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Introgression is a widespread evolutionary process leading to phylogenetic inconsistencies among distinct parts of the genomes, particularly between mitochondrial and nuclear-based phylogenetic reconstructions (e.g., mito-nuclear discordances). Here, we used mtDNA and genome-wide nuclear sites to provide the first phylogenomic-based hypothesis on the evolutionary relationships within the killifish genus Kryptolebias. In addition, we tested for evidence of past introgression in the genus given the multiple reports of undergoing hybridization between its members. Our mtDNA phylogeny generally agreed with the relationships previously proposed for the genus. However, our reconstruction based on nuclear DNA revealed an unknown lineage - Kryptolebias sp. \'ESP\' - as the sister group of the self-fertilizing mangrove killifishes, K. marmoratus and K. hermaphroditus. All individuals sequenced of Kryptolebias sp. \'ESP\' had the same mtDNA haplotype commonly observed in K. hermaphroditus, demonstrating a clear case of mito-nuclear discordance. Our analysis further confirmed extensive history of introgression between Kryptolebias sp. \'ESP\' and K. hermaphroditus. Population genomics analyses indicate no current gene flow between the two lineages, despite their current sympatry and history of introgression. We also confirmed introgression between other species pairs in the genus that have been recently reported to form hybrid zones. Overall, our study provides a phylogenomic reconstruction covering most of the Kryptolebias species, reveals a new lineage hidden in a case of mito-nuclear discordance, and provides evidence of multiple events of ancestral introgression in the genus. These findings underscore the importance of investigating different genomic information in a phylogenetic framework, particularly in taxa where introgression is common as in the sexually diverse mangrove killifishes.

Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.

Volcanic and tectonic activities in conjunction with Quaternary climate are the main events that shaped the geographical distribution of genetic variation of many lineages. Poeciliopsis infans is the only poeciliid species that was able to colonize the temperate highlands of central Mexico. We inferred the phylogenetic relationships, biogeographic history, and historical demography in the widespread Neotropical species P. infans and correlated this with geological events and the Quaternary glacial-interglacial climate in the highlands of central Mexico, using the mitochondrial genes Cytochrome b and Cytochrome oxidase I and two nuclear loci, Rhodopsin and ribosomal protein S7.
Populations of P. infans were recovered in two well-differentiated clades. The maximum genetic distances between the two clades were 3.3% for cytb, and 1.9% for coxI. The divergence of the two clades occurred ca. 2.83 Myr. Ancestral area reconstruction revealed a complex biogeographical history for P. infans. The Bayesian Skyline Plot showed a demographic decline, although more visible for clade A, and more recently showed a population expansion in the last 0.025 Myr. Finally, the habitat suitability modelling showed that during the LIG, clade B had more areas with high probabilities of presence in comparison to clade A, whereas for the LGM, clade A showed more areas with high probabilities of presence in comparisons to clade B.
Poeciliopsis infans has had a complex evolutionary and biogeographic history, which, as in other co-distributed freshwater fishes, seems to be linked to the volcanic and tectonic activities during the Pliocene or early Pleistocene. Populations of P. infans distributed in lowlands showed a higher level of genetic diversity than populations distributed in highlands, which could be linked to more stable and higher temperatures in lowland areas. The fluctuations in population size through time are in agreement with the continuous fluctuations of the climate of central Mexico.

Studies on parental aging are a very attractive field, although it is poorly understood how parental age affects embryonic development and adult traits of the offspring. In this study, we used the turquoise killifish Nothobranchius furzeri, as is the vertebrate with shortest captive lifespan and an interesting model. The embryos of N. furzeri can follow two distinct developmental pathways either entering diapause or proceeding through direct development. Thus, this embryonic plasticity allows this model to be used to study different factors that could affect their embryonic development, including parental age. The first goal of the present study was to investigate whether parental aging could affect the embryo development. To do this, we collected F1 embryos from two breeder groups (old parents and young parents). We monitored the duration of embryonic development and analyzed genes involved in dorsalization process. The second goal was to investigate if embryonic developmental plasticity could be modulated by an epigenetic process. To this end, the expression of DNMTs genes was examined. Our data support the hypothesis that diapause, occurring more frequently in embryos from old parents, is associated with increased expression of DNMT3A and DNMT3B suggesting an epigenetic control. Finally, we analyzed whether parental age could affect metabolism and growth during adult life. Morphometric results and qPCR analysis of genes from IGF system showed a slower growth in adults from old breeders. Moreover, a gender-specificity effect on growth emerged. In conclusion, these results may contribute to the better understanding of the complex mechanism of aging.

In recent years, the use of biochemical markers, especially in the assessment of toxic effects and modes of action, under controlled laboratory conditions has increased. However, transposing their use to in situ monitoring or risk assessment evaluations has encountered barriers, mainly related to the difficulty in interpreting the meaning of biochemical variation. In this work, we aimed at understanding if biochemical marker activities (cholinesterase, glutathione S-transferase and lactate dehydrogenase) can be used to monitor the health status of natural populations of fish (Gambusia affinis) and daphnids (Daphnia magna). For that, two ponds with different water properties were chosen as study sites, and organisms collected at four sampling periods along the year. The pattern of biochemical marker responses was not the same in the two species, showing higher integrated biochemical marker response values in the winter for G. affinis and in the autumn for D. magna, suggesting specificities that must be taken into account in biomonitoring programmes by including representative species of several trophic levels. In the case of G. affinis, the differences in key physicochemical parameters between the two ponds (especially dissolved oxygen levels) did not seem to affect biochemical marker levels as if organisms were already perfectly adapted to their environment. In general, seasonal variation of water quality seems to have an important role on biochemical marker responses. Several parameters above Environmental Quality Standards were identified such as dissolved oxygen (DO), ammonia, nitrites, sulphides and metals, but eventual responses to these stressors could not be discriminated from natural variation except for particular cases.

BACKGROUND: Annual Nothobranchius fishes are distributed in East and Southern Africa and inhabit ephemeral pools filled during the monsoon season. Nothobranchius show extreme life-history adaptations: embryos survive by entering diapause and they are the vertebrates with the fastest maturation and the shortest lifespan. The distribution of Nothobranchius overlaps with the East Africa Rift System. The geological and paleoclimatic history of this region is known in detail: in particular, aridification of East Africa and expansion of grassland habitats started 8 Mya and three humid periods between 3 and 1 Mya are superimposed on the longer-term aridification. These climatic oscillations are thought to have shaped evolution of savannah African mammals. We reconstructed the phylogeny of Nothobranchius and dated the different stages of diversification in relation to these paleoclimatic events.
RESULTS: We sequenced one mitochondrial locus and five nuclear loci in 63 specimens and obtained a robust phylogeny. Nothobranchius can be divided in four geographically separated clades whose boundaries largely correspond to the East Africa Rift system. Statistical analysis of dispersal and vicariance identifies a Nilo-Sudan origin with southwards dispersion and confirmed that these four clades are the result of vicariance events In the absence of fossil Nothobranchius, molecular clock was calibrated using more distant outgroups (secondary calibration). This method estimates the age of the Nothobranchius genus to be 8.3 (6.0 - 10.7) My and the separation of the four clades 4.8 (2.7-7.0) Mya. Diversification within the clades was estimated to have started ~3 Mya and most species pairs were estimated to have an age of 0.5-1 My.
CONCLUSIONS: The mechanism of Nothobranchius diversification was allopatric and driven by geographic isolation. We propose a scenario where diversification of Nothobranchius started in rough coincidence with aridification of East Africa, establishment of grassland habitats and the appearance of the typical African bovid fauna of the savannah. Although confidence intervals for the estimated ages of the four Nothobranchius clades are quite large, this scenario is compatible with the biology of extant Nothobranchius that are critically dependent on savannah habitats. Therefore, Nothobranchius diversification might have been shaped by the same paleoclimatic events that shaped African ungulate evolution.

The poeciliid Cnesterodon decemmaculatus is one of the native species of southern South America recently recommended for use as a test species in biomonitoring. Therefore, it is important to characterize its responses to stress conditions caused by pollution. The aim of this work was to determine the toxicity of the reference toxicant cadmium (Cd) and to evaluate the lethality response of juveniles of C. decemmaculatus exposed to an environmental sample with a high degree of pollution (Luján River, Buenos Aires, Argentina). The LC₅₀ values at 24 and 96 h were 6.00 and 2.27 mg Cd/L, respectively. The uptake of Cd was significantly greater in the first 24 h in relation to the total time of exposure in the bioassay. The toxicity of the water was in agreement with the level of contamination. A Cd contaminant pulse exerted an important additive effect on the toxicity of the environmental sample. The results provide information regarding the sensitivity of a native species to be used as a test organism in environmental monitoring.

Previous studies showed that caffeine, diphenhydramine, and carbamazepine were bioconcentrated by mosquito fish (Gambusia holbrooki) from freshwater bodies directly affected by reclaimed water. To understand the uptake, depuration, and bioconcentration factors (BCFs) under the worst-case conditions, the authors exposed 84 mosquito fish to reclaimed water under static renewal for 7 d, followed by a 14-d depuration phase in clean water. Characterization of the exposure media revealed the presence of 26 pharmaceuticals, whereas only 5 pharmaceuticals-caffeine, diphenhydramine, diltiazem, carbamazepine, and ibuprofen-were present in the organisms after only 5 h of exposure. Caffeine, diltiazem, and carbamazepine were quickly taken up by mosquito fish following a similar uptake curve. Diphenhydramine and ibuprofen, on the other hand, were more gradually taken up by mosquito fish but were also eliminated fairly quickly, resulting in the 2 shortest depuration half-lives at 34 h and 32 h, respectively. For comparison, BCFs based on rate constants (BCFb ), steady-state concentrations (BCFa ), and saturation-state concentrations (BCFc ) were calculated. Values of BCFb ranged from 0.23 to 29 and increased in the order of caffeine < carbamazepine < diltiazem < diphenhydramine < ibuprofen. Values of BCFa and BCFc ranged from 2.0 to 28 and increased in the order of carbamazepine < caffeine < diltiazem < diphenhydramine < ibuprofen. This is the first study using a nonartificial exposure-treated wastewater matrix to generate pharmacokinetic data for pharmaceutical mixtures in aquatic organisms. Environ Toxicol Chem 2013;32:1752-1758. © 2013 SETAC.