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. In this work, environmental assessments were conducted in the Port of Gijon, Northern Spain, using eDNA metabarcoding, and the gAMBI (genetics based AZTI Marine Biotic Index) was estimated. Results indicate a high/good ecological status within the port. However, nine non-indigenous species and five invasive species were found, and a modification of the gAMBI that includes species invasiveness was proposed: Blue-gNIS. The index was preliminary tested against existing validated indices such as gAMBI, BENTIX (based on the ecology of macroinvertebrates) and ALEX (based on the invasiveness of the species). Blue-gNIS classified the port in a good ecological status and showed its potential usefulness to achieve more complete water quality assessments of ports.

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. Their effects are studied in the Lidia cattle traditionally selected for agonistic behaviour compared with Spanish breeds showing tamed behaviour. Two different approaches, BayeScan and SelEstim, were applied using genotypic 50K SNP BeadChip data. Both procedures detected two genomic regions bearing genes previously related to behavioural traits. The frequencies of the selected allele in these two regions in Lidia breed were opposite to those found in the tamed breeds. In these genomic regions, several putative genes associated with enriched metabolic pathways related to the behavioural development were identified, as neurochondrin gene (NCDN) or glutamate ionotropic receptor kainate type subunit 3 (GRIK3) both located at BTA3 or leucine-rich repeat and Ig domain containing 2 (LINGO2) and phospholipase A2-activating protein (PLAA) at BTA8.

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). In addition, all the significant correlations found in this work were negative, indicating that heterozygotes had lower fitness than their homozygote counterparts. Marker location could not explain the observed HFCs. Evidence of inbreeding, outbreeding or population and family structuring was not found in this work. The presence of undetected general effects that may lead to the appearance of HFCs, however, cannot be ruled out. These results seem to be best explained by the occurrence of local effects (due to linkage) or even by possible direct locus advantages.

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 0.49 to 0.63), which fully agrees with previous estimates for this breed. The genetic correlations between EW and SW were 0.86, and lower between EW and LW at 0.543 to 0.622, using MAM and RRM models, respectively. Ranking of sires displayed changes depending on age at weaning of their offspring, which could explain the modest genetic progress reached using MAM evaluation. The first 2 eigenvalues of the random regression coefficient matrix explained 66 and 30% of the genetic variance, which implies important genetic variation underlying the form of the growth curve of the animals during the weaning period. The evaluation of sires according to the official method, as currently carried out by the breeders' association (WW adjusted previously to the age of 180 d), does not exploit the genetic differences in response to their production system where the calf is weaned at variable ages.

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. Linkage studies in outbred populations have traditionally exploited half-sib family designs; within the animal production context, half-sibships provide large families that are highly suitable for DNA pooling. Estimators for QTL position and effect have been proposed that make use of information from flanking markers. We present formulas derived by the delta method for the asymptotic variance of these estimators.

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. The study of genetic linkage was its first goal, though a design so general as possible has been meant. Fuzzy-valued phenotypes are handled by means of fuzzy numbers. AVAILABILITY: ftp://carleos.etsiig.uniovi.es/pub/falin ftp://fisher.ciencias.uniovi.es/pub/falin ftp://bellman.ciencias.uniovi.es/pub/falin Licensed under the GNU General Public License version 2 (see http://www.gnu.org/licenses/gpl.html).

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. Simulations showed that a relatively low number of marker systems (e.g. 20) are enough to accept the hypothesis of sib parentage with a reasonable power for usual significance levels, but that a higher number would be necessary if full-sib against half-sib parentage is the contrast to be carried out. The effect of sampling variation on the allele frequencies on power calculations is also analysed.

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. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams.

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 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean F(st) = 0.07; P<0.01). Five different genetic distances were computed and compared with no correlation found to be significantly different from 0 between distances based on the effective size of the population and those which use the size of the alleles. The Weitzman recursive approach and a multivariate analysis were used to measure the contribution of the breeds diversity. The Weitzman approach suggests that the most important breeds to be preserved are those grouped into two clusters: the cluster formed by the Mirandesa and Alistana breeds and that of the Sayaguesa and Tudanca breeds. The hypothetical extinction of one of those clusters represents a 17% loss of diversity. A correspondence analysis not only distinguished four breed groups but also confirmed results of previous studies classifying the important breeds contributing to diversity. In addition, the variation between breeds was sufficiently high so as to allow individuals to be assigned to their breed of origin with a probability of 99% for simulated samples.

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. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from the Balearic Islands breeds and among the former only two form a clear clustering, while the rest of Atlantic breeds (Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.