Luana S. F. Lins

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes’ tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower cellular freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes′ tandem array structure and consequently poor resolution of these repetitive regions. Here we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B and show that AFP copies expanded under low temperature, but also decreased with depth, which reduces freezing point via pressure. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which Zoarcoidei AFP arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

The mantis shrimp superfamily Squilloidea, with over 185 described species, is the largest superfamily in the crustacean order Stomatopoda. To date, phylogenetic relationships within this superfamily have been comprehensively analysed using morphological data, with six major generic groupings being recovered. Here, we infer the phylogeny of Squilloidea using a combined dataset comprising 75 somatic morphological characters and four molecular markers. Nodal support is low when the morphological and molecular datasets are analysed separately but improves substantially when combined in a total-evidence phylogenetic analysis. We obtain a well resolved and strongly supported phylogeny that is largely congruent with previous estimates except that the Anchisquilloides-group, rather than the Meiosquilla-group, is the earliest-branching lineage in Squilloidea. The splits among the Anchisquilloides- and Meiosquilla-groups are followed by those of the Clorida-, Harpiosquilla-, Squilla- and Oratosquilla-groups. Most of the generic groups are recovered as monophyletic, with the exception of the Squilla- and Oratosquilla-groups. However, many genera within the Oratosquilla-group are not recovered as monophyletic. Further exploration with more extensive molecular sampling will be needed to resolve relationships within the Oratosquilla-group and to investigate the adaptive radiation of squilloids. Overall, our results demonstrate the merit of combining morphological and molecular datasets for resolving phylogenetic relationships.

The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional individuals within and among lineages.

The worldwide population of the leatherback turtle (Dermochelys coriacea) encompasses seven subpopulations among the Pacific, Atlantic and Indian Oceans. It has experienced declines across parts of its distribution, with the subpopulation of the South-west Atlantic listed as critically endangered by the IUCN Red List. The main threats to this subpopulation include its interaction with fisheries, coastal development, pollution and climate change. In this study, we sequenced mitochondrial DNA from 52 leatherback turtles in Brazil and combined these with published data from other Atlantic Ocean rookeries. The haplotype diversities of the Atlantic population rookeries ranged from 0.112 to 0.533 and are not directly proportional to current rookery sizes. The Brazilian rookery, despite recording low nest numbers per year, had the second-highest haplotype diversity among all Atlantic rookeries (h = 0.532). A mixed-stock analysis revealed that the South American pelagic aggregate is primarily composed of individuals from West Africa (84%), with contributions from the North Atlantic rookeries (14%). Leatherback turtles appear to have a complex phylogeographic pattern, showing evidence of multiple colonization events and a lack of isolation by distance. Our novel dataset, based on DNA sequences of 695 base pairs, will provide baseline data needed to understand population dynamics in the region, building comprehensive population assessments to support and develop management strategies. Having both the only known regular rookery in the South-west Atlantic, and a mixed-origin foraging area for the species along its coast, Brazil has a key role in the conservation of the leatherback turtle.

The molecular clock is a valuable and widely used tool for estimating evolutionary rates and timescales in biological research. There has been considerable progress in the theory and practice of molecular clocks over the past five decades. Although the idea of a molecular clock was originally put forward in the context of protein evolution and advanced using various biochemical techniques, it is now primarily applied to analyses of DNA sequences. An interesting but very underappreciated aspect of molecular clocks is that they can be based on genetic data other than DNA or protein sequences. For example, evolutionary timescales can be estimated using microsatellites, protein folds, and even the extent of recombination. These genome features hold great potential for molecular dating, particularly in cases where nucleotide sequences might be uninformative or unreliable. Here we present an outline of the different genetic data types that have been used for molecular dating, and we describe the features that good molecular clocks should possess. We hope that our article inspires further work on the genome as an evolutionary timepiece.

The deep sea is one of the largest ecosystems on Earth and is home to a highly diverse fauna, with polychaetes, molluscs and peracarid crustaceans as dominant groups. A number of studies have proposed that this fauna did not survive the anoxic events that occurred during the Mesozoic Era. Accordingly, the modern fauna is thought to be relatively young, perhaps having colonized the deep sea after the Eocene/Oligocene boundary. To test this hypothesis, we performed phylogenetic analyses of nuclear ribosomal 18S and 28S and mitochondrial cytochrome oxidase I and 16S sequences from isopod crustaceans. Using a molecular clock calibrated with multiple isopod fossils, we estimated the timing of deep-sea colonization events by isopods. Our results show that some groups have an ancient origin in the deep sea, with the earliest estimated dates spanning 232–314 Myr ago. Therefore, anoxic events at the Permian–Triassic boundary and during the Mesozoic did not cause the extinction of all the deep-sea fauna; some species may have gone extinct while others survived and proliferated. The monophyly of the ‘munnopsid radiation’ within the isopods suggests that the ancestors of this group evolved in the deep sea and did not move to shallow-water refugia during anoxic events.

The population of Catapaguroides microps A. Milne-Edwards and Bouvier, 1892 in the Campos Basin was studied with an emphasis on its composition in the Northern and Southern parts of the Basin, the different gender sizes, sex ratio, and size class distribution. Specimens were collected under the "Program for the Environmental Characterization of the deep waters of the Campos Basin" ("Programa de Caracterização Ambiental das Águas Profundas da Bacia de Campos") in February and August 2003. A total of 339 hermit crabs were analyzed. Individual abundance was higher in the North. C. microps shows sexual dimorphism for body size, the males being larger than the females. The sex ratio is skewed in the female's favor (1:0.7), as shown by previous studies on shallow-water populations.