Contribution à la cytotaxonomie des Soricidés (Mammalia, Insectivora) de l'Afrique occidentale.

Chromosomes analysis of 28 shrews belonging to the genus Crocidura from West Africa allowed the detection of five new karyotypes: C. wimmeri (2n = 50, NF = 84), C. cf. gracilipes (56/86), C. cf. nimbae (46/68), and C. cf. planiceps (44/72). Among the individuals identified morphologically as C. poensis (52/70) a distinct species was recognized on the basis of its chromosome complement, C. nigeriae (50/76). The karyotype of C. occidentalis was confirmed with the study of another subspecies, C. occidentalis manni (50/66). An identical chromosome set characterizes C. odorata giffardi and provides evidence for its relationship with C. occidentalis.

The genome of the fire ant Solenopsis invicta.

Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothers. We used comparative genomic methods to obtain insight into the unique features of the S. invicta genome. For example, we found that this genome harbors four adjacent copies of vitellogenin. A phylogenetic analysis revealed that an ancestral vitellogenin gene first underwent a duplication that was followed by possibly independent duplications of each of the daughter vitellogenins. The vitellogenin genes have undergone subfunctionalization with queen- and worker-specific expression, possibly reflecting differential selection acting on the queen and worker castes. Additionally, we identified more than 400 putative olfactory receptors of which at least 297 are intact. This represents the largest repertoire reported so far in insects. S. invicta also harbors an expansion of a specific family of lipid-processing genes, two putative orthologs to the transformer/feminizer sex differentiation gene, a functional DNA methylation system, and a single putative telomerase ortholog. EST data indicate that this S. invicta telomerase ortholog has at least four spliceforms that differ in their use of two sets of mutually exclusive exons. Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species.

Reinitialization of evolutionary clocks during sublethal environmental stress in some invertebrates

This paper describes the influence of high environmental stress on evolutionary trends in some selected Mesozoic ammonite lineages and some protists. During extinction periods, many ammonoids are affected by drastic simplifications of their shell geometry, ornamentation and suture line. We observe that relatively tightly coiled ammonites can give rise to highly evolute forms or uncoiled heteromorphs with simple ornamentation and almost ceratitic suture line-a phenomenon called "proteromorphosis". Such simplifications often correspond to a reappearance of ancestral geometries (primitive ornamentation, evolute coiling or uncoiling) which suggest that the evolutionary clock of these organisms can be reinitialized by extreme, sublethal, environmental stress such as giant volcanism (including its consequences on diverse pollutions and on climatic changes) and major regressive events. (c) 2006 Elsevier B.V. All rights reserved.

Human nature and institutional analysis

This essay reviews some findings in cognition sciences and examines their consequences for the analysis of institutions. It starts by exploring how humans specialization in producing knowledge ensures our success in dominating the environment but also changes fast our environment. So fast that it did not give time to natural selection to adapt our biology, causing it to be potentially maladapted in important dimensions. A main function of institutions is therefore to fill the gap between the demands of our relatively new environment and our biology, still adapted to our ancestral environment as hunter-gatherers. Moreover, institutions are built with the available elements, which include our instincts. A deeper understanding of both aspects, their adaptive function and this recruitment of ancestral instincts, will add greatly to our ability to manage institutions.

Adaptive sequence evolution in a color gene involved in the formation of the characteristic egg-dummies of male haplochromine cichlid fishes.

BACKGROUND: The exceptionally diverse species flocks of cichlid fishes in East Africa are prime examples of parallel adaptive radiations. About 80% of East Africa's more than 1 800 endemic cichlid species, and all species of the flocks of Lakes Victoria and Malawi, belong to a particularly rapidly evolving lineage, the haplochromines. One characteristic feature of the haplochromines is their possession of egg-dummies on the males' anal fins. These egg-spots mimic real eggs and play an important role in the mating system of these maternal mouthbrooding fish. RESULTS: Here, we show that the egg-spots of haplochromines are made up of yellow pigment cells, xanthophores, and that a gene coding for a type III receptor tyrosine kinase, colony-stimulating factor 1 receptor a (csf1ra), is expressed in egg-spot tissue. Molecular evolutionary analyses reveal that the extracellular ligand-binding and receptor-interacting domain of csf1ra underwent adaptive sequence evolution in the ancestral lineage of the haplochromines, coinciding with the emergence of egg-dummies. We also find that csf1ra is expressed in the egg-dummies of a distantly related cichlid species, the ectodine cichlid Ophthalmotilapia ventralis, in which markings with similar functions evolved on the pelvic fin in convergence to those of the haplochromines. CONCLUSION: We conclude that modifications of existing signal transduction mechanisms might have evolved in the haplochromine lineage in association with the origination of anal fin egg-dummies. That positive selection has acted during the evolution of a color gene that seems to be involved in the morphogenesis of a sexually selected trait, the egg-dummies, highlights the importance of further investigations of the comparative genomic basis of the phenotypic diversification of cichlid fishes.

Extensive gene traffic on the mammalian X chromosome.

Mammalian sex chromosomes have undergone profound changes since evolving from ancestral autosomes. By examining retroposed genes in the human and mouse genomes, we demonstrate that, during evolution, the mammalian X chromosome has generated and recruited a disproportionately high number of functional retroposed genes, whereas the autosomes experienced lower gene turnover. Most autosomal copies originating from X-linked genes exhibited testis-biased expression. Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias.

A burst of segmental duplications in the genome of the African great ape ancestor

It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there are few rearrangements that distinguish ape-human chromosomes, and rates of single-base-pair change and retrotransposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gain are enriched within the primate lineage. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.

Unexpected findings on the taxonomic status of Est Mediterranean Crocidura russula auct. (Mammalaia, Insectivora)

With an approach, based on chromosomal, biochemical and morphological analysis, we show that the animals wich are classically attributed to C. r. gueldenstaedti and/or to C. r. monacha belong in fact to the taxon C. suaveolens. The oriental forms, formely seen as C. russula, are of the same karyotype as C. suaveolens and are biochemically close to C. suaveolens in Central Europe. The origin of the taxonomical confusion might stem from the large morphological variation in and between populations of C. suaveolens in the Near East. Based on our results C. russula monacha Thomas, 1906 belongs to the polymorphic species C. suaveolens Pallas, 1811 and we propose to consider C. (russula) gueldenstaedti Pallas, 1881 as "incertae sedis".

Shield morphology of curly overhair in 22 genera of Soricidae (Insectivora, Mammalia)

The structure of the shield of curly overhairs was studied in 22 genera of shrews, using scanning electron microscopy. The cross section of the shield is quadriconcave with two sides showing particular scale patterns or a relief which can be grouped into 4 morphological types: 1) a smooth type with, at most, shallow U-shaped notches; 2) a type with uniserial, V-shaped tiled notches; 3) a type with a groove and irregular notches; 4) a type with a deep ridged groove. Myosorex, which occupies a basal phyletic position, shows type 3. This type is therefore interpreted as an ancestral character state. It is found also in Feroculus and in some Sylvisorex. In the Crocidurinae, this type evolved into type 2 (Scutisorex and some Indomalayan Crocidura), and finally into type 1 (Suncus and most Crocidura). In the Soricinae, it evolved into type 4, which is common to all genera except Megasorex and Notiosorex. These two genera possess type 1 which is interpreted as being a synapomorphous character of these genera. The regression of the complex structure under dry climatic conditions supports the hypothesis that the function of the grooved form of hair is water repulsion.

Microsomal triglyceride transfer protein promotes the secretion of Xenopus laevis vitellogenin A1.

Vitellogenins (Vtg) are ancient lipid transport and storage proteins and members of the large lipid transfer protein (LLTP) gene family, which includes insect apolipophorin II/I, apolipoprotein B (apoB), and the microsomal triglyceride transfer protein (MTP). Lipidation of Vtg occurs at its site of synthesis in vertebrate liver, insect fat body, and nematode intestine; however, the mechanism of Vtg lipid acquisition is unknown. To explore whether Vtg biogenesis requires the apoB cofactor and LLTP family member, MTP, Vtg was expressed in COS cells with and without coexpression of the 97-kDa subunit of human MTP. Expression of Vtg alone gave rise to a approximately 220-kDa apoprotein, which was predominantly confined to an intracellular location. Coexpression of Vtg with human MTP enhanced Vtg secretion by 5-fold, without dramatically affecting its intracellular stability. A comparison of wild type and a triglyceride transfer-defective form of MTP revealed that both were capable of promoting Vtg secretion, whereas only wild type MTP could promote the secretion of apoB41 (amino-terminal 41% of apoB). These studies demonstrate that the biogenesis of Vtg is MTP-dependent and that MTP is the likely ancestral member of the LLTP gene family.

Le caryotype de Crocidura bolivari (Mammalia, Soricidae) Morales Agacino, 1934 (Mammalia, Soricidae)

The karyotype of Crocidura bolivari from Morocco is characterized by 2n = 50, NF = 66 and NFa = 62, and therefore corresponds to that of Crocidura occidentalis (Pucheran, 1855). Preliminary results on the standard genetic distances revealed by enzyme electrophoresis confirm the close relationship with the African giant shrews.

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.

The function of most proteins is not determined experimentally, but is extrapolated from homologs. According to the "ortholog conjecture", or standard model of phylogenomics, protein function changes rapidly after duplication, leading to paralogs with different functions, while orthologs retain the ancestral function. We report here that a comparison of experimentally supported functional annotations among homologs from 13 genomes mostly supports this model. We show that to analyze GO annotation effectively, several confounding factors need to be controlled: authorship bias, variation of GO term frequency among species, variation of background similarity among species pairs, and propagated annotation bias. After controlling for these biases, we observe that orthologs have generally more similar functional annotations than paralogs. This is especially strong for sub-cellular localization. We observe only a weak decrease in functional similarity with increasing sequence divergence. These findings hold over a large diversity of species; notably orthologs from model organisms such as E. coli, yeast or mouse have conserved function with human proteins.

Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein

Gene duplication was prevalent during hominoid evolution, yet little is known about the functional fate of new ape gene copies. We characterized the CDC14B cell cycle gene and the functional evolution of its hominoid-specific daughter gene, CDC14Bretro. We found that CDC14B encodes four different splice isoforms that show different subcellular localizations (nucleus or microtubule-associated) and functional properties. A microtubular CDC14B variant spawned CDC14Bretro through retroposition in the hominoid ancestor 18-25 million years ago (Mya). CDC14Bretro evolved brain-/testis-specific expression after the duplication event and experienced a short period of intense positive selection in the African ape ancestor 7-12 Mya. Using resurrected ancestral protein variants, we demonstrate that by virtue of amino acid substitutions in distinct protein regions during this time, the subcellular localization of CDC14Bretro progressively shifted from the association with microtubules (stabilizing them) to an association with the endoplasmic reticulum. CDC14Bretro evolution represents a paradigm example of rapid, selectively driven subcellular relocalization, thus revealing a novel mode for the emergence of new gene function

Speciation in the Sorex araneus (Mammalia, Insectivora)

The seven cytologically known species of the Sorex araneus complex each show a different karyotype. The three European species are genetically and morphologically very close, and mostly allopatric, thus having similar ecological requirements. It is suggested that chromosomic changes occasion a stasipatric speciation, the formation of chromosomic races in S. araneus being an illustration of this process. Neither small demes nor high inbreeding are likely in Sorex; thus the Robertsonian changes should spread out by meiotic drive alone, and the hybrids for a change should be almost fully fertile. Chromosomic speciation occurs when two incompatible metacentrics meet together. This model explains the separation between S. araneus and S. coronatus, but geographical isolation must have occured in the case of S. granarius, which keeps a primitive karyotype.

Postglacial recolonization at a snail's pace (Trochulus villosus): confronting competing refugia hypotheses using model selection.

The localization of Last Glacial Maximum (LGM) refugia is crucial information to understand a species' history and predict its reaction to future climate changes. However, many phylogeographical studies often lack sampling designs intensive enough to precisely localize these refugia. The hairy land snail Trochulus villosus has a small range centred on Switzerland, which could be intensively covered by sampling 455 individuals from 52 populations. Based on mitochondrial DNA sequences (COI and 16S), we identified two divergent lineages with distinct geographical distributions. Bayesian skyline plots suggested that both lineages expanded at the end of the LGM. To find where the origin populations were located, we applied the principles of ancestral character reconstruction and identified a candidate refugium for each mtDNA lineage: the French Jura and Central Switzerland, both ice-free during the LGM. Additional refugia, however, could not be excluded, as suggested by the microsatellite analysis of a population subset. Modelling the LGM niche of T. villosus, we showed that suitable climatic conditions were expected in the inferred refugia, but potentially also in the nunataks of the alpine ice shield. In a model selection approach, we compared several alternative recolonization scenarios by estimating the Akaike information criterion for their respective maximum-likelihood migration rates. The 'two refugia' scenario received by far the best support given the distribution of genetic diversity in T. villosus populations. Provided that fine-scale sampling designs and various analytical approaches are combined, it is possible to refine our necessary understanding of species responses to environmental changes.