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[EN] Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploidy frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.

Aim: We investigated the historical biogeography and diversification of Gentiana L. (Gentianaceae). Our study depicts the origin and dispersal routes of this alpine genus, and the role of the uplift of the Qinghai—Tibet Plateau (QTP) and past climate changes as triggers for its diversification. Location: Tibeto-Himalayan region and world-wide mountain habitats. Methods: Our sampling represents more than 50% of the extant Gentiana species, including all sections across their entire geographical ranges. We investigated the evolutionary history of Gentiana using phylogenetic reconstructions (maximum likelihood and Bayesian inference) of ITS, atpB—rbcl and trnL—trnF sequences, as well as molecular dating with BEAST. We tested two approaches of ancestral area reconstructions (DEC, DIVA) in BioGeoBEARS and investigated diversification rates using BAMM. Results: The common ancestor of Gentiana and subtribe Gentianinae lived in the QTP region at around 34 (25—45) million years ago (Ma), and 40 (29—52) Ma respectively. From the surroundings of the QTP, Gentiana lineages dispersed to eastern China, Taiwan, Europe, North and South America, Australia and New Guinea, from mid-Miocene onward (c. 15 Ma—present), with only one older dispersal event to Europe (c. 37—21 Ma). Diversification rates gradually increased over time, and two switches of diversification rates were identified in Gentianinae (c. 7 Ma, simultaneously in the Pneumonanthe/Cruciata lineage and in Tripterospermum). Main conclusions: Gentiana existed in the QTP region throughout most of its uplift history following the India-Asia collision. This region acted as the primary source area for dispersals to many areas of the world. Because steady increase in diversification rates coincides with the extension of the QTP, we argue that the museum theory rather than the explosive radiation theory prevails for gentians in this region, although rare shifts of diversification rates are associated with niche shifts across the alpine/subalpine ecotone.

This article is a Commentary on Li et al. (2021), 232: 1424–1435.

Recently, the \"mountain-geobiodiversity hypothesis\" (MGH) was proposed as a key concept for explaining the high levels of biodiversity found in mountain systems of the Tibeto-Himalayan region (THR), which comprises the Qinghai-Tibetan Plateau, the Himalayas, and the biodiversity hotspot known as the \"Mountains of Southwest China\" (Hengduan Mountains region). In addition to the MGH, which covers the entire life span of a mountain system, a complementary concept, the so-called \"flickering connectivity system\" (FCS), was recently proposed for the period of the Quaternary. The FCS focuses on connectivity dynamics in alpine ecosystems caused by the drastic climatic changes during the past ca. 2.6 million years, emphasizing that range fragmentation and allopatric speciation are not the sole factors for accelerated evolution of species richness and endemism in mountains. I here provide a review of the current state of knowledge concerning geological uplift, Quaternary glaciation, and the main phylogeographic patterns (\"contraction/recolonization,\" \"platform refugia/local expansion,\" and \"microrefugia\") of seed plant species in the THR. In addition, I make specific suggestions as to which factors future avenues of phylogeographic research should take into account based on the fundamentals presented by the MGH and FCS, and associated complementary paradigm shifts.

AIM: We investigated the biogeography of the subtropical mountain genus Tripterospermum Blume (Gentianaceae), disjunctly distributed at the southern fringe of the Qinghai–Tibetan Plateau (QTP) and other mountain systems within the biodiversity hotspots of Southeast Asia. This study reveals dispersal routes among these areas. LOCATION: East China, Indochina, Japan, the Philippines, southeastern fringe of the Qinghai–Tibetan Plateau (southern Himalaya and Hengduanshan), Taiwan, Wallacea. METHODS: The evolutionary history of Tripterospermum was studied using the phylogenetic reconstructions (Maximum Likelihood and Bayesian Inference using ITS, atpB–rbcL and trnL–trnF), molecular dating (using BEAST with a relaxed clock model and fossil constraints), and two approaches of ancestral area reconstructions (DEC, S‐DIVA). Our sampling design included 82% of the extant species of subtropical Gentianinae (Tripterospermum, Metagentiana, Sinogentiana and Crawfurdia) as ingroup, and Kuepferia, Gentiana and other Gentianaceae genera as outgroups. RESULTS: Subtropical Gentianinae originated at the southeastern fringe of the QTP (the southern Himalaya and Hengduanshan) between 16 and 35 million years ago (Ma). With a crown age estimated to be 2.7–8.8 million years (Myr), Tripterospermum originated at the southeastern fringe of the QTP, from where it dispersed to East China, Indochina, Sundaland, Taiwan, Japan and Wallacea. MAIN CONCLUSIONS: For Tripterospermum, the southern Himalaya and the Hengduanshan have acted as a source area for the colonization of East and Southeast Asia. This study depicts dispersal routes among the biodiversity hotspots neighbouring the QTP and those located on Sundaland and Wallacea. Mountain plants seem to have colonized Wallacea using a northern route via Taiwan rather than a more southern route via Sundaland. The latter route has previously been recorded for many lowland lineages. Because Tripterospermum species‐producing berries have dispersed more often across geographical barriers than those producing capsules, we hypothesize that avian transportation of berry‐like fruits might have facilitated their dispersal.

Aim Our objective is to analyse global‐scale patterns of mountain biodiversity and the driving forces leading to the observed patterns. More specifically, we test the ‘mountain geobiodiversity hypothesis’ (MGH) which is based on the assumption that it is not mountain‐uplift alone which drives the evolution of mountain biodiversity, but rather the combination of geodiversity evolution and Neogene and Pleistocene climate changes. We address the following questions: (a) Do areas of high geodiversity and high biodiversity in mountains overlap, that is can mountain geodiversity predict mountain biodiversity? (b) What is the role of Pleistocene climate change in shaping mountain biodiversity? (c) Did diversification rate shifts occur predominantly with the onset of more pronounced climate fluctuations in the late Neogene and Pleistocene fostering a ‘species pump’ effect, as predicted by the MGH? Location Global. Taxon Vascular plants. Methods We used generalized linear models to test to what extent vascular plant species diversity in mountains is explained by net primary productivity (NPP), geodiversity and Pleistocene climate fluctuations (i.e. changes in temperature between the Last Glacial Maximum [LGM] and today). In addition, we compiled dates of diversification rate shifts from mountain systems and investigated whether these shifts occurred predominantly before or after the global major climatic fluctuations of the late Neogene and Pleistocene. Results Both NPP and elevation range show a positive relationship, whereas Pleistocene climatic fluctuations show a negative impact on plant species diversity. The availability of climatic niche space during the LGM differs markedly among mountain systems. Shifts to higher diversification rates or starts of radiations showed the highest concentration from the late Miocene towards the Pleistocene, supporting the MGH. The most commonly inferred drivers of diversification were key innovations, geological processes (uplift) and climate. Main conclusions Our analyses point towards an important role of historical factors on mountain plant species richness. Mountain systems characterized by small elevational ranges and strong modifications of temperature profiles appear to harbour fewer radiations, and fewer species. In contrast, mountain systems with the largest elevational ranges and stronger overlap between today´s and LGM temperature profiles are also those where most plant radiations and highest species numbers were identified.

Aim We investigated whether the fossil‐rich and cosmopolitan buckthorn family (Rhamnaceae, dating back to the Cretaceous) was influenced by vicariance events following the Gondwanan breakup. To answer this question, we focused on the ziziphoid lineage of the buckthorn family, because extant ziziphoid taxa comprise tribes and genera exclusively or at least predominantly distributed in the Southern Hemisphere (Australia, Africa, and South America). Location World‐wide. Methods We generated a DNA alignment of 26,989 bp (from plastid, mitochondrial, and nuclear genomes), comprising 575 taxa of Rhamnaceae and related families, including all major lineages within Rhamnaceae and closely related families. We used nine internal fossils to set constraints in our molecular dating analyses. We used ‘BioGeoBEARS’ in R to reconstruct ancestral areas in order to infer the impact of vicariance events on the ziziphoids caused by Gondwanan fragmentation. Results Our biogeographic analyses illustrate that the ziziphoid lineage was influenced by both long‐distance dispersal and Gondwanan breakup vicariance events. Yet, these vicariance events cannot explain all divergence events at the backbone of this lineage. Main conclusions Our study highlights that a taxon's distribution throughout the Northern Hemisphere can be the result of vicariance, but this process may be obliterated by more recent long‐distance dispersal (LDD). Our study also highlights that sufficiently old taxa may sometimes constitute better models to investigate the impact of Gondwanan‐driven vicariance than taxa with a current disjunct distribution in the Southern Hemisphere.

• Premise of the Study: Climatic and geological changes have been considered as major drivers of biological diversification. However, it has been generally assumed that lineages retain common environmental affinities, suggesting a limited capacity to switch their climatic niche. We tested this assumption with a study of the evolution of climatic niches in the Neotropical tree genus Cedrela (Meliaceae).• Methods: We combined distribution models of extant Cedrela with a dated molecular phylogeny based on one nuclear (ITS) and three plastid markers (psbA-trnH, trnS-G and psbB-T-N) to reconstruct the evolutionary dynamics of climatic niches. We calculated relative disparity of climatic tolerances over time to test for niche evolution within subclades or divergence between subclades and conservatism among closely related groups. Published fossil records and studies on paleosols were evaluated for the distribution and climatic conditions of extinct Cedrela.• Key results: The fossil record of Cedrela suggested a major biome shift from paratropical conditions into warm-temperate seasonal climates in the Early Oligocene of western North America. In the Miocene, Cedrela extended from North America (John Day Formation, Oregon, USA) to southern Central America (Gatún, Panama). Diversification in the early evolutionary history was mainly driven by changes in precipitation. Temperature had an increasing impact on ecological diversification of the genus from the Miocene onwards. Sister-species comparisons revealed that recent speciation events may be related to divergence of climatic tolerances.• Conclusions: Our study highlights the complexity of climatic niche dynamics, and shows how conservatism and evolution have acted on different temporal scales and climatic parameters in Cedrela.

Plastome genomics and phylogenomics are essential tools for understanding plant diversity and evolution. Here we report the complete plastomes of Polylepis australis and P. microphylla , two species of the Andean tree genus Polylepis which forms the world’s highest treelines, using a whole-genome sequencing approach. The assembled plastomes (ca. 155 kb) exhibit the typical quadripartite structure of angiosperms with highly conserved gene content and organization. A total of 117 unique genes (81 protein-coding, 32 tRNA, and 4 rRNA) were annotated in the assembled plastomes. Comparative analysis revealed significant differences from previously reported partial plastomes of Polylepis , which lacked one copy of the inverted repeat (IR) region due to the limitations of long-range PCR methods. Phylogenetic analysis of whole-plastome data of Rosaceae species across subfamilies using Maximum Likelihood (ML) confirmed the monophyly of Polylepis and its placement within the tribe Agrimonieae. Our results highlight the reliability of whole-genome sequencing for generating complete, high-quality plastome sequence information. This provides a foundation for broader phylogenomic studies across the genus to test species boundaries, evaluate hybridization events and evolutionary trajectories, and develop conservation and restoration strategies.

Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow—contributes significantly to overall diversity within mountain systems, but the origins of alpine plant diversity are poorly understood. Here, we quantify the processes that generate alpine plant diversity and their changing dynamics through time in Saxifraga (Saxifragaceae), an angiosperm genus that occurs predominantly in mountain systems. We present a time-calibrated molecular phylogenetic tree for the genus that is inferred from 329 low-copy nuclear loci and incorporates 73% (407) of known species. We show that upslope biome shifts into the alpine zone are considerably more prevalent than dispersal of alpine specialists between regions, and that the rate of upslope biome shifts increased markedly in the last 5 Myr, a timeframe concordant with a cooling and fluctuating climate that is likely to have increased the extent of the alpine zone. Furthermore, alpine zone specialists have lower speciation rates than generalists that occur inside and outside the alpine zone, and major speciation rate increases within Saxifraga significantly pre-date increased rates of upslope biome shifts. Specialisation to the alpine zone is not therefore associated with speciation rate increases. Taken together, this study presents a quantified and broad scale perspective of processes underpinning alpine plant diversity. The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga , a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.