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A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.In this Perspective, the authors discuss how regulated alternative splicing can generate phenotypic diversity and outline emerging evidence that alternative splicing contributes to adaptation and species divergence.

Key Points Polyploidy, or whole-genome duplication (WGD), is usually an evolutionary dead end. Although polyploidy is a frequent and recurrent phenomenon, the number of WGDs that have become established in the long term is low. The occurrence of WGDs in the tree of life is not random and seems to correlate with periods of environmental upheaval. WGDs increase the adaptive potential of cells and organisms exposed to stressful conditions. The biased retention of genes following WGDs offers a unique evolutionary potential to evolve key innovations and to increase biological complexity in the long term. In cancer, WGD is a transient state that promotes aneuploidy, and is responsible for increased genetic variation and subsequent adaptive potential. Polyploidy occurs frequently but is usually detrimental to survival; thus, few polyploids survive in the long term. Here, evidence linking the short-term evolutionary success of polyploids to environmental upheaval is reviewed and possible longer-term evolutionary benefits of polyploidy are discussed. Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions 1 – 3 . Here we address these issues by analysing the genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies. Using intergenic regions and coalescent methods to analyse the genomes of 363 bird species, the authors present a well-supported tree confirming that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary.

Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This ‘genetic load’ has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components — the realized load (or expressed load) and the masked load (or inbreeding load) — can improve our understanding of the population genetics of deleterious mutations.The reduction in individual and mean population fitness induced by novel deleterious genetic variation is known as the genetic load. Bertorelle et al. review the definition of the genetic load and its components as well as the impact of whole-genome sequencing on the theoretical and applied study of the genetic load.

Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.Genetic improvement of production traits in aquaculture has great potential to help meet the rising seafood demands driven by human population growth. The authors review how genomics is being applied to aquaculture species at all stages of the domestication process to optimize selective breeding.

Key Points Recent evidence increasingly supports the idea that certain ancestral life experiences acquired in the environment can be inherited by offspring; paternally acquired characteristics can be encoded in the sperm in the form of epigenetic information in addition to DNA sequences. Sperm RNAs, in particular sperm microRNAs (miRNAs) and tRNA-derived small RNAs (tsRNAs), can mediate intergenerational transmission of paternally acquired phenotypes such as diet-induced metabolic disorders and mental stress phenotypes. The mechanisms by which sperm RNAs respond to environmental changes and encode the acquired traits remain unclear but may involve environmental–somatic–germline interactions that may be mediated by extracellular vesicles (EVs) and mobile RNAs, and involve a breach of the somatic–germline barrier. Sperm RNAs may initiate a transcriptional cascade of effects throughout embryonic development to induce a paternally acquired phenotype in offspring; how the initial effects caused by sperm RNAs are converted to a stable form of information to allow transgenerational inheritance remains a major puzzle but possibly involves interplay among transposable elements, DNA methylation and chromatin structure. Emerging evidence suggests that RNA modifications in sperm RNAs have an essential role in modulating epigenetic memory. Novel methods are required to map the locations of multiple RNA modifications in each RNA species, especially for tsRNAs and miRNAs that can induce offspring phenotypes. It remains unknown how many types of acquired traits can be transmitted to offspring through the germ line and under what circumstances this is likely to occur. Studies have demonstrated that paternal traits acquired in response to environmental conditions can be inherited by the offspring, sometimes persisting for multiple generations. In this Review, the authors discuss the accumulating evidence of a major role for sperm RNAs and RNA modifications in the inheritance of acquired traits and the mechanisms that may underlie this. Once deemed heretical, emerging evidence now supports the notion that the inheritance of acquired characteristics can occur through ancestral exposures or experiences and that certain paternally acquired traits can be 'memorized' in the sperm as epigenetic information. The search for epigenetic factors in mammalian sperm that transmit acquired phenotypes has recently focused on RNAs and, more recently, RNA modifications. Here, we review insights that have been gained from studying sperm RNAs and RNA modifications, and their roles in influencing offspring phenotypes. We discuss the possible mechanisms by which sperm become acquisitive following environmental–somatic–germline interactions, and how they transmit paternally acquired phenotypes by shaping early embryonic development.

The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself 1 . However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies 2 . Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent–offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis 3 . The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates. Using sequencing and comparing high-coverage genomes, the germline mutation rates across vertebrates are quantified.

Key Points The Archaea was recognized as a third domain of life 40 years ago. Molecular evidence soon suggested that the Eukarya represented a sister group to the Archaea or that eukaryotes descended from archaea. Culture-independent genomics has revealed the vast diversity existing among the Archaea, including the recently described Asgard superphylum. Phylogenomic analyses have placed the Asgard archaea as the closest prokaryotic relatives of eukaryotes. Comparative genomic analyses have reconstructed a complex last eukaryotic common ancestor. However, how and in which order these complex eukaryotic features evolved in an Asgard archaea-related ancestor remains largely unclear. Genomic investigation of Asgard archaea showed that they carry several genes formerly believed to be eukaryotic specific, illuminating early events during eukaryogenesis. Fully understanding the process of eukaryogenesis requires finding answers to several challenging and intertwined questions. Although we have seemingly answered some of these questions, others remain fiercely debated, and new questions continue to arise. The Archaea was recognized as a third domain of life 40 years ago. In this Review, Eme et al . outline a brief history of the changing shape of the tree of life and examine how the recent discovery of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of the eukaryotic cell. Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.

Primates and rodents, which descended from a common ancestor around 90 million years ago 1 , exhibit profound differences in behaviour and cognitive capacity; the cellular basis for these differences is unknown. Here we use single-nucleus RNA sequencing to profile RNA expression in 188,776 individual interneurons across homologous brain regions from three primates (human, macaque and marmoset), a rodent (mouse) and a weasel (ferret). Homologous interneuron types—which were readily identified by their RNA-expression patterns—varied in abundance and RNA expression among ferrets, mice and primates, but varied less among primates. Only a modest fraction of the genes identified as ‘markers’ of specific interneuron subtypes in any one species had this property in another species. In the primate neocortex, dozens of genes showed spatial expression gradients among interneurons of the same type, which suggests that regional variation in cortical contexts shapes the RNA expression patterns of adult neocortical interneurons. We found that an interneuron type that was previously associated with the mouse hippocampus—the ‘ivy cell’, which has neurogliaform characteristics—has become abundant across the neocortex of humans, macaques and marmosets but not mice or ferrets. We also found a notable subcortical innovation: an abundant striatal interneuron type in primates that had no molecularly homologous counterpart in mice or ferrets. These interneurons expressed a unique combination of genes that encode transcription factors, receptors and neuropeptides and constituted around 30% of striatal interneurons in marmosets and humans. Single-nucleus RNA-sequencing analyses of brain from humans, macaques, marmosets, mice and ferrets reveal diverse ways that interneuron populations have changed during evolution.

Key Points Speciation is a central and fundamental process in evolution that concerns the origin of reproductive isolation. The latest generation of genomic approaches provide remarkable opportunities to describe speciation and to learn about its underlying mechanisms. Genome scans, which can now be carried out in a truly genome-wide scale and at base-pair resolution, reveal substantial genomic divergence among incipient species even in the face of gene flow and show that there is extensive genomic heterogeneity in the extent of differentiation, especially at early stages of speciation, both in sympatry and in allopatry. The sources of this heterogeneity remain incompletely understood. The combination of genome scans with sophisticated population genetic modelling, quantitative trait locus mapping, admixture analyses and ecology has the potential to distinguish the influence of selection from demographic, historical and structural effects and to link these sources of genomic divergence to phenotypes and to reproductive isolation. Available empirical data suggest that differentiation between parapatric populations can be restricted to few genomic islands, whereas incipient species that coexist in sympatry show differentiation that is widely distributed across the genome. This suggests that genomically widespread selection is required to permit the maintenance and perhaps the build-up of genetic differentiation in sympatry. Recent genomic studies reveal that the genetic basis of reproductive isolation is often complex. The effects of pleiotropy, genetic correlations and patterns of recombination need to be considered alongside effects of ecological and sexual selection as well as genomic conflict. A surprising recent discovery is the re-use of ancient genetic variants in speciation, which are acquired either from standing genetic variation or by introgressive hybridization. In this Review, we propose a 'roadmap' for the development of speciation genomics towards answering classical and emerging questions in speciation research. Genomic approaches are an increasingly important aspect of speciation research. The authors review recent insights from speciation genomics and propose a roadmap for this field, which is aimed at addressing both long-standing and emerging questions about speciation. Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.