Christiane Denys

Comparative phylogeography of two sibling species of forest‐dwelling rodent (Praomys rostratus and P. tullbergi) in West Africa: different reactions to past forest fragmentation

Two sibling species of the rodent genus Praomys occur in West African forests: P. tullbergi and P. rostratus. By sampling across their geographical ranges (459 individuals from 77 localities), we test the hypothesis that climatic oscillations during the Quaternary made an impact on the observed pattern of cytochrome b sequence variation. We show that, although these two species have parapatric geographical distributions, their phylogeographical histories are dissimilar, which could be related to their distinct ecological requirements. Since the arid phases of the Pleistocene were characterized by isolated forest patches, and intervening wetter periods by forest expansion, these changes in forest cover may be the common mechanism responsible for the observed phylogeographical patterns in both of these species. For example, in both species, most clades had either allopatric or parapatric geographical distributions; however, genetic diversity was much lower in P. tullbergi than in P. rostratus. The genetic pattern of P. tullbergi fits the refuge hypothesis, indicating that a very small number of populations survived in distinct forest blocks during the arid phases, then expanded again with forest recovery. In contrast, a number of populations of P. rostratus appear to have survived during the dry periods in more fragmented forest habitats, with varying levels of gene flow between these patches depending on climatic conditions and forest extent. In addition, historical variations of the West African hydrographic network could also have contributed to the pattern of genetic differentiation observed in both species.

Host evolution in Mastomys natalensis (Rodentia: Muridae): an integrative approach using geometric morphometrics and genetics

The commensal rodent Mastomys natalensis is the natural reservoir of Lassa arenavirus (LASV), which causes hemorrhagic fever in West Africa. To study a possible effect of the virus on phenotypic and genotypic variation of its persistently infected host, we compared LASV-positive and non-infected wild-caught M. natalensis. The LASV effects on the phenotypic variation were explored using standard external morphometric measurements, geometric morphometric analyses of the cranial size and shape, and brain case volume. The genetic variability of M. natalensis specimens was assessed using 9 polymorphic microsatellite markers. Independent of sex and age, LASV-infected animals had smaller external body measurements, reproductive organs, skull size and brain case volume. Cranial shape differences between the 2 groups are represented by a lateral constriction of the entire skull. The genetic variability revealed consanguinity only among the LASV-positive rodents. We hypothesize that growth impairment may result in a selective disadvantage for LASV-infected M. natalensis, leading to a preferably commensal lifestyle in areas where the LAVS is endemic and, thereby, increasing the risk of LASV transmission to humans.

Identifying predation on rodent teeth through structure and composition: A case from Morocco.

Predation by nocturnal birds of prey is one of the most frequent modes leading to the concentration of rodents in fossil assemblages. This mode of accumulation leaves characteristic surface alterations on bones and teeth. In order to evaluate and characterize the effects of these pre-diagenesis alterations on rodent fossil samples, we have carried out microstructural and chemical analyses on incisors collected from present day Moroccan wild animals and owl pellets. The microstructure of both dentine and enamel was well preserved, but chemical changes were evident in pellet samples and depended on the particular tissue and the nature of the predator. The comparison of compositional data obtained from electron microprobe chemical analyses and infrared spectrometry has allowed us to assign a possible predator to an incisor extracted from a pellet of an unknown origin. This method has further implications for the understanding of taphonomy and palaeoecology of archaeological and fossil sites.

Flightless scaly-tailed squirrels never learned how to fly: A reappraisal of Anomaluridae phylogeny

Anomaluroidea, commonly known as the “scaly‐tailed squirrels,” are an emblematic group of tropical African mammals that includes gliding forms. The family Anomaluridae was until recently represented by three genera: the flying scaly‐tailed squirrels (Anomalurus), the flying mouse (Idiurus) and the flightless scaly‐tailed squirrels (Zenkerella). Idiurus and Zenkerella have long been grouped into the Zenkerellinae subfamily, and Zenkerella was interpreted as a rare case of evolutionary reversal to non‐gliding lifestyle. Recent studies have demonstrated that Zenkerella is sister to all other modern anomalurids, and represents in fact the monogeneric family Zenkerellidae. The Anomalurus genus was split into Anomalurus and Anomalurops, but no study has ever considered all Anomalurus species together in a phylogeny to test the status of Anomalurops. Here, we used mitogenomic next‐generation sequencing to infer the phylogenetic relationships among all extant anomalurids and to estimate their divergence ages. We found that the arboreal Zenkerella is the sister group of all extant gliding anomalurids (Idiurus and Anomalurus). We confirmed that Anomaluroidea only evolved the gliding adaptation once. A comparison based on morphological traits indicates that Zenkerella harbours several unique morphological features. We propose new morphological characters for the novel classification of modern Anomaluroidea, which includes the families Zenkerellidae and Anomaluridae. Using different calibration schemes, we demonstrated that classical dating methods relying only on mitogenomes provide rather young Miocene estimates between Zenkerellidae and the Anomaluridae. The use of published nuclear genes, internal calibrations and tip dating converged towards an Eocene split between gliding and non‐gliding scaly‐tailed squirrels, which is in agreement with the African fossil record. Finally, we provide the first exhaustive species‐level molecular phylogenetic inference for the genus Anomalurus. We found that Anomalurus beecrofti is the sister group of all other species of Anomalurus and branched off during the Miocene.

What is taphonomy and What is not

Efremov’s original definition (1940, p. 85) – ‘the study of the transition (in all its details) of animal remains from the biosphere into the lithosphere’ – set the boundaries of Taphonomy at natural processes affecting remains between death and preservation in the rock record. Since its origins, the field of taphonomy has expanded to include all types of organic remains and traces, changes that occur after burial (diagenesis) and during exposure on outcrop surfaces, and even changes caused by collecting, museum storage, preparation and analysis (e.g. Fernandez-Jalvo and Marin-Monfort 2008). For some researchers, taphonomy covers the transition of organic remains from biosphere to lithosphere to laboratory, ending only when the taphonomic data and analyses appear in the printed pages of a scientific journal. In archeology, taphonomy also includes cultural artifacts and the changes that affect them during accumulation and burial (‘site formation processes’) (e.g. Lyman 2010; Dominguez-Rodrigo et al. 2011; Denys and Patou-Mathis 2014; Brugal 2017). An even broader viewpoint could extend taphonomy to the study of all types of changes in dead biological AND physical materials over time – transformations in biomolecules, iron particles, building materials, fermented food and drink, human garbage – both in the past and into the future. Since the time of Efremov, taphonomy’s conceptual territory has expanded in two directions, one extending the sequence of processes affecting individual specimens, the other encompassing many more kinds of materials and objects than originally specified. If Taphonomy is so broadly defined, does this dilute its original and important focus on processes and biases that affect organic remains and traces between death and preservation in the lithosphere? Should we propose a new term for the degradation and preservation of cultural materials that are not strictly ‘biological?’ Where should we draw the line between what is, and is not, ‘Taphonomy?’ On one side of this debate is the important concept of natural change over time, which taphonomy has championed since its beginning. Understanding that dead remains have an active ‘life after death’ that affects information preserved in the fossil record was one of Efremov’s most important contributions. Extending this idea to all types of non-living materials, organic or inorganic, makes sense from a conceptual standpoint. It also focuses attention on the fact that virtually everything on Earth’s surface is changing. The same processes that control what becomes a fossil, such as animal activity, climate, water flow and sedimentation, also affect non-biological materials. Everything ‘dead’ around us is subject to alteration over time. Is it useful to extend the meaning of taphonomy to include all biological, physical, and chemical processes that interact with non-living substances? On the other side of the argument is a more pragmatic and empirical approach to ‘What is Taphonomy?’ Taphonomy as a field of science consists of the sum of investigations that have expanded understanding of the ‘biosphere to lithosphere’ transition for all types of organic remains. There is now a huge body of published and unpublished research across the globe, representing marine and terrestrial environments from the beginning of life to the present day. The papers in this special issue of Historical Biology represent the most recent part of the geological time column, with a wide range of innovative taphonomic research on archeological sites, faunal accumulations, and biological processes in Europe, Africa, and South America. Many of these papers focus on evidence that helps us distinguish non-human from human processes of bone accumulation and modification. It is clear from this research and other presentations at the 2016 ICAZ Taphonomy Working Group meeting that archeo-biological taphonomy is in a growth phase, inspiring new insights and methods for understanding the past, especially the human past. Those who see taphonomy as a field of study that is key to understanding preservation and bias in paleontology and archeology have a solid foundation of evidence and interpretations to answer the question, ‘What is Taphonomy?’ Another view of ‘What is Taphonomy?’ involves bias in the fossil record. Many workers think of taphonomy as the study of bias, a scientific investigation of the long-standing realization that the fossil record is an ‘unfaithful’ recorder of life and death in the past. In latter part of the twentieth century, understanding and correcting for taphonomic biases was regarded as a necessary but rather negative (‘wet-blanket’) issue in paleontology, particularly as the field expanded into the realms of big databases and macro-evolutionary analyses. More recently, there has been a shift to ‘positive’ taphonomy, in which the study of live-dead bias reveals important ecological changes relating

General to specific Quaternary taphonomy

At the transition between the biosphere and the Lithosphere, Taphonomy is an essential discipline of Historical Biology. Knowing the origins and formation mechanisms of paleontological and archaeological sites constitutes one of the first tasks of Taphonomy, but it also aim to illuminate paleoecological implications of a better understanding of bone diagenesis, taphonomic agents. Because many taphonomic studies have been devoted to Quaternary sites and also because of important recent developments in Zooarcheology, we felt it was time to organize a conference around the following theme: ‘General to Specific Quaternary Taphonomy’. The 4th Meeting of the ICAZ Taphonomy Working Group addressed this topic and we present some of the representative contributions. The Meeting was hold in Paris from 7 to 10th September 2016, thanks to the supports of Aix-Marseille University, CNRS-INEE, MNHN Paris, the GDR 3591 ‘Taphonomie, Environnement & Archéologie’, (TaphEnA) (http://lampea.cnrs.fr/spip.php?article3149). More specifically among the most recent developments of Quaternary taphonomy we focused upon three interrelated themes. The first was devoted to new Methodological developments in Taphonomy. This session, regarding all animal and cultural groups, envisions modern analogs/proxies as well as interactions involved in sediment-fossil accumulations. This allowed A.B. Marín-Arroyo & D. Ocio to propose a new Bayesian method to analyze the faunal skeletal profiles from archaeological assemblages and improve the determination of the agents of bone accumulations. Similarly J.M. Geiling et al. highlighted the importance of taking into account the spatial distribution of bone micro-fragments and their taphonomic features in the analyses of past hunters lifestyle and uses of hunted prey. M.J. Gabucio et al. highlighted the importance of taking into account bone refits to better understand the settlement dynamics and intra-site behavior of humans groups of the past. Not only new methods but also new experiments were proposed. An original experimental study by E. Turner et al. allowed interpretation of the origins of bone staining in waterlogged deposits and showed how this could be applied to the lower Paleolithic site of Schöningen 13II-4 (Germany). The second theme concerned distinguishing Human and Animal Predation, which is a major issue in Quaternary period. All kind of predation process, in the past and/or modern environments were proposed among which the importance of Carnivore taphonomy in South America was synthetized by M. Mondini while other contributions were devoted more specifically either to human activities on different types of prey and how to distinguish this from other predators. This approach was applied to an Upper Paleolithic site of South Catalonia by A. Rufa et al. Another Upper Pleistocene site near Barcelona has yielded many coprolites that were integrated by Montserrat M. Sanz & J. Daura to an archeozoological and taphonomical study, providing a comprehensive view of human/carnivores interactions during that time. Also on Iberian Pleistocene sites, V. Sauqué et al. propose that leopards (Panthera pardus) played a very important role as bone accumulators of these sites. Besides human activity and large carnivore accumulations, avian predation also plays an important role in concentrating bones. L. Lloveras et al. showed the characteristics of the taphonomic signature by the Golden Eagle (Aquila chrysaetos) as an important agent of concentration while Z.M. Bochenski et al. monitored bird-carcass accumulations in South Poland and found traces of different avian predators. The third focal theme was Taphonomy and Paleoenvironments, a session dealing with fundamental or applied studies in relation with the concepts of ecology, from metacommunities, communities, populations with evidence of competition, multi-site analysis, considered in terms of possible taphonomic signatures that can be applied over long periods of time or across long distances. Such a community approach was proposed by C. Denys et al. for a neo-taphonomic assemblage of small mammals from Morocco and applied to Plio-Pleistocene sites of El Harhoura II in Morocco. The multitaxonomic taphonomic study contributes more paleoecological information than a taxon-centered study. M.D. Pesquero et al. investigated experimentally the microbial activity and microstructural changes on bones in different environments.

Out of Africa: demographic and colonization history of the Algerian mouse ( Mus spretus Lataste)

North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lataste) is an endemic species from this basin, with its distribution restricted to North Africa (from Libya to Morocco), Iberian Peninsula and South of France. A rich paleontological record of M. spretus exists in North Africa, suggesting hypotheses concerning colonization pathways, and the demographic and morphologic history of this species. Here we combined genetic (3 mitochondrial DNA loci and 18 microsatellites) and climatic niche modeling data to infer the evolutionary history of the Algerian mouse. We collected 646 new individuals in 51 localities. Our results are consistent with an anthropogenic translocation of the Algerian mouse from North Africa to the Iberian Peninsula via Neolithic navigators, probably from the Tingitane Peninsula. Once arrived in Spain, suitable climatic conditions would then have favored the dispersion of the Algerian mice to France. The morphological differentiation observed between Spanish, French and North African populations could be explained by a founder effect and possibly local adaptation. This article helps to better understand the role of climate versus human-mediated changes on the evolutionary history of mammal species in the Mediterranean Basin.