Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers.

Behavioural and socio-cultural traits are recognized in the restriction of gene flow in species with high cognitive capacity and complex societies. This isolation by social barriers has been generally overlooked in threatened species by assuming disrupted gene flow due to population fragmentation and decline. We examine the genetic structure and ecology of the global population of the Critically Endangered red-fronted macaw (Ara rubrogenys), an endemic species to the inter-Andean valleys of Bolivia. We found a fine-scale genetic structuring in four genetic clusters. Genetic diversity was higher in wild compared to captive-bred macaws, but similar to that of captive wild-caught macaws. We found no clear evidence of severe genetic erosion in the population in recent decades, but it was patent in historic times, overlapping with drastic human habitat transformation and macaw persecution over millennia. We found no evidence of geographical and ecological barriers, owing to the high dispersal ability, nesting and foraging habits between genetic clusters. The lack of genetic intermixing despite long-distance foraging and seasonal movements suggests recruitment in natal colonies and other social factors reinforcing philopatry-related genetic structure. Conservation efforts should be specifically focussed on major threats in each genetic cluster as independent conservation units, and also considered in ex-situ management.

From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon.

The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next-generation sequencing approaches have prompted the transition to genome-wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double-digest restriction-associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild-born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.

Fine-Scale Habitat Segregation between Two Ecologically Similar Top Predators.

Similar, coexisting species often segregate along the spatial ecological axis. Here, we examine if two top predators (jaguars and pumas) present different fine-scale habitat use in areas of coexistence, and discuss if the observed pattern can be explained by the risk of interference competition between them. Interference competition theory predicts that pumas should avoid habitats or areas used by jaguars (the dominant species), and as a consequence should present more variability of niche parameters across study areas. We used non-invasive genetic sampling of faeces in 12 different areas and sensor satellite fine-scale habitat indices to answer these questions. Meta-analysis confirmed differences in fine-scale habitat use between jaguars and pumas. Furthermore, average marginality of the realized niches of pumas was more variable than those of jaguars, and tolerance (a measure of niche breadth) was on average 2.2 times higher in pumas than in jaguars, as expected under the interference competition risk hypothesis. The use of sensor satellite fine-scale habitat indices allowed the detection of subtle differences in the environmental characteristics of the habitats used by these two similar top predators, which, as a rule, until now were recorded using the same general habitat types. The detection of fine spatial segregation between these two top predators was scale-dependent.

Shared genetic diversity across the global invasive range of the monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection.

While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained by (i) the native source populations from which they were derived and (ii) demographic bottlenecks during introduction. Genetic data indicated a localized source area for most sampled invasive populations, with limited evidence for admixing of native source populations. This pattern largely coincides with historical data on pet trade exports. However, the invasive populations are genetically more similar than predicted from the export data alone. The extent of bottleneck effects varied among invasive populations. The observed low genetic diversity, evidence of demographic contraction and restricted source area do not support the hypothesis that invasion is favoured by the mixing and recombining of genetic variation from multiple source populations. Instead, they suggest that reduced genetic variation through random processes may not inhibit successful establishment and invasion in this species. However, convergent selection across invasive sites could also explain the observed patterns of reduction and similarity in genetic variation and/or the restricted source area. In general, the alternative explanation of intraspecific variation in invasive potential among genotypes or geographic areas is neglected, but warrants more attention as it could inform comparative studies and management of biological invaders.

High urban breeding densities do not disrupt genetic monogamy in a bird species.

Urbanization causes widespread endangerment of biodiversity worldwide. However, some species successfully colonize cities reaching higher densities than in their rural habitats. In these cases, although urban city dwellers may apparently be taking advantage of these new environments, they also face new ecological conditions that may induce behavioural changes. For example, the frequency of alternative reproductive behaviours such as extra-pair paternity and intraspecific brood parasitism might increase with breeding densities. Here, using a panel of 17 microsatellites, we tested whether increments in breeding densities such as those associated with urban invasion processes alter genetic monogamy in the burrowing owl Athene cunicularia. Our results show low rates of extra-pair paternity (1.47%), but relatively high levels of intraspecific brood parasitism (8.82%). However, we were not able to detect differences in the frequency at which either alternative reproductive behaviour occurs along a strong breeding density gradient. Further research is needed to properly ascertain the role of other social and ecological factors in the frequency at which this species presents alternative reproductive strategies. Meanwhile, our results suggest that genetic monogamy is maintained despite the increment in conspecific density associated with a recent urban invasion process.

Possible extinction vortex for a population of Iberian lynx on the verge of extirpation.

Theory suggests that demographic and genetic traits deteriorate (i.e., fitness and genetic diversity decrease) when populations become small, and that such deterioration could precipitate positive feedback loops called extinction vortices. We examined whether demographic attributes and genetic traits have changed over time in one of the 2 remaining small populations of the highly endangered Iberian lynx (Lynx pardinus) in Doñana, Spain. From 1983 to 2008, we recorded nontraumatic mortality rates, litter size, offspring survival, age at territory acquisition, and sex ratio. We combined these demographic attributes with measures of inbreeding and genetic diversity at neutral loci (microsatellites) and genes subjected to selection (major histocompatibility complex). Data on demographic traits were obtained through capture and radio tracking, checking dens during breeding, track surveys, and camera trapping. For genetic analyses, we obtained blood or tissue samples from captured or necropsied individuals or from museum specimens. Over time a female-biased sex ratio developed, age of territory acquisition decreased, mean litter size decreased, and rates of nontraumatic mortality increased, but there were no significant changes in overall mortality rates, standardized individual heterozygosity declined steadily, and allelic diversity of exon 2 of class II major histocompatibility complex DRB genes remained constant (2 allelic variants present in all individuals analyzed). Changes in sex ratio and age of territory acquisition may have resulted from demographic stochasticity, whereas changes in litter size and nontraumatic mortality may be related to observed increases in inbreeding. Concomitant deterioration of both demographic attributes and genetic traits is consistent with an extinction vortex. The co-occurrence, with or without interaction, of demographic and genetic deterioration may explain the lack of success of conservation efforts with the Doñana population of Iberian lynx.

High proportion of male faeces in jaguar populations.

Faeces provide relevant biological information which includes, with the application of genetic techniques, the sex and identity of individuals that defecated, thus providing potentially useful data on the behaviour and ecology of individuals, as well as the dynamics and structure of populations. This paper presents estimates of the sex ratio of different felid species (jaguar, Panthera onca; puma, Puma concolor; and ocelot/margay, Leopardus pardalis/Leopardus wiedi) as observed in field collected faeces, and proposes several hypotheses that could explain the strikingly high proportion of faeces from male jaguars. The proportion of male and female faeces was estimated using a non-invasive faecal sampling method in 14 study areas in Mexico and Brazil. Faecal samples were genetically analysed to identify the species, the sex and the individual (the latter only for samples identified as belonging to jaguars). Considering the three species, 72.6% of faeces (n = 493) were from males; however, there were significant differences among them, with the proportion from males being higher for jaguars than for pumas and ocelots/margays. A male-bias was consistently observed in all study areas for jaguar faeces, but not for the other species. For jaguars the trend was the same when considering the number of individuals identified (n = 68), with an average of 4.2±0.56 faeces per male and 2.0±0.36 per female. The observed faecal marking patterns might be related to the behaviour of female jaguars directed toward protecting litters from males, and in both male and female pumas, to prevent interspecific aggressions from male jaguars. The hypothesis that there are effectively more males than females in jaguar populations cannot be discarded, which could be due to the fact that females are territorial and males are not, or a tendency for males to disperse into suboptimal areas for the species.

The influence of oceanographic fronts and early-life-history traits on connectivity among littoral fish species.

The spatial distribution of neutral genetic diversity is mainly influenced by barriers to dispersal. The nature of such barriers varies according to the dispersal means and capabilities of the organisms concerned. Although these barriers are often obvious on land, in the ocean they can be more difficult to identify. Determining the relative influence of physical and biotic factors on genetic connectivity remains a major challenge for marine ecologists. Here, we compare gene flow patterns of 7 littoral fish species from 6 families with a range of early-life-history traits sampled at the same geographic locations across common environmental discontinuities in the form of oceanic fronts in the Western Mediterranean. We show that these fronts represent major barriers to gene flow and have a strong influence on the population genetic structure of some fish species. We also found no significant relation between the early-life-history traits most commonly investigated (egg type, pelagic larval duration, and inshore-offshore spawning) and gene flow patterns, suggesting that other life-history factors should deserve attention. The fronts analyzed and the underlying physical mechanisms are not site-specific but common among the oceans, suggesting the generality of our findings.

The complete mitochondrial genome of the whiting, Merlangius merlangus and the haddock, Melanogrammus aeglefinus: a detailed genomic comparison among closely related species of the Gadidae family.

We determined the first complete mitochondrial DNA (mtDNA) sequences for the whiting (Merlangius merlangus, family Gadidae, order Gadiformes) and the haddock (Melanogrammus aeglefinus, family Gadidae, order Gadiformes). The entire mitogenomes were amplified and sequenced by primer walking using newly designed specific internal primers. Lengths were 16,569 and 16,585 bases for whiting and haddock respectively, lengths which lie within the range of previously reported gadiform sequences from Atlantic cod (Gadus morhua, 16,696 bases) and walleye pollock (Theragra chalcogramma, 16,570 bases). Gene arrangement in both species conformed to the order seen in most vertebrate mitochondrial genomes. We identified a long intergenic spacer located between the tRNA(Thr) and tRNA(Pro) genes (of 100 and 70 bp long for whiting and haddock, respectively), as previously described for other species of the order Gadiformes. Using nucleotide and amino acid divergence data of four complete gadoid mitogenomes (M. merlangius, M. aeglefinus, G. morhua and T. chalcogramma), we examined in detail the relative mtDNA mutation patterns across genes and among Gadidae species and tested for the performance of each protein-coding, transfer RNA and ribosomal RNA gene in depicting the expected phylogeny among the four species, as compared with the whole genome dataset. This comparison may be particularly useful in phylogenetic analyses of such a diverse fish family, as well as for the understanding of the patterns of nucleotide substitution of the mtDNA at low levels of divergence.