The genomic signature of wild‐to‐crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.)

The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties

The significance of prey avoidance behaviour for the maintenance of a predator colour polymorphism

The existence of conspicuous colour polymorphisms in animals provides an ideal opportunity to examine the mechanisms which determine genetic and phenotypic variation in populations. It is well known that directional and negative frequency-dependent selection by predators can influence the persistence of colour polymorphisms in their prey, but much less attention has been paid to the idea that prey behaviour could generate selection on predator colour morphs. In this study, we examine the role that avoidance behaviour by honeybees might play in selection on a colour-polymorphic sit-and-wait predator, the crab spider Synema globosum. In two field experiments, we offered flowers harbouring spiders of different colour morphs to foraging honeybees. In the first, we tested for a pre-existing propensity in honeybees to avoid one spider morph over another, and whether this behaviour is influenced by the flower species on which spiders hunt. In the second, we tested the ability of bees to learn to avoid spider morphs associated with a previous simulated attack. Our results suggest that honeybees do not impose strong directional selection on spider morphs in our study population, and that avoidance behaviour is not influenced by flower species. However, we find evidence that honeybees learn to avoid spiders of a colour morph that has previously been associated with a simulated attack. These findings are the first empirical evidence for a mechanism by which prey behaviour might generate negative frequency-dependent selection on predator colour morphs, and hence potentially influence the long-term persistence of genetic and phenotypic diversity in predator populations

Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. The assumption that the most abundant tandem repeat is the centromere DNA was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and in length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond ~50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution, including the appearance of higher order repeat structures in which several polymorphic monomers make up a larger repeating unit. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animals and plants. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes

An FPTAS for Stochastic Unbounded Min-Knapsack Problem

In this paper, we study the stochastic unbounded min-knapsack problem ($\textbf{Min-SUKP}$). The ordinary unbounded min-knapsack problem states that: There are $n$ types of items, and there is an infinite number of items of each type. The items of the same type have the same cost and weight. We want to choose a set of items such that the total weight is at least $W$ and the total cost is minimized. The \prob~generalizes the ordinary unbounded min-knapsack problem to the stochastic setting, where the weight of each item is a random variable following a known distribution and the items of the same type follow the same weight distribution. In \prob, different types of items may have different cost and weight distributions. In this paper, we provide an FPTAS for $\textbf{Min-SUKP}$, i.e., the approximate value our algorithm computes is at most $(1+\epsilon)$ times the optimum, and our algorithm runs in $poly(1/\epsilon,n,\log W)$ time.Comment: 24 page

Parallel altitudinal clines reveal trends in adaptive evolution of genome size in \u3ci\u3eZea mays\u3c/i\u3e

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes

Reproductive biology of Macleania rupestris (Ericaceae), a pollen-limited Neotropical cloud-forest species in Costa Rica

Sin abstractVicerrectoría de Investigación, Universidad de Costa Rica, MICIT-CONICYTUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biologí

The Genomic Signature of Crop-Wild Introgression in Maize

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes were particularly resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly informing our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies