Ex situorigins and dispersal of taxa have played important roles in the assembly of island-like biodiversity hotspots. Insular limestone karsts in Southeast Asia are hotspots of biodiversity and endemism, but the immigration processes of their unique floras are still poorly known. Here, we used Gesneriaceae as a proxy to investigate the immigration dynamics of tropical and subtropical Southeast Asian karst floras. We present the most comprehensive phylogenetic analysis of the Old World gesneriads to date based on twelve loci. By estimating divergence times and reconstructing ancestral states (habitat, soil type and range), we found that immigration into subtropical Southeast Asian karst floras first occurred in the Early Miocene, with two peaks in the Early–Middle Miocene and the Pliocene–Early Pleistocene, whereas immigration into tropical Southeast Asian karsts initiated in the Late Eocene, with two peaks in the Late Oligocene and the Late Miocene. We also discover that Southeast Asian karst biodiversity comprises immigrant pre-adapted lineages and descendants from local acid soil ancestors, although niche shift from acid soil to karst in tropical Southeast Asian islands was lacking. This study advances our understanding of the historical assembly of Southeast Asian karst floras.

Chloranthaceae is a pantropical family of flowering plants distributed mainly across Central and South America, East Asia, and the Pacific, encompassing approximately 73 species belonging to four extant genera—Ascarina, Chloranthus, Hedyosmum, and Sarcandra. As one of the most ancient lineages of extant angiosperms, Chloranthaceae holds substantial value in traditional medicine globally and offers major insights into the evolutionary history of flowering plants. However, phylogenetic relationships within this family remain partially resolved, and its origin continues to be debated. We here sequenced, assembled, annotated, and compared the chloroplast genomes (plastomes) of 22 Chloranthaceae species to investigate their plastome evolution and reconstructed the family’s phylogeny by using both plastome and nuclear ribosomal DNA (nrDNA). Additionally, we employed the divergence-extinction-cladogenesis model to infer the ancestral area and historical migration patterns of Chloranthaceae. Results The plastomes of Chloranthaceae exhibit a typical quadripartite structure, with genome sizes ranging from 157,449 bp to 159,218 bp and encoding 113 unique genes, including 17–18 genes duplicated in inverted repeat (IR) regions. Interestingly, the genus Hedyosmum demonstrated notable IR expansions, resulting in trnHGUG duplication in five species. A comparative analysis unveiled substantial variations in simple sequence repeats (SSRs) and tandem repeats across different species, whereas interspersed repeats remained relatively stable. Correlation analyses revealed positive correlations between plastome size and both IR length and SSR count. Furthermore, our phylogenetic reconstruction based on plastome and nrDNA (18 S-ITS1-5.8 S-ITS2-26 S) data provided robust support for the intergeneric relationships, confirming the monophyly of each genus and resolving long-standing uncertainties in the intrageneric relationships of Chloranthus and Hedyosmum. Notably, H. orientale, the sole Hedyosmum species found in Asia, was phylogenetically embedded within the genus, rather than occupying a basal position contrary to previous results. Our biogeographical reconstruction, incorporating both extant and fossil evidence, supports a Laurasian origin of Chloranthaceae and its subsequent dispersal to the tropics. Conclusions This study provides the most comprehensive plastome-based phylogenomic analysis of Chloranthaceae to date, offering novel insights into its plastome evolution, resolving long-standing ambiguities in interspecific and phylogenetic relationships and reconstructing the probable biogeographic origin and historical migrations of this family. The proposed resources establish a robust framework for future evolutionary investigations within the realm of Chloranthaceae.

​Alignment problems may be complicated and diverse and the performance of the existing alignment-filtering tools, particularly their potential effect on phylogenetic reconstruction, have remained debated or limitedly explored. ​In the present study, we developed a new R package named alignmentFilter to treat the diverse alignment problems, especially masking ambiguously-aligned or overly divergent segments using a newly devised grouping-regrouping algorithms acting on sequence divergence in each of sliding windows throughout alignment. Then we tested and compared the power and accuracy of the prevalent alignment-filtering tools, particularly the effect on phylogeny based on Angiospermae genome-scale data and simulated data. ​The results indicate the alignment-filtering methods alone may affect the phylogeny decisively, producing (strongly-supported) phylogenetic conflicts. In most cases, alignmentFilter most efficiently improves phylogeny, yielding more congruent phylogeny regardless of phylogeny-reconstruction methods, producing phylogeny more concordant to the priori tree regarding to both topology and branch length in simulation, and most efficiently decreasing the root-to-tip length heterogeneity that is implied to be negatively correlated with topological accuracy. ​The concepts and algorithms of alignmentFilter are quite distinct from existing alignment-filtering methods. It is not susceptible to specific types of alignment errors that usually baffle other methods and can reach the optimal solution frequently with lowest computation complexity. The biological or statistical sense of the key optional stringency-controlling parameter is more straightforward and the setting and outcome may be more adjustable or predictable. A better and more comprehensive solution of alignment problems in this study will benefit tremendous downstream analyses sourced from alignment and phylogeny.

Petrocosmea funingensis, a new species from southeastern Yunnan, China is here described and illustrated. Based on morphological characters it is assumed to belong to section Anisochilus, because of the shallow or slight split of the corolla lobes with the upper lip being nearly half as long as the lower one. Within the section, the new species is associated with the species from series Iodioides, due to the particularly extensive fusion of the two adaxial lobes and is morphologically most similar to P. huanjiangensis and P. iodioides, especially in floral structure and traits, but can be distinguished from these species by several quantitative and qualitative characters of the leaves, peduncles, calices, stamens, staminodes and styles.