Linked vs unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression

We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, F(ST) based on unlinked loci indicated small (0.032-0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed.     

Molecular phylogeography and evolutionary history of Picea likiangensis in the Qinghai-Tibetan Plateau inferred from mitochondrial and chloroplast DNA sequence variation

The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis,a dominant species of the conifer forests in the eastern declivity of the Qinghai-Tibetan Plateau. We collected 422 individuals from 42 natural populations of three major varieties classified under this species.In conifers,mitochondrial(mt) DNA and chloroplast(cp) DNA dispersed by seeds or pollen experience very different levels of gene flow.To this end,we examined the sequence variation of two mtDNA fragments(nad5 intron 1 and nad1 intron b/c) and three cpDNA fragments(trnL-trnF,trnS-trnG and nadhK/C).We found that cpDNA probably introgressed from P.purpurea into remote populations of P.likiangensis through long-distance dispersal. Multiple refugia seem to have been maintained for P.likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions.Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations.However,genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions,which may result from the long-distance dispersal of the cpDNA,as well as its fast lineage sorting during intraspecific divergences.Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers,which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa.Together,the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion,long-distance dispersal,and intraspecific divergences at two sets of DNA genomes with different rates of gene flow.     

Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani

Plethodon shermani comprises a series of geographically disjunct populations occupying high-elevation mountain isolates. These populations hybridize at their borders with salamanders of the Plethodon glutinosus species complex, and past range expansions inferred from Pleistocene climatic cycles may have increased the possible genetic interactions between P. shermani and species of the P. glutinosus complex. Because mitochondrial DNA haplotypes often show introgression across species borders, we survey mtDNA variation for evidence of past and ongoing genetic interactions between P. shermani, its close relative Plethodon cheoah, and species of the P. glutinosus complex. Ongoing hybridization with the P. glutinosus-complex species Plethodon teyahalee is accompanied by extensive mitochondrial introgression in some Unicoi populations of P. shermani, but it has little genetic impact on P. shermani populations outside hybrid zones at three other isolates (Tusquitee, Wayah Bald, Standing Indian). Some Unicoi populations of P. shermani exhibit mtDNA evidence of past hybridization with diverse lineages from P. aureolus and P. glutinosus. The Tusquitee isolate of P. shermani is also characterized by mtDNA haplotypes most closely related to Plethodon aureolus and P. glutinosus, presumably introduced by past genetic contact with these species or with introgressed populations of Unicoi P. shermani. The mtDNA variation in sampled populations of the Wayah Bald and Standing Indian isolates of P. shermani appears largely unaffected by ongoing hybridization. Principal components analyses of allozymic data indicate that P. shermani isolates collectively form a genetically homogeneous unit clearly demarcated from species with which they have had current or past genetic interactions. Rapid mtDNA introgression associated with transient contacts between P. shermani and other species permits a fine-level resolution of evolutionary lineages not evident from allozymic data.     

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito‐nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation–migration analyses, however, revealed near‐zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.     

转基因水稻外源基因向近缘种群漂流和渐渗的研究进展

水稻是我国最重要的粮食作物之一,我国有8亿以上的人口以稻米作为主食。但在水稻生产中,由于病、虫、草害及不良气候等逆境因子的影响,严重制约了水稻的高产、稳产。转基因生物技术的迅速发展,为水稻抗性育种提供了新途径。自20世纪80年代以来,我国全方位地开展了转基因水稻的研发,目前已经培育出大量的抗病、抗虫、抗除草剂和抗逆的转基因水稻品种,这将为提高我国水稻的生产力和确保粮食安全做出重要的贡献。但转基因水稻的基因漂流及其可能带来的生物安全问题备受关注。已有报道证明,外源转基因可以通过异交向非转基因品种和野生近缘种漂流。在不同的试验条件下,抗除草剂基因有0．05％-0．53％逃逸的可能,其向不育系的最大漂移频率可达4．518％。抗虫基因向相邻非转基因水稻的平均漂移频率最高为0．875％。因此,本文对水稻与其近缘野生种的杂交情况,转基因水稻外源基因向非转基因品种、野生近缘种以及野生非近缘种的漂流和渐渗及其潜在的生态环境风险等方面进行了简要分析,并对转基因水稻的发展进行了展望,以期为转基因水稻的安全应用提供参考。     

Phylogeographic patterns and high levels of chloroplast DNA diversity in four Packera (asteraceae) species in southwestern Alberta

Chloroplast DNA (cpDNA) haplotype variation is compared among alpine and prairie/montane species of Packera from a region in southwestern Alberta that straddles the boundary of Pleistocene glaciation. The phylogeny of the 15 haplotypes identified reveals the presence of two groups: one generally found in coastal and northern species and the other from species in drier habitats. The presence of both groups in all four species and most populations from southwestern Alberta is evidence of past hybridization involving species or lineages that may no longer be present in the region. With the exception of the alpine P. subnuda (phiST = 1.0), interpopulational subdivision of haplotype variation is low (phiST < 0.350), suggesting that interpopulational gene flow is high. However, based on haplotype distribution patterns, we propose that Pleistocene hybridization and incomplete lineage sorting have resulted in reduced subdivision of interpopulational variation so that gene flow may not be as high as indicated. Drift has been more important in the alpine species populations, especially P. subnuda.     

Sandflies of the Phlebotomus perniciosus complex: mitochondrial introgression and a new sibling species of P. longicuspis in the Moroccan Rif

The bloodsucking adult females of Phlebotomus perniciosus Newstead and P. longicuspis Nitzulescu (Diptera: Psychodidae) are important vectors of the protozoan Leishmania infantum Nicolle (Kinetoplastida: Trypanosomatidae) in western Mediterranean countries. The species status of the two phlebotomine sandflies was assessed, along with the epidemiological implications. Individual sandflies from three Moroccan Rif populations were characterized morphologically, isoenzymatically (by the isoelectrofocusing of alleles at the polymorphic enzyme loci of HK, GPI and PGM), and by comparative DNA sequence analysis of a fragment of mitochondrial Cytochrome b (mtDNA). By reference to the character profiles of specimens from other locations, including southern Spain and the type-locality countries, the Moroccan flies were placed in three lineages: first, the lineage of P. perniciosus, which contained two mtDNA sublineages, one (pnt) widely distributed and associated with the morphology of the male types from Malta, and the other (pna) associated with a P. longicuspis-like male morphology; second, the lineage of P. longicuspis sensu stricto, including typical forms from Tunisia; and third, a new sibling species of P. longicuspis. The mtDNA sublineage (pnt) of typical P. perniciosus was also found in some P. longicuspis from Morocco, indicating interspecific hybridization. The typical race of P. perniciosus occurs in Italy as well as in Malta, Tunisia and Morocco. It is replaced in southern Spain by the Iberian race (with the pni mtDNA sublineage). The discovery of interspecific gene introgression and a new sibling species mean that previous records of the two morphospecies do not necessarily reflect their true vectorial roles or geographical and ecological distributions.     

Species diversity of freshwater shrimp in Henan Province,China, based on morphological characters and COI mitochondrial gene

Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree‐based methods (NJ, ML, and bPTP) and distance‐based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p‐distances had similar results. Mean K2P distances and p‐distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.     

Differential gene flow of mitochondrial and nuclear DNA markers among chromosomal races of Australian morabine grasshoppers (Vandiemenella, viatica species group)

Recent theoretical developments have led to a renewed interest in the potential role of chromosomal rearrangements in speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) provide an excellent study system to test this potential role of chromosomal rearrangements because they show extensive chromosomal variation and formed the basis of a classic chromosomal speciation model. There are three chromosomal races, viatica19, viatica17, and P24(XY), on Kangaroo Island, South Australia, forming five parapatric populations with four putative contact zones among them. We investigate the extent to which chromosomal variation among these populations may be associated with barriers to gene flow. Population genetic and phylogeographical analyses using 15 variable allozyme loci and the elongation factor-1alpha (EF-1alpha) gene indicate that the three races represent genetically distinct taxa. In contrast, analyses of the mitochondrial cytochrome c oxidase subunit I (COI) gene show the presence of three distinctive and geographically localized groups that do not correspond with the distribution of the chromosomal races. These discordant population genetic patterns are likely to result from introgressive hybridization between the chromosomal races and range expansions/contractions. Overall, these results suggest that reduction of nuclear gene flow may be associated with chromosomal variation, or underlying genetic variation linked with chromosomal variation, whereas mitochondrial gene flow appears to be independent of this variation in these morabine grasshoppers. The identification of an intact contact zone between P24(XY) and viatica17 offers considerable potential for further investigation of molecular mechanisms that maintain distinct nuclear genomes among the chromosomal races.     

Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequences

Salamander populations of the Plethodon jordani species complex form a challenging system for applying the general lineage concept of species to diagnose population-level lineages. The present study reports and analyses mitochondrial-DNA haplotypes (∼1200 nucleotide bases from the genes encoding ND2, tRNA^Trp, and tRNA^Ala from 438 salamanders) from 100 populations representing six species of the P. jordani complex ( Plethodon amplus , Plethodon cheoah , Plethodon jordani , Plethodon meridianus , Plethodon metcalfi , and Plethodon montanus ) with comparative analyses of previously published allozymic data to reconstruct the evolutionary history of this group and to diagnose species lineages. Analyses of mitochondrial haplotypic data include nested-cladistic analysis of phylogeography, analysis of molecular variance, hierarchical analysis of nucleotide-diversity measures, and likelihood-based estimates of recent temporal changes in population size. New analyses of allozymic data include multidimensional scaling and principal component analyses, and both data sets are analysed and compared for congruent genetic structure using Mantel correlation tests. These analyses in combination identify the six named species as distinct evolutionary lineages despite sporadic genetic exchanges among them and some discordance between mitochondrial DNA and allozymic markers. Sexual isolation is not complete for any pair of these six species, but they replace each other geographically and appear to block the geographical spreading of their neighbours. The P. jordani complex is a strong study system for investigating the genetic and ecological processes responsible for vicariant speciation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 25–51.     

A wide geographical survey of mitochondrial DNA variation in the great spotted woodpecker complex,Dendrocopos major (Aves: Picidae)

One of the fundamental goals of phylogeographical studies should be to achieve a comprehensive geographical sampling of any investigated group. In this study, we conducted the most comprehensive geographical investigation to date for the great spotted woodpecker complex (Dendrocopos major), including populations from North Africa and Eurasia [including specimens from China, Japan and southern Caucasia (Anatolia, Azerbaijan and Iran)], in order to evaluate its genetic structure and population history. At the same time, we tested species limits within the D. major complex, which currently includes 14 recognized subspecies based on morphology and coloration. We based our study on haplotypes for the mitochondrial gene NADH dehydrogenase subunit 2 (ND2). Most haplotypes were obtained from museum toe pads, although we also used some previously published data. We also tested gene flow through MDIV, and estimated divergence dates among lineages using BEAST. The analysis of 352 base pairs of the ND2 gene from 155 individuals sampled from 33 populations showed significant phylogeographical structure across the breeding range. Our results found four distinct and reciprocally monophyletic clades: China, Japan, Iran–Azerbaijan and Eurasia–North Africa, with no phylogeographical structure within them. Coalescent‐based gene flow analysis showed restricted gene flow between China and Japan and between Japan and Eurasia. On the basis of the gene flow and phylogenetic analysis results, we propose the recognition of at least four different species within the complex. We also propose that, within the Eurasia–North Africa clade, a rapid population expansion through ‘leading edge expansion’ from refugia in Iberia, Kursk and North Africa, as well as irruptive and loop migration, can explain the lack of phylogeographical structure. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

The complex evolutionary history of apricots: Species divergence,gene flow and multiple domestication events

Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long‐lived perennial fruit trees.     

Plant DNA barcodes and the influence of gene flow

Success of species assignment using DNA barcodes has been shown to vary among plant lineages because of a wide range of different factors. In this study, we confirm the theoretical prediction that gene flow influences species assignment with simulations and a literature survey. We show that the genome experiencing the highest gene flow is, in the majority of the cases, the best suited for species delimitation. Our results clearly suggest that, for most angiosperm groups, plastid markers will not be the most appropriate for use as DNA barcodes. We therefore advocate shifting the focus from plastid to nuclear markers to achieve an overall higher success using DNA barcodes.     

Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae)

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well-resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock-crevice-dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock-crevice-dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.     

Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus)

We investigated the genetic population structure and species status of a relatively sedentary bird that is a permanent resident of western North American forests, the blue grouse (Dendragapus obscurus). Phylogenetic analysis of complete mitochondrial control region DNA sequences resulted in the identification of three basal clades of haplotypes that were largely congruent with well-known biogeographical regions. These clades corresponded to the parapatric sooty (D. o. fuliginosus) and dusky (D. o. obscurus) subspecies groups of blue grouse plus a previously unrecognized division between northern and southern dusky grouse populations; the latter does not correspond closely to any currently recognized subspecies boundary. Approximately 66% of the total genetic variation was distributed among these three regions. Maximum likelihood estimates of gene flow between the regions were low or asymmetric; gene flow has been insufficient to prevent genetic divergence between dusky and sooty grouse. Estimates of gene flow among populations within sooty grouse were large except across the Columbia River valley. Among populations of dusky grouse, estimates of gene flow were heterogeneous and asymmetrical, reflecting large-scale fragmentation of the distribution due to landscape features and associated vegetation. Genetic, morphological and behavioural evidence suggest that sooty and dusky grouse are species-level taxa; the specific status of a third clade remains ambiguous.     

Genome-wide nuclear data confirm two species in the Alpine endemic land snail Noricella oreinos s.l. (Gastropoda,Hygromiidae)

The Austrian endemic land snail species Noricella oreinos (formerly Trochulus oreinos) occurs in the Northeastern Calcareous Alps at high elevations. Two morphologically highly similar subspecies N. o. oreinos and N. o. scheerpeltzi have been described. First analyses of mitochondrial and nuclear marker sequences indicated a high genetic divergence between them. In the present study, we aimed to assess gene flow between the two subspecies which should help to re-evaluate their taxonomic status. Sequence data and amplified fragment length polymorphism (AFLP) markers of 255 Noricella specimens covering the whole distribution range were analyzed. A clear geographic separation was found within the potential contact zone, the Haller Mauern mountain range. Samples of all western sites were part of the clade representing N. o. scheerpeltzi and almost all samples from the eastern sites clustered with N. o. oreinos. However, within two sampling sites of the eastern Haller Mauern, a few individuals possessed a COI sequence matching the N. o. oreinos clade whereas at the ITS2 locus they were heterozygous possessing the alleles of both taxa. Contrary to the ITS2 results indicating historical and/or ongoing hybridization, AFLP analyses of 202 individuals confirmed a clear separation of the two taxa congruent with the mitochondrial data. Although they occur on the same mountain range without any physical barrier, no indication of ongoing gene flow between the two taxa was found. Thus, we conclude that the two taxa are separate species N. oreinos and N. scheerpeltzi.     

Hybridization and introgression between Callicarpa japonica and C. mollis (Verbenaceae) in central Japan, as inferred from nuclear and chloroplast DNA sequences

Callicarpa x shirasawana is a natural hybrid between C. japonica and C. mollis, and has a morphology that is intermediate between those of the parent species. Characterization of natural Callicarpa populations in the Atsumi Peninsula of central Japan, which all three of the above species inhabit sympatrically, revealed hybrids with various morphologies. Molecular analysis revealed a high occurrence of introgression of the C. japonica genome into that of C. mollis. Moreover, all individuals examined with morphology similar to that of C. mollis had genetic traces of hybridization with C. japonica. Molecular analysis of individual C. mollis and C. japonica from five other areas of Japan showed that introgression of C. japonica into C. mollis occurs widely. Molecular data also strongly suggested that the previously recognized C. x shirasawana individuals with intermediate morphology are not F1 hybrids between C. japonica and C. mollis, but instead are progeny of C. x shirasawana backcrossed with C. japonica. Moreover, it was revealed that individuals with F1-type genotypes are indistinguishable morphologically from pure C. mollis. The results of the present study point to the need for re-evaluation of natural populations of C. mollis and C. x shirasawana.     

Gene flow,divergent selection and resistance to introgression in two species of morning glories (Ipomoea)

Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.     

Geographical variation of Plutella xylostella (Lepidoptera: Plutellidae) populations revealed by mitochondrial COI gene in China

The diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), is one of the most serious pests for cruciferous vegetable growers worldwide. To determine the relations of local and regional populations, we performed a mitochondrial COI gene analysis of eight P. xylostella populations from different locations in or around the Qinling Mountains and two other populations, one from Beijing and the other from Guangdong. The mtDNA divergences among the 10 populations were high, and 32 haplotypes were detected in 149 adults. The mean haplotype divergence was 1.7% (range 0.04–4.1%). Haplotype diversity in the 10 populations varied from 0.571 (AK) to 0.885 (HZ), and the nucleotide diversity varied from 0.00286 (AK) to 0.0117 (HZ). The results also did not show significant correlation between genetic and geographical distance. Also, the effective number of migrants between populations (Nm) ranged from 1.43 to infinite, suggesting that population exchange and gene flow among the P. xylostella populations occurred. However, principal component analysis (PCA) showed that the TB and TC populations were differentiated from other populations, indicating possible across‐mountain barrier to migration and gene flow.