New methods are revealing the character of epistatic interactions within proteins and their impacts on evolution. Variation in biochemical phenotypes across protein sequences is determined primarily by the context-independent effects of amino acids and global nonlinearities imposed by biophysical mechanisms. Specific epistasis - primarily pairwise interactions - plays a subsidiary role, but collectively has a major impact on evolution. Every substitution in an evolving protein changes the effects of many potential mutations at epistatically coupled sites. As homologs diverge from common ancestors, the constraints that determine the accessibility of subsequent mutations gradually drift apart. Opportunities for adaptation and functional innovation also change over time, because each substitution epistatically modifies the effects of mutations on existing and new protein phenotypes. Over moderate evolutionary timescales, the outcomes of protein evolution - both their sequences and biochemical properties - thus become strongly contingent on the substitutions that happen to occur in each lineage. This interplay between random chance and each proteins' epistatic architecture helps explain widely observed lineage-specific patterns of conservation and variation that are not expected under the dominant schools of thought in molecular evolution.

Modern humans exhibit marked musculoskeletal changes when compared to those of our African ape relatives, such as chimpanzees, bonobos, and gorillas. These changes reflect adaptive shifts during hominin evolution in spine, pelvis, knee, and foot morphology toward obligate bipedalism, shoulder, elbow, and hand morphology for propulsive throwing and precision object manipulation, and brain size expansion and craniofacial morphology for enhanced cognition related to complex culture and language. The molecular basis for these traits remains unknown, in part owing to the experimental difficulties in connecting DNA base-pairs to phenotypes. Here, we discuss recent methodological advances in the life sciences that help to connect genotype to phenotype and pave the way for understanding the molecular basis for human skeletal evolution. In this context, we also discuss the importance of recent findings in how adaptive evolution shapes modern disease risk.

Transposable elements (TEs) are abundant and dynamic components of eukaryotic genomes, subject to regulation by equally adaptive regulatory systems. A coevolution of TEs and zinc finger genes can be documented throughout metazoan evolution. In humans, TEs account for half of the genome, and nearly all TE subfamilies are preferentially bound by at least one of the approximately 400 KRAB zinc finger proteins (ZFPs). The majority of human KRAB-ZFPs appear to tame the cis-regulatory activities of TEs, thereby facilitating their integration within gene regulatory networks. In turn, throughout vertebrate evolution, TE protein domains have fused repeatedly with ZFPs to give rise to new classes of regulatory proteins. Thus, the TE-ZFP interplay has been a powerful catalyst of biological innovation.

Immune genes show remarkably consistent evidence of selection, modification, and diversification across the tree of life. Parasites are a key force in this process, but many questions remain about the genetic and phenotypic targets of parasite-mediated selection and how these connect to each other. Ecological immunology - the study of immune variation in natural settings - can complement genetic inference by providing an organismal perspective on immune evolution, including how immune adaptation may be explained or constrained by host life history and ecological context. In this review, we outline key questions in immune evolution where ecological immunology offers insights for evolutionary geneticists, and we explore the value of evolutionary genetic approaches for testing fundamental assumptions in ecological immunology.

Nonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA decay mechanism that serves the purpose of controlling both mRNA quality and quantity. As a quality control mechanism, NMD protects organisms against the deleterious effects of mRNAs that encode premature termination codons, which arise through either transcriptional errors or genetic variation. NMD is also employed as a major regulator of physiological gene expression levels, and complete knockouts of multiple NMD genes are embryonic lethal in model organisms. The identification of genes that contribute to human Mendelian disease has now highlighted that gene variants that impact NMD function contribute to a spectrum of neurodevelopmental disorders (NDDs). Here, we capture the current landscape of NMD genes and gene variants implicated in NDDs with a focus on recent discoveries. The survey highlighted the involvement of more than half of all NMD and NMD-related genes in NDDs, representing a significant enrichment. That compromised NMD is a likely convergent pathogenic mechanism across multiple genetic causes of NDDs warrants ongoing investigation into the role of NMD in brain development.

Centromeres are essential for genome inheritance, serving as sites for kinetochore assembly and for final sister chromatid cohesion to ensure accurate chromosome segregation during cell division. These roles must persist through radical physical changes to chromosomes and other biological challenges presented by specialized processes in the germlines of both sexes and during early embryonic development. Centromeres in most organisms are epigenetically defined by the presence of a histone H3 variant, CENP-A. Therefore, to maintain centromeres, CENP-A nucleosomes must be inherited across generations through the germline. However, unique aspects of gametogenesis, including asymmetric meiosis and prolonged cell cycle arrest in the female germline and extensive chromatin reorganization in the male germline, introduce additional layers of complexity to the process of centromere inheritance. Here, we review the implications of these processes for centromere regulation during gametogenesis and early embryonic development, drawing on findings from mouse and fruit fly models.

The genomic information is insulated in the nucleus of all eukaryotic cells. Error-free transcription needs to be followed by an efficient export of the messenger RNAs (mRNA) to facilitate the regulated synthesis of proteins for carrying out cellular functions. The functionally conserved Transcription-Export (TREX) complex is a key player in mediating mRNA export from the nucleus to the cytoplasm, along with RNA processing steps including 3'-end processing, 5' capping, transcriptional regulation, R-loop resolution, and splicing. TREX, a multifunctional complex, has important roles in stress response, mitotic progression, embryonic stem cell self-renewal and differentiation, and maintaining genome stability. Most of these processes are essential for the appropriate development and function of the brain. Consistent with this notion, partial loss of function variants in the TREX components THOC2, THOC6, and DDX39B were implicated in neurodevelopmental disorders. Furthermore, a growing body of evidence also highlighted the involvement of defective nucleocytoplasmic RNA transport in the development of neurodegenerative diseases. Overall, the TREX complex is emerging as a crucial player in neurological diseases, making it a critical target for both diagnosis and therapeutic intervention.

As the origin of the development, a fertilized egg owns the ability to generate a whole new organism, including both embryonic and extraembryonic tissues, representing the highest developmental potency, totipotency. For more than 40 years, pluripotent stem cells, with differentiation potential weaker than that of totipotent cells, have been easily derived from inner cell mass and maintained in vitro. Until now, capturing totipotent stem cells is still challenging. Recently, the stable culture of mouse and human totipotent blastomere-like cells was achieved for the first time using spliceosomal repression. Subsequently, other methods, particularly epigenetic manipulation, have also succeeded in culturing mouse totipotent stem cells. These advancements provide an excellent system for studying early embryonic development and offer new possibilities for regenerative medicine. However, the in vitro culture of totipotent stem cells has only been recently realized, and much further exploration is needed in this field. This review aims to compare different totipotent stem cells and discuss their potential applications in regenerative medicine and disease modeling.

The microbial community colonizing the animal gut includes all domains of life, including eukaryotic microbes. Historically viewed as pathogens, increasing evidence has revealed that many protists are commensal members of the microbiome with diverse ecological functions. This review synthesizes recent advances in our understanding of the ecology and evolution of these organisms, with a focus on phylogenetic diversity, microbial interactions, and genomic signatures of adaptation. New technologies such as single-cell genomics and transcriptomics, long-read sequencing technologies, and co-culture strategies have made these new findings possible, but much remains to be investigated. Further work is needed to understand how these diverse organisms contribute to the gut environment and evolve to colonize animal hosts.

Mitochondrial DNA (mtDNA) is inherited maternally across animals, yet the evolutionary rationale behind this unusual mode of inheritance remains a longstanding mystery. Understanding the processes that prevent the transmission of paternal mtDNA and thus ensure maternal-only inheritance is crucial to uncovering the evolutionary significance of this widespread phenomenon. Historically, research has focused on mechanisms that act within eggs to destroy sperm mitochondria via autophagy and the ubiquitin-proteasome degradation system. However, recent discoveries across multiple animal species, including humans, reveal a surprising twist: paternal mtDNA is actively degraded within mitochondria independently of and prior to the complete breakdown of the organelle itself, often even prior to fertilization. Only a few studies have begun to illuminate the molecular machinery responsible for this early mtDNA elimination. In this review, we explore the emerging landscape of paternal mtDNA elimination mechanisms across species, highlighting newly discovered pathways, evolutionary implications, and open questions that are furthering our understanding of mitochondrial inheritance.

Comparative genomics is a powerful approach to illuminate the genetic basis of phenotypic diversity across macro-evolutionary timescales. Recent advances in sequencing, genome assembly, annotation, and comparative methods promoted large-scale analyses that unveiled genomic determinants contributing to differences in cognition, metabolism, and body plans as well as phenotypes with biomedical relevance, such as cancer resistance, longevity, and viral tolerance. These studies highlight joint contributions of multiple molecular mechanisms and indicate an underappreciated role for gene and enhancer losses driving phenotypic change. However, challenges remain, including comprehensive phenotype databases and genome annotations, improved approaches for identifying lineage-specific adaptations, and functional tests. Here, we review recent progress, highlight major discoveries, and discuss future directions for linking phenotype to genotype using comparative genomics.

Germ cells are unique in their ability to acquire totipotency. Toward this end, they reorganize their three-dimensional (3D) epigenome during their development, including epigenetic reprogramming in primordial germ cells that differentiate mitotic prospermatogonia and ensuing unique epigenetic programming for generating undifferentiated spermatogonia/spermatogonial stem cells (SSCs). Advances in low-input epigenomic and 3D genomic techniques, along with complementary in-depth characterization of scalable in vitro reconstitution systems for germ cell development, that is, in vitro gametogenesis, have elucidated a number of fundamental events during these processes, including insulation augmentation in highly open chromatin following epigenetic reprogramming in mitotic prospermatogonia and insulation erasure and further euchromatization accompanied by chromosomal radial repositioning in undifferentiated spermatogonia/SSCs. These 3D epigenomic organizations likely serve as a foundation for generating fully functional gametes. Elucidating the mechanisms underlying 3D epigenomic reorganization during germ cell development will be instrumental not only for understanding the basis for totipotency but also for further advancing in vitro gametogenesis.

The primary objective of life is to ensure the faithful transmission of genetic material across generations, despite the constant threat posed by DNA-damaging factors. To counter these challenges, life has evolved intricate mechanisms to detect, signal, and repair DNA damage, thereby preventing mutations that can cause developmental abnormalities or diseases. DNA repair is especially vital during development - a period of rapid cell proliferation and differentiation. Failure to repair DNA damage in somatic cells can result in tissue dysfunction, while during embryonic development, it is often fatal. Transcription machinery plays a key role in the mechanisms of DNA repair. This review highlights current insights into DNA repair pathways that are driven or facilitated by transcription and their essential contribution to preserving genome stability.

Comparative transcriptomic studies are key to understanding how molecular evolution drives phenotypic divergence across the tree of life. Here, we discuss three major directions in which the field of comparative transcriptomics is evolving. The first one is enabled by advances in sequencing technologies. Bulk RNA sequencing emerged two decades ago as a key tool to characterize transcriptomic states, enabling evolutionary comparisons at the tissue and organ levels. However, single-cell and spatial transcriptomics are now driving a shift toward a paradigm centered around cell types. Second, while comparative transcriptomic studies have historically focused on a few key model organisms and on species closely related to humans, recent trends have shifted toward both broader phylogenetic coverage and deeper sampling within clades. In parallel, the growing amount of transcriptomic data, together with the advent of machine learning approaches, are leading to the development of new modeling frameworks. These frameworks range from reconstruction of cell type phylogenies to prediction of RNA coverage from genomic sequence alone and have propelled significant progress in evolutionary biology and its biomedical applications.

Genomic instability is a significant challenge in early mammalian development and a cause for developmental failure and abnormalities, particularly in humans. Here, we review our knowledge and explore its significance of genome instability in early embryos across multiple mammalian species, including humans, rhesus macaques, mice, bovines, equines, and porcine. All these species but mice share one feature: frequent chromosomal aberrations, aneuploidy, and developmental failure. We discuss the impact of genome instability on embryonic development, the applicability of gene editing using Cas9, and potential evolutionary implications. We also explore the role of germ cell and early embryo mutations and the bottleneck effect in mammals in comparison to lower vertebrates. Understanding genome stability in mammalian embryos can contribute to our understanding of genetic variation in development and evolution.

The gastrointestinal (GI) tract evolved in response to dietary changes and pathogen exposures that varied throughout history. As a major interface between the host and environment, the GI epithelia have evolved specialized barrier and immune functions while optimizing nutrient processing and absorption. Recent technological breakthroughs in modeling human biology in vitro and comparative single-cell genomics are providing novel insights into the genetic, cellular, and ontogenic basis of human evolution. In this review, we provide a broad overview of human-specific gut changes and how GI organoids and single-cell technologies can offer a mechanistic understanding of the specific features of human GI tract physiology.

Recent advances in single-cell genomics are propelling a flurry of discoveries about the cellular composition of the brain and other organs across species. These discoveries, coupled with experimental manipulations, have begun to reveal how variation between species in the proportion of cell types, including the outright disappearance of some cell types and the emergence of new ones, contributes to the evolution of behavior. This review highlights these emerging findings in the context of more traditional approaches to study the evolution of behavior and discusses important outstanding questions in this field.

The global replacement of nucleosomes with nonhistone chromosomal proteins during sperm differentiation is a widespread phenomenon in sexually reproducing animals. In mammals, for instance, sperm chromatin is essentially packaged with protamines, a type of sperm nuclear basic proteins (SNBPs). In contrast to vertebrates, where many taxa retain variable levels of histones in their sperm chromatin, insects seem to systematically eliminate histones during spermiogenesis. This diversity of sperm packaging across metazoa raises questions about the functional significance of the histone-to-protamine transition that occurs during spermiogenesis. Recent studies in Drosophila and other insects have shed light on the function of SNBPs in packaging ultracompact sperm DNA and preparing paternal chromosomes for their integration into the diploid zygote.

Ancient DNA has revolutionized our understanding of human history and clarified many aspects of human evolution on a molecular level. In this article, I describe recent efforts to translate this into descriptions of phenotypic change over time and to predict phenotypes of ancient groups and individuals. I do not discuss the more challenging problem of distinguishing between adaptive and neutral evolution and instead focus entirely on whether phenotypes and their evolution can be accurately reconstructed. I begin by describing the conceptual and technical limitations of current approaches, and then discuss efforts to reconstruct various phenotypes and the extent to which they are reliable.