Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain.

Rivers are crucial ecosystems supporting biodiversity and human well-being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms of taxonomic resolution and scalability. This study explores the application of DNA metabarcoding analysis in both bulk and environmental DNA (eDNA) samples for comprehensive assessment of macrozoobenthic biodiversity, detection of invasive and endangered species, and evaluation of river ecological status in northwestern Spain.

Inbreeding depression and runs of homozygosity islands in Asturiana de los Valles cattle breed after 30 years of selection.

Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree-based inbreeding coefficients. However, with the development of single-nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression.

Building on gAMBI in ports for a challenging biological invasions scenario: Blue-gNIS as a proof of concept.

The status of aquatic ecosystems has historically been monitored by the use of biotic indices. However, few biotic measures consider the presence of non-indigenous species as a sign of anthropogenic pollution and habitat disturbance even when this may seriously affect the metric scores and ecological status classifications of an environment. Today, biological invasions are currently one of the greatest threats to biodiversity and sustainable blue economies around the world.

Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas.

A set of five local bovine breeds in danger of extinction named Cachena, Caldelá, Limiá, Frieiresa, and Vianesa and included in the group of Morenas Gallegas are located in the Autonomous Community of Galicia at the Northwest of Spain. Local authorities launched a conservation plan at the end of the 21th century in order to preserve this important genetic reservoir. However, Morenas Gallegas bovine breeds never have been analyzed with genomic tools and this information may be crucial to develop conservation plans.

Detection of selection signatures for agonistic behaviour in cattle.

The identification of genomic regions including signatures of selection produced by domestication and its subsequent artificial selection processes allows the understanding of the evolution of bovine breeds. Although several studies describe the genomic variability among meat or milk production cattle breeds, there are limited studies orientated towards bovine behavioural features. This study is focused on mapping genomic signatures of selection which may provide insights of differentiation between neutral and selected polymorphisms.

Heterozygosity-fitness correlations in the gilthead sea bream Sparus aurata using microsatellite loci from unknown and gene-rich genomic locations.

Heterozygosity-fitness correlations (HFC) were assessed for a sample of a gilthead sea bream Sparus aurata population. Two hundred and seventy-one fish were genotyped at 22 known and novel microsatellite loci, from which correlations between the multilocus heterozygosity index (I(MLH) ) and various fitness traits (fork length, mass and specific growth rates) were calculated. Significant global HFCs were found in this sample (0·02 ≤r(2) ≤ 0·08).

Multi-trait and random regression approaches for addressing the wide range of weaning ages in Asturiana de los Valles beef cattle for genetic parameter estimation.

Weaning weight (WW) records of 24,066 Asturiana de los Valles beef cattle, including the progeny of 557 sires and 10,653 dams, were analyzed using a multitrait animal model (MAM) and a random regression model (RRM) in order to estimate the variance components and the breeding value of the animals. Three definitions of WW were used: early weaning (EW) for animals weaned before the age of 180 d; standard weaning (SW) for animals weaned between 180 and 240 d old; and late weaning (LW) for animals weaned between the ages of 240 and 365 d. The heritabilities (h(2)) were high (from 0.

Video microscopy as an alternative method for somatic cell count in milk.

This paper presents an alternative method to estimate somatic cell count (SCC) in cows' milk. SCC is an important indicator in the detection of inflammatory reactions within the udder in cows and Direct Optical Microscopy (DOM) is the present reference method for SCC but, owing to its dependence on human operators, it is extremely costly, time-consuming and potentially subjective. The industrial method of choice is Epifluorescence (EF), which has the potential for impressive throughput and acceptable precision, but requires huge inversions and handling of highly toxic reactives and waste.

Asymptotic variances of QTL estimators with selective DNA pooling.

Investigation on QTL-marker linkage usually requires a great number of observed recombinations, inferred from combined analysis of phenotypes and genotypes. To avoid costly individual genotyping, inferences on QTL position and effects can instead make use of marker allele frequencies. DNA pooling of selected samples makes allele frequency estimation feasible for studies involving large sample sizes.

Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations.

Motivation: Methods involving fuzzy theory have been rarely applied to genetics. We present an open platform for experimentation with fuzzy numbers as a tool to represent imprecise phenotypes in genetic modeling.

Results: A C++ library for simulation of genetic information transmission is introduced.

Sib-parentage testing using molecular markers when parents are unknown.

The formulae for computing the so-called Sib Index using codominant alleles for (1) full-sib and (2) half-sib parentage are given. Hypothesis testing is based on the distribution of conditional likelihood ratio or Bayes' factor. Thresholds for rejecting the null hypothesis and P-values were obtained in function of the number of alleles and their frequency distributions.

Genetic diversity measures of local European beef cattle breeds for conservation purposes.

This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.

Power analysis of QTL detection in half-sib families using selective DNA pooling.

Individual loci of economic importance (QTL) can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers). Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL.

The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data.

Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds.