Joana L. Rocha

The 17q21.31 locus in humans harbors several complex structural haplotypes including a ~ 970 kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650 kb, encompasses 5 additional genes, and is ~2 million years younger than the human inversion. Using short read sequencing data we characterize 17q21.31 haplotype diversity worldwide in ~5174 individuals from 107 populations finding increased frequencies of KANSL1 duplication-containing haplotypes in both European and South Asian populations as well as 8 double recombination events between inverted and non-inverted haplotypes ranging in size from 20-180 kb. Finally, using 626 ancient Eurasian human genomes we show the frequency of haplotypes containing KANSL1 duplications has increased ~6-fold over the past 12 thousand years in Europe. Together, our results highlight the dynamics, complexity, and recurrent, independent evolution of a medically relevant locus across humans and great apes.

Tandem repeats (TRs) are highly mutable DNA elements that influence gene regulation ¹ , protein structure ² , and disease ³ . Until recently, their repetitive nature has hindered accurate TR sequencing and genotyping, resulting in sparse comparative data across species. In addition, we lack population-aware approaches to analyze TR conservation, divergence, and mutational dynamics. Here, leveraging telomere-to-telomere primate genomes and long-read data from 46 humans and 23 chimpanzees, we constructed a catalog of homologous TR loci, and developed an analytical framework to jointly analyze TR variation within- and between-species. Across primates, TR diversity and conservation vary strongly with genomic context, with coding and 5’ UTR TRs exhibiting reduced polymorphism and constraint across species, consistent with stabilizing selection. Yet, while TRs are depleted in coding sequence, they are enriched in 5’ UTRs, suggesting functional roles that outweighs mutational risks. TR heterozygosity varies across motif lengths and is concordant with both evolutionary and trio-based mutation rate estimates ⁴ . Introducing an HKA-like approach to control for locus-specific mutation rates, we identified TRs with signatures of directional and balancing selection. These candidates are significantly enriched in genes involved in nervous system development and synaptic function, highlighting TRs as potential contributors to neural evolution. Further, TR divergence correlates with gene expression divergence, particularly for promoter-related TRs and expression in organoids related to neurodevelopment, implicating a subset of regulatory TRs as candidates for adaptive expression evolution. Finally, trait-associated TRs display longer alleles and higher diversity in humans compared to chimpanzees, consistent with lineage-specific runaway mutations and/or directional selection ⁵ . Together, our results establish a comparative framework for TR evolutionary analyses, revealing how mutational processes and selection jointly shape repeat variation, and supporting their role as both conserved functional elements and as drivers of evolutionary innovation.

Human SAMD9 and SAMD9L are duplicated genes that encode innate immune proteins restricting poxviruses and lentiviruses, such as human immunodeficiency virus (HIV). Mutations in these genes are implicated in genetic diseases and cancer. Here we combined structural similarity searches, phylogenetics and population genomics with experimental assays of SAMD9/9L functions to resolve the evolutionary and functional dynamics of these immune proteins, spanning from prokaryotes to primates. We discovered structural analogues of SAMD9/9L in the antibacteriophage defence system, Avs, resulting from convergent evolution. Further, the predicted nuclease site was conserved in bacterial analogues and was essential for cell death, suggesting a fundamental role in defence across different life kingdoms. Despite this shared immunity, we identified genomic signatures of evolutionary arms races in mammals, with remarkable gene copy number variations. We further unveiled that the absence of SAMD9 in bonobos corresponds to a recent gene loss still segregating in the population. Finally, we found that chimpanzee and bonobo SAMD9Ls have enhanced anti-HIV-1 functions compared with the human orthologue. These SAMD9/9L adaptations probably resulted from strong viral selective pressures, including by lentiviruses, and could contribute to lentiviral resistance in bonobos. Evolutionary characterization of Avs9 and SAMD9/9L provides a deeper understanding of how the immune system adapts to fight viruses over billions of years of evolution.

The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies^1–3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.

Summary: TRACK is a user-friendly command-line pipeline designed to consolidate the discovery and comparison of tandem repeats (TRs) across species. TRACK facilitates the cataloging and filtering of TRs based on reference genomes or T2T transcripts, and applies reciprocal LiftOver and sequence alignment methods to identify putative homologous TRs between species. For further streamlined analyses, TRACK can be used to genotype TRs and subsequently estimate and plot basic population genetic statistics. By integrating existing tools into one integrated workflow, TRACK enhances TR analysis accessibility and reproducibility, while offering flexibility for the user. Availability: The TRACK toolkit with step-by-step tutorial is freely available at https://github.com/caroladam/track .

The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations¹. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake², although evidence of recent selection is lacking^3,4. Here, using 94 long-read haplotype-resolved assemblies and short-read data from approximately 5,600 contemporary and ancient humans, we resolve the diversity and evolutionary history of structural variation at the amylase locus. We find that amylase genes have higher copy numbers in agricultural populations than in fishing, hunting and pastoral populations. We identify 28 distinct amylase structural architectures and demonstrate that nearly identical structures have arisen recurrently on different haplotype backgrounds throughout recent human history. AMY1 and AMY2A genes each underwent multiple duplication/deletion events with mutation rates up to more than 10,000-fold the single-nucleotide polymorphism mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome-based approach, we infer structural haplotypes across thousands of humans identifying extensively duplicated haplotypes at higher frequency in modern agricultural populations. Leveraging 533 ancient human genomes, we find that duplication-containing haplotypes (with more gene copies than the ancestral haplotype) have rapidly increased in frequency over the past 12,000 years in West Eurasians, suggestive of positive selection. Together, our study highlights the potential effects of the agricultural revolution on human genomes and the importance of structural variation in human adaptation.

We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.

Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility¹. The X chromosome is vital for reproduction and cognition². Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements—owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.

Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell’s fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.

One of the most celebrated textbook examples of physiological adaptations to desert environments is the unique ability that desert mammals have to produce hyperosmotic urine. Commonly perceived as an adaptation mainly observed in small rodents, the extent to which urine‐concentrating ability has evolved independently in distinct mammalian lineages has not previously been assessed using modern phylogenetic approaches. We review urine‐concentrating ability data from the literature in 121 mammalian species with geographic ranges encompassing varying climatic conditions. We explicitly test the general hypothesis that desert‐dwelling mammals have evolved greater ability to concentrate urine than non‐desert species, controlling for body mass, phylogenetic affinity and other covariates. Ancestral state reconstruction across our dataset’s phylogeny shows that the ability to produce hyperosmotic urine, measured as maximum urine osmolality, has evolved convergently in mammalian species with geographic ranges characterised by low mean annual aridity index. Phylogenetic generalised least‐squares (PGLS) models show that the mean annual aridity index of a species’ geographic range largely predicts its urine‐concentrating ability, even when accounting for body mass differences, phylogenetic correlations, the specific condition under which urine osmolality was measured, the method used to measure urine osmolality, and the species’ diet. In contrast, we find much weaker correlations between mass‐adjusted basal metabolic rate and environmental variables when analysing 84 of the species included in the urine osmolality analysis. Taken together, our results not only show that desert mammals effectively concentrate more urine than non‐desert mammals, but further suggest that aridity is likely to have been one of the main selective pressures leading to increasing maximum urine‐concentrating ability and driving its repeated evolution in different desert mammalian lineages.