Deon de Jager

@ddj-sa.bsky.social

800 Followers 434 Following

Postdoc at Globe Institute, University of Copenhagen | Wildlife genetics | Ancient DNA | Conservation | Birding | Sport. He/him. Opinions my own.

A screenshot of a 3D model of a Cape grysbok fossil mandible with teeth.
A two-panel plot showing the read length distribution obtained for two samples (A and B) by using two different DNA library building protocols: SCR and BEST. The graphs show that SCR (single-stranded) libraries contain a much higher proportion of shorter reads than the double-stranded BEST libraries. This is particularly important in contexts where DNA preservation is poor and ancient DNA fragments are very short, such as in Africa.
Biomolecular preservation. A Endogenous DNA proportion as a function of specimen age for the whole dataset (n = 144). The text inside the plot indicates the proportion of specimens that were genetically identifiable (“Yes”) in the Holocene and Pleistocene. B Collagen yield as a percentage of total dentine/bone powder, as a function of specimen age. C The relationship between DNA and collagen preservation, as represented by collagen yield in percentage and endogenous DNA proportion. Note that for B and C, only Phase 1 specimens (n = 54) are shown, for which we had both collagen and DNA data. D Mean length of endogenous reads as a function of specimen age (n = 65). Only genetically identifiable specimens are shown, as these have endogenous DNA from which to calculate read length. The vertical dashed line indicates the boundary between the Pleistocene and Holocene (11,700 years ago) in all plots. Species identifiable refers to whether the species could be genetically identified.
A photo of a skull with one horn of the extinct long-horned buffalo with a skull of the extant Cape buffalo for comparison. The long-horned buffalo horn is several times longer, and the skull much larger, than that of the Cape buffalo.
A plot showing endogenous DNA content on the y-axis and age of fossil specimens on the x-axis in log scale, from 0 to 100,000 years. Triangular points representing fossils are coloured green if DNA was retrieved and light grey if not. The trend shows that younger fossils, especially those from the Holocene (<11,700 years old) contain more endogenous, while older fossils tend to contain less DNA. Four Pleistocene fossil, older than 11,700 years, contain endogenous DNA, though at very low proportions.
A 3-panel plot, where panels A and B show fossils collected in Phase 1 and 2 of the study, with species on the x-axis and age of fossils on the y-axis in six sub-panels corresponding to sampling sites. Panel C is a map of southern South Africa showing the location of the archaeological sites where the fossils originated.
A schematic where five circles are connected to a central bovid tooth with dotted lines. Each circle represents something done with the tooth: Photography, 3D scanning, DNA preseservation evaluation, collagen preservation evaluation , and recording of its occurrence on GBIF.
A dated phylogeny of mitogenomes from African buffalo and several outgroup species.
A haplotype network of African buffalo mitogenomes.
Three scatterplots of stable carbon-13 and nitrogen-15 values from mammoths at the site, compared to other published data.
A three-panel figure showing a phylogenetic tree of mammoth mitochondrial haplotypes, with clades shown in different colours (top left), a mitochondrial DNA haplotype network with clades again coloured (top right), and five polar projection maps showing the distribution of the five major mammoth mitochondrial clades across their range (bottom).
A plot showing the biomolecular sex (male or female) of the mammoth specimens sampled from the circular structure.
A plot showing the modelled age of some mammoth specimens, based on their radiocarbon ages.
A grid of four photos showing a big circular collection of mammoth bones (top left), a close-up of a mammoth mandible in this structure with an embedded tooth (top right), a slightly more zoomed-out photo showing several mammoth mandibles (bottom left), and another close-up of a mammoth tooth in the structure (bottom right).
A photo of a molecular biology lab bench with tubes and a pipette.
Figure showing 18 plots the classic ancient DNA damage pattern of DNA from mammoth samples.
A poster adverstising the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE) in Puerto Vallarta, Mexico from July 7-11, 2024. It has an aerial photo of the town with the beach, ocean and surrounding hills in view.
Figure 2. Mitochondrial genome maps of R. melanotis (Cape grysbok) and R. sharpei (Sharpe’s grysbok) produced in Geneious Prime and further edited in Inkscape v1.2 (https://inkscape.org/).
Figure 1. Photographs and range map of the three Raphicerus species. A R. melanotis (Cape grysbok) female in Robertson, Western Cape Province, South Africa (©Barbara Claassen), B R. sharpei (Sharpe’s grysbok) female in Kruger National Park, South Africa (©Paulette Bloomer), C R. campestris (steenbok) female in Etosha National Park, Namibia (by Yathin S. Krishnappa - Own work, CC by-SA 3.0, https://creativecommons.org/licenses/by-sa/3.0/, https://commons.wikimedia.org/w/index.php?curid=24567649), included for comparative purposes. The original photo was cropped for this figure. Both grysbok species have conspicuous white hairs scattered throughout their coat, which are absent in steenbok. D Distribution range map of the three Raphicerus species. Distribution data were obtained from the IUCN Red List page for each species (IUCN (International Union for Conservation of Nature) Citation2017, Citation2008a, Citation2008b). the map was generated in QGIS v3.22.2 (https://qgis.org/en/site/).