Parallel evolution of fish bi-modal breathing and expansion of olfactory receptor (OR) genes: toward a universal ORs nomenclature.

Olfactory receptors (ORs) play a key role in the prime sensorial perception, being highly relevant for intra/interspecific interactions. ORs are a subgroup of G-protein coupled receptors that exhibit highly complex subgenomes in vertebrates. However, OR repertoires remain poorly studied in fish lineages, precluding finely retracing their origin, evolution, and diversification, especially in the most basal groups. Here, we conduct an exhaustive gene screening upon 43 high-quality fish genomes exhibiting varied gene repertoires (2-583 genes). While the early vertebrates performed gas exchange through gills, we hypothesize that the emergence of new breathing structures (swim bladder and paired lungs) in early osteichthyans may be associated with expansions in the ORs gene families sensitive to airborne molecules. Additionally, we verify that the OR repertoire of moderns actinopterygians has not increased as expected following a whole genome duplication, likely due to regulatory mechanisms compensating the gene load excess. Finally, we identify 25 distinct OR families, allowing us to propose an updated universal nomenclature for the fish ORs.

The genes from the pseudoautosomal region 1 (PAR1) of the mammalian sex chromosomes: Synteny, phylogeny and selection.

Sex chromosomes recombine restrictly in their homologous area, the pseudoautosomal region (PAR), represented by PAR1 and PAR2, which behave like an autosome in both pairing and recombination. The PAR1, common to most of the eutherian mammals, is located at the terminus of the sex chromosomes short arm and exhibit recombination rates ~20 times higher than the autosomes. Here, we assessed the interspecific evolutionary genomic dynamics of 15 genes of the PAR1 across 41 mammalian genera (representing six orders). The strong negative selection detected in most of the assessed groups reinforces the presence of evolutionary constraints, imposed by the important function of the PAR1 genes. Indeed, mutations in these genes are associated with various diseases in humans, including stature problems (Klinefelter Syndrome), leukemia and mental diseases. Yet, a few genes exhibiting positive selection (ω-value >1) were depicted in Rodentia (ASMT and ZBED1) and Primates (CRLF2 and CSF2RA). Rodents have the smallest described PAR1, while that of simian primates/humans underwent a 3 to 5 fold size reduction. The assessment of the PAR1 genes synteny revealed differences among the mammalian species, especially in the Rodentia order where chromosomic translocations from the sex chromosomes to the autosomes were observed. Such syntenic changes may be an evidence of the rapid evolution in rodents, as previous referred in other papers, also depicted by their increased branch lengths in the phylogenetic analyses. Concluding, we suggest that genome migration is an important factor influencing the evolution of mammals and may result in changes of the selective pressures operating on the genome.

Strong Sexual Selection Does Not Induce Population Differentiation in a Fish Species with High Dispersal Potential: The Curious Case of the Worm Pipefish Nerophis lumbriciformis (Teleostei: Syngnathidae).

High levels of population differentiation are a common demographic pattern in syngnathids, even at small geographical scales. This is probably the end result of the common life history traits observed within the family, involving limited dispersal capabilities and strong habitat dependency. The worm pipefish, Nerophis lumbriciformis, which displays all these characteristics, also presents an additional variable potentially able to promote population differentiation: high sexual selection intensity, especially at the extremes of its distribution. Nevertheless, an early life pelagic stage, which presumably allows for admixture, could prevent population structuring. Here, we assessed the phylogeography of N. lumbriciformis through the amplification of the cytochrome b, 12S, and 16S rDNA mitochondrial markers as well as the rhodopsin nuclear marker, performed upon 119 individuals. We observed a genetically homogeneous population with indications of extensive gene flow. We tentatively attribute this finding to the dispersal potential of the species' pelagic larvae, supported by marine currents acting as major dispersal vectors. We also detected a signal of expansion towards the poles, consistent with the current climate change scenario. Despite the marked latitudinal differences in the phenotype of reproducing worm pipefish, the absence of clear population structuring suggests that phenotypic plasticity can have a significant role in the expression of sexual selection-related traits.

Acquisition of social behavior in mammalian lineages is related with duplication events of FPR genes.

Formyl peptide receptors (FPRs) were firstly detected in immune cells where they act as key mediators of leukocyte chemotaxis, promoting the host defense against pathogens. Recently, three paralogs were reported in Homo sapiens (FPR1-3) and seven paralogs in Mus musculus (FPR1, FPRrs1-4, FPRrs6 and FPRrs7), but information from other mammalian lineages is scarce, including ambiguities in the current nomenclature system (e.g. absence of an orthologous relation between human and mouse FPR3). Here, we explored the FPR gene repertoire across 175 mammalian genomes using integrative phylogenetic and synteny analyses to describe the evolutionary history of FPRs in all mammalian orders. FPRs present a well conserved synteny but showed dynamic episodes of duplication events specific to several mammalian orders (Chiroptera, Perissodactyla, Primates and Rodentia), with up to 11 paralogs in some cases. Despite FPRs could be expressed in a panoply of tissues, there is a suggestion that they maintain an exclusive immunological function. However, we observed that species with social behavior have higher repertoire of FPRs in contrast with species with solitary lifestyle. Such evidence suggests a strict relationship between the optimization of the immunological system (by FPR duplication patterns) and the mammalian social behavior.

Neofunctionalization of the UCP1 mediated the non-shivering thermogenesis in the evolution of small-sized placental mammals.

The acquisition of UCP1-mediated non-shivering thermogenesis (NST) was an important event during the evolution of mammals. Here, we assessed the thermogenic neofunctionalization that occurred in the mammalian UCP1, by performing detailed comparative evolutionary genomics analyses (including phylogenetic and selection analyses) of the UCP family members across all major vertebrate classes. Heterogeneously distributed positive selection signatures were found in several UCPs, being preferably located in the mitochondrial matrix domains. Additionally, comparisons with non-mammalian orthologs showed increased evolutionary rates of the mammalian UCP1, not observable in the phylogenetically related UCP2 and UCP3 paralogs. Also, parallel signatures of episodic positive selection (ω > 1) were found in the ancestral branches of both Glires (rodents and lagomorphs) and Afroinsectivores (afrosoricids and macroscelids), underlining the importance of the UCP1 thermogenic activity in these mammalian groups. Finally, we hypothesize that the independent positive selection events that occurred in these two lineages resulted in two UCP1-mediated NST approaches, namely the cold acute response in the Glires and the reproduction success enhancement in the Afroinsectivores.

Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae) (Müller, 1774) in Portugal.

The Asian clam, Corbicula fluminea, is an invasive alien species (IAS) originally from Asia that has spread worldwide causing major ecological and economic impacts in aquatic ecosystems. Here, we evaluated C. fluminea genetic (using COI mtDNA, CYTb mtDNA and 18S rDNA gene markers), morphometric and sperm morphology variation in Portuguese freshwater ecosystems. The COI marker revealed a single haplotype, which belongs to the Asian FW5 invasive lineage, suggesting a common origin for all the 13 Portuguese C. fluminea populations analysed. Morphometric analyses showed differences between the populations colonizing the North (with the exception of the Lima River) and the Centre/South ecosystems. The sperm morphology examination revealed the presence of biflagellate sperm, a distinctive character of the invasive androgenetic lineages. The low genetic variability of the Portuguese C. fluminea populations and the pattern of sperm morphology have been illuminating for understanding the demographic history of this invasive species. We hypothesize that these populations were derived from a unique introductory event of a Corbicula fluminea FW5 invasive androgenic lineage in the Tejo River, which subsequently dispersed to other Portuguese freshwater ecosystems. The C. fluminea asexual reproductive mode may have assisted these populations to become highly invasive despite the low genetic diversity.

Biochemical and physiological responses of Carcinus maenas to temperature and the fungicide azoxystrobin.

Research on the effects of thermal stress is currently pertinent as climate change is expected to cause more severe climate-driven events. Carcinus maenas, a recognised estuarine model organism, was selected to test temperature-dependence of azoxystrobin toxicity, a widely applied fungicide. Crabs' responses were assessed after a 10-d acclimation at different temperatures (5°C, 22°C, and 27°C) of which the last 72h were of exposure to an environmental concentration of azoxystrobin. SOD and GST activities, mitochondrial oxygen consumption rates and protein content, as well as the Coupling Index were determined. The hypothesis proposed that extreme temperatures (5°C and 27°C) and azoxystrobin would affect crabs' responses. Results showed statistically significant different effects of SOD and all oxygen rates measured promoted by temperature, and that neither 30.3µgL(-1) of azoxystrobin nor the combined effect were crab-responsive. Protein content at 5°C was statistically higher when compared with the control temperature (22°C). The Coupling Index revealed both a slight and a drastic decrease of this index promoted by 5°C and 27°C, respectively. Regarding azoxystrobin effects, at 22°C, this index only decreased slightly. However, at extreme temperatures it fell 47% at 5°C and slightly increased at 27°C. Results provided evidence that crabs' responses to cope with low temperatures were more effective than their responses to cope with high temperatures, which are expected in future climate projections. Moreover, crabs are capable of handling environmental concentrations of azoxystrobin. However, the Coupling Index showed that combined stress factors unbalance crabs' natural capability to handle a single stressor.