) to determine whether this species is highly clonal and whether the distance between prairie patches influences genetic differentiation. In the Edge of Appalachia Preserve System, Ohio, this species is restricted to prairie patches that have a clumped distribution in the forest matrix. Data from this insect-pollinated forb with gravity-dispersed seed were compared to data from the same patches for Asclepias verticillata, an insect-pollinated species with wind-dispersed seed. Allozyme electrophoresis was used to collect genetic data from H. occidentalis samples from eight patches in four regions. Genetic data from three polymorphic loci indicted that this species is not highly clonal. Genetic differentiation was greater among patches within a region than among regions, suggesting that gene flow among patches is more limited in H. occidentalis than in A. verticillata. Founder effect may also have contributed to observed genetic differences among patches as some of these populations may have re-established after release from human use. As habitat fragmentation is increasing in the preserve, it is also likely that genetic differentiation may be increasing. Therefore, monitoring of genetic structure is necessary to further assess the effect of fragmentation.     

Potential selection in native grass populations by exotic invasion

Ecological impacts of invasive plant species are well documented, but the genetic response of native species to invasive dominance has been often overlooked. Invasive plants can drastically alter site conditions where they reach dominance, potentially exerting novel selective pressures on persistent native plant populations. Do native plant populations in old exotic invasions show evidence of selection when compared to conspecific populations in adjacent, noninvaded areas? We employ amplified fragment length polymorphism (AFLP) analysis to screen a large number of loci from two native grass species (Hesperostipa comata (Trin. & Rupr.) Barkworth and Sporobolus airoides Torr.) that occur in old infestations of the invasive forb Acroptilon repens. We then compare observed locus by locus F_ST values with distributions of F_ST estimated from simulation models under expectation of neutrality. We also compare the proportion of loci possibly linked to selection and those not linked to selection which exhibit parallel trends in divergence between two community types (invaded, noninvaded). Few loci (H. comata, 2.6%; S. airoides, 8.7%) in the two native grasses may be linked to genes under the influence of selection. Also, loci linked to selection showed a greater portion of parallel trends in divergence than neutral loci. Genetic similarities between community types were less than genetic similarity within community types suggesting differentiation in response to community alteration. These results indicate that a small portion of scored AFLP loci may be linked to genes undergoing selection tied to community dominance by an invasive species. We propose that native plants in communities dominated by exotic invasives may be undergoing natural selection.     

Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modelling indicated that the two species diverged with gene flow. The best‐supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (F _ST) and sequence divergence (d _XY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between‐species population pairs, isolation by distance was stronger for genomic regions with low between‐species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated, suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow.     

Genetic variation and phylogenetic relationship between two species of yellow catfish, <Emphasis Type="Italic">Horabagrus brachysoma</Emphasis> and <Emphasis Type="Italic">H. nigricollaris</Emphasis> (Teleostei: Horabagridae) based on RAPD and microsatellite markers

The two species of yellow catfish, Horabagrus brachysoma and H. nigricollaris are categorized as ‘endangered’ and ‘critically endangered’ respectively in their wild habitat. Proper knowledge of genetic structure and variability of these endangered species are highly essential for the management, conservation and improvement of fish stocks. Therefore, genetic variation and phylogenetic relationships between these species of yellow catfish sampled from Chalakkudy River in the hot spot of biodiversity-Western Ghats region, Kerala, India were analyzed by using Random amplified polymorphic DNA (RAPD) and microsatellite markers. 85 RAPD and five microsatellites loci were detected to analyze the genetic variation and phylogenetic relationships among these species. Out of 85 RAPD loci produced only 52.94% were polymorphic whereas in microsatellite, all 5 loci were polymorphic (100%). Species-specific RAPD bands were found in both species studied. In microsatellite, the number of alleles across the five loci ranged from 1 to 8. The observed heterozygosities in H. brachysoma and H. nigricollaris were 0.463 and 0.443, respectively. Here, both RAPD and microsatellite methods reported a low degree of gene diversity and lack of genetic heterogeneity in both species of Horabagrus which strongly emphasize the need of fishery management, conservation and rehabilitation of these species.     

Genetic structure of island populations of <Emphasis Type="Italic">Prunus lannesiana</Emphasis> var. <Emphasis Type="Italic">speciosa</Emphasis> revealed by chloroplast DNA,AFLP and nuclear SSR loci analyses

The wild flowering cherry Prunus lannesiana var. speciosa is highly geographically restricted, being confined to the Izu Islands and neighboring peninsulas in Japan. In an attempt to elucidate how populations of this species have established we investigated the genetic diversity and differentiation in seven populations (sampling 408 individuals in total), using three kinds of genetic markers: chloroplast DNA (cpDNA), amplified fragment length polymorphisms (AFLPs), and 11 nuclear SSR polymorphic loci. Eight haplotypes were identified based on the cpDNA sequence variations, 64 polymorphic fragments were scored for the AFLP markers, and a total of 154 alleles were detected at the 11 nuclear SSR loci. Analysis of molecular variance showed that among-population variation accounted for 16.55, 15.04 and 7.45% of the total detected variation at the cpDNA, AFLPs, and SSR loci, respectively. Thus, variation within populations accounted for most of the genetic variance for all types of markers, although the genetic differentiation among populations was also highly significant. For cpDNA variation, no clear structure was found among the populations, except that of the most distant island, although an “isolation by distance” pattern was found for each marker. Both neighbor-joining trees and structure analysis indicate that the genetic relationships between populations reflect geological variations between the peninsula and the islands and among the islands. Furthermore, hybridization with related species may have affected the genetic structure, and some genetic introgression is likely to have occurred.     

Population Genetic Structure of Astyanax scabripinnis (Teleostei, Characidae) from an Urban Stream

Despite the great anthropogenic interference on urban streams, information is still scarce about the genetic variability and structure of native fish populations inhabiting such streams. In the present study, random amplified polymorphic DNA (RAPD) markers were used to analyze genetic variability and structure of populations assigned to the Neotropical fish species Astyanax scabripinnis from an urban stream located in Londrina, Paraná State, southern Brazil. Thirty individuals of this species were collected from three sites throughout the upper Cambé stream. A total of 10 primers amplified 159 loci, of which 128 (80.5%) were polymorphic. Each of the three populations showed very similar proportions of polymorphic loci, which ranged from 63.5 to 64.8%. Unbiased genetic distances varied from 0.0612 to 0.0646. Theta_p-test values indicated moderate to high genetic differentiation among individuals from different localities. The number of migrants varied from 1.34 to 1.46, suggesting a low gene flow between populations. The genetic similarity among all individuals studied ranged from 0.424 to 0.848. The results suggest that populations of A. scabripinnis in Cambé stream are undergoing genetic differentiation.     

The genetic variability of the red king crab, <Emphasis Type="Italic">Paralithodes camtschatica</Emphasis> (Tilesius, 1815) (Anomura,Lithodidae) introduced into the Barents Sea compared with samples from the Bering Sea and Kamchatka region using eleven microsatellite loci

The intentional introduction of red king crab, Paralithodes camtschatica (Tilesius, 1815) in the Barents Sea represent one of a few successful cases and one that now supports a commercial fishery. Introductions of alien species into new environments are often associated with genetic bottlenecks, which cause a reduction in the genetic variation, and this could be important for the spreading potential of the species in the Atlantic Ocean. Red king crab samples collected in the Varangerfjord located on the Barents Sea (northern Norway) were compared with reference crab samples collected from the Bering Sea and Kamchatka regions in the Pacific Ocean. All samples were screened for eleven microsatellite loci, based on the development of species-specific primers. The observed number of alleles per locus was similar, and no reduction in genetic variation, including gene diversity and allelic richness, was detected between the Varangerfjord sample and the reference sample from Okhotsk Sea near Kamchatka, indicating no genetic bottlenecking at least for the microsatellite loci investigated. The same results were found in comparison with the sample from Bering Sea. The level of genetic differentiation among the samples, measured as overall F _ST across all loci, was relatively low (0.0238) with a range of 0.0035–0.1000 for the various loci investigated. The largest pairwise F _ST values were found between the Bering Sea and Varangerfjord/Barents Sea samples, with a value of 0.0194 across all loci tested. The lowest value (0.0101) was found between the Varangerfjord and Kamchatka samples. Genetic differentiation based on exact tests on allele frequencies revealed highly significant differences between all pairwise comparisons. The high level of genetic variation found in the Varangerfjord/Barents Sea sample could be of significance with respect to further spreading of the species to other regions in the North Atlantic Ocean.     

A CHROMATOGRAPHIC INVESTIGATION OF INTERSPECIFIC RELATIONSHIPS IN PINUS (SUBSECTION SYLVESTRES)

The foliage polyphenols of 16 Pinus species were compared by two-dimensional paper chromatography. The general patterns of chemical similarity were correlated with the geographic distributions of the species; sympatric species generally had greater chemical affinity than did allotropic species. This relationship did not always correspond to hybridization patterns and morphological similarities. The distinctive chromatographic patterns of the Southeast Asian species (P. insularis, P. luchuensis, P. merkusii) and their generally low affinities with species of Europe and the Asian mainland suggest that further investigation of the morphological relationships and the genetic compatibility of these species with other Sylvestres species is warranted. The chemical relationships of P. halepensis and P. heldreichii to other Sylvestres species were also unclear. The qualitative differences in polyphenols among species are consistent and of sufficient magnitude to enable the application of chromatographic analysis to studies of interspecific hybridization in Pinus.     

Genetic divergence in four species of the genus Raphanus: Implications for the ancestry of the domestic radish R. sativus

Four species of radish of the genus Raphanus were examined by electrophoresis of water soluble proteins. This technique was used to provide information about the degree of genetic differentiation of the species over a range of gene loci coding for various enzymes. These results give genetic distance estimates showing all four radish species to be closely related. From this data a simple dendrogram is constructed to show the possible interrelationships and evolutionary divergence of these species. The domestic radish Raphanus sativus shows the greatest genetic similarity when compared with an Italian population of R. landra.     

Unexpected low genetic differentiation among Allopatric species of section Algarobia of Prosopis (Leguminosae)

The Chaqueña Biogeographic Province, in South America, is the main diversity centre of Prosopis. A group of sympatric species of Section Algarobia in this region constitutes a syngameon, characterised by frequent hybridization and introgression. These processes have been postulated as responsible for the low genetic differentiation observed among species within this group. In this study genetic variability and differentiation among geographically isolated species of the same section was analysed through isoenzyme electrophoresis. Variability parameters and fixation indices were estimated to determine the genetic structure of populations. Two Argentinean, P. ruscifolia (‘vinal’) and P. flexuosa (‘algarrobo amarillo’), and one North American species, P. glandulosa (honey mesquite) were studied. All of them showed, similarly to other species of the same section, high genetic variability and exhibit homozygote excess, probably due to population substructure and low rates of selfing. In contrast to our hypothesis, genetic similarity among species is not related to geographic distance. Genetic distances between P. glandulosa and South American species are similar to those observed among species of this subcontinent. The results obtained suggest that the high genetic similarity among the species of the section Algarobia studied is not due to hybridization.     

Low genetic differentiation among populations ofArabis serrata (Brassicaceae) along an altitudinal gradient

We investigated the extent of genetic differentiation among populations of fujihatazao,Arabis serrata along an altitudinal gradient at Mt. Fuji in Shizuoka Prefecture. This species is a perennial plant, widely distributed in Japan forming small isolated populations. However, at Mt. Fuji, this species constitutes a large population distributed from 1440 to 2400 m altitude. A total of 411 individuals were sampled from ten subpopulations. Eighteen loci were detected on eleven enzyme systems. Eleven loci were monomorphic and seven loci were polymorphic with a mean of 2.11 alleles per loci. Nei's genetic distance (mean 0.01) and genetic identity (mean 0.968) were very similar among populations indicating a low genetic differentiation. The total genetic diversity (H _T ) estimated for the polymorphic loci was, in average, 0.396. The mean gene differentiation (G_ST=0.091) was very low. Gene frequency of seven polymorphic loci was analyzed by spatial autocorrelation methods based on Moran's indexes. Only Pgi-3 exhibited a significant negative autocorrelation (−0.160;P<0.05); other loci values ranged from −0.134 to 0.027. Gene flow estimated by indirect methods varied between genes but most of the values were high (meanNm=20.8) suggesting that subpopulations at different altitudes are probably connected. Despite plants at different altitudes present different ecological traits (e.g., differences in phenology, growth and reproductive traits), subpopulations ofA. serrata are still low differentiated, at least for the loci studied. This may be explained by the recent origin of some habitats (e.g., second crater and surrounded areas) in this locality.     

Genetic diversity of Typha latifolia (Typhaceae) and the impact of pollutants examined with tandem-repetitive DNA probes

Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated “core” sequences (GACA, GATA, and GCAC). The principal objectives of this investigation were to determine whether: (1) the previously reported almost complete lack of polymorphism at allozyme loci in this species was indicative of a reduced amount of genetic diversity at VNTR loci as well; (2) VNTR markers were informative about possible clonal propagation; and (3) significant differences in genetic structure of sampling sites were associated with differences in environmental levels of pollutants at those sites. Previously, widespread sampling across the eastern United States, surveying across ten allozyme loci, has detected only two genotypes, involving a difference at a single locus, among 104 populations. In this study, the amount of genetic diversity detected at VNTR loci: (1) among ramets (N = 40; 40 genotypes detected) collected at ∼8-km intervals along a 320-km transect; (2) among ramets (N = 220; 117 genotypes detected) from five study sites separated by 50–3000 m; and (3) even among ramets within each study site [N = 44 per site; from 13 to 34 genotypes detected per site (270 m²)] exceeds that previously found in those more geographically widespread allozyme surveys. Among the 260 ramets analyzed here, the mean number of bands scored per individual was 48.61 (SD = 2.80). Mean genetic similarity among ramets collected along the 320-km transect was 0.91, which was within the range of mean genetic similarity within the five study sites (range: 0.89–0.95). Among the five study sites, 61% of the samples analyzed appeared to be clonal ramets, with up to 12 clones detected for 44 ramets sampled within a site. Clones grew intermingled and ranged up to 39 m in extent. Permutation tests of genetic similarity revealed significant genetic differentiation between each of the five study sites. Consistent with the previous allozyme studies, T. latifolia was characterized by extremely low genetic variation relative to levels of polymorphism detected at VNTR loci in other plant species. Estimated heterozygosity among ramets along the 320-km transect ranged from 0.11 to 0.13, while that within the five study sites ranged from 0.05 to 0.12. Estimates of F_st (0.32–0.41) also indicated considerable genetic subdivision among these stands. Significantly higher genetic diversity was detected at the two study sites that chemistry and toxicity data indicate to be the most severely impacted by pollutants. Although this correlation does not establish cause and effect, the results of this study indicate that the analysis of genetic diversity at VNTR loci may be a useful tool for monitoring anthropogenic-induced changes in the genetic structure of natural populations of plants.     

Microsatellite variation and population structure of a recovering Tree frog (Hyla arborea L.) metapopulation

Numbers and sizes of populations of the European tree frog in The Netherlands have dramatically decreased in the second half of the last century due to extensive habitat destruction and fragmentation. We have studied the genetic structure of a slowly recovering meta-population. Strong genetic differentiation, estimated at eight microsatellite loci, was found between clusters of populations (F _st-values above 0.2). Within clusters, consisting of ponds within a radius of about 5 km, European tree frog populations were less differentiated (F _st<0.08) and exact tests showed that most of the ponds within clusters were not significantly differentiated. Although local population sizes have been increasing since 1989, and some new ponds have been colonised in the direct vicinity of ponds that have been populated continuously, little evidence for gene flow between clusters of ponds was found (only one exception). Furthermore, levels of genetic diversity were low compared to populations in comparable areas elsewhere in Europe. Therefore, a continuous conservation effort is needed to prevent any further loss of genetic diversity. The alleviation of important barriers to dispersal between the clusters should be given a high priority for the restoration of the meta-population as a whole.     

Geographic variation in hybridization and ecological differentiation between three syntopic,morphologically similar species of montane lizards

To understand factors shaping species boundaries in closely related taxa, a powerful approach is to compare levels of genetic admixture at multiple points of contact and determine how this relates to intrinsic and extrinsic factors, such as genetic, morphological and ecological differentiation. In the Australian Alps, the threatened alpine bog skink Pseudemoia cryodroma co‐occurs with two morphologically and ecologically similar congeners, P. entrecasteauxii and P. pagenstecheri, and all three species are suspected to hybridize. We predicted that the frequency of hybridization should be negatively correlated with genetic divergence, morphological differentiation and microhabitat separation. We tested this hypothesis using a mitochondrial locus, 13 microsatellite loci, morphological and microhabitat data and compared results across three geographically isolated sites. Despite strong genetic structure between species, we detected hybridization between all species pairs, including evidence of backcrossed individuals at the two sites where all three species are syntopic. Hybridization frequencies were not consistently associated with genetic, morphological or ecological differentiation. Furthermore, P. entrecasteauxii and P. pagenstecheri only hybridized at the two sites where they are syntopic with P. cryodroma, but not at the largest site where P. cryodroma was not recorded, suggesting that P. cryodroma may serve as a bridging species. This study reveals the complex dynamics within a three species hybrid zone and provides a baseline for assessing the impact of climate change and anthropogenic habitat modification on future hybridization frequencies.     

Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.     

Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local‐level species separation is recognized by Bayesian clustering and neighbor‐joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F_ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H_E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H_E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.