Periodic Reporting for period 1 - PalaeoBovids (Palaeogenomes of a lost world: Ancient bovids of the submerged Palaeo-Agulhas Plain of southern Africa)
Okres sprawozdawczy: 2021-12-01 do 2023-11-30
The Palaeo-Agulhas Plain (PAP) is a now-submerged ecosystem off the southern coast of South Africa. The plain was exposed during the last ice age (~29,000 to 11,700 years ago) because the sea levels were much lower due to water being trapped in ice at the poles. This meant that the coastline was, in some places, almost 100 km further south than it is today, resulting in almost 85,000 square kilometres (approximately the size of Ireland) of extra habitat for both ancient humans and animals, supporting large populations in an ecosystem very different to what is found in southern South Africa today. As the last ice age ended, the sea levels rose and drowned this ecosystem, with the sea level rising to the same level as today approximately 11,700 years ago. This loss of habitat was accompanied by significant changes in the climatic and environmental conditions, leading to changes in both the abundance and composition of species in this area of South Africa. Notably, grazers (herbivores feeding on grass) became much less abundant than browsers (herbivores feeding on leaves). This is visible in the fossil record and has contributed to the understanding that the climate and habitat became more suitable for browsers than for grazers, resulting in large declines of grazer populations.
While these changes are well understood at the species level, how the genetic diversity within these species changed along with their population sizes has not been investigated. Evolutionary theory predicts that genetic diversity decreases with decreasing population sizes. Genetic diversity is a fundamental part of biodiversity, and it provides the substrate on which evolution by natural selection acts. In other words, genetic diversity within a species allows it to adapt to changing climatic conditions, and if genetic diversity decreases too much, it impairs a species’ ability to adapt to climate change. In this project, our objective was to measure whether and by how much the genetic diversity changed between ~20,000 years ago and today of six species that occur in southern South Africa and lived on the PAP during the last ice age, using ancient DNA techniques. We wanted to compare the changes in genetic diversity of grazers and browsers, to determine whether the changes in abundance of these two broad groups seen in the fossil record were also reflected at the genetic level. This could provide valuable insights into how wildlife responded to climate change and habitat loss in the past, to help us predict how those species might respond to ongoing human-caused climate change and habitat destruction. This could help us better manage and conserve species, resulting in more stable ecosystems, which in turn will help buffer against the effects of climate change. While the project may be focused on southern Africa, the results will be instructive for species conservation in general and the conclusions drawn will be relevant at a global scale.
Due to technical challenges and delays we have not yet been able to answer this important question. However, the project will continue beyond this funding stream. Nonetheless, an important outcome of this project was that we were able to obtain ancient DNA and reconstruct mitochondrial genomes from African fossils up to ~7,000 years ago – an important achievement, given the poor preservation conditions for DNA at palaeontological sites in sub-tropical regions and the few studies that have been done at such sites. This shows that it will be possible for us to at least answer the question related to climate change and genetic diversity of wildlife.
While these changes are well understood at the species level, how the genetic diversity within these species changed along with their population sizes has not been investigated. Evolutionary theory predicts that genetic diversity decreases with decreasing population sizes. Genetic diversity is a fundamental part of biodiversity, and it provides the substrate on which evolution by natural selection acts. In other words, genetic diversity within a species allows it to adapt to changing climatic conditions, and if genetic diversity decreases too much, it impairs a species’ ability to adapt to climate change. In this project, our objective was to measure whether and by how much the genetic diversity changed between ~20,000 years ago and today of six species that occur in southern South Africa and lived on the PAP during the last ice age, using ancient DNA techniques. We wanted to compare the changes in genetic diversity of grazers and browsers, to determine whether the changes in abundance of these two broad groups seen in the fossil record were also reflected at the genetic level. This could provide valuable insights into how wildlife responded to climate change and habitat loss in the past, to help us predict how those species might respond to ongoing human-caused climate change and habitat destruction. This could help us better manage and conserve species, resulting in more stable ecosystems, which in turn will help buffer against the effects of climate change. While the project may be focused on southern Africa, the results will be instructive for species conservation in general and the conclusions drawn will be relevant at a global scale.
Due to technical challenges and delays we have not yet been able to answer this important question. However, the project will continue beyond this funding stream. Nonetheless, an important outcome of this project was that we were able to obtain ancient DNA and reconstruct mitochondrial genomes from African fossils up to ~7,000 years ago – an important achievement, given the poor preservation conditions for DNA at palaeontological sites in sub-tropical regions and the few studies that have been done at such sites. This shows that it will be possible for us to at least answer the question related to climate change and genetic diversity of wildlife.
We collected a total of 478 samples from five extant and one extinct species (3 grazers, 1 intermediate feeder, 2 browsers) – grazers: African Cape buffalo (Syncerus caffer caffer), long-horned buffalo (Syncerus antiquus, extinct), and southern reedbuck (Redunca arundinum); browsers: grey rhebok (Pelea capreolus) and Cape grysbok (Raphicerus melanotis); intermediate feeder: common eland (Tragelaphus oryx). This included 324 ancient samples (fossils) and 154 historical and modern samples. Due to challenges referred to above and expanded on in the detailed report, only 58 ancient samples could be processed for ancient DNA during this funding period.
Nonetheless, 3D models were generated for all 324 fossil specimens, as a prerequisite for destructive ancient DNA sampling. These 3D models will be made publicly available on an online repository and can be used by palaeontologists to investigate morphology and make measurements digitally, thus expanding the use and impact of the collection from which the specimens were sourced. The museums from which the specimens were sourced can also use these 3D models for outreach, education, or training activities.
From the 58 fossil samples, we were able to evaluate the level of ancient DNA preservation across time and archaeological sites. We found that ancient DNA was mostly preserved in specimens younger than ~7,000 years old, with only two samples older than this providing a limited amount of ancient DNA data. After enrichment of mitochondrial DNA, we were able to generate enough data to reconstruct the mitogenomes of 21 of the 58 ancient samples.
From the 154 historical and modern samples, we generated 90 mitochondrial genomes against which to compare the ancient genetic diversity. This included the novel mitochondrial genome of the Cape grysbok, which has not been sequenced before, and resulted in a peer-reviewed publication. This aspect of the project also includes the first population-level genetic datasets for the grey rhebok and the southern reedbuck, thereby contributing novel genetic data for understudied species in Africa. These data will be published along with the ancient DNA results in upcoming peer-reviewed publications.
The results of the project have been presented at two international and one local conference. The genetic results will be useful to the museums as it identifies some specimens to species level where only genus level classification was possible before, it confirms the species identity of other specimens, and in some cases corrects the species of incorrectly identified specimens. This improves the scientific accuracy and reliability of the collections. The project is continuing in 2024 and the main results will be published open-access in peer-reviewed publications in due course.
Nonetheless, 3D models were generated for all 324 fossil specimens, as a prerequisite for destructive ancient DNA sampling. These 3D models will be made publicly available on an online repository and can be used by palaeontologists to investigate morphology and make measurements digitally, thus expanding the use and impact of the collection from which the specimens were sourced. The museums from which the specimens were sourced can also use these 3D models for outreach, education, or training activities.
From the 58 fossil samples, we were able to evaluate the level of ancient DNA preservation across time and archaeological sites. We found that ancient DNA was mostly preserved in specimens younger than ~7,000 years old, with only two samples older than this providing a limited amount of ancient DNA data. After enrichment of mitochondrial DNA, we were able to generate enough data to reconstruct the mitogenomes of 21 of the 58 ancient samples.
From the 154 historical and modern samples, we generated 90 mitochondrial genomes against which to compare the ancient genetic diversity. This included the novel mitochondrial genome of the Cape grysbok, which has not been sequenced before, and resulted in a peer-reviewed publication. This aspect of the project also includes the first population-level genetic datasets for the grey rhebok and the southern reedbuck, thereby contributing novel genetic data for understudied species in Africa. These data will be published along with the ancient DNA results in upcoming peer-reviewed publications.
The results of the project have been presented at two international and one local conference. The genetic results will be useful to the museums as it identifies some specimens to species level where only genus level classification was possible before, it confirms the species identity of other specimens, and in some cases corrects the species of incorrectly identified specimens. This improves the scientific accuracy and reliability of the collections. The project is continuing in 2024 and the main results will be published open-access in peer-reviewed publications in due course.
The generation of ancient DNA data from African subfossils remains a rare occurrence in the field of paleogenetics. A search on Scopus with the terms [“ancient DNA” AND “Africa” AND “fossil”] finds 42 research articles, many of which only refer to Africa and took place outside the continent or are focused on a couple of specimens from a single species. Therefore, this project is one of few that is pushing the boundaries of ancient DNA research in Africa, particularly in terms of the age of specimens and the number of species investigated. Having so far generated 21 ancient mitogenomes from four species across different feeding guilds and from samples up to 7,000 years old is already an immensely novel contribution to the field, both in Africa and globally. At the completion of the project, the dataset will be highly unique in its spatial, temporal, and species composition, and the insights to be gained from its analysis will be singular and uniquely impactful in the fields of paleogenetics, paleobiology, and biodiversity conservation.