Methods development
Software and Bioinformatic Development
I develop bioinformatic toolsets for analyzing and interpreting genetic and genomic datasets in a multi-disciplinary framework. Below I list some examples of software that I’ve developed, and also examples of how they have been used in practice. You can also find information on my GitHub page!
Computational programs such as Numt Parser are broadly applicable to any research that uses Genomics because it Increases the accuracy of biological datasets
Numt Parser also has potential for application in other study systems and questions (e.g. human numt analysis for biomedical research)
Numt Parser
Mondrial DNA is often used for phylogenetic studies that investigate matrilineal inheritance patterns (Chaitanya et al. 2014), inter- and intraspecific divergences (Cronin et al. 1991; Gill et al. 1993; Bowers et al. 1994), and for studies that use samples with low DNA copy numbers (Hofreiter et al. 2001; Merheb et al. 2019). However, the presence of nuclear mitochondrial (numt) pseudogenes (designated as Numt by Lopez et al. 1994) may hinder the identification of true cytoplasmic mitochondrial (cymt) DNA sequences and the reliability of mtDNA for phylogenetic and population genetic comparisons (Bensasson et al. 2001). Numts arise when mitochondrial DNA is incorporated into the nuclear genome during chromosomal double-strand break repair by nonhomologous recombination (Bensasson et al. 2001).
Together with Dr. Angel Rivera-Colón, I have co-developed, tested, and co-published a freely available program, Numt Parser:
(https://github.com/adeflamingh/NuMt_parser)
Numt Parser allows for the identification and filtering of DNA sequences that likely originate from numts in short-read sequencing datasets. Sequencing reads are classified as putatively originating from either cytoplasmic mtDNA or numt DNA by direct comparison against known cytoplasmic mt and numt reference sequences.
This program has been applied in other systems - e.g. a Pleistocene jaguar sample
GenSID
(GeneticSexID)
I developed a R-based software that allows for the genomics sex identification through an estimation of read coverage of the X chromosome normalized by read coverage of autosomal chromosomes.
I tested this methodology using African elephant genomic data from individuals with known sexes (red for XX, blue for XY in the graph), and then identified the unknown sex of elephant tusks from a 500-year old shipwreck (gray) who we found to be mostly genomically male (XY).
This methodology advances current approaches;
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It works for species with reference chromosomes from genetically female individuals
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It works for low coverage data, for example ancient DNA datasets
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It provides an confidence estimate of the genomic sex identified for each individual
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It has been broadly adapted to many ancient DNA study systems (some listed below)
Examples of studies using GenSID
Molecular wet-laboratory protocol development and testing
I develop DNA collection and analysis methodologies that focus on increasing accessibility to researchers working in challenging field conditions, and for advanced ancient DNA analysis and museuomics. Below I showcase one example of each of these focal areas.
Accessible methods for Conservation Genetics
I developed a methodology to generate complete (4X) elephant genomes using fecal cards that do not require cold storage and are easily collected in the field by any person with no specialized training. Beyond endogenous genomes, I also developed complementary computational methodologies to analyze pathogens, parasites and other organisms for which DNA was collected as part of the elephant fecal card sampling process.
This new protocol allows us to do non-invasive health assesmments of the individual, but also from the gut microbiome and of the elephant population in large
Advanced methods for Paleogenomics
I developed a new wet-lab approach for decontaminating, extracting and analyzing DNA from ancient hair samples . I tested this methodology using hairs from tooth cavities from two lion museum specimens, and was able to generate complete mitogenomes for various species that these lions ate. Below I link the four step protocol which is also detailed in the associated pre-print currently under review:
de Flamingh, Alida, et al. "Compacted Hair in Broken Carnivore Teeth Reveal Dietary Prey of Historic Lions." Available at SSRN 4839630.
