ZooMS confirms geometric morphometrics species identification of ancient sheep and goat.

Geometric morphometrics can effectively distinguish isolated third lower molars of present-day sheep and goat, but its applicability to archaeological specimens has yet to be established. Using a modern reference collection of 743 sheep and goats and a two-dimensional landmark-based geometric morphometric (GMM) protocol, this study aimed to morphometrically identify 109 archaeological specimens, used as case studies, dating from the Late Neolithic to the modern period/era. These morphometric identifications were then compared to molecular identifications via collagen peptide mass fingerprinting, known as Zooarcheology by Mass Spectrometry (ZooMS). ZooMS confirmed the morphometric identifications for 104 specimens, with the five misidentified specimens all morphometrically identified as goat. Modern sheep and goats have larger teeth and distinct shapes compared to their archaeological counterparts, suggesting strong differences between archaeological and modern specimens potentially linked with recent breed improvement or geographical origin of the specimens. In addition, for both species, some of the archaeological dental morphologies do not match with any of our modern references. This study validates the applicability of geometric morphometrics for identifying isolated archaeological sheep and goat teeth. It represents a stepping stone for future, non-destructive, bioarchaeological studies of the two species.

Barley systematics and taxonomy foreseen by seed morphometric variation.

Since its Neolithic domestication in the Fertile Crescent, barley has spread to all continents and represents a major cereal in many modern agrarian systems. Current barley diversity includes thousands of varieties divided into four main categories corresponding to 2-row and 6-row subspecies and naked and hulled types, each of them with winter and spring varieties. This diversity is associated to different uses and allow cultivation in diverse environments. We used a large dataset of 58 varieties of French origin, (1) to assess the taxonomic signal in barley grain measurements comparing 2-row and 6-row subspecies, and naked and hulled types; (2) to test the impact of the sowing period and interannual variation on the grains size and shape; (3) to investigate the existence of morphological differences between winter and spring types; and finally (4) to contrast the relationship between the morphometric and genetic proximity. Size and shape of 1980 modern barley caryopses were quantified through elliptic Fourier Transforms and traditional size measurements. Our results indicate that barley grains record morphological diversity of the ear (89.3% classification accuracy between 2-row/6-row subspecies; 85.2% between hulled and naked type), sowing time of the grains (from 65.6% to 73.3% within barley groups), and environmental conditions during its cultivation and varietal diversity. This study opens perspectives for studying archaeological barley seeds and tracing the barley diversity and evolution since the Neolithic.

Morphometrics of waterlogged archaeological seeds give new insights into the domestication and spread of Papaver somniferum L. in Western Europe.

Domesticated opium poppy Papaver somniferum L. subsp. somniferum probably originated in the Western Mediterranean from its possible wild progenitor, Papaver somniferum L. subsp. setigerum and spread to other European regions. Seeds of opium poppy have been identified in different European regions since the Early Neolithic (from the 6th millennium cal. BC onwards) period. However, until recently, the absence of morphological identification criteria has prevented the discrimination between wild and domestic morphotypes. New morphometric approaches to distinguish modern subspecies have been proven to be applicable to waterlogged archaeological remains, opening the possibility of understanding the process of domestication of the plant in both time and space. This paper applies seed outline analyses, namely elliptic Fourier transforms, combined with size and number of cells to archaeological waterlogged Papaver seeds throughout the Neolithic period in the NW Mediterranean and the surroundings of the Alps. Furthermore, one example from the Late Bronze Age (LBA) was added to see what kind of differences appeared during the >1000 years between the end of the Neolithic and the LBA. The aim of the study is to classify the archaeological seeds as domestic or wild morphotypes and observe morphometric changes in connection to geographical and chronological patterns that can explain the spread and domestication process(es) of this important crop. A total of 295 archaeological seeds coming from 10 waterlogged sites dating between 5300-2300 cal. BC (Neolithic), and one LBA site dating to 1070 cal. BC were analysed. The results indicate the presence of seeds, similar to the wild morphotype, in the Mediterranean sites and larger seeds, similar to the domestic morphotype, in the regions surrounding the Alps. The number of cells mainly increased during the Late Neolithic (3300 to 2300 cal. BC) and, finally, in the Late Bronze Age (ca. 1050-800 cal. BC), larger, morphologically domesticated seeds are clearly predominant. A change in the shape of the seeds is only clearly visible in the LBA material. Altogether our results suggest that opium poppy seeds show no sign of domestication in the early periods of the Neolithic, despite the fact that the plant was very probably already cultivated at that time in the western Mediterranean region.

Size and shape of the semicircular canal of the inner ear: A new marker of pig domestication?

Domestication has led to many changes in domestic animal biology, including their anatomy. The shape of the inner ear, part of the mammalian ear, has been found particularly relevant for discriminating domesticated species, their hybrids or differentiating the wild and domestic populations of a single species. Here we assessed the use of the size and shape of the semicircular canals (SCC) of the inner ear as a marker of pig domestication. We studied a total of 63 petrosal bones belonging to wild boar (Sus scrofa, two populations) and domestic pigs (extensively and intensively reared specimens) that were µCT-scanned and from which the size and the shape of the inner ear were quantified through geometric morphometrics, analyzing the 3D coordinates of 6 landmarks and 60 sliding semilandmarks localized on the SCC and the common crus. The domestic pigs have larger SCC than the wild boar from which they also strongly differ in shape (correct cross validation of 95.5%, confidence interval: 92.3%-98.1%). Strong shape differences were detected between the two populations of wild boar, as well as a sexual size dimorphism. All together the results highlight the taxonomic discriminant power of the SCC of the inner ear shape, and its relevance for domestication studies.

Pip shape echoes grapevine domestication history.

The pip, as the most common grapevine archaeological remain, is extensively used to document past viticulture dynamics. This paper uses state of the art morphological analyses to analyse the largest reference collection of modern pips to date, representative of the present-day diversity of the domesticated grapevine from Western Eurasia. We tested for a costructure between the form of the modern pips and the: destination use (table/wine), geographical origins, and populational labels obtained through two molecular approaches. Significant structuring is demonstrated for each of these cofactors and for the first time it is possible to infer properties of varieties without going through the parallel with modern varieties. These results provide a unique tool that can be applied to archaeological pips in order to reconstruct the spatio-temporal dynamics of grape diversity on a large scale and to better understand viticulture history. The models obtained were then used to infer the affiliations with archaeobotanical remains recovered in Mas de Vignoles XIV (Nîmes, France). The results show a twofold shift between the Late Iron Age and the Middle Ages, from table to wine grape varieties and from eastern to western origins which correlates with previous palaeogenomic results.

Bones geometric morphometrics illustrate 10th millennium cal. BP domestication of autochthonous Cypriot wild boar (Sus scrofa circeus nov. ssp).

Epipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild descendants of these boars. However, the geographic origin of the Cypriot boar and how they were integrated into the earliest forms of pig husbandry remain unsolved. Here, we present data on 11,000 to 9000 cal. BP Sus scrofa from the PPN sites of Klimonas and Shillourokambos. We compared them to contemporaneous populations from the Near East and to Neolithic and modern populations in Corsica, exploring their origin and evolution using biosystematic signals from molar teeth and heel bones (calcanei), using 2D and 3D geometric morphometrics. We found that the Cypriot PPN lineage of Sus scrofa originates from the Northern Levant. Yet, their phenotypic idiosyncrasy suggest that they evolved into an insular sub-species that we named Sus scrofa circeus, referring to Circe, the metamorphosis goddess that changed Ulysses companions into pigs. The phenotypic homogeneity among PPNA Klimonas wild boars and managed populations of PPNB Shillourokambos suggests that local domestication has been undertaken on the endemic S. s. circeus, strengthening the idea that Cyprus was integrated into the core region of animal domestication.

A morphometric approach to track opium poppy domestication.

Opium poppy (Papaver somniferum L. subsp. somniferum) was likely domesticated in the Western Mediterranean, where its putative wild ancestor is indigenous, and then spread to central and northern Europe. While opium poppy seeds are regularly identified in archaeobotanical studies, the absence of morphological criteria to distinguish the seeds of wild and domestic forms prevents the documentation of their respective historical and geographical occurrences and of the process of opium domestication as a whole. To fill this gap and better understand the status of this crop in the Neolithic, we combined seed outline analyses, namely elliptic Fourier transforms, with other morphometric descriptors to describe and identify Papaver setigerum, Papaver somniferum and other Papaver taxa. The combination of all measured parameters gives the most precise predictions for the identification of all seven taxa. We finally provide a case study on a Neolithic assemblage from a pile-dwelling site in Switzerland (Zurich-Parkhaus Opéra, ca. 3170 BC). Our results indicate the presence of mixed populations of domestic and wild seeds belonging to the P. somniferum group, suggesting that the plant was already in the process of domestication at the end of 4th millennium BC. Altogether, these results pave the way to understand the geography and history of the poppy domestication and its spread into Europe.

Dire wolves were the last of an ancient New World canid lineage.

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 results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

Optimizing digitalization effort in morphometrics.

Quantifying phenotypes is a common practice for addressing questions regarding morphological variation. The time dedicated to data acquisition can vary greatly depending on methods and on the required quantity of information. Optimizing digitization effort can be done either by pooling datasets among users, by automatizing data collection, or by reducing the number of measurements. Pooling datasets among users is not without risk since potential errors arising from multiple operators in data acquisition prevent combining morphometric datasets. We present an analytical workflow to estimate within and among operator biases and to assess whether morphometric datasets can be pooled. We show that pooling and sharing data requires careful examination of the errors occurring during data acquisition, that the choice of morphometric approach influences amount of error, and that in some cases pooling data should be avoided. The demonstration is based on a worked example (Sus scrofa teeth) using a combinations of 18 morphometric approaches and datasets for which we identified and quantified several potential sources of errors in the workflow. We show that it is possible to estimate the analytical power of a study using a small subset of data to select the best morphometric protocol and to optimize the number of variables necessary for analysis. In particular, we focus on semi-landmarks, which often produce an inflation of variables in contrast to the number of available observations use in statistical testing. We show how the workflow can be used for optimizing digitization efforts and provide recommendations for best practices in error management.

Eco-evo-devo implications and archaeobiological perspectives of trait covariance in fruits of wild and domesticated grapevines.

The phenotypic changes that occurred during the domestication and diversification of grapevine are well known, particularly changes in seed morphology, but the functional causes and consequences behind these variations are poorly understood. Wild and domesticate grapes differ, among others, in the form of their pips: wild grapes produce roundish pips with short stalks and cultivated varieties have more elongated pips with longer stalks. Such variations of form are of first importance for archaeobotany since the pip form is, most often, the only remaining information in archaeological settings. This study aims to enlighten archaeobotanical record and grapevine pip development by better understanding how size and shape (co)variates between pip and berry in both wild and domesticated Vitis vinifera. The covariation of berry size, number of seeds per berry ("piposity"), pip size and pip shape were explored on 49 grapevine accessions sampled among Euro-Mediterranean traditional cultivars and wild grapevines. We show that for wild grapevine, the higher the piposity, the bigger the berry and the more elongated the pip. For both wild and domesticated grapevine, the longer is the pip, the more it has a "domesticated" shape. Consequences for archaeobotanical studies are tested and discussed, and these covariations allowed the inference of berry dimensions from archaeological pips from a Southern France Roman site. This systematic exploration sheds light on new aspects of pip-berry relationship, in both size and shape, on grapevine eco-evo-devo changes during domestication, and invites to explore further the functional ecology of grapevine pip and berry and notably the impact of cultivation practices and human selection on grapevine morphology.

3D Geometric Morphometrics Reveals Convergent Character Displacement in the Central European Contact Zone between Two Species of Hedgehogs (Genus Erinaceus).

Hedgehogs, as medium-sized plantigrade insectivores with low basal metabolic rates and related defensive anti-predator strategies, are quite sensitive to temperature and ecosystem productivity. Their ranges therefore changed dramatically due to Pleistocene climate oscillations, resulting in allopatric speciation and the subsequent formation of secondary contact zones. Such interactions between closely related species are known to generate strong evolutionary forces responsible for niche differentiation. In this connection, here, we detail the results of research on the phenotypic evolution in the two species of hedgehog present in central Europe, as based on genetics and geometric morphometrics in samples along a longitudinal transect that includes the contact zone between the species. While in allopatry, Erinaceus europaeus is found to have a larger skull than E. roumanicus and distinct cranial and mandibular shapes; the members of the two species in sympatry are smaller and more similar to each other, with a convergent shape of the mandible. The relevant data fail to reveal any major role for either hybridisation or clinal variation. We, therefore, hypothesise that competitive pressure exerted on the studied species does not generate divergent selection sufficient for divergent character displacement to evolve, instead giving rise to convergent selection in the face of resource limitation in the direction of smaller skull size. Considering the multi-factorial constraints present in the relevant adaptive landscape, reduction in size could also be facilitated by predator pressure in ecosystems characterised by mesopredator release and other anthropogenic factors. As the function of the animals' lower jaw is mainly connected with feeding (in contrast to the cranium whose functions are obviously more complex), we interpret the similarity in shape as reflecting local adaptations to overlapping dietary resources in the two species and hence as convergent character displacement.

The intraspecific diversity of tooth morphology in the large-spotted catshark Scyliorhinus stellaris: insights into the ontogenetic cues driving sexual dimorphism.

Teeth in sharks are shed and replaced throughout their lifetime. Morphological dental changes through ontogeny have been identified in several species and have been correlated with shifts in diet and the acquisition of sexual maturity. However, these changes were rarely quantified in detail along multiple ontogenetic stages, which makes it difficult to infer the developmental processes responsible for the observed plasticity. In this work, we use micro-computed tomography and 3D geometric morphometrics to describe and analyze the tooth size and shape diversity across three ontogenetic stages (hatchling, juvenile, and sexually mature) in the large-spotted catshark Scyliorhinus stellaris (Linnaeus, 1758). We first describe the intra-individual variation of tooth form for each sex at each ontogenetic stage. We provide a tooth morphospace for palatoquadrate and Meckelian teeth and identify dental features, such as relative size and number of cusps, involved in the range of variation of the observed morphologies. We then use these shape data to draw developmental trajectories between ontogenetic stages and for each tooth position within the jaw to characterize ontogenetic patterns of sexual dimorphism. We highlight the emergence of gynandric heterodonty between the juvenile and mature ontogenetic stages, with mature females having tooth morphologies more similar to juveniles' than mature males that display regression in the number of accessory cusps. From these data, we speculate on the developmental processes that could account for such developmental plasticity in S. stellaris.

Exploring Rattus praetor (Rodentia, Muridae) as a possible species complex using geometric morphometrics on dental morphology.

Taxonomic uncertainties in the Rattus genus persist due to among-species morphological conservatism coupled with within-species environmental variation in morphology. As a result, this genus contains a number of possible cryptic species. One important example can be found in R. praetor, where morphological studies indicate it is a possible species complex. Genetic studies of R. praetor (limited to analysis of mitochondrial DNA) have been inconclusive, but do indicate such subdivision. Here we use geometric morphometrics to explore this possible species complex by analysing the dental traits of 48 specimens from New Guinea and neighbouring regions. We find separate molar morphologies for Bougainsville Island, central New Guinea and west New Guinea which cannot be easily explained by different environmental factors (climate, precipitation and altitude), strongly suggesting the existence of a number of evolutionarily distinct taxa within what is currently called R. praetor thus supporting previous suggestions that R. praetor is a species complex. Our findings demonstrate the potential of advanced morphological analyses in identifying separate species, contrary to the claims of morphological conservatism. Future analyses should combine geometric morphometrics with genetic analyses over the species range and include sub-fossil specimens from the Bismarck archipelago and Solomon Islands to resolve the evolutionary history of R. praetor.

Shape variation and modularity of skull and teeth in domesticated horses and wild equids.

BACKGROUND: In horses, the morphological changes induced by the process of domestication are reportedly less pronounced than in other species, such as dogs or pigs - although the horses' disparity has rarely been empirically tested. We investigated shape differences and modularity of domesticated horses, Przewalski's horses, donkeys and zebras. Mandibular and tooth shape have been shown to be valuable features for differentiating wild and domesticated forms in some mammals. RESULTS: Both mandible and teeth, show a pattern of shape space occupation analogous to that of the cranium, with domesticated horses occupying a similar extension in shape space to that of wild equids. Only cranial shape data exhibit a tendency to separate domesticated horses and Przewalski's horses from donkeys and zebras. Maximum likelihood model-based tests confirm the horse cranium is composed of six developmental modules, as reported for placental mammals in general. The magnitude of integration in domesticated horse skull was lower than in wild equids across all six cranial modules, and lower values of integration were associated with higher disparity values across all modules. CONCLUSION: This is the first study that combines different skeletal features for the description and comparison of shape changes in all living equid groups using geometric morphometrics. We support Darwin's hypothesis that the shape variation in the skull of domesticated horses is similar to the shape variation of all wild equid species existing today. Lower magnitudes of module integration are recovered in domesticated horses compared to their wild relatives.

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events.

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

Neomorphosis and heterochrony of skull shape in dog domestication.

The overall similarity of the skull shape of some dog breeds with that of juvenile wolves begs the question if and how ontogenetic changes such as paedomorphosis (evolutionary juvenilisation) played a role in domestication. Here we test for changes in patterns of development and growth during dog domestication. We present the first geometric morphometric study using ontogenetic series of dog and wolf crania, and samples of dogs with relatively ancestral morphology and from different time periods. We show that patterns of juvenile-to-adult morphological change are largely similar in wolves and domestic dogs, but differ in two ways. First, dog skulls show unique (neomorphic) features already shortly after birth, and these features persist throughout postnatal ontogeny. Second, at any given age, juvenile dogs exhibit skull shapes that resemble those of consistently younger wolves, even in dog breeds that do not exhibit a 'juvenilized' morphology as adults. These patterns exemplify the complex nature of evolutionary changes during dog domestication: the cranial morphology of adult dogs cannot simply be explained as either neomorphic or paedomorphic. The key to our understanding of dog domestication may lie in a closer comparative examination of developmental phases.

A test for paedomorphism in domestic pig cranial morphology.

Domestic animals are often described as paedomorphic, meaning that they retain juvenile characteristics into adulthood. Through a three-dimensional landmark-based geometric morphometric analysis of cranial morphology at three growth stages, we demonstrate that wild boar (n = 138) and domestic pigs (n = 106) (Sus scrofa) follow distinct ontogenetic trajectories. With the exception of the size ratio between facial and neurocranial regions, paedomorphism does not appear to be the primary pattern describing the observed differences between wild and domestic pig cranial morphologies. The cranial phenotype of domestic pigs instead involves developmental innovation during domestication. This result questions the long-standing assumption that domestic animal phenotypes are paedomorphic forms of their wild counterparts.

Earliest "Domestic" Cats in China Identified as Leopard Cat (Prionailurus bengalensis).

The ancestor of all modern domestic cats is the wildcat, Felis silvestris lybica, with archaeological evidence indicating it was domesticated as early as 10,000 years ago in South-West Asia. A recent study, however, claims that cat domestication also occurred in China some 5,000 years ago and involved the same wildcat ancestor (F. silvestris). The application of geometric morphometric analyses to ancient small felid bones from China dating between 5,500 to 4,900 BP, instead reveal these and other remains to be that of the leopard cat (Prionailurus bengalensis). These data clearly indicate that the origins of a human-cat 'domestic' relationship in Neolithic China began independently from South-West Asia and involved a different wild felid species altogether. The leopard cat's 'domestic' status, however, appears to have been short-lived--its apparent subsequent replacement shown by the fact that today all domestic cats in China are genetically related to F. silvestris.