Biology subjects

Battey, C. J.

Publications and source records attributed to Battey, C. J..

9 recordsLinked to original sources

bioRxiv2020

Visualizing Population Structure with Variational Autoencoders

Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs) - generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data - for visualizing population genetic variation. VAEs incorporate non-linear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae, is available as a command-line python program at github.com/kr-colab/popvae. The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population.

genetics↗

bioRxiv2019

Predicting Geographic Location From Genetic Variation with Deep Neural Networks

Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here we describe a deep learning method, which we call Locator, to accomplish this task faster and more accurately than existing approaches. In simulations, Locator infers sample location to within 4.1 generations of dispersal and runs at least an order of magnitude faster than a recent model-based approach. We leverage Locators computational efficiency to predict locations separately in windows across the genome, which allows us to both quantify uncertainty and describe the mosaic ancestry and patterns of geographic mixing that characterize many populations. Applied to whole-genome sequence data from Plasmodium parasites, Anopheles mosquitoes, and global human populations, this approach yields median test errors of 16.9km, 5.7km, and 85km, respectively.

genetics↗

bioRxiv2019

Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii. We analysed whole genomes of 1,142 individual mosquitoes sampled from the wild in 13 African countries, and a further 234 individuals comprising parents and progeny of 11 lab crosses. The data resource includes high confidence single nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We used these data to analyse genetic population structure, and characterise genetic diversity within and between populations. We also illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance, and for accelerating research and development of new vector control tools.

genomics↗

bioRxiv2019

On the relative ease of speciation with periodic gene flow

AO_SCPLOWBSTRACTC_SCPLOWCommon models of speciation with gene flow consider constant migration or admixture on secondary contact, but earths recent climatic history suggests many populations have experienced cycles of isolation and contact over the last million years. How does this process impact the rate of speciation, and how much can we learn about its dynamics by analyzing the genomes of modern populations? Here we develop a simple model of speciation through Bateson-Dobzhansky-Muller incompatibilities in the face of periodic gene flow and validate our model with forward time simulations. We then use empirical atmospheric CO2 concentration data from the Vostok Ice Cores to simulate cycles of isolation and secondary contact in a tropical montane landscape, and ask whether they can be distinguished from a standard isolation-with-migration model by summary statistics or joint site frequency spectrum-based demographic inference. We find speciation occurs much faster under periodic than constant gene flow with equivalent effective migration rates (Nm). These processes can be distinguished through combinations of summary statistics or demographic inference from the site frequency spectrum, but parameter estimates appear to have little resolution beyond the most recent cycle of isolation and migration. Our results suggest speciation with periodic gene flow is a common force in generating species diversity through Pleistocene climate cycles, and highlight the limits of current inference techniques for demographic models mimicking the complexity of earths recent climatic history.

evolutionary biology↗

bioRxiv2019

Why Montane Anolis Lizards Are Moving Downhill While Puerto Rico Warms

1Because Puerto Rico has warmed in recent decades, ectotherms there should have shifted their elevational ranges uphill. However, by comparing historical versus recent distributional records of Anolis lizards, we found that three \"montane-forest\" species have instead moved downhill in recent decades, almost to sea level. This downward shift appears related to the massive regeneration of Puerto Rican forests - especially in lowland areas - which started in the mid-20th century when the islands economy began shifting from agriculture to manufacturing. The magnitude of local cooling caused by regenerated forests swamps recent climate warming, seemingly enabling cool-adapted \"montane\" lizards to track forests as they spread downhill from mountain refugia into abandoned plantations. Thus, contemporary distributional patterns are likely converging to those prior to the arrival of European settlers, who cleared most lowland forests for agriculture, thereby restricting forests and associated fauna to high-elevation remnants. In contrast with the montane species, three lowland species expanded their ranges to higher elevations in recent decades; but whether this movement reflects warming, land-use shifts, or hurricane-induced destruction of upland forests is unclear.

ecology↗

bioRxiv2019

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data

Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies. We find that most common summary statistics have distributions that differ substantially from that seen in well-mixed populations, especially when Wrights neighborhood size is less than 100 and sampling is spatially clustered. Stepping-stone models reproduce some of these effects, but discretizing the landscape introduces artifacts which in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations were surprisingly robust to isolation by distance. We also show that the combination of spatially autocorrelated environments and limited dispersal causes genome-wide association studies to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms.

genetics↗

bioRxiv2018

Time Lags and Niche Shifts in a Biological Invasion of Hummingbirds

Shifts in a species realized niche can lead to rapid population growth by increasing the carrying capacity of local habitats and allowing colonization of new areas. This process is well known in \"invasive\" species introduced to novel ranges by humans, but can also occur when native species expand their range. In these cases expansions may be driven either by a shift in the available environment or by a shift in the species use of existing niche space, but identifying the specific environmental or behavioral changes involved is often hindered by time lags in the process of colonization. Here I document a century of range shifts in the Annas Hummingbird (Calypte anna) and show that recent abundance in the Pacific Northwest is the product of a series of range and niche expansions that started in the early 20th century following the spread of garden cultivation and introduced plant species in California. Demographic trends in the northwest have tracked simple models of exponential growth since populations became established in the 1960s and 70s, and nest records suggest that the species has delayed the beginning of the breeding season by at least 18 days in the north. Niche models trained on historic climate and occurrence data fail to predict the modern range, suggesting that climate change is not the primary cause of the expansion. Range expansions in the Annas Hummingbird thus closely track the dynamics of an invasive species spreading across a novel range, and were made possible by a mix of introduced plants, phenological acclimation, and an expansion of the realized climatic niche.

ecology↗

bioRxiv2017

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

One common method of minimizing errors in large DNA sequence datasets is to drop variable sites with a minor allele frequency below some specified threshold. Though widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical SNP dataset to demonstrate the impacts of minor allele frequency (MAF) thresholds on inference of population structure. We find that model-based inference of population structure is confounded when singletons are included in the alignment, and that both model-based and multivariate analyses infer less distinct clusters when more stringent MAF cutoffs are applied. We propose that this behavior is caused by the combination of a drop in the total size of the data matrix and by correlations between allele frequencies and mutational age. We recommend a set of best practices for applying MAF filters in studies seeking to describe population structure with genomic data.

genomics↗

bioRxiv2017

A Migratory Divide In The Painted Bunting (Passerina ciris)

Divergence in migratory behavior is a potential mechanism of lineage divergence in sympatric populations and a key life history trait used in the identification of demographically independent units for conservation purposes. In the Painted Bunting (Passerina ciris), a North American songbird, populations on the Atlantic coast and interior southern United States are known to be allopatric during the breeding season, but efforts to map connectivity with wintering ranges in Mexico, Florida, and the Caribbean have been largely inconclusive. Using genomic and morphological data from natural history specimens and banded birds, we found evidence of three genetically differentiated populations with distinct wintering ranges and molt-migration phenologies. In addition to confirming that the Atlantic coast population remains allopatric throughout the annual cycle, we identified an unexpected migratory divide within the interior breeding range. Populations breeding in the Lower Mississippi River Valley winter on the Yucatan Peninsula, and are parapatric with other interior populations that winter in mainland Mexico and Central America. Across the interior breeding range, genetic ancestry is also associated with variation in wing length; suggesting that selective pressures may be promoting morphological divergence in populations with different migration strategies.

zoology↗