Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.
Montane regions can promote allopatric speciation and harbor unique species with small ranges. The southern Appalachians are a biodiversity hotspot for salamanders, and several montane endemics occur in the region. Here, we present the first DNA sequence data for Plethodon sherando, a terrestrial salamander recently discovered in the Blue Ridge Mountains of Virginia. We sequenced two mitochondrial regions (cyt-b and CO1) from salamanders at reference sites near the center of P. sherando's range and from two contact zones where P. sherando populations are replaced by Plethodon cinereus, the Northern Red-Backed salamander. We then used these sequence data to examine divergence and hybridization between the two taxa. We found P. sherando and P. cinereus morphotypes from contact zones to be reciprocally monophyletic and highly divergent (*17%). P. sherando exhibited very low sequence diversity (p = 0.0010) as compared to P. cinereus from the same locations (p = 0.0096). Salamander morphology in the contact zone was as distinct as morphology at reference sites, and discriminant function analysis based on morphology successfully classified 98% of salamanders to their mitochondrial lineage. Phylogenetic analysis of cyt-b sequences showed P. sherando to be sister to Plethodon serratus (the Southern Red-Backed salamander) rather than P. cinereus or any nearby mountaintop endemics. Our results suggest that P. sherando is a distinct lineage that is not subject to substantial introgression from P. cinereus and that may have a history of geographic isolation. Given its limited range (\80 km 2 ), we believe P. sherando should merit a conservation status similar to that of other mountaintop salamanders in the region.
Understanding the impact of hatchery supplementation on the genetics of wild fish populations is important for designing and evaluating ecologically sound stocking practices. For species such as brook trout Salvelinus fontinalis, which are a high priority for conservation and restoration in their native range, understanding the potential impacts of stocking on the functional diversity of wild populations is critical. We sought to determine whether brook trout stocked in low-order reservoirs colonize impoundment feeder streams and if they naturally reproduce and interbreed with established native populations in these tributaries. Analysis of microsatellite DNA allowed us to distinguish hatcheryorigin brook trout and putative native strains among tributaries of three stocked reservoirs and one unstocked stream. Hatchery-origin fish were found in tributaries of all stocked reservoirs, mixed with native populations; none were found in an unstocked reference stream that supported wild brook trout. Age-1 brook trout genetically matching a known hatchery strain were found in tributaries of stocked reservoirs, although none of this age were stocked, suggesting that stocked trout have successfully reproduced in these streams. Assignment tests indicated that 4 of the 98 brook trout collected from mixed stocked-native streams were probably hybrids (∼4.1%; 95% confidence interval = 1.3-10.0%). These results suggest that to date the direct impacts of stocking on the genetics of these native populations have been limited but that indirect impacts through competition or similar interactions may still be occurring.Conservation of populations of wild and putative native brook trout Salvelinus fontinalis is of considerable concern within its native range. Hudy et al. (2008) recently documented extensive loss of suitable brook trout habitat in the eastern United States and extirpation of populations from 28% of historically occupied subwatersheds in this region. In the Commonwealth of Virginia, extirpation from 38% of the subwatersheds was documented, and only 9% of historically occupied watersheds retain "intact" populations (EBTJV 2006;Hudy et al. 2008). In many areas, inadequate thermal regimes in higherorder streams have caused brook trout populations to persist
Climate change poses several challenges to biological communities including changes in the frequency of encounters between closely related congeners as a result of range shifts. When climate change leads to increased hybridization, hybrid dysfunction or genetic swamping may increase extinction risk—particularly in range‐restricted species with low vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully terrestrial woodland salamander that is restricted to ~18 km of ridgeline in the mountains of southwestern Virginia, and its range is surrounded by the abundant and widespread Eastern Red‐backed Salamander, Plethodon cinereus. In order to determine whether these two species are hybridizing and how their range limits may be shifting, we assessed variation at eight microsatellite loci and a 1,008 bp region of Cytochrome B in both species at allopatric reference sites and within a contact zone. Our results show that hybridization between P. hubrichti and P. cinereus either does not occur or is very rare. However, we find that diversity and differentiation are substantially higher in the mountaintop endemic P. hubrichti than in the widespread P. cinereus, despite similar movement ability for the two species as assessed by a homing experiment. Furthermore, estimation of divergence times between reference and contact zone populations via approximate Bayesian computation is consistent with the idea that P. cinereus has expanded into the range of P. hubrichti. Given the apparent recent colonization of the contact zone by P. cinereus, future monitoring of P. cinereus range limits should be a priority for the management of P. hubrichti populations.
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