Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.)

Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards

The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.

A Small Set of Nuclear Markers for Reliable Differentiation of the Two Closely Related Oak Species Quercus Robur and Q. Petraea

Quercus robur and Q. petraea are, in addition to Fagus sylvatica, the main economically used deciduous tree species in Europe. Identification of these two species is crucial because they differ in their ecological demands. Because of a changing climate, foresters must know more than ever which species will perform better under given environmental conditions. The search for differentiating molecular markers between these two species has already lasted for decades. Until now, differentiation has only been possible in approaches with a combination of several molecular markers and a subsequent statistical analysis to calculate the probability of being one or the other species. Here, we used MiSeq Illumina data from pools of Q. robur and Q. petraea specimens and identified nuclear SNPs and small InDels versus the Q. robur reference genome. Selected sequence variants with 100% allele frequency difference between the two pools were further validated in an extended set of Q. robur and Q. petraea specimens, and then the number of markers was deliberately reduced to the smallest possible set for species differentiation. A combination of six markers from four nuclear regions is enough to identify Q. robur, Q. petraea or hybrids between these two species quite well and represents a marker set that is cost-efficient and useable in every laboratory.

Genetic Variability and Admixture Zones in the Italian Populations of Turkey Oak (Quercus cerris L.)

The Turkey oak (Quercus cerris L.) is widely distributed in Italy, where it is the ecologically dominant oak on sandy and acidic soil. In this work, we analysed 23 natural populations by means of eight SSR (microsatellite) markers, to obtain the first synthetic map of genetic variability for this species and to study its dispersion during the Holocene, due to the possibility that at least one refugium during the Last Glacial Maximum was in Italy. The analyses showed a good amount of genetic variability together with fair differentiation between populations, as indicated by F_ST = 0.059. A Bayesian analysis of the amount of admixture among populations revealed the presence of four putative gene pools of origin and a rough subdivision of the populations according to their geographic location, as confirmed by the spatial analysis. No evidence for the existence of putative refugial populations was found; however, this study paves the way for the planning of conservation strategies also with regard to the relationship between Turkey oak and other oak species in Italy.

Identifying of Quercus vulcanica and Q. frainetto growing in different environments through deep learning analysis

Quercus is one of the important elements of forests worldwide. But the diagnosis of the species in this genus in particular using leaves is pretty challenging due to the presence of natural hybrids and phenotypically plastic trait expression. In this sense, this study aims to classify the leaves of Q. vulcanica and Q. frainetto using convolutional neural networks, VGG16 and VGG19, and Xception deep learning architectures to determine which method has the best performance in species assignment. For this purpose, leaf samples were collected from a total of 300 trees of 6 natural populations using a total of 1459 leaf images, 491 from Q. frainetto and 968 from Q. vulcanica. Before exporting images to the deep learning model, RGB/gray filters are applied and images are optimized with contrast limited adaptive histogram equalization to achieve maximum performance in the deep learning model. Accuracy rates of deep learning architectures varied from 79% (Xception) to 95% (VGG16). The VGG16 deep learning model provided superior performance compared to the others. Developing a mobile device using images from natural populations of many oak species will be beneficial not only for practitioners but also for scientists and local people.

The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm

Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi's genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.

Genetic Diversity and Differentiation of Pedunculate Oak (Quercus robur L.) Populations at the Southern Margin of Its Distribution Range—Implications for Conservation

Understanding intraspecific genetic variation is one of the principal requirements for the evaluation of tree species capacity to cope with intensive climatic changes, as well as designing long-term conservation programs. Herein, we evaluated the genetic diversity and genetic structure of seven pedunculate oak (Quercus robur L.) populations, located at the southern margin of its distribution range on the Balkan Peninsula (Serbia). The objective of the study was to propose future in situ conservation measures aimed at protection of pedunculate oak adaptive and neutral genetic diversity at the species rear-edge. Genetic diversity and structure were estimated using twelve highly polymorphic simple sequence repeat (SSR) markers. The mean expected heterozygosity (He) was 0.769, allelic richness (AR) 9.63, and private allelic richness (pAR) 0.79, indicating high genetic diversity in the studied populations. Genetic differentiation among the populations was low (Fst = 0.032). Structure analysis, the unweighted pair group method with arithmetic mean (UPGMA) showed the existence of two gene pools unrelated to the populations’ area of occurrence. Taking into consideration the results of the current study and previous conservation activities on the pedunculate oak in Serbia, as well as the importance of rear-edge populations in the long-term conservation of the species genetic diversity, we suggested establishing three additional gene conservation units for securing long-term sustainability of the species.

Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa

Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.

Isolation of Metrosideros ('Ohi'a) Taxa on O'ahu Increases with Elevation and Extreme Environments

Species radiations should be facilitated by short generation times and limited dispersal among discontinuous populations. Hawaii's hyper-diverse, landscape-dominant tree, Metrosideros, is unique among the islands' radiations for its massive populations that occur continuously over space and time within islands, its exceptional capacity for gene flow by both pollen and seed, and its extended life span (ca. >650 years). Metrosideros shows the greatest phenotypic and microsatellite DNA diversity on O'ahu, where taxa occur in tight sympatry or parapatry in mesic and montane wet forest on 2 volcanoes. We document the nonrandom distributions of 12 taxa (including unnamed morphotypes) along elevation gradients, measure phenotypes of ~6-year-old common-garden plants of 8 taxa to verify heritability of phenotypes, and examine genotypes of 476 wild adults at 9 microsatellite loci to compare the strengths of isolation across taxa, volcanoes, and distance. All 8 taxa retained their diagnostic phenotypes in the common garden. Populations were isolated by taxon to a range of degrees (pairwise FST between taxa: 0.004-0.267), and there was no pattern of isolation by distance or by elevation; however, significant isolation between volcanoes was observed within monotypic species, suggesting limited gene flow between volcanoes. Among the infraspecific taxa of Metrosideros polymorpha, genetic diversity and isolation significantly decreased and increased, respectively, with elevation. Overall, 5 of the 6 most isolated taxa were associated with highest elevations or otherwise extreme environments. These findings suggest a principal role for selection in the origin and maintenance of the exceptional diversity that occurs within continuous Metrosideros stands on O'ahu.

Comparative analysis of spatial genetic structures in sympatric populations of two riparian plants, Saxifraga acerifolia and Saxifraga fortunei

PREMISE

The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures.

METHODS

To reveal genetic structures, we examined chloroplast microsatellite variations and genome-wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences.

RESULTS

We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation.

CONCLUSIONS

Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures.

From allozymes to NGS: population genetics of forest trees in Slovakia in the past 40 years

This review summarizes the development of population genetics and population genomics studies of forest trees in Slovakia during the past 40 years. Various protein and DNA markers have been applied during this period to address several topics in evolutionary genetics and biogeography of trees: allozymes, uniparentally inherited chloroplast and mitochondrial markers, simple sequence repeats and single nucleotide polymorphisms. The main object of studies of phylogeny and postglacial migration were Fagus sylvatica s.l. and eastern-Mediterranean firs (Abies Mill. section Abies), where the divergence of genetic lineages (species and subspecific taxa) in time, as well as colonization of the current ranges during the Holocene were reconstructed. The studies on intraspecific gene flow and homoploid hybridization focused on hybrid swarms Pinus sylvestris/P. mugo and firs. Unusual maternal inheritance of chloroplast DNA was revealed in P. mugo × P. sylvestris crosses. Contrasting geographical structures of hybrid zones were revealed in wind-dispersed vs. animal-dispersed trees. Within the studies of adaptation, signals of selection were identified both in field observations and common-garden experiments on Picea abies, F. sylvatica and A. alba. Perspectives of ongoing research employing next-generation sequencing were shortly outlined.

High-throughput sequencing of 5S-IGS in oaks: Exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples

Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high-throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum-likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium- to high-abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide.

Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus

Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the "true" picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology-although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence.

Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan

Introgression from one species in a specific environment to another may facilitate colonization of the environment by the recipient species. However, such environment-dependent introgression has been clarified in limited plant taxa. In northern Japan, there are two interfertile oak species: Quercus dentata (Qd) in coastal areas and Q. mongolica var. crispula (Qc) in inland areas. However, at higher latitudes where Qd is rare, a coastal Qc ecotype with Qd-like traits is distributed in the coastal areas. We distinguished inland Qc, coastal Qc, and coastal Qd populations based on genome-wide genotypes and multitrait phenotypes and verified introgression from coastal Qd to coastal Qc using reduced library sequencing. Genotypes and phenotypes differed among the populations, and coastal Qc was intermediate between inland Qc and coastal Qd. The ABBA-BABA test showed introgression from coastal Qd to coastal Qc. In coastal Qc, we found various stages of introgression after the first generation of backcross but detected no genomic regions where introgression was enhanced. Overall, we show evidence for introgression from a coastal species to an ecotype of an inland species, which has colonized the coastal environment. It remains unclear whether introgressed alleles are selected in the coastal environment.

A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture

BACKGROUND AND AIMS

Hybridization and introgression play an important role in the evolution and diversification of plants. To assess the degree of past and current hybridization, the level of genetic admixture in populations needs to be investigated. Ongoing hybridization and blurred species separation have made it challenging to assign European white oak taxa based on leaf morphology and/or genetic markers and to assess the level of admixture. Therefore, there is a need for powerful markers that differentiate between taxa. Here, we established a condensed set of single-nucleotide polymorphism (SNP) markers to reliably differentiate between the three most common oak species in temperate European forests (Quercus robur, Q. petraea, Q. pubescens) and to assess the degree of admixture in a large set of selected Swiss populations.

METHODS

A training set of 194 presumably pure reference samples from Switzerland and Europe was used to assign 633 test individuals with two different approaches (population genetic-based/Bayesian vs. assumption-free/discriminative classifier) using 58 selected SNPs from coding regions. Admixture was calculated at the individual and population level with the Shannon diversity index based on individual assignment probabilities.

KEY RESULTS

Depending on the approach, 97.5-100 % of training individuals were assigned correctly, and additional analyses showed that the established SNP set could be further reduced while maintaining its discriminatory power. The two assignment approaches showed high overlap (99 %) in assigning training individuals and slightly less overlap in test individuals (84 %). Levels of admixture varied widely among populations. Mixed stands of Q. petraea and Q. pubescens revealed much higher degrees of admixture than mixed stands of the other two taxon pairs, accentuating high levels of gene flow between these two taxa in Switzerland.

CONCLUSIONS

Our set of SNPs warrants reliable taxon discrimination with great potential for further applications. We show that the three European white oak taxa have largely retained their species integrity in Switzerland despite high levels of admixture.

Demographic Inference of Divergence and Gene Exchange Between Castanopsis fabri and Castanopsis lamontii

The cytoplasmic genome of one species may be replaced by that of another species without leaving any trace of past hybridization in its nuclear genome, which can thus confuse the inference of genealogical relationship and evolutionary history of many congeneric species. In this study, we used sequence variations of chloroplast DNA and restriction site-associated DNA to investigate gene exchange between Castanopsis fabri and Castanopsis lamontii, and to infer the divergence history of the two species by comparing different divergence models based on the joint allele frequency spectrum. We evaluated climatic niche similarity of the two species using climatic variables across their entire distribution range in subtropical China. Clear genetic differentiation was revealed between C. fabri and C. lamontii, and gene exchange between the two species was discovered as a consequence of secondary contact. The gene exchange rates were variable across the genome. Gene exchange could allow C. fabri to widen its habitat through pollen swamping and broaden its climatic niche, and the chloroplast genome of C. lamontii is captured by C. fabri during this process. These results further our understanding of the timing and contribution of gene exchange to species divergence in forests.

Radial growth-based assessment of sites effects on pedunculate and greyish oak in southern Romania

This study focuses on the climate growth drivers of Quercus robur L. (pedunculate oak) and Q. robur subsp. pedunculiflora K. Koch. (greyish oak), occurring in the biodiversity of three sites in southern Romania. We determined the degree of tolerance of the greyish oak, between the tardive and praecox varieties, to environmental stress, between 1951 and 2016. Total tree ring-width (RW), and earlywood (EW) and latewood (LW) measurements were subject of periodical and monthly climate-growth analysis. Our results revealed a moderate relationship between climate and tree-growth. A significant and positive relationship was observed between RW and previous growing season precipitation. Mean and minimum temperatures affected both positive and negative tree-rings during the growing season. We also observed that winter and spring represent key seasons for differentiating tardive from praecox varieties, affecting the intra-annual variability of ring-width, and EW and LW parameters. The correlation between the tree-ring measurements and daily climate data shows a clear offset of the starting growth between greyish oak varieties. A weak influence of stressors on tree-growth at the sites was observed through pointer year and resilience components analysis.

Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages

BACKGROUND

Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures.

RESULTS

Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America.

CONCLUSIONS

Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.

Influence of a climatic gradient on genetic exchange between two oak species

PREMISE

In plant groups with limited intrinsic barriers to gene flow, it is thought that environmental conditions can modulate interspecific genetic exchange. Oaks are known for limited barriers to gene flow among closely related species. Here, we use Quercus as a living laboratory in which to pursue a fundamental question in plant evolution: Do environmental gradients restrict or promote genetic exchange between species?

METHODS

We focused on two North American oaks, the rare Quercus dumosa and the widespread Q. berberidifolia. We sampled intensively along a contact zone in California, USA. We sequenced restriction site-associated DNA markers and measured vegetative phenotype. We tested for genetic exchange, the association with climate, and the effect on phenotype.

RESULTS

There is evidence for genetic exchange between the species. Admixed plants are found in areas of intermediate climate, while less admixed plants are found at the extremes of the climatic gradient. Genetic and phenotypic patterns are out of phase in the contact zone; some plants display the phenotype of one species but are genetically associated with another.

CONCLUSIONS

Our results support the hypothesis that a strong climatic gradient can promote genetic exchange between species. The overall weak correlation between genotype and phenotype in the contact zone between the species suggests that genetic exchange can lead to the breakdown of trait combinations used to define species. This incongruency predicts ongoing problems for conservation of Q. dumosa, with implications for conservation of other oaks.

Challenges of next-generation sequencing in conservation management: Insights from long-term monitoring of corridor effects on the genetic diversity of mouse lemurs in a fragmented landscape

Long-term genetic monitoring of populations is essential for efforts aimed at preserving genetic diversity of endangered species. Here, we employ a framework of long-term genetic monitoring to evaluate the effects of fragmentation and the effectiveness of the establishment of corridors in restoring population connectivity and genetic diversity of mouse lemurs Microcebus ganzhorni. To this end, we supplement estimates of neutral genetic diversity with the assessment of adaptive genetic variability of the major histocompatibility complex (MHC). In addition, we address the challenges of long-term genetic monitoring of functional diversity by comparing the genotyping performance and estimates of MHC variability generated by single-stranded conformation polymorphism (SSCP)/Sanger sequencing with those obtained by high-throughput sequencing (next-generation sequencing [NGS], Illumina), an issue that is particularly relevant when previous work serves as a baseline for planning management strategies that aim to ensure the viability of a population. We report that SSCP greatly underestimates individual diversity and that discrepancies in estimates of MHC diversity attributable to the comparisons of traditional and NGS genotyping techniques can influence the conclusions drawn from conservation management scenarios. Evidence of migration among fragments in Mandena suggests that mouse lemurs are robust to the process of fragmentation and that the effect of corridors is masked by ongoing gene flow. Nonetheless, results based on a larger number of shared private alleles at neutral loci between fragment pairs found after the establishment of corridors in Mandena suggest that gene flow is augmented as a result of enhanced connectivity. Our data point out that despite low effective population size, M. ganzhorni maintains high individual heterozygosity at neutral loci and at MHC II DRB gene and that selection plays a predominant role in maintaining MHC diversity. These findings highlight the importance of long-term genetic monitoring in order to disentangle between the processes of drift and selection maintaining adaptive genetic diversity in small populations.

An admixture of Quercus dentata in the coastal ecotype of Q. mongolica var. crispula in northern Hokkaido and genetic and environmental effects on their traits

In northern Japan, coastal oak forests consist of Quercus dentata (Qd) on the coastal side and Q. mongolica var. crispula (Qc) on the inland side. In the forests of northern Hokkaido, Qd is rare, and a coastal ecotype of Qc with some Qd-like traits grows on the coastal side. To reveal the genetic background of this ecotype, nuclear microsatellite genotypes in closely related oak taxa were obtained from the Eurasian continent, Sakhalin, and Hokkaido. The clustering of these genotypes suggests an admixture of Qd in the coastal ecotype of Qc. Next, we evaluated the effects of admixture and coastal stress on the leaf and shoot traits of Qc and Qd along coastal-inland gradients in northern Hokkaido. The admixture of Qd in Qc was quantified by the Qd ancestry proportions. Coastal stress causes bud mortality in the upper parts of shoots and was quantified by the survival patterns of buds in shoots. The genetic and environmental effects on the traits at Qd-abundant and Qd-rare sites were estimated using linear mixed models. The genetic effect was detected in all traits. Both genetic and environmental effects were detected in most traits. Some traits differed between Qd-abundant and Qd-rare sites in addition to these effects, indicating more Qd-like traits at Qd-rare sites. The findings suggest that an admixture of Qd characterizes the genetic background of the coastal ecotype of Qc and that not only the coastal stress but also the genetic background is responsible for the leaf and shoot traits of Qc and Qd in northern Hokkaido.

Genetic structuring of the coastal herb Arthropodium cirratum (Asparagaceae) is shaped by low gene flow, hybridization and prehistoric translocation

We examined the genetic structuring of rengarenga (Arthropodium cirratum; Asparagaceae), an endemic New Zealand coastal herb, using nuclear microsatellite markers. This species was brought into cultivation by Māori within the last 700–800 years for its edible roots and was transplanted beyond its natural distribution as part of its cultivation. We found very high levels of genetic structuring in the natural populations (F_ST = 0.84), indicating low levels of gene flow. Reduced genetic diversity was found in the translocated populations, suggesting a large loss of genetic diversity early in the domestication process. The data indicates that rengarenga was brought into cultivation independently at least three times, with the sources of these introductions located within a narrow area encompassing about 250km of coastline. Hybridization was inferred between A. cirratum and the closely related A. bifurcatum, despite A. birfucatum not occurring in the vicinity.

Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus)

Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.

Relative contributions of neutral and non-neutral processes to clinal variation in calyx lobe length in the series Sakawanum (Asarum: Aristolochiaceae)

Background and Aims

Clines, the gradual variation in measurable traits along a geographical axis, play a major role in evolution and can contribute to our understanding of the relative roles of selective and neutral process in trait variation. Using genetic and morphological analyses, the relative contributions of neutral and non-neutral processes were explored to infer the evolutionary history of species of the series Sakawanum (genus Asarum), which shows significant clinal variation in calyx lobe length.

Methods

A total of 27 populations covering the natural geographical distribution of the series Sakawanum were sampled. Six nuclear microsatellite markers were used to investigate genetic structure and genetic diversity. The lengths of calyx lobes of multiple populations were measured to quantify their geographical and taxonomic differentiation. To detect the potential impact of selective pressure, morphological differentiation was compared with genetic differentiation (QCT-FST comparison).

Key Results

Average calyx lobe length of A. minamitanianum was 124.11 mm, while that of A. costatum was 13.80 mm. Though gradually changing along the geographical axis within series, calyx lobe lengths were significantly differentiated among the taxa. Genetic differentiation between taxa was low (FST = 0.099), but a significant geographical structure along the morphological cline was detected. Except for one taxon pair, pairwise QCT values were significantly higher than the neutral genetic measures of FST and G'ST.

Conclusions

Divergent selection may have driven the calyx lobe length variation in series Sakawanum taxa, although the underlying mechanism is still not clear. The low genetic differentiation indicates recent divergence and/or gene flows between geographically close taxa. These neutral processes would also affect the clinal variation in calyx lobe lengths. Overall, this study implies the roles of population history and divergent selection in shaping the current cline of a flower trait in the series Sakawanum.

Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes

Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa. In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa, evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini. Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini. By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa, and a cryptic species may also exist in Q. boulengeri. However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri. Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa.

Impacts of human-induced environmental disturbances on hybridization between two ecologically differentiated Californian oak species

Natural hybridization, which can be involved in local adaptation and in speciation processes, has been linked to different sources of anthropogenic disturbance. Here, we use genotypic data to study range-wide patterns of genetic admixture between the serpentine-soil specialist leather oak (Quercus durata) and the widespread Californian scrub oak (Quercus berberidifolia). First, we estimated hybridization rates and the direction of gene flow. Second, we tested the hypothesis that genetic admixture increases with different sources of environmental disturbance, namely anthropogenic destruction of natural habitats and wildfire frequency estimated from long-term records of fire occurrence. Our analyses indicate considerable rates of hybridization (> 25%), asymmetric gene flow from Q. durata into Q. berberidifolia, and a higher occurrence of hybrids in areas where both species live in close parapatry. In accordance with the environmental disturbance hypothesis, we found that genetic admixture increases with wildfire frequency, but we did not find a significant effect of other sources of human-induced habitat alteration (urbanization, land clearing for agriculture) or a suite of ecological factors (climate, elevation, soil type). Our findings highlight that wildfires constitute an important source of environmental disturbance, promoting hybridization between two ecologically well-differentiated native species.

Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions

Genetic variation shared between closely related species may be due to retention of ancestral polymorphisms because of incomplete lineage sorting (ILS) and/or introgression following secondary contact. It is challenging to distinguish ILS and introgression because they generate similar patterns of shared genetic diversity, but this is nonetheless essential for inferring accurately the history of species with overlapping distributions. To address this issue, we sequenced 33 independent intron loci across the genome of two closely related pine species (Pinus massoniana Lamb. and Pinus hwangshanensis Hisa) from Southeast China. Population structure analyses revealed that the species showed slightly more admixture in parapatric populations than in allopatric populations. Levels of interspecific differentiation were lower in parapatry than in allopatry. Approximate Bayesian computation suggested that the most likely speciation scenario explaining this pattern was a long period of isolation followed by a secondary contact. Ecological niche modeling suggested that a gradual range expansion of P. hwangshanensis during the Pleistocene climatic oscillations could have been the cause of the overlap. Our study therefore suggests that secondary introgression, rather than ILS, explains most of the shared nuclear genomic variation between these two species and demonstrates the complementarity of population genetics and ecological niche modeling in understanding gene flow history. Finally, we discuss the importance of contrasting results from markers with different dynamics of migration, namely nuclear, chloroplast and mitochondrial DNA.

The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative.

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation-with-migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.

Revisiting the evolutionary events in Allium subgenus Cyathophora (Amaryllidaceae): Insights into the effect of the Hengduan Mountains Region (HMR) uplift and Quaternary climatic fluctuations to the environmental changes in the Qinghai-Tibet Plateau

The respective roles that the Hengduan Mountains Region (HMR) uplift around 4-3 Ma and Quaternary climatic oscillations played in causing the environmental changes in the Qinghai-Tibet Plateau (QTP) remain unknown. Here, we reconstruct the evolutionary history of two varieties of Allium cyathophorum and A. spicatum of subgenus Cyathophora, restricted to the HMR and the western QTP, respectively. Forty-five populations were surveyed for chloroplast and nuclear sequence variation to evaluate phylogenetic relationships, dates of divergence and ancestral area/inflorescence reconstructions. In addition, analyses were conducted on discernable micromorphologies, cytotypes and seed size variation. Our results indicated that two varieties of A. cyathophorum are separate species, i.e. A. farreri and A. cyathophorum, and the initial split of Cyathophora was triggered by the HMR uplift around 4-3 Ma. Subsequently, A. spicatum originated through the strengthened aridification in the western QTP induced vicariance of the ancestral populations in the HMR during the early Pleistocene. A self-sustaining allotetraploid species from A. farreri and A. cyathophorum was established during an interglacial period of penultimate glaciation of the QTP. Seed size variation also supports these by the colonization-competition tradeoff among small and large seeds. Our findings appear to suggest that the HMR uplift could have strengthened the development of the Asian monsoon regimes in this region and aridification in the western QTP, while the Quaternary climatic oscillations spurred the allopatric species' range shifts and created new open microhabitat for the alloploid species.

Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio-Pleistocene range dynamics of evergreen forest in subtropical China

Warm-temperate evergreen (WTE) forest represents the typical vegetation type of subtropical China, but how its component species responded to past environmental change remains largely unknown. Here, we reconstruct the evolutionary history of Tetrastigma hemsleyanum, an herbaceous climber restricted to the WTE forest. Twenty populations were genotyped using chloroplast DNA sequences and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and ecological niche modeling (ENM) of the species distributions during the Last Glacial Maximum (LGM) and at present. Lineages in Southwest vs Central-South-East China diverged through climate/tectonic-induced vicariance of an ancestral southern range during the early Pliocene. Long-term stability in the Southwest contrasts with latitudinal range shifts in the Central-South-East region during the early-to-mid-Pleistocene. Genetic and ENM data strongly suggest refugial persistence in situ at the LGM. Pre-Quaternary environmental changes appear to have had a persistent influence on the population genetic structure of this subtropical WTE forest species. Our findings suggest relative demographic stability of this biome in China over the last glacial-interglacial cycle, in contrast with palaeobiome reconstructions showing that this forest biome retreated to areas of today's tropical South China during the LGM.

Incipient radiation within the dominant Hawaiian tree Metrosideros polymorpha

Although trees comprise a primary component of terrestrial species richness, the drivers and temporal scale of divergence in trees remain poorly understood. We examined the landscape-dominant tree, Metrosideros polymorpha, for variation at nine microsatellite loci across 23 populations on young Hawai'i Island, sampling each of the island's five varieties throughout its full geographic range. For four varieties, principal coordinate analysis revealed strong clustering of populations by variety across the 10 430 km(2) island, indicating partitioning of the species into multiple evolutionarily significant units. The single island-endemic form, riparian var. newellii, showed especially strong differentiation from other varieties despite occurring in sympatry with other varieties and likely evolved from a bog form on the oldest volcano, Kohala, within the past 500 000 years. Along with comparable riparian forms on other Pacific Islands, var. newellii appears to represent parallel incipient ecological speciation within Metrosideros. Greater genetic distance among the more common varieties on the oldest volcano and an inverse relationship between allelic diversity and substrate age appear consistent with colonization of Hawai'i Island by older, partially diverged varieties followed by increased hybridization among varieties on younger volcanoes. This study demonstrates that broad population-level sampling is required to uncover patterns of diversification within a ubiquitous and long-lived tree species. Hawaiian Metrosideros appears to be a case of incipient radiation in trees and thus should be useful for studies of divergence and the evolution of reproductive isolating barriers at the early stages of speciation.

Novel SNP development and analysis at a NADP+ -specific IDH enzyme gene in a four species mixed oak forest

Closely related Quercus species generally exhibit low levels of genetic differentiation despite their ecological and morphological differences. However, at a few so-called 'outlier' loci they seem to remain genetically distinct. Isocitrate dehydrogenases (IDH) are key enzymes involved in the metabolic pathway of the citrate cycle. IDH has also been characterised as an 'outlier' marker, significantly differentiating the closely related Q. robur and Q. petraea with the isozyme technique. This ability to differentiate the species was tested here at molecular level: 13 single nucleotide polymorphism (SNP) markers were identified and developed within a NADP(+) -specific IDH gene in Quercus spp. and applied as molecular markers in a four species mixed oak forest in eastern Europe, where Q. robur, Q. petraea, Q. pubescens and Q. frainetto naturally co-exist. From the 13 developed SNPs, three groups were formed: non-synonymous, synonymous and non-coding SNPs. The levels of total gene diversity were moderate for all species investigated. The non-synonymous SNPs showed lower levels of gene diversity. Overall, the four closely related Quercus spp. were significantly differentiated (except Q. petraea with Q. frainetto). Analysis of non-random association of alleles revealed no clear physical clustering of the SNP sites in significant linkage disequilibrium (LD). However, separate LD analysis for each species showed a lower number of sites in significant LD for Q. robur than for the other species, possibly reflecting the history of the species in this specific geographical site and less efficient recombination effect due to the larger effective population size of Q. robur. Eleven statistically significant associations were found between seven SNPs and morphological traits that are commonly used to differentiate oak species.

Detecting the footprints of divergent selection in oaks with linked markers

Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 nuclear microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process.

The role of genetic structure in the adaptive divergence of populations experiencing saltwater intrusion due to relative sea-level rise

Saltwater intrusion into estuaries creates stressful conditions for nektonic species. Previous studies have shown that Gambusia affinis populations with exposure to saline environments develop genetic adaptations for increased survival during salinity stress. Here, we evaluate the genetic structure of G. affinis populations, previously shown to have adaptations for increased salinity tolerance, and determine the impact of selection and gene flow on structure of these populations. We found that gene flow was higher between populations experiencing different salinity regimes within an estuary than between similar marsh types in different estuaries, suggesting the development of saline-tolerant phenotypes due to local adaptation. There was limited evidence of genetic structure along a salinity gradient, and only some of the genetic variation among sites was correlated with salinity. Our results suggest limited structure, combined with selection to saltwater intrusion, results in phenotypic divergence in spite of a lack of physical barriers to gene flow.

Phylogeography of the Korean pine (Pinus koraiensis) in northeast Asia: inferences from organelle gene sequences

Range-wide genetic variation of Korean pine (Pinus koraiensis) was assessed using maternally inherited mtDNA and paternally inherited cpDNA for 16 natural populations throughout northeast Asia in order to study its phylogeographical history during the Quaternary. The cpDNA variation indicated that there was no difference between populations on the Asian continent and those in the Japanese archipelago. In contrast, the mtDNA variation indicated that there was significant difference between the populations from the two regions, with each region having a different lineage. The continental populations exhibited no diversity in the mtDNA examined despite the species' current extensive range and large populations. Conversely, while the Korean pine is rare in Japan, the Japanese populations exhibited greater levels of mtDNA diversity (H (T) = 0.502). The higher mtDNA diversity and evidence from numerous Korean pine macrofossil remains dated to the Pleistocene and recovered various sites in Japan suggest that the Japanese archipelago once served as a refugium to a much larger Korean pine population with a more extensive range than is the case today. The presence of the single mtDNA haplotype across the Asian continent suggests that the present widespread populations could have expanded from a single refugium population after the last glacial periods.

A European phylogeography of Rhinanthus minor compared to Rhinanthus angustifolius: unexpected splits and signs of hybridization

Rhinanthus minor and Rhinanthus angustifolius (Orobanchaceae) are annual hemiparasites, which occur sympatrically in Europe and are known to hybridize. We studied chloroplast and nuclear (amplified fragment length polymorphism [AFLP]) diversity in R. minor and compared genetic structuring in this species with R. angustifolius by analyzing the AFLP data for both species simultaneously. The AFLP data revealed that populations in Italy, Greece, and southeast Russia initially identified as R. minor were so distant from the other R. minor populations that they probably belong to another, yet unidentified taxon, and we refer to them as Rhinanthus sp. R. minor s.s. showed a clear geographic genetic structure in both the chloroplast DNA (cpDNA) and nuclear genome. The simultaneous analysis of both species shed new light on the previously published findings for R. angustifolius, because some populations now turned out to belong to R. minor. The admixture analysis revealed very few individuals of mixed R. minor–R.angustifolius ancestry in the natural populations in the west of Europe, while admixture levels were higher in the east. The combined haplotype network showed that haplotype H1 was shared among all species and is likely to be ancestral. H2 was more abundant in R. angustifolius and H3 in R. minor, and the latter probably arose from H1 in this species in the east of Europe. The occurrence of H3 in R. angustifolius may be explained by introgression from R. minor, but without interspecific admixture, these are likely to have been old hybridization events. Our study underlines the importance of including related species in phylogeographic studies.

Inferring multiple refugia and phylogeographical patterns in Pinus massoniana based on nucleotide sequence variation and DNA fingerprinting

BACKGROUND

Pinus massoniana, an ecologically and economically important conifer, is widespread across central and southern mainland China and Taiwan. In this study, we tested the central-marginal paradigm that predicts that the marginal populations tend to be less polymorphic than the central ones in their genetic composition, and examined a founders' effect in the island population.

METHODOLOGY/PRINCIPAL FINDINGS

We examined the phylogeography and population structuring of the P. massoniana based on nucleotide sequences of cpDNA atpB-rbcL intergenic spacer, intron regions of the AdhC2 locus, and microsatellite fingerprints. SAMOVA analysis of nucleotide sequences indicated that most genetic variants resided among geographical regions. High levels of genetic diversity in the marginal populations in the south region, a pattern seemingly contradicting the central-marginal paradigm, and the fixation of private haplotypes in most populations indicate that multiple refugia may have existed over the glacial maxima. STRUCTURE analyses on microsatellites revealed that genetic structure of mainland populations was mediated with recent genetic exchanges mostly via pollen flow, and that the genetic composition in east region was intermixed between south and west regions, a pattern likely shaped by gene introgression and maintenance of ancestral polymorphisms. As expected, the small island population in Taiwan was genetically differentiated from mainland populations.

CONCLUSIONS/SIGNIFICANCE

The marginal populations in south region possessed divergent gene pools, suggesting that the past glaciations might have low impacts on these populations at low latitudes. Estimates of ancestral population sizes interestingly reflect a recent expansion in mainland from a rather smaller population, a pattern that seemingly agrees with the pollen record.

Tracing the origin of Gulf Coast Phragmites (Poaceae): a story of long-distance dispersal and hybridization

PREMISE OF THE STUDY

Long-distance dispersal can affect speciation processes in two opposing ways. Dispersal can promote geographic isolation or it can bring together geographically distant and distantly related genotypes, thus counteracting local differentiation. We used the Gulf Coast of North America (GC), a "hot spot" of reed diversity and evolutionary dynamics, as a model system to study the diversification processes within the invasive, cosmopolitan, polyploid grass Phragmites.

METHODS

Genetic diversity was studied using collections representing all species of the genus and from all continents (except Antarctica). A range of molecular markers, including chloroplast and nuclear sequences, microsatellites, and AFLPs, was analyzed to detect DNA variation from the population to the species level and to infer phylogenetic relationships across continents.

KEY RESULTS

An interspecific hybrid, Phragmites mauritianus × P. australis, and four P. australis cp-DNA haplotypes from Africa, Europe, and North America have been dispersed to the GC and interbreed with each other.

CONCLUSIONS

Long-distance dispersal and weak breeding barriers appear to be recurring phenomena, not only in the GC, but worldwide. We present data strongly suggesting that interspecific hybridization and introgression among different Phragmites species take place and appear to have contributed significantly to the diversification processes within the genus. Hence, the application of traditional species concepts within Phragmites might be inappropriate.

Next-generation hybridization and introgression

Hybridization has a major role in evolution-from the introgression of important phenotypic traits between species, to the creation of new species through hybrid speciation. Molecular studies of hybridization aim to understand the class of hybrids and the frequency of introgression, detect the signature of ancient hybridization, and understand the behaviour of introgressed loci in their new genomic background. This often involves a large investment in the design and application of molecular markers, leading to a compromise between the depth and breadth of genomic data. New techniques designed to assay a large sub-section of the genome, in association with next-generation sequencing (NGS) technologies, will allow genome-wide hybridization and introgression studies in organisms with no prior sequence data. These detailed genotypic data will unite the breadth of sampling of loci characteristic of population genetics with the depth of sequence information associated with molecular phylogenetics. In this review, we assess the theoretical and methodological constraints that limit our understanding of natural hybridization, and promote the use of NGS for detecting hybridization and introgression between non-model organisms. We also make recommendations for the ways in which emerging techniques, such as pooled barcoded amplicon sequencing and restriction site-associated DNA tags, should be used to overcome current limitations, and enhance our understanding of this evolutionary significant process.

Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae)

PREMISE OF THE STUDY

Hybridization is pervasive in many plant taxa, with consequences for species taxonomy, local adaptation, and management. Oaks (Quercus spp.) are thought to hybridize readily yet retain distinct traits, drawing into question the biological species concept for such taxa, but the true extent of gene flow is controversial. Genetic data are beginning to shed new light on this issue, but red oaks (section Lobatae), an important component of North American forests, have largely been neglected. Moreover, gene flow estimates may be sensitive to the choice of life stage, marker type, or genetic structure statistic.

METHODS

We coupled genetic structure data with parentage analyses for two mixed-species stands in North Carolina. Genetic structure analyses of adults (including F(ST), R(ST), G'(ST), and structure) reflect long-term patterns of gene flow, while the percentage of seedlings with parents of two different species reflect current levels of gene flow.

KEY RESULTS

Genetic structure analyses revealed low differentiation in microsatellite allele frequencies between co-occurring species, suggesting past gene flow. However, methods differed in their sensitivity to differentiation, indicating a need for caution when drawing conclusions from a single method. Parentage analyses identified >20% of seedlings as potential hybrids. The species examined exhibit distinct morphologies, suggesting selection against intermediate phenotypes.

CONCLUSIONS

Our results suggest that hybridization between co-occurring red oaks occurs, but that selection may limit introgression, especially at functional loci. However, by providing a source of genetic variation, hybridization could influence the response of oaks and other hybridizing taxa to environmental change.

Asymmetric introgression between the M and S forms of the malaria vector, Anopheles gambiae, maintains divergence despite extensive hybridization

The suggestion that genetic divergence can arise and/or be maintained in the face of gene flow has been contentious since first proposed. This controversy and a rarity of good examples have limited our understanding of this process. Partially reproductively isolated taxa have been highlighted as offering unique opportunities for identifying the mechanisms underlying divergence with gene flow. The African malaria vector, Anopheles gambiae s.s., is widely regarded as consisting of two sympatric forms, thought by many to represent incipient species, the M and S molecular forms. However, there has been much debate about the extent of reproductive isolation between M and S, with one view positing that divergence may have arisen and is being maintained in the presence of gene flow, and the other proposing a more advanced speciation process with little realized gene flow because of low hybrid fitness. These hypotheses have been difficult to address because hybrids are typically rare (<1%). Here, we assess samples from an area of high hybridization and demonstrate that hybrids are fit and responsible for extensive introgression. Nonetheless, we show that strong divergent selection at a subset of loci combined with highly asymmetric introgression has enabled M and S to remain genetically differentiated despite extensive gene flow. We propose that the extent of reproductive isolation between M and S varies across West Africa resulting in a 'geographic mosaic of reproductive isolation'; a finding which adds further complexity to our understanding of divergence in this taxon and which has considerable implications for transgenic control strategies.

Allopolyploid origin of highly invasive Centaurea stoebe s.l. (Asteraceae)

Spotted knapweed (Centaurea stoebe) occurs from Western Asia to Western Europe both as diploid and tetraploid cytotypes, predominantly in single-cytotype populations with higher frequency of diploid populations. Interestingly, only tetraploids have been recorded so far from its introduced range in North America where they became highly invasive. We performed phylogenetic and network analyses of more than 40 accessions of the C. stoebe and C. paniculata groups and other related taxa using cloned internal transcribed spacer (ITS) and sequences of the chloroplast trnT-trnL and atpBrbcL regions to (i) assess the evolutionary origin of tetraploid C. stoebe s.l., and (ii) uncover the phylogeny of the C. stoebe group. Both issues have not been studied so far and thus remained controversial. Cloned ITS sequences showed the presence of two slightly divergent ribotypes occurring in tetraploid cytotype, while only one major ribotype was present in diploid C. stoebe s.str. This pattern suggests an allopolyploid origin of tetraploids with contribution of the diploid C. stoebe s.str. genome. Although we were not able to detect the second parental taxon, we hypothesize that hybridization might have triggered important changes in morphology and life history traits, which in turn may explain the colonization success of the tetraploid taxon. Bayesian relaxed clock estimations indicate a relatively recent--Pleistocene origin of the tetraploid C. stoebe s.l. Furthermore, our analyses showed a deep split between the C. paniculata and C. stoebe groups, and a young diversification of the taxa within the C. stoebe group. In contrast to nrDNA analyses, the observed pattern based on two cpDNA regions was inconclusive with respect to the origin and phylogeny of the studied taxa, most likely due to shared ancient polymorphism and frequent homoplasies.