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

Vývojové tendencie v rastlinnej výrobe na Slovensku po roku 2004 – regionálne diferenciácie

One of the key milestones of joining European Union was to decrease disparities within economical and social environment in Slovakia. On the contrary, disparities are still growing, also in agriculture. Structural changes in agriculture between 2004 and 2014 are explained based on several stages of development, leading to regional differentiations. Based on indicators of crop production such as – gross crop production, crop production (cereals, oil plants, potatoes, sugar beet and perennial fodder crops), production per one hectare of selected crops, per capita production of selected crops and per 1 hectare of agricultural land this paper shows trends in crop production in Slovakia between 2004 and 2014. Individual regions and their ranking in Slovakia are analysed based on the level NUTS (Nomenclature of territorial units for statistics) III (regions). The classification of development of indicators of crop production in regions of Slovakia in relation to the calculated average value of Slovak Republic from 2004 to 2014 is based on calculated average values for the monitored period. Selected stasticial methods (standard deviation, coefficient of variation, the ratio of the data set and the relative size of the data file) are applied to analyse, study and interpret development of regional disparities in crop production in Slovakia.I napriek tomu, že jedným zo základných atribútov vstupu Slovenska do Európskej únie (EÚ) bolo zníženie regionálnych disparít v ekonomickom a sociálnom prostredí, naďalej dochádza k ich prehlbovaniu, nevynímajúc ani poľnohospodárstvo. Štrukturálne zmeny, ktoré nastali v poľnohospodárstve v tomto období sa premietli do jeho vývoja vo viacerých oblastiach a navonok sa prejavili v regionálnych diferenciáciách. V príspevku pomocou zvolených ukazovateľov rastlinnej výroby – hrubá rastlinná produkcia, produkcia plodín (obilniny, olejniny, zemiaky, cukrová repa a viacročné krmoviny), hektárová úroda vybraných plodín, výroba vybraných plodín na 1 obyvateľa a na 1 ha poľnohospodárskej pôdy) poukážeme na vývojové tendencie v rastlinnej výrobe Slovenska v období rokov 2004 – 2014. Na úrovni regiónov NUTS (Nomenklatúra územných štatistických jednotiek) III (samosprávnych krajov) predstavíme postavenie jednotlivých krajov Slovenska v produkcii skúmaných plodín. Na základe vypočítaných priemerných hodnôt za sledované časové obdobie rokov klasifikujeme vývoj ukazovateľov rastlinnej výroby v krajoch Slovenska vo vzťahu k vypočítanej priemernej hodnote za SR v časovom horizonte rokov 2004 – 2014. S pomocou využitia zvolených štatistických metód (smerodajná odchýlka, variačný koeficient, pomer dátového súboru a relatívny rozsah dátového súboru) interpretujeme vývoj regionálnych disparít ukazovateľov v rastlinnej výrobe Slovenska

Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants

The file attached is the published version of the article. Revised LorP 22/5/2017©The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected]

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