The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical data sets

The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE out- put, the ΔK method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of K and is sensitive to uneven sampling. If this finding holds for empirical data sets, conclusions about the scale of gene flow may have to be revised for a large number of studies. To determine the impact of method choice, we applied recently described es- timators of K to re-estimate genetic structure in 41 empirical microsatellite data sets; 15 from a broad range of taxa and 26 from one phylogenetic group, coral. We com- pared alternative estimates of K (Puechmaille statistics) with traditional (ΔK and pos- terior probability) estimates and found widespread disagreement of estimators across data sets. Thus, one estimator alone is insufficient for determining the optimal num- ber of clusters; this was regardless of study organism or evenness of sampling scheme. Subsequent analysis of molecular variance (AMOVA) did not necessarily clarify which clustering solution was best. To better infer population structure, we suggest a com- bination of visual inspection of STRUCTURE plots and calculation of the alternative estimators at various thresholds in addition to ΔK. Disagreement between traditional and recent estimators may have important biological implications, such as previously unrecognized population structure, as was the case for many studies reanalysed here

Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes

The study of the interplay between speciation and hybridization is of primary importance in evolutionary biology. Octocorals are ecologically important species whose shallow phylogenetic relationships often remain to be studied. In the Mediterranean Sea, three congeneric octocorals can be observed in sympatry: Eunicella verrucosa, Eunicella cavolini and Eunicella singularis. They display morphological differences and E.singularis hosts photosynthetic Symbiodinium, contrary to the two other species. Two nuclear sequence markers were used to study speciation and gene flow between these species, through network analysis and Approximate Bayesian Computation (ABC). Shared sequences indicated the possibility of hybridization or incomplete lineage sorting. According to ABC, a scenario of gene flow through secondary contact was the best model to explain these results. At the intraspecific level, neither geographical nor ecological isolation corresponded to distinct genetic lineages in E.cavolini. These results are discussed in the light of the potential role of ecology and genetic incompatibilities in the persistence of species limits.French National Research Agency (ANR) program Adacni (ANR) [ANR-12-ADAP-0016]CNRSHubert Curien 'Tassili' program [12MDU853]CCMAR Strategic Plan from Fundacao para a Ciencia e a Tecnologia-FCT [PEst-C/MAR/LA0015/2011,FEDERinfo:eu-repo/semantics/publishedVersio

An efficient method to find potentially universal population genetic markers, applied to metazoans

<p>Abstract</p> <p>Background</p> <p>Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families.</p> <p>Results</p> <p>In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the <it>Homolens </it>databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals.</p> <p>Conclusions</p> <p>Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.</p

The Deep‐water corals of Cyprus: Environmental settings and ecological features (CYprus Cold‐corals Levantine SeA, Eastern MEditerraneaN: CYCLAMEN)

The recently started research project CYCLAMEN (CYprus Cold-corals Levantine SeA, Eastern MEditerraneaN), will conduct the first detailed study of cold-water coral communities in eastern Cypriot waters. Cold-water coral habitats have been found during exploratory surveys. The 2-yr long project will include the environmental characterization of the area, as well as the study of the spatial distribution of cold-water coral communities. In addition to the study of the biology of the coral species, genetic and eco-physiological studies will be included. This project is the first of its kind in Cyprus and will additionally have an associated scientific outreach programme in order to bring these ecosystems, still poorly known, to the general public. The project is led by the Spanish Institute of Oceanography (IEO), and relies on the participation of research Institutions in Cyprus: The Cyprus Institute (CyI) and the NGO Enalia Physis Environmental Research Centre (EPERC); France: Aix-Marseille University – Mediterranean Institute for Biodiversity & Ecology (AMU-IMBE); Greece: The Hellenic Centre for Marine Research (HCMR); Mónaco: Centre Scientifique de Monaco (CSM); United Kingdom: National Oceanography Centre (NOC), and Spain: Universitat de Barcelona (UB). Here we present the conceptual frame of the project, the background knowledge and the first obtained results in the oceanographic cruise carried out in summer 2015

A well-kept treasure at depth: precious red coral rediscovered in Atlantic deep coral gardens (SW Portugal) after 300 years

The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed. Its occurrence has not been reported for the last 300 years.info:eu-repo/semantics/publishedVersio

Analyses de la spéciation et l'hybridation chez les octocoralliaires méditerranéens

Scripts for the analysis of transcriptome data to study speciation and hybridization in octocoralsScripts for the analysis of transcriptome data from the article on hybridization in Mediterranean octocorals. See information and scripts in the markdown file. License CC-BY 4.0 https://creativecommons.org/licenses/by/4.0

L’espèce incertaine et les taxons flous

The question of the " good " definition of species, which unites biologists, naturalists and all those involved in the use or conservation of biodiversity, is constantly being updated by advances in knowledge of evolution and speciation. This question is far from being resolved because speciation is ongoing in current biodiversity, and taxa of specific rank are therefore not definite species, but rather hypotheses which often remain to be tested. Darwin emphasized the importance of "doubtful species" for his argument on variation. We illustrate this property of living organisms to resist classification with the example of fuzzy taxa, which can be summarized in two main types: syngameon and incipient species. The variety of case-studies reporting gene flow between species, sometimes between genera, and its ecological role, underline the fact that the uncertain species is a major aspect of biodiversity issues.La question de la « bonne » définition de l’espèce, qui unit les biologistes, les naturalistes et les personnes impliquées dans l’usage ou la conservation de la biodiversité, est constamment réactualisée par les progrès des connaissances sur l’évolution et la spéciation. Cette question est loin d’être résolue parce que la spéciation est à l’œuvre dans la biodiversité actuelle et que les taxons de rang spécifique ne sont donc pas des espèces certaines mais plutôt des hypothèses d’espèces qui restent souvent à tester. Darwin soulignait l’importance des « espèces douteuses » pour son argumentation sur la variation. Nous illustrons cette propriété du vivant à résister à la classification par l’exemple des taxons flous qui peuvent être résumés en deux grands types, le syngaméon et les espèces naissantes. La variété des cas d’études rapportant des flux de gènes entre espèces, parfois entre genres, le rôle écologique de ceux-ci, soulignent que l’espèce incertaine constitue un aspect majeur des problématiques de la biodiversité