Molecular biology and evolution最新文献

Mitochondrial function can be affected by mutations in mitochondrial DNA (mtDNA). However, detecting de novo mutations in mtDNA has been challenging due to its high copy number, particularly in germline cells, and the low accuracy of conventional next-generation sequencing technologies. Using highly accurate duplex sequencing, we study the frequency of de novo insertion and deletion (indel) mtDNA mutations across multiple age groups in somatic and germline tissues of three mammalian species-mouse, macaque, and human. We demonstrate that, similar to de novo nucleotide substitutions, indels accumulate rapidly with age in somatic tissues with high energetic demand (brain and skeletal muscle) or high proliferation (liver). However, in oocytes, indels accumulate slower with age than nucleotide substitutions (or do not accumulate at all). The increases in indel frequency with age are driven mostly by deletions. Short tandem repeats are highly enriched for indels, implicating DNA replication slippage as a major driver of indel formation in mtDNA. For some species and tissues, indels are depleted at protein-coding sequences, however, indels that are multiples of 3 bp are not overrepresented. omfOurs is the most detailed study of de novo small indels in mtDNA to date. It provides parameters for models of mtDNA evolution, informs molecular mechanisms for a multitude of human genetic diseases, and illuminates the accumulation of indel mutations with age. Such accumulation may have functional consequences, as it affects reproduction later in life and drives the decline of mitochondrial function during aging.

In teleosts, homologs of Anti-Müllerian Hormone (Amhy) and its type II receptor (Amhr2/Amhr2y) have been independently recruited as master sex-determination genes in about 50% of known cases. However, it remains unknown whether a conserved transducer pair exists, as the requisite type I receptors and R-Smad effectors remain unidentified amidst their diversity and potential redundancy. In this study, we employed an in vitro reporter assay to screen five type I receptors (Alk2a, Alk2b, Alk3, Alk6a, Alk6b) and three R-Smads (Smad1, Smad5, Smad8), discovering that only Alk3, Alk6a, or Alk6b, in combination with Smad5, significantly activated Amhy/Amhr2 signaling. In Nile tilapia, levels of phosphorylated Smad5 (p-Smad5) were notably elevated in XY gonads compared to XX gonads during the critical sex-determination window (8-15 dpf), while total Alk3 and Smad5 expression did not exhibit sexual dimorphism. The inhibition of type I receptors in XY fish resulted in feminization or complete sex reversal. Similarly, CRISPR/Cas9 mutagenesis of alk3 or smad5 led to male-to-female sex reversal in F0 mosaic mutants. Importantly, homozygous mutations in alk3 or smad5 resulted in embryonic lethality at the gastrula stage, whereas mutations in other type I receptors or R-Smads were viable and demonstrated normal sexual development. The conservation of this pathway was further substantiated in Southern catfish, where mutations in alk3a or smad5 also induced sex reversal in XY individuals. Collectively, our findings establish Alk3 and Smad5 as essential and specific transducers of the Amhy/Amhr2-mediated sex-determination pathway, revealing a potentially conserved signaling axis across teleosts.

Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutational dynamics in Daphnia obtusa, we generated a chromosome-level genome assembly spanning 129.4 Mb across 12 chromosomes, encompassing 15,321 predicted protein-coding genes. Leveraging whole-genome sequencing of eight mutation-accumulation (MA) lines propagated for an average of 482 generations (spanning over 20 years), we estimated a spontaneous single-nucleotide mutation (SNM) rate of 2.45 × 10-9 and an indel mutation rate of 3.34 × 10-10 per site per generation. The SNM spectrum was strongly biased toward C:G > T:A transitions. Despite the design of MA experiments to minimize selection, nonsynonymous mutations were strongly underrepresented, providing rare evidence that purifying selection can act detectably even during mutation accumulation. Comparative analyses with natural population data revealed that exonic mutations observed in the MA lines were significantly less likely to be present in standing variation than intronic or intergenic mutations, suggesting that purifying selection in natural populations acts to remove deleterious alleles. We also identified 48 loss-of-heterozygosity (LOH) events, comprising 8 heterozygous deletions and 40 gene-conversion events, yet found no evidence of GC-biased gene conversion. Instead, while mutation predicts a substantially lower equilibrium GC content, the observed GC level is maintained at higher values, implicating natural selection as the primary force stabilizing base composition. Together, these results provide one of the most comprehensive assessments of the interplay among mutation, selection, and genome stability in an ecologically important species.

Nuclear receptor subfamilies are comprised of members that can have markedly different ligand preferences. The NR1H subfamily contains the farnesoid X receptor (FXR) and liver X receptors (LXR) which regulate myriad metabolic processes, often in a coordinated fashion. As sensors for bile acids and oxysterols respectively, it is not known what ligand(s) activated the precursor of FXR and LXR. We reconstruct the common FXR/LXR vertebrate ancestor and determine that it responds to neither class of ligands for the extant receptors. Using structural and functional analysis, we identify the set of evolutionary substitutions that recapitulate the shift in ligand preference from the FXR/LXR ancestor to the ancestral vertebrate FXR. We show that the substitutions reshaped the ligand binding pocket to drive this functional shift. Subsequent evolutionary mutations altered the secondary structure of FXR to scaffold the binding pocket and support functional specialization.

Cave burial is a funerary practice believed to be associated with modern Kra-Dai (KD) and Hmong-Mien (HM) speakers for thousands of years. However, the extent to which these ancient cave burial practitioners contributed to the formation of modern ethnic minority groups remains poorly understood due to the limited ancient genomic data. We generated 14 newly sequenced ancient human genomes from cave burial sites in Guangxi. The findings reveal continuous gene flow from northern lineages into ancient cave burial populations, shaping their genetic profiles over time. We observed a significant genetic distinction in HM populations: Southeast Asian HM groups derive 74.8-100% of their ancestry from cave burials, preserving a robust ancient southern genetic signature, while Chinese HM populations exhibit only 11.1-37.2% ancient cave burial ancestry, but heavily admixed with Yellow River-related populations (14.7-52.1%), reflecting differential historical interactions with northern migrants. In contrast, most KD speakers maintain tight genetic clustering with Guangxi ancestors (28.5-100% contribution from cave burials). The HM formation involved admixture between ancient cave burials, northern farmers, and local KD-related groups, which is evident in the genetic cline of She and Miao populations.

Holosteans (gars and bowfins) have emerged as valuable models for understanding early vertebrate evolution, offering insights into diverse topics ranging from genomic architecture to molecular processes. These lineages also exhibit unusual features in their immune response, combining molecular elements seen in both tetrapods and ray-finned fishes. However, the immune repertoire of holosteans remains relatively unexplored. Here, we investigate the evolution of PSMB8, a core component of the immunoproteasome responsible for cleaving intracellular proteins into peptides for presentation by MHC class I molecules. We identify two holostean PSMB8 types-S type and K type-that are unique among vertebrates. These types likely cause significant biochemical changes to the S1 binding pocket involved in antigen cleavage which could result in the presentation of novel peptides by MHC class I. Integrating comparative analyses across major ray-finned fish lineages demonstrates that bowfins and gars independently evolved the PSMB8 S type within separate PSMB8 paralog lineages, while the PSMB8-K type is an evolutionary novelty found only in gars. Our results provide new perspectives into PSMB8 haplotypes and their role in peptide antigen processing, offering unique insights into the molecular evolution of the vertebrate immunity and antigen presentation.

Duffy antigen receptor for chemokines (DARC) is the primary red blood cell (RBC) receptor for invasion of human RBCs by Plasmodium vivax and Plasmodium knowlesi parasites. By contrast, Plasmodium falciparum parasites use multiple RBC receptors for invasion. Whether DARC is one of these receptors has never been systematically explored. We used flow cytometry and microscopy-based approaches to investigate whether P. falciparum parasites preferentially invade specific Duffy RBC phenotypes and explored two potential explanations for invasion preference - differences in RBC biophysical properties and surface protein composition. P. falciparum parasites showed a consistent preference for Duffy-positive RBCs, and some biophysical properties and surface protein expression varied between Duffy-positive and Duffy-negative RBCs. We then used our in vitro invasion data to parametrise an evolutionary-epidemiological model of the relationship between P. falciparum and the FYBES allele. Our model accounts for immunity against P. falciparum virulence, gained through exposure, and thus mutations that impede infection are not always advantageous. The inhibition of P. falciparum invasion that we observed in vitro leads to FYBES frequencies increasing at low levels of P. falciparum transmission but decreasing at high levels of transmission. The impact of P. falciparum on the prevalence of Duffy negativity may therefore be most apparent in lower transmission settings. Our findings are the first to show a link between Duffy negativity and P. falciparum and suggest that DARC may directly or indirectly be involved in P. falciparum invasion of human RBCs which could, together with P. vivax, explain the distribution of Duffy negativity in sub-Saharan Africa.

Understanding how biological sequences give rise to observable traits, that is, how genotype maps to phenotype, is a central goal in biology. Yet our knowledge of genotype-phenotype maps in natural systems remains limited by the high dimensionality of sequence space and the context-dependent effects of mutations. The emergence of Multiplex assays of variant effect (MAVEs) and the availability of ever growing collections of natural sequences offer new opportunities to characterize these maps at an unprecedented scale. However, tools for statistical and exploratory analyses of such high-dimensional data are still needed. To address this gap, we developed gpmap-tools (https://github.com/cmarti/gpmap-tools), a python library integrating models for inference, phenotypic imputation, and error estimation from MAVE data or natural sequences in the presence of genetic interactions of any order. gpmap-tools also provides methods for summarizing patterns of epistasis across sites and visualization of genotype-phenotype maps with millions of genotypes. We demonstrate its utility by inferring genotype-phenotype maps containing 262,144 variants of the Shine-Dalgarno sequence, a key motif for mRNA translation in bacteria, from both genomic 5'UTR sequences and MAVE data. Visualization of the inferred landscapes consistently revealed high-fitness ridges that link core motifs at different distances from the start codon, motivating a new, highly interpretable thermodynamic model for this system. In summary, gpmap-tools provides a flexible, interpretable framework for studying complex genotype-phenotype maps, offering new insights into the architecture of genetic interactions and their evolutionary consequences.

Chromosomal fusion and fission are widespread across species, yet the underlying genomic mechanisms and their evolutionary implications remain poorly understood. Here, we present high-quality chromosome-level genome assemblies for two closely related subterranean rodent species, Eospalax rufescens and E. rothschildi. Through comparative genomic and synteny analyses, we identified two species-specific chromosomal fusions in E. rothschildi, likely mediated by ectopic recombination through repetitive elements and by mutations affecting genome stability. Despite minimal changes in base-level genomic features, the fused chromosomes are associated with altered three-dimensional (3D) chromatin architecture, including increased chromatin entropy, topologically associating domain (TAD) rearrangement, and compartment switching. Reduced gene flow on the fused chromosomes suggests a role in reproductive isolation. Additionally, molecular signals of relaxed selection and adaptive evolution in pathways related to DNA repair, chromatin dynamics, and environmental sensing highlight the interplay between structural and ecological factors in shaping divergence. Together, our findings provide a mechanistic and evolutionary framework linking chromosomal fusions with genome architecture remodeling, epigenetic changes, and barriers to gene flow in mammals, offering a valuable resource for future evolutionary genomics studies.

Archipelagos and oceanic islands have remarkably high levels of endemism, which is associated with rapid speciation. The Malayan pangolin (Manis javanica), one of critically endangered Asia pangolin species, occurs in southern Yunnan, China, and on oceanic islands via the Malay peninsula. The question of whether the distribution of Malayan pangolins between the mainland and nearby marine islands has led to deep population differentiation is not well addressed. In-depth investigation of population structure and genetic consequences is of vital importance for protection and conservation of Malayan pangolins. Here we carried out a large-scale population genomic analysis for Malayan pangolins, which revealed three highly distinct genetic populations. The largest population was found to be distributed over a wide area extending from mainland China to almost the whole of South East Asia. The other two smaller populations reported in this study were inferred from Borneo. In addition, based on multiple lines of genomic and skull morphological evidences, we confirmed the existence of a fifth Asian pangolin species (M. mysteria). Genetic diversity and genome-wide inbreeding were at moderate levels, indicating that anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins. However, Malayan pangolins from northeastern Borneo exhibited low genetic diversity, high levels of inbreeding and mutational load, thereby necessitating attention to their protection.