Matthew James Collins

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Verified

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• Bachelor of Science Zoology with Marine Zoology
• Professor at University of Cambridge

The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Genomes from Central Türkiye ~8000 BCE are genetically proximal to the domestic origins of sheep but do not fully explain the ancestry of later populati...

Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developingnovel strategies for the analyses and interpretations of complex, degraded protein mixtures.The community has also established standards of good practice to interrogate our data. How-ever, there is a lack of a systematic exploration of how these affect the...

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia¹. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs—European, Southwe...

Background Natural history museum specimens of historical honeybees have been successfully used to explore the species’ genomic past, indicating fast and rapid changes between historical and modern specimens, possibly as a response to current challenges. In our study we explore a potential new untapped archive from natural history collections - spe...

It is a strange observation, given the cultural co-evolution of dairying, that milk proteins are more commonly reported than any other food proteins in the archaeological record. The whey protein β-lactoglobulin and in particular its eleven amino acid long peptide T125PEVDXEALEK135 seems to be preferentially preserved in both ceramic vessels and te...

Funerary masks played a crucial role in ancient Egyptian burial practices, as part of the rituals to ensure a successful afterlife. This study presents the first comprehensive analysis of a gilded mummy mask from the Roman period in Egypt from the collections of The Ny Carlsberg Glyptotek in Copenhagen. Portraying a young female, the mask belongs t...

This study investigates the efficacy of proteomic analysis of human remains to identify active infections in the past through the detection of pathogens and the host response to infection. We advance leprosy as a case study due to the sequestering of sufferers in leprosaria and the suggestive skeletal lesions that can result from the disease. Here...

Leather was one of the most important materials of nomadic Scythians, used for clothing, shoes, and quivers, amongst other objects. However, our knowledge regarding the specific animal species used in Scythian leather production remains limited. In this first systematic study, we used palaeoproteomics methods to analyse the species in 45 samples of...

Ancient protein studies have demonstrated their utility for looking at a wide range of evolutionary and historical questions. The majority of palaeoproteomics studies to date have been restricted to high latitudes with relatively temperate environments. A better understanding of protein preservation at lower latitudes is critical for disentangling...

Proteins are the most stable of the macromolecules that carry genetic information over long periods of time. Closed systems are more likely to retain endogenous proteins or their degradation products. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate c...

Historical evidence suggests that social status played a major role in all aspects of society in eighteenth–nineteenth century England. We present an insight into how socioeconomic status affected the dietary habits of two post-medieval urban populations from Greater Manchester, northwest England. Stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope ra...

Marine historical ecology provides a means to establish baselines to inform current fisheries management. Groupers (Epinephelidae) are key species for fisheries in the Mediterranean, which have been heavily overfished. Species abundance and distribution prior to the 20th century in the Mediterranean remains poorly known. To reconstruct the past bio...

Poor preservation of collagen in dry and/or arid environments has hindered the application of Zooarchaeology by mass spectrometry (ZooMS) analysis in many regions of the world. As a result, many zooarchaeological investigations have relied exclusively on morphological assessment of fragmentary remains due to the inadequate preservation of biomolecu...

Taxonomic identification of whale bones found during archaeological excavations is problematic due to their typically fragmented state. This difficulty limits understanding of both the past spatio-temporal distributions of whale populations and of possible early whaling activities. To overcome this challenge, we performed zooarchaeology by mass spe...

In 2018, a well-constructed cist-type grave was discovered at Ba`ja, a Neolithic village (7,400–6,800 BCE) in Southern Jordan. Underneath multiple grave layers, an 8-year-old child was buried in a fetal position. Over 2,500 beads were found on the chest and neck, along with a double perforated stone pendant and a delicately engraved mother-of-pearl...

The Neolithic burial of Grotta di Pietra Sant’Angelo (CS) represents a unique archaeological finding for the prehistory of Southern Italy. The unusual placement of the inhumation at a rather high altitude and far from inhabited areas, the lack of funerary equipment and the prone deposition of the body find limited similarities in coeval Italian sit...

Objectives: We evaluate the potential of paired isotopic analysis of bone carbonate and collagen to examine the diet of post-medieval human and animal populations from England (17th-19th c.), including, for the first time, manufacturing towns in northern England. The potential for identifying C 4 crop consumption is explored alongside regional and...

In the Middle Ages, texts were recorded and preserved on parchment, an animal-derived material. When this resource was scarce, older manuscripts were sometimes recycled to write new manuscripts. In the process, the ancient text was erased, creating what is known as a palimpsest. Here, we explore the potential of peptide mass fingerprinting (PMF), w...

The systematics of Madagascar’s extinct elephant birds remains controversial due to large gaps in the fossil record and poor biomolecular preservation of skeletal specimens. Here, a molecular analysis of 1000-year-old fossil eggshells provides the first description of elephant bird phylogeography and offers insight into the ecology and evolution of...

Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)2. During liming, collagen peptides containing Glutamine (Q) undergo deamidation resulting in a mass shift of 0.984 Da. Assessing the extent of deamidation can inform us about parchment production patterns and quality. In this study...

Beeswax is a product of honeybees (Apis mellifera) and has been used extensively through time, especially as the primary component in medieval sealing wax for authenticating millions of documents. Today, these seals form large collections which, along with the historical information in the documents that the seals are attached to, could be a potent...

Between the sixteenth and nineteenth century, British agriculture underwent a ‘revolutionary’ transformation. Yet despite over a century of research and the recognised centrality of agricultural developments to industrialisation and population growth, the character or chronology of any ‘revolution’ during this period remains contentious. Enquiry ha...

Previously we showed that authentic peptide sequences could be obtained from 3.8-Ma-old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we show that the same sequences survive in a > 6.5 Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in extant s...

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago¹ had climates resembling those forecasted under future warming². Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known...

The oldest authenticated peptide sequences to date were reported in 2016 from 3.8 Ma old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we demonstrate survival of the same sequences in 6.5-9 Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in ext...

Fur is known from contemporary written sources to have been a key commodity in the Viking Age. Nevertheless, the fur trade has been notoriously difficult to study archaeologically as fur rarely survives in the archaeological record. In Denmark, fur finds are rare and fur in clothing has been limited to a few reports and not recorded systematically....

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA,...

This study compares histological preservation in archaeological bones from different burial types to unravel the histotaphonomy‐to‐funerary practices relationship. Αn intra‐skeletal approach is also adopted to explore intra‐individual (inner ear part of the petrous bone vs upper/lower limb long bones) and intra‐bone (proximal vs distal diaphysis) v...

One of the greatest successes of the application of Palaeoproteomics to Archaeology is its use by a number of authors to track evidence of dairying practice, both in terms of its origin and the selection of animal species. To this end, the whey protein β-lactoglobulin entrapped in pottery and dental calculus is widely studied because it is so frequ...

Significance The controversy over the taxonomic identity of the eggs exploited by Australia’s first people around 50,000 y ago is resolved. The birds that laid these eggs are extinct, and distinguishing between two main candidates, a giant flightless “mihirung” Genyornis and a large megapode Progura , had proven impossible using morphological and g...

The investigation and conservation of the Vienna Genesis, a Late Antique manuscript on purple parchment, included the study of parchment production and purple dyeing in the sixth century. The process of parchment making and of purple dyeing was recreated and compared with the Vienna Genesis and other manuscripts from the sixth and eighth centuries....

Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH) 2 . During liming, collagen peptides containing Glutamine (Q) undergo deamidation resulting in a mass shift of 0.984 Da. Assessing the extent of deamidation can inform us about parchment production patterns and quality. In this stu...

RATIONALE Dental calculus (mineralized dental plaque) is composed primarily of hydroxyapatite. We hypothesize that the carbonate component of dental calculus will reflect the isotopic composition of ingested simple carbohydrates. Therefore, dental calculus carbonates may be an indicator for sugar consumption, and an alternative to bone carbonate in...

The dataset contains the first-ever comprehensive biocodicological analysis of medieval library books and charters using Zooarchaeological Mass Spectrometry (ZooMS). Here, we analyze 68 codices and 59 charters (1490+59 samples in total) from one single monastic institution, namely the Cistercian abbey of Orval in present-day Belgium. The data entai...

We present the isotopic discrimination between paired skin and bone collagen from animals of known life history, providing a modern baseline for the interpretation of archaeological isotopic data. At present, the interpretation of inter-tissue variation (Δ(skin–bone)) in mummified remains is based on comparisons with other archaeological material,...

Next Generation Lab turns large and hitherto unstudied urban assemblages of archaeological leather and bone into a laboratory learning experience for high school students. The students, in turn, provide species identifications and thus increase knowledge on medieval and Renaissance livestock exploitation and material selection by craftsmen.

Mollusc shells represent excellent systems for the preservation and retrieval of genuine biomolecules from archaeological or palaeontological samples. As a consequence, the post-mortem breakdown of intracrystalline mollusc shell proteins has been extensively investigated, particularly with regard to its potential use as a “molecular clock” for geoc...

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope an...

Biocodicological analysis of parchments from manuscript books and archives offers unprecedented insight into the materiality of medieval literacy. Using ZooMS for animal species identification, we explored almost the entire library and all the preserved single leaf charters of a single medieval Cistercian monastery (Orval Abbey, Belgium). Systemati...

The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from arch...

Historic legal deeds are one of the most abundant resources in British archives, but also one of the most neglected. Despite the millions that survive, we know remarkably little about their manufacture, including the species of animal on which they were written. Here we present the species identification of 645 sixteenth-twentieth century skins via...

We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok—southe...

In this paper, we describe palaeoproteomic evidence obtained from a stained medieval birth girdle using a previously developed dry non-invasive sampling technique. The parchment birth girdle studied (Wellcome Collection Western MS. 632) was made in England in the late fifteenth century and was thought to be used by pregnant women while giving birth...

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America¹, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our res...

Parchment is one of the most abundant resources in archives across the world and is a unique time-sensitive material through which centuries of livestock economies, trade and craft can be explored. We examine the impact of structural and chemical modifications during production to δ¹³C and δ¹⁵N values in the skin, particularly the removal of cutane...

The degradation of archaeological bones is influenced by many variables. The bone material itself is a composite of both organic and inorganic components, and their degradation depends on processes occurring both before and after burial, and on both intrinsic bone characteristics as well as extrinsic environmental parameters. In this study we attem...

Paleoproteomics and the study of ancient proteins has become an important consideration in bioarchaeological research as we seek to understand the relationship between the physical skeleton and its underlying biochemistry. Osteocalcin is an abundant, non-collagenous protein that is accessible archaeologically due to its affinity for hydroxyapatite...

Zooarchaeology by Mass Spectrometry (ZooMS) is rapidly becoming a staple in archaeological and cultural heritage science. Developed a decade ago, this peptide mass fingerprinting technique is expanding from a small group of researchers mainly involved in method development to a broader group of scientists using it as another tool in their toolboxes...

In this paper we describe a dry non-invasive extraction method to detect palaeoproteomic evidence from stained manuscripts. The manuscript analysed in this study is a medieval parchment birth girdle (Wellcome Collection Western MS. 632) made in England and thought to be used by pregnant women while giving birth. Using a dry non-invasive sampling me...

Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their diversity throughout the exposure period. We genetically profiled the bacterial community in an experimental series of pig bone frag...

The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, with one of the most iconic artefacts being the bone point. Although great in number they remain understudied. Here we present a combined investigation of the typology, protein-based species composition, and absolute chronology of Maglemosian bo...

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...

Brain tissue is ubiquitous in the archaeological record. Multiple, independent studies report the finding of black, resinous or shiny brain tissue, and Petrone et al. [2020 "Heat-induced Brain Vitrification from the Vesuvius Eruption in C.E. 79." N Engl J Med. 382: 383-384; doi:10.1056/ NEJMc1909867] raise the intriguing prospect of a role for vitr...

Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three diff...

Abstract We report a simple histological study on skin biopsies from young domestic sheep following each step in transformation from skin to parchment production. During the recreation of historical parchment manufacture, histological analyses were conducted; before and after lime treatment, hair removal, and stretching. Sections were fixed and sta...

The Vienna Genesis: Material analysis and conservation of a Late Antique illuminated manuscript on purple parchment Abstract The Vienna Genesis (Austrian National Library, Codex Theologicus graecus 31) is a fragmentary Greek manuscript of the Book of Genesis written on purple dyed parchment with silver ink. It is assumed that the book was created i...

Ancient protein analysis is providing new insights into the evolutionary relationships between hominin fossils across the Pleistocene. Protein identification commonly relies on the proteolysis of a protein extract using a single protease, trypsin. As with modern proteome studies, alternative or additional proteases have the potential to increase bo...

The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to...

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...

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neand...

We report a simple histological study on skin biopsies from young domestic sheep following each step in transformation from skin to parchment production. Histological analyses were conducted; before and after lime treatment, hair removal, and stretching. Sections were fixed and stained using a variety of histological stains to identify the presence...

We report a simple histological study on skin biopsies from young domestic sheep following each step in transformation from skin to parchment production. During the recreation of historical parchment manufacture, histological analyses were conducted; before and after lime treatment, hair removal, and stretching. Sections were fixed and stained usin...

Motivation: Classification of archaeological animal samples is commonly achieved via manual examination of MALDI-ToF spectra. This is a time-consuming process which requires significant training and which does not produce a measure of confidence in the classification. We present a new, automated method for arriving at a classification of a MALDI-T...

We investigated the rate at which endogenous DNA from differently prepared (butchered, boiled and baked) compact pig bones degrades in five different Danish terrestrial and marine environments over a period of 12 months. Although >70% of the estimated endogenous mtDNA is lost after just four weeks of exposure, no cytosine deamination of DNA was obs...

Contamination is a potential problem in the study of ancient proteins, either from prior handling of the sample, laboratory consumables, or cross-sample carryover from mass spectrometers. Recently, deamidation of glutamine has been proposed as a measure for assessing the degradation of ancient proteins. Here, we present deamiDATE 1.0, a method for...

Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zea...

Extraction of environmental DNA from sediments are providing ground-breaking views of the past ecosystems and biodiversity. Despite this rich source of information, we do not yet know much about which sediments favour preservation and why. Here we used atomic force microscopy and molecular dynamics simulations to explore the DNA-mineral binding in...

We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterize the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liq...