Andrew David Foote

• Nickel, Jana Helene; Laine, Jan Tapio & Foote, Andrew David (2026). Complex Patterns of Hitchhiking Mutation Load Among Stickleback Populations. Genome Biology and Evolution (GBE). 18(4). doi: 10.1093/gbe/evag088. Full text in Research Archive Show summary

  Positive selection causes beneficial alleles to rise to high frequency in a population. This can cause linked genetic variation to “hitchhike,” and thereby also rise in frequency. This linked variation may include deleterious recessive alleles, previously neutrally harbored at low frequency and in heterozygous genotypes. Modeling studies have shown that local effective population size and reduced recombination rate should contribute to the probability of deleterious mutations being swept to high frequency by being linked to beneficial alleles in selective sweeps or selection on inversion karyotypes. Marine sticklebacks have repeatedly adapted to thousands of freshwater habitats that became available after the last ice age, resulting in the formation of distinct marine and freshwater ecotypes. Selection acts on ancient standing genetic variation present in marine populations, causing freshwater-adaptive alleles to increase rapidly over tens of generations. These genomic regions play a key role in the repeated freshwater adaptation of morphological, physiological, and behavioral traits, and evolve under strong selection. Thus, threespine stickleback is an ideal system for investigating the impact of hitchhiking mutation load. We estimate the mutation load in regions of low recombination, including inversions and the Eda haplotype. We find some evidence for increased accumulation of deleterious alleles in one inversion, while this is not the case for two other inversions. Inversions deviated from Hardy–Weinberg equilibrium in several populations due to an excess of homozygotes.

• Foote, Andrew David & Croft, Darren Paul (2025). Sexually antagonistic selection, X-chromosome relatedness and the evolution of menopause in killer whales. Biology Letters. ISSN 1744-9561. 21(12). doi: 10.1098/rsbl.2025.0528. Full text in Research Archive Show summary

  The human menopause is hypothesized to be an adaptive trait that allows post-reproductive females to invest in, and avoid reproductive conflict with, their existing offspring and grand-offspring, thereby increasing their survival. Thus, the sacrifice of an early cessation of reproduction can result in increased inclusive fitness. However, the genetic basis of menopause remains largely unknown. Given that a mid-life menopause is a rare trait in terrestrial social species, there is a need to consider alternative taxa to move beyond a single datapoint to test theoretical frameworks upon. One aquatic taxonomic group, toothed whales, comprises five matrilineal species with menopause, thereby providing a crucial comparative system for understanding the evolution of menopause. The kinship dynamics in killer whale Orcinus orca societies, maximize the inclusive fitness of post-reproductive females when they invest in their son’s reproductive success. Specifically, inclusive fitness is maximized at the X-chromosome (over the autosomes) through a post-reproductive female’s son siring daughters. This raises the question of how selection favours a female trait that primarily benefits male offspring? Due to its inheritance pattern and ploidy, the X-chromosome is a candidate target for sexual antagonistic selection, which could act on the female-specific traits of increased lifespan and reproductive cessation. We therefore propose that the X-chromosome is a promising marker to explore the genetic underpinning of menopause in matrilineal whale species and could provide a key comparison (and contrast) to the genetic basis of menopause in humans. Lastly, we expand these ideas to autosomal regions with female biased recombination.

• A., Morin, Phillip; Bernhard, Bein,; Chiara, Bortoluzzi,; V., Bukhman, Yury; Taylor, Hains, & Dorothea, Heimeier, [Show all 53 contributors for this article] (2025). Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life. Frontiers in Marine Science. 12, p. 1–24. doi: 10.3389/fmars.2025.1562045. Full text in Research Archive Show summary

  Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project (CGP) began in early 2020 to facilitate the generation of near error-free, chromosome-resolved reference genomes for all cetacean species. Towards that goal, and using the methods, goals and genome assembly quality standards of the Vertebrate Genomes Project (VGP), we generated 13 new reference genomes across eight of the 14 cetacean families. Additionally, we summarize the genome assembly characteristics for 18 species, including these newly-generated and five published genome assemblies that meet the completeness and quality standards. We infer ancestral linkage groups (ALG) for cetaceans, showing that the ancestral karyotype of 22 ALGs is largely conserved in extant species, except for Ziphiidae, and for Balaenidae and Kogiidae, which exhibit similar independent fusions. Gene annotation, characterization of historical demography, heterozygosity and runs of homozygosity (ROH) reveal important information for conservation applications. By comparing the new reference genomes to previous draft assemblies, we show that the reference genomes have enhanced characteristics that will support and promote scientific research. Specifically, the genomes improve resolution and characterization of repetitive elements, provide validation (or exclusion) of genes linked to complex traits, and allow more complete characterization of gene regions such as the highly complex Major Histocompatibility Complex (MHC) Class I and II gene clusters that are important for population health.

• Laine, Jan Tapio; Nickel, Jana Helene; Romundset, Anders & Foote, Andrew David (2025). Ancient stickleback genomes reveal the early stages of parallel adaptation. Evolution. ISSN 0014-3820. 79(11), p. 2446–2459. doi: 10.1093/evolut/qpaf164. Full text in Research Archive Show summary

  The parallel evolution of traits and their underlying genetic basis is well studied; however, studies of the parallel chronology of adaptive genetic changes remain scarce. The probability of parallel genetic change should be increased by the clustering of adaptive alleles in regions of suppressed recombination, particularly for genes that have large fitness or phenotypic effects. The threespine stickleback is a model system for studying parallel evolution, here we present genomic data from nine subfossil stickleback bones dated to 14.8-0.7 KYR BP in age. Comparing the four highest coverage genomes, which represent different stages along the marine–freshwater divergence continuum, we find that the accumulation of freshwater ancestry is clustered rather than randomly distributed throughout the marine–freshwater divergent regions of the genome. We consistently find freshwater ancestry on chromosome IV at the early stages of freshwater adaptation. Regions of chromosome IV contain the greatest genetic differentiation between marine and freshwater ecotypes and among the highest density of quantitative trait loci. These include Ectodysplasin (EDA), a large-effect pleiotropic locus associated with defensive armor and variation in neurosensory and behavioral traits. Freshwater ancestry in the subfossils is also consistently found at inversions and X chromosome early in the adaptive process. Our findings add to emerging evidence that freshwater adaptation in threespine stickleback could have a staggered but predictable temporal dynamic.

• Foote, Andrew David; Gilbert, Marcus Thomas Pius; Shyam, Gopalakrishnan,; Marie, Louis,; Martin, Michael David & A., Morin, Phillip [Show all 9 contributors for this article] (2025). Evidence of long-term purging of mutation burden in killer whale Orcinus orca genomes. Heredity. ISSN 0018-067X. 134, p. 671–679. doi: 10.1038/s41437-025-00806-5. Full text in Research Archive Show summary

  Genomes of high latitude killer whales (Orcinus orca) harbour signatures of post-glacial founding and expansion. Here, we investigate whether reduced efficacy of selection increased the predicted mutation burden in founder populations with low Ne, or whether recessive deleterious mutations exposed to selection in homozygous genotypes were purged. Comparing the accumulation of synonymous and non-synonymous mutations across pairs of globally sampled genomes reveals that high latitude North Atlantic genomes have accumulated proportionally fewer non-synonymous mutations than other populations. The genome of a 7.5-Kyr-old North Atlantic killer whale, inferred to be closely related to the direct ancestors of the present-day Icelandic and Norwegian populations, was used to calibrate the timing of the action of selection on non-synonymous mutations predominantly to the Holocene. Non-synonymous mutations purged in modern Norwegian killer whale genomes are found as globally shared standing variation in heterozygote genotypes more often than expected, suggesting associative- or pseudo-overdominance. Taken together, our findings are consistent with purging of recessive non-synonymous mutations exposed to selection in founder-associated homozygous genotypes.

• Filatova, Olga A.; Fedutin, Ivan D.; Borisova, Ekaterina A.; Meschersky, Ilya G.; Shitova, Marina V. & Hoyt, Erich [Show all 7 contributors for this article] (2025). Complete Mitochondrial Genomes Provide Evidence of a Killer Whale Refugium Off the Coast of Japan During the Last Glacial Maximum. Journal of Biogeography. ISSN 0305-0270. 52(8). doi: 10.1111/jbi.15159. Full text in Research Archive Show summary

  Aim During glacial periods, highly mobile species often shifted to warmer, ice-free regions known as refugia, which frequently maintained higher genetic diversity than newly colonised areas after glacial retreat. We analyse complete mitogenome sequences from 11 killer whale samples in Nemuro Strait to test the hypothesis that waters around Japan may have preserved a refugial population of killer whales that retained historical genetic diversity. Location Western North Pacific. Taxon Orcinus orca ater, Cetacea. Methods Sequencing of complete mitochondrial genomes (16,387 bp) from 11 killer whale samples collected in the Nemuro Strait, southern Okhotsk Sea. Distribution of haplotypes in the social network was visualised using the data on social associations. The probability of individuals belonging to one or more possible reproductive groups was estimated based on 17 microsatellite loci. Results Seven samples shared a haplotype common in the western North Pacific, one had a haplotype previously found only in the eastern North Pacific, and three exhibited novel haplotypes. Killer whales with different haplotypes were connected into a single social network, but some degree of social segregation is evident within the network. No significant genetic clustering based on microsatellite markers was detected between Nemuro Strait and areas near the Kamchatka Peninsula. Main Conclusions With five distinct mitogenomes, Nemuro Strait now ranks second in mitogenomic diversity after the central Aleutian Islands. These findings support the hypothesis of a glacial refugium off Japan preserving a portion of pre-glacial genetic diversity. The lack of genetic clustering between Nemuro Strait and areas near the Kamchatka Peninsula indicates that all R-type killer whales in the western North Pacific belong to a single population. The low mitogenomic diversity north of Nemuro Strait likely reflects a founder effect, where a few groups colonised the region after the LGM, while most of the population with higher genetic diversity remained near Japan.

• Baumgartner, Chérine D.; Jourdain, Eve Marie; Bonhoeffer, Sebastian; Borgå, Katrine; Heide-Jørgensen, Mads P. & Karoliussen, Richard [Show all 13 contributors for this article] (2025). Kinship clustering within an ecologically diverse killer whale metapopulation. Heredity. ISSN 0018-067X. 134, p. 109–119. doi: 10.1038/s41437-024-00740-y. Full text in Research Archive Show summary

  Metapopulation dynamics can be shaped by foraging ecology, and thus be sensitive to shifts in prey availability. Genotyping 204 North Atlantic killer whales at 1346 loci, we investigated whether spatio-temporal population structuring is linked to prey type and distribution. Using population-based methods (reflecting evolutionary means), we report a widespread metapopulation connected across ecological groups based upon nuclear genome SNPs, yet spatial structuring based upon mitogenome haplotypes. These contrasting patterns of markers with maternal and biparental inheritance are consistent with matrilineal site fidelity and philopatry, and male-mediated gene flow among demes. Connectivity between fish-eating and ‘mixed-diet’ (eating both fish and mammal prey) killer whales, marks a deviation within a species renowned for its marked structure associated with ecology. However, relatedness estimates suggest distinct spatial clusters, and heterogeneity in recent gene flow between them. The contrasting patterns between inference of structure and inference of relatedness suggest that gene flow has been partially restricted over the past two to three generations (50–70 years). This coincides with the collapse of North Atlantic herring stocks in the late 1960s and the subsequent cessation of their seasonal connectivity. Statistically significant association between diet types and assignment of Icelandic killer whales to relatedness-based clusters indicated limited gene flow was maintained through Icelandic ‘mixed-diet’ whales when herring-mediated connectivity was diminished. Thus, conservation of dietary variation within this metapopulation is critical to ensure genetic health. Our study highlights the role of resource dynamics and foraging ecology in shaping population structure and emphasises the need for transnational management of this widespread migratory species and its prey.

• Reeves, Isabella M.; Totterdell, John A.; Sandoval-Castillo, Jonathan; Betty, Emma L.; Stockin, Karen A. & Stewart, Ramari Oliphant [Show all 8 contributors for this article] (2025). Admixture Increases Genetic Diversity and Adaptive Potential in Australasian Killer Whales. Molecular Ecology. ISSN 0962-1083. 34(23). doi: 10.1111/mec.17689. Full text in Research Archive Show summary

  Admixture is the exchange of genetic variation between differentiated demes, resulting in ancestry within a population coalescing in multiple ancestral source populations. Low-latitude killer whales (Orcinus orca) populations typically have higher genetic diversity than those in more densely populated, high productivity and high-latitude regions. This has been hypothesized to be due to episodic admixture between populations with distinct genetic backgrounds. We test this hypothesis by estimating variation in local ancestry of whole genome sequences from three genetically differentiated, low-latitude killer whale populations and comparing them to global genetic variation. We find ‘Antarctic-like’ ancestry tracts in the genomes of southwestern Australia (SWA) population including recent (within the last 2–4 generations) admixture. Admixed individuals had, on average, shorter and fewer runs of homozygosity than unadmixed individuals and increased effective population size (Ne). Thus, connectivity between demes results in the maintenance of Ne of relatively small demes at a level comparable to the sum of Ne across demes. A subset of the admixed regions was inferred to be evolving under selection in the SWA population, suggesting that this admixed variation may be contributing to the population's adaptive potential. This study provides important and rare empirical evidence that small populations can maintain genetic diversity due to sporadic admixture between different genetic backgrounds and that admixed ancestry can promote the long-term stability of Ne.

• Laine, Jan Tapio; Mak, Sarah S.T.; Martins, Nuno F.G.; Chen, Xihan; Gilbert, Marcus Thomas Pius & Jones, Felicity C. [Show all 9 contributors for this article] (2024). Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Current Biology. ISSN 0960-9822. 34(5), p. 1142–1147. doi: 10.1016/j.cub.2024.01.056. Full text in Research Archive Show summary

  Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective “evolve and resequence” natural experiments using sedaDNA.

• Jourdain, Eve Marie; Karoliussen, Richard; Martin, Sarah Louise; Langangen, Øystein Ole Gahr; Robeck, Todd & Borgå, Katrine [Show all 8 contributors for this article] (2024). Social and genetic connectivity despite ecological variation in a killer whale network. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 291(2021). doi: 10.1098/rspb.2024.0524. Full text in Research Archive Show summary

  Philopatric kin-based societies encourage a narrow breadth of conservative behaviours owing to individuals primarily learning from close kin, promoting behavioural homogeneity. However, weaker social ties beyond kin, and across a behaviourally diverse social landscape, could be sufficient to induce variation and a greater ecological niche breadth. We investigated a network of 457 photo-identified killer whales from Norway (548 encounters in 2008–2021) with diet data available (46 mixed-diet individuals feeding on both fish and mammals, and 411 exclusive fish-eaters) to quantify patterns of association within and between diet groups, and to identify underlying correlates. We genotyped a subset of 106 whales to assess patterns of genetic differentiation. Our results suggested kinship as main driver of social bonds within and among cohesive social units, while diet was most likely a consequence reflective of cultural diffusion, rather than a driver. Flexible associations within and between ecologically diverse social units led to a highly connected network, reducing social and genetic differentiation between diet groups. Our study points to a role of social connectivity, in combination with individual behavioural variation, in influencing population ecology in killer whales.

• Meyer, Laura; Barry, Pierre; Riquet, Florentine; Foote, Andrew David; Der Sarkissian, Clio & Cunha, Regina L. [Show all 13 contributors for this article] (2024). Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.17277. Full text in Research Archive Show summary

  Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.

• Garroway, Colin J.; Greef, Evelien de; Lefort, Kyle J.; Thorstensen, Matt J.; Foote, Andrew David & Matthews, Cory J. D. [Show all 13 contributors for this article] (2024). Climate change introduces threatened killer whale populations and conservation challenges to the Arctic. Global Change Biology. ISSN 1354-1013. 30(6). doi: 10.1111/gcb.17352. Full text in Research Archive Show summary

  The Arctic is the fastest-warming region on the planet, and the lengthening ice-free season is opening Arctic waters to sub-Arctic species such as the killer whale (Orcinus orca). As apex predators, killer whales can cause significant ecosystem-scale changes. Setting conservation priorities for killer whales and their Arctic prey species requires knowledge of their evolutionary history and demographic trajectory. Using whole-genome resequencing of 24 killer whales sampled in the northwest Atlantic, we first explored the population structure and demographic history of Arctic killer whales. To better understand the broader geographic relationship of these Arctic killer whales to other populations, we compared them to a globally sampled dataset. Finally, we assessed threats to Arctic killer whales due to anthropogenic harvest by reviewing the peer-reviewed and gray literature. We found that there are two highly genetically distinct, non-interbreeding populations of killer whales using the eastern Canadian Arctic. These populations appear to be as genetically different from each other as are ecotypes described elsewhere in the killer whale range; however, our data cannot speak to ecological differences between these populations. One population is newly identified as globally genetically distinct, and the second is genetically similar to individuals sampled from Greenland. The effective sizes of both populations recently declined, and both appear vulnerable to inbreeding and reduced adaptive potential. Our survey of human-caused mortalities suggests that harvest poses an ongoing threat to both populations. The dynamic Arctic environment complicates conservation and management efforts, with killer whales adding top-down pressure on Arctic food webs crucial to northern communities' social and economic well-being. While killer whales represent a conservation priority, they also complicate decisions surrounding wildlife conservation and resource management in the Arctic amid the effects of climate change.

• Foote, Andrew David; Alexander, Alana; Ballance, Lisa T.; Constantine, Rochelle; Muñoz, Bárbara Galletti Vernazzani & Guinet, Christophe [Show all 15 contributors for this article] (2023). "Type D" killer whale genomes reveal long-term small population size and low genetic diversity. Journal of Heredity. ISSN 0022-1503. 114(2), p. 94–109. doi: 10.1093/jhered/esac070. Full text in Research Archive
• Reeves, Isabella; Totterdell, John A.; Betty, Emma; Donnelly, David M.; George, Angela & Holmes, Steven [Show all 11 contributors for this article] (2023). Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers. Journal of Heredity. ISSN 0022-1503. 114(6), p. 598–611. doi: 10.1093/jhered/esad058. Full text in Research Archive Show summary

  Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as “Old Tom,” washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom’s genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.

• Louis, Marie; Korlević, Petra; Nykänen, Milaja; Archer, Frederick; Berrow, Simon & Brownlow, Andrew [Show all 18 contributors for this article] (2023). Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nature Communications. 14(1). doi: 10.1038/s41467-023-39532-z. Full text in Research Archive Show summary

  Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.

• Louis, Marie; Korlević, Petra; Nykänen, Milaja; Archer, Frederick I.; Berrow, Simon & Brownlow, Andrew [Show all 18 contributors for this article] (2022). Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. BioRxiv. ISSN 0362-4331. doi: 10.1101/2022.11.03.515020. Full text in Research Archive
• Foote, Andrew; Bunskoek, Paulien & Sanger, Wellcome (2022). The genome sequence of the killer whale, Orcinus orca (Linnaeus, 1758). Wellcome Open Research. 7. doi: 10.12688/wellcomeopenres.18278.1. Full text in Research Archive Show summary

  We present a genome assembly from an individual female Orcinus orca (the killer whale; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence is 2.65 gigabases in span. The majority of the assembly (93.76%) is scaffolded into 22 chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length.

• Foote, Andrew (2022). Are “Type 2” killer whales long in the tooth? A critical reflection on the discrete categorization of Northeast Atlantic killer whales. Marine mammal science. ISSN 0824-0469. 39, p. 345–350. doi: 10.1111/mms.12964. Full text in Research Archive
• Kirch, Melanie; Romundset, Anders; Gilbert, Marcus Thomas Pius; Jones, Felicity C. & Foote, Andrew (2021). Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Current Biology. ISSN 0960-9822. 31, p. 2027–2036. doi: 10.1016/j.cub.2021.02.027. Full text in Research Archive Show summary

  Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.1 To address this, we applied a paleogenomics approach2 to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes3 and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.4 The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.

• Louis, Marie; Galimberti, Marco; Archer, Frederick; Berrow, Simon; Brownlow, Andrew & Fallon, Ramon [Show all 15 contributors for this article] (2021). Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. Science Advances. 7(44). doi: 10.1126/sciadv.abg1245. Full text in Research Archive Show summary

  Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.

• Foote, Andrew; Hooper, Rebecca; Alexander, Alana; Baird, Robin; Baker, Charles Scott & Ballance, Lisa [Show all 34 contributors for this article] (2021). Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Molecular Ecology. ISSN 0962-1083. 30(23), p. 6162–6177. doi: 10.1111/mec.16137. Full text in Research Archive Show summary

  Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.

• Foote, Andrew; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam; Louis, Marie; Martin, Michael David & Morin, Phillip A. [Show all 9 contributors for this article] (2021). Evidence of long-term purging of mutation load in killer whale genomes. BioRxiv. ISSN 0362-4331. doi: 10.1101/2021.08.21.457186. Full text in Research Archive
• Papadopulos, Alexander; Helmstetter, A.; Osborne, Owen; Comeault, Aaron; Wood, Daniel & Straw, Edward [Show all 13 contributors for this article] (2021). Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 38(9), p. 3724–3736. doi: 10.1093/molbev/msab141. Full text in Research Archive Show summary

  The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species’ capacities to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonised isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonisation of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

• Dehasque, Marianne; Ávila-Arcos, María C; Díez-del-Molino, David; Fumagalli, Matteo; Guschanski, Katerina & Lorenzen, Eline D. [Show all 15 contributors for this article] (2020). Inference of natural selection from ancient DNA. Evolution Letters. 4(2), p. 94–108. doi: 10.1002/evl3.165. Full text in Research Archive Show summary

  Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.

• Morin, Phillip A.; Alexander, Alana; Blaxter, Mark; Caballero, Susana; Fedrigo, Olivier & Fontaine, Michaël C. [Show all 16 contributors for this article] (2020). Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species. Marine mammal science. ISSN 0824-0469. 36(4), p. 1356–1366. doi: 10.1111/mms.12721. Full text in Research Archive
• Hosegood, Jane; Humble, Emily; Ogden, Rob; Bruyn, Mark de; Creer, Simon & Stevens, Guy [Show all 25 contributors for this article] (2020). Phylogenomics and species delimitation for effective conservation of manta and devil rays. Molecular Ecology. ISSN 0962-1083. 29(24), p. 4783–4796. doi: 10.1111/mec.15683. Full text in Research Archive Show summary

  Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome‐wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide‐ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

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• Croft, Darren P.; Foote, Andrew David; Garland, Ellen C. & King, Stephanie L. (2026). The Evolution of Cetacean Societies. University of Chicago Press. ISBN 9780226840574. 436 p. doi: https:/press.uchicago.edu/ucp/books/book/chicago/E/bo257312594.html. Full text in Research Archive Show summary

  Cetaceans—whales, dolphins, and porpoises—represent an evolutionary peak with respect to their advanced cognitive capacities; flexible communication systems; and structured, multilevel societies. Indeed, the social lives of whales and dolphins have long fascinated scientists and the public alike. The Evolution of Cetacean Societies provides a comprehensive overview of the significant advancements made in studying cetacean behavior and ecology over the last twenty-five years, focusing on our growing understanding of these animals’ complex social lives. Bringing together scientists from multiple disciplines, the volume summarizes key innovations and progress related to studying cetacean societies’ cultural and genetic basis, their complex social structures, their use of cooperation and patterns of social conflict, and their significant interactions with humans. Each chapter provides an in-depth account of the social lives of whales and dolphins, incorporating the latest cutting-edge research from genomics, communication, network analysis, and animal culture to explain how these animals form societies, maintain relationships, and share information. The final chapters focus on the existential threats facing these diverse and charismatic species, how human-cetacean interactions have shaped our perceptions, and what scientists can learn from their diverse social lives by championing researcher diversity in marine mammal science. The result is an essential and forward-looking book that both contextualizes the lessons of the past two decades and questions the challenges these enigmatic species might face in the future.

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• Foote, Andrew David (2026). Museum collections provide a temporal record of past genetic variation. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 123(2). doi: 10.1073/pnas.2530586122. Full text in Research Archive Show summary

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• Taylor, Rebecca S.; Jensen, Evelyn L.; Coltman, David; Foote, Andrew & Lamichhaney, Sangeet (2021). Seeing the whole picture: What molecular ecology is gaining from whole genomes. Molecular Ecology. ISSN 0962-1083. 30, p. 5917–5922. doi: 10.1111/mec.16282. Full text in Research Archive
• Taylor, Rebecca S.; Jensen, Evelyn L.; Coltman, David; Foote, Andrew & Lamichhaney, Sangeet (2021). Seeing the whole picture: What molecular ecology is gaining from whole genomes. Molecular Ecology. ISSN 0962-1083. 30(23), p. 5917–5922. doi: 10.1111/mec.16282. Full text in Research Archive

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