The mechanism by which a new species arises and adapts to its environment is a fundamental question in evolutionary biology. Seed characteristics such as seed size and nutrient composition are important fitness-related traits and have been shown to vary greatly among populations and species. However, the significance of variation in seed traits in plant adaptation and speciation remains unclear. We carried out a population genetic study on nucleotide variation of one 11S seed storage protein gene (Pss) of Oryza rufipogon Griff. and O. nivara Sharma & Shastry, two closely related wild rice species. By comparatively examining the genetic variation pattern of the regulatory and coding regions of Pss and fragments of six reference loci across different chromosomes, we found significantly lower polymorphisms at coding regions of the gene (PssI) in O. nivara relative to O. rufipogon. Neutrality tests indicated that the reduction of polymorphisms at PssI in O. nivara was caused by positive selection rather than population demography, implying a role of selection on the 11S seed protein gene. Further phylogenetic and principal component analyses also support the hypotheses that the origin of O. nivara was associated with the adaptive divergence on the coding region of Pss. It is most likely that higher reproductive effort would be favored when O. nivara arose from O. rufipogon populations and adapted to the environment change.

Populus euphratica Olivier and P. pruinosa Schrenk are known for their tolerance to highly saline and arid habitats, and overlapping distribution. We examined interspecific differentiation and gene flow between these two species at six loci that encode vacuolar Na⁺/H⁺ exchanger genes. Interspecific divergence varied greatly between sampled loci and could collectively delimit the two species well. Simulations based on the isolation–migration model suggested gene flow primarily from P. euphratica into P. pruinosa. This asymmetrical gene flow may be related to the adaptive survival of the introgressed individuals. Our findings suggest that these species may have diverged in the presence of gene flow and that local adaptation may have played an important role in maintaining the distinct species lineages by restricting gene flow between them. Our results together indicate that interspecific divergence and gene flow differ greatly between members of the same gene family, possibly due to differential subfunctionalization and/or neofunctionalization during ongoing speciation of these two poplar species.

Truncated receptor ectodomains have been described for several classes of cell surface receptors, including those that bind to growth factors, cytokines, immunoglobulins, and adhesion molecules. Soluble receptor isoforms are typically generated by proteolytic cleavage of the cell surface receptor or by alternative splicing of RNA transcripts arising from the same gene encoding the full-length receptor. Both the epidermal growth factor receptor (EGFR) and the insulin receptor (INSR) families produce soluble receptor splice variants in vertebrates and truncated forms of insulin receptor-like sequences have previously been described inDrosophila. The EGFR and INSR ectodomains share significant sequence homology with each other suggestive of a common evolutionary origin. We discovered novel truncated insulin receptor-like variants in several arthropod species. We carried out a phylogenetic analysis of the conserved extracellular receptor L1 and L2 subdomains in invertebrate species. Although the segregation of insulin receptor-like L1 and L2 domains indicated that an internal domain duplication had occurred only once, the generation of truncated insulin receptor-like sequences has occurred multiple times. The significance of this work is the previously unknown and widespread occurrence of truncated isoforms in arthropods, signifying that these isoforms play an important functional role, potentially related to such isoforms in mammals.

Hainan, an island linking mainland East Asia and Southeast Asia, lay in one of the routes of early migration to East Asia. The largest indigenous group of Hainan is called Hlai, possibly direct descendants of the earliest migrants. However, there are no sufficient genetic data to assess the population history of Hainan Island. Here, we have analyzed mitochondrial DNA control-region and coding-region sequence variations in 566 Hlai individuals from all five subgroups, Ha, Gei, Zwn, Moifau, and Jiamao. Our results suggest three phases for the peopling of Hainan. The first phase represents the initial settlement of the island as part of the African dispersal approximately 50 000 years ago. The second phase reflects colonization events from mainland Asia before the Last Glacial Maximum, which was recorded by wide distributed lineages, such as F*, B4a, and D4a.The third phase reflects population expansions under lineages F1b, M7b, and R9b after the Last Glacial Maximum and Neolithic migrations in and out of Hainan Island. Selection also started to play a role during the last phase. We also detected different distributions between paternal Y chromosome and maternal mitochondrial DNA among isolated Hlai populations, which might be caused by sex-biased cultural practices.

Gene duplication and diversification is a significant aspect of gene and genome evolution, even though the evolutionary mechanism following duplication almost certainly varies by genes or gene families. We have identified three PISTILLATA (PI)-like genes, HoPI_1, HoPI_2, and HoPI_3, from basal angiosperm Hedyosmum orientale (Chloranthaceae) and found a functional divergence of these duplicate paralogs in the B-function process. However, the mechanism underlying the divergence of the three HoPI copies remains unclear. In this study, we carefully compared the coding sequence of the three duplicate HoPI paralogs, and investigated their evolutionary process after duplication. Molecular evolutionary analyses suggested that the coding sequence of the relatively recent duplicate paralogs HoPI_1and HoPI_3 may evolve under purifying selection, but the functional constraint that acted on the coding sequence of HoPI_2 may have been relaxed. Domain swapping and site-directed mutagenesis experiments further showed that HoPI_2 has lost class B-function activity through a gradual process of mutational degradation in MADS and I domains. Although we currently have no direct in vivo evidence that HoPI_2 has lost function in floral development, the relaxed selection, in combination with its inability to rescue pi-1 mutant phenotype, indicate that this distant paralog HoPI_2 might have been converted to be functionless in the B-function process. This study provides a detailed molecular characterization of duplicate PI lineage gene divergence in a single individual level, and our results suggest that mutations in the MI region are more likely to have negative effects on the biochemical activity of PI-like proteins.

The secondary cell wall in plant cells is a highly organized structure that provides mechanical support to the tissue and the entire plant body. Glycine soja, the presumed ancestor of domesticated soybean, differs from the domesticated soybean in an array of morphological characters. The remarkable difference is the stem phenotype, which is often attributed to the thickness of secondary cell walls. Hence, it is of great importance to understand the genetic basis underlying the regulation of secondary wall thickening in these two species. Here, we report that GlycineNST1A/B are functional orthologs of AtNST1/2, which have been shown to act as the master switches of secondary cell wall thickening. GlycineNST1A/B are preferentially expressed in organs undergoing secondary wall deposition, and GmNST1A/Bare expressed at twofold the level of GsNST1A/B in mature stem. The overexpression of GsNST1A/B disrupts overall plant development by inducing ectopic deposition of massive secondary walls in normally parenchyma cells in Arabidopsis. Furthermore, expression analyses suggest that the ectopic secondary wall is achieved by upregulating the expression of a series of cell wall-associated transcription factors and secondary wall biosynthetic genes. Together, these results indicate that GsNST1A/B, as the key regulators, are capable of activating the entire secondary wall biosynthetic pathway in Arabidopsis, and also suggest that the genetic circuit of secondary wall development is conserved between Fabaceae and Brassiaceae.

The phylogenetic position of the genus Hanabusaya was verified using the internal transcribed spacer (ITS) sequences data of 181 individuals of 176 taxa in Campanulaceae, including allied genera such as genus Campanula, Adenophora, Symphyandra, and Zeugandra. The phylogenetic analysis showed thatHanabusaya is more closely allied to Adenophora than to Symphyandra, Zeugandra, and Campanula. Accordingly, the connate anthers of Hanabusaya are considered to have evolved independently of Symphyandra or Zeugandra. However, Hanabusaya and sect. Remotiflorae of Adenophora were unresolved within a clade. Therefore, the relationship between Hanabusaya and its allies should be more accurately determined through a broader study on diverse genetic regions.

Allele variation of ten low-polymorphic enzyme-encoding genes were analyzed among 349 accessions of Aegilops tauschii Coss., 183 of ssp. tauschii and 166 of ssp.strangulata (Eig) Tzvelev, representing all the species area. The data obtained indicated that both of these subspecies had originated and occupied their areas in ancient times. In ssp. tauschii and ssp. strangulata geographic occurrence of rare allozymes was sporadic and rather even through the subspecies areas. The probability of finding a rare allele of some of the ten loci studied in Ae. tauschii accession was also similar in the two subspecies and made up 0.066 and 0.060 for ssp. tauschii and ssp. strangulata, respectively. In both ssp. tauschii and ssp. strangulata an accession was found (k-1954 and t-9¹s, respectively) having more than one rare allele. Both accessions are of Caucasian origin, indicating that Ae. tauschii originated in this geographic region. Geographic distribution of rare allozymes occurrences reveals that genetic exchange between ssp. tauschii and ssp. strangulata takes place. Also this distribution indicates that in Ae. tauschii the same allozymes could have originated independently in different local populations: there are examples when the same rare allele was found in local populations located geographically very far from one another and belonging to different subspecies. Therefore it seems that the genetic system of Ae. tauschii local populations are in stochastic steady state. This makes this species a perfect model object for the studies of genetic basis of adaptive divergence.

Ancient trees remaining in natural areas from once widespread forest due to overexploitation and habitat modification would naturally regenerate to form small isolated populations after the halting of disturbance. The genetic processes and consequence of this regeneration are generally unknown, which prevents the effective conservation and management of these populations. One such population, an Erythrophleum fordii population, is located in Dinghushan National Nature Reserve (China). Owing to the remarkably huge trunk of the sole ancient tree (KG) relative to the other individuals in the population, the local people and local tourism administration presume that this population has developed solely from KG. We found, using genetic diversity analyses, that contrary to this presumption, the population might have regenerated from several founders with diverse genetic backgrounds. Severe degradation of genetic diversity within the population did not take place, rather, it possessed the potential ability to maintain and recover gradually with population development. According to the results of simulations, we found that the longevity of tree species with iteroparity offers the potential to maintain genetic diversity in small isolated populations. The results from this study will benefit the restoration and conservation of the endangered species E. fordii, and of other congener species and tree species with similar life history traits.

Distyly is a genetically controlled flower dimorphism. Most species in Mussaenda are distylous or functionally dioecious. Mussaenda shikokiana Makino consisted of one floral morph only in the populations studied in southern China. The present study aimed at illuminating the characteristics of floral monomorphism in M. shikokiana, and elucidating the mechanism behind the evolution of monomorphism from distyly. We examined floral morphology in five natural populations across the species' distribution range. Experiments and observations on the floral biology, pollinating fauna, and breeding system were carried out in two to four natural populations. We also screened allozyme markers to estimate the degree of outcrossing. The results indicated that M. shikokiana was a self-compatible, partially autogamous species and pollinators were required to maximize seed set. Anthers dehisced and pollen showed the highest viability 8–12 h before flower opening, and stigmas were receptive in bud, resulting in bud-selfing. Pollen viability decreased sharply after flower opening, whereas stigma receptivity lasted to the third day. Pollinators including bees, butterflies, and hawkmoths visited the flowers of M. shikokiana frequently at the study sites. There was no significant difference among pollen tube growth rates in selfing and outcrossing; pollen tubes reached ovules within 16 h in all treatments, indicating lack of typical self-incompatibility or cryptic self-incompatibility. Our results suggested that M. shikokiana is a homostylous species, and that homostyly promoting self-pollination was selected in its evolutionary history.

There are 26 phylogenetic studies for Bromeliaceae based on different sources of evidence. Despite this broad phylogenetic coverage of Bromeliaceae, however, the available phylogenetic data display a scattered sampling, with little overlap among different types of evidence. The aim of this study is to integrate the available phylogenetic information of the Bromeliaceae in one hypothesis using a supertree. To test which of them integrates best the information for Bromeliaceae, nine supertree methods were employed: Avcon, MSS, MinFlip, MMC, MRP, PhySIC_IST, Robinson–Foulds Supertree, Sfit, and SuperFine. Supertrees were compared with a reference tree, generated from the maximum likelihood (ML) analysis of a supermatrix integrated by 120 taxa of Bromeliaceae and seven cpDNA regions. In order to select which method best reconstructs the most robust phylogeny, two different sets of source trees were used: (i) those generated from the analysis of each individual DNA regions; and (ii) four selected phylogenies (from the 26 published works). We used the consensus fork index, normalized partition metric, patristic distance coefficient, and the Shimodaira–Hasegawa test to compare supertrees with the reference tree. The best performing methods were used to construct a supertree using all phylogenies of Bromeliaceae. The SuperFine method generated the best supertree. The lack of overlapping among phylogenies was the major limiting factor for the integration of the phylogenetic information of Bromeliaceae. Nonetheless, supertree methods helped in the identification of poorly sampled groups, as well as to explore levels of agreement among published phylogenetic studies for Bromeliaceae.

The microsoroid ferns make up a large group in the family Polypodiaceae, easily characterized by the combination of at least partly clathrate rhizome scales and anastomosing reticulate venation. The diversification of this clade is poorly known, both because of unresolved generic delimitations and the lack of fossil records. In this work, we describe the first microsoroid macrofossil: Palaeosorum ellipticum sp. nov. F. M. B. Jacques & Z. K. Zhou. The fossil specimen, represented by part and counterpart, was found in the middle Miocene sediment of the Dajie Formation in Ailsohan, central Yunnan, southwest China. Epiphytic ferns belonging to Drynariaare found in different locations in Yunnan during the Pliocene. The fossil described in this study deepens the occurrence of epiphytic ferns in Yunnan back to the middle Miocene. It demonstrates that forests with complex ecological relationships have existed in southwest China for more than 10 million years.

The herbaceous lycopsid Drepanophycus minor sp. nov. is described from the late Mid Devonian Hujiersite Formation of Xinjiang, Northwest China. The new species is characterized by minor sized, falcate microphylls, and kidney-shaped sporangia, with rhizome, K-shaped branching, and developed lateral buds. Stomatal apparatuses are observed from the axis surface of the new species. The habit and the rhizome structure of D. minor are discussed.