Reconstruction phylogénétique de Salmonidae : portrait de famille par augmentation de l'échantillonnage des taxons

Tableau d’honneur de la Faculté des études supérieures et postdoctorales, 2009-2010Les poissons de la famille Salmonidae ont posé de nombreuses difficultés aux systématiciens qui ont tenté d'élucider leurs relations évolutives. Plusieurs ambiguïtés persistent à tous les niveaux de la phylogénie de cette famille et un portrait phylogénétique exhaustif comprenant de nombreux représentants de Salmonidae n'a toujours pas été obtenu. Différentes causes ont été suggérées pour expliquer les difficultés à obtenir un consensus phylogénétique, mais la portion relativement restreinte des taxons échantillonnée jusqu'ici pour effectuer les inferences milite en faveur de cette nouvelle stratégie. Dans le cadre de ce projet de maîtrise, des séquences mitochondriales (gènes cytochrome b et cytochrome c oxydase I; 2403 pb) et des AFLP (3304 loci) ont été produits afin de conduire des analyses phylogénétiques sur 107 taxons représentant une portion importante de la biodiversité spécifique de la famille. Afin de vérifier la congruence et la robustesse des différents signaux, de diminuer l'influence d'erreurs stochastiques et d'évaluer l'apport de l'échantillonnage des taxons sur la phylogénie, une supermatrice comprenant l'ensemble des séquences mitochondriales et nucléaires disponibles sur GenBank a été élaborée à partir de ce vecteur de taxons, constituant ainsi le plus grand nombre d'évidences (taxons et caractères) ayant été amenées dans un cadre phylogénétique jusqu'à ce jour. Cette stratégie a permis d'améliorer la résolution phylogénétique par l'augmentation du signal historique et la détection de biais systématiques, mettant en évidence certaines des difficultés biologiques (par ex.: hybridation, radiations) et méthodologiques ayant mené aux nombreuses contradictions entre les hypothèses phylogénétiques précédentes. En plus d'offrir un portrait qui fait plus que doubler le nombre d'espèces incluses dans la phylogénie et d'avoir inféré avec robustesse la séquence évolutive des genres de Salmoninae, la reconstruction temporelle de l'évolution et des taux de diversification obtenue par l'enracinement de l'arbre phylogénétique avec le groupe Esociformes et l'inclusion de cinq points de calibration fossile témoigne de l'ampleur temporelle de l'évolution dans Salmonidae et demande de considérer une nouvelle hypothèse pour l'enracinement de la famille et la séquence évolutive de ses sous-familles

Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish:Proof of concept for key components of the insulin-like growth factor axis

Acknowledgements This study was funded by a Natural Environment Research Council grant (NERC, project code: NBAF704). FML is funded by a NERC Doctoral Training Grant (Project Reference: NE/L50175X/1). RLS was an undergraduate student at the University of Aberdeen and benefitted from financial support from the School of Biological Sciences. DJM is indebted to Dr. Steven Weiss (University of Graz, Austria), Dr. Takashi Yada (National Research Institute of Fisheries Science, Japan), Dr. Robert Devlin (Fisheries and Oceans Canada, Canada), Prof. Samuel Martin (University of Aberdeen, UK), Mr. Neil Lincoln (Environment Agency, UK) and Prof. Colin Adams/Mr. Stuart Wilson (University of Glasgow, UK) for providing salmonid material or assisting with its sampling. We are grateful to staff at the Centre for Genomics Research (University of Liverpool, UK) (i.e. NERC Biomolecular Analysis Facility – Liverpool; NBAF-Liverpool) for performing sequence capture/Illumina sequencing and providing us with details on associated methods that were incorporated into the manuscript. Finally, we are grateful to the organizers of the Society of Experimental Biology Satellite meeting 'Genome-powered perspectives in integrative physiology and evolutionary biology' (held in Prague, July 2015) for inviting us to contribute to this special edition of Marine Genomics and hosting a really stimulating meeting.Peer reviewedPublisher PD

Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss

microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation

Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling.

Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63) to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY) old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ~0.31%/MY (CI: 0.27-0.36%/MY). Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our findings represent an important contribution to the systematics of Salmonidae, and provide a useful tool for addressing questions related to fundamental and applied evolutionary issues

Strict consensus of 48 MP trees inferred using MitoNuc-NT showing the distribution of sequences across taxa.

<p>Bootstrap support values are indicated above branches; Bremer support indices are shown below branches. Underlined Bremer support indices indicate nodes that support significant clades. Nodes with bootstrap values less than 75% are indicated with open circles, as are nodes where conflicts between mitochondrial and nuclear genes were detected (n = 5; Bremer supports partitioned by genomic compartment are annotated in the following order: Mitochondrial/Nuclear).</p

ML tree inferred by the MitoNuc-NT data set with 1 model of molecular evolution.

<p>A: Nodes with less than 75% bootstrap support are indicated by open circles (n = 24). Bootstrap values less than 100% are denoted above branches and posterior probabilities less than 100% for BAY analyses are shown under branches. B: Radial view of the same tree.</p

Unrooted ML phylogram based on the cytochromes data set.

<p>A: Nodes with bootstrap values less than 75% are indicated with open circles (n = 29). For some deep nodes, ML bootstrap support/BAY posterior probabilities/MP bootstrap supports are shown above the node. B: Radial view of the same tree. Abbreviations: <i>B</i> = <i>Brachymystax</i>, <i>C = Coregonus</i>, <i>H = Hucho</i>, <i>O = Oncorhynchus</i>, <i>Pa = Parahucho perryi</i>, <i>P = Prosopium</i>, <i>Sm = Salmo</i>, <i>Sv = Salvelinus</i>, <i>Svth = Salvethymus svetovidovi</i>, <i>St = Stenodus leucichthys</i> and <i>T = Thymallus</i>. Numbers beside each sample correspond to identification numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046662#pone.0046662.s001" target="_blank">Table S1</a>.</p

Alternative rooting for Salmonidae based on posterior probabilities of 10,000 MC³ trees.

<p>Boxes on radial phylograms indicated the location of the magnified areas to the left of each tree. The width of the branches indicates posterior probabilities for the position of the outgroup and the length of the branches represents the average of the posterior distributions. Trees in the left column show inferences for NT matrices; trees in the right column show inferences for RY matrices. A: Esociformes: NT 99.1% RY 57.9% (Thymallinae); NT 0.9% RY 35.2% (Salmoninae); RY 6.9% (Coregoninae); B: Alepocephaloidea: NT 3.5% RY 11.8% (Thymallinae); NT 61.6% RY 4.8% (Salmoninae); NT 34.8% RY 42.6% (Coregoninae); C: Argentinoidea: NT 22.5% RY 67.8% (Thymallinae); NT 41.4% RY 13.9% (Salmoninae); NT 33.1% RY 7.3% (Coregoninae); D: Osmeroidei: RY 0.3% (Thymallinae); RY 0.1% (Salmoninae); NET 2.2% RY 2.2% (Coregoninae).</p