Publications

Giant Galápagos tortoises on the island of Española have been the focus of an intensive captive breeding-repatriation programme for over 35 years that saved the taxon from extinction. However, analysis of 118 samples from released individuals indicated that the bias sex ratio and large variance in reproductive success among the 15 breeders has severely reduced the effective population size (Ne).

Because head regeneration occurs in nerve-free hydra mutants, neurogenesis was regarded as dispensable for this process. Here, in wild-type hydra, we tested the function of the ParaHox gsx homolog gene, cnox-2, which is a specific marker for bipotent neuronal progenitors, expressed in cycling interstitial cells that give rise to apical neurons and gastric nematoblasts (i.e. sensory mechanoreceptor precursors). cnox-2 RNAi silencing leads to a dramatic downregulation of hyZic, prdl-a, gsc and cnASH, whereas hyCOUP-TF is upregulated. cnox-2 indeed acts as an upstream regulator of the neuronal and nematocyte differentiation pathways, as cnox-2(-) hydra display a drastic reduction in apical neurons and gastric nematoblasts, a disorganized apical nervous system and a decreased body size. During head regeneration, the locally restricted de novo neurogenesis that precedes head formation is cnox-2 dependent: cnox-2 expression is induced in neuronal precursors and differentiating neurons that appear in the regenerating tip; cnox-2 RNAi silencing reduces this de novo neurogenesis and delays head formation. Similarly, the disappearance of cnox-2(+) cells in sf-1 mutants also correlates with head regeneration blockade. Hence in wild-type hydra, head regeneration requires the cnox-2 neurogenic function. When neurogenesis is missing, an alternative, slower and less efficient, head developmental program is possibly activated.

We describe a new species of lungfish, Ferganoceratodus martini sp. nov., based on a single specimen discovered in the Late Jurassic - Early Cretaceous of the Phu Nam Jun locality, north-eastern Thailand. The material comprises an almost complete skull roof with associated upper and lower jaws, as well as some postcranial remains. F. martini shows characters unexpected and/or unknown in other Mesozoic lungfishes, such as pieces of a ‘hard snout’. The microstructure of the ‘hard snout’ provides support to the Bemis and Northcutt interpretation of the cosmine tissue of Palaeozoic lungfishes as homologous to the complex cutaneous vasculature of the living Neoceratodus. Because the homologies of the ossifications of the skull roof among lungfishes and among piscian sarcopterygians are unsatisfactorily understood, we use a topological nomenclature in the description of the specimen and in the discussion of post-Devonian dipnoan skull roof characters. We define a few characters for the cladistic analysis only, but these are regarded as less theory-laden. We propose a hypothesis of phylogenetic relationships for most of the post-Devonian forms known by skull remains. The main feature is the ancient dichotomy between the Neoceratodus lineage and most of the other Mesozoic forms, including the Lepidosirenids. The palaeobiogeographical pattern shows a series of vicariant events between Laurasia and Gondwana in the Late Triassic - Early Jurassic, followed by a vicariant event between Africa and South America.

Mitochondrial genomes have recently become widely used in animal phylogeny, mainly to infer the relationships between vertebrates and other bilaterians. However, only 11 of 723 complete mitochondrial genomes available in the public databases are of early metazoans, including cnidarians (Anthozoa, mainly Scleractinia) and sponges. Although some cnidarians (Medusozoa) are known to possess atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization is similar to that of other metazoans. Because the phylogenetic relationships among Anthozoa as well as their relation to other early metazoans still need to be clarified, we tested whether sequencing the complete mitochondrial genome of Savalia savaglia, an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such relationships. Compared to other anthozoans, S. savaglia's genome is unusually long (20,766 bp) due to the presence of several noncoding intergenic regions (3691 bp). The genome contains all 13 protein coding genes commonly found in metazoans, but like other Anthozoa it lacks most of the tRNAs. Phylogenetic analyses of S. savaglia mitochondrial sequences show Zoantharia branching closely to other Hexacorallia, either as a sister group to Actiniaria or as a sister group to Actiniaria and Scleractinia. The close relationships suggested between Zoantharia and Actiniaria are reinforced by strong similarities in their gene order and the presence of similar introns in the COI and ND5 genes. Our study suggests that mitochondrial genomes can be a source of potentially valuable information on the phylogeny of Hexacorallia and may provide new insights into the evolution of early metazoans.

Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using the sequence data of the ENCODE consortium, which include 1% of mammalian genomes in 18 species belonging to all main mammalian lineages. Phylogenetic reconstructions based on an unprecedented amount of coding sequences taken from 218 genes resulted in a highly supported tree placing the root of Placentalia between Afrotheria and Exafroplacentalia (Afrotheria hypothesis). This topology was validated by the phylogenetic analysis of a new class of genomic phylogenetic markers, the conserved noncoding sequences. Applying the tests of alternative topologies on the coding sequence dataset resulted in the rejection of the Atlantogenata hypothesis (Xenarthra grouping with Afrotheria), while this test rejected the second alternative scenario, the Epitheria hypothesis (Xenarthra at the base), when using the noncoding sequence dataset. Thus, the two datasets support the Afrotheria hypothesis; however, none can reject both of the remaining topological alternatives.

The development of suitable intervention strategies to control Salmonella populations at the farm level requires reliable data on the occurrence and prevalence of the pathogen. Previous studies on Salmonella prevalence have focused on acquiring data from specific farm types and/or selected regions. The purpose of this study was to evaluate the distribution of this pathogen across a variety of farm types and regions in order to generate comparative data from a diverse group of environmental samples. Farm samples (n = 2,496) were collected quarterly from 18 different farms across five states (Tennessee, North Carolina, Alabama, California, and Washington) over a 24-month period. The participating farms included beef and dairy cattle operations, swine production and farrowing facilities, and poultry farms (both broiler chicken and turkey). The samples were analyzed for the presence of Salmonella by means of the U.S. Food and Drug Administration's Bacteriological Analytical Manual methods optimized for farm samples. Salmonella isolates were characterized by automated riboprinting. Salmonella serovars were recovered from 4.7% of all samples. The majority of positive findings were isolated from swine farms (57.3%). The occurrence of Salmonella was lower on dairy farms (17.9%), poultry farms (16.2%), and beef cattle farms (8.5%). The most commonly isolated serovar was Salmonella Anatum (48.4%), which was isolated notably more frequently than the next most common Salmonella serovars, Arizonae (12.1%) and Javiana (8.8%). The results of this study suggest that significant reservoirs of Salmonella populations still exist on swine production facilities and to a lesser extent in other animal production facilities. Data showed that the surrounding farm environment could be an important source of contamination.