Hybridization and introgression in sympatric and allopatric populations of four oak species

Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses

Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.

Does selection favour the maintenance of porous species boundaries?

The endpoint of speciation has been viewed as complete isolation and the absence of gene flow between species. If the influx of genes from another species is maladaptive because species have different adaptations and genetic backgrounds, selection should favour the closing of species boundaries and zero gene flow, a process known as reinforcement. Recently, numerous cases of gene flow between species have been identified, many of which involved adaptive introgression of beneficial alleles. These cases could reflect transient states on the way to closed species boundaries or the result of declining strength or efficacy of selection for reinforcement as the level of gene flow approaches zero. An alternative hypothesis, however, is that selection favours porous species boundaries that allow beneficial alleles to cross, especially in changing environments. This perspective evaluates the conditions that would be needed for selection to favour porous species boundaries and the evidence for them. A contrast is made between hybridization in sexual eukaryotes and gene transfer via homologous recombination in bacteria. Current evidence is inconclusive on whether non-zero gene flow is favoured by selection. Studies are needed that quantify selection gradients on rates of gene flow and test for evolution towards intermediate values, especially experiments that manipulate conditions and track evolution for multiple generations. Estimation of gene flow networks for more clades and regional assemblages using emerging genome data will also allow the evolutionary determinants of interspecific gene flow to be better understood.

Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: genetic, phenotypic, and environmental insights

Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.

Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae)

BACKGROUND AND AIMS

Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico.

METHODS

Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages.

KEY RESULTS

The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages.

CONCLUSIONS

The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

Spatial Distribution and Ecological Determinants of Coexisting Hybrid Oak Species: A Study in Yushan's Mixed Forest

Ecological niche partitioning is crucial in reducing interspecific competition, fostering species coexistence, and preserving biodiversity. Our research, conducted in a hybrid mixed oak forest in Yushan, Jiangsu, China, focuses on Quercus acutissima, Q. variabilis, Q. fabri, and Q. serrata var. brevipetiolata. Using Point Pattern Analysis, we investigated the spatial relationships and ecological trait autocorrelation, including total carbon (TC), nitrogen (TN), phosphorus (TP), potassium (TK), and breast height diameter (DBH). Our findings show aggregated distribution patterns within the oak populations. The Inhomogeneous Poisson Point model highlights the impact of environmental heterogeneity on Q. variabilis, leading to distinct distribution patterns, while other species showed wider dispersion. This study reveals aggregated interspecific interactions, with a notable dispersal pattern between Q. acutissima and Q. variabilis. We observed significant variability in nutrient elements, indicating distinct nutrient dynamics and uptake processes. The variations in total carbon (TC), nitrogen (TN), phosphorus (TP), and potassium (TK) suggest distinct nutrient dynamics, with TK showing the highest variability. Despite variations in TC, TK, and TP, the species did not form distinct classes, suggesting overlapping nutritional strategies and environmental adaptations. Furthermore, spatial autocorrelation analysis indicates strong positive correlations for DBH, TC, and TP, whereas TK and TN correlations are non-significant. The results suggest habitat filtering as a key driver in intraspecific relationships, with a finer spatial scale of ecological niche division through TC and TP, which is crucial for maintaining coexistence among these oak species.

Enhanced and asymmetric signatures of hybridization at climatic margins: Evidence from closely related dioecious fig species

Hybridization plays a significant role in biological evolution. However, it is not clear whether ecological contingency differentially influences likelihood of hybridization, particularly at ecological margins where parental species may exhibit reduced fitnesses. Moreover, it is unknown whether future ecosystem change will increase the prevalence of hybridization. Ficus heterostyla and F. squamosa are closely related species co-distributed from southern Thailand to southwest China where hybridization, yielding viable seeds, has been documented. As a robust test of ecological factors driving hybridization, we investigated spatial hybridization signatures based on nuclear microsatellites from extensive population sampling across a widespread contact range. Both species showed high population differentiation and strong patterns of isolation by distance. Admixture estimates exposed asymmetric interspecific gene flow. Signatures of hybridization increase significantly towards higher latitude zones, peaking at the northern climatic margins. Geographic variation in reproductive phenology combined with ecologically challenging marginal habitats may promote this phenomenon. Our work is a first systematic evaluation of such patterns in a comprehensive, latitudinally-based clinal context, and indicates that tendency to hybridize appears strongly influenced by environmental conditions. Moreover, that future climate change scenarios will likely alter and possibly augment cases of hybridization at ecosystem scales.

Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing

This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.

Genome-wide analyses of introgression between two sympatric Asian oak species

Introgression can be an important source of new alleles for adaption under rapidly changing environments, perhaps even more important than standing variation. Though introgression has been extensively studied in many plants and animals, key questions on the underlying mechanisms of introgression still remain unanswered. In particular, we are yet to determine the genomic distribution of introgressed regions along the genome; whether the extent and patterns of introgression are influenced by ecological factors; and when and how introgression contributes to adaptation. Here, we generated high-quality genomic resources for two sympatric widespread Asian oak species, Quercus acutissima and Q. variabilis, sampled in multiple forests to study introgression between them. We show that introgressed regions are broadly distributed across the genome. Introgression was affected by genetic divergence between pairs of populations and by the similarity of the environments in which they live-populations occupying similar ecological sites tended to share the same introgressed regions. Introgressed genomic footprints of adaptation were preferentially located in regions with suppressed recombination rate. Introgression probably confers adaptation in these oak populations by introducing allelic variation in cis-regulatory elements, in particular through transposable element insertions, thereby altering the regulation of genes related to stress. Our results provide new avenues of research for uncovering mechanisms of adaptation due to hybridization in sympatric species.

The Syngameon Enigma

Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.