Multiple domestications of asian rice

In their recent Correspondence about our study showingthat there were three origins of Asian rice2, Huang and Han suggest that the methodology that we used to infer multiple domestications was flawed as it did not take account of the strong genetic bottleneck in japonica

The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models

The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte-dominant lineages, namely the hornworts, liverworts, and mosses, collectively known as bryophytes, and a sporophyte-dominant lineage, the vascular plants, or tracheophytes. In recent decades, the prevailing view of evolutionary relationships among these four lineages has been that the tracheophytes were derived from a bryophyte ancestor. However, recent phylogenetic evidence has suggested that bryophytes are monophyletic, and thus that the first split among land plants gave rise to the lineages that today we recognize as the bryophytes and tracheophytes. We present a phylogenetic analysis of chloroplast protein-coding data that also supports the monophyly of bryophytes. This newly compiled data set consists of 83 chloroplast genes sampled across 30 taxa that include chlorophytes and charophytes, including four members of the Zygnematophyceae, and land plants, that were sampled following a balanced representation of the main bryophyte and tracheophyte lineages. Analyses of non-synonymous site nucleotide data and amino acid translation data result in congruent phylogenetic trees showing the monophyly of bryophytes, with the Zygnematophyceae as the charophyte group most closely related to land plants. Analyses showing that bryophytes and tracheophytes evolved separately from a common terrestrial ancestor have profound implications for the way we understand the evolution of plant life cycles on land and how we interpret the early land plant fossil record.This work was supported by FCT (Portuguese Foundation for Science and Technology) through project grant PTDC/BIA-EVF/1499/2014 to CC and national funds through project UIDB/04326/2020, and from the operational programs CRESC Algarve 2020 and COMPETE 2020 through projects EMBRC.PT ALG-01-0145-FEDER-022121 and BIODATA.PT ALG-01-0145-FEDER-022231.info:eu-repo/semantics/publishedVersio

The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models

Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.UIDB/04326/2020, PTDC/BIA-EVF/1499/2014, EMBRC.PT ALG-01-0145-FEDER-022121, BIODATA.PT ALG-01-0145-FEDER-022231info:eu-repo/semantics/publishedVersio

Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces

Background: Understanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm. Results: The evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture. Conclusions: The discovery of population structure, combined with knowledge of associated phenotypes and environmental adaptations, enables a rational approach to identification of landraces that might be used as sources of germplasm for breeding programs. The population structure also enables hypotheses concerning the prehistoric spread and development of agriculture to be addressed

Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the fertile crescent

We used supernetworks with datasets of nuclear gene sequences and novel markers detecting retrotransposon insertions in ribosomal DNA loci to reassess the evolutionary relationships among tetraploid wheats. We show that domesticated emmer has a reticulated genetic ancestry, sharing phylogenetic signals with wild populations from all parts of the wild range. The extent of the genetic reticulation cannot be explained by post-domestication gene flow between cultivated emmer and wild plants, and the phylogenetic relationships among tetraploid wheats are incompatible with simple linear descent of the domesticates from a single wild population. A more parsimonious explanation of the data is that domesticated emmer originates from a hybridized population of different wild lineages. The observed diversity and reticulation patterns indicate that wild emmer evolved in the southern Levant, and that the wild emmer populations in south-eastern Turkey and the Zagros Mountains are relatively recent reticulate descendants of a subset of the Levantine wild populations. Based on our results we propose a new model for the emergence of domesticated emmer. During a pre-domestication period, diverse wild populations were collected from a large area west of the Euphrates and cultivated in mixed stands. Within these cultivated stands, hybridization gave rise to lineages displaying reticulated genealogical relationships with their ancestral populations. Gradual movement of early farmers out of the Levant introduced the pre-domesticated reticulated lineages to the northern and eastern parts of the Fertile Crescent, giving rise to the local wild populations but also facilitating fixation of domestication traits. Our model is consistent with the protracted and dispersed transition to agriculture indicated by the archaeobotanical evidence, and also with previous genetic data affiliating domesticated emmer with the wild populations in southeast Turkey. Unlike other protracted models, we assume that humans played an intuitive role throughout the process.Natural Environment Research Council [NE/E015948/1]; Slovak Research and Development Agency [APVV-0661-10, APVV-0197-10]info:eu-repo/semantics/publishedVersio

Meeting the challenges facing wheat production: The strategic research agenda of the Global Wheat Initiative

Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper

Additional file 2: of Role of genetic introgression during the evolution of cultivated rice (Oryza sativa L.)

Supporting figures. Figure S1. Schematic summary of the data processing and analysis pipeline. Figure S2. Variants shared and fixed in cultivated groups. Alleles that are simultaneously fixed in indica, japonica and aus (counts shown on y axis) are always found in wild populations, usually with high allelic frequencies (x axis). Figure S3. Histogram of SNP densities. Histograms show the number of sites per 100 kb window used for the calculation of the introgression index shown on Fig. 4. Mean number of sites per window is shown for each dataset in corresponding colours. (PDF 119 kb

Data from: Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

Plants are the primary producers of the terrestrial ecosystems that dominate much of the natural environment. Occurring approximately 480 MYA (Sanderson 2003; Kenrick et. al. 2012), the evolutionary transition of plants from an aquatic to a terrestrial environment was accompanied by several major developmental innovations. The freshwater charophyte ancestors of land plants have a haplobiontic life cycle with a single haploid multicellular stage, whereas land plants, which include the bryophytes (liverworts, hornworts, and mosses) and tracheophytes (also called vascular plants, namely, lycopods, ferns, and seed plants), exhibit a marked alternation of generations with a diplobiontic life-cycle with both haploid and diploid multicellular stages and where the embryo remains attached to, and is nourished by, the gametophyte (Haig 2008). The interjection of a multicellular diploid phase into the land plant life cycle was an important adaptation that enabled long-distance dispersal via mitotic spores where water-borne male gametes have restricted motility in dry terrestrial environments. Despite the similarity among land-plant life-cycles, they differ in one significant aspect: in the three bryophyte groups, the haploid gametophytic stage is the dominant vegetative stage, whereas in vascular plants the diploid sporophyte dominates. A common assumption, and one implied by the tradition of referring to bryophytes as “lower plants” - in contrast to the “higher plants”, the tracheophytes - is that the bryophytes and their life-cycle are primitive (Kato and Akiyama 2005). However, without a strong phylogenetic hypothesis of land-plant relationships, it is not clear which (if either) of the gametophyte or sporophyte was the dominant ancestral vegetative state present in the earliest land plants (Renzaglia et al. 2007; Qiu et al. 2012). Early land plants have a relatively poor fossil record with few intermediate forms (Kenrick and Crane 1997; Wellman et al. 2003; Clarke et al. 2011), so most of the evidence for early land plant evolution has been based upon the patterns of morphological change that are implied by phylogenetic trees of relationships among extant land plant and algal groups. In this context, several recent studies based on large molecular data sets have converged upon a phylogenetic solution to land plant origins wherein tracheophytes are derived from bryophyte ancestors (Karol et al. 2001; Qiu et al. 2006; Gao et al. 2010; Karol et al. 2010; Chang and Graham 2011). In this hypothesis, the three bryophyte groups, namely liverworts, mosses, and hornworts, diverged sequentially and form a paraphyletic group with the hornworts sister to the tracheophytes. This phylogeny supports an intuitively elegant evolutionary trajectory whereby plants increased in morphological complexity from single-celled algae to seed plants via bryophyte intermediates (Karol et al. 2001; McCourt et al. 2004). Specifically, it implies that the gametophyte-dominant bryophyte life-cycle was ancestral among land plants and that the complex modular growth form of the vascular plant sporophyte evolved from the simplistic bryophyte sporophyte that consists only of a single growth module (Kato and Akiyama 2005; Barthélémy and Caraglio 2007)