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1. On the number of genealogical ancestors tracing to the source groups of an admixed population

   https://doi.org/10.1093/genetics/iyad079  

   Mooney, Jazlyn A; Agranat-Tamir, Lily; Pritchard, Jonathan K; Rosenberg, Noah A (July 2023, GENETICS)

   Novembre, J (Ed.)

   Abstract Members of genetically admixed populations possess ancestry from multiple source groups, and studies of human genetic admixture frequently estimate ancestry components corresponding to fractions of individual genomes that trace to specific ancestral populations. However, the same numerical ancestry fraction can represent a wide array of admixture scenarios within an individual’s genealogy. Using a mechanistic model of admixture, we consider admixture genealogically: how many ancestors from the source populations does the admixture represent? We consider African-Americans, for whom continent-level estimates produce a 75–85% value for African ancestry on average and 15–25% for European ancestry. Genetic studies together with key features of African-American demographic history suggest ranges for parameters of a simple three-epoch model. Considering parameter sets compatible with estimates of current ancestry levels, we infer that if all genealogical lines of a random African-American born during 1960–1965 are traced back until they reach members of source populations, the mean over parameter sets of the expected number of genealogical lines terminating with African individuals is 314 (interquartile range 240–376), and the mean of the expected number terminating in Europeans is 51 (interquartile range 32–69). Across discrete generations, the peak number of African genealogical ancestors occurs in birth cohorts from the early 1700s, and the probability exceeds 50% that at least one European ancestor was born more recently than 1835. Our genealogical perspective can contribute to further understanding the admixture processes that underlie admixed populations. For African-Americans, the results provide insight both on how many of the ancestors of a typical African-American might have been forcibly displaced in the Transatlantic Slave Trade and on how many separate European admixture events might exist in a typical African-American genealogy. 

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2. Genetic mixing facilitates adaptation to a novel environmental constraint

   https://doi.org/10.1111/een.13242  

   Durkee, Lily F.; Olazcuaga, Laure; Szymanski, Rachael; Melbourne, Brett A.; Hufbauer, Ruth A. (August 2023, Ecological Entomology)

   Abstract Climate change can affect the length and timing of seasons, which in turn can alter the time available for insects to complete their life cycles and successfully reproduce. Intraspecific hybridization between individuals from genetically distinct populations, or admixture, can boost fitness in populations experiencing environmental challenges. Admixture can particularly benefit small and isolated populations that may have high genetic load by masking deleterious alleles, thereby immediately increasing fitness, and also by increasing the genetic variation available for adaptive evolution. To evaluate the effects of admixture on populations exposed to a novel life cycle constraint, we used the red flour beetle,Tribolium castaneum, as a model system. Distinct laboratory lineages were kept isolated or mixed together to create populations containing 1–4 lineages. We then compared the fitness of admixed populations to 1‐lineage populations while subjecting them to a shortened generation time for three generations. Admixture did not influence fitness after two generations. In contrast, in the third generation, admixed populations had significantly greater fitness compared with 1‐lineage populations. The timing of the increase in fitness for the admixed populations suggests that adaptation to the novel environmental constraint occurred in the experimental populations. Our study highlights the importance of admixture for facilitating rapid adaptation to changes in seasonality, and more broadly to environmental change. 

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3. Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination

   https://doi.org/10.1371/journal.pcbi.1010422  

   Guo, Fangfang; Carbone, Ignazio; Rasmussen, David A. (August 2022, PLOS Computational Biology)

   Schiffels, Stephan (Ed.)

   Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungus Aspergillus flavus sampled across the United States to explore patterns of recombination and migration across the genome. 

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4. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs ( Occidozyga laevis )

   https://doi.org/10.1093/sysbio/syab034  

   Chan, Kin Onn; Hutter, Carl R; Wood, Perry L; Su, Yong-Chao; Brown, Rafe M (May 2021, Systematic Biology)

   Burbrink, Frank (Ed.)

   Abstract In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs—a group that is widespread, phenotypically conserved, and exhibits high levels of geographically based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: 1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and 2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear $$p$$-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow. [Cryptic species; gene flow; introgression; isolation-by-distance; isolation-by-environment; phylogenetic network; species delimitation.] 

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5. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

   KIN ONN CHAN, CARL R. (January 2021, Systematic biology)

   null (Ed.)

   In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs—a group that is widespread, phenotypically conserved, and exhibits high levels of geographically based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specificways in which gene flowcan cause overestimations of species diversity: 1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and 2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-bydistance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow. 

   more » « less