Biology subjects

Coop, G.

Publications and source records attributed to Coop, G..

At least 19 recordsLinked to original sources

bioRxiv2026

The Genome-Wide Effect of Drift and Selection over a Single Generation

The relative importance of genetic drift versus selection to evolutionary change has long been debated. This debate has mainly focused over long-time-scales (e.g. hundreds of thousands of generations), leaving the question of short-term evolutionary change relatively unaddressed. Our knowledge about the effects of selection on genetic change over short time scales is often based on identifying major allele frequency changes at few loci with large selective advantage. Yet selection often acts on polygenic traits where the short-term response is shaped by small shifts in allele frequency at many loci that will be difficult to distinguish from genetic drift. Here, we quantify the genome-wide effects of polygenic selection over a single generation, using the idea that alleles in stronger genetic correlation (LD) with selected alleles are expected to show greater variance in allele frequency change than expected under genetic drift. We derive expressions relating variation in LD among loci to the variance in allele frequency change due to linked selection and genetic drift and leverage this theory to quantify the contribution of linked selection to a single generation of allele frequency change. To demonstrate our approach, we decompose the genome-wide allele frequency change in the UK Biobank using fitness proxy phenotypes. We show that selection makes a small, but significant, contribution, with genetic drift making up the large majority of the change in allele frequencies. Our framework could be applied to other organisms for which data on number of offspring or allele frequencies over consecutive generations are available, enabling investigations of the short-term, genome-wide effects of polygenic selection across a wide range of species.

evolutionary biology↗

bioRxiv2026

Maize genetic diversity is largely unstructured by human ethnolinguistic diversity in its center of origin

Population structure and environmental features often capture major axes of genetic variation in many species. Yet the impacts of human activity often remain unquantified. For domesticated species that rely on human activity for survival and dispersal, human movements and cultural differences may play key roles patterning genetic diversity. Maize is a staple crop of enormous cultural importance to indigenous peoples of the Americas, but cannot survive or disperse without farmers. Using publicly available genotyping and passport data from almost 2,000 traditional maize varieties, more than 500 whole genome sequences of humans from Mexico, and indigenous linguistic maps, we quantify anthropogenic effects on maize genetic diversity in the Americas. Maize shows very little overall structure, highlighting the effectiveness of indigenous farmers in moving and mixing maize populations. While principal components of maize diversity show meaningful correlations to human genetic diversity, our linear modeling suggests little additional impact of human population structure beyond shared geography. Though differences in maize diversity are often patterned by language locally, we find only weak genome-wide effects at larger spatial scales. Despite the relatively weak global signal of anthropogenic effects, linguistic GWAS, outlier FST analyses, and selection scans identified loci associated with specific languages. Leveraging landscape-level sequencing data, we highlight how anthropogenic factors have shaped patterns of maize genetic diversity across Mesoamerica.

evolutionary biology↗

bioRxiv2025

Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado

In avocado and certain wild relatives in Lauraceae, pollination occurs via a synchronized rhythm of floral sex timing between two hermaphroditic flowering types. A-type plants present female-phase flowers in the morning and male-phase flowers in the afternoon, while B-types show the complementary pattern, a form of heterodichogamy. We map this dimorphism in avocado to a genomic region overlapping a single strong candidate gene, SDMYB, where a dominant haplotype confers A-type flowering. SDMYB belongs to a subgroup of R2R3 MYB transcription factors established as key regulators of floral maturation in diverse species with links to circadian jasmonate signaling. Haplotypes at this locus form an ancient trans-species polymorphism maintained by negative frequency-dependent balancing selection over 44 million years, and they segregate in at least 26 non-avocado species, including in a genus where this mating system has not been reported. Across several species examined, rhythmic diel SDMYB expression is associated with biphasic floral anthesis, and the dominant allele, which contains nonsynonymous changes in conserved functional domains, exhibits a cis-regulated phase delay, corresponding to the delayed 2nd anthesis of A-types. The coupling of dichogamy with diel flower movements, widespread among magnoliids, is a likely precursor to daily forms of heterodichogamy. Absence of the SDMYB polymorphism in true cinnamon, which exhibits a highly similar mating system, suggests the possibility that heterodichogamy has convergently evolved within Lauraceae.

evolutionary biology↗

bioRxiv2025

Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum

A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a bottom-up approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the genomic landscape of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans, and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avallenet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasizing the need to distinguish between historical divergence and recent introgression.

evolutionary biology↗

bioRxiv2025

Allelic turnover and dominance reversal at a single-gene balanced polymorphism controlling heterodichogamous flowering in wingnuts (Juglandaceae)

Angiosperms have evolved a wide variety of spatial and temporal developmental mechanisms to limit sexual interference and inbreeding. In heterodichogamy, two hermaphroditic morphs exploit distinct temporal reproductive niches by alternating phases of male and female flowering, promoting disassortative mating. This system is widespread within Juglandaceae, and known to be controlled by ancient balanced polymorphisms in walnuts (Juglans) and hickories (Carya). Here we identify distinct inheritance mechanisms controlling heterodichogamy in two separate Juglandaceae genera, the wingnuts (Pterocarya and Cyclocarya). We first document the occurrence of heterodichogamy in Pterocarya and map its genomic basis to haplotypes overlapping a single candidate gene in the FANTASTIC FOUR superfamily (GFAFL). These haplotypes segregate throughout the entire genus and the dominant haplotype controls female-first flowering. We show heterodichogamy in the sister genus Cyclocarya is associated with a distinct pair of ancient haplotypes at the same locus in both diploids and tetraploids, but with a dominant allele controlling male-first flowering. We infer a well-resolved fossil-calibrated phylogeny of Juglandaceae and date the divergence of the Pterocarya and Cyclocarya haplotypes to 51 and 44 million years ago, more recent than the divergence of these genera. In Pterocarya female-first heterozygotes, the dominant haplotype is associated with allele-specific suppression of the recessive copy of GFAFL during early male flower development. In Cyclocarya male-first heterozygotes, the dominant haplotype is associated with allele-specific activation of the recessive copy of GFAFL during male flower development, while the dominant copy itself shows higher expression in female flowers. We propose a model for the evolution of reciprocal sex matching in heterodichogamy through the combination of cis-regulatory divergence and allelic interactions involving fast and slow alleles at a single gene regulating flowering time. The non-independent expression of alleles in both systems is reminiscent of trans-sensing phenomena in other systems and suggests a mechanism mediated by DNA homology or an RNA intermediary. Notably, the dominant haplotypes in both genera show parallel architecture with a hemizygous region containing tandem duplicates of the same 1 kb motif downstream of the transcribed region of GFAFL which may be linked with such a mechanism. Our findings shed light on the molecular basis of heterodichogamy and contribute to an emerging view that diverse genetic pathways can be co-opted during its evolution and facilitate turnover in its genetic control.

evolutionary biology↗

bioRxiv2025

The distribution of highly deleterious variants across human ancestry groups

A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry group, so as not to miss "ancestry-specific variants." Here, we argue that this focus is unwarranted. We start with first principles considerations, based on models of mutation-drift-selection balance, which suggest highly pathogenic mutations should be at similarly low frequencies across ancestry groups. Severe disease mutations tend to be strongly deleterious, and thus evolutionarily young, and are kept at relatively constant frequency through recurrent mutation. Therefore, highly pathogenic alleles are shared identical by descent within extended families, not broad ancestry groups, and sequencing more people should yield similar numbers regardless of ancestry. We illustrate these points using gnomAD genetic ancestry groupings, and show that the classes of variants most likely to be highly pathogenic, notably sets of loss of function alleles at strongly constrained genes, conform well to these predictions. While there are many important reasons to diversify genomic research, strongly deleterious alleles will be found at comparable rates in people of all ancestries, and the information they provide about human biology is shared across ancestries.

genetics↗

bioRxiv2024

Inferring the geographic history of recombinant lineages using the full ancestral recombination graph

Spatial patterns of genetic relatedness among samples reflect the past movements of their ancestors. Our ability to untangle this history has the potential to improve dramatically given that we can now infer the ultimate description of genetic relatedness, the ancestral recombination graph (ARG). By extending spatial theory previously applied to trees, we generalize the common model of Brownian motion to full ARGs, thereby accounting for correlations in trees along a chromosome while efficiently computing likelihood-based estimates of dispersal rate and genetic ancestor locations, with associated uncertainties. We evaluate this models ability to reconstruct spatial histories using individual-based simulations and unfortunately find a clear bias in the estimates of dispersal rate and ancestor locations. We investigate the causes of this bias, pinpointing a discrepancy between the model and the true spatial process at recombination events. This highlights a key hurdle in extending the ubiquitous and analytically-tractable model of Brownian motion from trees to ARGs, which otherwise has the potential to provide an efficient method for spatial inference, with uncertainties, using all the information available in the full ARG.

evolutionary biology↗

bioRxiv2023

Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). In both genera, heterodichogamy is controlled by a single dominant allele. We fine-map the locus in each genus, and find two ancient (>50 Mya) structural variants involving different genes that both segregate as genus-wide trans-species polymorphisms. The Juglans locus maps to a ca. 20 kb structural variant adjacent to a probable trehalose phosphate phosphatase (TPPD-1), homologs of which regulate floral development in model systems. TPPD-1 is differentially expressed between morphs in developing male flowers, with increased allele-specific expression of the dominant haplotype copy. Across species, the dominant haplotype contains a tandem array of duplicated sequence motifs, part of which is an inverted copy of the TPPD-1 3 UTR. These repeats generate various distinct small RNAs matching sequences within the 3 UTR and further downstream. In contrast to the single-gene Juglans locus, the Carya heterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in developing flowers. The dominant haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows markedly reduced genetic diversity and is over twice as long as its recessive counterpart due to accumulation of various types of transposable elements. We did not detect either genetic system in other heterodichogamous genera within Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.

evolutionary biology↗

bioRxiv2023

Causal interpretations of family GWAS in the presence of heterogeneous effects

Family-based genome-wide association studies (GWAS) have emerged as a gold standard for assessing causal effects of alleles and polygenic scores. Notably, family studies are often claimed to provide an unbiased estimate of the average causal effect (or average treatment effect; ATE) of an allele, on the basis of an analogy between the random transmission of alleles from parents to children and a randomized controlled trial. Here, we show that this interpretation does not hold in general. Because Mendelian segregation only randomizes alleles among children of heterozygotes, the effects of alleles in the children of homozygotes are not observable. Consequently, if an allele has different average effects in the children of homozygotes and heterozygotes, as can arise in the presence of gene-by-environment interactions, gene-by-gene interactions, or differences in LD patterns, family studies provide a biased estimate of the average effect in the sample. At a single locus, family-based association studies can be thought of as providing an unbiased estimate of the average effect in the children of heterozygotes (i.e., a local average treatment effect; LATE). This interpretation does not extend to polygenic scores, however, because different sets of SNPs are heterozygous in each family. Therefore, other than under specific conditions, the within-family regression slope of a PGS cannot be assumed to provide an un-biased estimate for any subset or weighted average of families. Instead, family-based studies can be reinterpreted as enabling an unbiased estimate of the extent to which Mendelian segregation at loci in the PGS contributes to the population-level variance in the trait. Because this estimate does not include the between-family variance, however, this interpretation applies to only (roughly) half of the sample PGS variance. In practice, the potential biases of a family-based GWAS are likely smaller than those arising from confounding in a standard, population-based GWAS, and so family studies remain important for the dissection of genetic contributions to phenotypic variation. Nonetheless, the causal interpretation of family-based GWAS estimates is less straightforward than has been widely appreciated.

genetics↗

bioRxiv2023

The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change

Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets. Significance statementThe relative contribution of random genetic drift and natural selection to the change in allele frequencies through time is a long standing question in Evolutionary Biology. We show through theory and simulation how genomic time series - such as ancient DNA datasets - can be used to decompose the genome-wide contributions of selection, gene flow, and genetic drift to allele frequency change. We apply these methods to two time time series from ancient Europeans and show that gene flow accounts for most allele frequency change over the last few thousand years, with genetic drift and not selection making up much of the rest of the contribution to genome-wide evolutionary change.

evolutionary biology↗

bioRxiv2023

Demographic inference for spatially heterogeneous populations using long shared haplotypes

We introduce a modified spatial {Lambda}-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.

genetics↗

bioRxiv2023

The temporal and genomic scale of selection following hybridization

1Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the dynamics underlying these patterns within hybrid populations have been lacking. Here, we develop methods based on the Wavelet Transform to understand the spatial genomic scale of local ancestry variation and its association with recombination rates. We present theory and use simulations to show how wavelet-based decompositions of ancestry variance along the genome and the correlation between ancestry and recombination reflect the joint effects of recombination, genetic drift, and genome-wide selection against introgressed alleles. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of local ancestry variation at varying spatial genomic scales through time. Using wavelet approaches to identify the genomic scale of variance in ancestry and its correlates, we show that these methods can detect temporally localized effects of drift and selection. We apply these methods to previously published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio), and to inferred Neanderthal introgression in modern humans. Across systems, we find that upwards of 20% of the variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. We also see signals of selection at fine genomic scales and much longer time scales. However, we show that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available, and can help shed light on generalities of the genomic consequences of interspecific hybridization.

evolutionary biology↗

bioRxiv2023

Polygenic outcomes of sexually antagonistic selection

Sexual antagonism occurs when males and females have different fitness optima for a phenotype, but are constrained from evolving to these optima because of their shared genome. We study the response of a polygenic phenotype to the onset of sexually antagonistic selection, modeling a phenotype initially under stabilizing selection around an optimum, followed by a sudden divergence of the male and female optima. We observe rapid phenotypic evolution to these new optima via small changes in allele frequencies genome-wide. We study the role of sex chromosomes in this divergence and find that, in the absence of dosage compensation, the X chromosome favors evolution toward the female optimum, inducing co-evolutionary male-biased responses on the autosomes. However, dosage compensation obscures the female-biased interests of the X, causing it to contribute equally to male and female phenotypic change. In both scenarios, we see little effect of dominance in the genetic variation utilized by the X chromosome vs. the autosomes. We go on to examine the dynamics of stabilizing selection once the male and female optima have been reached, exploring a subtle mechanism through which the X chromosome, via the Bulmer effect, can cause higher equilibrium phenotypic variance in males than females. Finally, we consider how sexual antagonistic selection might persist across longer time scales, demonstrating that random fluctuations in an adaptive landscape can generate prolonged intragenomic conflict. Overall, our results provide insight into the response of complex phenotypes to sexually antagonistic selection and the evolution of sexual dimorphism.

evolutionary biology↗

bioRxiv2023

Interpreting population and family-based genome-wide association studies in the presence of confounding

A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individuals phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding, and can also absorb the indirect genetic effects of relatives genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of Mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect size estimates are used in polygenic scores. We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. In addition to known biases that can arise in family-based GWASs when interactions between family members are ignored, we show that biases can also arise from gene-by-environment (GxE) interactions when parental genotypes are not distributed identically across interacting environmental and genetic backgrounds. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding and interactions.

genetics↗

bioRxiv2022

A complex evolutionary history of genetic barriers to gene flow in hybridizing warblers

The Setophaga warbler sister species in western North America, Setophaga occidentalis and S. townsendi provide a rare opportunity to explore how the accumulation of genetic barriers to gene flow contributes to speciation. These sister species are at the very early stages of speciation, as their genome-wide divergence is limited, and they hybridize extensively upon secondary contact. However, there are several well-characterized loci involved in speciation. There is a plumage difference between the species controlled by mutations close to the agouti signaling protein (ASIP), which generates underdominance due to compromised hybrid territorial signaling. A second large region (~2Mb) on chromosome 5 encodes many mitochondrial-interacting genes and coevolves with the mitochondrial genome. Here we reconstructed the ancestral recombination graphs of these genomic regions relative to the genome-wide background to learn about the evolutionary history of these barriers. We find signatures of long-lasting barrier effects that lasted for ~190 K generations, and recent selective sweeps in chr5 mitonuclear genetic block in both species within the past 60 K generations ago. We further observed heterogeneity within the long-lasting mitonuclear barrier with localized signals of much more recent selective sweeps unique one of the species. The divergence of ASIP is elevated by a species-specific selective sweep within S. occidentalis that occurred 21 K generations ago. However, the signature of long-lasting barrier effect is much weaker at ASIP suggesting that it may have arisen later than the mitonuclear system. Associating the evolutionary history of these genetic barriers with Pleistocene climate change history sheds light on the intrinsic and extrinsic reciprocity underlying the origin of species.

evolutionary biology↗

bioRxiv2021

Population differentiation of polygenic score predictions under stabilizing selection

1Given the many small-effect loci uncovered by genome-wide association studies (GWAS), polygenic scores have become central to the drive for genomic medicine and have spread into various areas including evolutionary studies of adaptation. While promising, these scores are fraught with issues of portability across populations, due to mis-estimated effect sizes and missing causal loci across populations unrepresented in large-scale GWAS. The poor portability of polygenic scores at first seems at odds with the view that much of common genetic variation is shared among populations. Here we investigate one potential cause of this discrepancy, stabilizing selection on complex traits. Somewhat counter-intuitively, while stabilizing selection to the same optimum phenotype leads to lower phenotypic differentiation among populations, it increases genetic differentiation at GWAS loci because it accelerates the turnover of polymorphisms underlying trait variation within populations. We develop theory to show how stabilizing selection impacts the utility of polygenic scores when applied to unrepresented populations. Specifically, we quantify their reduced prediction accuracy and find they can substantially overstate average genetic differences of phenotypes among populations. Our work emphasizes stabilizing selection to the same optimum as a useful null evolutionary model to draw connections between patterns of allele frequency and polygenic score differentiation.

evolutionary biology↗

bioRxiv2021

Mate choice enhances post-zygotic barriers to gene flow via ancestry bundling

Hybridization and subsequent genetic introgression are now known to be common features of the histories of many species, including our own. Following hybridization, selection often purges introgressed DNA genome-wide. While mate choice can prevent hybridization in the first place, it is also known to play an important role in post-zygotic selection against hybrids, and thus the purging of introgressed DNA. However, this role is usually thought of as a direct one: a mating preference for conspecifics reduces the sexual fitness of hybrids, reducing the transmission of introgressed ancestry. Here, we explore a second, indirect role of mate choice as a barrier to gene flow. Under assortative mating, parents covary in their ancestry, causing ancestry to be "bundled" in their offspring and later generations. This bundling effect increases ancestry variance in the population, enhancing the efficiency with which post-zygotic selection purges introgressed DNA. Using whole-genome simulations, we show that the bundling effect can comprise a substantial portion of mate choices overall effect as a post-zygotic barrier to gene flow, and that it is driven by ancestry covariances between and within maternally and paternally inherited genomes. We derive a simple method for estimating the impact of the bundling effect from standard measures of assortative mating. Applying this method to data from a diverse set of hybrid zones, we find that the bundling effect increases the purging of introgressed DNA by between 1.2-fold (in a baboon system with weak assortative mating) and 14-fold (in a swordtail system with strong assortative mating). Thus, the bundling effect of mate choice contributes substantially to the genetic isolation of species.

evolutionary biology↗

bioRxiv2021

Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies

Spatial patterns in genetic diversity are shaped by individuals dispersing from their parents and larger-scale population movements. It has long been appreciated that these patterns of movement shape the underlying genealogies along the genome leading to geographic patterns of isolation by distance in contemporary population genetic data. However, extracting the enormous amount of information contained in genealogies along recombining sequences has, until recently, not been computationally feasible. Here we capitalize on important recent advances in genome-wide gene-genealogy reconstruction and develop methods to use thousands of trees to estimate per-generation dispersal rates and to locate the genetic ancestors of a sample back through time. We take a likelihood approach in continuous space using a simple approximate model (branching Brownian motion) as our prior distribution of spatial genealogies. After testing our method with simulations we apply it to Arabidopsis thaliana. We estimate a dispersal rate of roughly 60km2 per generation, slightly higher across latitude than across longitude, potentially reflecting a northward post-glacial expansion. Locating ancestors allows us to visualize major geographic movements, alternative geographic histories, and admixture. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.

evolutionary biology↗