Comparative cytogenetics of two endangered leuciscine fish, Squalius aradensis and S. torgalensis (Teleostei, Cyprinidae), from the Iberian Peninsula

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

BACKGROUND

The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock - positive loop) and repress expression (cryptochrome (cry) and period (per) - negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type.

RESULTS

We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes.

CONCLUSIONS

Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.

Using asexual vertebrates to study genome evolution and animal physiology: Banded (Fundulus diaphanus) x Common Killifish (F. heteroclitus) hybrid lineages as a model system

Wild, asexual, vertebrate hybrids have many characteristics that make them good model systems for studying how genomes evolve and epigenetic modifications influence animal physiology. In particular, the formation of asexual hybrid lineages is a form of reproductive incompatibility, but we know little about the genetic and genomic mechanisms by which this mode of reproductive isolation proceeds in animals. Asexual lineages also provide researchers with the ability to produce genetically identical individuals, enabling the study of autonomous epigenetic modifications without the confounds of genetic variation. Here, we briefly review the cellular and molecular mechanisms leading to asexual reproduction in vertebrates and the known genetic and epigenetic consequences of the loss of sex. We then specifically discuss what is known about asexual lineages of Fundulus diaphanus x F. heteroclitus to highlight gaps in our knowledge of the biology of these clones. Our preliminary studies of F. diaphanus and F. heteroclitus karyotypes from Porter's Lake (Nova Scotia, Canada) agree with data from other populations, suggesting a conserved interspecific chromosomal arrangement. In addition, genetic analyses suggest that: (a) the same major clonal lineage (Clone A) of F. diaphanus x F. heteroclitus has remained dominant over the past decade, (b) some minor clones have also persisted, (c) new clones may have recently formed, and iv) wild clones still mainly descend from F. diaphanus ♀ x F. heteroclitus ♂ crosses (96% in 2017-2018). These data suggest that clone formation may be a relatively rare, but continuous process, and there are persistent environmental or genetic factors causing a bias in cross direction. We end by describing our current research on the genomic causes and consequences of a transition to asexuality and the potential physiological consequences of epigenetic variation.

Nucleolar organizer region banding in crossbred and non-descript pigs of India

Aim:

The objective of this experiment was to study the nucleolar organizer region (NOR)-banding pattern in Large White Yorkshire (LWY) crossbred and non-descript pigs and finding differences in the number of NORs between animals and between genetic groups.

Materials and Methods:

The experiment was carried out on 15 females, and 15 males of LWY crossbred and non-descript pigs to study NOR-banding pattern by employing ammoniacal silver staining technique.

Results:

A total of 63 and 65 number of good metaphases were prepared in LWY crossbred, and non-descript pigs and a total of 168 and 143 number of NORs were detected on the 8th and 10th chromosomes in both genetic groups, respectively. The mean number of NORs per metaphase was 2.67 and 2.20 in LWY crossbred and non-descript pigs, respectively. LWY crossbred pig had high mean number of silver-stained NORs (Ag-NORs) per metaphase compared to non-descript pig. In general, it was observed that the highest frequency of metaphases (%) examined had two number of NORs, while the lowest frequency (%) had four number of NORs. The number of NORs observed per metaphase on secondary constrictions of the 8th and 10th chromosome pair in both genetic groups ranged from 2 to 4. The Chi-square test of significance revealed that the observed frequencies do not differ significantly from the expected frequencies.

Conclusion:

The results confirmed differences across breeds in occurrence and number of NORs on chromosomes in pigs. The mean numbers of NORs present per metaphase vary between the animals indicating the existence of polymorphism for the number of NORs. A higher number of Ag-NORs were observed on chromosome pair 10 in both the genetic groups. It was concluded that NORs were more morphologically distinct and greater on chromosome pair 10 than on pair 8, which suggests a dominant role of chromosome 10 in the global production of ribosomal RNA.

Karyotype, C-banding and AgNORs of two endemic leuciscine fish, Pseudophoxinuscrassus (Ladiges, 1960) and P.hittitorum Freyhof & Özulug, 2010 (Teleostei, Cyprinidae)

The genus Pseudophoxinus Bleeker, 1860 is found in a wide range of habitats in central Anatolia, but it is not well known from a cytogenetic aspect. In this study the first karyotypic description of the spring minnows Pseudophoxinuscrassus (Ladiges, 1960) and Pseudophoxinushittitorum Freyhof & Özulug, 2010 by means of conventional methods (Giemsa staining, C-banding, silver nitrate impregnation (Ag-NORs)) was performed. Both species are endemic and have restricted distributions in Central Anatolia. Pseudophoxinuscrassus and Pseudophoxinushittitorum have the same diploid chromosome number, 2n = 50, patterns of distribution of constitutive heterochromatin (CH), and localization of nucleolus organizer regions (NORs), but differ in their karyotypic formulae (KFs). The C-banding technique revealed clear pericentromeric blocks of CH in many chromosomes; Ag-NORs treatment revealed consistent positive signals at the end of the short arms of a submetacentric chromosome pair, likely homologous in both species. The karyotypic differences found between these species can be used for their taxonomical study.