Genetic diversity of the largest African mole-rat genus, Bathyergus. One, two or four species?

Recent advances in sequencing technology and phylogenetic methods allow us to solve puzzling taxonomic questions using detailed analyses of genetic diversity of populations and gene flow between them. The genus of solitary-living dune mole-rat, Bathyergus, is quite unique among six genera of African mole-rats. The animals are by far the largest and the only scratch digging mole-rat genus possessing a skull less adapted to digging, grooved upper incisors, and more surface locomotor activity. Most authors recognize two species of dune mole-rats, B. suillus and B. janetta, but according to others, the genus is monotypic. In addition, recent molecular studies have revealed cryptic genetic diversity and suggested the existence of up to four species. In our study, we used mitochondrial and genome-wide nuclear data collected throughout the distribution of the genus to investigate the number of species. In agreement with previous studies, we found Bathyergus to be differentiated into several distinct lineages, but we also found evidence for a degree of gene flow between some of them. Furthermore, we confirmed that B. janetta is nested within B. suillus, making the latter paraphyletic and we documented an instance of local mitochondrial introgression between these two nominal species. Phylogeographic structure of the genus was found to be very shallow. Although traditionally dated to the Miocene, we found the first split within the genus to be much younger estimated to 0.82 Ma before present. Genealogical distinctiveness of some lineages was very low, and the coancestry matrix showed extensive sharing of closely related haplotypes throughout the genus. Accordingly, Infomap clustering on the matrix showed all populations to form a single cluster. Overall, our study tends to support the existence of only one species of Bathyergus namely, B. suillus. Environmental niche modelling confirmed its dependence on sandy soils and the preference for soils with relatively high carbon content. Bayesian skyline plots indicate recent population decline in the janetta lineage, probably related to global environmental change.

The taxonomic and phylogenetic status of digeneans from the genus Timoniella (Digenea: Cryptogonimidae) in the Black and Baltic seas.

Timoniella spp. are cryptogonimid flukes (Digenea: Cryptogonimidae) that parasitize the guts of fish in brackish waters. Timoniella imbutiforme, a species from the Mediterranean Sea, is recorded in the Black Sea, while T. balthica has been described from the Baltic Sea. In this paper, we clarify the taxonomic status of Timoniella populations in the Baltic and Black seas. Adults and metacercariae of Timoniella spp. were sampled from localities in the Mediterranean Sea (France), Black Sea (Ukraine) and Baltic Sea (Germany) and subjected to molecular and morphological analysis, including Bayesian phylogenetic reconstruction based on concatenated sequences of ITS1-ITS2-28S. This allowed us to construct a new key to species of the genus Timoniella. Our results suggest that T. balthica forms part of the Boreal-Atlantic relict fauna of the Black Sea and should now be considered a junior synonym of T. imbutiforme.

Expression, function and regulation of Evi-1 during embryonic avian development.

Ecotropical viral integration site 1 (Evi-1) is a transcription factor essential for vascularisation and cell proliferation during embryonic development. The chimeric transcription factor AML1-EVI-1 is activated in leukaemia where it plays a role as a differentiation block and stimulator of proliferation. Here, we cloned chicken Evi-1 and analysed its expression during embryonic development. There was early expression in the pharyngeal arches, in the brain and intermediate mesoderm of chicken embryos at stage 15. Later at stage 20, Evi-1 mesenchymal expression was concentrated in the second pharyngeal arch, and weaker expression was found in the mandibular and maxillary prominences. Facial expression decreased in intensity during development. Evi-1 expression in the limb was also limited to the mesenchyme with the most prominent expression in the anterior margin. Evi-1 was not detectable in the posterior limb bud. At later stages, Evi-1 was expressed in the peripheral mesenchyme of the limb but not in the developing precartilage blastema. At stage 29, the expression became restricted to the perichondrium and interdigital areas; however, the cartilage condensations themselves were negative. To study the function of Evi-1 in chondrogenesis, we knocked down expression in limb micromass cultures using siRNA. Chondrogenesis was significantly reduced in both anterior and posterior cultures. Since Evi-1 was expressed adjacent to the apical ectodermal ridge and this area is a source of FGFs, we tested whether endogenous FGF receptor signalling was necessary to maintain its expression. Inhibitors of FGFRs (PD161570 and SU5402) were applied to wing mesenchyme, and downregulation of Evi-1 expression was observed after treatment with both inhibitors. Therefore, Evi-1 may be a transcription factor mediating the effects of FGF and may also be defining the size of cartilage elements in the limb.

Identification of the first Toll-like receptor gene in passerine birds: TLR4 orthologue in zebra finch (Taeniopygia guttata).

Toll-like receptors (TLRs) are the basic components of the vertebrate pathogen recognition system. Despite uniform general structure, remarkable variability in domain composition can be found in individual TLRs among species. Knowledge of interspecific differences is of particular importance to our understanding of selective pressures on TLRs. Currently, most TLRs are characterized only in a limited number of model species, including domestic chicken as a universal avian model. Here, we describe structure and expression pattern of TLR4 in zebra finch, a widely used passerine model species. The tgTlr4 gene consists of three exons (204, 167 and 3033-3043 bp) that are transcribed into messenger RNA with a relatively long 3'-untranslated region (788 bp). Predicted protein is composed of 842 amino acids (aas) forming extracellular domain with nine leucine-rich repeat (LRR) motives flanked at the carboxy-terminal end by leucine-rich repeat carboxy-terminal domain, transmembrane domain and cytoplasmic toll/interleukin-1 receptor domain. The overall structure is similar to other known TLR4 molecules with 32%-49% aa identity to various mammals and 74% to chicken. Although the position of most of the domains in zebra finch TLR4 resembles their position in chicken, there is one extra LRR at the aa position 207-229 in tgTLR4 and one LRR known in chTLR4 is missing. The gene is highly expressed in the bone marrow and in the spleen, intermediately in the gut and low expression was found in the liver and lungs. For the first time in birds, expression of tgTLR4 in peritoneal macrophages was found to be enhanced by the Escherichia coli lipopolysaccharide treatment.