Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.

Manioc-also called cassava and yuca-is among the world's most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality.

Plant domestication and agricultural ecologies.

Plant life defines the environments to which animals adapt and provides the basis of food webs. This was equally true for hunter-gatherer economies of ancestral humans, yet through the domestication of plants and the creation of agricultural ecologies based around them, human societies transformed vegetation and transported plant taxa into new geographical regions. These human-plant interactions ultimately co-evolved, increasing human population densities, technologies of farming, and the diversification of landraces and crop complexes.

Two domestications for grapes.

Glacial cycles and wild adaptations shaped grape domestication and the rise of wine.

A stepwise route to domesticate rice by controlling seed shattering and panicle shape.

Asian rice ( L.) is consumed by more than half of the world's population. Despite its global importance, the process of early rice domestication remains unclear.

A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication.

Most models of selection incorporate some notion of environmental degradation where the majority of the population becomes less fit concerning a character resulting in pressure to adapt. Such models have been variously associated with an adaptation cost, the substitution load. Conversely, adaptative mutations that represent an improvement in fitness in the absence of environmental change have generally been assumed to be associated with negligible cost.

Emerging evidence of plant domestication as a landscape-level process.

The evidence from ancient crops over the past decade challenges some of our most basic assumptions about the process of domestication. The emergence of crops has been viewed as a technologically progressive process in which single or multiple localized populations adapt to human environments in response to cultivation. By contrast, new genetic and archaeological evidence reveals a slow process that involved large populations over wide areas with unexpectedly sustained cultural connections in deep time.

Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava.

The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only c. 6 million years ago have significantly complicated previous phylogenetic analyses.

The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae).

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied.

Archaeological Central American maize genomes suggest ancient gene flow from South America.

Maize ( ssp. ) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal.

Microsatellite marker development in the crop wild relative using genome skimming.

Premise: Nuclear microsatellite markers were developed for , the sister species of the crop , to provide molecular genetic tools for the investigation of genetic diversity and structure.

Methods And Results: Fifty microsatellite loci were identified in by means of genome skimming, and 44 loci successfully amplified. Of these, 16 loci evenly spread across the reference nuclear genome were used for genotyping six populations.

Guano morphology has the potential to inform conservation strategies in British bats.

Bats are primary consumers of nocturnal insects, disperse nutrients across landscapes, and are excellent bioindicators of an ecosystem's health, however four of the seventeen Great British species are listed as declining. In this study we aim to investigate the link between bat guano morphology and diet, specifically looking at the ability to predict 1) species, 2) dietary guild, and 3) bat size, using guano morphology alone. Guano from 16 bat species sampled from across Great Britain were analysed to determine various morphological metrics.

A domestication history of dynamic adaptation and genomic deterioration in Sorghum.

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia.

Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production.

After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture.

A re-evaluation of the domestication bottleneck from archaeogenomic evidence.

Domesticated crops show a reduced level of diversity that is commonly attributed to the "domestication bottleneck"; a drastic reduction in the population size associated with subsampling the wild progenitor species and the imposition of selection pressures associated with the domestication syndrome. A prediction of the domestication bottleneck is a sharp decline in genetic diversity early in the domestication process. Surprisingly, archaeological genomes of three major annual crops do not indicate that such a drop in diversity occurred early in the domestication process.

Geographic mosaics and changing rates of cereal domestication.

Domestication is the process by which plants or animals evolved to fit a human-managed environment, and it is marked by innovations in plant morphology and anatomy that are in turn correlated with new human behaviours and technologies for harvesting, storage and field preparation. Archaeobotanical evidence has revealed that domestication was a protracted process taking thousands of plant generations. Within this protracted process there were changes in the selection pressures for domestication traits as well as variation across a geographic mosaic of wild and cultivated populations.

Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment.

The recovery of ancient RNA from archeological material could enable the direct study of microevolutionary processes. Small RNAs are a rich source of information because their small size is compatible with biomolecular preservation, and their roles in gene regulation make them likely foci of evolutionary change. We present here the small RNA fraction from a sample of archeological barley generated using high-throughput sequencing that has previously been associated with localized adaptation to drought.

Uncovering the dispersion history, adaptive evolution and selection of wheat in China.

Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27 933 DArTseq (for 717 landraces) and 312 831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China.

Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific.

Background And Aims: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent.

A new model for ancient DNA decay based on paleogenomic meta-analysis.

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables.

Barley domestication: the end of a central dogma?

Genomic analysis of barley paints a picture of diffuse origins of this crop, with different regional wild populations contributing putative adaptive variations.

Archaeology. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago.

The Mesolithic-to-Neolithic transition marked the time when a hunter-gatherer economy gave way to agriculture, coinciding with rising sea levels. Bouldnor Cliff, is a submarine archaeological site off the Isle of Wight in the United Kingdom that has a well-preserved Mesolithic paleosol dated to 8000 years before the present. We analyzed a core obtained from sealed sediments, combining evidence from microgeomorphology and microfossils with sedimentary ancient DNA (sedaDNA) analyses to reconstruct floral and faunal changes during the occupation of this site, before it was submerged.

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant-hominin co-evolution back to the Pliocene.

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment.