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Species delimitation detected by molecular markers is complicated by introgression and incomplete lineage sorting between species. Recent modeling suggests that fixed genetic differences between species are highly related to rates of intraspecific gene flow. However, it remains unclear whether such differences are due to high levels of intraspecific gene flow overriding the spread of introgressed alleles or favoring rapid lineage sorting between species. In pines, chloroplast (cp) and mitochondrial (mt) DNAs are normally paternally and maternally inherited, respectively, and thus their relative rates of intraspecific gene flow are expected to be high and low, respectively. In this study, we used two pine species with overlapping geographical distributions in southeast China, P. massoniana and P. hwangshanensis, as a model system to examine the association between organelle gene flow and variation within and between species. We found that cpDNA variation across these two pine species is more species specific than mtDNA variation and almost delimits taxonomic boundaries. The shared mt/cp DNA genetic variation between species shows no bias in regard to parapatric versus allopatric species' distributions. Our results therefore support the hypothesis that high intraspecific gene flow has accelerated cpDNA lineage sorting between these two pine species.

Recent work has suggested that rates of introgression should be inversely related to levels of gene flow because introgressed populations cannot be 'rescued' by intraspecific gene flow if it is too low. Mitochondrial and chloroplast DNA (mtDNA and cpDNA) experience very different levels of gene flow in conifers due to their contrasted maternal and paternal modes of transmission, hence the prediction that mtDNA should introgress more readily than cpDNA in this group. Here, we use sequence data from both mtDNA and cpDNA to test this hypothesis in a group of closely related spruces species, the Picea asperata complex from China. Nine mitochondrial and nine chloroplast haplotypes were recovered from 459 individuals in 46 natural populations belonging to five species of the Picea asperata complex. Low variation was found in the two mtDNA introns along with a high level of differentiation among populations (G(ST) = 0.90). In contrast, we detected higher variation and lower differentiation among populations at cpDNA markers (G(ST) = 0.56), a trend shared by most conifer species studied so far. We found that cpDNA variation, although far from being fully diagnostic, is more species-specific than mtDNA variation: four groups of populations were identified using cpDNA markers, all of them related to species or groups of species, whereas for mtDNA, geographical variation prevails over species differentiation. The literature suggests that mtDNA haplotypes are often shared among related conifer species, whereas cpDNA haplotypes are more species-specific. Hence, increased intraspecific gene flow appears to decrease differentiation within species but not among species.

The development of next‐generation sequencing technologies allows researchers to address complex problems in species delimitation, especially for non‐model organisms. The taxonomic status of North American Nyssa species has long been debated and remains controversial. To elucidate the genetic structure and phylogenetic relationships of the five currently recognized North American Nyssa species, we conducted whole‐genome sequencing of representative individuals and identified genome‐wide single‐nucleotide polymorphisms (SNPs) by utilizing the recently released chromosome‐level assembly of Nyssa sinensis genome. Population genetic and phylogenetic analyses consistently inferred four well‐supported genetic clusters from our sampled individuals, that is, N. aquatica, N. ogeche, N. sylvatica, and N. biflora–N. ursina. Although the identification of N. biflora and N. ursina is primarily based on the morphological characteristics of leaves and drupes, the present evidence, including our principal components analysis of leaf morphological traits, strongly supports the taxonomic designation of N. biflora and N. ursina as a single species. In addition, these four genetic clusters were grouped into two major clades, that is, clade 1 (N. aquatica and N. ogeche) and clade 2 (N. sylvatica and N. biflora–N. ursina). Despite the fact that no evidence of widespread gene flow was found between these two major clades, our analyses revealed the possibility of introgression from N. sylvatica into N. biflora, albeit at a relatively low frequency. This study demonstrates the use of whole‐genome sequences as a promising avenue for delimiting species boundaries and further advocates for an integrative approach in the assessment of species delimitation. [ABSTRACT FROM AUTHOR]

The distinction between hybrids and species of hybrid origin is significant for plant diversity conservation. Interspecific hybridization within the genus Rosa is a common phenomenon. Based on field observation, we hypothesized that one previously published species, Rosa pseudobanksiae (endangered category: CR) might be a hybrid. In this study, we utilized molecular approaches involving three nuclear markers and four plastid markers to examine the origin of R. pseudobanksiae. Our evidence shows that it is indeed a natural homoploid hybrid between R. banksiae var. normalis and R. multiflora var. cathayensis, and that gene flows bidirectionally. Our multivariate morphometric analyses provide strong evidence for a matrocliny in R. × pseudobanksiae individuals. R. × pseudobanksiae has diverse morphological variations among individuals andshares the overlapped distributions with its parental progenitors. This taxon has not developed into a stabilized and self-evolving lineage with the high sterility in seed sets. [ABSTRACT FROM AUTHOR]

"Sky island" species diversification contributes greatly to mountainous biodiversity. However, the underlying genomic divergence and the inferred drivers remain largely unknown. In this study, we examined the diversification history of five diploid species with three exclusively endemic to the sky islands (mountains) of the Himalaya–Hengduan Mountains biodiversity hotspot. All of them together comprise a clade of the genus Eutrema (Brassicaceae). We resequenced genomes of multiple individuals of the found populations for each species. We recovered the inconsistent phylogenetic relationships between plastome and nuclear‐genome trees for one species. Based on nuclear population genomic data, we detected high genetic divergence between five species with limited gene flow. Four species seemed to diverge mainly through geographical isolation, whereas one arose through hybrid origin. The origins of the sampled five species were dated to within the late Miocene when mountains were uplifted and climates oscillated. All species decreased their population sizes since the inferred origin of each species initially, but only two of them expanded after the Last Glacial Maximum. Together, these findings suggest that geographic isolation plays an important role in driving the sky island species diversification of the sampled species in addition to the occasional gene flow that might have led to the hybrid origin of some sky island species, similar to the species diversification of sea islands. [ABSTRACT FROM AUTHOR]

Accurate species delimitation of sampled biological material is critical for a range of studies. Although the DNA barcodes developed in recent years are useful for identifying numerous well differentiated species that have not experienced frequent gene flow, they fail to delimit recently diverged species, especially those with extensive introgressions. Here we use five Rhododendron species growing together on the same mountain as a model system to compare the species delimitation effectiveness of the DNA barcodes (internal transcribed spacer, matK, psbA‐trnH, and rbcL) previously proposed versus 15 pairs of microsatellite markers. Using these markers, we genotyped 129 individuals, which were members of five species according to morphological identification. We identified five simple sequence repeat genetic clusters (independently evolving lineages) corresponding to the morphological identification. However, we found that numerous individuals contained cryptic hybrid introgressions from the other species. The four DNA barcodes could not delimit three out of four closely related species that showed clear morphological differentiation and cryptic introgressions. Even after excluding all cryptic hybrids, two closely related species could not be successfully identified. The low discrimination ability of the DNA barcodes for closely related Rhododendron species could result from two, not mutually exclusive factors: introgressive hybridization and incomplete lineage sorting. Our results highlight the importance of simple sequence repeat markers in delimiting closely related species and identifying cryptic introgressions in the absence of morphological changes. [ABSTRACT FROM AUTHOR]

Pleistocene climate change has had an important effect in shaping intraspecific genetic variation in many species; however, its role in driving speciation is less clear. We examined the possibility of a Pleistocene origin of the only two representatives of the genus Pugionium ( Brassicaceae), Pugionium cornutum and Pugionium dolabratum, which occupy different desert habitats in northwest China., We surveyed sequence variation for internal transcribed spacer ( ITS), three chloroplast (cp) DNA fragments, and eight low-copy nuclear genes among individuals sampled from 11 populations of each species across their geographic ranges., One ITS mutation distinguished the two species, whereas mutations in cp DNA and the eight low-copy nuclear gene sequences were not species-specific. Although interspecific divergence varied greatly among nuclear gene sequences, in each case divergence was estimated to have occurred within the Pleistocene when deserts expanded in northwest China., Our findings point to the importance of Pleistocene climate change, in this case an increase in aridity, as a cause of speciation in Pugionium as a result of divergence in different habitats that formed in association with the expansion of deserts in China. [ABSTRACT FROM AUTHOR]