Species delimitation and hybridization history of a hazel species complex

Phylogeny, species delimitation, and biogeographical history of Bredia

Species delimitation in plants is sometimes challenging due to morphological convergence, interspecific gene flow, and historically limited sampling. Bredia Blume as currently defined comprises 27 species and has been resolved as monophyletic in previous phylogenomic studies. However, relationships among several major lineages in the genus remain elusive, and the species boundaries of some problematic taxa have not been tested. In this study, we employed comprehensive taxon sampling and reconstructed the phylogeny of Bredia using single-copy orthologs (SCOs), genomic single nucleotide polymorphisms (SNPs), and whole plastomes. The species tree derived from SCOs provided the highest resolution, strongly supporting all interspecific relationships. We identified instances of morphological convergence and potential hybridization/introgression within groups of interest and discussed species limits based on monophyly, genetic divergence, and morphological diagnosability. Using this robust phylogeny, we inferred divergence times and biogeographical history for Bredia. The genus originated in the Yunnan-Myanmar-Thailand Border region and the Beibu Gulf region during the middle Miocene, initially adapting to karst habitats. Over time, certain lineages shifted to non-karst environments. One such lineage migrated to the southeastern part of the Eastern Asiatic Kingdom in the late Miocene, where it rapidly diversified forming several major lineages. Subsequently, a mainland lineage reached Taiwan via a land bridge between the late Pliocene and the early Pleistocene and diversified in the region, eventually spreading to the Ryukyu Islands in the middle Pleistocene.

Species delimitation in the Populus laurifolia complex (Salicaceae) based on phylogenetic and morphometric evidence

Due to significant morphological differences and extensive interspecific hybridization, there are numerous species complexes with taxonomic challenges in the genus Populus. Integrative taxonomy, which combines evidence of morphology, molecular phylogeny, niche differentiation, and reproductive isolation, provides the most effective approaches for species delimitation. The Populus laurifolia complex, which belongs to Populus subg. Tacamahaca (Salicaceae), is distributed in the Altai Mountains and Tianshan Mountains. This complex exhibits morphological variability, making species delimitation challenging. Due to limited sampling and systematic studies, its taxonomy has remained unresolved. In this study, 337 specimens, along with online digital samples representing nearly all wild populations, were collected. Morphological analyses were performed to evaluate key traits and clarify species boundaries. Phylogenetic relationships were reconstructed using concatenation and coalescent methods based on 566,375 nuclear single-nucleotide polymorphisms (SNPs). Ecological niche differentiation was assessed, and ABBA-BABA analysis was used to examine interspecific hybridization. The results revealed that this complex, based on a series of significant character states, could be morphologically distinguished into three species-P. laurifolia (Populus pilosa considered a synonym of P. laurifolia), Populus talassica, and Populus pamirica-which also correspond to three well-supported clades in the phylogenetic trees. P. pamirica exhibits some degree of ecological niche differentiation from P. talassica and P. laurifolia, whereas the latter two show minimal differentiation. Gene flow within the complex remains limited. This research underscores the importance of integrating multiple lines of evidence in the classification of Populus, providing a framework for future taxonomic studies.

Population genomics reveals demographic history and selection signatures of hazelnut (Corylus)

Hazelnut (Corylus spp.) is known as one of the four famous tree nuts in the world due to its pleasant taste and nutritional benefits. However, hazelnut promotion worldwide is increasingly challenged by global climate change, limiting its production to a few regions. Focusing on the eurytopic Section Phyllochlamys, we conducted whole-genome resequencing of 125 diverse accessions from five geo-ecological zones in Eurasia to elucidate the genomic basis of adaptation and improvement. Population structure inference outlined five distinct genetic lineages corresponding to climate conditions and breeding background, and highlighted the differentiation between European and Asian lineages. Demographic dynamics and ecological niche modeling revealed that Pleistocene climatic oscillations dominantly shaped the extant genetic patterns, and multiple environmental factors have contributed to the lineage divergence. Whole-genome scans identified 279, 111, and 164 selective sweeps that underlie local adaptation in Corylus heterophylla, Corylus kweichowensis, and Corylus yunnanensis, respectively. Relevant positively selected genes were mainly involved in regulating signaling pathways, growth and development, and stress resistance. The improvement signatures of hybrid hazelnut were concentrated in 312 and 316 selected genes, when compared to C. heterophylla and Corylus avellana, respectively, including those that regulate protein polymerization, photosynthesis, and response to water deprivation. Among these loci, 22 candidate genes were highly associated with the regulation of biological quality. Our study provides insights into evolutionary processes and the molecular basis of how sibling species adapt to contrasting environments, and offers valuable resources for future climate-resilient breeding.

A Model-Based Assessment for the Ability of National Nature Reserves to Conserve the Picea Species in China under Predicted Climate Conditions

Climate change has a profound impact on the conservation and management of the Picea species, and establishing more nature reserves would be an effective way to conserve wild species in general. Based on a novel computational method using ecological niche modeling to predict the potential geographical distribution of species and a spatial decision support system, the planning process could predict the future distribution of the Picea species and thus select appropriate nature reserves. In this research, we utilized systematic conservation planning to define priority conservation areas for the Picea species in China according to future climate predictions. We hypothesized that: (1) the distribution of the Picea species could be changed under predicted climate conditions in China; (2) the current national nature reserves had sufficient capacity to conserve Picea species under predicted climate conditions in China; and (3) there were still deficiencies in the planned conservation for the Picea species based on predicted climate predictions in China. The results of a spatial analysis showed that the predicted climate would have an impact on the area of distribution of the Picea species. Current nature reserves have a strong potential to conserve the Picea species. However, the conservation of the Picea species in the existing nature reserves was not adequate. There were still many Picea specimens outside the reserve that would be threatened. This research systematically improved the research on the Picea species, and it also scientifically identified the suitable growth and conserved areas of the Picea species in China to provide an empirical basis for the conservation and management of the Picea species.

Taxonomic delimitation and molecular identification of clusters within the species Zanthoxylumnitidum (Rutaceae) in China

Zanthoxylumnitidum, known as Liang-Mian-Zhen in China, is a traditional Chinese medicinal plant used to treat traumatic injury, rheumatism, paralysis, toothache, stomach ache, and venomous snake bites. Two varieties of the species have been described and three morphological types have been reported within the original variety. However, taxonomic delimitation and molecular markers for distinguishing these varieties and types within this species remain unknown. Since different populations exhibit varying chemical compositions, easy identification of intraspecific taxa is crucial. We collected 420 individuals from 38 natural populations, 3 samples of standard medicinal material, and 17 folk-medicine samples to perform classification and identification within Zanthoxylumnitidum. Four distinct genetic clusters (A, B, C, and D) were highly supported by the nuclear barcode. Two distinct chloroplast clusters (A1 and A2) were further detected within A, and three others had one-to-one correspondence with the remaining nuclear clusters. Molecular identification showed that the 17 folk samples comprised A1, A2, B, and D, while the 3 standard samples belonged to A2. The internal transcribed spacer (ITS) region and rbcL gene are proposed as barcodes for rapid and accurate identification of the different Liang-Mian-Zhen lineages in China. This study highlights the importance of accurate taxonomic delimitation in combination with rapid and accurate molecular identification of medicinal plants.

Species Delimitation of Asteropyrum (Ranunculaceae) Based on Morphological, Molecular, and Ecological Variation

Objectively evaluating different lines of evidence within a formalized framework is the most efficient and theoretically grounded approach for defining robust species hypotheses. Asteropyrum Drumm. et Hutch. is a small genus of perennial herb containing two species, A. cavaleriei and A. peltatum. The distinction of these two species mainly lies in the shape and size of leaf blades. However, these characters have been considered labile and could not differentiate the two species reliably. In this study, we investigated the variation of the leaf blades of 28 populations across the whole range of Asteropyrum using the landmark-based geometric morphometrics (GMM), sought genetic gaps within this genus using DNA barcoding, phylogenetic reconstruction and population genetic methods, and compared the predicted ecological niches of the two species. The results showed that the leaf form (shape and size) was overlapped between the two species; barcode gap was not detected within the genus Asteropyrum; and little ecological and geographical differentiation was found between the two taxa. Two genetic clusters detected by population genetic analysis did not match the two morphospecies. The results suggest that there are no distinct boundaries between the two species of Asteropyrum in terms of morphology, genetics and ecology and this present classification should be abandoned. We anticipate that range-wide population genomic studies would properly delineate the species boundaries and help to understand the evolution and speciation within Asteropyrum.