Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure

Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex (B. liuyanii, B. longgangensis, B. masoniana and B. variegata) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between B. liuyanii and B. longgangensis occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of B. masoniana have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

How diverse are the mountain karst forests of Mexico?

Tropical forests on karstic relief (tropical karst forest) are among the most species-rich biomes. These forests play pivotal roles as global climate regulators and for human wellbeing. Their long-term conservation could be central to global climate mitigation and biodiversity conservation. In Mexico, karst landscapes occupy 20% of the total land surface and are distributed mainly in the southeast of the country, along the eastern slope, and in the Yucatan Peninsula. Within each of these areas, the following types of karst occur: coastal karst, plain karst, hill karst, and mountain karst (low, medium, high). Mountain karst cover 2.07% of Mexico's land surface and are covered by tropical rainforests, montane cloud forests, and tropical deciduous forests. These are probably one of the most diverse biomes in Mexico. However, the mountain karst forests of Mexico have received little attention, and very little is known about their diversity. Here, we evaluated the vascular plant species richness within the mountain karst forests of Mexico. We assembled the first, largest, and most comprehensive datasets of Mexican mountain karst forest species, from different public databases (CONABIO, GBIF, IBdata-UNAM), which included a critical review of all data. We compiled a list of the families, genera, and species present within the mountain karst forests of Mexico. Taxa that best characterize these forests were identified based on their spatial correlation with this biome. We explored biodiversity patterns, identifying areas with the highest species richness, endemism centers, and areas of relatively low sampling intensity. We found that within the mountain karst forests of Mexico there are representatives of 11,771 vascular plant species (253 families and 2,254 genera), ca. 50% of the Mexican flora. We identified 372 species endemic to these forests. According to preliminary IUCN red list criteria, 2,477 species are under some category of conservation risk, of which 456 (3.8%) are endangered. Most of the Mexican mountain karst forests have been extensively explored and six allopatric, species-rich areas were identified. Compared to other regions in the world, the mountain karst forests of Mexico are one of the most diverse biomes. They contain more species than some entire montane systems in Mexico such as Sierra Madre Oriental, and Sierra Madre del Sur. Also, the mountain karst forests of Mexico are most diverse than similar forests of South America and Asia, even if considering the effect of different sampling areas. The fact that mountain karst forests are embedded in areas of high biotic diversity, probably contributes to their great floristic diversity. Thus, the mountain karst forests of Mexico are an important source of diversity and shelters a large percentage of the Mexican flora.

Spatial genetic patterns and distribution dynamics of Begonia grandis (Begoniaceae), a widespread herbaceous species in China

Introduction

Begonia L., one of the 10 largest plant genera, contains over 2,100 species, most of which have a very limited distribution range. Understanding the spatial genetic structure and distribution dynamics of a widespread species in this genus will contribute to clarifying the mechanism responsible for Begonia speciation.

Methods

In this study, we used three chloroplast DNA markers (ndhF-rpl32, atpI-atpH, and ndhA intron), coupled with species distribution modeling (SDM), to investigate the population genetic structure and distribution dynamics of Begonia grandis Dryand., the species of Begonia with the widest distribution in China.

Results

Thirty-five haplotypes from 44 populations clustered into two groups, and haplotype divergence began in the Pleistocene (1.75 Mya). High genetic diversity (H _d = 0.894, H _T = 0.910), strong genetic differentiation (F _ST = 0.835), and significant phylogeographical structure (G _ST/N _ST = 0.848/0.917, P < 0.05) were observed. The distribution range of B. grandis migrated northwards after the last glacial maximum, but its core distribution area remained stable.

Discussion

Combined, the observed spatial genetic patterns and SDM results identified the Yunnan-Guizhou Plateau, the Three Gorges region, and the Daba Mountains as potential refugia of B. grandis. BEAST-derived chronogram and haplotype network analysis do not support the Flora Reipublicae Popularis Sinicae and Flora of China for subspecies classification based on morphological characteristics. Our results support the hypothesis that population-level allopatric differentiation may be an important speciation process for the Begonia genus and a key contributor to its rich diversity.

Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China

Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.

Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae

Petrocodon and Primulina are two characteristic genera of Gesneriaceae that exhibit remarkable species and floral diversity, and high endemism across the Sino-Vietnamese Limestone Karsts. To better understand the evolution of limestone gesneriad plastomes, we report nine complete plastomes of seven Primulina and two Petrocodon which have never been assembled before. The newly generated plastomes range from 152,323 to 153,786 bp in size and display a typical quadripartite structure. To further explore the plastome evolution across Gesneriaceae, we assembled five additional plastomes from public reads data and incorporated 38 complete Gesneriaceae plastomes available online into comparative and phylogenomic analyses. The comparison of 52 Gesneriaceae plastomes reveals that not only Primulina and Petrocodon but all gesneriad genera analyzed are highly conserved in genome size, genome structure, gene contents, IR boundary configurations, and codon usage bias. Additionally, sliding window analyses were implemented across alignments of Primulina and Petrocodon for identifying highly variable regions, providing informative markers for future studies. Meanwhile, the SSRs and long repeats of Gesneriaceae plastomes were characterized, serving as useful data in studying population and repetitive sequence evolutions. The results of plastome phylogenetics represent a preliminary but highly resolved maternal backbone genealogy of Primulina and the Old World subtribes of Gesneriaceae.

Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus)

Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed.

Six new species of Begonia from Guangxi, China

BACKGROUND

With currently 1980 described species, the mega-diverse Begonia is now perhaps the 5th largest flowering plant genus, expanding rapidly from ca. 900 species in 1997 to its current size in merely two decades. In continuation of our studies of Asian Begonia, we report six additional new species from Guangxi, the region/province harboring the second richest Begonia flora of China.

RESULTS

Based on morphological and molecular data, the new species B. aurora belongs to Begonia sect. Platycentrum, while the other five new species (viz. B. larvata, B. longiornithophylla, B. lui, B. scabrifolia, and B. zhuoyuniae) are members of Sect. Coelocentrum. Somatic chromosome numbers of B. longiornithophylla and B. zhuoyuniae at metaphase were counted as 2n = 30, consistent with previously reports for Sect. Coelocentrum.

CONCLUSIONS

With the addition of the six new species, the total number of Begonia species in Guangxi increases from 86 to 92. Detailed description, line drawings, and color plates are provided to aid in identification.

In memoriam Ching-I Peng (1950-2018)-an outstanding scientist and mentor with a remarkable legacy

Ching-I Peng, the most prolific and internationally recognized Taiwanese plant taxonomist of his generation, passed away on May 1, 2018. Dr. Peng was an eminent worker on the taxonomy of East Asian plants and the genus Ludwigia, and the foremost expert on Asian Begonia. He served as associate editor, co-editor in chief, and editor-in-chief of Botanical Studies and its predecessor Botanical Bulletin of Academia Sinica during the period 1992-2016. He gathered over 25,000 plant specimens, name 121 plant taxa, and has left a remarkable legacy of literature, collaborations and collections. This article summarizes Dr. Peng's academic career and commemorates his enduring contribution.

Molecular systematics of Chiritopsis-like Primulina (Gesneriaceae): one new species, one new name, two new combinations, and new synonyms

BACKGROUND

The Gesneriaceae genus Chiritopsis, confined almost exclusively to cave or cave-like microhabitats of limestone karsts of southern China, was described to distinguish it from Chirita by much smaller flowers and generally miniature plant sizes in the former genus. However, molecular phylogenetic analyses showed that Chiritopsis is polyphyletic and its species delimitation has been problematic. To understand how many times Chiritopsis-like species have evolved from within the recircumscribed Primulina and to further clarify their species identification, we sampled all but two recently described species of Chiritopsis-like Primulina and reconstructed their phylogenetic relationship based on DNA sequences of nuclear ITS and chloroplast trnL-F and trnH-psbA.

RESULTS

With 182 accessions of 165 taxa of Primulina sampled, our analyses placed the 40 accessions of 25 taxa of Chiritopsis-like Primulina in 17 unrelated positions, indicating at least 17 independent origins of the traits associated with caves or cave-like microhabitats. Of the 17 clades containing Chiritopsis-like Primulina, Clade 1 is composed of P. bipinnatifida, P. cangwuensis, P. jianghuaensis, P. lingchuanensis, and P. zhoui, as well as additional samples that show variable and overlapping morphology in leaf shapes. Clade 10 includes P. cordifolia, P. huangii, and P. repanda, while Primulina repanda var. guilinensis is not placed within Clade 10. Primulina glandulosa var. yangshuoensis is not placed in the same clade of P. glandulosa.

CONCLUSIONS

Based on our data, P. cangwuensis, P. jianghuaensis, and P. lingchuanensis are proposed to synonymize under P. bipinnatifida, with P. zhoui treated as a variety of P. bipinnatifida. Primulina repanda var. guilinensis is transferred as P. subulata var. guilinensis comb. nov. and Primulina pseudoglandulosa nom. nov. is proposed for P. glandulosa var. yangshuoensis. One new species is named P. chingipengii to honor the late Dr. Ching-I Peng (1950-2018).