Biology subjects

Campana, M. G.

Publications and source records attributed to Campana, M. G..

6 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↗

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

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↗

bioRxiv2021

A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes

Understanding patterns of diversification, genetic exchange, and pesticide resistance in insect species of human health concern is necessary for effective population reduction and management. With the broad availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for large numbers of genetic markers from across the known genome. To this end, the targeting of gene sequences of known function or inheritance can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens that are detrimental to endangered vertebrate species such as bird malaria. Here we describe our development of a targeted gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we examined taxonomic divergence among samples from several members of the complex, as well as distinct populations of the relatively under-studied Culex quinquefasciatus, an urban pantropical species. We also examined the presence of known insecticide-resistance conferring alleles. Broadly, our developed gene-based assay proved effective for examining patterns of taxonomic and geographic clustering within the species complex, as well as for surveying genetic variants that have been associated with insecticide resistance. This assay will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of ubiquitous and increasingly damaging disease vectors.

genomics↗

bioRxiv2017

Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico

Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Using a metagenomic tool called MALT to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked to the 1545-1550 CE epidemic locally known as \"cocoliztli\", the cause of which has been debated for over a century. Here we present two reconstructed ancient genomes for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C contributed to the population decline during the 1545 cocoliztli outbreak in Mexico.\n\nOne Sentence SummaryGenomic evidence of enteric fever identified in an indigenous population from early contact period Mexico.

genomics↗