The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection.

The effective population size (Ne) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in Ne across time using measures of genome diversity or linkage disequilibrium between markers. Directional selection is expected to reduce diversity and Ne, and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and recombination rate heterogeneity in the estimation of historical Ne. We also investigate the relationship between diversity parameters and Ne across the different regions of the genome using human marker data. We show that the estimates of historical Ne obtained from linkage disequilibrium between markers (NeLD) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of NeLD obtained for particular genomic regions do not correlate, or they do it very weakly, with recombination rate, nucleotide diversity, proportion of polymorphic sites, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that NeLD measures mainly reflect demographic changes in population size across generations.

Impact of population structure in the estimation of recent historical effective population size by the software GONE.

BACKGROUND: Effective population size (Ne) is a crucial parameter in conservation genetics and animal breeding. A recent method, implemented by the software GONE, has been shown to be rather accurate in estimating recent historical changes in Ne from a single sample of individuals. However, GONE estimations assume that the population being studied has remained isolated for a period of time, that is, without migration or confluence of other populations. If this occurs, the estimates of Ne can be heavily biased. In this paper, we evaluate the impact of migration and admixture on the estimates of historical Ne provided by GONE through a series of computer simulations considering several scenarios: (a) the mixture of two or more ancestral populations; (b) subpopulations that continuously exchange individuals through migration; (c) populations receiving migrants from a large source; and (d) populations with balanced systems of chromosomal inversions, which also generate genetic structure. RESULTS: Our results indicate that the estimates of historical Ne provided by GONE may be substantially biased when there has been a recent mixture of populations that were previously separated for a long period of time. Similarly, biases may occur when the rate of continued migration between populations is low, or when chromosomal inversions are present at high frequencies. However, some biases due to population structuring can be eliminated by conducting population structure analyses and restricting the estimation to the differentiated groups. In addition, disregarding the genomic regions that are involved in inversions can also remove biases in the estimates of Ne. CONCLUSIONS: Different kinds of deviations from isolation and panmixia of the populations can generate biases in the recent historical estimates of Ne. Therefore, estimation of past demography could benefit from performing population structure analyses beforehand, by mitigating the impact of these biases on historical Ne estimates.

A comparison of marker-based estimators of inbreeding and inbreeding depression.

BACKGROUND: The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (FLH1 and FLH2), VanRaden (FVR1 and FVR2), Yang and colleagues (FYA1 and FYA2), marker homozygosity (FHOM), runs of homozygosity (FROH) and estimates based on pedigree (FPED) in comparison with estimates obtained from IBD measures (FIBD). RESULTS: If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with FIBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with FIBD is generally obtained by FLH1 and the best estimator of ΔID is FYA2. The estimators FVR2 and FLH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with FIBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (FHOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (FROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (FPED) show a lower correlation with FIBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations. CONCLUSIONS: When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with FIBD and provide good estimates of ΔID. When base population allele frequencies are unknown, FLH1 is the marker frequency-based estimator that is most correlated with FIBD, and FYA2 provides the most accurate estimates of ΔID. Estimates from FROH are also very precise in most scenarios. The estimators FVR2 and FLH2 have the poorest performances.

Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium.

Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.

Highly pleiotropic variants of human traits are enriched in genomic regions with strong background selection.

Recent studies have shown the ubiquity of pleiotropy for variants affecting human complex traits. These studies also show that rare variants tend to be less pleiotropic than common ones, suggesting that purifying natural selection acts against highly pleiotropic variants of large effect. Here, we investigate the mean frequency, effect size and recombination rate associated with pleiotropic variants, and focus particularly on whether highly pleiotropic variants are enriched in regions with putative strong background selection. We evaluate variants for 41 human traits using data from the NHGRI-EBI GWAS Catalog, as well as data from other three studies. Our results show that variants involving a higher degree of pleiotropy tend to be more common, have larger mean effect sizes, and contribute more to heritability than variants with a lower degree of pleiotropy. This is consistent with the fact that variants of large effect and frequency are more likely detected by GWAS. Using data from four different studies, we also show that more pleiotropic variants are enriched in genome regions with stronger background selection than less pleiotropic variants, suggesting that highly pleiotropic variants are subjected to strong purifying selection. From the above results, we hypothesized that a number of highly pleiotropic variants of low effect/frequency may pass undetected by GWAS.

An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree.

The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (FUNI) or on the genomic relationships (FGRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (FHOM), homozygous-by-descent segments (FHBD), runs-of-homozygosity (FROH) or on the known genealogy (FPED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that FUNI and FGRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as FHBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, FPED was uncorrelated with locus-specific homozygosity.

Long-term exhaustion of the inbreeding load in Drosophila melanogaster.

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.

The value of genomic relationship matrices to estimate levels of inbreeding.

BACKGROUND: Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs. RESULTS: Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign. CONCLUSIONS: Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.

Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

BACKGROUND: The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. METHODS: Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. RESULTS: Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. CONCLUSIONS: Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes.

Use of a Humanized Anti-CD6 Monoclonal Antibody (Itolizumab) in Elderly Patients with Moderate COVID-19.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a recent outbreak of coronavirus disease (COVID-19). In Cuba, the first case of COVID-19 was reported on March 11, 2020. Elderly individuals with multiple comorbidities are particularly susceptible to adverse clinical outcomes in the course of SARS-CoV-2 infection. During the outbreak, a local transmission event took place in a nursing home in Villa Clara province, Cuba, in which 19 elderly residents tested positive for SARS-CoV-2. METHODS: Based on the increased susceptibility to cytokine release syndrome, inducing respiratory and systemic complications in this population, 19 patients were included in an expanded access clinical trial to receive itolizumab, an anti-CD6 monoclonal antibody. RESULTS: All patients had underlying medical conditions. The product was well tolerated. After the first dose, the course of the disease was favorable, and 18 of the 19 patients (94.7%) were discharged clinically recovered with negative real-time reverse transcription polymerase chain reaction test results at 13 days. After one dose of itolizumab, circulating IL-6 decreased within the first 24-48 h in patients with high baseline values, whereas in patients with low levels, this concentration remained over low values. To preliminarily assess the effect of itolizumab, a control group was selected among the Cuban COVID-19 patients that did not receive immunomodulatory therapy. The control subjects were well matched regarding age, comorbidities, and severity of the disease. The percentage of itolizumab-treated, moderately ill patients who needed to be admitted to the intensive care unit was only one-third of that of the control group not treated with itolizumab. Additionally, treatment with itolizumab reduced the risk of death 10 times as compared with the control group. CONCLUSION: This study corroborates that the timely use of itolizumab in combination with other antivirals reduces COVID-19 disease worsening and mortality. The humanized antibody itolizumab emerges as a therapeutic alternative for patients with COVID-19. Our results suggest the possible use of itolizumab in patients with cytokine release syndrome from other pathologies.

An anti-CD6 monoclonal antibody (itolizumab) reduces circulating IL-6 in severe COVID-19 elderly patients.

BACKGROUND: Since the COVID-19 outbreak an unprecedented challenge for healthcare systems around the world has been placed. In Cuba, the first case of COVID-19 was reported on March 11. Elderly with multiple comorbidities have been the most risky population. Although most patients present a mild to moderate disease, some have developed severe symptoms. One of the possible mechanisms underlying rapid disease progression is a cytokine storm, in which interleukin (IL) -6 seems to be a major mediator. Itolizumab is a humanized recombinant anti-CD6 monoclonal antibody (MAb), with the ability of reducing serum interferon gamma (INF-γ), tumour necrosis factor alpha (TNFα) and IL-6. Based on these previous results in patients with psoriasis and rheumatoid arthritis, an expanded access clinical trial was approved by the Cuban regulatory agency for COVID-19 critically, severely and moderately ill patients. RESULTS: We show here a short kinetic of IL-6 serum concentration in the first 24 COVID-19 patients treated with itolizumab. Most of patients were elderly with multiple comorbidities. We found that with one itolizumab dose, the circulating IL-6 decreased in critically and severely ill patients, whereas in moderately ill patients the values didn't rise as compared to their low baseline levels. CONCLUSION: These findings suggest that itolizumab could be an attractive therapeutic option to decrease the negative outcome of the cytokine storm in COVID-19 patients. TRIAL REGISTRATION: CECMED IIC RD-EC 179, RPCEC00000311. Registered 4 May 2020 - Retrospectively registered, http://rpcec.sld.cu/ensayos/RPCEC00000311-Sp or http://rpcec.sld.cu/trials/RPCEC00000311-En.

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster.

Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.

Variation in phenotypic resistance to gastrointestinal nematodes in hair sheep in the humid tropics of Mexico.

The objective of the study was to evaluate phenotypic resistance against gastrointestinal nematodes in Blackbelly, Pelibuey and Katahdin ewes before pregnancy in the humid tropics of Mexico. Individual faecal and blood samples were taken in 59 Pelibuey, 69 Blackbelly and 73 Katahdin ewes. The egg count per gram of faeces (EPG) of gastrointestinal nematodes (GINs) was determined. The percentage of packed cell volume (PCV) and body condition score (BCS) of each animal were also recorded. The ewes were segregated as susceptible, intermediate or resistant based on the EPG using the quartile method. The data were analysed using the general linear method, and the means between breeds were compared by Tukey's test. The relationships between the EPG, PCV and BCS were evaluated by Spearman correlation. The Katahdin ewes showed the highest EPG counts (3613.6 ± 5649) compared to the Blackbelly and Pelibuey ewes (576.1 ± 1009 and 56.8 ± 187, respectively, P < 0.01). The PCV values between breeds were similar (P > 0.05). The susceptible ewes had the highest EPG counts and the lowest PCV percentage (5069 ± 6404 and 22.8% ± 8.1% respectively) compared to the resistant ewes (P < 0.01). A higher percentage of Katahdin ewes were susceptible compared to the other breeds (P < 0.05). The main GIN species were Haemonchus contortus, Trichostrongylus colubriformis and Cooperia curticei. In conclusion, Katahdin ewes showed susceptibility to GIN compared to Blackbelly and Pelibuey ewes before the pregnancy period in the humid tropics of Mexico.

Prevalence of gastrointestinal nematode infections in goat flocks on semi-arid rangelands of northeastern Mexico.

The objective of this study was to determine the prevalence of gastrointestinal nematode (GIN) infection in goat flocks on semi-arid rangelands of northeastern Mexico (25° N, 350-400 mm annual precipitation). The study included 668 pluriparous goats from 18 herds in five municipalities of Coahuila and Nuevo Leon, Mexico. Five genetic groups were considered (predominance of Boer, Nubian, Alpine, Saanen, and Toggenburg). Fecal samples were taken from the rectum of each animal to determine the number of eggs per gram (EPG) of GIN. The prevalence of flocks with GIN infections was 88.9%. Similar results were observed for the number of goats infected in the flocks. The Alpine breed presented the highest prevalence and highest EPG loads of GIN, whereas Boer and Nubian were the genetic groups with the lowest (P < 0.05) EPG. There was a negative effect of GIN infection on the live weight of goats (P < 0.05). The GIN genera found were Trichostrongylus spp. and Haemonchus spp. It was concluded that in the goat flocks of the semi-arid zones of Mexico was found a high prevalence of infections with gastrointestinal nematodes. The municipality and the breed of the animals were factors that showed influence on this prevalence and the level of infection of the goats.

Can parallel ecological speciation be detected with phylogenetic analyses?

Distinguishing parallel divergence from vicariance scenarios is crucial to establish the determinism of natural selection in the formation of new species. It has been proposed that phylogenetic methods can be used to disentangle a single origin in allopatry and multiple origins in sympatry for ecological speciation. However, a key issue is to what extent introgression in a patchy environment may complicate the distinction between both origins through the analysis of variation at neutral markers. While divergence at environmentally-based selected loci retains the initial correlation with ecological variables, such association may be lost at neutral loci unlinked to any selected locus. Thus, neutral divergence might reflect in the long-term the molecular fingerprint of isolation by distance regardless of the model of speciation considered, and a question arises as to whether phylogenetic analyses of neutral markers are able or not to retrieve the signals acquired in the ancestral populations. Here, we use computer simulations to show that the detection of the original signal using a phylogenetic method strongly depends on the migration rates among populations. Recombination accelerates the loss of the initial phylogenetic signal, but this effect is rather small compared with the effect of migration, and only substantial when recombination is very large. For model species with reduced gene flow between distant populations and between populations adapted to different habitats, the phylogenetic approach is able to distinguish a single origin in allopatry from multiple origins in sympatry.

Effect of the combination of male effect with PGF2α on estrus synchronization of hair sheep in Mexican tropic.

The aim of this study was to evaluate the "male effect" at the end of protocol with prostaglandins (PG) on estrus synchronization of hair sheep during breeding season (November-December) in Yucatan, Mexico. Twenty female Pelibuey sheep (weighting 38.2 ± 1.6 kg and body condition score of 2.5 ± 0.5) were randomly distributed in two groups (n = 10). Group T1 (control, PG), two doses of 50 µg of cloprostenol with 12 days between applications were applied; in the second group T2 (PG-ME), ewes received the same PG protocol plus the introduction of a male at the end of treatment. The interval of end treatment-onset of estrus was analyzed using survival test; the number of sheep with presence/absence of estrus was analyzed using Fisher's exact test. Ewes in estrus for groups T1 and T2 were 5 vs. 8, respectively. No significant differences were found as regards the interval end of treatment-onset of estrus (P > 0.05), as well as in total proportion of ewes with estrus and likewise in the duration of it (P > 0.05). We conclude that the protocol based on double dose of PGF2α with interval of 12 days combined with the male effect is efficient to induce luteolysis and estrus synchronization in hair sheep.

Evaluation of different models to segregate Pelibuey and Katahdin ewes into resistant or susceptible to gastrointestinal nematodes.

This study evaluated four models based on the number of eggs per gram of faeces (EPG) to segregate Pelibuey or Katahdin ewes during the lactation period into resistant or susceptible to gastrointestinal nematodes (GIN) in tropical Mexico. Nine hundred and thirty EPG counts of Pelibuey ewes and 710 of Katahdin ewes were obtained during 10 weeks of lactation. Ewes were segregated into resistant, intermediate and susceptible, using their individual EPG every week. Then, data of every ewe was used to provide a reference classification, which included all the EPG values of each animal. Then, four models were evaluated against such reference. Model 1 was based on the 10-week mean EPG count ± 2 SE. Models 2, 3 and 4 were based on the mean EPG count of 10, 5 and 2 weeks of lactation. The cutoff points for the segregation of ewe in those three models were the quartiles ≤Q1 (low elimination) and ≥Q3 (high elimination). In all the models evaluated, the ewes classified as resistant had lower EPG than intermediates and susceptible (P < 0.001) while ewes classified as susceptible had higher EPG than intermediate and resistant (P < 0.001). According to J Youden test, models presented concordance with the reference group (>70 %). Model 3 tended to show higher sensitivity and specificity with the reference data, but no difference was found with other models. The present study showed that the phenotypic marker EPG might serve to identify and segregate populations of adult ewes during the lactation period. All models used served to segregate Pelibuey and Katahdin ewes into resistant, intermediate and susceptible. The model 3 (mean of 5 weeks) could be used because it required less sampling effort without losing sensitivity or specificity in the segregation of animals. However, model 2 (mean of 2 weeks) was less labour-intensive.

Allelic diversity for neutral markers retains a higher adaptive potential for quantitative traits than expected heterozygosity.

The adaptive potential of a population depends on the amount of additive genetic variance for quantitative traits of evolutionary importance. This variance is a direct function of the expected frequency of heterozygotes for the loci which affect the trait (QTL). It has been argued, but not demonstrated experimentally, that long-term response to selection is more dependent on QTL allelic diversity than on QTL heterozygosity. Conservation programmes, aimed at preserving this variation, usually rely on neutral markers rather than on quantitative traits for making decisions on management. Here, we address, both through simulation analyses and experimental studies with Drosophila melanogaster, the question of whether allelic diversity for neutral markers is a better indicator of a high adaptive potential than expected heterozygosity. In both experimental and simulation studies, we established synthetic populations for which either heterozygosity or allelic diversity was maximized using information from QTL (simulations) or unlinked neutral markers (simulations and experiment). The synthetic populations were selected for the quantitative trait to evaluate the evolutionary potential provided by the two optimization methods. Our results show that maximizing the number of alleles of a low number of markers implies higher responses to selection than maximizing their heterozygosity.

Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers.

Deep coalescence and the nongenealogical pattern of descent caused by recombination have emerged as a common problem for phylogenetic inference at the species level. Here we use computer simulations to assess whether AFLP-based phylogenies are robust to the uncertainties introduced by these factors. Our results indicate that phylogenetic signal can prevail even in the face of extensive deep coalescence allowing recovering the correct species tree topology. The impact of recombination on tree accuracy was related to total tree depth and species effective population size. The correct tree topology could be recovered upon many simulation settings due to a trade-off between the conflicting signals resulting from intra-locus recombination and the benefits of the joint consideration of unlinked loci that better matched overall the true species tree. Errors in tree topology were not only determined by deep coalescence, but also by the timing of divergence and the tree-building errors arising from an insufficient number of characters. DNA sequences generally outperformed AFLPs upon any simulated scenario, but this difference in performance was nearly negligible when a sufficient number of AFLP characters were sampled. Our simulations suggest that the impact of deep coalescence and intra-locus recombination on the reliability of AFLP trees could be minimal for effective population sizes equal to or lower than 10,000 (typical of many vertebrates and tree plants) given tree depths above 0.02 substitutions per site.