The deciduous habit of northern temperate trees and shrubs provides one of the most obvious examples of convergent evolution, but how did it evolve? Hypotheses based on the fossil record posit that deciduousness evolved first in response to drought or darkness and preadapted certain lineages as cold climates spread. An alternative is that evergreens first established in freezing environments and later evolved the deciduous habit. We monitored phenological patterns of 20 species of Viburnum spanning tropical, lucidophyllous (subtropical montane and warm temperate), and cool temperate Asian forests. In lucidophyllous forests, all viburnums were evergreen plants that exhibited coordinated leaf flushes with the onset of the rainy season but varied greatly in the timing of leaf senescence. In contrast, deciduous species exhibited tight coordination of both flushing and senescence, and we found a perfect correlation between the deciduous habit and prolonged annual freezing. In contrast to previous stepwise hypotheses, a consilience of independent lines of evidence supports a lockstep model in which deciduousness evolved in situ, in parallel, and concurrent with a gradual cooling climate. A pervasive selective force combined with the elevated evolutionary accessibility of a particular response may explain the massive convergence of adaptive strategies that characterizes the world's biomes.

The ecology and genetic diversity of model yeast Saccharomyces cerevisiae prior to human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace where the most divergent natural lineage was discovered. Here, we extensively sampled the broad-leaf forests across this continental island to probe the ancestral species diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between natural lineages and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions which contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.

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Background Sino-Vietnamese limestone karsts (SVLK) are a biodiversity hotspot rich in endemic plant species associated with caves and cave-like microhabitats. Based on phylogenetic studies of Begonia sect. Coelocentrum , a species-rich and characteristic SVLK clade, geographic isolation caused by extensive and continuous karstification was proposed as the major driving force triggering population diversification and geographic speciation. To test this proposition, population genetics and phylogeography of Begonia luzhaiensis were investigated using EST-SSR markers and the chloroplast trnC - ycf6 intergenic spacer. Results F statistics, Bayesian clustering analysis, AMOVA, and PCoA of both data sets all indicated substantial population differentiation and significant isolation by distance. Nested clade phylogeographic analyses inferred that historical fragmentations have been prominent, congruent with Guangxi’s geohistory of karstification as well as suggesting a mountain chain in northeastern Guangxi could have also acted as a major geographic barrier. A Bayesian skyline plot (BSP) indicated a slight decline in effective population size at 75,000 years ago (75 Kya), coinciding with the last glacial period during which the increased aridity in East Asia had retarded karstification, negatively affecting the populations of B. luzhaiensis . However, BSP detected a continuous and further population decline until the present time even though summer monsoons have resumed since the end of the last glacial maximum. Conclusions The microevolution patterns of B. luzhaiensis support that limited gene flow would have greatly enhanced the effects of random genetic drift and has been a major factor promoting diversification in Begonia , highly congruent with previous proposition. Based our study, we further propose that the arrival of Paleolithic Homo sapiens whose activities centered around limestone caves could have had further impacts on the populations of B. luzhaiensis , resulting in additional population decline. Further habitat destruction could have resulted from the transition from hunter gathering to food-producing societies ca. 20–10 Kya and the development of agriculture ca. 10 Kya in South China. Implications of the current study for SVLK plant conservation are also discussed. Electronic supplementary material The online version of this article (10.1186/s40529-019-0267-9) contains supplementary material, which is available to authorized users.

Previous chromosome information is restricted to 13 species in the Asian Begonia sect. Diploclinium.Here we present the first chromosome counts of three species, as well as confirmed their chromosome numbers of five species. Among three species investigated for the first time, the chromosome number of 2n=18 and 2n=32 are new counts in the section. Additionally, we provide the karyotypes of eight species for the first time. Among ca. 135 species in sect. Diploclinium, chromosome numbers of 16 species are available together with the present and previous reports. Among 16 species, they show diverse chromosome numbers with 2n=18, 22, 24, 26, 30, 32, 36, 46, and 54. B. wenshanensis with 2n=18 is the lowest chromosome number in the section and the third lowest chromosome number in Begonia. We suggest that B. coptidimontana with 2n=32 is tetraploid origin with the basic chromosome number of x=8. We discussed the chromosome evolution in Begonia sect. Diploclinium.

Begonia sect. Baryandra is distributed mainly in the Philippines with a few species in Borneo and New Guinea. Previous chromosome information of sect. Baryandra has restricted to ca. 16 species and their karyotypes have never been investigated. Here we report the cytological investigations of 26 species of sect. Baryandra, including five karyotype analyses that are the first report in sect. Baryandra, 24 species were reported cytologically for the first time, and two species were re-examined. Incorporating previous and present studies, chromosome numbers of 40 of the 78 species in sect. Baryandra are now available. Except for some intraspecific variant counts of 2n=26 and 44, and a tetraploid number of 2n=56, 39 species have the chromosome number of either 2n=28 or 30. The karyotypic formula of the three investigated species is uniform as 2n=28=10m+18sm(st), and two as 2n=30=8m+22sm(st). Based on molecular phylogenetic relationships, ancestral state reconstruction suggests that 2n=30 is the most likely ancestral chromosome number of sect. Baryandra, with 2n=28 a derived number. Based on our and previous studies, the chromosome evolution in Begonia sect. Baryandra is discussed.

The alpine ecosystem is the only terrestrial biogeographic unit that is distributed globally. Studying phylogenetics of the plant species in this widespread ecosystem can provide insights into the historical biogeographic processes that have shaped the global biodiversity. The trans-Pacific disjunct alpine genus Oreomyrrhis (Apiaceae) was investigated using nrDNA ITS sequences to test the taxonomic and biogeographic hypotheses. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference revealed that species of Oreomyrrhis form a weakly supported monophyletic clade that is nested within Chaerophyllum sect. Chaerophyllum (subtribe Scandicinae, tribe Scandiceae). The optimal solutions of dispersal-vicariance analysis indicate that the ancestor of Chaerophyllum sect. Chaerophyllum (including Oreomyrrhis) was distributed in Eurasia and subsequently dispersed to North America and southern Pacific Rim. Based on dating using ITS sequence variation, these dispersal events were most likely recent, probably during late Tertiary to Quaternary. The structure of the ITS haplotype network suggests that a rapid range expansion via long-distance dispersal had been crucial in generating the trans-Pacific disjunction of Oreomyrrhis. Furthermore, evolution toward smaller mericarp size and a transition from outcrossing to selfing during Oreomyrrhis's evolution might have increased the chances for long-distance dispersal, facilitating its range expansion and occupation on alpine environments.

The Philippine island of Palawan is highly biodiverse. During fieldwork there in 2011 & 2014 we found five unknown species in the large genus Begonia. The species are similar in their rhizomatous stems, four-tepaled flowers, inferior two- or three-locular ovaries with bilamellate placentas, and are assignable to Begonia sect. Baryandra. Our observations support the recognition of these as five new species endemic to Palawan: B. elnidoensis, B. gironellae, B. quinquealata, B. tabonensis and B. tenuibracteata which are described here. The five new species were added to phylogenies based Bayesian analysis of nrDNA (ITS) and chloroplast DNA (ndhA, ndhF-rpl32, rpl32-trnL, trnC-trnD), along with 45 other allied ingroup species. A majority of the species show incongruent positions in the two phylogenies, with evidence of prevalent chloroplast capture. Models show chloroplast capture is more likely in plant populations with high levels of inbreeding following a reduction in selfing rate after hybridisation; we suggest that this is a possible explanation for the massive amount of chloroplast exchange seen in our phylogeny, as Begonia species often exist as small isolated populations and may be prone to inbreeding depression. Our data also indicate a level of nuclear genetic exchange between species. The high prevalence of hybrid events in Begonia is potentially an important factor in driving genomic change and species evolution in this mega-diverse genus.