Biology subjects

Vicente, M.

Publications and source records attributed to Vicente, M..

8 recordsLinked to original sources

bioRxiv2024

Spatial and seasonal biodiversity variation in a large Mediterranean lagoon using environmental DNA metabarcoding through sponge tissue collection

Ecosystem monitoring is a fundamental tool to avert biodiversity loss, gathering valuable information that can be used to develop conservation policies, evaluating management outcomes, and guiding science-based decision-making. The Mar Menor costal lagoon (South-East of Spain) has experienced episodes of eutrophication due to intensive agriculture and other human activities, causing mass mortalities of marine fauna. In this scenario, biodiversity monitoring is crucial to evaluate the status of fauna and flora and take appropriate measures. Here, our main objective was to assess faunal composition and its spatial and temporal structure associated with the pillars used to support the built recreational well-being facilities along the Mar Menor. We capitalised on the many sea sponges that settle on these structures by collecting tissue samples for subsequent extraction of filtered environmental DNA (i.e. natural sampler DNA, nsDNA) in northern and southern areas of the lagoon, both in spring and summer. We metabarcoded all samples at the cytochrome oxidase subunit I gene (COI), and reliably identified 76 taxa belonging to nine different phyla, with annelids, poriferans, molluscs and cnidarians being the richest groups. We detected emblematic species of threatened status, such as pipefishes (genus Syngnathus) and the piddock clam, Pholas dactylus, and others known to become invasive, such as the ascidians Styela canopus and Botrylloides niger, the barnacle Amphibalanus amphitrite, and the polychaetes Branchiomma bairdi and Branchiomma boholense. The use of common and widely distributed sponges as natural eDNA samplers allowed us to characterise both spatial and temporal diversity, further emphasizing the importance of this low-cost approach to monitoring biological communities in shallow coastal ecosystems.

ecology↗

bioRxiv2023

The genetic legacy of the expansion of Bantu-speaking peoples in Africa

With the largest genomic dataset to date of Bantu-speaking populations, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we shed fresh light on the expansion of peoples speaking Bantu languages that started [~]4000 years ago in western Africa. We have genotyped 1,740 participants, including 1,487 Bantu speakers from 143 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals. Our results show that Bantu speakers received significant gene-flow from local groups in regions they expanded into. We show for the first time that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the DRC as possible crossroads of interaction. Using spatially explicit methods and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial founder migration model. Finally, we discuss the utility of our dataset as an exhaustive modern-day African comparative dataset for ancient DNA studies. These new findings and data will be important to a wide range of disciplines from science and humanities as well as to the medical sector studying human genetic variation and health in African and African-descendant populations. One-sentence summaryA comprehensive genetic analysis of the expansion of people speaking Bantu languages reveals a complex history of serial founder events, variable levels of contact with local groups, and spread-over-spread events.

evolutionary biology↗

bioRxiv2022

aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow

Analysis of microbial data from archaeological samples is a rapidly growing field with a great potential for understanding ancient environments, lifestyles and disease spread in the past. However, high error rates have been a long-standing challenge in ancient metagenomics analysis. This is also complicated by a limited choice of ancient microbiome specific computational frameworks that meet the growing computational demands of the field. Here, we propose aMeta, an accurate ancient Metagenomic profiling workflow designed primarily to minimize the amount of false discoveries and computer memory requirements. Using simulated ancient metagenomic samples, we benchmark aMeta against a current state-of-the-art workflow, and demonstrate its superior sensitivity and specificity in both microbial detection and authentication, as well as substantially lower usage of computer memory. aMeta is implemented as a Snakemake workflow to facilitate use and reproducibility.

bioinformatics↗

bioRxiv2021

Cardioluminescence in transgenic zebrafish embryos: a calcium imaging tool to study drug effects and pathological modeling

The zebrafish embryo has emerged as an excellent model in cardiovascular research. The existing techniques to monitor Ca2+ in the heart based on fluorescent Ca2+ biosensors are limited due to phototoxicity and photobleaching. To overcome these issues, we have used bioluminescence. We generated a transgenic line expressing GFP-Aequorin in the heart, Tg(cmlc2:GA), and optimized an in vivo aequorin reconstitution protocol to improve the luminescence capacity. This allowed imaging Ca2+ in long duration recordings in embryos of 3 to 5 days post-fertilization. The analogs diacetyl h-coelenterazine and f-coelenterazine enhanced the light output and signal-to-noise ratio from the embryos. With this cardioluminescence model, we monitored the time-averaged Ca2+ levels and beat-to-beat Ca2+ oscillations. Changes in Ca2+ levels were observed by incubation with BayK8644, an L-type Ca2+ channel agonist, the channel blocker nifedipine, and {beta}-adrenergic blocker propranolol. Treatment of zebrafish embryos with terfenadine for 24 hours has been proposed as a model of heart failure. Tg(cmlc2:GA) embryos treated with terfenadine showed a 2:1 atrioventricular block and a decrease in the ventricular Ca2+ levels.

physiology↗

bioRxiv2020

Sleep deprivation triggers somatostatin neurons in prefrontal cortex to initiate nesting and sleep via the preoptic and lateral hypothalamus

Animals undertake specific behaviors before sleep. Little is known about whether these innate behaviors, such as nest building, are actually an intrinsic part of the sleep-inducing circuitry. We found, using activity-tagging genetics, that mouse prefrontal cortex (PFC) somatostatin/GABAergic (SOM/GABA) neurons, which become activated during sleep deprivation, induce nest building when opto-activated. These tagged neurons induce sustained global NREM sleep if their activation is prolonged metabotropically. Sleep-deprivation-tagged PFC SOM/GABA neurons have long-range projections to the lateral preoptic (LPO) and lateral hypothalamus (LH). Local activation of tagged PFC SOM/GABA terminals in LPO and the LH induced nesting and NREM sleep respectively. Our findings provide a circuit link for how the PFC responds to sleep deprivation by coordinating sleep preparatory behavior and subsequent sleep.

neuroscience↗

bioRxiv2019

Population history and genetic adaptation of the Fulani nomads: Inferences from genome-wide data and the lactase persistence trait

Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt. Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. Our findings further suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first Genome Wide Association study (GWAS) of the lactase persistence trait. We also further explored signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

evolutionary biology↗

bioRxiv2019

Patterns of African and Asian admixture in the Afrikaner population of South Africa

The Afrikaner population of South Africa are the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the "Coloured" populations of South Africa. Ancestry, social class, culture, sex ratio and geographic structure affected admixture patterns and caused different ancestry and admixture patterns in Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records estimated the non-European contributions into the Afrikaners to 5.5%-7.2%. To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization) we genotyped ~5 million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture among diverse groups during early colonial times might have counterbalanced the effects of a founding population with a small census size. SIGNIFICANCE STATEMENTAfrikaners are a southern African ethnic group primarily descended from colonial settlers (population ~2.8-3.5 million). Genome-wide studies might offer interesting insights into their ancestry, not the least due to South Africas history of segregationist laws known as "apartheid", resulting in an expectation of low levels of admixture with other groups. Originating from a small founder population, their genetic diversity is also interesting. In our genome-wide study of 77 Afrikaners we found their majority ancestry (average 95.3%) came from Europeans, but almost all Afrikaners had admixture from non-Europeans (Africans and Asians). Despite their small founding population, we found no signs of decreased genetic diversity. Admixture among diverse groups during colonial times might have counterbalanced effects of a small founding population.

evolutionary biology↗

bioRxiv2017

Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

genomics↗