Biology subjects

Chaves, C.

Publications and source records attributed to Chaves, C..

3 recordsLinked to original sources

bioRxiv2024

Disparate demographic impacts of the Roman Colonization and the Migration Period in the Iberian Peninsula.

It has been unclear how the periods of Roman and later Germanic political control shaped the demography of the Iberian Peninsula and how Iberia differs in these respects from other parts of the Roman Empire. We report genome-wide data from 248 ancient individuals from the largely unsampled period 100-800 CE and co-analyze them with previously reported data. In the Roman era, we document profound demographic transformation, with an influx of people with ancestry from the Central and Eastern Mediterranean in all the areas under study and of North Africans, especially in central and southern Iberia. Germanic (Buri, Suebi, Vandals & Visigoths) and Sarmatian (Alans) took over political control beginning in the 5th century, and although we identify individuals with Germanic-associated ancestry at sites with Germanic-style ornaments and observe that such individuals were closely related across large distances as in the case of two siblings separated by 700 km, for Iberia as a whole, we observe high continuity with the previous Hispano-Roman population. The demographic patterns in Iberia contrast sharply with those in Britain, which showed the opposite pattern of little change in the Roman period followed by great change in the Migration period, and also from demographic patterns in the central Mediterranean where both periods were associated with profound transformation, raising broader questions about the forces that precipitated change over this time.

genomics↗

bioRxiv2024

Eco-Anthropological factors explaining forest patch use by 3 species of wild Atelid monkeys co-existing with a small-scale farming community in Northeastern Costa Rica, Central America

The main conservation risks for wild non-human primates (NHP) in Costa Rica, Mesoamerica, is deforestation and the allocation of lands for agriculture. This is because they result in a mosaic of forest patches that differ in size and ecological properties. NHP, being the vertebrates with the highest risk and rate of extinction, slowly adapt to this rapid environmental change, optimizing their metabolic costs to survive and reproduce. One way to balance these costs is to use forest patches depending on the benefits they provide, such as food, shelter, or social contact. To understand the possible environmental factors that predict the usage of a series of 8 connected forest patches by Ateles geoffroyi, Alouata paliatta, and Sapajus imitator we collected demographic, behavioral, climatological and other environmental data from 2018 until 2021. We used information-theoretic metrics to identify the factors that best explained the presence and behavior of the species of interest in the forest patches studied, and fit the data to a set of models built informed a priori. Using the best explanatory factors, we k-fold cross-validated 9 classifier algorithms to identify the best predictive models for the presence of the monkeys studied and their behavioral patterns given the data. Presence was highest in warmer, more humid days, especially when other groups were present in the same patch. Behavioral patterns were different in each patch; monkeys rested more often when other groups of the same species were present, and foraged more during warmer, more humid days, and smaller groups. Predictive models for the presence of the species studied, trained with the 3 best explanatory factors, reached an accuracy between 70-96%, with Gradient Boost Classifier performing the best. In contrast, behavioral patterns were more unpredictable, with the the algorithms tested only reaching between 43-51% accuracy, the AdaBoost Classifier being the best. Our findings suggest that the usage of the 8 forest patches monitored by the monkeys studied depends on patch characteristics, not related to size nor the presence of a reserve, by the presence of other NHP in the patch and the meteorological conditions. Further work on the ecological characteristics of these patches can clarify the mechanisms modulating behavioral patterns.

zoology↗

bioRxiv2020

Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were [≥] 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples. The approach can be easily adapted for other metabarcoding applications, such as biodiversity assessment, ecosystem health assessment and diet studies.

ecology↗