Céline Bonillo

Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.

Although much progress has been made recently in teleostean phylogeny, relationships among the main lineages of the higher teleosts (Acanthomorpha), containing more than 60% of all fish species, remain poorly defined. This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes. We compiled and analyzed three independent data sets, including: (i) mitochondrial ribosomal fragments from 12S and 16s (814bp for 97 taxa); (ii) nuclear ribosomal 28S sequences (847bp for 74 taxa); and (iii) a nuclear protein-coding gene, rhodopsin (759bp for 86 taxa). Detailed analyses were conducted on each data set separately and the principle of taxonomic congruence without consensus trees was used to assess confidence in the results as follows. Repeatability of clades from separate analyses was considered the primary criterion to establish reliability, rather than bootstrap proportions from a single combined (total evidence) data matrix. The new and reliable clades emerging from this study of the acanthomorph radiation were: Gadiformes (cods) with Zeioids (dories); Beloniformes (needlefishes) with Atheriniformes (silversides); blenioids (blennies) with Gobiesocoidei (clingfishes); Channoidei (snakeheads) with Anabantoidei (climbing gouramies); Mastacembeloidei (spiny eels) with Synbranchioidei (swamp-eels); the last two pairs of taxa grouping together, Syngnathoidei (aulostomids, macroramphosids) with Dactylopteridae (flying gurnards); Scombroidei (mackerels) plus Stromatoidei plus Chiasmodontidae; Ammodytidae (sand lances) with Cheimarrhichthyidae (torrentfish); Zoarcoidei (eelpouts) with Cottoidei; Percidae (perches) with Notothenioidei (Antarctic fishes); and a clade grouping Carangidae (jacks), Echeneidae (remoras), Sphyraenidae (barracudas), Menidae (moonfish), Polynemidae (threadfins), Centropomidae (snooks), and Pleuronectiformes (flatfishes).

A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

BackgroundThe Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited.ResultsWe have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish.ConclusionThe RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.

Genome dynamics and chromosomal localization of the non-LTR retrotransposons Rex1 and Rex3 in Antarctic fish

The non-long terminal repeat retrotransposons Rex1 and Rex3 were identified in 13 species of Antarctic fishes from five families of the suborder Notothenioidei. Partial reverse transcriptase gene sequences were characterized for Notothenia coriiceps, Trematomus newnesi and Dissostichus mawsoni (Nototheniidae), and Gymnodraco acuticeps (Bathydraconidae). Rex1 and Rex3 both formed a notothenioid-specific monophyletic group compared to the corresponding elements from other fishes. They globally evolved under purifying selection, showing their activity during notothenioid evolution. Fluorescence in situ hybridization analysis of the chromosomal distribution of Rex1 and Rex3 was performed for several notothenioid fish species. Rex1 was generally less abundant than Rex3, which was widely scattered on the chromosomes with more intense hybridization patterns in some specific zones. Particularly, Rex3 accumulated in Chionodraco hamatus in pericentromeric areas, short arms of some pairs as well as in an intercalary band in the long arm of the Y chromosome similarly to a previously described DNA transposon. Such pattern similarities suggest the presence of autosomal and gonosomal regions of preferential accumulation for different types of repeated elements in notothenioid genomes. To the best of our knowledge, this report is the first description and analysis of retrotransposable elements in Antarctic fish genomes.

Molecular evidence for the origins of Antarctic fishes: paraphyly of the Bovichtidae and no indication for the monophyly of the Notothenioidei (Teleostei)

Abstract The notothenioids are an Antarctic suborder of perciform fishes to which increasing interest is being devoted. To investigate their origin, one must address two questions. First, are Bovichtidae (Bovichtus, Cottoperca, Pseudaphritis), the sister-group of the rest of the suborder, monophyletic ? Secondly, what is the sister-group of the Notothenioidei ? These questions were addressed by determining the complete nucleotide sequence of the D2 and D8 domains of 28S rDNA (759 sites, among which 158 informative for parsimony), for 6 notothenioids and a collection of 6 outgroup taxa including the Trachinoidei and Zoarcoidei. Different outgroups (or combinations of outgroups) and different weighting schemes support the inference that Pseudaphritis is closer to the rest of the Notothenioidei than Cottoperca and Bovichtus are. Relationships of Cottoperca and Bovichtus remain unclear with respect to outgroups. Our molecular data therefore clearly show that the Bovichtidae are paraphyletic, but their relationships are not those suggested by Balushkin in 1992. Our data provide no indication of the monophyly of the Notothenioidei in its classical sense. Most of the homoplasy is due to outgroup sequences and interrelationships of outgroups are unresolved. Some morphological synapomorphies shared by Pseudaphritis and the rest of the non-bovichtid Notothenioidei are proposed, including some that were identified by Voskoboynikova in 1993.

Phylogeny of the Channichthyidae (Notothenioidei, Teleostei) Based on Two Mitochondrial Genes

The family Channichthyidae contains 11 genera and 15 species [1] and is considered monophyletic [2,3, 4, 5]. Interrelationships of channichthyids were first investigated by Iwami [2] based on morphological characters.

Molecular and morphological phylogenies of the Antarctic teleostean family Nototheniidae, with emphasis on the Trematominae

Four independent molecular data sets were sequenced in order to solve longstanding phylogenetic problems among Antarctic teleosts of the family Nototheniidae. The anatomical data of Balushkin (2000) were also coded into a matrix of 106 characters in order to test the parsimony of his taxonomic conclusions. Molecular results confirm Balushkin’s Pleuragrammatinae but not his Nototheniinae. Different genes used here found the “clade A” establishing the paraphyly of the Nototheniinae sensu lato; i.e. Lepidonotothen and Patagonotothen are more closely related to the Trematominae than to Notothenia. The genus Notothenia is paraphyletic and Paranotothenia should become Notothenia. Previously no molecular data set could assign a reliable position for the genus Gobionotothen. For the first time robust results are obtained for the phylogeny among the Trematominae. Trematomus scotti is the sister-group of all others, then Trematomus newnesi emerges, then Trematomus eulepidotus. Among the crown group, three clades emerge: 1: Trematomus hansoni + Trematomus bernacchii + Trematomus vicarius; 2: Trematomus pennellii + Trematomus lepidorhinus + Trematomus loennbergii; 3: Trematomus (Pagothenia) borchgrevinki + Trematomus nicolai. Pagothenia should become Trematomus to make the genus Trematomus monophyletic. The Trematomus tree found here did not match the topology obtained with Balushkin’s morphological matrix. The tree shows that the tendencies shown by some trematomines to secondarily colonize the water column are not gained through common ancestry.

Comparisons between mitochondrial genomes of domestic goat (Capra hircus) reveal the presence of numts and multiple sequencing errors

Materials and methods. In the present study, we amplified and sequenced the complete mitochondrial genome from a Vietnamese domestic goat (Capra hircus). The data were compared with mtDNA sequences available in the nucleotide databases. Results. The results revealed many problems in the goat mitochondrial reference genome (GenBank accession number NC_005044). Firstly, the authors did not sequence the complete genome, simply 44.5% of its total length. Secondly, two fragments (representing 1201 and 2384 nt) contained an unusually high percentage of sequencing errors. Thirdly, a segment of 1881 nt, covering most of nd5 and the 5′ part of nd6, was shown to be a nuclear sequence of mitochondrial origin (Numt). Surprisingly, a similar Numt was also detected in four other goat mitochondrial genomes available in GenBank (GU22978-81). Two primers were designed specially to amplify ∼960 nt of the Numt identified in goat mtDNA genomes. After cloning, two Numts were detected for C. hircus. Several Numts, most of them with stop codon or frameshift mutations, were also found in Hemitragus jemlahicus (Himalayan tahr) and Pseudois nayaur (bharal). Phylogenetic analyses suggest that a nuclear integration occurred in the common ancestor of Ammotragus, Arabitragus, Capra, Hemitragus and Pseudois, followed by several subsequent duplication events. Conclusion. As poor-quality sequences can produce misleading interpretations of both phylogeny and molecular evolution, we propose including a new link to each accession number in the nucleotide databases, named “external expertise”, which could be openly and continually updated by non-anonymous searchers in order to validate good-quality data, or, conversely, to indicate possible problems in the sequence, such as DNA contamination or sequencing errors. This information could prove very useful over time to select good-quality sequences for in silico analyses.

Assessment of otocephalan and protacanthopterygian concepts in the light of multiple molecular phylogenies

The rise of cladistics in ichthyology has dramatically improved our knowledge of teleostean basal interrelationships. However, some questions have remained open, among them the reliability of the Otocephala, a clade grouping clupeomorphs and ostariophysans, and the relationships of the Esocoidei. These two questions have been investigated in the light of new DNA sequences (from 28S and rhodopsin genes) and sequences from data banks (cytochrome b, 12-16S, 18S, MLL and RAG1). The ability of each of these markers to resolve basal teleostean interrelationships is assessed, and the cytochrome b was not found appropriate. Practical (i.e. different taxonomic samplings) and epistemological grounds led us to perform multiple separated phylogenetic analyses, in order to estimate the reliability of the above clades from their repeatability among trees from independent sequence data. The Otocephala are found monophyletic from most of the datasets; otherwise, they are not significantly contradicted from the others, which exhibit unresolved relationships. We conclude that the evidence provided here favours the sister-group relationship of clupeomorphs and ostariophysans. Morphological evidence including fossils is discussed, concluding that morphological works have not yet provided sufficient data to support this group. Salmonids and esocoids are found sister-groups from every molecular dataset in which these groups were sampled. Based on these convincing results, the Protacanthopterygii of Johnson and Patterson [1] are redefined, including the Esocoidei.

Is the Species Flock Concept Operational? The Antarctic Shelf Case

There has been a significant body of literature on species flock definition but not so much about practical means to appraise them. We here apply the five criteria of Eastman and McCune for detecting species flocks in four taxonomic components of the benthic fauna of the Antarctic shelf: teleost fishes, crinoids (feather stars), echinoids (sea urchins) and crustacean arthropods. Practical limitations led us to prioritize the three historical criteria (endemicity, monophyly, species richness) over the two ecological ones (ecological diversity and habitat dominance). We propose a new protocol which includes an iterative fine-tuning of the monophyly and endemicity criteria in order to discover unsuspected flocks. As a result nine « full » species flocks (fulfilling the five criteria) are briefly described. Eight other flocks fit the three historical criteria but need to be further investigated from the ecological point of view (here called « core flocks »). The approach also shows that some candidate taxonomic components are no species flocks at all. The present study contradicts the paradigm that marine species flocks are rare. The hypothesis according to which the Antarctic shelf acts as a species flocks generator is supported, and the approach indicates paths for further ecological studies and may serve as a starting point to investigate the processes leading to flock-like patterning of biodiversity.

LINE-1 amplification accompanies explosive genome repatterning in rodents.

Transposable elements (TEs) sometimes induce karyotypic changes following recombination, breakage and rearrangement. We used FISH and Southern blot analyses to investigate the amount and distribution of LINE-1 retrotransposons in rodents (genus Taterillus, Muridae, Gerbillinae) that have recently undergone an important genome repatterning. Our results were interpreted in a known phylogenetic framework and clearly showed that LINE-1 elements were greatly amplified and non-randomly distributed in the most rearranged karyotypes. A comparison between FISH and conventional banding patterns provided evidence that LINE-1 insertion sites and chromosome breakpoints were not strongly correlated, thus suggesting that LINE-1 amplification subsequently accompanied Taterillus chromosome evolution. Similar patterns are observed in some cases of genomic stresses (hybrid genomes, cancer and DNA-damaged cells) and usually associated with DNA hypomethylation. We propose that intensively repatterned genomes face transient stress phases during which some epigenetic features, such as DNA methylation, are relaxed, thus allowing TE amplification.