Parallel domestication has been widely acknowledged but its genetic basis remains largely unclear. As an important rice ecotype, upland rice was assumedly domesticated multiple times in two rice subspecies (Indica and Japonica) and provides a feasible system to explore the genetic basis of parallel domestication. To uncover the genome‐wide pattern of genetic differentiation between upland and lowland rice and explore the parallelism of genetic changes during upland rice domestication, we obtained whole‐genome sequences of 95 rice landraces and yielded genome‐wide expression data for five tissues of representative accessions of upland and lowland rice. Our phylogenetic analyses confirmed multiple domestications of the upland ecotype in two rice subspecies. Genomic scans based on resequencing data identified substantial differentiation between the upland and lowland ecotypes with 11.4% and 14.8% of the genome diverged between the two ecotypes in Indica and Japonica, respectively. Further genome‐wide gene expression analyses found that 30% of effectively expressed genes were significantly differentiated between two ecotypes, indicating the importance of regulation changes in the domestication of upland rice. Importantly, we found that only 1.8% of differentiated genomes and 1.6% of differentially expressed genes were shared by upland Indica and upland Japonica, suggestive of largely unparallel genetic alterations during upland rice domestication. These findings not only provide new insights into the genetic basis of parallel domestication at the genome scale but could also facilitate genetic improvement and breeding of rice and crops in general.

This study attempts to understand the biogeographic history of the Western Ghats forests by investigating decoupling between phylogenetic and taxonomic diversity. We specifically test whether the deciduous forests have been recently established, whether the southern region was a refuge, and whether the deciduous and evergreen forest species have disparate evolutionary histories. We used species composition data from 23 forest types along the Western Ghats for all woody angiosperms above 10‐cm diameter at breast height. Forests were broadly grouped as either evergreen or deciduous. Mean phylogenetic distances corrected for species richness and mean phylogenetic beta diversity corrected for shared species were assessed using z‐scores from null distributions. Null distributions were generated by randomizing the species relationships on the phylogeny. We found that all evergreen forests showed a greater phylogenetic diversity as compared with null expectations. Deciduous forests showed the inverse pattern. Within the evergreen belt, there was a decreasing phylogenetic diversity from south to north, as predicted by the southern refuge hypothesis. The phylogenetic beta diversity across evergreen–deciduous forests was lesser than the null expectation, whereas it was much higher across forests within the evergreen belt. This study provides the first phylogenetic evidence for the antiquity of evergreen forests as well as the southern refuge hypothesis in the Western Ghats. The deciduous forests species have shared evolutionary histories with the evergreen forest species, suggesting multiple shifts between evergreen and deciduous states through the lineages. Conversely, the evergreen species exhibited a disparate evolutionary history across these forests, possibly owing to sharper ecological or climatic gradients.

The karst landform in southern China is renowned for its high levels of species diversity and endemism. Globally, karst ecosystems are under threat from unsustainable anthropogenic disturbance and climate changes and are among the most threatened ecosystems worldwide. In this study, we used the typical karst endemic genus in southern China, Primulina Hance, as a model to identify areas within the karst landform with high diversity and to investigate congruence between phylogenetic and species‐based measures of diversity. Using phylogenetic information and species distribution data, we measured geographical patterns of diversity with four metrics: species richness (SR), corrected weighted endemism (CWE), phylogenetic diversity (PD), and phylogenetic endemism (PE). Our results revealed a high spatial congruence among SR, PD, and PE, with hotspot areas identified in the Nanling Mountains (i.e., north Guangdong and northeast Guangxi) and southeast Yungui Plateau (i.e., north and southwest Guangxi), whereas the hotspots of CWE are comparatively uniform throughout the geographic extent. The categorical analysis of neo‐ and paleoendemism identified a pattern of mixed neo‐ and paleoendemism in numerous grid cells, suggesting that karst areas in southern China have acted as both “museums” and “cradles” of plant evolution. Conservation gap analysis of hotspots revealed that the majority of prioritized hotspots (>90%) of the genus are outside of protected areas, therefore indicating the limited effectiveness of national nature reserves for the karst flora. Overall, our results suggest that the karst flora merits more conservation attention and SR can be an effective surrogate to capture PD in conservation planning.

Accurate inference in phylogeography requires appropriate sampling strategies. Complex questions demand a large sample size at both the population and genetic levels to obtain precise reconstructions. This is the case of the phylogeographic history of Cistus monspeliensis, a plant that displays low plastid (cpDNA) diversity in the Mediterranean Basin but high diversity in the Canary Islands. Here, we aimed to identify Mediterranean refugial areas and to accurately quantify inter‐island colonization events in the Canaries. Using a previous study as starting point, we increased sample size in two ways: (i) additional sampling of plastid genetic markers (from 1041 to 1899 bp); and (ii) additional sampling of populations (from 47 to 69) in long‐term persistence areas suggested by species distribution modeling (SDM). The synergy between SDM and extended population sampling helped find higher genetic diversity. Our deeper phylogeographic sampling of C. monspeliensis revealed the following: (i) potential refugia in long‐term persistence areas with high cpDNA diversity in western Europe and the Canary Islands; and (ii) a significant increase (from 7 to 12) in the number of inferred inter‐island colonization events across the archipelago. Our results stress the usefulness of SDM to identify the genetic signature associated with potential refugial areas. We herein propose a field sampling approach based on SDM that, in combination with a larger cpDNA sampling, can help answer a wide array of phylogeographic questions, such as the location of Quaternary refugia and number of colonizations across archipelagos.

Fungi are essential components of all terrestrial ecosystems. Despite the crucial ecological role of soil fungi in grasslands, knowledge about fungal community diversity and structure in Mediterranean meadow habitats is still fragmentary. We analyzed macrofungal communities in three geographically distinct Mediterranean montane calcareous grasslands and surrounding forests, by means of fruit body surveys. We investigated a number of biotic and abiotic factors influencing the studied fungal communities, including plant species composition. Out of 6365 fruit bodies, a total of 268 species belonging to 84 genera were found. In general, there was a significant correlation between plant species richness and fungal richness. Variation in vegetation and plant community structure accounted for approximately 20% of variance in fungal community structure. Tree and shrub vegetation played a dominant role in shaping the analyzed fungal communities, both in meadows and surrounding forests, with particular influence on ectomycorrhizal, litter, and lignicolous saprotrophic fungi. Fungal biodiversity in the studied meadows was increased by the presence of tree and shrub species from the adjacent forests, but was reduced by the increasing vegetation cover.

Allopolyploidization usually causes prominent genomic and transcriptional changes, and consequently, promotes the occurrence of phenotypic modifications and/or novelties. The tetraploid Achillea alpina L. species complex in the daisy family has been clearly studied concerning genetic variations and parentage. Population genetic data point to their progenitors as the diploid A. acuminata (Ledeb.) Sch. Bip. and A. asiatica Serg., and show that they have kept two distinct parental genomes relatively intact. Phenotypically, this complex displays a range of leaf form variation between the parental species. To better understand the source of variation at the transcriptional level of the allotetraploid species, we undertook morphological and gene expression analyses with regard to leaf dissection patterns. Morphometrics of leaf traits were carried out on two members of the tetraploid complex, A. alpina and A. wilsoniana Heimerl ex Hand.‐Mazz. and their diploid progenitor species, A. acuminata and A. asiatica. In parallel, the expression patterns of a dozen leaf dissection‐related genes were detected using reverse transcription real‐time quantitative polymerase chain reaction (RT‐qPCR) method. In the allotetraploid species, important leaf dissection‐related genes, such as NAM and PIN, were expressed at the intermediate level between the two diploid species. In general, most of the genes examined in the allotetraploids were expressed at mid‐parent levels or close to one of the parental species. Considering the relative contribution of parental homeologs to the allotetraploids, there is no consistent pattern among the genes analyzed. Overall, lack of transgressive expression of leaf dissection‐related genes could be correlated with the intermediate leaf phenotypes of the allotetraploids A. alpina and A. wilsoniana between their parental species.

Phylogeographic and evolutionary studies are necessary to establish solid taxonomic treatments and to implement effective conservation programs. Unfortunately, a well‐argued and well‐founded taxonomic framework is still lacking for some Mediterranean taxa. This is the case of Arenaria section Pseudomoehringia, a group that currently comprises three species endemic to the Iberian Peninsula (A. funiculata, A. suffruticosa, and A. tejedensis) and A. glochidisperma, which is restricted to the Rif mountains, North Africa. However, the taxonomic boundaries and phylogenetic relationships among these species are still uncertain. To explore the evolutionary history and phylogeographic patterns within this section, analyses based on nuclear (amplified fragment length polymorphism and internal transcribed spacer) and plastid DNA markers (psbA‐3’ trnK‐matK and rps16) were performed. Our study has confirmed the monophyly of the section, in which two species are clearly identified (A. funiculata and A. glochidisperma) and an additional species complex (“A. suffruticosa + A. tejedensis complex”) is also supported as a monophyletic clade. The phylogeographic results point toward a dispersal event of a common ancestor of the group from the Iberian Peninsula, giving rise to A. glochidisperma in North Africa. Moreover, A. funiculata and A. glochidisperma are identified as closely related species edaphically differentiated across the Strait of Gibraltar. Our study indicates low levels of a recent gene flow among populations of the “A. suffruticosa + A. tejedensis complex,” which are genetically highly structured and suggest an isolation by distance pattern, probably due to a combination of ecological and geographic barriers. Furthermore, the taxonomic and conservation status of taxa included in Arenaria section Pseudomoehringia has been reviewed.

Conspecific weeds that permanently infest worldwide agroecosystems are evolved from their crop species. These weeds cause substantial problems for crop production by competing for resources in agricultural fields. Weedy rice represents such a conspecific weed infesting rice ecosystems, and causing tremendous rice yield losses owing to its strong competitiveness and abundant genetic diversity, likely resulted from its complex origins. Here, we report the use of chloroplast DNA (cpDNA) fingerprints to determine whether weedy rice is evolved from its wild (exo‐feral) or cultivated (endo‐feral) rice progenitor as the maternal donor in recent hybridization events. In addition, we also applied nuclear simple sequence repeat (SSR) markers to confirm the exo‐feral or endo‐feral origins of weedy rice accessions determined by the cpDNA fingerprints. We found that the studied weedy rice accessions evolved either from their wild or cultivated rice progenitor, as the maternal donor, based on the cpDNA network and structure analyses. Combined analyses of cpDNA and nuclear SSR markers indicated that a much greater proportion of weedy rice accessions had the endo‐feral origin. In addition, results from the genetic structure of nuclear SSR markers indicated that weedy rice accessions from the endo‐feral pathway are distinctly associated with either indica or japonica rice cultivars, suggesting their complex origins through crop–weed introgression. The complex pathways of origin and evolution could greatly promote genetic diversity of weedy rice. Therefore, innovative methods should be developed for effective weedy rice control.

Plant sigma factors (SIGs) are key regulators of chloroplast gene expression and chloroplast differentiation. Despite their functional importance, the evolutionary history of these factors remains unclear. Using newly available genomic and transcriptomic data, we undertook a detailed and comprehensive phylogenetic analysis of SIG homologues from land plants and algae. Our results reveal that plants have acquired sigma factors from ancestor cyanobacteria through endosymbiotic gene transfers, forming four major clades, namely, super‐SIG2 (SIG2/3/4/6/SIG2‐like), SIG1, SIG5, and SIGX. The super‐SIG2 clade was confirmed to have evolved from cyanobacterial SIGA factors, and a novel clade (SIGX) specific to non‐angiosperms was revealed here. Gene duplications (mainly whole genome duplications) within lineages and species have contributed to the expansion of sigma factors in plants, especially flowering plants. We hypothesize that plant sigma factors originated from different endosymbiotic ancestors and evolved diverse functions. This not only sheds new light on the evolution of plant SIG genes but also paves the way for understanding the functional diversification of these genes.

Orphan genes are genetic innovations that lack homologs in other lineages. Orphan genes can rapidly originate and become substantially functional, yet the mechanisms underlying their origins are still largely unknown in plants. Here, we investigated the origin of orphan genes in the Oryza sativa ssp. japonica “Nipponbare” genome using genome‐wide comparisons with 10 closely related Oryza species. We identified a total of 37 orphan genes in the Nipponbare genome that show short sequence lengths, elevated GC content, and absence of introns. Interestingly, half of the identified orphan genes originated by way of a distinctive mechanism that involved the generation of new coding sequences through independent and rapid divergence within the inserted transposable element. Our results provide valuable insight into genetic innovations in the model rice genome that formed on a very short timescale.

The modern genus Dacrycarpus (Endl.) de Laub. of the family Podocarpaceae, containing nine species, is mainly distributed in tropical mountain rainforests of the southwestern Pacific region, ranging from New Zealand to low‐latitude Asia. This genus has abundant fossil records in both hemispheres, but all the known megafossils were limited to Australasia and South America. Here we report on Dacrycarpus guipingensis sp. nov. from the Miocene Erzitang Formation of Guangxi, South China. This is the first megafossil of Dacrycarpus in the Northern Hemisphere. The new species is represented by mummified dimorphic foliage, ovuliferous shoots, and a male cone with in situ pollen. It resembles the extant Dacrycarpus imbricatus (Blume) de Laub., which is common in rainforests from southern China and northern Myanmar to Fiji. This paper presents the first data on the anatomical structure of seed cone and exine ultrastructure of Dacrycarpus in situ pollen grains from a fossil material by using computed tomography scanning and ultrathin sectioning. For comparative purpose, data on the pollen morphology and ultrastructure were obtained for modern D. imbricatus for the first time. The D. guipingensis fossils strongly suggest the Miocene arrival of Dacrycarpus in Asia from the Southern Hemisphere. Based on the modern ecological niche and related fossil elements, this fossil locality was probably covered by conifer–broad‐leaved mountain rainforests during the Miocene.

A new species of the Osmundaceae, Plenasium xiei sp. nov., is herein described from the Cretaceous of Northeast China. The specimens examined here represent the earliest unequivocal record of the extant genus Plenasium in Eurasia based on fossil rhizomes. The rhizome consists of a central stem with a mantle of petiole bases and adventitious roots. The stem contains an ectophloic‐dictyoxylic siphonostele and a two‐layered cortex. The C‐shaped leaf trace bears two protoxylem bundles at the point of separation from the stele. The pith is heterogeneous. The parenchymatous inner cortex is thinner than the sclerenchymatous outer cortex. Lobed sclerenchyma bands occur at the adaxial sides of the stem xylem strands, in the concavity of the leaf trace, and along the adaxial side of the vascular bundles of the petiole base. In distal petiole portions, the sclerenchyma band splits into several groups in the transverse view. Sclerenchyma rings are heterogeneous with an abaxial sclerenchymatous arc of thick‐walled fibers. Numerous sclerenchyma strands of thick‐walled fibers appear in the petiolar inner cortex and the stipular wing. These fossils provide unambiguous evidence for the existence of subgenus Plenasium of modern Plenasium by at least the Late Cretaceous, demonstrating the longevity of this extant subgenus. Altogether the leaf and rhizome fossil records of Plenasium indicate that this genus was widely distributed across North America and Eurasia from the Early Cretaceous to the Early Cenozoic, followed by a range restriction to Eurasia in the Late Cenozoic. Extant Plenasium species are only known from East and Southeast Asia.

The co‐occurrence of mutational events including substitutions and insertions–deletions (InDels) with oligonucleotide repeats has previously been reported for a limited number of prokaryotic, eukaryotic, and organelle genomes. In this study, the correlations among these mutational events in chloroplast genomes of species in the eudicot family Malvaceae were investigated. This study also reported chloroplast genome sequences of Hibiscus mutabilis, Malva parviflora, and Malvastrum coromandelianum. These three genomes and 16 other publicly available chloroplast genomes from 12 genera of Malvaceae were used to calculate the correlation coefficients among the mutational events at family, subfamily, and genus levels. In these comparisons, chloroplast genomes were pairwise aligned to record the substitutions and the InDels in mutually exclusive, 250 nucleotide long bins. Taking one among the two genomes as a reference, the coordinate positions of oligonucleotide repeats in the reference genome were recorded. The extent of correlations among repeats, substitutions, and InDels was calculated and categorized as follows: very weak (0.1–0.19), weak (0.20–0.29), moderate (0.30–0.39), and strong (0.4–0.69). The extent of correlations ranged 0.201–0.6 between “InDels and single‐nucleotide polymorphism (SNP)”, 0.182–0.513 between “InDels and repeat” and 0.055–0.403 between “SNPs and repeats”. At family‐ and subfamily‐level comparisons, 88%–96% of the repeats showed co‐occurrence with SNPs, whereas at the genus level, 23%–86% of the repeats co‐occurred with SNPs in same bins. Our findings support the previous hypothesis suggesting the use of oligonucleotide repeats as a proxy for finding the mutational hotspots.

Phylogenetic stemminess is one of the most popular metrics of tree shape among evolutionary biologists. The index was originally described by Fiala & Sokal (1985) as the proportion of the total length of the branches of a phylogenetic clade (including the subtending branch or “stem”) that is accounted for by the length of the subtending branch of the clade. Accordingly, phylogenies with high stemminess would show accumulation of speciation events toward the present, whereas those with low‐stemminess values would reflect the opposite pattern (i.e., speciation events skewed toward the root node, Fig. 1).

The dwarf dogwoods (subgenus Arctocrania) have been widely known to consist of three circumboreal species Cornus suecica, Cornus canadensis, and Cornus unalaschkensis. A fourth putative species was discovered from the northern Myanmar in 1937, but it had never been formally reported on. Here, we formally report the species on the basis of phylogenetic and morphological evidence and name it Cornus wardiana Rushforth & Wahlsteen (sp. nov.). We conducted phylogenetic and morphometric analyses to determine its evolutionary relationship and differentiation from the existing relatives. We dated the phylogeny using molecular data and conducted a biogeographic analysis to gain insights into the evolution and biogeography of the Arctic‐Sino‐Himalayan disjunction. The phylogenetic analysis used sequences of the nrITS and plastid matK and rbcL genes and included all four dwarf dogwoods and 20 other species representing the three other major lineages of Cornus and the outgroup. The morphometric analyses included 60 populations and 102 specimens of dwarf dogwood, representing the entire range of the subgenus. The results showed that C. wardiana diverged first within subgenus Arctocrania in the Miocene, from a wide‐spread ancestor. Results from principal component analysis and discriminant analysis also showed that the Myanmar samples are well separated from the others. Taken together, these results suggest that the dwarf dogwood lineage split from the big‐bracted dogwoods in Asia or Asia‐western North America during the late Paleocene and spread widely to form a Eurasia‐North America distribution; the Arctic‐Sino‐Himalayan disjunction was the result of southward migration in the Miocene followed by extinction in the intervening highland areas.