Publications

The evolution of tetrapod limbs from fish fins enabled the conquest of land by vertebrates and thus represents a key step in evolution. Despite the use of comparative gene expression analyses, critical aspects of this transformation remain controversial, in particular the origin of digits. Hoxa and Hoxd genes are essential for the specification of the different limb segments and their functional abrogation leads to large truncations of the appendages. Here we show that the selective transcription of mouse Hoxa genes in proximal and distal limbs is related to a bimodal higher order chromatin structure, similar to that reported for Hoxd genes, thus revealing a generic regulatory strategy implemented by both gene clusters during limb development. We found the same bimodal chromatin architecture in fish embryos, indicating that the regulatory mechanism used to pattern tetrapod limbs may predate the divergence between fish and tetrapods. However, when assessed in mice, both fish regulatory landscapes triggered transcription in proximal rather than distal limb territories, supporting an evolutionary scenario whereby digits arose as tetrapod novelties through genetic retrofitting of preexisting regulatory landscapes. We discuss the possibility to consider regulatory circuitries, rather than expression patterns, as essential parameters to define evolutionary synapomorphies.

Genetic differences between Northeast Asian (NEA) and Southeast Asian (SEA) populations have been observed in numerous studies. At the among-population level, despite a clear north-south differentiation observed for many genetic markers, debates were led between abrupt differences and a continuous pattern. At the within-population level, whether NEA or SEA populations have higher genetic diversity is also highly controversial. In this study, we analyzed a large set of HLA data from East Asia in order to map the genetic variation among and within populations in this continent and to clarify the distribution pattern of HLA lineages and alleles. We observed a genetic differentiation between NEA and SEA populations following a continuous pattern from north to south, and we show a significant and continuous decrease of HLA diversity by the same direction. This continuity is shaped by clinal distributions of many HLA lineages and alleles with increasing or decreasing frequencies along the latitude. These results bring new evidence in favor of the "overlapping model" proposed previously for East Asian peopling history, whereby modern humans migrated eastward from western Eurasia via two independent routes along each side of the Himalayas and, later, overlapped in East Asia across open land areas. Our study strongly suggests that intensive gene flow between NEA and SEA populations occurred and shaped the latitude-related continuous pattern of genetic variation and the peculiar HLA lineage and allele distributions observed in this continent. Probably for a very long period, the exact duration of these events remains to be estimated.

The prevalence of rheumatoid arthritis and its specific autoantibodies varies in different populations. This variability depends on the genetic polymorphism of the immune response genes among which the HLA system plays a major role. In this context, we studied the HLA-DRB1 and HLA-DQB1 first-level allele frequencies in 100 Albanian patients with rheumatoid arthritis (RA), and taking into account their rheumatoid factor (RF) and anticitrullinated peptide antibodies (ACPA) serologic subgroups, we compared them with the respective frequencies in a population of 191 Albanian individuals without known pathology. No differences were found between the controls and the RA patient group as a whole, but three statistically significant differences were found: an increase in DRB1*04 among ACPA+, RF+ and ACPA+/RF+ patients, a significant decrease in DRB1*11 among ACPA+/RF+ and also a decrease in DRB1*13 among RF+ patient subgroups. Comparing allele frequencies of putatively associated RA alleles in different European populations revealed a significant negative correlation between the RA predisposing DRB1*04 and protective DRB1*11 allele frequencies. A statistically significant correlation was also found between RA prevalence rates and DRB1*04 as well as DRB1*11 frequencies. The relatively low frequencies of DRB1*04 and high DRB1*11 in the Albanian population might explain the rather low positivity rate of ACPA and RF antibodies among the Albanian RA patients. These specific association patterns suggest that this first study of RA in an Albanian population should be followed up to include second level or higher definition of HLA alleles and to compare RA patterns among European populations.

Explaining the genetic diversity of past and present European populations Although it is the continent with the lowest genomic diversity, Europe embraces a significant degree of variation, shaped by complex demographic events and locus-specific selective factors linked to environmental conditions. The European genetic diversity observed today has also important clinical and epidemiological implications. Different questions related to these topics are addressed in this special topic issue of eight excellent papers written by specialized European teams. The papers document the remarkable progress achieved in the last years in exploring human genomic diversity, both in past and present populations, in reconstructing complex scenarios of European peopling history using sophisticated data analyses and computer simulations, in identifying signatures of adaptive selection in milk digestion- and immune-related genes, and in applying this knowledge to crucial health issues, from tissue transplantation to disease associations. Genetic Diversity in European Populations: Evolutionary Evidence and Medical Implications is of special interest to researchers and students in biological and medical sciences and clinicians, who wish to update their knowledge in the field of European genetic diversity for basic research and medical applications.

The Early Triassic witnessed the highest taxic diversity of coelacanths (or Actinistia), a clade with a single liv- ing genus today. This peak of diversity is accentuated here with the description of a new coelacanth discovered in the lower Spathian (Upper Olenekian, Lower Triassic) cropping out in the Tulcea Veche (Old Tulcea) promon- tory, in the city of Tulcea, in North Dobrogea, Romania. The bone remains were preserved in a block of limestone, which was chemically dissolved. The resulting 3D and matrix-free ossifications correspond mostly to elements of the skull and branchial apparatus. Posterior parietals, postparietal with associated prootic and basisphenoid allow a precise description of the neurocranium. Ossifications of the lower jaw, together with branchial and pec- toral elements, complete the description of this coelacanth and support the coining of a new generic and specific name, Dobrogeria aegyssensis. A phylogenetic analysis of actinistians with the new species recovers clades which were found in most recent analyses, i.e. the Sasseniidae, the Laugiidae, the Coelacanthiformes, the Latimerioidei, the Mawsoniidae and the Latimeriidae, and identifies the new taxon as a non-latimerioid coelacanthiform.

A new ginglymodian fish, Isanichthys lertboosi, is described from the Phu Kradung Formation, north-eastern Thailand, a freshwater deposit of probable Late Jurassic age. The species is represented by four specimens, from the Phu Noi locality, associated with a rich fauna of sharks, turtles, crocodiles, and theropod and sauropod dinosaurs. One specimen is an isolated braincase, which provides characters rarely observed in extinct ginglymodians. The species is referred to the genus Isanichthys, a taxon originally described on the basis of a single specimen from the Phu Nam Jun locality, a slightly younger site approximately 75 km from Phu Noi. Isanichthys is mainly distinguished by frontals slightly narrower anteriorly than posteriorly, two anterior infraorbitals not in contact with the orbit, reduced preorbital region, and a small orbit and a cheek region completely covered by bones. The new species is characterized, among other characters, by a dermal component of the sphenotic visible on the cheek, one pair of extrascapulars plus a small median one, the presence of few suborbitals (ca. 4 or 6) arranged in one row, and a median dorsal row of scales with spine. Comparisons with other ginglymodian taxa and a cladistic analysis indicates that Isanichthys (Lepidotes) latifrons from the Late Jurassic of England, as well as probably Isanichthys (Lepidotes) luchowensis from the Early or Middle Jurassic of Sichuan, China, form a clade with both Thai species of Isanichthys. The new species provides evidence of the high diversity of ginglymodian fishes in the Phu Kradung Formation and suggests a new hypothesis of phylogenetic relationships among extinct ginglymodians.

DNA barcoding is the molecular identification of species using short, standardized gene sequences. Numerous applications of DNA barcoding in taxonomy, ecology, bioconservation, and biosafety contributed to a spectacular development of this initiative administered by the Consortium for the Barcode of Life (CBOL). Reference databases that assign DNA barcodes to particular morphospecies have been developed for almost all groups of animals, plants, and fungi, as well as some groups of protists (i.e., diatoms, ciliates, amoebae). However, such a database does not exist for foraminifera, despite large numbers of DNA sequences being available. To fill this gap, we initiated the Foram Barcoding (FB) project, whose objective is to create a curated molecular database for modern foraminifera. Each species included in our database is represented by one or several specimens, from which DNA was extracted and sequenced. Species entries include photos of processed specimens, taxonomic references, and DNA barcode sequences. A fragment of the 18S rRNA gene, commonly used in foraminiferal molecular studies, was chosen as the DNA barcode. We believe that the FB project will help resolve at least some misidentification problems that plague foraminiferal taxonomy. We also foresee its further applications in such domains of foraminiferal research as diversity assessment, ecology, biogeography, and biomonitoring. However, we are aware that the impact of the FB database depends mainly on its completeness and accuracy, and thus we appeal to the community of foraminiferologists to support this project by providing material for genetic studies and by contributing their taxonomic expertise in species identification and documentation.