Joint effects of population size and isolation on genetic erosion in fragmented populations: finding fragmentation thresholds for management

Size and isolation of local populations are main parameters of interest when assessing the genetic consequences of habitat fragmentation. However, their relative influence on the genetic erosion of local populations remains unclear. In this study, we first analysed how size and isolation of habitat patches influence the genetic variation of local populations of the Dupont's lark (Chersophilus duponti), an endangered songbird. An information-theoretic approach to model selection allowed us to address the importance of interactions between habitat variables, an aspect seldom considered in fragmentation studies, but which explained up to 65% of the variance in genetic parameters. Genetic diversity and inbreeding were influenced by the size of local populations depending on their degree of isolation, and genetic differentiation was positively related to isolation. We then identified a minimum local population of 19 male territories and a maximum distance of 30km to the nearest population as thresholds from which genetic erosion becomes apparent. Our results alert on possibly misleading conclusions and suboptimal management recommendations when only additive effects are taken into account and encourage the use of most explanatory but easy-to-measure variables for the evaluation of genetic risks in conservation programmes.Peer Reviewe

Restricted gene flow and genetic drift in recently fragmented populations of an endangered steppe bird

Identifying the genetic processes derived from habitat fragmentation is critical for the conservation of endangered species. We conducted an integrated analysis of genetic patterns in the endangered Dupont’s lark (Chersophilus duponti), a circum-Mediterranean songbird threatened by the loss and fragmentation of natural steppes in recent decades. After sampling all the remaining Spanish populations and the two clos¬est North African ones, we found that the Mediterranean Sea acts as a major barrier against gene flow and that recent habitat fragmentation is isolating Spanish populations at different spatial scales. While we found a historical signal of gene flow among Spanish regions, a coalescent model supported that the ancestral panmictic population is evolving into several different units in the absence of current gene flow, genetic drift being more intense in the smaller and more isolated populations. Moreover, small-scale spa¬tial autocorrelation analyses showed that genetic differentiation is also acting within populations. The spatial genetic structure, significant levels of inbreeding and high relatedness within patches raise con¬cerns on the viability of most of the extant populations. We highlight the urgency for steppe patches to be protected, expanded and reconnected, considering the genetic clusters identified here rather than the previously considered eco-geographic regions occupied by the species. Meanwhile, translocations could be considered as a complementary, faster management action to attenuate the crowding and genetic effects of population fragmentation and the extinction risk of small populations without compromising the current local adaptations, culture diversity and genetic clusters already known for the species.Peer Reviewe

Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals

Bioprocesses conducted under conditions with restricted O2 supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative aerobe Escherichia coli, the microbial cell factory par excellence, has elaborate sensing and signal transduction mechanisms that respond to the availability of electron acceptors and alternative carbon sources in the surrounding environment. In particular, the ArcBA and CreBC two-component signal transduction systems are largely responsible for the metabolic regulation of redox control in response to O2 availability and carbon source utilization, respectively. Significant advances in the understanding of the biochemical, genetic, and physiological duties of these regulatory systems have been achieved in recent years. This situation allowed to rationally-design novel engineering approaches that ensure optimal carbon and energy flows within central metabolism, as well as to manipulate redox homeostasis, in order to optimize the production of industrially-relevant metabolites. In particular, metabolic flux analysis provided new clues to understand the metabolic regulation mediated by the ArcBA and CreBC systems. Genetic manipulation of these regulators proved useful for designing microbial cells factories tailored for the synthesis of reduced biochemicals with added value, such as poly(3-hydroxybutyrate), under conditions with restricted O2 supply. This network-wide strategy is in contrast with traditional metabolic engineering approaches, that entail direct modification of the pathway(s) at stake, and opens new avenues for the targeted modulation of central catabolic pathways at the transcriptional level

A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5′ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel

The signatures of Anthropocene defaunation: cascading effects of the seed dispersal collapse

Anthropogenic activity is driving population declines and extinctions of large-bodied, fruit-eating animals worldwide. Loss of these frugivores is expected to trigger negative cascading effects on plant populations if remnant species fail to replace the seed dispersal services provided by the extinct frugivores. A collapse of seed dispersal may not only affect plant demography (i.e., lack of recruitment), but should also supress gene flow via seed dispersal. Yet little empirical data still exist demonstrating the genetic consequences of defaunation for animal-dispersed plant species. Here, we first document a significant reduction of seed dispersal distances along a gradient of human-driven defaunation, with increasing loss of large- and medium-bodied frugivores. We then show that local plant neighbourhoods have higher genetic similarity and smaller effective population sizes when large seed dispersers become extinct (i.e., only small frugivores remain) or are even partially downgraded (i.e., medium-sized frugivores providing less efficient seed dispersal). Our results demonstrate that preservation of large frugivores is crucial to maintain functional seed dispersal services and their associated genetic imprints, a central conservation target. Early signals of reduced dispersal distances that accompany the Anthropogenic defaunation forecast multiple, cascading effects on plant populations

Polymorphisms associated with the risk of lung cancer in a healthy Mexican Mestizo population: Application of the additive model for cancer

Lung cancer is the leading cause of cancer mortality in Mexico and worldwide. In the past decade, there has been an increase in the number of lung cancer cases in young people, which suggests an important role for genetic background in the etiology of this disease. In this study, we genetically characterized 16 polymorphisms in 12 low penetrance genes (AhR, CYP1A1, CYP2E1, EPHX1, GSTM1, GSTT1, GSTPI, XRCC1, ERCC2, MGMT, CCND1 and TP53) in 382 healthy Mexican Mestizos as the first step in elucidating the genetic structure of this population and identifying high risk individuals. All of the genotypes analyzed were in Hardy-Weinberg equilibrium, but different degrees of linkage were observed for polymorphisms in the CYP1A1 and EPHX1 genes. The genetic variability of this population was distributed in six clusters that were defined based on their genetic characteristics. The use of a polygenic model to assess the additive effect of low penetrance risk alleles identified combinations of risk genotypes that could be useful in predicting a predisposition to lung cancer. Estimation of the level of genetic susceptibility showed that the individual calculated risk value (iCRV) ranged from 1 to 16, with a higher iCRV indicating a greater genetic susceptibility to lung cancer

Social factors related to the clinical severity of influenza cases in Spain during the A(H1N1)2009 virus pandemic

Background During the 2009 influenza pandemic, a change in the type of patients most often affected by influenza was observed. The objective of this study was to assess the role of individual and social determinants in hospitalizations due to influenza A (H1N1) 2009 infection. Methods We studied hospitalized patients (cases) and outpatients (controls) with confirmed influenza A (H1N1) 2009 infection. A standardized questionnaire was used to collect data. Variables that might be related to the hospitalization of influenza cases were compared by estimation of the odds ratio (OR) and 95% confidence intervals (CI) and the variables entered into binomial logistic regression models. Results Hospitalization due to pandemic A (H1N1) 2009 influenza virus infections was associated with non-Caucasian ethnicity (OR: 2.18, 95% CI 1.17 − 4.08), overcrowding (OR: 2.84, 95% CI 1.20 − 6.72), comorbidity and the lack of previous preventive information (OR: 2.69, 95% CI: 1.50 − 4.83). Secondary or higher education was associated with a lower risk of hospitalization (OR 0.56, 95% CI: 0.36 − 0.87) Conclusions In addition to individual factors such as comorbidity, other factors such as educational level, ethnicity or overcrowding were associated with hospitalization due to A (H1N1) 2009 influenza virus infections

Isolation and characterization of twenty polymorphic microsatellite markers for the endangered Dupont's lark (Chersophilus duponti) and cross-amplification in crested lark (Galerida cristata) and thekla lark (Galerida theklae)

We developed twenty microsatellite markers for the Dupont0 s lark (Chersophilus duponti), one of the most endangered European bird species, and tested in two related, more widely distributed species: crested lark (Galerida cristata) and thekla lark (Galerida theklae). 14 markers amplified and were polymorphic in Dupont0 s lark, 11 in crested lark and 6 in thekla lark. Microsatellite var- iability analyses were carried out on Dupont0 s lark (N = 23–28 individuals), crested lark (N = 9–10) and thekla lark (N = 14) populations in NE Spain showing moderate/high diversity, ranging from 1 to 13 alleles per locus. The mean allelic richness in Dupont’s lark was 6.21 and expected and observed heterozygosities ranged from 0.195 to 0.848 and from 0.071 to 0.889, respectively. Crested and thekla larks showed moderate/high diversity with a mean allelic richness of 4.36 and 4.67, respectively. This microsatellite set could be useful for population genetic studies of lark species widely differing in popula- tion fragmentation and conservation status across the Old World.Peer Reviewe

Sex determination of Dupont's lark Chersophilus duponti using molecular sexing and discriminant funtions

Aims: To test for sexual size dimorphism in external measurements of the Dupont's lark Chersophilus duponti, using a sample of live birds previously sexed by molecular techniques, and to obtain discriminant functions to easily sex birds in hand. Location: Birds were captured in different populations throughout Spain and Morocco. Most birds were trapped in the Ebro Valley (north-eastern Spain). Methods: A total of 317 adult and 42 yearlings were captured, banded, weighted and measured. A drop of blood was extracted for molecular sexing. After testing for sex differences in body size, discriminant function analyses were performed to identify the best traits for sexing both juveniles and adults. Results: All the measured parameters differed significantly between sexes in adult Dupont's larks. The best discriminant function accurately assigned sex to 99.0 % of the adults. The parameter which gave the best single factor correlation with sex was wing length, and the discriminant function with only this variable classified correctly 97.5 % of all the adults. An adult would be a male if wing length > 97 mm and a female if wing length < 97 mm. Sex had a significant effect on all parameters of juvenile individuals as well, except for bill depth. The best discriminant function, using wing length and cranium size, predicted correctly the sex of 97.6 % of the juveniles. Conclusions: Dupont's lark showed clear size dimorphism, males being heavier and larger than females in nearly all measured traits. From an evolutionary perspective, this difference could be explained by processes of intra- and inter-sexual competition, and even by potential costs linked to song flight in males. In any case, the discriminant functions produced using morphometry of individuals previously sexed by molecular procedures provided a highly accurate, inexpensive and fast method for sexing this threatened species in hand, which can help to interpret and understand many questions about its behavioural and population ecology.Peer Reviewe

Individual identification of endangered species using mosquito blood meals: a proof-of-concept study in Iberian lynx

Host identification from mosquito blood meals has been routinely used to identify the feeding preferences of insects in studies on transmission of vector-borne pathogens. Here, we identified for the first time the susceptibility of the endangered Iberian lynx (Lynx pardinus) to the attack of a wild mosquito female, the mosquito Anopheles atroparvus. Furthermore, we used 11 microsatellite markers to test for the utility of vertebrate DNA isolated from insect blood meals for individual identification of wildlife. Only the three smallest markers were successfully amplified; however, this genotype did not match with any of the previously genotyped individuals in southern Spain. These results support the use of DNA from mosquito blood meals as a non-invasive source of DNA and a powerful tool on epidemiological and conservation biology studies. However, as may be the case of other non-invasive sampling methods, the utility of this technique is probably limited by the quantity and quality of vertebrate DNAPeer reviewe