Browsing by Subject "population genetics"

Admixture occurs when previously isolated populations come together to form a new population with genetic ancestry from those sources. Admixture is ubiquitous across the tree of life, including humans, and is often associated with migration and exposure to new environments and selective pressures. Admixed populations provide a unique opportunity to study adaptation on short timescales by introducing beneficial alleles at high frequency. However, admixed populations are often excluded from genomic studies due to lack of applicable methodology. Instead of relying on classical methods confounded by the process of admixture itself, we can detect changes in patterns of genetics ancestry that are informative about selection in admixed populations and at the short timescales often relevant for post-admixture selection. However, we lack theoretical expectations and methods to detect and characterize ancestry-based genomic signals indicative of post-admixture selection and adaptation. Common ancestry outlier approaches discard information about the surrounding genomic context and are prone to false positives due to drift and demography. Here, I present three studies which leverage patterns of genetic ancestry to investigate the evolutionary history of admixed populations. First, I develop a suite of ancestry-based summary statistics and computational methods to detect post-admixture adaptation, and demonstrate their application in a case study of human adaptation to malaria. In particular, these summary statistics incorporate patterns of ancestry beyond the site under selection, such as the length of contiguous ancestry tracts surrounding the locus, and are informative about the strength and timing of selection in admixed populations. I observe one of the strongest signals of recent selection in humans at the malaria protective Duffy-null allele, and show that this mode of strong single-locus selection over 20 generations has impacted genome-wide patterns of ancestry. Next, I move beyond summary statistics to develop a deep learning strategy for localizing regions of the genome under selection. This method takes images of chromosomes painted by ancestry as input to avoid the loss of information and bias that can occur when relying on user-defined summary statistics. I demonstrate this approach on simulated admixture scenarios and find that the method successfully localizes variants under selection 95% percent of the time, outperforms the common ancestry outlier approach, and is robust to demographic misspecification. Lastly, I present the first Illyrian genome sequences available from the Iron Age in a study of the ancestry and genetic relationships of five neonates buried in Korčula, Croatia. I find genetic support for classifying these individuals as Illyrian, and show that patterns of ancestry and genetic variation are consistent with their geographic location between Italy and the mainland Balkans. In the combined work presented here, I advance our ability to study the evolutionary history of admixed populations, which has implications for our understanding of phenotypic variation, disease risk, and conservation genetics across many study systems. Further, these methods tailored to the mosaic ancestry of admixed populations is a step towards expanding the diversity of populations, especially humans, who benefit from discoveries and advancement in genomic research.

Genetic diversity, population structure, and connectivity influence interactions among communities and populations. At hydrothermal vents in the western pacific, population structure in vent-associated species could occur at spatial scales ranging from vent sites separated by a few hundred meters to oceanic basins separated by more than 3000 kilometers. The spatial scale of population structure has important conservation implications; species that are well-connected across large geographic regions are more resilient to natural and anthropogenic disturbance. This dissertation examines the genetic diversity, population structure, and connectivity of 3 vent-associated species in the western Pacific. It first presents results from the development of microsatellite primers for Ifremeria nautilei, a deep-sea vent associated snail, then uses mitochondrial COI sequences and a suite of microsatellite markers to examine the broader connectivity of three vent-associated species, Ifremeria nautilei, Chorocaris sp. 2, and Olgasolaris tollmanni, across three back-arc basins in the western Pacific.

Within Manus Basin, no significant genetic differentiation was detected in populations of Ifremeria nautilei (based on COI and microsatellite), Chorocaris sp. 2 (based on COI and microsatellite), or Olgasolaris tollmanni (based on COI). A previously documented low-abundance cryptic species, Chorocaris sp. 1, was detected from a single site, South Su (based on COI). The population of I. nautilei in Manus Basin was found to be significantly differentiated from a second population that appeared to be panmictic across North Fiji and Lau Basin (based on COI and microsatellites). Chorocaris sp. 2 was also found to be significantly differentiated between Manus and North Fiji Basin (based on COI). Both I. nautilei and Chorocaris sp. 2 showed signs of potential low-level migration between Manus and other southwestern Pacific basins. O. tollmanni was undifferentiated between Manus and Lau Basin (based on COI). It is likely that a variable impedance filter exists that limits the realized dispersal of some, but not all species between Manus Basin and other western Pacific back-arc basins. The presence of a variable filter has implications for the conservation and management of hydrothermal vents in Manus Basin, as it is unclear what effects sustained anthropogenic disturbance will have on isolated populations of I. nautilei and Chorocaris sp. 2.

Human migrations over many centuries have resulted in considerable movements of organisms beyond their natural ranges. Study of these exotic introductions can help us to understand their ecology and biology as well as provide clues for the management of biological invasions. Suillus luteus is one of the most abundant globally introduced symbiotic fungi associated with exotic pine afforestation. I studied the population genomics of native and introduced populations of this ectomycorrhizal fungus to understand its evolution and genetics. Whole genomes of 274 S. luteus strains along with strains of closely related sister species were sequenced using the Illumina sequencing platform. These strains represent native populations of S. luteus from its native range across Europe and Asia as well as from five introduced populations in North America, South America, Australia, New Zealand, and Africa. Taking advantage of this rich dataset, I analyzed and compared the genetic relationships, population genetic parameters, and signatures of selection across populations to understand the natural history of S. luteus, the processes of its introductions, and the evolutionary consequences in the introduced populations.Using the sister species S. brunnescens as an outgroup, phylogenomic, multi-species coalescent model, and admixture analyses of SNP data revealed three genetically divergent clades in the native range, which likely represent at least two cryptic species within the single morphological species S. luteus. Phylogenomic analyses showed that all introduced populations belong to the Central Europe clade, and multiple independent introductions for exotic populations in Australia, New Zealand, South America, Africa, and North America. North American introduced populations were found to be the least differentiated from the Central Europe population, implying a more recent introduction and/or limited sexual reproduction since the introduction. The introduced population from South America was the most isolated from others, with little evidence of gene flow with other populations. All introduced populations experienced different levels of loss in genetic diversity and had more limited numbers of mating types, which suggests those exotic population experienced genetic bottlenecks during the introductions. Demographic analyses revealed significant expansion of population size for introduced populations in Western Australia and Argentina. Higher inbreeding coefficients were observed in all introduced populations, likely as a result of smaller founder population sizes. However, high rates of outcrossing in the introduced populations and selfing only observed in one introduced population indicate the changes in mating system of S. luteus is not common in introduction contexts. I examined the occurrence of local adaptation in each population by scanning genome regions of high divergence and selective sweeps. Several genes associated with regulatory functions were observed to have shared signatures of selections among multiple introduced populations, implying their important roles in adaptation for diverse exotic environments. The genomics approach used to study the mating type loci of S. luteus was applied to genomes of other Suillus and Rhizopogon species to understand the evolution of the self-incompatibility system in suilloid fungi. I employed a novel method of de novo assembly to assemble the highly divergent self-incompatibility loci and then recovered haplotypes from the genomes. Strong patterns of trans-specific polymorphisms and high sequence divergence in the HD MAT locus suggest that this locus is under strong balancing selection and confirm that this locus functions to control mating types in suilloid fungi. Phylogenetic analyses of HD MAT haplotypes showed that HD MAT loci were multiallelic in suilloid fungi and that the origins of some mating types predated the split between Rhizopogon and Suillus. Population genomics of native and introduced populations provides new insight into the evolution of S. luteus, the process and consequences of introduction, and the evolution associated with global exotic introductions. This study also demonstrates how the genomics and theories of molecular evolution can be used to study the evolution and genetics of fungi albeit the difficulties in ecological survey and limited genetic methods in ectomycorrhizal fungi.

Many molecular ecological and evolutionary studies sample wild populations at a single point in time, failing to consider that data they collect represents genetic variation from a potentially unrepresentative snapshot in time. Variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. However, many studies of rapid contemporary microevolution examine phenotypic trait divergence as opposed to molecular evolutionary divergence. Here, we compare genetic diversity in wild caught populations of Drosophila persimilis and D. pseudoobscura collected 16 years apart at the same time of year and same site at four X-linked and two mitochondrial loci to assess genetic stability. We found no major changes in nucleotide diversity in either species, but we observed a drastic shift in Tajima’s D between D. pseudoobscura timepoints at one locus associated with the increased abundance of a set of related haplotypes. Our data also suggests that D. persimilis may have recently accelerated its demographic expansion. While the changes we observed were modest, this study reinforces the importance of considering potential temporal variation in genetic parameters within single populations over short evolutionary timescales.