Population structure, genomic diversity and demographic history of Komodo dragons inferred from whole-genome sequencing.

Population and conservation genetics studies have greatly benefited from the development of new techniques and bioinformatic tools associated with next-generation sequencing. Analysis of extensive data sets from whole-genome sequencing of even a few individuals allows the detection of patterns of fine-scale population structure and detailed reconstruction of demographic dynamics through time. In this study, we investigated the population structure, genomic diversity and demographic history of the Komodo dragon (Varanus komodoensis), the world's largest lizard, by sequencing the whole genomes of 24 individuals from the five main Indonesian islands comprising the entire range of the species. Three main genomic groups were observed. The populations of the Island of Komodo and the northern coast of Flores, in particular, were identified as two distinct conservation units. Degrees of genomic divergence among island populations were interpreted as a result of changes in sea level affecting connectivity across islands. Demographic inference suggested that Komodo dragons probably experienced a relatively steep population decline over the last million years, reaching a relatively stable Ne during the Saalian glacial cycle (400-150 thousand years ago) followed by a rapid Ne decrease. Genomic diversity of Komodo dragons was similar to that found in endangered or already extinct reptile species. Overall, this study provides an example of how whole-genome analysis of a few individuals per population can help define population structure and intraspecific demographic dynamics. This is particularly important when applying population genomics data to conservation of rare or elusive endangered species.

High expressions of the cytoglobin and PGC-1α genes during the tissue regeneration of house gecko (Hemidactylus platyurus) tails.

BACKGROUND: The tissue regeneration process requires high oxygen and energy levels. Cytoglobin (Cygb) is a member of the globin family, which has the ability to bind oxygen, plays a role in dealing with oxidative stress, and carries oxygen into the mitochondria. Energy production for tissue regeneration is associated with mitochondria-especially mitochondrial biogenesis. The peroxisome proliferator-activated receptor-gamma coactivator (PGC)-1alpha protein helps to regulate mitochondrial biogenesis. House geckos (Hemidactylus platyurus) are reptiles that have the ability to regenerate the tissue in their tails. House geckos were selected as the animal models for this study in order to analyze the association of Cygb with oxygen supply and the association of PGC-1α with energy production for tissue regeneration. RESULTS: The growth of house gecko tails showed a slow growth at the wound healing phase, then followed by a fast growth after wound healing phase of the regeneration process. While Cygb mRNA expression reached its peak at the wound healing phase and slowly decreased until the end of the observation. PGC-1α mRNA was expressed and reached its peak earlier than Cygb. CONCLUSIONS: The expressions of both the Cygb and PGC-1α genes were relatively high compared to the control group. We therefore suggest that Cygb and PGC-1α play an important role during the tissue regeneration process.

Expression and role of HIF-1α and HIF-2α in tissue regeneration: a study of hypoxia in house gecko tail regeneration.

The house gecko (Hemidactylus platyurus) has evolved the ability to autotomize its tail when threatened. The lost part is then regrown via epimorphic regeneration in a process that requires high energy and oxygen levels. Oxygen demand is therefore likely to outstrip supply and this can result in relative hypoxia in the tissues of the regenerating tail. The hypoxic state is stabilized by the Hypoxia Inducible Factor-1α (HIF-1α) and HIF-2α proteins. We induced tail autotomy in 30 mal H. platyurus adults using a standard procedure and then collected samples of the regenerated tail tissue on days 1, 3, 5, 8, 10, 13, 17, 21, 25, and 30 post autotomy. For each sample, mRNA expression was analyzed by qPCR, proteins were analyzed using Western Blot tests and immunohistochemistry, and the histological structure was analyzed using Hematoxylin and Eosin staining. On day 1, HIF-1α mRNA expression increased and the tissue was dominated by leucocyte and erythrocyte cells. HIF-1α mRNA expression peaked on day 3, at which time some cells were actively proliferating, migrating, and differentiating. At the same time as HIF-1α expression decreased, HIF-2α mRNA expression increased, as did overall cellular activity. HIF-2α expression increased more gradually but was present over a longer period of time than HIF-1α. We hypothesize that HIF-1α helps to initially stimulate the tissue regeneration process while HIF-2α functionally takes over the role of HIF-1α after HIF-1α succumbs to the oxygen conditions, but we suspect that both HIF-1α and HIF-2α play a role in overcoming the tissue's hypoxic state.