Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize

Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Demonstration of local adaptation in maize landraces by reciprocal transplantation.

Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparisons between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (Q ST) was greater than neutral allele frequency differentiation (F ST) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces' native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits were stronger in the highland site than the lowland site, supporting their status as highland-adaptive. These results give substance to the long-held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America

Why dispersal should be maximized at intermediate scales of heterogeneity

Citation: Skelsey, P., . . . & Garret, K. (2013). Why dispersal should be maximized at intermediate scales of heterogeneity. Theoretical Ecology, 6(2), 203-211. https://doi.org/10.1007/s12080-012-0171-3Dispersal is a fundamental biological process that results in the redistribution of organisms due to the interplay between the mode of dispersal, the range of scales over which movement occurs, and the scale of spatial heterogeneity, in which patchiness may occur across a broad range of scales. Despite the diversity of dispersal mechanisms and dispersal length scales in nature, we posit that a fundamental scaling relationship should exist between dispersal and spatial heterogeneity. We present both a conceptual model and mathematical formalization of this expected relationship between the scale of dispersal and the scale of patchiness, which predicts that the magnitude of dispersal (number of individuals) among patches should be maximized when the scale of spatial heterogeneity (defined in terms of patch size and isolation) is neither too fine nor too coarse relative to the gap-crossing abilities of a species. We call this the “dispersal scaling hypothesis” (DSH). We demonstrate congruence in the functional form of this relationship under fundamentally different dispersal assumptions, using well-documented isotropic dispersal kernels and empirically derived dispersal parameters from diverse species, in order to explore the generality of this finding. The DSH generates testable hypotheses as to when and under what landscape scenarios dispersal is most likely to be successful. This provides insights into what management scenarios might be necessary to either restore landscape connectivity, as in certain conservation applications, or disrupt connectivity, as when attempting to manage landscapes to impede the spread of an invasive species, pest, or pathogen

Competition from unseen or unheard novel words: Lexical consolidation across modalities

Item does not contain fulltextIn four experiments we investigated the formation of novel word memories across modalities, using competition between novel words and their existing phonological/orthographic neighbours as a test of lexical integration. Auditorily acquired novel words entered into competition both in the spoken modality (Experiment 1) and in the written modality (Experiment 4) after a consolidation period of 24 h. Words acquired from print, on the other hand, showed competition effects after 24 h in a visual word recognition task (Experiment 3) but required additional training and a consolidation period of a week before entering into spoken-word competition (Experiment 2). These cross-modal effects support the hypothesis that lexicalised rather than episodic representations underlie post-consolidation competition effects. We suggest that sublexical phoneme-grapheme conversion during novel word encoding and/or offline consolidation enables the formation of modality-specific lexemes in the untrained modality, which subsequently undergo the same cortical integration process as explicitly perceived word forms in the trained modality. Although conversion takes place in both directions, speech input showed an advantage over print both in terms of lexicalisation and explicit memory performance. In conclusion, the brain is able to integrate and consolidate internally generated lexical information as well as external perceptual input.15 p