Biology subjects

Plaza, M.

Publications and source records attributed to Plaza, M..

4 recordsLinked to original sources

bioRxiv2026

Expanded unbiased population-genomic summary statistics in pixy

Estimates of population-genetic summary statistics are often computed from variant-only VCFs, which commonly omit invariant sites (i.e. sites with only homozygous reference genotypes across all samples). However, these sites are critical for correctly estimating per site statistics such as nucleotide diversity ({pi}) and between population divergence (dxy). Our software pixy addressed this issue by providing support for computing statistics directly from "all-sites" VCFs that encode invariant positions explicitly (Korunes and Samuk 2021). pixy has since been widely adopted and used in a large variety of population genetic studies. Here we present a major update to pixy, which expands the original tool in four major areas. First, we provide implementations of new estimators of Wattersons {theta} and Tajimas D that are unbiased with respect to missing data. Secondly, we provide support for arbitrary ploidy and multiallelic sites. Third, we introduce a variety of optimizations, including multicore execution and a roughly order-of-magnitude reduction in per-worker memory footprint. Finally, we have broadly modernized our code base, test suite, and community contribution pathway. We validate these new features on simulated polyploid and multiallelic datasets, as well as two empirical datasets (one diploid and one autotetraploid), and benchmark the new multicore scaling. We position pixy relative to contemporary tools and discuss shared limitations of VCF-based estimators. By integrating support for diverse ploidies, allelic complexity, and genome-wide scale in one workflow, pixy provides the population genetics community with a straightforward tool for estimates of key summary statistics that are unbiased with respect to missing data. pixy remains completely open-source (MIT-licensed) and easily installable with the conda package management system.

bioinformatics↗

bioRxiv2021

Plant-associate interactions and diversification across trophic levels

Interactions between species are widely understood to have promoted the diversification of life on Earth, but how interactions spur the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled population genetic studies of host plants and intimately associated herbivores, parasites, and mutualists. We used Bayesian multiple regressions and the BEDASSLE modeling framework to test whether host and associate population structures were correlated over and above the potentially confounding effects of geography and shared environmental variation. We found that associates population structure often paralleled their hosts population structure, and that this effect is robust to accounting for geographic distance and climate. Associate genetic structure was significantly explained by plant genetic structure somewhat more often in antagonistic interactions than in mutualistic ones. This aligns with a key prediction of coevolutionary theory, that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions more often promote diversity via the effect of hosts geographic distribution on mutualists dispersal.

evolutionary biology↗

bioRxiv2020

Dispersal ability of Neophilaenus campestris, a vector of Xylella fastidiosa, from olive groves to over-summering hosts

Neophilaenus campestris is one of the recently identified spittlebugs (Hemiptera: Cercopoidea) able to transmit Xylella fastidiosa to olive trees. Considering its vector ability and the wide distribution of this species in Spain, N. campestris should be considered a serious threat to key crops that are vital for Spanish agriculture such as olive, almonds and grapevines. Migration and dispersal abilities of insect vectors have profound implications in the spread of vector-borne diseases. Thus, knowledge on the dispersal ability of N. campestris is essential to model, predict and limit the spread of the diseases caused by X. fastidiosa. A mark-release-recapture technique was developed to track between-field movements of N. campestris during its late spring migration from the ground cover grasses within olive groves to sheltered areas dominated by pine trees. An indoor assay showed that the fluorescent dust used for marking did not affect the survival nor the flying ability of N. campestris. Spittlebug adults captured in olive groves at Los Santos de la Humosa (Madrid, Spain) during late spring, 2019 were dusted with four fluorescent colours and released in four different locations. Six recapture samplings were performed 23 to 42 days after release in 12 different sites located within a maximum distance of 2.8 km from the release point. Results indicated that N. campestris was able to disperse a maximum distance of 2473 m in 35 days from the olive groves to areas dominated by pine trees. Furthermore, our flight mill studies also showed that N. campestris was able to fly long distances, reaching almost 1.4 km in an 82 minutes single flight. Moreover, we carried out a survey of directional movement of potential vectors of X. fastidiosa in an olive grove located in Villa del Prado (Madrid). We used yellow sticky bands, a Malaise trap and a vertical yellow sticky net to assess the directional movement from olive groves to surrounding managed and unmanaged areas. The captures obtained in the yellow sticky bands showed that spittlebugs dispersal from the olive grove to surrounding vegetation matched with the time when the ground cover dried out. The highest number of spittlebugs was captured in the border between the olive grove and a vineyard close by. Altogether, our findings suggest that eradication measures by rooting-up X. fastidiosa-infected and non-infected trees in a radius of 100 m are of limited value because vectors are able to disperse rapidly over distances much longer than expected.

ecology↗

bioRxiv2019

No evidence for kin recognition in a passerine bird.

Theory predicts that individuals behave altruistically towards their relatives. Hence, some form of kin recognition is useful for individuals to optimize their behaviour. In species displaying bi-parental care and subject to extra-pair matings, kin recognition theoretically allows cuckolded fathers to reduce their parental investment, and thus optimize their fitness, but whether this is possible remains unclear in birds. This study investigates the ability of male sparrows to recognize their own chicks, using a large cross-foster experiment, parental care as an indicator and House Sparrows (Passer domesticus) as a model organism. We cross-fostered chicks after hatching, and then expected that fathers would show a decrease in their parental efforts when tending to a clutch of unrelated offspring. However, there was no significant effect of relatedness on provisioning rates. This suggests that sparrows may not be capable of kin recognition, or at least do not display kin discrimination despite its apparent evolutionary advantage.

animal behavior and cognition↗