International Journal of Primatology, Mar 12, 2019
It has become apparent that natural hybridization is far more common and may play a much greater ... more It has become apparent that natural hybridization is far more common and may play a much greater role in evolution than has historically been recognized. The skeletal morphology of hybrid primates is notoriously variable and difficult to predict. Indeed, before the advent of genetic sequencing techniques, many wild hybrid populations went undetected. Though many species of primates are now known to hybridize naturally and are likely to have done so for millions of years, anthropogenic alterations to the environment are increasingly restricting or altering primate species ranges and contact zones and driving hybridization between populations that may otherwise never have come into contact. The case of hybridizing Japanese and Taiwanese macaques (Macaca fuscata and Macaca cyclopis) is an excellent example of this, as these two island species could not have come into contact without human interference. Here we apply 3D geometric morphometrics and nonmetric trait analysis to the crania and dentition of hybrid macaques (N = 70) and their parental species, M. fuscata (N = 57) and M. cyclopis (N = 51). The exploration of 3D shape variation identifies mildly transgressive morphology in the hybrids and a general tendency toward the M. fuscata morphotype overall, but less variability in the hybrid morphotype than has been identified in previous studies of primate hybrids. We also identify a small number of nonmetric traits that differentiate the hybrids from the parental species, although the power of these traits to distinguish between groups is weak and their relationship with hybridity is unclear. We conclude that the relatively short divergence time between the parent species is likely to help explain the observed differences in hybrid morphotype, and that further exploration of the relationship between degree of evolutionary divergence and hybrid morphology may help us to better explain and predict hybrid morphology in other taxa.
Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology... more Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology and Anthropology, in conjunction with the
International Journal of Molecular Sciences, Sep 3, 2020
The transitioning of cells during the systemic demise of an organism is poorly understood. Here, ... more The transitioning of cells during the systemic demise of an organism is poorly understood. Here, we present evidence that organismal death is accompanied by a common and sequential molecular flood of stress-induced events that propagate the senescence phenotype, and this phenotype is preserved in the proteome after death. We demonstrate activation of "death" pathways involvement in diseases of ageing, with biochemical mechanisms mapping onto neurological damage, embryonic development, the inflammatory response, cardiac disease and ultimately cancer with increased significance. There is sufficient bioavailability of the building blocks required to support the continued translation, energy, and functional catalytic activity of proteins. Significant abundance changes occur in 1258 proteins across 1 to 720 h post-mortem of the 12-week-old mouse mandible. Protein abundance increases concord with enzyme activity, while mitochondrial dysfunction is evident with metabolic reprogramming. This study reveals differences in protein abundances which are akin to states of stress-induced premature senescence (SIPS). The control of these pathways is significant for a large number of biological scenarios. Understanding how these pathways function during the process of cellular death holds promise in generating novel solutions capable of overcoming disease complications, maintaining organ transplant viability and could influence the findings of proteomics through "deep-time" of individuals with no historically recorded cause of death.
Where the possibility of hybridisation in the human lineage was once largely speculative and ulti... more Where the possibility of hybridisation in the human lineage was once largely speculative and ultimately untestable, recent advancements in genome sequencing techniques have brought it to the forefront of palaeoanthropological research. A genetic mode of investigation has some clear advantages over a morphologically based one, and undoubtedly has a great deal left to contribute to our understanding of human evolution. Nevertheless, insurmountable limitations on the preservation of DNA mean that anatomically based research remains perpetually indispensable. The ability to identify hybrids based upon skeletal morphology has enormous potential for palaeontological research, but has proven to be notoriously difficult. In the human fossil record particularly, possible hybrids have typically been identified based upon unusual mosaics of modern and archaic features. Though suggestive, these claims remain contentious; ultimately, we have very little idea what a hybrid in the human lineage ac...
Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology... more Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology and Anthropology, in conjunction with the
The burial mound of Le Tumulus des Sables, southwest France, contains archaeological artefacts sp... more The burial mound of Le Tumulus des Sables, southwest France, contains archaeological artefacts spanning from the Neolithic to the Iron Age. Human remains have been found throughout the burial mound, however their highly fragmented state complicates the association between the burial mound structure and the archaeological material. Radiocarbon dating and isotopic analyses of human teeth have been used to investigate the chronology, diet and mobility of the occupants. Radiocarbon dating shows that the site was used for burials from the Neolithic to Iron Age, consistent with the range of archaeological artefacts recovered. δ13C and δ15N values (from dentine collagen) suggest a predominately terrestrial diet for the population, unchanging through time. 87Sr/86Sr (on enamel and dentine) and δ18O (on enamel) values are consistent with occupation of the surrounding region, with one individual having a δ18O value consistent with a childhood spent elsewhere, in a colder climate region. These results showcase the complex reuse of this burial mound by a mostly local population over a period of about 2000 years.
It has become apparent that natural hybridization is far more common and may play a much greater ... more It has become apparent that natural hybridization is far more common and may play a much greater role in evolution than has historically been recognized. The skeletal morphology of hybrid primates is notoriously variable and difficult to predict. Indeed, before the advent of genetic sequencing techniques, many wild hybrid populations went undetected. Though many species of primates are now known to hybridize naturally and are likely to have done so for millions of years, anthropogenic alterations to the environment are increasingly restricting or altering primate species ranges and contact zones and driving hybridization between populations that may otherwise never have come into contact. The case of hybridizing Japanese and Taiwanese macaques (Macaca fuscata and Macaca cyclopis) is an excellent example of this, as these two island species could not have come into contact without human interference. Here we apply 3D geometric morphometrics and nonmetric trait analysis to the crania and dentition of hybrid macaques (N = 70) and their parental species, M. fuscata (N = 57) and M. cyclopis (N = 51). The exploration of 3D shape variation identifies mildly transgressive morphology in the hybrids and a general tendency toward the M. fuscata morphotype overall, but less variability in the hybrid morphotype than has been identified in previous studies of primate hybrids. We also identify a small number of nonmetric traits that differentiate the hybrids from the parental species, although the power of these traits to distinguish between groups is weak and their relationship with hybridity is unclear. We conclude that the relatively short divergence time between the parent species is likely to help explain the observed differences in hybrid morphotype, and that further exploration of the relationship between degree of evolutionary divergence and hybrid morphology may help us to better explain and predict hybrid morphology in other taxa.
The first dental proteomic profile of Iron Age individuals (ca. 2000-1000 years B.P.), collected ... more The first dental proteomic profile of Iron Age individuals (ca. 2000-1000 years B.P.), collected from the site of Long Long Rak rock shelter in northwest Thailand is described. A bias toward the preservation of the positively charged aromatic, and polar amino acids is observed. It is evident that the 212 proteins identified (2 peptide, FDR <1%) comprise a palimpsest of alterations that occurred both ante-mortem and post-mortem. Conservation of amino acids within the taphonomically resistant crystalline matrix enabled the identification of both X and Y chromosome linked amelogenin peptides. A novel multiple reaction monitoring method using the sex specific amelogenin protein isoforms is described and indicate the teeth are of male origin. Functional analysis shows an enrichment of pathways associated with metabolic disorders and shows a capacity for harboring these conditions prior to death. Stable isotope analysis using carbon isotopes highlights the strongly C 3 based (80%) diet of the Long Long Rak cemetery people, which probably comprised rice combined with protein from freshwater fish among other food items. The combination of proteomics and stable isotope analysis provides a complementary strategy for assessing the demography, diet, lifestyle, and possible diseases experienced by ancient populations.
Oxygen (δ 18 O) and strontium (87 Sr/ 86 Sr) isotopes were used as tools to investigate human mig... more Oxygen (δ 18 O) and strontium (87 Sr/ 86 Sr) isotopes were used as tools to investigate human migration at the early Bell Beaker site (2500-2000 BC) Le Tumulus des Sables, Saint-Laurent-Médoc, southwest France. The O and Sr isotope ratios measured in tooth enamel record the average dietary isotope signature ingested by that individual during their childhood. When this data is compared to the isotope signature of the burial site it can be used to indicate if the individual migrated into this area during their lifetime. The O isotopic composition of meteoric water changes depending on climate, temperature and quantity of precipitation. O isotope ratios in skeletal and dental remains are related to body water, which in turn is influenced by diet, physiology and climate. Most of the water consumed by large mammals comes from drinking water, typically sourced locally. Sr isotope ratios on the other hand vary between different geologic regions, depending on their age and composition. Sr is released through weathering and transported into the soil, ground and surface water, where it becomes available for uptake by plants, enters the food cycle and eventually ends up in skeletal and dental tissue where it substitutes for calcium.
ABSTRACT Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and ani... more ABSTRACT Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and animal migrations across geologically different terrains. Sr isotope ratios in rocks are a product of age and composition and thus vary between geologic units. From the eroding environment Sr is transported into the soils, plants and rivers of a region. Humans and animals incorporate Sr from their diet into their bones and teeth, where it substitutes for calcium. Tooth enamel contains Sr isotope signatures acquired during childhood and is most resistant to weathering and overprinting, while the dentine is often diagenetically altered towards the local Sr signature. For the reconstruction of human and animal migrations the tooth enamel 87Sr/86Sr ratio is compared to the Sr isotope signature in the vicinity of the burial site and the surrounding area. This study focuses on the establishment of a comprehensive reference map of bioavailable 87Sr/86Sr ratios for France. In a next step we will compare human and animal teeth from key archaeological sites to this reference map to investigate mobility. So far, we have analysed plant and soil samples from ~200 locations across France including the Aquitaine basin, the western and northern parts of the Paris basin, as well as three transects through the Pyrenees Mountains. The isotope data, geologic background information (BRGM 1:1M), field images, and detailed method descriptions are available through our online database iRhum (http://rses.anu.edu.au/research/ee). This database can also be used in forensic studies and food sciences. As an archaeological case study teeth from 16 adult and 8 juvenile individuals were investigated from an early Bell Beaker (2500-2000 BC) site at Le Tumulus des Sables, south-west France (Gironde). The teeth were analysed for Sr isotope ratios using laser ablation ICP-MS. Four teeth were also analysed using solution ICP-MS, which showed a significant offset to the laser ablation results. This requires further detailed investigation. Nevertheless, the teeth showed clear differences between enamel and diagenetically overprinted dentine, which suggests mobility. Unfortunately, the sandy sediment units in the close vicinity of Le Tumulus des Sables show large variations in their 87Sr/86Sr ratios so it is currently not possible to distinguish between migration from outside of the Médoc region from mobility within the region based solely on Sr isotope ratios. The case study illustrates the importance of detailed reference maps, which are required for any isotope studies used for the reconstruction of migrations. Other isotope data, such as O and Pb, will complement the investigation at Tumulus de Sables and may enable us to tie down the range of mobility of the humans that were buried at Le Tumulus des Sables.
The transitioning of cells during the systemic demise of an organism is poorly understood. Here, ... more The transitioning of cells during the systemic demise of an organism is poorly understood. Here, we present evidence that organismal death is accompanied by a common and sequential molecular flood of stress-induced events that propagate the senescence phenotype, and this phenotype is preserved in the proteome after death. We demonstrate activation of “death” pathways involvement in diseases of ageing, with biochemical mechanisms mapping onto neurological damage, embryonic development, the inflammatory response, cardiac disease and ultimately cancer with increased significance. There is sufficient bioavailability of the building blocks required to support the continued translation, energy, and functional catalytic activity of proteins. Significant abundance changes occur in 1258 proteins across 1 to 720 h post-mortem of the 12-week-old mouse mandible. Protein abundance increases concord with enzyme activity, while mitochondrial dysfunction is evident with metabolic reprogramming. Thi...
International Journal of Primatology, Mar 12, 2019
It has become apparent that natural hybridization is far more common and may play a much greater ... more It has become apparent that natural hybridization is far more common and may play a much greater role in evolution than has historically been recognized. The skeletal morphology of hybrid primates is notoriously variable and difficult to predict. Indeed, before the advent of genetic sequencing techniques, many wild hybrid populations went undetected. Though many species of primates are now known to hybridize naturally and are likely to have done so for millions of years, anthropogenic alterations to the environment are increasingly restricting or altering primate species ranges and contact zones and driving hybridization between populations that may otherwise never have come into contact. The case of hybridizing Japanese and Taiwanese macaques (Macaca fuscata and Macaca cyclopis) is an excellent example of this, as these two island species could not have come into contact without human interference. Here we apply 3D geometric morphometrics and nonmetric trait analysis to the crania and dentition of hybrid macaques (N = 70) and their parental species, M. fuscata (N = 57) and M. cyclopis (N = 51). The exploration of 3D shape variation identifies mildly transgressive morphology in the hybrids and a general tendency toward the M. fuscata morphotype overall, but less variability in the hybrid morphotype than has been identified in previous studies of primate hybrids. We also identify a small number of nonmetric traits that differentiate the hybrids from the parental species, although the power of these traits to distinguish between groups is weak and their relationship with hybridity is unclear. We conclude that the relatively short divergence time between the parent species is likely to help explain the observed differences in hybrid morphotype, and that further exploration of the relationship between degree of evolutionary divergence and hybrid morphology may help us to better explain and predict hybrid morphology in other taxa.
Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology... more Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology and Anthropology, in conjunction with the
International Journal of Molecular Sciences, Sep 3, 2020
The transitioning of cells during the systemic demise of an organism is poorly understood. Here, ... more The transitioning of cells during the systemic demise of an organism is poorly understood. Here, we present evidence that organismal death is accompanied by a common and sequential molecular flood of stress-induced events that propagate the senescence phenotype, and this phenotype is preserved in the proteome after death. We demonstrate activation of "death" pathways involvement in diseases of ageing, with biochemical mechanisms mapping onto neurological damage, embryonic development, the inflammatory response, cardiac disease and ultimately cancer with increased significance. There is sufficient bioavailability of the building blocks required to support the continued translation, energy, and functional catalytic activity of proteins. Significant abundance changes occur in 1258 proteins across 1 to 720 h post-mortem of the 12-week-old mouse mandible. Protein abundance increases concord with enzyme activity, while mitochondrial dysfunction is evident with metabolic reprogramming. This study reveals differences in protein abundances which are akin to states of stress-induced premature senescence (SIPS). The control of these pathways is significant for a large number of biological scenarios. Understanding how these pathways function during the process of cellular death holds promise in generating novel solutions capable of overcoming disease complications, maintaining organ transplant viability and could influence the findings of proteomics through "deep-time" of individuals with no historically recorded cause of death.
Where the possibility of hybridisation in the human lineage was once largely speculative and ulti... more Where the possibility of hybridisation in the human lineage was once largely speculative and ultimately untestable, recent advancements in genome sequencing techniques have brought it to the forefront of palaeoanthropological research. A genetic mode of investigation has some clear advantages over a morphologically based one, and undoubtedly has a great deal left to contribute to our understanding of human evolution. Nevertheless, insurmountable limitations on the preservation of DNA mean that anatomically based research remains perpetually indispensable. The ability to identify hybrids based upon skeletal morphology has enormous potential for palaeontological research, but has proven to be notoriously difficult. In the human fossil record particularly, possible hybrids have typically been identified based upon unusual mosaics of modern and archaic features. Though suggestive, these claims remain contentious; ultimately, we have very little idea what a hybrid in the human lineage ac...
Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology... more Honours thesis submitted as part of the B.A. (Hons) degree completed in the School of Archaeology and Anthropology, in conjunction with the
The burial mound of Le Tumulus des Sables, southwest France, contains archaeological artefacts sp... more The burial mound of Le Tumulus des Sables, southwest France, contains archaeological artefacts spanning from the Neolithic to the Iron Age. Human remains have been found throughout the burial mound, however their highly fragmented state complicates the association between the burial mound structure and the archaeological material. Radiocarbon dating and isotopic analyses of human teeth have been used to investigate the chronology, diet and mobility of the occupants. Radiocarbon dating shows that the site was used for burials from the Neolithic to Iron Age, consistent with the range of archaeological artefacts recovered. δ13C and δ15N values (from dentine collagen) suggest a predominately terrestrial diet for the population, unchanging through time. 87Sr/86Sr (on enamel and dentine) and δ18O (on enamel) values are consistent with occupation of the surrounding region, with one individual having a δ18O value consistent with a childhood spent elsewhere, in a colder climate region. These results showcase the complex reuse of this burial mound by a mostly local population over a period of about 2000 years.
It has become apparent that natural hybridization is far more common and may play a much greater ... more It has become apparent that natural hybridization is far more common and may play a much greater role in evolution than has historically been recognized. The skeletal morphology of hybrid primates is notoriously variable and difficult to predict. Indeed, before the advent of genetic sequencing techniques, many wild hybrid populations went undetected. Though many species of primates are now known to hybridize naturally and are likely to have done so for millions of years, anthropogenic alterations to the environment are increasingly restricting or altering primate species ranges and contact zones and driving hybridization between populations that may otherwise never have come into contact. The case of hybridizing Japanese and Taiwanese macaques (Macaca fuscata and Macaca cyclopis) is an excellent example of this, as these two island species could not have come into contact without human interference. Here we apply 3D geometric morphometrics and nonmetric trait analysis to the crania and dentition of hybrid macaques (N = 70) and their parental species, M. fuscata (N = 57) and M. cyclopis (N = 51). The exploration of 3D shape variation identifies mildly transgressive morphology in the hybrids and a general tendency toward the M. fuscata morphotype overall, but less variability in the hybrid morphotype than has been identified in previous studies of primate hybrids. We also identify a small number of nonmetric traits that differentiate the hybrids from the parental species, although the power of these traits to distinguish between groups is weak and their relationship with hybridity is unclear. We conclude that the relatively short divergence time between the parent species is likely to help explain the observed differences in hybrid morphotype, and that further exploration of the relationship between degree of evolutionary divergence and hybrid morphology may help us to better explain and predict hybrid morphology in other taxa.
The first dental proteomic profile of Iron Age individuals (ca. 2000-1000 years B.P.), collected ... more The first dental proteomic profile of Iron Age individuals (ca. 2000-1000 years B.P.), collected from the site of Long Long Rak rock shelter in northwest Thailand is described. A bias toward the preservation of the positively charged aromatic, and polar amino acids is observed. It is evident that the 212 proteins identified (2 peptide, FDR <1%) comprise a palimpsest of alterations that occurred both ante-mortem and post-mortem. Conservation of amino acids within the taphonomically resistant crystalline matrix enabled the identification of both X and Y chromosome linked amelogenin peptides. A novel multiple reaction monitoring method using the sex specific amelogenin protein isoforms is described and indicate the teeth are of male origin. Functional analysis shows an enrichment of pathways associated with metabolic disorders and shows a capacity for harboring these conditions prior to death. Stable isotope analysis using carbon isotopes highlights the strongly C 3 based (80%) diet of the Long Long Rak cemetery people, which probably comprised rice combined with protein from freshwater fish among other food items. The combination of proteomics and stable isotope analysis provides a complementary strategy for assessing the demography, diet, lifestyle, and possible diseases experienced by ancient populations.
Oxygen (δ 18 O) and strontium (87 Sr/ 86 Sr) isotopes were used as tools to investigate human mig... more Oxygen (δ 18 O) and strontium (87 Sr/ 86 Sr) isotopes were used as tools to investigate human migration at the early Bell Beaker site (2500-2000 BC) Le Tumulus des Sables, Saint-Laurent-Médoc, southwest France. The O and Sr isotope ratios measured in tooth enamel record the average dietary isotope signature ingested by that individual during their childhood. When this data is compared to the isotope signature of the burial site it can be used to indicate if the individual migrated into this area during their lifetime. The O isotopic composition of meteoric water changes depending on climate, temperature and quantity of precipitation. O isotope ratios in skeletal and dental remains are related to body water, which in turn is influenced by diet, physiology and climate. Most of the water consumed by large mammals comes from drinking water, typically sourced locally. Sr isotope ratios on the other hand vary between different geologic regions, depending on their age and composition. Sr is released through weathering and transported into the soil, ground and surface water, where it becomes available for uptake by plants, enters the food cycle and eventually ends up in skeletal and dental tissue where it substitutes for calcium.
ABSTRACT Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and ani... more ABSTRACT Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and animal migrations across geologically different terrains. Sr isotope ratios in rocks are a product of age and composition and thus vary between geologic units. From the eroding environment Sr is transported into the soils, plants and rivers of a region. Humans and animals incorporate Sr from their diet into their bones and teeth, where it substitutes for calcium. Tooth enamel contains Sr isotope signatures acquired during childhood and is most resistant to weathering and overprinting, while the dentine is often diagenetically altered towards the local Sr signature. For the reconstruction of human and animal migrations the tooth enamel 87Sr/86Sr ratio is compared to the Sr isotope signature in the vicinity of the burial site and the surrounding area. This study focuses on the establishment of a comprehensive reference map of bioavailable 87Sr/86Sr ratios for France. In a next step we will compare human and animal teeth from key archaeological sites to this reference map to investigate mobility. So far, we have analysed plant and soil samples from ~200 locations across France including the Aquitaine basin, the western and northern parts of the Paris basin, as well as three transects through the Pyrenees Mountains. The isotope data, geologic background information (BRGM 1:1M), field images, and detailed method descriptions are available through our online database iRhum (http://rses.anu.edu.au/research/ee). This database can also be used in forensic studies and food sciences. As an archaeological case study teeth from 16 adult and 8 juvenile individuals were investigated from an early Bell Beaker (2500-2000 BC) site at Le Tumulus des Sables, south-west France (Gironde). The teeth were analysed for Sr isotope ratios using laser ablation ICP-MS. Four teeth were also analysed using solution ICP-MS, which showed a significant offset to the laser ablation results. This requires further detailed investigation. Nevertheless, the teeth showed clear differences between enamel and diagenetically overprinted dentine, which suggests mobility. Unfortunately, the sandy sediment units in the close vicinity of Le Tumulus des Sables show large variations in their 87Sr/86Sr ratios so it is currently not possible to distinguish between migration from outside of the Médoc region from mobility within the region based solely on Sr isotope ratios. The case study illustrates the importance of detailed reference maps, which are required for any isotope studies used for the reconstruction of migrations. Other isotope data, such as O and Pb, will complement the investigation at Tumulus de Sables and may enable us to tie down the range of mobility of the humans that were buried at Le Tumulus des Sables.
The transitioning of cells during the systemic demise of an organism is poorly understood. Here, ... more The transitioning of cells during the systemic demise of an organism is poorly understood. Here, we present evidence that organismal death is accompanied by a common and sequential molecular flood of stress-induced events that propagate the senescence phenotype, and this phenotype is preserved in the proteome after death. We demonstrate activation of “death” pathways involvement in diseases of ageing, with biochemical mechanisms mapping onto neurological damage, embryonic development, the inflammatory response, cardiac disease and ultimately cancer with increased significance. There is sufficient bioavailability of the building blocks required to support the continued translation, energy, and functional catalytic activity of proteins. Significant abundance changes occur in 1258 proteins across 1 to 720 h post-mortem of the 12-week-old mouse mandible. Protein abundance increases concord with enzyme activity, while mitochondrial dysfunction is evident with metabolic reprogramming. Thi...
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