The evolutionary relationships among extinct African hominin taxa are highly debated and largely ... more The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. ForParanthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa1,2and the nature of intraspecific variation3–6are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically toP. robustus,from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern A...
Despite the vast array of different geochronological tools available, dating the Paleolithic rema... more Despite the vast array of different geochronological tools available, dating the Paleolithic remains one of the discipline’s greatest challenges. This review focuses on two different dating approaches: trapped charge and amino acid geochronology. While differing in their fundamental principles, both exploit time-dependent changes in signals found within crystals to generate a chronology for the material dated and hence, the associated deposits. Within each method, there is a diverse range of signals that can be analyzed, each covering different time ranges, applicable to different materials and suitable for different paleoenvironmental and archaeological contexts. This multiplicity of signals can at first sight appear confusing, but it is a fundamental strength of the techniques, allowing internal checks for consistency and providing more information than simply a chronology. For each technique, we present an overview of the basis for the time-dependent signals and the types of mate...
Estimating the dwarfing rate of an extinct Sicilian elephant Highlights d We present mitochondria... more Estimating the dwarfing rate of an extinct Sicilian elephant Highlights d We present mitochondrial genome data from an extinct Mediterranean dwarf elephant d Dwarf elephant DNA diverged 0.4 million years ago from the large-bodied ancestor d Multidisciplinary evidence places a minimum and maximum boundary on dwarfing rate d We find a size reduction between 0.74 and 200.95 kg and 0.15 and 41.49 mm per generation
Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic p... more Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, the...
Fossils were thought to lack original organic molecules, but chemical analyses show that some can... more Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These ‘soft tissues’ have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil ‘soft tissues’ differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize i...
Fossils were long thought to lack original organic material, but the discovery of organic molecul... more Fossils were long thought to lack original organic material, but the discovery of organic molecules in fossils and sub-fossils, thousands to millions of years old, has demonstrated the potential of fossil organics to provide radical new insights into the fossil record. How long different organics can persist remains unclear, however. Non-avian dinosaur bone has been hypothesised to preserve endogenous organics including collagen, osteocytes, and blood vessels, but proteins and labile lipids are unstable during diagenesis or over long periods of time. Furthermore, bone is porous and an open system, allowing microbial and organic flux. Some of these organics within fossil bone have therefore been identified as either contamination or microbial biofilm, rather than original organics. Here, we use biological and chemical analyses of Late Cretaceous dinosaur bones and sediment matrix to show that dinosaur bone hosts a diverse microbiome. Fossils and matrix were freshly-excavated, aseptic...
This data accession contains:1) Genomic BAM files of selected regions in the genomes of extant an... more This data accession contains:1) Genomic BAM files of selected regions in the genomes of extant and extinct rhinoceroses used for protein translation.2) Protein sequence alignment of all considered extant and extinct species, per gene.A description of research design, methods, and results can be found at:https://doi.org/10.1038/s41586-019-1555-y
Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables ... more Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables age estimation over the Quaternary, but to date, its application to mammalian remains has been challenging. It has been postulated that enamel is a suitable biomineral for the long-term survival of endogenous amino acids and thus, it can be used for age estimation. Directly dating mammalian remains is integral to understanding mammalian evolution and for understanding palaeoecology and palaeoclimatology. Analysis of multiple amino acids for geochronological studies is typically achieved using a RP-HPLC method. However, the low concentrations of amino acids coupled with high concentrations of inorganic species makes accurate determination of amino concentrations challenging. The initial focus of this thesis covers the development of a novel method for the separation of amino acids from inorganic species. This was initially attempted via a HILIC SPE, but was later superseded by a biphasic ...
Evolution on islands, together with the often extreme phenotypic changes associated with it, has ... more Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily).1 Despite the challenges associated with recovering ancient DNA from warm climates,2 we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived3 to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 and 200.95 kg and height reduction between 0.15 and 41.49 mm per generation. We ...
Processed data sets for the experiments included in the manuscript: A new method for amino acid r... more Processed data sets for the experiments included in the manuscript: A new method for amino acid racemization dating: a closed system approach
The evolutionary relationships among extinct African hominin taxa are highly debated and largely ... more The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. ForParanthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa1,2and the nature of intraspecific variation3–6are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically toP. robustus,from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern A...
Despite the vast array of different geochronological tools available, dating the Paleolithic rema... more Despite the vast array of different geochronological tools available, dating the Paleolithic remains one of the discipline’s greatest challenges. This review focuses on two different dating approaches: trapped charge and amino acid geochronology. While differing in their fundamental principles, both exploit time-dependent changes in signals found within crystals to generate a chronology for the material dated and hence, the associated deposits. Within each method, there is a diverse range of signals that can be analyzed, each covering different time ranges, applicable to different materials and suitable for different paleoenvironmental and archaeological contexts. This multiplicity of signals can at first sight appear confusing, but it is a fundamental strength of the techniques, allowing internal checks for consistency and providing more information than simply a chronology. For each technique, we present an overview of the basis for the time-dependent signals and the types of mate...
Estimating the dwarfing rate of an extinct Sicilian elephant Highlights d We present mitochondria... more Estimating the dwarfing rate of an extinct Sicilian elephant Highlights d We present mitochondrial genome data from an extinct Mediterranean dwarf elephant d Dwarf elephant DNA diverged 0.4 million years ago from the large-bodied ancestor d Multidisciplinary evidence places a minimum and maximum boundary on dwarfing rate d We find a size reduction between 0.74 and 200.95 kg and 0.15 and 41.49 mm per generation
Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic p... more Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, the...
Fossils were thought to lack original organic molecules, but chemical analyses show that some can... more Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These ‘soft tissues’ have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil ‘soft tissues’ differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize i...
Fossils were long thought to lack original organic material, but the discovery of organic molecul... more Fossils were long thought to lack original organic material, but the discovery of organic molecules in fossils and sub-fossils, thousands to millions of years old, has demonstrated the potential of fossil organics to provide radical new insights into the fossil record. How long different organics can persist remains unclear, however. Non-avian dinosaur bone has been hypothesised to preserve endogenous organics including collagen, osteocytes, and blood vessels, but proteins and labile lipids are unstable during diagenesis or over long periods of time. Furthermore, bone is porous and an open system, allowing microbial and organic flux. Some of these organics within fossil bone have therefore been identified as either contamination or microbial biofilm, rather than original organics. Here, we use biological and chemical analyses of Late Cretaceous dinosaur bones and sediment matrix to show that dinosaur bone hosts a diverse microbiome. Fossils and matrix were freshly-excavated, aseptic...
This data accession contains:1) Genomic BAM files of selected regions in the genomes of extant an... more This data accession contains:1) Genomic BAM files of selected regions in the genomes of extant and extinct rhinoceroses used for protein translation.2) Protein sequence alignment of all considered extant and extinct species, per gene.A description of research design, methods, and results can be found at:https://doi.org/10.1038/s41586-019-1555-y
Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables ... more Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables age estimation over the Quaternary, but to date, its application to mammalian remains has been challenging. It has been postulated that enamel is a suitable biomineral for the long-term survival of endogenous amino acids and thus, it can be used for age estimation. Directly dating mammalian remains is integral to understanding mammalian evolution and for understanding palaeoecology and palaeoclimatology. Analysis of multiple amino acids for geochronological studies is typically achieved using a RP-HPLC method. However, the low concentrations of amino acids coupled with high concentrations of inorganic species makes accurate determination of amino concentrations challenging. The initial focus of this thesis covers the development of a novel method for the separation of amino acids from inorganic species. This was initially attempted via a HILIC SPE, but was later superseded by a biphasic ...
Evolution on islands, together with the often extreme phenotypic changes associated with it, has ... more Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily).1 Despite the challenges associated with recovering ancient DNA from warm climates,2 we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived3 to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 and 200.95 kg and height reduction between 0.15 and 41.49 mm per generation. We ...
Processed data sets for the experiments included in the manuscript: A new method for amino acid r... more Processed data sets for the experiments included in the manuscript: A new method for amino acid racemization dating: a closed system approach
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