Biology subjects

Solari, K. A.

Publications and source records attributed to Solari, K. A..

8 recordsLinked to original sources

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

Biocultural vulnerability of traditional crops in the Indian Trans Himalaya

Traditional agricultural landscapes are critical for conserving biocultural and ecological diversity. Despite their significance, traditional systems have often been overlooked, leading to genetic erosion of crop landraces. Using the fragile ecosystems of northwest Himalaya as case study, we examine the ecological and genetic resilience of an understudied and lesser-known traditional crop, black pea, and barley (Hordeum vulgare) and compare them to the introduced cash crop of green pea (Pisum sativum L.). We co-designed field experiments with local farmers to assess survival and reproductive traits for the crops. We performed whole-genome sequencing to investigate the genetic diversity of black pea and describe their nutritional profile. Our findings indicate that traditional crops are better adapted to local climatic conditions and hold considerable genetic diversity and nutritional potential. We emphasize the importance of integrating traditional knowledge with scientific research to promote sustainable food systems and socio-ecological stability in vulnerable mountain regions.

plant 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

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↗

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↗