Search publications of the members of the Royal Belgian institute of natural Sciences
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New data on the distribution and phylogenetic position of Mastomys awashensis (Rodentia, Muridae)
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New metallothionein mRNAs in Gobio gobio reveal at least three gene duplication events in cyprinid metallothionein evolution.
- This paper reports the identification and analysis of the primary structure of three novel metallothionein cDNA sequences in the gudgeon, Gobio gobio (Cyprinidae). Two different 180 bp coding regions were identified, resulting in two MT isoforms differing in one amino acid. The primary structure of the amino acid sequence was compared to other cyprinid MT sequences. Furthermore, two differently sized cDNAs were discovered in one of the two transcripts. We present a phylogenetic comparison of our sequences to other, previously published cyprinid MT gene sequences. Our analysis reveals an unexpected complexity in cyprinid MT evolution, with at least three gene duplication events. Differences and homologies between the evolution of cyprinid MT genes are compared to other teleost families. Finally, possible implications for metallothionein classification are discussed.
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On the phylogeny of Lake Baikal amphipods in the light of mitochondrial and nuclear DNA sequence data
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Origin of the superflock of cichlid fishes from Lake Victoria, East Africa.
- Lake Victoria harbors a unique species-rich flock of more than 500 endemic haplochromine cichlid fishes. The origin, age, and mechanism of diversification of this extraordinary radiation are still debated. Geological evidence suggests that the lake dried out completely about 14,700 years ago. On the basis of phylogenetic analyses of almost 300 DNA sequences of the mitochondrial control region of East African cichlids, we find that the Lake Victoria cichlid flock is derived from the geologically older Lake Kivu. We suggest that the two seeding lineages may have already been lake-adapted when they colonized Lake Victoria. A haplotype analysis further shows that the most recent desiccation of Lake Victoria did not lead to a complete extinction of its endemic cichlid fauna and that the major lineage diversification took place about 100,000 years ago.
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Ostracoda as Proxies for Quaternary Climate Change
- We explore how molecular techniques can be applied to ostracod DNA to infer past climatic and environmental fluctuations at several time scales. Cladoceran DNA has been extracted from resting eggs up to several thousand years old but no such work onOstracoda has yet been published.Ostracod eggs are not encased in large protective ephippia as in Cladocera, and only some are pro- tected by thick walls. Collapsed eggs with thin walls will be more difficult to sort individually from sediments; direct extraction of DNA is likely to work only on thick-walled eggs, but could also be possible fromjuveniles hatched fromeggs several hundred years old. The potential for direct extraction of DNA fromfossils (valves, remnant soft parts) is considered. A potential method to infer large climate-induced effects on ancient lakes (e.g. large lake-level fluc- tuations) involves DNA analyses of extant populations, combining phylogenetic and population genetic (coalescent) techniques.
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Out of Tanganyika: genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes.
- The adaptive radiations of cichlid fishes in East Africa are well known for their spectacular diversity and their astonishingly fast rates of speciation. About 80\% of all 2,500 cichlid species in East Africa, and virtually all cichlid species from Lakes Victoria (approximately 500 species) and Malawi (approximately 1,000 species) are haplochromines. Here, we present the most extensive phylogenetic and phylogeographic analysis so far that includes about 100 species and is based on about 2,000 bp of the mitochondrial DNA.
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Over 100 years of biodiversity research on Lake Tanganyika fishes
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Patterns of evolutionary change in Baikalian gammarids inferred from DNA sequences (Crustacea, Amphipoda).
- The Baikalian gammarids (Crustacea, Amphipoda) are the most widely known and most spectacular example of an adaptive radiation among contemporary freshwater invertebrates. To study the phylogeny of the Baikalian gammarids we sequenced a 622-bp-long fragment of the nuclear gene coding for 18S rRNA from species of 18 endemic Baikalian genera and Gammarus pulex-a non-Baikalian taxon. Some important morphological characters appear independently in both lineages and suggest parallelism in the development of gigantism and body armament. The first lineage comprises benthic, mostly unarmed taxa. The second lineage contains predominantly armed taxa, most of which are detrivorous or carnivorous.
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Phylogeny and evolution of African shrews (Mammalia: Soricidae) inferred from 16s rRNA sequences.
- Current phylogenetic hypotheses on the African Crocidurinae (Soricidae) are based upon morpho-anatomical, karyological, and allozyme studies. The present study attempts to resolve the interrelationships among African Crocidurinae and their relationships to Eurasian Crocidurinae and to the subfamily Soricinae, on the basis of partial mitochondrial 16s rRNA sequences (549 bp). This is the first molecular study to include all but one of the nine currently recognized African shrew genera. In agreement with current views, two major lineages emerge. The first lineage includes Myosorex and Congosorex and supports the existence of a myosoricine taxon. The second lineage includes the six remaining genera. The genus Sylvisorex appears to be polyphyletic, whereas species of the controversial genus Crocidura are monophyletic. The genus Suncus presumably originated in Africa. The monospecific genera Ruwenzorisorex and Scutisorex and the two representatives of Paracrocidura cluster with species of other genera. Grouping patterns of species from different continents suggest that there have been multiple exchanges between Africa and Eurasia. The time estimates of these exchanges, inferred from two independent fossil-based calibrations of a molecular clock, coincide with the time estimates for migration events in other mammalian taxa.
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Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the Central and East African haplochromine cichlid fish faunas.
- Lake Tanganyika, the oldest of the East African Great Lakes, harbors the ecologically, morphologically, and behaviorally most complex of all assemblages of cichlid fishes, consisting of about 200 described species. The evolutionary old age of the cichlid assemblage, its extreme degree of morphological differentiation, the lack of species with intermediate morphologies, and the rapidity of lineage formation have made evolutionary reconstruction difficult. The number and origin of seeding lineages, particularly the possible contribution of riverine haplochromine cichlids to endemic lacustrine lineages, remains unclear. Our phylogenetic analyses, based on mitochondrial DNA sequences of three gene segments of 49 species (25\% of all described species, up to 2,400 bp each), yield robust phylogenies that provide new insights into the Lake Tanganyika adaptive radiation as well as into the origin of the Central- and East-African haplochromine faunas. Our data suggest that eight ancient African lineages may have seeded the Tanganyikan cichlid radiation. One of these seeding lineages, probably comprising substrate spawning Lamprologus-like species, diversified into six lineages that evolved mouthbrooding during the initial stage of the radiation. All analyzed haplochromines from surrounding rivers and lakes seem to have evolved within the radiating Tanganyikan lineages. Thus, our findings contradict the current hypothesis that ancestral riverine haplochromines colonized Lake Tanganyika to give rise to at least part of its spectacular endemic cichlid species assemblage. Instead, the early phases of the Tanganyikan radiation affected Central and East African rivers and lakes. The haplochromines may have evolved in the Tanganyikan basin before the lake became a hydrologically and ecologically closed system and then secondarily colonized surrounding rivers. Apparently, therefore, the current diversity of Central and East African haplochromines represents a relatively young and polyphyletic fauna that evolved from or in parallel to lineages now endemic to Lake Tanganyika.
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Phylogeographic structure and regional history of Lemniscomys striatus (Rodentia: Muridae) in tropical Africa
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Phylogeographical patterns of genetic divergence and speciation in African mole-rats (Family: Bathyergidae)
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Phylogeography and cryptic diversity of the solitary-dwelling silvery mole-rat, genus Heliophobius (family: Bathyergidae)
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Pleistocene desiccation in East Africa bottlenecked but did not extirpate the adaptive radiation of Lake Victoria haplochromine cichlid fishes.
- The Great Lakes region of East Africa, including Lake Victoria, is the center of diversity of the mega-diverse cichlid fishes (Perciformes: Teleostei). Paleolimnological evidence indicates dramatic desiccation of this lake ca. 18,000-15,000 years ago. Consequently, the hundreds of extant endemic haplochromine species in the lake must have either evolved since then or refugia must have existed, within that lake basin or elsewhere, from which Lake Victoria was recolonized. We studied the population history of the Lake Victoria region superflock (LVRS) of haplochromine cichlids based on nuclear genetic analysis (12 microsatellite loci from 400 haplochomines) of populations from Lake Kivu, Lake Victoria, and the connected and surrounding rivers and lakes. Population genetic analyses confirmed that Lake Kivu haplochromines colonized Lake Victoria. Coalescent analyses show a 30- to 50-fold decline in the haplochromine populations of Lake Victoria, Lake Kivu, and the region ca. 18,000-15,000 years ago. We suggest that this coincides with drastic climatic and geological changes in the late Pleistocene. The most recent common ancestor of the Lake Victoria region haplochromines was estimated to have existed about 4.5 million years ago, which corresponds to the first radiation of cichlids in Lake Tanganyika and the origin of the tribe Haplochrominii. This relatively old evolutionary origin may explain the high levels of polymorphism still found in modern haplochromines. This degree of polymorphism might have acted as a "genetic reservoir" that permitted the explosive radiation of hundreds of haplochromines and their array of contemporary adaptive morphologies.
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Population structure in two sympatric species of the Lake Tanganyika cichlid tribe Eretmodini: evidence for introgression.
- Patterns of genetic differentiation were analysed and compared in two sympatric species of the endemic Lake Tanganyika cichlid tribe Eretmodini by means of mitochondrial DNA (mtDNA) sequences of the control region and six microsatellite DNA loci. The sample area covers a total of 138 km of mostly uninterrupted rocky shoreline in the Democratic Republic of Congo and includes the entire distribution range of Tanganicodus cf. irsacae that stretches over a distance of 35 km. Both markers detected significant genetic differentiation within and between the two species. T. cf. irsacae contained lower overall genetic variation than Eretmoduscyanostictus, possibly due to its more restricted range of distribution and its smaller effective population sizes. Complete fixation of Tanganicodus mtDNA haplotypes was observed in Eretmodus at two localities, while at two other localities some Tanganicodus individuals possessed Eretmodus mtDNA haplotypes. Taking into account the relatively large average sequence divergence of 6.2\% between the two species, as well as the geographical distribution of mtDNA haplotypes in the lake, the observed pattern is more likely to be a consequence of asymmetric introgression than of shared ancestral polymorphism. As there is significant population differentiation between sympatric Tanganicodus and Eretmodus populations, the events of introgressions may have happened after secondary contact, but our data provide no evidence for ongoing gene flow and suggest that both species are reproductively isolated at present time.
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Providing access to Albertine Rift biodiversity data: a queryable website on taxon and specimen information for selected Albertine Rift species: birds, butterflies (Papilionidae (Papilio, Graphium), Nymphalidae (Charaxes)), flowering plants (coffee family, Rubiaceae), and lacustrine fishes (Cichlidae)
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Rapid chromosomal evolution in the mesic four-striped grass rat Rhabdomys dilectus (Rodentia, Muridae) revealed by mtDNA phylogeographic analysis
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Rapidly evolving lineages impede the resolution of phylogenetic relationships among Clitellata (Annelida).
- The phylogenetic relationships of the Clitellata were investigated using a data set with published and new complete or partial 18S rRNA and mtCOI gene sequences of 13 and 49 taxa representing 8 and 14 families, respectively. Three different alignments were considered for 18S, and the possible influence of departures from rate constancy among sites was evaluated by analyses using a Gamma model of rate heterogeneity. Maximum-likelihood estimates of the shape parameter alpha of the Gamma distribution were very low, whatever the alignment or the gene considered, suggesting that phylogenetic reconstructions taking into account the rate heterogeneity among sites are likely to be the most reliable. Analyzed separately, the two genes did not resolve the relationships among the Clitellata, but the consensus tree was congruent with the morphology-based relationships. Our data suggest the inclusion of the Euhirudinea, Acanthobdellida, and Branchiobdellida in the Oligochaeta and suggest the Lumbriculidae as the link between both assemblages. Although separate analyses of both genes, as well as different alignments for the 18S rRNA sequences, yielded conflicting results concerning the phylogenetic position of leeches and leech-like worms vis-à-vis the Oligochaeta, subsequent analyses using the Gamma model greatly reduced the observed inconsistencies. Our analyses show that among the Clitellata, the leeches and the leech-like and gutless worms represent significantly faster evolving lineages. It is suggested that the observed higher mutation rates may be explained by the fact that these lineages contain almost exclusively commensal and/or parasitic taxa.
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Recensie: PW Hochachka & TP Mommsen (eds.): Molecular biology frontiers
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Reduced gene flow at pericentromeric loci in a hybrid zone involving chromosomal races of the house mouse Mus musculus domesticus.
- The West European house mouse, Mus musculus domesticus, is a particularly suitable model to investigate the role of chromosomal rearrangements in reproductive isolation. In fact, it exhibits a broad range of chromosomal polymorphism due to Robertsonian (Rb) fusions leading to various types of contact zones between different chromosomal races. In the present study, we analyzed a parapatric contact in central Italy between the Cittaducale chromosomal race (CD: 2n= 22) and the surrounding populations with standard karyotype (2n= 40) to understand if Rb fusions play a causative role in speciation. One hundred forty-seven mice from 17 localities were genotyped by means of 12 microsatellite loci. A telomeric and a pericentromeric locus situated on six chromosome arms (four Rbs and one telocentric) were selected to detect differences in the amount of gene flow for each locus in different chromosomal positions. The analyses performed on the two subsets of loci show differences in the level of gene flow, which is more restricted near the centromeres of Rb chromosomes. This effect is less pronounced in the homozygotes populations settled at the border of the hybrid zone. We discuss the possible cause of the differential porosity of gene flow in Rbs considering "hybrid dysfunctions" and "suppressed recombination" models.
