Proteome Evolution of Deep-Sea Hydrothermal Vent Alvinellid Polychaetes Supports the Ancestry of Thermophily and Subsequent Adaptation to Cold in Some Lineages

The effectiveness of selection in a species affects the direction of amino acid frequency evolution

Nearly neutral theory predicts that species with higher effective population size (N e ) are better able to purge slightly deleterious mutations. We compare evolution in high-N e vs. low-N e vertebrates to reveal which amino acid frequencies are subject to subtle selective preferences. We take three complementary approaches, two measuring flux and one measuring outcomes. First, we fit non-stationary substitution models of amino acid flux using maximum likelihood, comparing the high-N e clade of rodents and lagomorphs to its low-N e sister clade of primates and colugos. Second, we compare evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies and N e . Third, we dissect the details of flux in human, chimpanzee, mouse, and rat, as scored by parsimony - this also enables comparison to a historical paper. All three methods agree on which amino acids are preferred under more effective selection. Preferred amino acids tend to be smaller, less costly to synthesize, and to promote intrinsic structural disorder. Parsimony-induced bias in the historical study produces an apparent reduction in structural disorder, perhaps driven by slightly deleterious substitutions. Within highly exchangeable pairs of amino acids, arginine is strongly preferred over lysine, and valine over isoleucine, consistent with more effective selection preferring a marginally larger free energy of folding. These two preferences match differences between thermophiles and mesophilic relatives. These results reveal the biophysical consequences of mutation-selection-drift balance, and demonstrate the utility of nearly neutral theory for understanding protein evolution.

Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella

Background

The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to separate of vent populations, promoting local adaptation and contributing to bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution.

Results

We explored genomic patterns of divergence in the early and late stages of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement.

Conclusion

Our analyses highlight the non-negligible role of natural selection on both the early and late stages of speciation in the iconic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed light on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02057-y.

Inter-Specific Genetic Exchange Despite Strong Divergence in Deep-Sea Hydrothermal Vent Gastropods of the Genus Alviniconcha

Deep hydrothermal vents are highly fragmented and unstable habitats at all temporal and spatial scales. Such environmental dynamics likely play a non-negligible role in speciation. Little is, however, known about the evolutionary processes that drive population-level differentiation and vent species isolation and, more specifically, how geography and habitat specialisation interplay in the species history of divergence. In this study, the species range and divergence of Alviniconcha snails that occupy active Western Pacific vent fields was assessed by using sequence variation data of the mitochondrial Cox1 gene, RNAseq, and ddRAD-seq. Combining morphological description and sequence datasets of the three species across five basins, we confirmed that A. kojimai, A. boucheti, and A. strummeri, while partially overlapping over their range, display high levels of divergence in the three genomic compartments analysed that usually encompass values retrieved for reproductively isolated species with divergences rang from 9% to 12.5% (mtDNA) and from 2% to 3.1% (nuDNA). Moreover, the three species can be distinguished on the basis of their external morphology by observing the distribution of bristles and the shape of the columella. According to this sampling, A. boucheti and A. kojimai form an east-to-west species abundance gradient, whereas A. strummeri is restricted to the Futuna Arc/Lau and North Fiji Basins. Surprisingly, population models with both gene flow and population size heterogeneities among genomes indicated that these three species are still able to exchange genes due to secondary contacts at some localities after a long period of isolation.

Balanced Polymorphism at the Pgm-1 Locus of the Pompeii Worm Alvinella pompejana and Its Variant Adaptability Is Only Governed by Two QE Mutations at Linked Sites

The polychaete Alvinella pompejana lives exclusively on the walls of deep-sea hydrothermal chimneys along the East Pacific Rise (EPR), and displays specific adaptations to withstand the high temperatures and hypoxia associated with this highly variable habitat. Previous studies have revealed the existence of a balanced polymorphism on the enzyme phosphoglucomutase associated with thermal variations, where allozymes 90 and 100 exhibit different optimal activities and thermostabilities. Exploration of the mutational landscape of phosphoglucomutase 1 revealed the maintenance of four highly divergent allelic lineages encoding the three most frequent electromorphs over the geographic range of A. pompejana. This polymorphism is only governed by two linked amino acid replacements, located in exon 3 (E155Q and E190Q). A two-niche model of selection, including ‘cold’ and ‘hot’ conditions, represents the most likely scenario for the long-term persistence of these isoforms. Using directed mutagenesis and the expression of the three recombinant variants allowed us to test the additive effect of these two mutations on the biochemical properties of this enzyme. Our results are coherent with those previously obtained from native proteins, and reveal a thermodynamic trade-off between protein thermostability and catalysis, which is likely to have maintained these functional phenotypes prior to the geographic separation of populations across the Equator about 1.2 million years ago.

Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin

Human genome stability requires efficient repair of oxidized bases, which is initiated via damage recognition and excision by NEIL1 and other base excision repair (BER) pathway DNA glycosylases (DGs). However, the biological mechanisms underlying detection of damaged bases among the million-fold excess of undamaged bases remain enigmatic. Indeed, mutation rates vary greatly within individual genomes, and lesion recognition by purified DGs in the chromatin context is inefficient. Employing super-resolution microscopy and co-immunoprecipitation assays, we find that acetylated NEIL1 (AcNEIL1), but not its non-acetylated form, is predominantly localized in the nucleus in association with epigenetic marks of uncondensed chromatin. Furthermore, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed non-random AcNEIL1 binding near transcription start sites of weakly transcribed genes and along highly transcribed chromatin domains. Bioinformatic analyses revealed a striking correspondence between AcNEIL1 occupancy along the genome and mutation rates, with AcNEIL1-occupied sites exhibiting fewer mutations compared to AcNEIL1-free domains, both in cancer genomes and in population variation. Intriguingly, from the evolutionarily conserved unstructured domain that targets NEIL1 to open chromatin, its damage surveillance of highly oxidation-susceptible sites to preserve essential gene function and to limit instability and cancer likely originated ∼500 million years ago during the buildup of free atmospheric oxygen.

Spaghetti to a Tree: A Robust Phylogeny for Terebelliformia (Annelida) Based on Transcriptomes, Molecular and Morphological Data

Terebelliformia-"spaghetti worms" and their allies-are speciose and ubiquitous marine annelids but our understanding of how their morphological and ecological diversity evolved is hampered by an uncertain delineation of lineages and their phylogenetic relationships. Here, we analyzed transcriptomes of 20 terebelliforms and an outgroup to build a robust phylogeny of the main lineages grounded on 12,674 orthologous genes. We then supplemented this backbone phylogeny with a denser sampling of 121 species using five genes and 90 morphological characters to elucidate fine-scale relationships. The monophyly of six major taxa was supported: Pectinariidae, Ampharetinae, Alvinellidae, Trichobranchidae, Terebellidae and Melinninae. The latter, traditionally a subfamily of Ampharetidae, was unexpectedly the sister to Terebellidae, and hence becomes Melinnidae, and Ampharetinae becomes Ampharetidae. We found no support for the recently proposed separation of Telothelepodidae, Polycirridae and Thelepodidae from Terebellidae. Telothelepodidae was nested within Thelepodinae and is accordingly made its junior synonym. Terebellidae contained the subfamily-ranked taxa Terebellinae and Thelepodinae. The placement of the simplified Polycirridae within Terebellinae differed from previous hypotheses, warranting the division of Terebellinae into Lanicini, Procleini, Terebellini and Polycirrini. Ampharetidae (excluding Melinnidae) were well-supported as the sister group to Alvinellidae and we recognize three clades: Ampharetinae, Amaginae and Amphicteinae. Our analysis found several paraphyletic genera and undescribed species. Morphological transformations on the phylogeny supported the hypothesis of an ancestor that possessed both branchiae and chaetae, which is at odds with proposals of a "naked" ancestor. Our study demonstrates how a robust backbone phylogeny can be combined with dense taxon coverage and morphological traits to give insights into the evolutionary history and transformation of traits.

Comparative transcriptome analysis reveals potential evolutionary differences in adaptation of temperature and body shape among four Percidae species

Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch (Perca flavescens), Eurasian perch (Perca fluviatilis), pike perch (Sander lucioperca), and ruffe (Gymnocephalus cernua), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the D. rerio branch to the sub-branch clustered by P. flavescens and P. fluviatilis. The specific 93 fast-evolving genes and 57 positively selected genes in P. flavescens, compared with 22 shared fast-evolving genes among P. fluviatilis, G. cernua, and S. lucioperca, showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like “Cul4-RING E3 ubiquitin ligase complex.” Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in S. lucioperca drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.

Do ampharetids take sedimented steps between vents and seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems

BACKGROUND

A range of higher animal taxa are shared across various chemosynthesis-based ecosystems (CBEs), which demonstrates the evolutionary link between these habitats, but on a global scale the number of species inhabiting multiple CBEs is low. The factors shaping the distributions and habitat specificity of animals within CBEs are poorly understood, but geographic proximity of habitats, depth and substratum have been suggested as important. Biogeographic studies have indicated that intermediate habitats such as sedimented vents play an important part in the diversification of taxa within CBEs, but this has not been assessed in a phylogenetic framework. Ampharetid annelids are one of the most commonly encountered animal groups in CBEs, making them a good model taxon to study the evolution of habitat use in heterotrophic animals. Here we present a review of the habitat use of ampharetid species in CBEs, and a multi-gene phylogeny of Ampharetidae, with increased taxon sampling compared to previous studies.

RESULTS

The review of microhabitats showed that many ampharetid species have a wide niche in terms of temperature and substratum. Depth may be limiting some species to a certain habitat, and trophic ecology and/or competition are identified as other potentially relevant factors. The phylogeny revealed that ampharetids have adapted into CBEs at least four times independently, with subsequent diversification, and shifts between ecosystems have happened in each of these clades. Evolutionary transitions are found to occur both from seep to vent and vent to seep, and the results indicate a role of sedimented vents in the transition between bare-rock vents and seeps.

CONCLUSION

The high number of ampharetid species recently described from CBEs, and the putative new species included in the present phylogeny, indicates that there is considerable diversity still to be discovered. This study provides a molecular framework for future studies to build upon and identifies some ecological and evolutionary hypotheses to be tested as new data is produced.