Genetic structuring of Eunicella singularis populations along a bathymetric gradient

Phenotypic plasticity refers to the ability of an organism to express different morphologies depending on the abiotic and biotic environment. Depth integrating many variables (e.g. temperature, light and hydrodynamics), may affect population structure and dynamics of the populations, as well as connectivity patterns and genetic diversity. Eunicella singularis is a Mediterranean arborescent gorgonian who plays an important rule as engineer species providing biomass and complexity to coralligenous habitats. It has a wide bathymetric distribution ranging from shallow rocky bottoms to deep sublittoral reefs. The species shows two depth-related morphotypes which taxonomic status is not yet clarified. The aim of the study is to analyses genetic variability and/or structuring along a vertical gradient to test the presence of the two morphotypes. Furthermore, a preliminary analyses of the phylogenetic relationship among species of the genus Eunicella has been done. Six populations of Eunicella singularis were sampled from 10 to 60 m depth in Cap de Creus and individuals belonging to Eunicella cavolinii, E. verrucosa, E. racemosa and E. stricta aphyta were collected. The genetic analyses were carried out using five microsatellite loci and ITS-1 sequence polymorphism. The results showed a reduction of genetic variability along the vertical gradient. A threshold in connectivity was observed across 30 - 40 m depth, confirming the presence of two different Eunicella singularis morphotypes. The two morphological forms could be due to phenotypic plasticity, which allowed populations to suit different environmental conditions, or to a break in gene flow that determined the isolation of the two populations and an accumulation of genetic differences. The molecular markers used were not able to clarify the phylogenetic relationship among Eunicella species and the systematic position of the two morphotypes, conversely they risen the question on the existence of single species of Mediterranean Eunicella.

High genetic variability and low local diversity in a population of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are ecologically important root symbionts of most terrestrial plants. Ecological studies of AMF have concentrated on differences between species; largely assuming little variability within AMF species. Although AMF are clonal, they have evolved to contain a surprisingly high within-species genetic variability, and genetically different nuclei can coexist within individual spores. These traits could potentially lead to within-population genetic variation, causing differences in physiology and symbiotic function in AMF populations, a consequence that has been largely neglected. We found highly significant genetic and phenotypic variation among isolates of a population of Glomus intraradices but relatively low total observed genetic diversity. Because we maintained the isolated population in a constant environment, phenotypic variation can be considered as variation in quantitative genetic traits. In view of the large genetic differences among isolates by randomly sampling two individual spores, <50% of the total observed population genetic diversity is represented. Adding an isolate from a distant population did not increase total observed genetic diversity. Genetic variation exceeded variation in quantitative genetic traits, indicating that selection acted on the population to retain similar traits, which might be because of the multigenomic nature of AMF, where considerable genetic redundancy could buffer the effects of changes in the genetic content of phenotypic traits. These results have direct implications for ecological research and for studying AMF genes, improving commercial AMF inoculum, and understanding evolutionary mechanisms in multigenomic organisms.

A genetic isolation gradient of populations of the Balearic green toad (Bufo balearicus) follows rising eastward fragmentation of the rural landscapes on the island of Menorca.

We present the first approach to the genetic diversity and structure of the Balearic toad (Bufo balearicus Boettger, 1880) for the island of Menorca. Forty-one individ- uals from 21 localities were analyzed for ten microsatellite loci. We used geo-refer- enced individual multilocus genotypes and a model-based clustering method for the inference of the number of populations and of the spatial location of genetic dis- continuities between those populations.¦Only six of the microsatellites analyzed were polymorphic. We revealed a northwest- ern area inhabited by a single population with several well-connected localities and another set of populations in the southeast that includes a few unconnected small units with genetically significant differences among them as well as with the individ- uals from the northwest of the island. The observed fragmentation may be explained by shifts from agricultural to tourism practices that have been taking place on the island of Menorca since the 1960s. The abandonment of rural activities in favor of urbanization and concomitant service areas has mostly affected the southeast of the island and is currently threatening the overall geographic connectivity between the different farming areas of the island that are inhabited by the Balearic toad.

Do stacked species distribution models reflect altitudinal diversity patterns?

The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed.

Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic

A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels. Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts. The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe. Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north-south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera.

Divergence along a steep ecological gradient in lake whitefish (Coregonus sp.)

To understand mechanisms structuring diversity in young adaptive radiations, quantitative and unbiased information about genetic and phenotypic diversity is much needed. Here, we present the first in-depth investigation of whitefish diversity in a Swiss lake, with continuous spawning habitat sampling in both time and space. Our results show a clear cline like pattern in genetics and morphology of populations sampled along an ecological depth gradient in Lake Neuchâtel. Divergent natural selection appears to be involved in shaping this cline given that trait specific P(ST)-values are significantly higher than F(ST)-values when comparing populations caught at different depths. These differences also tend to increase with increasing differences in depth, indicating adaptive divergence along a depth gradient, which persists despite considerable gene flow between adjacent demes. It however remains unclear, whether the observed pattern is a result of currently stable selection-gene flow balance, incipient speciation, or reverse speciation due to anthropogenic habitat alteration causing two formerly divergent species to collapse into a single gene pool.

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Qualidade fisiológica de sementes e diversidade genética de maracujazeiros cultivados em diferentes altitudes no Espírito Santo

O maracujazeiro pertence à família Passifloraceae e ao gênero Passiflora que é o mais importante economicamente. Altitudes entre 100 a 900 m são indicadas para o plantio do maracujazeiro e estudos sobre localizações geográficas distintas possibilitam expressões do genótipo, influenciadas pelas condições ambientais. O gradiente altitudinal influencia a distribuição da variação genética dentro e entre populações de plantas e a diversidade genética muda com a altitude. O presente trabalho teve como objetivo avaliar a qualidade fisiológica de sementes e a diversidade genética de maracujazeiros cultivados em diferentes altitudes do Espírito Santo. Para avaliação da qualidade fisiológica das sementes, os frutos de Passiflora spp. maduros foram colhidos em pomares localizados em altitudes baixa (0-100 m), média (>100 até 600 m) e alta (>600 m) de diferentes municípios do Espírito Santo. Os tratamentos pré-germinativos nas sementes foram: T1- escarificação física, feita manualmente com lixa d´água nº 120; T2- tratamento com ácido giberélico (GA3) na concentração de 500 mg L-1 com embebição por 24 horas e T3- sementes sem escarificação realizados nas sementes em laboratório e em casa de vegetação. Foi avaliado o envelhecimento acelerado tradicional, envelhecimento acelerado com saturação salina e deterioração controlada em sementes de maracujá amarelo sem escarificação localizado em alta altitude e as condições que apresentaram menor deterioração das sementes para aplicação às demais espécies e altitudes com os respectivos tratamentos pré-germinativos que apresentaram maiores valores de germinação e vigor em laboratório e em casa de vegetação. Assim, para as sementes do maracujá amarelo utilizou-se o tratamento sem escarificação, para sementes de maracujá roxo, a escarificação física e para as sementes de maracujá doce, o tratamento com ácido giberélico. O teste de envelhecimento acelerado com saturação salina a 43 ºC por 72 horas e deterioração controlada a 25% de umidade expostas por 24 horas diferencia as espécies nas diferentes altitudes. Sementes de maracujá amarelo e sementes localizadas em alta altitude apresentam qualidade fisiológica superior. Para a avaliação da diversidade genética foram utilizadas folhas jovens de cinco plantas matrizes de Passiflora edulis Sims f. flavicarpa Degener, P. edulis Sims e P. alata Curtis cultivadas em três altitudes (baixa, média e alta) do Espírito Santo. Para SSR foi encontrado baixo número de alelos, alta heterozigosidade esperada e altos valores de PIC e para a análise ISSR detectou um elevado número de bandas por primer e alto polimorfismo. Há maior similaridade genética entre P. edulis f. flavicarpa Deg. e P. edulis. Passiflora alata apresenta maior distância genética em relação às espécies. As populações de baixa altitude se diferenciam das demais independente da espécie e do marcador utilizado.

Morphometric and genetic differentiation among populations of Eupemphix nattereri (Amphibia, Anura, Leiuperidae) from central Brazil

To assess genetic structure and phenotypic diversity of Eupemphix nattereri Steindachner, 1863, morphometric and molecular analyses were carried out for nine populations from the State of Goiás. A total of 11 morphometric traits were evaluated and genetic information was estimated using RAPD markers. Genetic and phenotypic distances were determined as a function of geographical origin. Correlation among genetic, morphometric, micro, and macroenviromental were analyzed by the Mantel test. Genetic data indicated high levels of genetic diversity (Φst= 0.3) among the nine populations. Mantel tests did not reveal a significant positive correlation between genetic and geographical distances, indicating that locally geographical populations were not genetically similar, even in distances smaller than 50 km. Discriminant analysis on 11 morphometric measurements showed a high divergence among the nine populations. However, a marginally significant correlation (P=0.08) between genetic and morphometric distances was found. The observed correlation was not causal in terms of the relationship between phenotype and genotype, but indicated common spatial structures. Thus, our results suggest that isolation-by-distance processes may explain population divergence in Eupemphix nattereri.

THE USE OF SIMULATIONS IN EVOLUTIONARY POPULATION GENETICS: APPLICATIONS ON HUMANS, OWLS AND VIRTUAL ORGANISMS

Summary (in English) Computer simulations provide a practical way to address scientific questions that would be otherwise intractable. In evolutionary biology, and in population genetics in particular, the investigation of evolutionary processes frequently involves the implementation of complex models, making simulations a particularly valuable tool in the area. In this thesis work, I explored three questions involving the geographical range expansion of populations, taking advantage of spatially explicit simulations coupled with approximate Bayesian computation. First, the neutral evolutionary history of the human spread around the world was investigated, leading to a surprisingly simple model: A straightforward diffusion process of migrations from east Africa throughout a world map with homogeneous landmasses replicated to very large extent the complex patterns observed in real human populations, suggesting a more continuous (as opposed to structured) view of the distribution of modern human genetic diversity, which may play a better role as a base model for further studies. Second, the postglacial evolution of the European barn owl, with the formation of a remarkable coat-color cline, was inspected with two rounds of simulations: (i) determine the demographic background history and (ii) test the probability of a phenotypic cline, like the one observed in the natural populations, to appear without natural selection. We verified that the modern barn owl population originated from a single Iberian refugium and that they formed their color cline, not due to neutral evolution, but with the necessary participation of selection. The third and last part of this thesis refers to a simulation-only study inspired by the barn owl case above. In this chapter, we showed that selection is, indeed, effective during range expansions and that it leaves a distinguished signature, which can then be used to detect and measure natural selection in range-expanding populations. Résumé (en français) Les simulations fournissent un moyen pratique pour répondre à des questions scientifiques qui seraient inabordable autrement. En génétique des populations, l'étude des processus évolutifs implique souvent la mise en oeuvre de modèles complexes, et les simulations sont un outil particulièrement précieux dans ce domaine. Dans cette thèse, j'ai exploré trois questions en utilisant des simulations spatialement explicites dans un cadre de calculs Bayésiens approximés (approximate Bayesian computation : ABC). Tout d'abord, l'histoire de la colonisation humaine mondiale et de l'évolution de parties neutres du génome a été étudiée grâce à un modèle étonnement simple. Un processus de diffusion des migrants de l'Afrique orientale à travers un monde avec des masses terrestres homogènes a reproduit, dans une très large mesure, les signatures génétiques complexes observées dans les populations humaines réelles. Un tel modèle continu (opposé à un modèle structuré en populations) pourrait être très utile comme modèle de base dans l'étude de génétique humaine à l'avenir. Deuxièmement, l'évolution postglaciaire d'un gradient de couleur chez l'Effraie des clocher (Tyto alba) Européenne, a été examiné avec deux séries de simulations pour : (i) déterminer l'histoire démographique de base et (ii) tester la probabilité qu'un gradient phénotypique, tel qu'observé dans les populations naturelles puisse apparaître sans sélection naturelle. Nous avons montré que la population actuelle des chouettes est sortie d'un unique refuge ibérique et que le gradient de couleur ne peux pas s'être formé de manière neutre (sans l'action de la sélection naturelle). La troisième partie de cette thèse se réfère à une étude par simulations inspirée par l'étude de l'Effraie. Dans ce dernier chapitre, nous avons montré que la sélection est, en effet, aussi efficace dans les cas d'expansion d'aire de distribution et qu'elle laisse une signature unique, qui peut être utilisée pour la détecter et estimer sa force.

Diversity of Chromobacterium violaceum isolates from aquatic environments of state of Pará, Brazilian Amazon

The present study intended to characterize the phenotypic and genetic diversity of Brazilian isolates of Chromobacterium violaceum from aquatic environments within the Amazon region. Nineteen isolates showed morphological properties of C. violaceum and the majority grew at 44°C. Low temperatures, in contrast, showed to be inhibitory to their growth, as eleven isolates did not grow at 10ºC and nine did not produce pigmentation, clearly indicating an inhibition of their metabolism. The largest variation among isolates was observed in the citrate test (Simmons), in which 12 isolates were positive, and in the oxidation/fermentation of sucrose, with six positives isolates. Chloramphenicol, gentamicin and sulfonamides efficiently inhibited bacterial growth. Amplified products of the recA gene were digested with HindII or PstI, which produced three or four restriction fragments patterns, respectively. The combined analysis arranged the isolates into six genospecies. The higher diversity observed in Belém (genotypes C, D, E and F) may be a consequence of intense human occupation, pollution of the aquatic environment or due to the higher diversity of the environments sampled in that region. In conclusion, a high level of genetic and phenotypic diversity was observed, and four new genospecies were described.

Tracing lineage by phenotypic and genotypic markers in Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- and Salmonella Typhimurium isolated in state of São Paulo, Brazil

Fifty-three Salmonella 1,4,[5],12:i:- and 45 Salmonella Typhimurium strains were characterised using phage typing, plasmid profiles and pulsed-field gel electrophoresis (PFGE) for comparison. The majority of the strains were subdivided into definitive type (DT) 41 (22.6%) and DT 193 (18%) and the 60-MDa plasmid was detected in 94.3% and 84.4% of strains, respectively. Genetic diversity was observed among all strains and 90% presented a > 70% similarity through PFGE analysis. These results suggest a close relationship between Salmonella 1,4,[5],12:i:- and Salmonella Typhimurium at the serotype level.

Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish.

BACKGROUND: Transgressive segregation describes the occurrence of novel phenotypes in hybrids with extreme trait values not observed in either parental species. A previously experimentally untested prediction is that the amount of transgression increases with the genetic distance between hybridizing species. This follows from QTL studies suggesting that transgression is most commonly due to complementary gene action or epistasis, which become more frequent at larger genetic distances. This is because the number of QTLs fixed for alleles with opposing signs in different species should increase with time since speciation provided that speciation is not driven by disruptive selection. We measured the amount of transgression occurring in hybrids of cichlid fish bred from species pairs with gradually increasing genetic distances and varying phenotypic similarity. Transgression in multi-trait shape phenotypes was quantified using landmark-based geometric morphometric methods. RESULTS: We found that genetic distance explained 52% and 78% of the variation in transgression frequency in F1 and F2 hybrids, respectively. Confirming theoretical predictions, transgression when measured in F2 hybrids, increased linearly with genetic distance between hybridizing species. Phenotypic similarity of species on the other hand was not related to the amount of transgression. CONCLUSION: The commonness and ease with which novel phenotypes are produced in cichlid hybrids between unrelated species has important implications for the interaction of hybridization with adaptation and speciation. Hybridization may generate new genotypes with adaptive potential that did not reside as standing genetic variation in either parental population, potentially enhancing a population's responsiveness to selection. Our results make it conceivable that hybridization contributed to the rapid rates of phenotypic evolution in the large and rapid adaptive radiations of haplochromine cichlids.

Y-chromosome diversity in native mexicans reveals continental transition of genetic structure in the Americas

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.

Subalpine-nival gradient of species richness for vascular plants, lichens and bryophytes in the Swiss Inner Alps

In the European GLORIA project, 12 summits (treeline to nival belt) were inventoried in three regions of Switzerland: two in the Swiss National Park Graubünden and one in Valais. Vascular plants were recorded in all three regions and bryophytes and lichens were recorded only in Valais. On each summit, vegetation and temperature data were sampled using sampling protocols for the GLORIA project (Global Observation Research Initiative in Alpine environment) on large summit sections and in clusters of four 1x1-m quadrats. We observed a general decrease of species richness for all three systematic groups with increasing elevation in the summit sections, but only for vascular plants in the quadrats. In Valais, there was higher species richness for vascular plants than for bryophytes and lichens on the lower summits, but as the decrease in species richness was less pronounced for cryptogams, the latter were more numerous than vascular plants on the highest summit. Vascular species showed a clear shift of the dominant life form with elevation, with chamaephytes replacing hemicryptophytes. Bryophytes and lichens showed a weak trend among the life forms at the summit section scale, but a stronger shift of the dominant forms was seen in the quadrats, with cushion replacing turf bryophytes and crustaceous replacing fruticose lichens. Altogether, these results sustain the temperature-physiographic hypothesis to explain the species richness decrease along the altitudinal gradient: the harsh climatic conditions of the alpine-nival belts act as a filter for species, but the diminishing diversity of microhabitats is also an important factor. Because cryptogams depend more on humidity than temperature and more on smaller microhabitats than vascular plants, the decrease of species richness is more gradual with elevation for bryophytes and lichens.