No abstract

Biological clocks have evolved as an adaptation to life on a rhythmic planet, synchronising physiological processes to the environmental light-dark cycle. Here we examine circadian clock function in Mexican blind cavefish Astyanax mexicanus and its surface counterpart. In the lab, adult surface fish show robust circadian rhythms in per1, which are retained in cave populations, but with substantial alterations. These changes may be due to increased levels of light-inducible genes in cavefish, including clock repressor per2. From a molecular standpoint, cavefish appear as if they experience 'constant light' rather than perpetual darkness. Micos River samples show similar per1 oscillations to those in the lab. However, data from Chica Cave shows complete repression of clock function, while expression of several lightresponsive genes is raised, including DNA repair genes. We propose that altered expression of light-inducible genes provides a selective advantage to cavefish at the expense of a damped circadian oscillator.

While Quaternary climatic changes are considered by some to have been a major factor promoting speciation within the neotropics, others suggest that much of the neotropical species diversity originated before the Pleistocene. Using mitochondrial and nuclear sequence data, we evaluate the relative importance of Pleistocene and pre-Pleistocene events within the evolutionary history of the Mexican iguana Ctenosaura pectinata, and related species. Results support the existence of cryptic lineages with strong mitochondrial divergence (> 4%) among them. Some of these lineages form zones of secondary contact, with one of them hybridizing with C. hemilopha. Evolutionary network analyses reveal the oldest populations of C. pectinata to be those of the northern and southern Mexican coastal regions. Inland and mid-latitudinal coastal populations are younger in age as a consequence of a history of local extinction within these regions followed by re-colonization. Estimated divergence times suggest that C. pectinata originated during the Pliocene, whereas geographically distinct mitochondrial DNA lineages first started to diverge during the Pliocene, with subsequent divergence continuing through the Pleistocene. Our results highlight the influence of both Pliocene and Pleistocene events in shaping the geographical distribution of genetic variation within neotropical lowland organisms. Areas of high genetic diversity in southern Mexico were detected, this finding plus the high levels of genetic diversity within C. pectinata, have implications for the conservation of this threatened species.

Aim Our aim was to investigate genetic structure in Neotropical populations of common green iguanas (Iguana iguana) and to compare that structure with past geological events and present barriers. Additionally, we compared levels of divergence between lineages within Iguana with those within closely related genera in the subfamily Iguaninae. Location Neotropics. Methods DNA sequence data were collected at four loci for up to 81 individuals from 35 localities in 21 countries. The four loci, one mitochondrial (ND4) and three nuclear (PAC, NT3, c‐mos), were chosen for their differences in coalescent and mutation rates. Each locus was analysed separately to generate gene trees, and in combination in a species‐level analysis. Results The pairwise divergence between Iguana delicatissima and I. iguana was much greater than that between sister species of Conolophus and Cyclura and non‐sister species of Sauromalus, at both mitochondrial (mean 10.5% vs. 1.5–4%, respectively) and nuclear loci (mean 1% vs. 0–0.18%, respectively). Furthermore, divergences within I. iguana were equal to or greater than those for interspecific comparisons within the outgroup genera. Phylogenetic analyses yielded four strongly supported, geographically defined mitochondrial clades (3.8–5% divergence) within I. iguana. Three of the four clades were found using PAC (0.18–1.65% divergence) and two using NT3 (0.6% divergence) alone. The primary divergence, recovered in three polymorphic loci, was between individuals north and south of the Isthmus of Panama. The southern group was differentiated into clades comprising individuals on either side of the northern Andes, using both PAC and ND4. Main conclusions Deep genetic divergences were found within I. iguana that are congruent with past and current geological barriers. These divisions are greater than sister species comparisons in other Iguaninae genera, indicating the possible presence of cryptic species. Geological changes from the mid‐Miocene through the Plio‐Pleistocene have shaped the pattern of divergence in I. iguana. The uplift of the northern Andes presented a barrier between South American I. iguana populations by 4 Ma. Populations north of the Isthmus of Panama form a clade that is distinct from those to the south, and may have expanded northwards following the closing of the Isthmus of Panama 2.5 Ma.

Matrix models and population viability analysis (PVA) have become useful tools to understand population attributes and dynamics. Demography analysis gives valuable information for the management of threatened species, and can be used to create action plans for their conservation. PVA is particularly useful in those species with small population sizes difficult to sample. By calculating the individual fate of each member of the population, PVA simulates temporal population changes and estimates extinction risk over a time period. Here we use these models to analyse the population of axolotl Ambystoma mexicanum, which has decreased more than six times within only 5 years. Its natural environment (the Xochimilco aquatic system within Mexico City) has deteriorated significantly in the last decades. The matrix analysis showed large oscillations in the axolotl population growth rate (damping behaviour), which could explain the fast density reduction in only few generations. Younger ages (eggs and larvae) showed the highest sensitivity and elasticity values, suggesting that the lack of food sources such as zooplankton or the increased predation by exotic carp and tilapia are capable to reduce axolotl density. PVA shows low extinction probabilities using laboratory data for younger ages. However, a small reduction in egg or larvae survival rate is capable to increase extinction probabilities to 100% in 20 years. Based on these results, we found that the best strategy to restore the axolotl population is to increase the survival rate of eggs and larvae by restoring the habitat, eradicating introduced fish and improving water quality, rather than implementing a reintroduction programme.