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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.

Aim The Hengduan Mountains (HDM) of southwest China is a biodiversity hotspot and harbours one of the world's richest temperate floras. However, the origin and evolution of its biota remain largely unresolved. Here we explore the impact of mountain uplift on the diversification process of biodiversity in this hotspot using alpine bamboos. Location The HDM region, southwest China. Taxon Alpine bamboos. Methods We used ddRAD‐seq data from the most complete sampling of alpine bamboos undertaken to date (79% of the species diversity), to investigate their evolutionary history. The ancestral area of these bamboos was reconstructed using a time‐calibrated phylogeny in BioGeoBEARS and diversification rates were inferred using BAMM analyses. In addition, the impact of mountain uplift on the divergence of alpine bamboos was evaluated using trait‐dependent models of diversification. Results The alpine bamboos were strongly supported as monophyletic, and the relationships within them were robustly resolved. Fargesia was found to be polyphyletic and Yushania was resolved as monophyletic. Alpine bamboos originated outside the HDM region during the late Miocene, and spread to this region in the Pliocene, undergoing a significant acceleration in net diversification, which is temporally congruent with the orogeny. The speciation rate increased with altitude and a high diversification rate, estimated to be 0.75 species per million years, was detected for alpine bamboos distributed in high elevations. Main Conclusions Our study demonstrates that heterogeneous mountain habitats and geographical isolation of alpine bamboos, which have limited dispersal ability, are important drivers for their rapid diversification. This study also highlights the power of complementary analyses in revealing the link between species diversification and past geological changes.

Translocating species is an important management tool to establish or expand the range of species. Success of translocations requires an understanding of potential consequences, including whether a sufficient number of individuals were used to minimize founder effects and if interspecific hybridization poses a threat. We provide an updated and comprehensive genetic assessment of a 1970s–1980s translocation and now established mottled duck (Anas fulvigula) population in South Carolina, USA. In addition to examining the population genetics of these mottled ducks, we simulated expected genetic assignments for generational hybrids (F1–F10), permitting formal purity assignment across samples to identify true hybrids and establish hybridization rates. In addition to wild mallards (A. platyrhynchos), we tested for presence of hybrids with migrant American black ducks (A. rubripes) and released domestic game-farm mallards (A. p. domesticus). We used wild reference populations of North American mallard-like ducks and sampled game-farm mallards from 2 sites in South Carolina that could potentially interbreed with mottled ducks. Despite 2 different subspecies of mottled duck (Florida [A. f. fulvigula] and the Western Gulf Coast [A. f. maculatlus]) used in original translocations, we determined the gene pool of the Western Gulf Coast mottled duck was overwhelmingly represented in South Carolina's current population. We found no evidence of founder effects or inbreeding and concluded the original translocation of 1,285 mottled ducks was sufficient to maintain current genetic diversity. We identified 7 hybrids, including an F1 and 3 late-staged (i.e., F2–F3 backcrosses) mottled duck ×black duck hybrids, 1 F2-mottled duck backcrossed with a wild mallard, and 2 F3-mottled ducks introgressed with gamefarm mallard. We estimated a 15% hybridization rate in our mottled duck dataset; however, the general lack of F1 and intermediate hybrids were inconsistent with scenarios of high hybridization rates or presence of a hybrid swarm. Instead, our results suggested a scenario of infrequent interspecific hybridization between South Carolina's mottled ducks and congeners. We concluded that South Carolina's mottled duck population is sufficiently large now to absorb current hybridization rates because 85% of sampled mottled ducks were pure. These results demonstrate the importance in managing and maintaining large parental populations to counter hybridization. As such, future population management of mottled ducks in South Carolina will benefit from increased geographical and continued sampling to monitor hybridization rates with closely related congeners. We also suggest that any future translocations of mottled ducks to coastal South Carolina should originate from the Western Gulf Coast.

Aim Cold‐adapted biotas from mid‐latitudes often show small population sizes, harbour low levels of local genetic diversity and are highly vulnerable to extinction due to ongoing climate warming and the progressive shrinking of montane and alpine ecosystems. In this study, we use a suite of analytical approaches to infer the demographic processes that have shaped contemporary patterns of genomic variation in Omocestus bolivari and Omocestus femoralis, two narrow‐endemic and red‐listed Iberian grasshoppers forming highly fragmented populations in the sky island archipelago of the Baetic System. Location South‐eastern Iberia. Methods We quantified genomic variation in the two focal taxa and coupled ecological niche models and a spatiotemporally explicit simulation approach based on coalescent theory to determine the relative statistical support of a suite of competing demographic scenarios representing contemporary population isolation (i.e. a predominant role of genetic drift) versus historical connectivity and post‐glacial colonization of sky islands (i.e. pulses of gene flow and genetic drift linked to Pleistocene glacial cycles). Results Inference of spatial patterns of genetic structure, environmental niche modelling and statistical evaluation of alternative species‐specific demographic models within an approximate Bayesian computation framework collectively supported genetic admixture during glacial periods and post‐glacial colonization of sky islands, rather than long‐term population isolation, as the scenario best explaining the current distribution of genomic variation in the two focal taxa. Moreover, our analyses revealed that isolation in sky islands has also led to extraordinary genetic fragmentation and contributed to reduce local levels of genetic diversity. Main conclusions This study exemplifies the potential of integrating genomic and environmental niche modelling data across biological and spatial replicates to determine whether organisms with similar habitat requirements have experienced concerted/idiosyncratic responses to Quaternary climatic oscillations, which can ultimately help to reach more general conclusions about the vulnerability of mountain biodiversity hotspots to ongoing climate warming.

Integrating population genetics with species distribution models provides powerful insights into species' evolutionary trajectories under climatic and geological contexts, and informs evidence‐based conservation strategies for endangered species. In this study, we characterized the population genetic structure of Primula wilsonii, a plant species with extremely small populations (PSESP) endemic to the mountains of Southwest China, to provide insights for the conservation of alpine endangered plants. Double‐digest restriction‐site associated DNA sequencing (ddRAD‐seq) generated 18,313 neutral and unlinked single‐nucleotide polymorphisms (SNPs) from 30 individuals across seven populations. Population genetic analysis revealed that these populations formed two major clusters. All populations exhibited low levels of genetic diversity (He = 0.00184–0.00271; π = 0.00176–0.00292), with one population (MG1) showing high genetic differentiation (FST > 0.7) from the other populations, possibly reflecting long‐term geographic isolation resulting in a small effective population size (Ne). Demographic history analysis indicated an expansion around 0.88 Ma, followed by sustained contraction since approximately 45 ka with low Ne levels maintained. Species distribution models further suggested range contraction from the Last Glacial Maximum to the mid‐Holocene and persistence of suitable refugia in the Hengduan Mountains under future warming scenarios. In conclusion, our results indicated that complex topography and Quaternary climatic oscillations have shaped a hierarchical genetic structure with deeply isolated lineages. We therefore recommend delineating at least three independent management units, consistent with patterns of genetic structure, differentiation, and demographic history. These findings highlight the importance of integrating genetic and environmental evidence in the conservation of P. wilsonii and other PSESPs. This study investigates the genetic erosion and conservation of Primula wilsonii, a plant species with extremely small populations in Southwest China. Using genomic sequencing and species distribution models, the research identifies distinct genetic clusters, low genetic diversity, and significant genetic differentiation among populations, in the text of complex topography and climatic oscillations. The findings highlight the need for targeted conservation efforts.

Rhododendron bailiense was identified as a new species in 2013, with approximately 150 individuals existing globally, found only in Dafang County and Panzhou City, Guizhou Province, China. Despite its discovery, the genetic diversity and population structure of this species remain poorly understood, hindering efforts to collect and conserve wild germplasm resources. In this study, double digest restriction‐site associated DNA sequencing was conducted on 26 samples from two populations of R. bailiense to identify single nucleotide polymorphism (SNP) loci. Using these data, the research explores the genetic diversity and structure of R. bailiense populations and infers their population dynamics and evolutionary history. The results indicate that R. bailiense has a moderate level of genetic diversity (π = 0.2489, Ho = 0.2039, He = 0.2331). Genetic differentiation between populations is relatively high (55.94%), with a genetic differentiation coefficient (FST) of 0.1907. This suggests that R. bailiense historically might have been a large population, which, due to geological historical events, became fragmented into the two existing populations. The Panzhou population demonstrates a heterozygote selection advantage. Conversely, the Dafang population faces the risk of inbreeding depression, further exacerbated by its limited gene flow. Consequently, in situ conservation is recommended for the Panzhou population, while ex‐situ conservation is suggested for the Dafang population. Additionally, research on breeding techniques is necessary to expand the population size while maintaining high genetic diversity. This study is the first to use ddRAD‐seq sequencing technology for Single Nucleotide Polymorphism (SNP) analysis, systematically analyzing the genetic background of R. bailiense. This species exhibits rich genetic diversity at both species and population levels. This study provides a theoretical basis for the conservation of wild resources of the R. bailiense and lay the foundation for the breeding or cultivation of this new species.

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the Callicarpa genus that is represented by three species: Callicarpa parvifolia and C. glabra exclusive to the Chichijima Islands, and Callicarpa subpubescens, distributed across the entire Bonin Islands. Notably, C. subpubescens exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size. In this study, we aimed to investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species within Callicarpa in the Bonin Islands using phenotypic and genetic data (double‐digest restriction site‐associated DNA sequencing). Genetic analysis revealed that C. parvifolia and C. glabra both formed single, distinct genetic groups. Conversely, C. subpubescens consisted of six genetic groups corresponding to different ecotypes and regions, and a hybrid group resulting from the hybridization between two of these genetic groups. Population demography analysis focusing on six Chichijima and Hahajima Islands‐based species/ecotypes indicated that all species and ecotypes except one ecotype diverged simultaneously around 73–77 kya. The star‐shaped neighbor‐net tree also suggests the simultaneous divergence of species and ecotypes. The species and ecotypes that simultaneously diverged adapted to dry environments and understory forests, suggesting that aridification may have contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species and one hybrid species within C. subpubescens. This study investigated the keystone endemic tree genus Callicarpa in the Bonin Islands, revealing two cryptic species and one hybrid species based on phenotypic, genotypic, and phylogenetic patterns. It provides evidence of simultaneous divergence of multiple species and ecotypes, offering definitive evidence of adaptive radiation and suggesting a link to global environmental changes.

Aim: A current model of rain forest population diversification in Sundaland specifies east–west vicariance into refugia during the early Pleistocene. In some taxa, this division was followed by dispersal and apparent secondary contact on Borneo in the late Pleistocene. To investigate genetic, morphological, spatial and temporal characteristics of the model, we compared genomic population and plumage variation among four bird species with east–west mtDNA and plumage structure. Location: Borneo and western Sundaland (Sumatra and the Malay Peninsula). Methods: We quantified plumage patterns among populations of two muscicapids (Copsychus saularis and Kittacincla malabarica) and two timaliids (Mixornis gularis and Trichastoma malaccense), and compared them with population genetic patterns determined from (1) SNPs produced by RAD-Seq and (2) previously sequenced mtDNA. Results: All four species exhibit east–west variation in morphological and some genetic characters, but patterns are idiosyncratic. Copsychus saularis' mtDNA and plumage change gradually across Borneo, but RAD-Seq comparisons indicate no population structure. In K. malabarica, all three characteristics change abruptly and concurrently on Borneo. In M. gularis, the main east–west break occurs between Borneo and western Sundaland, with marginal mtDNA, plumage and RAD-Seq structure on Borneo. T. malaccense exhibits two distinct mtDNA and genomic transitions, an early Pleistocene break between western Sundaland and Borneo, and a Pliocene break between the north-east and the rest of Borneo. Despite this deep genetic division, its plumage changes clinally across Borneo. Main conclusions: MtDNA, plumage and RAD-Seq patterns may vary depending on such factors as pre-Pleistocene distribution, habitat requirements and dispersal propensity, differential introgression among the three character types, selection on plumage and phylogenetic relationships.

The Burmese roofed turtle (Batagur trivittata) is one of the world's most endangered turtles. Only one wild population remains in Myanmar. There are thought to be 12 breeding turtles in the wild. Conservation efforts for the species have raised >700 captive turtles since 2002, predominantly from eggs collected in the wild. We collected tissue samples from 445 individuals (approximately 40% of the turtles' remaining global population), applied double-digest restriction-site associated DNA sequencing (ddRAD-Seq), and obtaine approximately 1500 unlinked genome-wide single nucleotide polymorphisms. Individuals fell into 5 distinct genetic clusters, 4 of which represented full-sib families. We inferred a low effective population size (≤10 individuals) but did not detect signs of severe inbreeding, possibly because the population bottleneck occurred recently. Two groups of 30 individuals from the captive pool that were the most genetically diverse were reintroduced to the wild, leading to an increase in the number of fertile eggs (n = 27) in the wild. Another 25 individuals, selected based on the same criteria, were transferred to the Singapore Zoo as an assurance colony. Our study demonstrates that the research-to-application gap in conservation can be bridged through application of cutting-edge genomic methods. La tortuga rugosa birmana (Batagur trivittata) es una de las tortugas en mayor peligro de extinción de todo el mundo. En Myanmar sólo permanece una población silvestre. Se cree que existen 12 tortugas reproductoras en vida libre. Los esfuerzos de conservación para la especie han criado > 700 tortugas en cautiverio desde 2002, principalmente a partir de huevos recolectados del hábitat natural. Colectamos muestras de tejido de 445 individuos (aproximadamente 40% de la permaneciente población mundial de la tortuga), aplicamos una secuenciación de ADN asociado de digestión-doble restringida al sitio (ddRAD-Seq, en inglés) y obtuvimos aproximadamente 1500 polimorfismos de nucleotido único, sin conexión y del ancho del genoma. Los individuos cayeron dentro de cinco agrupamientos genéticos distintos, cuatro de los cuales representaron familias de hermanos completos. Inferimos un tamaño reducido de población efectiva (≤10 individuos) pero no detectamos señales de endogamia severa, posiblemente porque el cuello de botella poblacional ocurrió recientemente. Dos grupos de 30 individuos del pool en cautiverio, que fueron los más diversos genéticamente, fueron reintroducidos a su habitat natural, resultando en un incremento del número de huevos fértiles (n = 27) en vida libre. Otros 25 individuos, seleccionados con base en los mismos criterios, fueron transferidos al Zoológico de Singapur una colonia de garantía. Nuestro estudio demuestra que el vacio de investigación-a-aplicación en la conservación puede remediarse por medio de la aplicación de métodos genómicos innovadores.

Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement.