Biology subjects

Castro, I.

Publications and source records attributed to Castro, I..

3 recordsLinked to original sources

bioRxiv2021

Evidence of post-domestication hybridization and adaptive introgression in Western European grapevine varieties

Grapevine (Vitis vinifera L.) is one of the most significant crops in the world. Todays richness in grapevine diversity results from a complex domestication history over multiple historical periods. Here, we employed whole genome resequencing to elucidate different aspects of the recent evolutionary history of this crop. Our results support a model in which a central domestication event in grapevine was followed by post-domestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties, which show large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by geneflow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.

plant biology↗

bioRxiv2021

The UCR Minicore: a valuable resource for cowpea research and breeding

Incorporation of new sources of genetic diversity into plant breeding programs is crucial for continuing to improve yield and quality, as well as tolerance to abiotic and biotic stresses. A minicore (the "UCR Minicore") composed of 368 worldwide accessions of cultivated cowpea has been assembled, having been derived from the University of California, Riverside cowpea collection. High-density genotyping with 51,128 SNPs followed by principal component and genetic assignment analyses identified six subpopulations in the UCR Minicore, mainly differentiated by cultivar group and geographic origin. All six subpopulations were present to some extent in West African material, suggesting that West Africa is a center of diversity for cultivated cowpea. Additionally, population structure analyses supported two routes of introduction of cowpea into the U.S.: (1) from Spain to the southwest U.S. through Northern Mexico, and (2) from Africa to the southeast U.S. via the Caribbean. Genome-wide association studies (GWAS) of important agronomic traits including flowering time, resulted in the identification of significant SNPs for all traits and environments. The mapping resolution achieved by high-density genotyping of this diverse minicore collection allowed the identification of strong candidate genes, including orthologs of the Arabidopsis FLOWERING LOCUS T. In summary, this diverse, yet compact cowpea collection constitutes a suitable resource to identify loci controlling complex traits, consequently providing markers to assist with breeding to improve this crop of high relevance to global food and nutritional security.

genetics↗

bioRxiv2020

Precision as a metric for acoustic survey design using occupancy or spatial capture-recapture

Passive acoustic surveys provide a convenient and cost-effective way to monitor animal populations. Methods for conducting and analysing such surveys, especially for performing automated call recognition from sound recordings, are undergoing rapid development. However, no standard metric exists to evaluate the proposed changes. Furthermore, most metrics that are currently used are specific to a single stage of the survey workflow, and therefore may not reflect the overall effects of a design choice. Here, we attempt to define and evaluate the effectiveness of surveys conducted in two common frameworks of population inference - occupancy modelling and spatially explicit capture-recapture (SCR). Specifically, we investigate precision (standard error of the final estimate) as a possible metric of survey performance, but we show that it does not lead to generally optimal designs in occupancy modelling. In contrast, precision of the SCR density estimate can be optimised with fewer experiment-specific parameters. We illustrate these issues using simulations. We further demonstrate how SCR precision can be used to evaluate design choices on a field survey of little spotted kiwi (Apteryx owenii). We show that precision correctly measures tradeoffs involving sampling effort. As a case study, we compare automated call recognition software with human annotations. The proposed metric captured the tradeoff between missed calls (8% loss of precision when using the software) and faster data through-put (60% gain), while common metrics based on per-second agreement failed to identify optimal improvements and could be inflated by deleting data. Due to the flexibility of SCR framework, the approach presented here can be applied to a wide range of different survey designs. As the precision is directly related to the power of detecting temporal trends or other effects in the subsequent inference, this metric evaluates design choices at the application level, and can capture tradeoffs that are missed by stage-specific metrics, thus enabling reliable comparison between different experimental designs and analysis methods.

ecology↗