Population genetic clustering methods are widely used to detect hybridization events between closely related populations within species, as well as between deeply diverged lineages across phylogenetic time-scales. Their strengths and limitations in the latter cases, however, remain poorly explored. This study presents a systematic evaluation of the performance of the most popular population clustering method, STRUCTURE, under a variety of cross-species hybridization scenarios, including hybrid speciation, as well as introgression involving ghost (i.e., extinct or unsampled) lineages or otherwise. Our simulations demonstrate that STRUCTURE performs well in identifying hybrids and their parental donors when admixture happens very recently between sampled extant lineages, but generally fails to detect signals of admixture when hybridization occurs in deep time or when gene flow stems from ghost lineages. We find that symmetrical parental contribution in cases of hybrid speciation will often be revealed as extremely asymmetrical in STRUCTURE, especially when the admixture event occurred a long time ago. Our results suggest that population-genetic clustering methods may be inefficient for detecting ancient or ghost admixtures, which may partly explain why ghost introgression has escaped the attention of evolutionary biologists until recently.

Carpesium (Asteraceae) represents the largest Asian genus within the subtribe Inulinae of the tribe Inuleae, exhibiting maximum species diversity in China. This study presents the first comprehensive phylogenetic analysis of Carpesium, utilizing nuclear ribosomal ITS, specific chloroplast DNA sequences (rps16-trnQ, rpl32-trnL and ndhF-rpl32), whole chloroplast genomes and chloroplast coding sequence (CDS). The results demonstrate that Carpesium, excluding C. abrotanoides, constitutes a monophyletic group. The Carpesium s.str. clade contains two well-supported lineages with distinct morphological characteristics. Based on morphological analyses, molecular phylogenetic evidence, and karyotypic studies, this research establishes Cladocarpesium gen. nov. to accommodate Carpesium abrotanoides. The comprehensive sampling approach has facilitated a thorough phylogenetic reconstruction of the Inula complex, establishing a robust systematic framework that clarifies previously uncertain relationships among constituent species. This multilocus methodology provides essential insights for reassessing infrageneric classifications within this taxonomically complex group.

While conducting a population genetic study aiming at refining previous conclusions about cladogenesis in the Oxera genus (Lamiaceae) in New Caledonia, we uncovered an unexpected result for the well-known Oxera palmatinervia Dubard species. To better understand the preliminary molecular results that revealed two distinct sister species, we performed extensive field studies in order to sample, measure, hand-pollinate and observe the flower and fruit visitors on different populations of O. palmatinervia and other species of the “robusta” clade. We found flower morphology differences to be congruent with the molecular results so that we propose to describe a new species as O. sympatrica Gâteblé & Karnadi sp. nov. The differences in flower morphology between the two species, that can grow in true sympatry and flower at the same time of the year, are striking so that flower visitors and pollination syndromes were investigated as far as possible. We find that two species of honeyeaters Glycifohia undulata and Philemon diemenensis are likely the preferred pollinators respectively of O. palmatinervia and O. sympatrica sp. nov. because of their respective sizes, bill and tongue lengths and behavior. Even though, to date, it cannot be proven that initial speciation of both Oxera occurred in sympatry, today’s sympatry is observed along with a remarkable supposed coevolution pollination syndrome. The new species is fully described, mapped, evaluated against Red List criteria and illustrated. Pollination syndromes are discussed and illustrated.

Fossil Ericales pollen from late Oligocene to Early Miocene sediments of the Ban Pa Kha Subbasin, Li Basin, northern Thailand, were examined using the single-grain method. A total of 24 different ericalean pollen types belonging to Ebenaceae (Diospyros), Ericaceae (Cassiope, Vaccinium, and Rhododendron), Pentaphylacaceae (Adinandra), Sapotaceae, Styracaceae (Rehderodendron and Styrax), and Symplocaceae (Symplocos) were identified. All the fossil pollen, except that of Sapotaceae, represent families/genera that are described for the first time from the Cenozoic of Thailand. By considering present terrestrial biome occupancy, Köppen–Geiger climate profiles, and vertical distributions of potential modern analogues of the parent plants producing the fossil pollen, the phytosociological and paleoecological preferences of the fossil taxa were assessed. Our results demonstrate that modern analogues of most of the ericalean taxa have wide ecological and climatic amplitudes with a broad zone of convergence in warm and cold temperate humid or seasonally dry climates. Exceptions are Sapotaceae, which rarely occur outside lowland tropical forests, and Cassiope, which at present occurs at high elevations and, besides Rehderodendron, is one of two modern analogues absent from the modern flora of Thailand. Along with a review of phytosociological studies in montane forests of northern Thailand and neighboring regions, this suggests that the assemblage of dispersed ericalean pollen of the Ban Pa Kha Subbasin likely derives from more than one vegetation type and possibly from different vertical zones.

The genetic structure and population history of ethno-linguistically diverse populations from the Yunnan-Guizhou Plateau remain underrepresented in human genomic research. We analyzed genome-wide data from 239 individuals in Guizhou, combined with modern and ancient datasets, to investigate their fine-scale genetic structure, demographic events, and functional consequences of adaptive genomic signatures. Our findings revealed three genetically distinct groups corresponding to linguistic categories, shaped by differential gene flow from ancient millet farmers and southern Chinese populations. We identified population-specific adaptive candidate genomic regions associated with immune, metabolic, and hematological functions. Additionally, we detected clinically relevant variants with implications for disease risk prediction and precision medicine. These findings underscore the importance of genetic diversity in understanding human adaptation and health disparities, offering a framework for equitable genomic research in underrepresented populations.

Karst area are well known as their extremely biodiversity and the investigation of plants adaptation in these unique environments is one of research hotspots. Previous studies primarily focused on the genomic adaptation of karst endemic species, but the special adaptation of facultative species remains unclear. Hemiboea subcapitata, a traditional medicinal plant growing in both karst and non-karst areas, serves as a valuable model for understanding the genomic mechanisms of this issue. Here, the genome of H. subcapitata was sequenced using the PacBio and Illumina platforms and de novo assembled with contig N50 value of 21.11 Mb. The assembled genomic size was 763.59 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) quality value was 98.10%, and 92.87% sequences were anchored to 16 chromosomes. Comparative genome analyses identified three whole-genome duplication (WGD) events: γ-WGT event (115–130 Ma) shared by all eudicots, WGD2 shared within Lamiales except Oleaceae (67.57 Ma) and the recently independent WGD1 unique to H. subcapitata (16.92 Ma). These three WGD events likely facilitated the expansion of stress-responsive gene families, which in turn influenced functional pathway regulation. Especially, genomic and transcriptome analyses identified 25 key genes in the flavonoid pathway and candidate MYB transcription factors related to environmental adaptation. Compared to the karst-endemic Primulina tabacum, H. subcapitata showed upregulation of 25 key flavonoid pathway genes (96% in roots, 92% in leaves, 88% in flowers). This mechanism of expanding ecological niches through metabolic pathway regulation was the unique adaptive strategy of H. subcapitata. This study provides valuable data for further resource utilization and conservation of Hemiboea.

Ectomycorrhizal (ECM) fungi form symbiotic relationships with woody plants, completing their life cycles through mutualistic associations. The evolution of this symbiosis involves genomic adaptations including gene gain and loss. However, how these genomic characteristics reflect speciation and adaptation throughout the evolutionary history of ECM fungi remains unclear. In the present study, we explored speciation and host adaptation in Tricholoma species, an ecologically relevant clade of ECM basidiomycetes. We compared the genomes of three species, Tricholoma matsutake, T. populinum, and T. bakamatsutake, which despite their close phylogenetic relationships, have different tree hosts. A phylogenetic tree constructed using single-copy orthologous genes estimated the divergence time of T. populinum to be approximately 28.48 Mya, coinciding with the diversification of subg. Eupopulus in East Asia. The split between T. matsutake and T. bakamatsutake was estimated at around 8.08 Mya, corresponding to the diversification period of evergreen broadleaved forests in East Asia. In this study, we identified 19, 13, and 13 positively selected genes in the genomes of T. bakamatsutake, T. matsutake, and T. populinum, respectively. Additionally, 2983, 2783, and 1548 genes have undergone rapid evolution in their genomes. GO enrichment analysis revealed the functions of these rapidly evolving genes, including those associated with cell cycle, cytoplasmic components, and GTPase mediation. Gene flow analysis indicated unidirectional migration from the ancestor of T. populinum to T. matsutake and T. bakamatsutake, whereas bidirectional gene flow was observed in the ancestors of T. matsutake and T. bakamatsutake. This study suggested that host-induced immigrant unviability in symbiotic fungi is the primary cause of prezygotic isolation. The combination of ecology-based genomic evidence and gene flow analysis offers new insight into the speciation and evolutionary mechanisms of symbiotic fungi.

The tribe Cunonieae comprises five genera and 214 species of shrubs and trees currently distributed in the Southern Hemisphere and the tropics, exhibiting an amphi-pacific disjunct distribution shared with Araucariaceae, Myrtaceae, Nothofagaceae, Podocarpaceae, and Proteaceae, among others. To address the central question of how historical geological forces have shaped the distribution of plant diversity in the southern hemisphere, we aimed to provide evidence from the biogeographical history of Cunonieae. We generated the most densely sampled phylogenetic trees of Cunonieae available to date, with 121 samples and 81 species, based on 404 new sequences of plastid and nuclear DNA regions with high hierarchical phylogenetic signal (matK, trnL-F, rpl16, and ITS). We included 184 samples of Rosids to estimate divergence times using fossil calibration points. For biogeographic inference, we employed a time-stratified model including fossils as tips. Cunonia and Pterophylla were paraphyletic in the ITS tree, and Cunonia was paraphyletic in the plastid tree. Pancheria, Vesselowskya, and Weinmannia were monophyletic, the latter with conflicting nuclear and plastid phylogenies. The crown group Cunonieae was dated at ~56 Mya and its ancestral areas were Antarctica and Patagonia. Antarctica acted as a bridge between Australia and South America before the consolidation of the Antarctic Ice Sheet, and the extinction of the lineage in Antarctica from Oligocene to Miocene. Following that, Cunonieae spread to lower latitudes via Zealandia/Oceania and Patagonia/South America. Geological changes during the Pliocene facilitated further burst in diversification along the Andes, in Madagascar, and New Caledonia where at least three colonization events occurred.

Neotropical catfishes of the genus Rhamdia are divided into cis- and trans-Andean/Middle American reciprocally monophyletic components, the latter notable for its considerable cave-dwelling diversity. Despite previous research, uncertainties remain regarding the systematics and historical biogeography of the Middle American clade. To test previous phylogenetic hypotheses and improve our understanding of the evolutionary history of this group of Middle American freshwater fishes, we generated and analyzed comparative mitogenome-wide data from most valid species and known cave-dwelling forms. Our results corroborate this clade as divided into two reciprocally monophyletic groups (split dated at ~9 Ma): a clade representing the species Rhamdia guatemalensis (crown group dated at ~2.8 Ma) and a clade consisting of the remaining Middle American species (i.e., the Rhamdia laticauda species group; crown group dated at ~4 Ma). Our results also confirm the notion that R. laticauda is deeply paraphyletic and that phylogenetically scattered geographic lineages of this taxon could represent different species. Our divergence time estimates coupled with present-day distribution patterns support the biogeographic scenario in which northward dispersal and colonization of Central America and southern North America by Rhamdia was catalyzed by the emergence of the Panamanian Isthmus land bridge and stream captures across Lower Central America. Cave colonization in Middle American Rhamdia is widespread, convergent, relatively recent (dating from the Pleistocene), and most likely opportunistic, with established cave-dwelling populations possibly representing “evolutionary dead ends”.

The 26 genera of aurantioids and the 28 species of one genus, Citrus, are mapped. The distributions are explained, not by using fossil-calibrated clade ages and ancestral-area algorithms, but by focusing on the geometry of the clade distributions and the tectonic history at the break-zones (nodes). Allopatry is attributed to vicariance, overlap to normal dispersal. Subfamily Aurantioideae is allopatric with its sister groups in Eurasia and the Americas. In contrast, the seven main clades within Aurantioideae show a high level of overlap. But within each of these seven main clades, there is again a high level of allopatry. The pattern is explained by vicariance events at the first and third levels. The overlap at the second level can be accounted for if vicariance (now obscured) generated the clades and subsequent dispersal caused secondary overlap of the clades. This latter phase of mobilism can be explained by the migration of coastlines and maritime flora far inland during marine transgressions, especially in the mid-Cretaceous. Many aurantioids inhabit mangrove-associate vegetation, beach thicket, limestone substrate, and areas with high levels of disturbance. Within Citrus, the five main clades overlap in south-central China (Nanling Mountains) and are allopatric elsewhere. The overlap-zone has been interpreted as a centre of origin, but it is explained here as a break-zone, the site of vicariance in a widespread ancestor, where localised, secondary overlap has developed later. The zone coincides with a belt of mid-Cretaceous deformation manifested in voluminous magmatism, subsidence, rifting, back-arc extension, and the opening of the East China sea.

Pinaceae are one of the most economically and ecologically important tree families and play a key role in boreal, temperate and montane forests of the Northern Hemisphere. The family have a rich fossil record with the earliest occurrence of the Pinaceae crown group probably from the Late Jurassic, and diverse seed cones, woods, leaves and pollen grains from the Early Cretaceous of the Northern Hemisphere. However, the origin and early evolutionary history of Pinaceae is not well understood, in part because of uncertainty about the phylogenetic position of early fossils. In this paper we describe a new woody stem of Pinaceae based on well-preserved material from the Early Cretaceous Huolinhe Formation in Jarud Banner, eastern Inner Mongolia, Northeast China. Piceoxylon jarudense sp. nov. has distinct growth rings with secondary xylem composed of tracheids, ray tracheids, ray parenchyma cells, axial parenchyma cells, and axial and radial resin canals. Pitting on radial walls of tracheids is abietinean; cross-field pitting is piceoid and taxodioid with 2–6 pits arranged in 1–2 rows per cross-field. Axial and radial resin canals are lined by thick-walled epithelial cells. Piceoxylon has been considered to include species with wood anatomy comparable to extant Larix, Pseudotsuga, Picea and Cathaya. Comparisons of wood anatomy and constrained phylogenetic analyses of Piceoxylon jarudense, one of the earliest records of Piceoxylon, both suggest that P. jarudense is most likely allied with Larix and Pseudotsuga within the pinoid clade suggesting divergence of the Larix-Pseudotsuga clade before ~125.6 Ma.

Apomixis can confer fertility upon spontaneous hybrids and allopolyploids, both of which have played a pivotal role in the evolutionary trajectory and diversification of flowering plants. We hypothesized that an unusual morphotype of Elatostema represents a viable hybrid species between E. scabrum and E. hirticaule, as opposed to a sterile F1 hybrid. To test this, we employed phylogenomic, flow cytometry, cytological, and morphological analyses. A two-step phylogenomic approach was used. Genome skimming was performed on one E. longpingii population, three populations of each parent (E. scabrum, E. hirticaule), and ten Elatostema and one Pilea species. Population genetic analyses were then conducted using RAD sequencing data from the type population of hybrid and parent species. Phylogenomic analyses using genome skimming and RAD sequencing data consistently supported a hybrid origin, placing E. longpingii close to or nested within E. scabrum and distant from E. hirticaule. Chromosome counts revealed pentaploid, triploid, and tetraploid ploidy levels in E. longpingii, E. scabrum, and E. hirticaule, respectively. Flow cytometry suggested apomixis in E. longpingii and E. scabrum, while E. hirticaule exhibited sexual reproduction. Morphological studies indicated that E. longpingii shares traits from both parents. Our findings demonstrate a novel reproductively viable hybrid species in Elatostema, likely originated through a natural hybridization event involving heteroploidy, coupled with the inheritance of an apomictic reproductive pathway from its maternal parent. These results provide compelling evidence that hybridization and apomixis have played pivotal roles in driving reticulate evolution and promoting diversification within the Elatostema.