Biology subjects

Armstrong, E. E.

Publications and source records attributed to Armstrong, E. E..

At least 19 recordsLinked to original sources

bioRxiv2026

Recombination accelerates adaptation across genetic architectures and demographic histories

According to classic population genetics theory, recombination shapes the efficacy of natural selection. However, whether variation in recombination rate itself translates into meaningful differences in adaptive capacity remains poorly understood. Here, we used forward-time simulations to examine polygenic adaptation in populations colonizing novel environments. We varied recombination rate eightfold, modeled QTL effect size distributions using three gamma distributions, and compared constant and contracted population sizes. Across all conditions, higher recombination rates modestly accelerated adaptation, reducing the time to reach a new phenotypic optimum by 2-15%. The benefit was substantially greater in constant-size populations than in those that had experienced a contraction, but did not differ across genetic architectures. To understand the mechanism of this acceleration, we tracked linkage disequilibrium among adaptation-related QTL throughout adaptation. We found that across simulations, beneficial alleles were consistently in repulsion phase with one another and in coupling phase with deleterious alleles, both signatures of Hill-Robertson interference. Higher recombination attenuated both forms of interference, indicating that the benefit of recombination operated primarily through relieving interference among QTL. These results implicate interference among linked loci as the primary constraint on polygenic adaptation in this context, and demographic history as a critical modulator of the benefit of recombination.

evolutionary biology↗

bioRxiv2026

Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator

BackgroundBlack-footed cats (Felis nigripes) are one of Africas least studied felines. The population dynamics and demographic history of this solitary species have not been well-described. Reports of ongoing decline of present-day populations resulted in the IUCN Red List categorizing the species as vulnerable to extinction. As populations decline and become isolated from each other, they become susceptible to strong genetic drift and inbreeding, which can lead to the accumulation of deleterious alleles and increased sextinction risk. However, the IUCN cited data deficiencies across the species range as a limitation in this categorization for black-footed cats. In cases where ecological surveys are lacking, range-wide population genomic surveys can improve our understanding of population dynamics. ResultsIn the first genomic study of free-roaming individuals, we sequenced whole genomes of black-footed cats (N=44) from across their distribution. To do so, we incorporated whole genome sequences generated from both modern biological samples and century-old museum specimens. We assembled a highly contiguous reference genome using a combination of PacBio HiFi data and publicly available Hi-C data and investigated the demographic history, population structure, and genetic diversity of wild black-footed cats. We found evidence of historical effective population sizes of [~]11,500 individuals, which is lower than estimates reported in other felid species. Consistent with modest historical population sizes, we found that present-day genome-wide diversity was low ({pi} {approx} 0.0004). However, despite low genetic diversity, we find that black-footed cat genomes do not harbor long runs of homozygosity. Simulation results indicate that low present-day genetic diversity may simply result from modest historical population size. However, other analyses point to evidence of a population contraction in the last 50 generations, which could contribute to future genomic erosion. We also compared genomic variation in populations across the range to evaluate patterns of population structure, finding evidence of higher genetic similarity between individuals in closer geographic proximity. ConclusionOverall, these results provide range-wide information about the demographic history and present-day genetic diversity of an understudied species. Together with analyses of population structure, we speculate that there may be greater connectivity between populations of black-footed cats than previously assumed. Our study underscores the utility of genomic data in providing insights into population dynamics for better conservation management.

evolutionary biology↗

bioRxiv2026

Over-representation of sperm-associated deleterious mutations across wild and ex situ cheetah (Acinonyx jubatus) populations

As purifying selection becomes less effective and inbreeding increases, small populations frequently develop an increased load of genome-wide deleterious mutations. Reflecting this pattern, deleterious mutations in genes associated with fertility and immunity have previously been identified in the cheetah (Acinonyx jubatus), which has had a low effective population size for at least the last 10,000 years. However, the distribution of deleterious mutations across cheetah populations is currently unknown. Here, we analysed novel whole genome resequencing data from 30 ex situ and 9 wild cheetahs. We investigated variation in genetic diversity, genomic measures of inbreeding, and the distribution of deleterious mutations across cheetah populations. South Sudanese and Tanzanian cheetahs showed higher inbreeding and realized load, while Namibian cheetahs had a higher proportion of population-specific deleterious mutations. Genes containing high- or moderate-impact deleterious mutations were significantly enriched for sperm-related functions, highlighting putative causative loci associated with poor sperm quality in cheetahs. Similar levels of genetic diversity and inbreeding were observed in ex situ cheetahs compared to their wild counterparts, providing empirical evidence of the efficacy of captive breeding programmes in maintaining genetic variation in ex situ populations.

genomics↗

bioRxiv2025

President Roosevelt's lions reveal a century of population fragmentation in Africa's largest carnivore

Over the past century, lion (Panthera leo) populations across Africa have experienced rapid and severe declines. Despite this, East Africa is considered a modern-day lion stronghold. Here, we use whole-genome sequencing of both recent and historical lion populations, primarily collected during the Smithsonians Roosevelt East African (1909-1911) and Rainey (1911-1912) Expeditions, to investigate changes in population structure, connectivity, and diversity over the last [~]100 years in East Africa. We find a clear signal of population fragmentation when comparing historical (1896-1946) and recent (1990-present) lion populations. Our analyses reveal genetic distinctions between remaining lion populations in Kenya and Tanzania and document loss of genetic diversity over time including reduced heterozygosity and the accumulation of runs of homozygosity. We detect a severe bottleneck in both Kenya and Tanzania approximately 25 generations ago, coinciding with a severe rinderpest outbreak in the region that is known to have decimated bovid and ultimately carnivore populations in the area. Nevertheless, modern lions in East Africa still exhibit overall high levels of diversity and low levels of inbreeding. Our results provide direct evidence of the effects of increasing habitat fragmentation and the significance of temporal data for contextualizing current patterns of population connectivity and diversity.

evolutionary biology↗

bioRxiv2024

Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics

Characterizing genetic variation in natural populations is vital to evolutionary biology, however many non-model species lack genomic resources. Here, we demonstrate that reference bias significantly affects population genomic analyses by mapping whole genome sequence data from gray foxes (Urocyon cinereoargenteus) to a conspecific reference and two heterospecific canid genomes (dog and Arctic fox). Mapping to the conspecific genome improved read pairing by [~]5%, detected 26-32% more SNPs, and 33-35% more singletons. Nucleotide diversity estimates increased over 30%, FST increased from 0.189 to 0.197, and effective population size estimates were 30-60% higher with the conspecific reference. Recombination rates varied by up to 3-fold at chromosome ends with heterospecific references. Importantly, FST outlier detection differed markedly, with heterospecific genomes identifying twice as many unique outlier windows. These findings highlight the impact of reference genome choice and the importance of conspecific genomic resources for accurate evolutionary inference. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/625554v2_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@1d717adorg.highwire.dtl.DTLVardef@537c85org.highwire.dtl.DTLVardef@1142d10org.highwire.dtl.DTLVardef@19a9f06_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA species-specific reference genome improves read mapping and variant detection C_LIO_LIReference bias underestimates genetic diversity and differentiation C_LIO_LIDivergent reference genomes distort demographic histories and recombination landscapes C_LIO_LIUnique FST outliers are detected across references, affecting functional interpretations C_LI

evolutionary biology↗

bioRxiv2024

Next-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from feces

Snow leopards, Panthera uncia, are under threat from numerous pressures and are the focus of a great deal of conservation efforts. However, their elusive nature makes it difficult to estimate population sizes. Current methods used to monitor local population sizes include visually identifying individuals from camera trap photos and genetically identifying individuals from fecal samples using microsatellite loci. Here, we present a new method for identifying snow leopard individuals from fecal samples using a multiplex PCR single nucleotide polymorphism (SNP) panel method. The SNP panel we present consists of 144 SNPs and utilizes next-generation sequencing technology, making it cheaper and easier than current microsatellite methods. We validate our SNP panel with paired tissue and fecal samples from zoo individuals, showing a minimum of 96.7% accuracy in allele calls per run. We then generate SNP data from 235 field-collected fecal samples from across Pakistan to show that the panel can reliably identify individuals from low-quality fecal samples of unknown age and is robust to contamination. We also show that our SNP panel has the capability to identify first-order relatives and provides insights into the geographic origin of samples. This SNP panel will empower the snow leopard research community in their efforts to assess local and global snow leopard population sizes. More broadly, we present a method for developing a SNP panel that utilizes open source software for SNP selection and primer design, Illumina sequencing technology, and a streamlined lab and bioinformatics protocol which can be used to create similar SNP panels for any species of interest for which adequate genomic reference data is available.

genetics↗

bioRxiv2024

Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species

Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favored for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for use in population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel user-friendly SNP selection pipeline for population assignment and individual identification, mPCRselect. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for species of conservation concern.

evolutionary biology↗

bioRxiv2024

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup Neofelis nebulosa, using pedigrees. We use a previously validated pipeline (RatesTools) to calculate mutation rate for each species and subsequently explore the impacts of the novel rates on historic effective population size estimates in each of these charismatic felids of conservation concern. Importantly, we find that the choice of reference genome, the data type and coverage, and the individual all impact estimates of the mutation rate. Despite these stochastic effects, we inferred that base pair mutation rates for all species fell between 0.5 and 1.4e-08 per generation per base pair (mean 0.81e-08 {+/-} 0.35-08 across Pantherinae). Our results provide a cautionary view on inter-species mutation rate comparisons, given the error associated with the reference genome choice and sequencing depth of coverage of the individuals.

evolutionary biology↗

bioRxiv2023

Extreme in Every Way: Exceedingly Low Genetic Diversity in Snow Leopards Due to Persistently Small Population Size

Snow leopards (Panthera uncia) serve as an umbrella species whose conservation benefits their high-elevation Asian habitat. Their numbers are believed to be in decline due to numerous Anthropogenic threats; however, their conservation is hindered by numerous knowledge gaps. They are the least studied genetically of all big cat species with more to learn regarding their population structure, historical population size, and current levels of genetic diversity. Here, we use whole-genome sequencing data for 41 snow leopards (37 newly sequenced) to offer new insights into these unresolved questions. Among our samples, we find evidence of a primary genetic divide between the northern and southern part of the range around the Dzungarian Basin, as previously identified, and a secondary divide south of Kyrgyzstan around the Taklamakan Desert. Most noteworthy, we find that snow leopards have the lowest genetic diversity of any big cat species, due to a persistently small population size (relative to other big cat species) throughout their evolutionary history rather than recent inbreeding. Without a large population size or ample standing genetic variation to help buffer them from any forthcoming Anthropogenic challenges, snow leopard persistence may be more tenuous than currently appreciated.

evolutionary biology↗

bioRxiv2023

What does the fox (genome) say? A chromosome-level assembly for the gray fox (Urocyon cinereoargenteus)

Reference genome assemblies have been created from multiple lineages within the Canidae family, however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases (Mb), respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern US and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.

genomics↗

bioRxiv2023

Unraveling the Genomic Diversity and Evolutionary History of Captive Tigers in the United States

Genomic studies of rare and endangered species have focused broadly on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated the genomic diversity potentially housed in captive populations. For tigers (Panthera tigris) in particular, captive individuals vastly outnumber those in the wild, yet the diversity of the captive population remains largely unexplored. Here, we present the first large-scale genetic study of the private (non-zoo) captive tiger population in the United States (U.S.), also known as Generic tigers. We find that the U.S. Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies (P. t. altaica, Amur; P. t. tigris, Bengal; P. t. corbetti, Indochinese; P. t. jacksoni, Malayan; P. t. amoyensis, South China; P. t. sumatrae, Sumatran). We show that the Generic tiger population has a comparable amount of genetic diversity to most wild subspecies, relatively few private variants, and fewer deleterious mutations. We also observe inbreeding coefficients that are similar to wild populations, suggesting that inbreeding in captive populations is not pervasive, although there are some individuals within the Generic population that are substantially inbred. Our results elucidate the admixture history of the Generic tiger population in the U.S. Additionally, we develop a reference panel for tigers and show that it can be used with imputation to accurately distinguish individuals and assign ancestry even with ultra-low coverage (0.25x) data. The study and reference panel will provide a resource to assist in tiger conservation efforts.

evolutionary biology↗

bioRxiv2023

Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae

Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genetic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families - genes directly mediating interactions with plant chemical defenses - underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many lineages are ancient (>150 million years ago [mya]), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several non-herbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza have among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on plants (bitter or electrophilic phytotoxins) or their ancestral diet (yeast and fruit volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight strong gene candidates that have also been linked to other dietary transitions in Drosophila.

evolutionary biology↗

bioRxiv2023

Genomic Resources for Asian (Elephas maximus) and African Savannah Elephant (Loxodonta africana) Conservation and Health Research

We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and non-invasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.

genomics↗

bioRxiv2022

RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data

SummaryHere, we introduce RatesTools, an automated pipeline to infer de novo mutation rates from parent-offspring trio data of diploid organisms. By providing a reference genome and high-coverage, whole-genome resequencing data of a minimum of three individuals (sire, dam, offspring), RatesTools provides a list of candidate de novo mutations and calculates a putative mutation rate. RatesTools uses several quality filtering steps, such as discarding sites with low mappability and highly repetitive regions, as well as sites with low genotype and mapping qualities to find potential de novo mutations. In addition, RatesTools implements several optional filters based on post hoc assumptions of the heterozygosity and mutation rate of the organism. Filters are highly customizable to user specifications in order to maximize utility across a wide-range of applications. AvailabilityRatesTools is freely available at https://github.com/campanam/RatesTools under a Creative Commons Zero (CC0) license. The pipeline is implemented in Nextflow (Di Tommaso et al. 2017), Ruby (http://www.ruby-lang.org), Bash (https://www.gnu.org/software/bash/), and R (R Core Team 2020) with reliance upon several other freely available tools. RatesTools is compatible with macOS and Linux operating systems. Supplementary InformationWe document RatesTools performance using published datasets in the online Supplementary information.

bioinformatics↗

bioRxiv2022

A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos)

The brown bear (Ursus arctos) is the second largest and most widespread extant terrestrial carnivore on Earth and has recently emerged as a medical model for human metabolic diseases. Here, we report a fully-phased chromosome-level assembly of a male North American brown bear built by combining Pacific Biosciences (PacBio) HiFi data and publicly available Hi-C data. The final genome size is 2.47 Gigabases (Gb) with a scaffold and contig N50 length of 70.08 and 43.94 Mb, respectively. BUSCO analysis revealed that 94.5% of single-copy orthologs from mammalia were present in the genome (the highest of any ursid genome to date). Repetitive elements accounted for 44.48% of the genome and a total of 20,480 protein coding genes were identified. Based on whole genome alignment, the brown bear is highly syntenic with the polar bear, and our phylogenetic analysis of 7,246 single-copy BUSCOs supports the currently proposed species tree for Ursidae. This highly contiguous genome assembly will support future research on both the evolutionary history of the bear family and the physiological mechanisms behind hibernation, the latter of which has broad medical implications. SignificanceBrown bears (Ursus arctos) are the most widespread, large terrestrial carnivore on the planet and represent an interesting example of speciation through hybridization, as well as a medical model for sedentary lifestyle-related disease. Although a previous genome for a brown bear has been published, the reported contig N50 was low (only [~]530 kb), despite being scaffolded into putative chromosomes. Genomes of this quality limit the accuracy of analyses which rely on long contiguous stretches of the genome to be assembled (such as with many demographic analyses) as well as attempts at connecting genotype to phenotype (such as in association analyses). In order to support studies on both the complex hybridization history of the brown bear and investigations into medically-relevant phenotypes, we generated a fully-phased, chromosome-level assembly from a male grizzly bear. The genome has a total size of 2.47 Gb and 90% of the genome is contained in 36 scaffolds, roughly corresponding to one autosome per scaffold. This high-quality genome will enable studies across a variety of disciplines, including conservation, evolution, and medicine.

genomics↗

bioRxiv2022

Chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris)

The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. Here, we assemble genomes from three members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.

genomics↗

bioRxiv2020

Widespread introgression across a phylogeny of 155 Drosophila genomes

Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across nine monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the nine clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.

evolutionary biology↗

bioRxiv2020

Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long read sequencing allow high quality genome assemblies for tens or even hundreds of species to be generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution within this key group.

evolutionary biology↗