Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Comparative analysis of jujube and sour jujube gave insight into their difference in genetic diversity and suitable habitat

Jujube (Ziziphus jujuba var. jujuba Mill.) and sour jujube (Z. jujuba var. spinosa (Bunge) Hu ex H.F.Chow.) are economically, nutritionally, and ecologically significant members of the Rhamnaceae family. Despite their importance, insufficient research on their genetics and habitats has impeded effective conservation and utilization. To address this knowledge gap, we conducted plastome sequencing, integrated distribution data from China, and assessed genetic diversity and suitable habitat. The plastomes of both species exhibited high conservation and low genetic diversity. A new-found 23 bp species-specific Indel in the petL-petG enabled us to develop a rapid Indel-based identification marker for species discrimination. Phylogenetic analysis and dating illuminated their genetic relationship, showing speciation occurred 6.9 million years ago, in a period of dramatic global temperature fluctuations. Substantial variations in suitable climatic conditions were observed, with the mean temperature of the coldest quarter as the primary factor influencing distributions (-3.16°C-12.73°C for jujube and -5.79°C to 4.11°C for sour jujube, suitability exceeding 0.6). Consequently, distinct conservation strategies are warranted due to differences in suitable habitats, with jujube having a broader distribution and sour jujube concentrated in Northern China. In conclusion, disparate habitats and climatic factors necessitate tailored conservation approaches. Comparing genetic diversity and developing rapid species-specific primers will further enhance the sustainable utilization of these valuable species.

Leaf morphometric analysis and potential distribution modelling contribute to taxonomic differentiation in the Quercus microphylla complex

Mexico is a major center of evolutionary radiation for the genus Quercus, with oak species occurring across different habitat types and showing a wide variation in morphology and growth form. Despite representing about 20% of Mexican species, scrub oaks have received little attention and even basic aspects of their taxonomy and geographic distribution remain unresolved. In this study, we analyzed the morphological and climatic niche differentiation of scrub oak populations forming a complex constituted by six named species, Quercus cordifolia, Quercus frutex, Quercus intricata, Quercus microphylla, Quercus repanda, Quercus striatula and a distinct morphotype of Q. striatula identified during field and herbarium work (hereafter named Q. striatula II). Samples were obtained from 35 sites covering the geographic distribution of the complex in northern and central Mexico. Morphological differentiation was analyzed through geometric morphometrics of leaf shape and quantification of trichome traits. Our results indicated the presence of two main morphological groups with geographic concordance. The first was formed by Q. frutex, Q. microphylla, Q. repanda and Q. striatula, distributed in the Trans-Mexican Volcanic Belt, the Sierra Madre Occidental and a little portion of the south of the Mexican Altiplano (MA). The second group consists of Q. cordifola, Q. intricata and Q. striatula II, found in the Sierra Madre Oriental and the MA. Therefore, our evidence supports the distinctness of the Q. striatula II morphotype, indicating the need for a taxonomic revision. Within the two groups, morphological differentiation among taxa varied from very clear to low or inexistent (i.e. Q. microphylla-Q. striatula and Q. cordifolia-Q. striatula II) but niche comparisons revealed significant niche differentiation in all pairwise comparisons, highlighting the relevance of integrative approaches for the taxonomic resolution of complicated groups such as the one studied here.

Genetic diversity and population divergence of Leonurus japonicus and its distribution dynamic changes from the last interglacial to the present in China

BACKGROUND

Leonurus japonicus, a significant medicinal plant known for its therapeutic effects on gynecological and cardiovascular diseases, has genetic diversity that forms the basis for germplasm preservation and utilization in medicine. Despite its economic value, limited research has focused on its genetic diversity and divergence.

RESULTS

The avg. nucleotide diversity of 59 accessions from China were 0.00029 and hotspot regions in petN-psbM and rpl32-trnL_(UAG) spacers, which can be used for genotype discrimination. These accessions divided into four clades with significant divergence. The four subclades, which split at approximately 7.36 Ma, were likely influenced by the Hengduan Mountains uplift and global temperature drop. The initial divergence gave rise to Clade D, with a crown age estimated at 4.27 Ma, followed by Clade C, with a crown age estimated at 3.39 Ma. The four clades were not showed a clear spatial distribution. Suitable climatic conditions for the species were identified, including warmest quarter precipitation 433.20 mm ~ 1,524.07 mm, driest month precipitation > 12.06 mm, and coldest month min temp > -4.34 °C. The high suitability distribution showed contraction in LIG to LGM, followed by expansion from LGM to present. The Hengduan Mountains acted as a glacial refuge for the species during climate changes.

CONCLUSIONS

Our findings reflected a clear phylogenetic relationships and divergence within species L. japonicus and the identified hotspot regions could facilitate the genotype discrimination. The divergence time estimation and suitable area simulation revealed evolution dynamics of this species and may propose conservation suggestions and exploitation approaches in the future.

Improving species delimitation for effective conservation: a case study in the endemic maple-leaf oak (Quercus acerifolia)

Species delimitation is challenging in lineages that exhibit both high plasticity and introgression. This challenge can be compounded by collection biases, which may downweight specimens morphologically intermediate between traditional species. Additionally, mismatch between named species and observable phenotypes can compromise species conservation. We studied the species boundaries of Quercus acerifolia, a tree endemic to Arkansas, U.S. We performed morphometric analyses of leaves and acorns from 527 field and 138 herbarium samples of Q. acerifolia and its close relatives, Q. shumardii and Q. rubra. We employed two novel approaches: sampling ex situ collections to detect phenotypic plasticity caused by environmental variation and comparing random field samples with historical herbarium samples to identify collection biases that might undermine species delimitation. To provide genetic evidence, we also performed molecular analyses on genome-wide SNPs. Quercus acerifolia shows distinctive morphological, ecological, and genomic characteristics, rejecting the hypothesis that Q. acerifolia is a phenotypic variant of Q. shumardii. We found mismatches between traditional taxonomy and phenotypic clusters. We detected underrepresentation of morphological intermediates in herbarium collections, which may bias species discovery and recognition. Rare species conservation requires considering and addressing taxonomic problems related to phenotypic plasticity, mismatch between taxonomy and morphological clusters, and collection biases.

Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks

Improving our knowledge of how past climate-driven selection has acted on present-day trait population divergence is essential to understand local adaptation processes and improve our predictions of evolutionary trajectories in the face of altered selection pressures resulting from climate change. In this study, we investigated signals of selection on traits related to drought tolerance and growth rates in two Mediterranean oak species (Quercus faginea and Q. lusitanica) with contrasting distribution ranges and climatic niches. We genotyped 182 individuals from 24 natural populations of the two species using restriction-site-associated DNA sequencing and conducted a thorough functional characterization in 1602 seedlings from 21 populations cultivated in common garden experiments under contrasting watering treatments. Our genomic data revealed that both Q. faginea and Q. lusitanica have very weak population genetic structure, probably as a result of high rates of pollen-mediated gene flow among populations and large effective population sizes. In contrast, common garden experiments showed evidence of climate-driven divergent selection among populations on traits related to leaf morphology, physiology and growth in both species. Overall, our study suggests that climate is an important selective factor for Mediterranean oaks and that ecophysiological traits have evolved in drought-prone environments even in a context of very high rates of gene flow among populations.

Postglacial colonization in the Great Lakes Region by the white-footed mouse (Peromyscus leucopus): conflicts between genomic and field data

For regions that were covered by ice during the Pleistocene glaciations, species must have emigrated from unglaciated regions. However, it can be difficult to discern when and from what ancestral source populations such expansions took place, especially since warming climates introduce the possibility of very recent expansions. For example, in the Great Lakes region, pronounced climatic change includes past glaciations as well as recent, rapid warming. Here we evaluate different expansion hypotheses with a genomic study of the white-footed mouse (Peromyscus leucopus noveboracensis), which is one of the most common mammals throughout the Great Lakes region. Ecological surveys coupled with historical museum records suggest a recent range expansion of P. leucopus associated with the warming climate over the last decades. These detailed records have yet to be complemented by genomic data that provide the requisite resolution for detecting recent expansion, although some mitochondrial DNA (mtDNA) sequences have suggested possible hypotheses about the geography of expansion. With more than 7,000 loci generated using RADseq, we evaluate support for multiple hypotheses of a geographic expansion in the Upper Peninsula of Michigan (UP). Analysis of a single random single-nucleotide polymorphism per locus revealed a fine-scale population structure separating the Lower Peninsula (LP) population from all other populations in the UP. We also detected a genetic structure that reflects an evolutionary history of postglacial colonization from two different origins into the UP, one coming from the LP and one coming from the west. Instead of supporting a climate-driven range expansion, as suggested by field surveys, our results support more ancient postglacial colonization of the UP from two different ancestral sources. With these results, we offer new insights about P. leucopus geographic expansion history, as well as a more general phylogeographic framework for testing range shifts in the Great Lakes region.

Species divergence and phylogeography of Corylus heterophylla Fisch complex (Betulaceae): Inferred from molecular, climatic and morphological data

Historical geo-climatic changes have shaped the geographical distributions and genetic diversity of numerous plant taxa in East Asia, which promote species divergence and ultimately speciation. Here, we integrated multiple approaches, including molecular phylogeography, ecological niche modeling, and morphological traits to examine the nucleotide diversity and interspecific divergence within Corylus heterophylla complex (C. heterophylla, C. kweichowensis, and C. yunnanensis). These three sibling taxa harbored similar high levels of nucleotide diversity at the species level. The molecular data (SCNG and cpDNA) unanimously supported the division of C. heterophylla complex into two major clades, with C. yunnanensis diverged earlier from the complex, whereas C. heterophylla and C. kweichowensis could hardly be separated. The split between the two clades (c. 12.89 Ma) coincided with the formation of Sichuan Basin in the middle Miocene, while the divergence among and within the five subclades (YUN1-YUN3, HK1-HK2) occurred from the late Miocene to the Pleistocene. C. heterophylla of northern China experienced glacial contraction and interglacial expansion during the Quaternary, whereas C. kweichowensis and C. yunnanensis of southern China presented population expansion even during the last glacial maximum. Despite of high levels of genetic admixture between C. heterophylla and C. kweichowensis, significant ecological and morphological discrepancy as well as incomplete geographic isolation indicated that adaptive evolution triggered by divergent selection may have played important roles in incipient ecological speciation.

Genetic Differentiation and Demographic History of Three Cerris Oak Species in China Based on Nuclear Microsatellite Makers

Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous Cerris oak species (Q. acutissima, Q. variabilis and Q. chenii) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that Q. acutissima and Q. chenii were clustered in the same group, whereas Q. variabilis formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that Q. variabilis and Q. acutissima diverged from their most common ancestor around 19.84 Ma, and subsequently Q. chenii diverged from Q. acutissima at about 9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three Cerris oak species repeatedly underwent considerable ‘expansion–contraction’ during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.

Quercus Conservation Genetics and Genomics: Past, Present, and Future

Quercus species (oaks) have been an integral part of the landscape in the northern hemisphere for millions of years. Their ability to adapt and spread across different environments and their contributions to many ecosystem services is well documented. Human activity has placed many oak species in peril by eliminating or adversely modifying habitats through exploitative land usage and by practices that have exacerbated climate change. The goal of this review is to compile a list of oak species of conservation concern, evaluate the genetic data that is available for these species, and to highlight the gaps that exist. We compiled a list of 124 Oaks of Concern based on the Red List of Oaks 2020 and the Conservation Gap Analysis for Native U.S. Oaks and their evaluations of each species. Of these, 57% have been the subject of some genetic analysis, but for most threatened species (72%), the only genetic analysis was done as part of a phylogenetic study. While nearly half (49%) of published genetic studies involved population genetic analysis, only 16 species of concern (13%) have been the subject of these studies. This is a critical gap considering that analysis of intraspecific genetic variability and genetic structure are essential for designing conservation management strategies. We review the published population genetic studies to highlight their application to conservation. Finally, we discuss future directions in Quercus conservation genetics and genomics.

Evolutionary legacy of a forest plantation tree species (Pinus armandii): Implications for widespread afforestation

Many natural systems are subject to profound and persistent anthropogenic influence. Human-induced gene movement through afforestation and the selective transportation of genotypes might enhance the potential for intraspecific hybridization, which could lead to outbreeding depression. However, the evolutionary legacy of afforestation on the spatial genetic structure of forest tree species has barely been investigated. To do this properly, the effects of anthropogenic and natural processes must be examined simultaneously. A multidisciplinary approach, integrating phylogeography, population genetics, species distribution modeling, and niche divergence would permit evaluation of potential anthropogenic impacts, such as mass planting near-native material. Here, these approaches were applied to Pinus armandii, a Chinese endemic coniferous tree species, that has been mass planted across its native range. Population genetic analyses showed that natural populations of P. armandii comprised three lineages that diverged around the late Miocene, during a period of massive uplifts of the Hengduan Mountains, and intensification of Asian Summer Monsoon. Only limited gene flow was detected between lineages, indicating that each largely maintained is genetic integrity. Moreover, most or all planted populations were found to have been sourced within the same region, minimizing disruption of large-scale spatial genetic structure within P. armandii. This might be because each of the three lineages had a distinct climatic niche, according to ecological niche modeling and niche divergence tests. The current study provides empirical genetic and ecological evidence for the site-species matching principle in forestry and will be useful to manage restoration efforts by identifying suitable areas and climates for introducing and planting new forests. Our results also highlight the urgent need to evaluate the genetic impacts of large-scale afforestation in other native tree species.

Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks

Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak's lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene-Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage.

Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees

Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.

Population genetic structure, migration, and polyploidy origin of a medicinal species Gynostemma pentaphyllum (Cucurbitaceae)

Gynostemma pentaphyllum, a member of family Cucurbitaceae, is a perennial creeping herb used as a traditional medicinal plant in China. In this study, six polymorphic nSSR and four EST-SSR primers were used to genotype 1,020 individuals in 72 wild populations of G. pentaphyllum. The genetic diversity and population structure were investigated, and ecological niche modeling was performed to reveal the evolution and demographic history of its natural populations. The results show that G. pentaphyllum has a low level of genetic diversity and high level of variation among populations because of pervasive asexual propagation, genetic drift, and long-term habitat isolation. Results of the Mantel test demonstrate that the genetic distance and geographic distance are significantly correlated among G. pentaphyllum natural populations. The populations can be divided into two clusters on the basis of genetic structure. Asymmetrical patterns of historical gene flow were observed among the clusters. For the contemporary, almost all the bidirectional gene flow of the related pairs was symmetrical with slight differences. Recent bottlenecks were experienced by 34.72% of the studied populations. The geographic range of G. pentaphyllum continues to expand northward and eastward from Hengduan Mountains. The present distribution of G. pentaphyllum is a consequence of its complex evolution. Polyploidy in G. pentaphyllum is inferred to be polygenetic. Finally, G. pentaphyllum is a species in need of protection, so in situ and ex situ measures should be considered in the future.

Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history

The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations.

Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus)

BACKGROUND

Hybridization and introgression are common phenomena among oak species. These processes can be beneficial by introducing favorable genetic variants across species (adaptive introgression). Given that drought is an important stress, impacting physiological and morphological variation and limiting distributions, our goal was to identify drought-related genes that might exhibit patterns of introgression influenced by natural selection. Using RNAseq, we sequenced whole transcriptomes of 24 individuals from three oaks in southern California: (Quercus engelmannii, Quercus berberidifolia, Quercus cornelius-mulleri) and identified genetic variants to estimate admixture rates of all variants and those in drought genes.

RESULTS

We found 398,042 variants across all loci and 4352 variants in 139 drought candidate genes. STRUCTURE analysis of all variants revealed the majority of our samples were assignable to a single species, but with several highly admixed individuals. When using drought-associated variants, the same individuals exhibited less admixture and their allele frequencies were more polarized between Engelmann and scrub oaks than when using the total gene set. These findings are consistent with the hypothesis that selection may act differently on functional genes, such as drought-associated genes, and point to candidate genes that are suggestive of divergent selection among species maintaining adaptive differences. For example, the drought genes that showed the strongest bias against engelmannii-fixed oak variants in scrub oaks were related to sugar transporter, coumarate-coA ligases, glutathione S-conjugation, and stress response.

CONCLUSION

This pilot study illustrates that whole transcriptomes of individuals will provide useful data for identifying functional genes that contribute to adaptive divergence among hybridizing species.

Effects of Geological and Environmental Events on the Diversity and Genetic Divergence of Four Closely Related Pines: Pinus koraiensis, P. armandii, P. griffithii, and P. pumila

The effects of mountain uplift and environmental oscillations on nucleotide variability and species divergence remain largely unknown in East Asia. In this study, based on multiple nuclear DNA markers, we investigated the levels and patterns of nucleotide diversity and interspecific divergence in four closely related pines in China, i.e., Pinus koraiensis, P. armandii, P. griffithii, and P. pumila. The four pine taxa shared low levels of nucleotide polymorphisms at the species level. P. pumila had the highest silent nucleotide diversity (πsil = 0.00661) whereas P. griffithii had the lowest (πsil = 0.00175), while the levels of genetic polymorphism in P. armandii (πsil = 0.00508) and P. koraiensis (πsil = 0.00652) were intermediate between the other two species. Population genetic structure analysis showed that variations primarily existed within populations of the four pine species, presumably due to habitat fragmentation or the island-like distributions of Pinus species. Population divergence (FST) analysis showed that the genetic divergence between P. griffithii and P. koraiensis was much greater than that between P. koraiensis and the other two pines species. Isolation-with-migration analysis suggested that asymmetric gene flow had occurred between any two pairs of pine species. Phylogenetic analyses indicated that the four allied species split into two groups about 1.37 million years ago, where P. armandii and P. pumila were closer and clustered as sister species, whereas P. koraiensis and P. griffithii were clustered on another branch. Our results and those obtained in previous studies suggest that mountain uplift and geological climate oscillations may have led to the patterns of genetic divergence and nucleotide variations in these four pine species.

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.

Ecological and Genetic Divergences with Gene Flow of Two Sister Species (Leucomeris decora and Nouelia insignis) Driving by Climatic Transition in Southwest China

Understanding of the processes of divergence and speciation is a major task for biodiversity researches and may offer clearer insight into mechanisms generating biological diversity. Here, we employ an integrative approach to explore genetic and ecological differentiation of Leucomeris decora and Nouelia insignis distributed allopatrically along the two sides of the biogeographic boundary 'Tanaka Line' in Southwest China. We addressed these questions using ten low-copy nuclear genes and nine plastid DNA regions sequenced among individuals sampled from 28 populations across their geographic ranges in China. Phylogenetic, coalescent-based population genetic analyses, approximate Bayesian computation (ABC) framework and ecological niche models (ENMs) were conducted. We identified a closer phylogenetic relationship in maternal lineage of L. decora with N. insignis than that between L. decora and congeneric Leucomeris spectabilis. A deep divergence between the two species was observed and occurred at the boundary between later Pliocene and early Pleistocene. However, the evidence of significant chloroplast DNA gene flow was also detected between the marginal populations of L. decora and N. insignis. Niche models and statistical analyses showed significant ecological differentiation, and two nuclear loci among the ten nuclear genes may be under divergent selection. These integrative results imply that the role of climatic shift from Pliocene to Pleistocene may be the prominent factor for the divergence of L. decora and N. insignis, and population expansion after divergence may have given rise to chloroplast DNA introgression. The divergence was maintained by differential selection despite in the face of gene flow.

Evolutionary lessons from California plant phylogeography

Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures-both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence in Four Endangered Notopterygium Herbs

Mountain uplift and climatic fluctuations are important driving forces that have affected the geographic distribution and population dynamics history of organisms. However, it is unclear how geological and climatic events might have affected the phylogeographic history and species divergence in high-alpine herbal plants. In this study, we analyzed the population demographic history and species differentiation of four endangered Notopterygium herbs on the high-altitude Qinghai-Tibetan Plateau (QTP) and adjacent areas. We combined phylogeographic analysis with species distribution modeling to detect the genetic variations in four Notopterygium species (N. incisum, N. franchetii, N. oviforme, and N. forrestii). In total, 559 individuals from 74 populations of the four species were analyzed based on three maternally inherited chloroplast fragments (matK, rbcL, and trnS-trnG) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-five chloroplast DNA (cpDNA) and 48 ITS haplotypes were identified in the four species. All of the cpDNA and ITS haplotypes were species-specific, except N. franchetii and N. oviforme shared one cpDNA haplotype, H32. Phylogenetic analysis suggested that all four species formed a monophyletic clade with high bootstrap support, where N. franchetii and N. oviforme were sisters. In addition, each Notopterygium species generated an individual clade that corresponded to their respective species in the ITS tree. Population dynamics analyses and species distribution modeling showed that the two widely distributed herbs N. incisum and N. franchetii exhibited obvious demographic expansions during the Pleistocene ice ages. Molecular dating suggested that the divergence of the four Notopterygium species occurred approximately between 3.6 and 1.2 Mya, and it was significantly associated with recent extensive uplifts of the QTP. Our results support the hypothesis that mountain uplift and Quaternary climatic oscillations profoundly shaped the population genetic divergence and demographic dynamics of Notopterygium species. The findings of this and previous studies provide important insights into the effects of QTP uplifts and climatic changes on phylogeography and species differentiation in high altitude mountainous areas. Our results may also facilitate the conservation of endangered herbaceous medicinal plants in the genus Notopterygium.

Inferring the demographic history of an oligophagous grasshopper: Effects of climatic niche stability and host-plant distribution

Understanding the consequences of past environmental changes on the abiotic and biotic components of the landscape and deciphering their impacts on the demographic trajectories of species is a major issue in evolutionary biogeography. In this study, we combine nuclear and mitochondrial genetic data to study the phylogeographical structure and lineage-specific demographic histories of the scrub-legume grasshopper (Chorthippus binotatus binotatus), a montane taxon distributed in the Iberian Peninsula and France that exclusively feeds on certain scrub-legume species. Genetic data and paleo-distribution modelling indicate the presence of four main lineages that seem to have diverged in allopatry and long-term persisted in Iberian and French refugia since the Mid Pleistocene. Comparisons of different demographic hypotheses in an Approximate Bayesian Computation (ABC) framework supported a population bottleneck in the northwestern French clade and paleo-distribution modelling indicate that the populations of this lineage have experienced more severe environmental fluctuations during the last 21 000 years than those from the Iberian Peninsula. Accordingly, we found that nuclear genetic diversity of the populations of scrub-legume grasshopper is positively associated with local stability of suitable habitats defined by both Pleistocene climate changes and historical distributional shifts of host-plant species. Overall, our study highlights the importance of integrating the potential effects of abiotic (i.e. climate and geography) and biotic components (i.e. inter-specific interactions) into the study of the evolutionary and demographic history of specialist taxa with narrow ecological requirements.

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)

The emergence of next generation sequencing has increased by several orders of magnitude the amount of data available for phylogenetics. Reduced representation approaches, such as restriction-sited associated DNA sequencing (RADseq), have proven useful for phylogenetic studies of non-model species at a wide range of phylogenetic depths. However, analysis of these datasets is not uniform and we know little about the potential benefits and drawbacks of de novo assembly versus assembly by mapping to a reference genome. Using RADseq data for 83 oak samples representing 16 taxa, we identified variants via three pipelines: mapping sequence reads to a recently published draft genome of Quercus lobata, and de novo assembly under two sets of locus filters. For each pipeline, we inferred the maximum likelihood phylogeny. All pipelines produced similar trees, with minor shifts in relationships within well-supported clades, despite the fact that they yielded different numbers of loci (68 000 – 111 000 loci) and different degrees of overlap with the reference genome. We conclude that both the reference-aligned and de novo assembly pipelines yield reliable results, and that advantages and disadvantages of these approaches pertain mainly to downstream uses of RADseq data, not to phylogenetic inference per se.

Exploring the potential of gametic reconstruction of parental genotypes by F1 hybrids as a bridge for rapid introgression

Interspecific hybridization and genetic introgression are commonly observed in natural populations of many species, especially trees. Among oaks, gene flow between closely related species has been well documented. And yet, hybridization does not lead to a "melting pot", i.e., the homogenization of phenotypic traits. Here, we explore how the combination of several common reproductive and genomic traits could create an avenue for interspecific gene flow that partially explains this apparent paradox. During meiosis, F₁ hybrids will produce approximately (½)ⁿ "reconstructed" parental gametes, where n equals the number of chromosomes. Crossing over would introduce a small amount of introgressive material. The resulting parental-type gametophytes would probably possess a similar fertilization advantage as conspecific pollen. The resulting "backcross" would actually be the genetic equivalent of a conspecific out-cross, with a small amount of heterospecific DNA captured through crossing over. Even with detailed genomic analysis, the resulting offspring would not appear to be a backcross. This avenue for rapid introgression between species through the F₁ hybrid will be viable for organisms that meet certain conditions: low base chromosome number, conserved genomic structure and size, production of billions of gametes/gametophytes during each reproductive event, and conspecific fertilization advantage.

Testing the role of ancient and contemporary landscapes on structuring genetic variation in a specialist grasshopper

Understanding the processes underlying spatial patterns of genetic diversity and structure of natural populations is a central topic in evolutionary biogeography. In this study, we combine data on ancient and contemporary landscape composition to get a comprehensive view of the factors shaping genetic variation across the populations of the scrub‐legume grasshopper (Chorthippus binotatus binotatus) from the biogeographically complex region of southeast Iberia. First, we examined geographical patterns of genetic structure and employed an approximate Bayesian computation (ABC) approach to compare different plausible scenarios of population divergence. Second, we used a landscape genetic framework to test for the effects of (1) Late Miocene paleogeography, (2) Pleistocene climate fluctuations, and (3) contemporary topographic complexity on the spatial patterns of population genetic differentiation. Genetic structure and ABC analyses supported the presence of three genetic clusters and a sequential west‐to‐east splitting model that predated the last glacial maximum (LGM, c. 21 Kya). Landscape genetic analyses revealed that population genetic differentiation was primarily shaped by contemporary topographic complexity, but was not explained by any paleogeographic scenario or resistance distances based on climate suitability in the present or during the LGM. Overall, this study emphasizes the need of integrating information on ancient and contemporary landscape composition to get a comprehensive view of their relative importance to explain spatial patterns of genetic variation in organisms inhabiting regions with complex biogeographical histories.

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.

Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the 'genomic islands' scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene.

Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions

The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides, and Quercus rehderiana) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG) to the last glacial maximum (LGM), which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.

Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions

The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides, and Quercus rehderiana) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG) to the last glacial maximum (LGM), which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.