Biology subjects

de Flamingh, A.

Publications and source records attributed to de Flamingh, A..

5 recordsLinked to original sources

bioRxiv2023

Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times

Mutually beneficial partnerships between genomics researchers and North American Indigenous Nations are rare. Here, we present one such partnership that provides insight into the peopling of the Americas and furnishes a new line of evidence that can be used to further treaty and Indigenous rights. We show that the genomics of sampled individuals from the Blackfoot Confederacy belong to a previously undescribed ancient lineage that diverged from other genomic lineages in the Americas in Late Pleistocene times. Using multiple complementary forms of knowledge, we provide a scenario for Blackfoot population history that fits with oral tradition and provides a plausible model for the evolutionary process of the peopling of the Americas. One-Sentence SummaryPreviously unknown genomic lineage in North America revealed in present-day Indigenous community and historic ancestors.

genomics↗

bioRxiv2023

Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants

Across Africa, space for conservation is sometimes limited to formally protected areas that have become progressively more isolated. There is a need for targeted conservation initiatives such as the demarcation of landscape connections, defined as areas that encompass environmental variables that promote the natural movement of individuals between populations, which can facilitate gene flow. Landscape connections can mitigate genetic isolation, genetic drift, and inbreeding, which can occur in isolated populations in protected areas. Promoting gene flow can reduce the risk of extirpation often associated with isolated populations. Here we develop and test models for identifying landscape connections among African savannah elephant (Loxodonta africana) populations by combining habitat suitability modeling with gene flow estimates across a large region including seven countries. We find a pronounced non-linear response to unsuitable habitat, consistent with previous studies showing that non-transformed habitat models are poor predictors of gene flow. We generated a landscape connections map that considers both suitable habitats based on telemetry occurrence data and gene flow estimated as the inverse of individual genetic distance, delineating areas that are important for maintaining elephant population connectivity. Our approach represents a novel framework for developing spatially and genetically informed conservation strategies for elephants and many other taxa distributed across heterogeneous and fragmented landscapes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/554325v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d8f639org.highwire.dtl.DTLVardef@10d31c0org.highwire.dtl.DTLVardef@13d421forg.highwire.dtl.DTLVardef@c0427c_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction

Extinct Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "Black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate extinct Cape lion genome characteristics, population dynamics and genetic distinctiveness prior to their extinction. We generated genomic data from two historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, but rather highlights how alternative knowledge-systems, e.g., Indigenous perspectives, could potentially further inform interpretations of species life histories.

evolutionary biology↗

bioRxiv2022

Non-invasive fecal DNA yields whole genome and metagenomic data for species conservation

Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, and/or dangerous species. Integrating genomic techniques that use non-invasive biological samples with advances in computational approaches can benefit and inform wildlife conservation and management. Here we present a molecular pipeline that uses non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at 6X coverage) and metagenomic sequences, combining in a novel fashion widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome and/or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated by this pipeline was demonstrated by the application of genome-scale analysis and metagenomics to zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses generated compositional taxon classifications that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of our approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular pipeline presented here extends applications beyond what has previously been shown for target-enriched datasets and contributes towards the expansion and application of genomic techniques to conservation science and practice.

genomics↗

bioRxiv2022

NUMT PARSER: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW to two other bioinformatic approaches that can be used to account for numt contamination. We found that NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.

evolutionary biology↗