Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries.

BACKGROUND: The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Here we performed a phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RADseq) in a total of twelve Patagonotothen species. RESULTS: We present a well-supported, time-calibrated phylogenetic hypothesis including closely and distantly related outgroups, confirming the monophyly of the genus Patagonotothen with an origin approximately 3 million years ago and the paraphyly of both the sister genus Lepidonotothen and the family Notothenidae. Our phylogenomic and population genetic analyses highlight a previously unrecognized linage and provide evidence for shared genetic variation between some closely related species. We also provide a mitochondrial phylogeny showing mitonuclear discordance. CONCLUSIONS: Based on a combination of phylogenomic and population genomic approaches, we provide evidence for the existence of a new, potentially cryptic, Patagonotothen species, and demonstrate that genetic boundaries between some closely related species are diffuse, likely due to recent introgression and/or incomplete linage sorting. The detected mitonuclear discordance highlights the limitations of relying on a single locus for species barcoding. In addition, our time-calibrated phylogenetic hypothesis shows that the early burst of diversification roughly coincides with the onset of the intensification of Quaternary glacial cycles and that the rate of species accumulation may have been stepwise rather than constant. Our phylogenetic framework not only advances our understanding of the origin of a high-latitude marine radiation, but also provides the basis for the study of the ecology and life history of the genus Patagonotothen, as well as for their conservation and commercial management.

A rapid approach for sex assignment by RAD-seq using a reference genome.

Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of two ad hoc indexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.

Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from north Patagonia.

Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor an important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that are currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of E. maclovinus. We used restriction site-associated DNA (RAD) sequencing and outlier tests to obtain neutral and adaptive loci, using FST and GEA approaches. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 (Chepu) to 14,454 (Chaitén) and were influenced more by locality than by salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in E. maclovinus populations. These results suggest a complex interaction between genetic drift, gene flow, and natural selection in this area. Our findings also suggest several evolutionary significant units in this area, and the information should be integrated into the management of this species. We discussed the significance of these results for fishery management and suggest future directions to improve our understanding of how E. maclovinus has adapted to the dynamic waters of Northern Patagonia.

Ontogenetic stage-dependent effect of temperature on developmental and metabolic rates in a holometabolous insect.

Different hypotheses attempt to explain how different stages of organisms with complex life cycles respond to environmental changes. Most studies have focused at the among-species level showing similar responses to temperature throughout ontogeny. However, there is no agreement about the pattern expected at the intraspecific scale where a strong selective effect is expected. In this paper, we studied the effects of thermal treatments on a life history trait (developmental rate) and a physiological trait (metabolic rate) during development in the fruitfly Drosophila buzzatii. First, we estimated the rate of development during larval life (LDR) and the pupal stage (PDR) in flies derived from two natural populations exposed to several thermal treatments. Our results showed that the developmental rate ratio, LDR/PDR, did not vary between populations, and that the effects of thermal treatments were stage specific. Second, we studied the relationship between developmental rate (DR) and metabolic rate (MR) in each life cycle stage. We found that allometric relationships between DR and MR varied throughout ontogeny, a pattern that shed light on the mechanisms responsible for thermal plasticity. We conclude that, although different populations may show developmental rate isomorphy; larvae and pupae may choose alternative "decisions" in terms of life-history evolution and physiological traits when confronted to different thermal environments.