Incomplete lineage sorting and local extinction shaped the complex evolutionary history of the Paleogene relict conifer genus, Chamaecyparis (Cupressaceae)

Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting in the rapidly radiated East Asian genus Nekemias (Vitaceae)

BACKGROUND AND AIMS

Nekemias is a small genus of the grape family, with nine species discontinuously distributed in temperate to subtropical zones of the Northern Hemisphere but mostly in East Asia. Previous phylogenetic studies on Nekemias have mainly been based on a few chloroplast markers, and the phylogenetic framework and systematic relationships are still highly contested.

METHODS

We carried out a systematic framework reconstruction of Nekemias and intra-generic reticulate evolutionary analyses based on extensive single-copy nuclear and chloroplast genomic data obtained by the Hyb-Seq approach, combining genome skimming and target enrichment.

KEY RESULTS

Both nuclear and chloroplast genomic data strongly support the monophyly of Nekemias with its division into two major lineages from East Asia and North America, respectively. There are strong and extensive topological conflicts among nuclear gene trees and between nuclear and chloroplast topologies within the genus, especially within the East Asian clade.

CONCLUSIONS

Rapid radiation through predominant incomplete lineage sorting (ILS) throughout the evolutionary history of the East Asian taxa is supported to explain the relatively high species diversity of Nekemias in East Asia. This study highlights the important role of short periods of rapid evolutionary radiations accompanied by ILS as a mechanism for the complex and fast species diversifications in the grape family as well as potentially in many other plant lineages in East Asia and beyond.

Integrative Taxonomy for Species Delimitation: A Case Study in Two Widely Accepted Yet Morphologically Confounding Rosa Species Within Sect. Pimpinellifoliae (Rosaceae)

The use of morphological traits as a practical approach for delimiting taxa at various ranks has long been regarded as a reliable basis for taxonomy. However, its efficacy has been increasingly called into question in many taxonomic groups due to its inherent limitations, such as failing to account for phenotypic plasticity, ecologically driven variation (e.g., ecotypes), and parallel evolution. These factors often introduce ambiguity or misleading similarities, thereby obscuring the true evolutionary relationships among taxa, particularly in the context of species delimitation. In the present study, we employ an integrated methodology that combines quantitative morphological analyses, whole-genome data, and ecological measurements to resolve the species boundaries of two morphologically similar roses, Rosa sericea and Rosa hugonis, which have long been considered as two distinct species but lack clear morphological boundaries. Our findings reveal that the unbiased analysis of morphological data based on a large and representative sample size was insufficient to identify effective diagnostic traits. However, when complemented with genome-wide population-level sequencing data or integrated with geographic and ecological niche assessments, the delineation of species boundaries was significantly improved. Furthermore, ecological data provide additional insight into the abiotic factors driving interspecific and intraspecific divergence. By integrating multiple lines of evidence-spanning genomic (intrinsic) and phenotypic (extrinsic) traits-and incorporating the interaction between species and their environments, species boundaries can be delineated with greater confidence. A well-defined species can thus be established through the mutual corroboration of diverse datasets, thereby ensuring a more rigorous and comprehensive taxonomic framework.

Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies

Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs. In this study, using 1,533 nuclear genes generated from transcriptome sequencing and a complete sampling of all widely recognized species, we have successfully reconstructed a robust phylogeny of global firs, in which four clades are strongly supported and all intersectional relationships are resolved, although phylogenetic discordance caused mainly by incomplete lineage sorting and hybridization was detected. Molecular dating and ancestral area reconstruction suggest a Northern Hemisphere high-latitude origin of Abies during the Late Cretaceous, but all extant firs diversified during the Miocene to the Pleistocene, and multiple continental and intercontinental dispersals took place in response to the late Neogene climate cooling and orogenic movements. Notably, four critically endangered firs endemic to subtropical mountains of China, including A. beshanzuensis, A. ziyuanensis, A. fanjingshanensis and A. yuanbaoshanensis from east to west, have different origins and evolutionary histories. Moreover, three hotspots of species richness, including western North America, central Japan, and the Hengduan Mountains, were identified in Abies. Elevation and precipitation, particularly precipitation of the coldest quarter, are the most significant environmental factors driving the global distribution pattern of fir species diversity. Some morphological traits are evolutionarily constrained, and those linked to elevational variation (e.g., purple cone) and cold resistance (e.g., pubescent branch and resinous bud) may have contributed to the diversification of global firs. Our study sheds new light on the spatiotemporal evolution of global firs, which will be of great help to forest management and species conservation in a warming world.

Phylogenomics of Brachystegia: Insights into the origin of African miombo woodlands

PREMISE

Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a dominant genus of trees in miombo woodlands, appears as a key witness of the history of the largest woodland and savanna biome of Africa.

METHODS

We reconstructed the evolutionary history of the genus using targeted-enrichment sequencing on 60 Brachystegia specimens for a nearly complete species sampling. Phylogenomic inferences used supermatrix (RAxML-NG) and summary-method (ASTRAL-III) approaches. Conflicts between species and gene trees were assessed, and the phylogeny was time-calibrated in BEAST. Introgression between species was explored using Phylonet.

RESULTS

The phylogenies were globally congruent regardless of the method used. Most of the species were recovered as monophyletic, unlike previous plastid phylogenetic reconstructions where lineages were shared among geographically close individuals independently of species identity. Still, most of the individual gene trees had low levels of phylogenetic information and, when informative, were mostly in conflict with the reconstructed species trees. These results suggest incomplete lineage sorting and/or reticulate evolution, which was supported by network analyses. The BEAST analysis supported a Pliocene origin for current Brachystegia lineages, with most of the diversification events dated to the Pliocene-Pleistocene.

CONCLUSIONS

These results suggest a recent origin of species of the miombo, congruently with their spatial expansion documented from plastid data. Brachystegia species appear to behave potentially as a syngameon, a group of interfertile but still relatively well-delineated species, an aspect that deserves further investigations.

Recent advances on phylogenomics of gymnosperms and a new classification

Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics. Here, we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms. This new classification includes three classes (Cycadopsida, Ginkgoopsida, and Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, and Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, and Welwitschiales), 13 families, and 86 genera. We also described six new tribes including Acmopyleae Y. Yang, Austrocedreae Y. Yang, Chamaecyparideae Y. Yang, Microcachrydeae Y. Yang, Papuacedreae Y. Yang, and Prumnopityeae Y. Yang, and made 27 new combinations in the genus Sabina.

Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus

Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.