Genome Biology and Evolution最新文献

Endoderm, one of three primary germ layers of vertebrate embryos, makes major contributions to the respiratory and gastrointestinal tracts and associated organs, including the liver and pancreas. In mammals, transcription factor (TF) SOX17 is vital for endoderm organ formation and can induce endoderm progenitor identity. Duplication of ancestral sox17 before or during the early evolution of ray-finned fishes produced paralogs sox32 and sox17 in zebrafish. Sox32 is required for specification of endoderm and progenitors of the left-right (LR) organizer (Kupffer's Vesicle, KV), with Sox17 a downstream target of Sox32 implicated in further KV development. Phenotypic evidence, therefore, suggests functional similarities between zebrafish Sox32 and Sox17 and mammalian SOX17. Here, we directly compare these orthologs and paralogs, using the early zebrafish embryo as a biological platform for functional testing. Our results indicate that, unlike Sox32, human SOX17 cannot induce endoderm specification in zebrafish. Furthermore, using hybrid protein functional analyses, we show that Sox32 specificity for the endoderm gene regulatory network is linked to evolutionary divergence in its DNA-binding High Mobility Group domain from its paralog Sox17. Additionally, changes in the C-terminal regions of Sox32 and Sox17 underpin their differing target specificities. Finally, we establish that specific conserved peptides in the Sox17 C-terminal domain are essential for its role in establishing correct organ asymmetry. Overall, our results illuminate the molecular basis for functional divergence of Sox32 and Sox17 in vertebrate endoderm development and LR patterning, and reveal that alterations in specific domains of both TFs at different points during the evolution of fish are critical to their distinct and essential functions.

The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners. Additionally, ratios between branch lengths in the gene tree can inform about the timing of transfers relative to each other. Using this approach, recent studies have proposed a relative chronology of gene acquisitions in the lineage leading to the last eukaryotic common ancestor. However, a recognized caveat of the branch-length ratio method are potential biases due to incomplete taxon sampling resulting in so-called "ghost" lineages. Here, we assessed the effect of ghost lineages on the inference of the relative ordering of gene acquisition events during eukaryogenesis. For this, we used a novel simulation framework that populates a dated Tree of Life with plausible "ghost" lineages and simulates their gene transfers to the lineage leading to last eukaryotic common ancestor. Our simulations suggest that a substantial majority of gene acquisitions from distinct ghost donors are inferred with the correct relative order. However, we identify phylogenetic placements where ghost lineages would be more likely to produce misleading results. Overall, our approach offers valuable guidance for the interpretation of future work on eukaryogenesis, and can be readily adapted to other evolutionary scenarios.

Bovines have a complex yet poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically widespread genetic data are currently limited. In mid-latitude Asia, Denisova Cave, located in the Altai, Siberia, and nearby paleontological sites have yielded a large collection of remains spanning the Middle to Late Pleistocene, many of which are identifiable as bovines via morphology or paleoproteomics. In this study, we screened these bovine bones for ancient DNA and generated mitogenomes, to refine knowledge of Pleistocene bovine diversity in the region. We found that bovines carrying a yak-like mitogenome were common residents of the Altai mountains, along with bison belonging to the clade X mitochondrial lineage and, more rarely, aurochs. The yak-like mitochondrial lineage identified in this study represents a previously unknown lineage sister to present-day yak mitogenome diversity. This yak-like mitochondrial lineage, termed yak X, was identified at several sites, and survived in mid-latitude Asia across climatic transitions for around 200,000 years. Our findings suggest that all three bovine taxa harbored diversity no longer present in extant populations, thus mirroring archaic hominin findings at Denisova Cave. The Altai mountains therefore appear to have been a hotspot of both bovine and hominin diversity.

Natural selection heavily influences the evolutionary trajectories of species by impacting their genotype-to-phenotype transitions. On the molecular level, these transitions are shaped by the regulatory sequences. In this study, we employed a combination of population and comparative genomics to investigate how natural selection affects specific regulatory sequence classes involved in the regulatory transcription factor-DNA interactions. These interactions consist of two motifs, namely: transcription factor-binding domains and transcription factor-binding sites. Using publicly available annotation data for Homo sapiens, Arabidopsis thaliana, and Drosophila melanogaster, we first constructed the species-specific lists of the transcription factor-binding domain regions. On applying some of the commonly used summary statistics, we found signals of purifying selection acting on transcription factor-binding domains, consistent with their functional importance. Next, using the biochemical assay-based annotations, we identified potential transcription factor-binding site regions and used variants within them as nonsynonymous equivalents. Interestingly, we also observed that noncoding transcription factor-binding site regions showed similar levels of constraint to that of coding regions for populations with large Ne. Signals of positive selection were limited. Nevertheless, McDonald-Kreitman estimates revealed that, in both fruit-fly and thale-cress, α for transcription factor-binding domains was consistently higher than for adjacent nonbinding domains, whereas no such difference was apparent in humans. Taken together, our comparative analysis shows that the efficiency of negative-and to a lesser extent positive-selection on transcription factor-DNA interface elements scales with effective population size. The dataset and analysis pipeline provide a baseline for future studies of regulatory evolution across coding and noncoding regions.

A novel mechanism of de novo gene origination from nongenic sequences was first proposed in the early 2000s. Subsequent studies have since provided evidence of de novo gene emergence across all domains of life, revealing its occurrence to be more frequent than initially anticipated. While studies mainly agree on the general concept of de novo emergence from nongenic DNA, the exact methods and definitions for detecting de novo genes differ significantly. Here, we provide a comprehensive step-by-step description of the most commonly used methods for de novo gene detection. In addition, we address the limitations of nomenclature and detection methods and clarify some complex concepts that are sometimes misused. This review is accompanied by the publication of a de novo gene annotation format to standardize the reporting of methodology, enable reproducibility and improve the comparability of datasets.

A lack of recombination in the heterogametic sex between parts or all of newly evolving sex chromosomes results in the gradual accumulation of deleterious mutations on proto-Y or proto-W chromosomes. This "genetic degeneration" is caused by several population genetic mechanisms. It can eventually lead to the loss of functionality and deletions of Y- or W-linked genes in species with male or female heterogamety, respectively, reducing the fitness of heterozygous XY males or ZW females. This creates selection to compensate for such degeneration. Contemporary studies of degeneration and dosage compensation are built on classical genetic work by HJ Muller, with molecular analyses of genomes and gene expression now revealing new details. We review these studies, integrating ideas about how degeneration and compensation evolve. We discuss whether these two processes evolve together, whether the initial changes involved in compensation occurred in individual sex-linked genes ("piecemeal"), and whether they were sex specific. We also discuss the idea that control of expression across larger chromosome regions reflects later changes, after increased expression of X- or Z-linked genes in both sexes favored reduced X expression in females (or Z expression in males with female heterogamety). We summarize the currently available empirical evidence and discuss difficulties involved in documenting the evolutionary changes that lead to the different types of dosage compensation, as well as limitations of the data for testing evolutionary hypotheses.

In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.

The genomic characteristics of adaptively radiated groups could contribute to their high species number and ecological disparity, by increasing their evolutionary potential. Here, we explored the genomic variation of Anolis lizards, focusing on three species with distinct phenotypes: Anolis auratus, one of the species with the longest tail; Anolis frenatus, one of the largest species; and Anolis carolinensis, one of the species that inhabits the coldest environments. We assembled and annotated two new chromosome-level reference genomes for A. auratus and A. frenatus and compared them with the available genomes of A. carolinensis and Anolis sagrei. We evaluated the presence of structural rearrangements, quantified the density of repeat elements, and identified potential signatures of positive selection in coding and regulatory regions. We detected substantial rearrangements in scaffolds 1, 2, and 3 of A. frenatus different from the other species, in which the rearrangement breakpoints corresponded to hotspots of developmental genes. Further, we detected an accumulation of repeats around key developmental genes in anoles and phrynosomatid outgroups. Finally, coding sequences and regulatory regions of genes relevant to development and physiology showed variation that could be associated with the unique phenotypes of the analyzed species. Our results show examples of the hierarchical genomic variation within anoles that could provide the substrate that promoted phenotypic disparity and contributed to their adaptive radiation.

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this, we used published high coverage (>8✕) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5✕ genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with ≥0.5✕ coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes.

Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to incomplete lineage sorting. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both gene duplication and loss and incomplete lineage sorting. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extending it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for horizontal gene transfer, we show that CASTLES-Pro is relatively robust to random horizontal gene transfer, though its accuracy can degrade at the highest levels of horizontal gene transfer.