Publications by authors named "Christiane Denys"

29 Publications

  • Page 1 of 1

Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini).

Mol Phylogenet Evol 2021 04 6;157:107069. Epub 2021 Jan 6.

Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic. Electronic address:

The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.
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http://dx.doi.org/10.1016/j.ympev.2021.107069DOI Listing
April 2021

Multilocus phylogeny of African striped grass mice (Lemniscomys): Stripe pattern only partly reflects evolutionary relationships.

Mol Phylogenet Evol 2021 02 5;155:107007. Epub 2020 Nov 5.

Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic. Electronic address:

Murine rodents are one of the most evolutionary successful groups of extant mammals. They are also important for human as vectors and reservoirs of zoonoses and agricultural pests. Unfortunately, their fast and relatively recent diversification impedes our understanding of phylogenetic relationships and species limits of many murine taxa, including those with very conspicuous phenotype that has been frequently used for taxonomic purposes. One of such groups are the striped grass mice (genus Lemniscomys), distributed across sub-Saharan Africa in 11 currently recognized species. These are traditionally classified into three morphological groups according to different pelage colouration on the back: (a) L. barbarus group (three species) with several continuous pale longitudinal stripes; (b) L. striatus group (four species) with pale stripes diffused into short lines or dots; and (c) L. griselda group (four species) with a single mid-dorsal black stripe. Here we reconstructed the most comprehensive molecular phylogeny of the genus Lemniscomys to date, using the largest currently available multi-locus genetic dataset of all but two species. The results show four main lineages (=species complexes) with the distribution corresponding to the major biogeographical regions of Africa. Surprisingly, the four phylogenetic lineages are only in partial agreement with the morphological classification, suggesting that the single-stripe and/or multi-striped phenotypes evolved independently in multiple lineages. Divergence dating showed the split of Lemniscomys and Arvicanthis genera at the beginning of Pleistocene; most of subsequent speciation processes within Lemniscomys were affected by Pleistocene climate oscillations, with predominantly allopatric diversification in fragmented savanna biome. We propose taxonomic suggestions and directions for future research of this striking group of African rodents.
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http://dx.doi.org/10.1016/j.ympev.2020.107007DOI Listing
February 2021

Life history and habitat do not mediate temporal changes in body size due to climate warming in rodents.

PeerJ 2020 24;8:e9792. Epub 2020 Sep 24.

South African Research Chair in Biodiversity Value and Change and Centre for Invasion Biology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, Limpopo, South Africa.

Temporal changes in body size have been documented in a number of vertebrate species, with different contested drivers being suggested to explain these changes. Among these are climate warming, resource availability, competition, predation risk, human population density, island effects and others. Both life history traits (intrinsic factors such as lifespan and reproductive rate) and habitat (extrinsic factors such as vegetation type, latitude and elevation) are expected to mediate the existence of a significant temporal response of body size to climate warming but neither have been widely investigated. Using examples of rodents, we predicted that both life history traits and habitat might explain the probability of temporal response using two tests of this hypothesis. Firstly, taking advantage of new data from museum collections spanning the last 106 years, we investigated geographical and temporal variation in cranial size (a proxy for body size) in six African rodent species of two murid subfamilies (Murinae and Gerbillinae) of varying life history, degree of commensality, range size, and habitat. Two species, the commensal and the non-commensal showed significant temporal changes in body size, with the former increasing and the latter decreasing, in relation with climate warming. Commensalism could explain the increase in size with time due to steadily increasing food availability through increased agricultural production. Apart from this, we found no general life history or habitat predictors of a temporal response in African rodents. Secondly, in order to further test this hypothesis, we incorporated our data into a meta-analysis based on published literature on temporal responses in rodents, resulting in a combined dataset for 50 species from seven families worldwide; among these, 29 species showed no significant change, eight showed a significant increase in size, and 13 showed a decline in size. Using a binomial logistic regression model for these metadata, we found that none of our chosen life history or habitat predictors could significantly explain the probability of a temporal response to climate warming, reinforcing our conclusion based on the more detailed data from the six African species.
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http://dx.doi.org/10.7717/peerj.9792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520088PMC
September 2020

Tracking the Near Eastern origins and European dispersal of the western house mouse.

Sci Rep 2020 05 19;10(1):8276. Epub 2020 May 19.

Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France.

The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks - 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe - which in turn may have driven the first human mediated dispersal of cats in Europe.
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http://dx.doi.org/10.1038/s41598-020-64939-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237409PMC
May 2020

Dating the skull from Broken Hill, Zambia, and its position in human evolution.

Nature 2020 04 1;580(7803):372-375. Epub 2020 Apr 1.

CHER, Department of Earth Sciences, Natural History Museum, London, UK.

The cranium from Broken Hill (Kabwe) was recovered from cave deposits in 1921, during metal ore mining in what is now Zambia. It is one of the best-preserved skulls of a fossil hominin, and was initially designated as the type specimen of Homo rhodesiensis, but recently it has often been included in the taxon Homo heidelbergensis. However, the original site has since been completely quarried away, and-although the cranium is often estimated to be around 500 thousand years old-its unsystematic recovery impedes its accurate dating and placement in human evolution. Here we carried out analyses directly on the skull and found a best age estimate of 299 ± 25 thousand years (mean ± 2σ). The result suggests that later Middle Pleistocene Africa contained multiple contemporaneous hominin lineages (that is, Homo sapiens, H. heidelbergensis/H. rhodesiensis and Homo naledi), similar to Eurasia, where Homo neanderthalensis, the Denisovans, Homo floresiensis, Homo luzonensis and perhaps also Homo heidelbergensis and Homo erectus were found contemporaneously. The age estimate also raises further questions about the mode of evolution of H. sapiens in Africa and whether H. heidelbergensis/H. rhodesiensis was a direct ancestor of our species.
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http://dx.doi.org/10.1038/s41586-020-2165-4DOI Listing
April 2020

The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity.

Mol Phylogenet Evol 2020 03 6;144:106703. Epub 2019 Dec 6.

College of Arts & Sciences, Roosevelt University, 430 S Michigan, Chicago, IL 60605, USA.

Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.
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http://dx.doi.org/10.1016/j.ympev.2019.106703DOI Listing
March 2020

Associated tympanic bullar and cochlear hypertrophy define adaptations to true deserts in African gerbils and laminate-toothed rats (Muridae: Gerbillinae and Murinae).

J Anat 2019 02 25;234(2):179-192. Epub 2018 Nov 25.

South African Research Chair in Biodiversity and Change and Centre for Invasion Biology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa.

Hearing capabilities in desert rodents such as gerbils and heteromyids have been inferred from both anatomical and ecological aspects and tested with experiments and theoretical models. However, very few studies have focused on other desert-adapted species. In this study, a refined three-dimensional morphometric approach was used on three African rodent tribes (Otomyini, Taterillini and Gerbillini) to describe the cochlear and tympanic bullar morphology, and to explore the role of phylogeny, allometry and ecology to better understand the underlying mechanism of any observed trends of hypertrophy in the bulla and associated changes in the cochlea. As a result, desert-adapted species could be distinguished from mesic and semi-arid taxa by the gross cochlear dimensions, particularly the oval window, which is larger in desert species. Bullar and cochlear modifications between species could be explained by environment (bulla and oval window), phylogeny (cochlear curvature gradient) and/or allometry (cochlear relative length, oval window and bulla) with some exceptions. Based on their ear anatomy, we predict that Desmodillus auricularis and Parotomys brantsii should be sensitive to low-frequency sounds, with D. auricularis sensitive to high-frequency sounds, too. This study concludes that in both arid and semi-arid adapted laminate-toothed rats and gerbils there is bulla and associated cochlea hypertrophy, particularly in true desert species. Gerbils also show tightly coiled cochlea but the significance of this is debatable and may have nothing to do with adaptations to any specific acoustics in the desert environment.
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http://dx.doi.org/10.1111/joa.12906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326829PMC
February 2019

Notes on the distribution and phylogeography of two rare small Gerbillinae (Rodentia, Muridae) in Morocco: Gerbillus simoni and Gerbillus henleyi.

C R Biol 2018 Sep - Oct;341(7-8):398-409. Epub 2018 Aug 25.

Laboratory 'Biodiversity, Ecology and Genome', Research Center 'Plant and Microbial Biotechnology, Biodiversity and Environment', Faculty of Sciences, Mohammed V University in Rabat, 4, avenue Ibn-Battouta, B.P. 1014 RP, Rabat, Morocco.

Even though Gerbillinae rodents represent an important part of the mammalian fauna in North Africa, many gaps remain in our understanding of the distribution, ecology, evolution, and systematics of some lesser known species in this family. We present in this study the most recent findings on two of these species. The first species, Gerbillus simoni Lataste, 1881, is a short-tailed, small gerbil, endemic to North Africa. In Morocco, it is present only in a small area in the northeast, where it has not been caught since 1970. In 2014, we captured a small gerbil in this region that was identified as G. simoni based on morphology and molecular data (cytochrome b gene sequencing). This study represents the first genetic characterization of G. simoni in Morocco and the first one outside Tunisia. Populations from Morocco and Tunisia (mainland and Kerkennah Islands) show very little genetic differentiation. The second species, Gerbillus henleyi de Winton, 1903, is a long-tailed small gerbil that lives in the Sahel and North Africa with an extension to the Middle East. In Morocco, this species was only known in the southwest. Between 2014 and 2015, we have captured four gerbils in the northeast of the country, which were confirmed genetically and morphologically as belonging to this species. This represents an extension of its known distribution of about 370km to the northeast of the country. These new Moroccan specimens form a distinct lineage. High genetic diversity is observed throughout the geographic range of G. henleyi, suggesting the existence of several cryptic species.
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http://dx.doi.org/10.1016/j.crvi.2018.08.001DOI Listing
November 2018

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

Heredity (Edinb) 2019 02 23;122(2):150-171. Epub 2018 May 23.

Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France.

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.
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http://dx.doi.org/10.1038/s41437-018-0089-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327062PMC
February 2019

[Craniometrical study of the species complex of Meriones shawii-grandis (Mammalia: Rodentia) in Morocco, in Algeria and in Tunisia].

C R Biol 2018 Jan 8;341(1):28-42. Epub 2017 Dec 8.

Université Mouloud Mammeri de Tizi Ouzou, B.P. 17 R.P., DZ, 14000 Algérie.

In North Africa, the rodents of the species complex Meriones shawii-grandis have a considerable ecological, economic and epidemiological importance. Until now, the systematics of these species was subject to discussion due to the presence of populations displaying high morphological variability. By means of an approach of traditional morphometrics based on cranial distances and by using the method of the log shape-ratio, we attempt to characterize morphologically these two taxa. The results show significant differences in size and shape between the specimens of Morocco, on the one hand, and those of Algeria and Tunisia, on the other hand. The samples of Morocco that have been molecularly typed and attributed to M. grandis have larger tooth rows and narrower skulls, as well as relatively small tympanic bullae. On the other hand, those of Algeria and Tunisia assigned to M. shawii are characterized by small tooth rows and wide skulls with well-developed tympanic bullae. The morphological distance is relatively strong between both clades (79.5%), which corresponds to the molecular distance. However, the discriminant analysis performed after molecularly-typed specimens allows the correct classification of only 91.8% of the individuals.
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http://dx.doi.org/10.1016/j.crvi.2017.11.001DOI Listing
January 2018

Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.

PLoS One 2017 17;12(8):e0182565. Epub 2017 Aug 17.

Max Planck Institute for the Science of Human History, Jena, Germany.

Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182565PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560628PMC
October 2017

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

Integr Zool 2015 Nov;10(6):505-14

UMR 7205 Institute of Systematic, Evolution and Biodiversity (ISYEB), National Museum of Natural History CNRS, Sorbonne Universities, Paris, France.

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.
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http://dx.doi.org/10.1111/1749-4877.12164DOI Listing
November 2015

Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa.

BMC Evol Biol 2015 Apr 23;15:71. Epub 2015 Apr 23.

Institut de Systématique, Évolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, 75005, Paris, France.

Background: This study aims to reconstruct the evolutionary history of African shrews referred to the Crocidura olivieri complex. We tested the respective role of forest retraction/expansion during the Pleistocene, rivers (allopatric models), ecological gradients (parapatric model) and anthropogenic factors in explaining the distribution and diversification within this species complex. We sequenced three mitochondrial and four nuclear markers from 565 specimens encompassing the known distribution of the complex, i.e. from Morocco to Egypt and south to Mozambique. We used Bayesian phylogenetic inference, genetic structure analyses and divergence time estimates to assess the phylogenetic relationships and evolutionary history of these animals.

Results: The C. olivieri complex (currently composed of C. olivieri, C. fulvastra, C. viaria and C. goliath) can be segregated into eight principal geographical clades, most exhibiting parapatric distributions. A decrease in genetic diversity was observed between central and western African clades and a marked signal of population expansion was detected for a broadly distributed clade occurring across central and eastern Africa and portions of Egypt (clade IV). The main cladogenesis events occurred within the complex between 1.37 and 0.48 Ma. Crocidura olivieri sensu stricto appears polyphyletic and C. viaria and C. fulvastra were not found to be monophyletic.

Conclusions: Climatic oscillations over the Pleistocene probably played a major role in shaping the genetic diversity within this species complex. Different factors can explain their diversification, including Pleistocene forest refuges, riverine barriers and differentiation along environmental gradients. The earliest postulated members of the complex originated in central/eastern Africa and the first radiations took place in rain forests of the Congo Basin. A dramatic shift in the ecological requirements in early members of the complex, in association with changing environments, took place sometime after 1.13 Ma. Some lineages then colonized a substantial portion of the African continent, including a variety of savannah and forest habitats. The low genetic divergence of certain populations, some in isolated localities, can be explained by their synanthropic habits. This study underlines the need to revise the taxonomy of the C. olivieri complex.
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http://dx.doi.org/10.1186/s12862-015-0344-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422046PMC
April 2015

[Importance of Shaw's Jird Meriones shawii within the trophic components of the Barn Owl Tyto alba in steppic areas of Algeria].

C R Biol 2014 Jun 12;337(6):405-15. Epub 2014 Jun 12.

Laboratoire d'ornithologie, Département de zoologie, École nationale des sciences agronomique, Alger, Algérie.

The study of the diet of the Barn Owl in two steppic regions (M'Sila and Djelfa) located in the Algerian highlands is based on the analysis of the pellets of rejections collected in six stations. The analysis of 706 pellets resulting from the various stations made it possible to count 1380 individuals, represented by seven classes, 12 orders, 32 families, and 76 species of preys. The mammals are consumed with variable abundance rates between 59.1 % and 90.0 % whose predominance is assigned to the rodents (relative abundance: AR > 58 %). The latter constitute the most advantageous preys in biomass (61.4 ≤ B % ≤ 99.2). The most consumed prey is Meriones shawii, with variable rates between 31.9 % and 76.6 %. Generally, Tyto alba presents a diversified diet in the majority of the stations (0.69 ≤ E ≤ 0.76), except the station of Ain El-Hadjel (E = 0.35), with a low diversity and dominance of M. shawii (AR = 76.6 %).
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http://dx.doi.org/10.1016/j.crvi.2014.04.005DOI Listing
June 2014

Molecular phylogeny of hantaviruses harbored by insectivorous bats in Côte d'Ivoire and Vietnam.

Viruses 2014 Apr 29;6(5):1897-910. Epub 2014 Apr 29.

Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.

The recent discovery of genetically distinct hantaviruses in multiple species of shrews and moles prompted a further exploration of their host diversification by analyzing frozen, ethanol-fixed and RNAlater®-preserved archival tissues and fecal samples from 533 bats (representing seven families, 28 genera and 53 species in the order Chiroptera), captured in Asia, Africa and the Americas in 1981-2012, using RT-PCR. Hantavirus RNA was detected in Pomona roundleaf bats (Hipposideros pomona) (family Hipposideridae), captured in Vietnam in 1997 and 1999, and in banana pipistrelles (Neoromicia nanus) (family Vespertilionidae), captured in Côte d'Ivoire in 2011. Phylogenetic analysis, based on the full-length S- and partial M- and L-segment sequences using maximum likelihood and Bayesian methods, demonstrated that the newfound hantaviruses formed highly divergent lineages, comprising other recently recognized bat-borne hantaviruses in Sierra Leone and China. The detection of bat-associated hantaviruses opens a new era in hantavirology and provides insights into their evolutionary origins.
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http://dx.doi.org/10.3390/v6051897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036548PMC
April 2014

Nonlinear projection methods for visualizing Barcode data and application on two data sets.

Mol Ecol Resour 2013 Nov 3;13(6):976-90. Epub 2013 Jan 3.

SAMM (Statistique, Analyse et Modélisation Multidisciplinaire), EA 4543, Université Paris 1 Panthéon Sorbonne, 90 rue de Tolbiac, Paris, 75013, France.

Developing tools for visualizing DNA sequences is an important issue in the Barcoding context. Visualizing Barcode data can be put in a purely statistical context, unsupervised learning. Clustering methods combined with projection methods have two closely linked objectives, visualizing and finding structure in the data. Multidimensional scaling (MDS) and Self-organizing maps (SOM) are unsupervised statistical tools for data visualization. Both algorithms map data onto a lower dimensional manifold: MDS looks for a projection that best preserves pairwise distances while SOM preserves the topology of the data. Both algorithms were initially developed for Euclidean data and the conditions necessary to their good implementation were not satisfied for Barcode data. We developed a workflow consisting in four steps: collapse data into distinct sequences; compute a dissimilarity matrix; run a modified version of SOM for dissimilarity matrices to structure the data and reduce dimensionality; project the results using MDS. This methodology was applied to Astraptes fulgerator and Hylomyscus, an African rodent with debated taxonomy. We obtained very good results for both data sets. The results were robust against unbalanced species. All the species in Astraptes were well displayed in very distinct groups in the various visualizations, except for LOHAMP and FABOV that were mixed up. For Hylomyscus, our findings were consistent with known species, confirmed the existence of four unnamed taxa and suggested the existence of potentially new species.
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http://dx.doi.org/10.1111/1755-0998.12047DOI Listing
November 2013

The impact of human conflict on the genetics of Mastomys natalensis and Lassa virus in West Africa.

PLoS One 2012 15;7(5):e37068. Epub 2012 May 15.

Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France.

Environmental changes have been shown to play an important role in the emergence of new human diseases of zoonotic origin. The contribution of social factors to their spread, especially conflicts followed by mass movement of populations, has not been extensively investigated. Here we reveal the effects of civil war on the phylogeography of a zoonotic emerging infectious disease by concomitantly studying the population structure, evolution and demography of Lassa virus and its natural reservoir, the rodent Mastomys natalensis, in Guinea, West Africa. Analysis of nucleoprotein gene sequences enabled us to reconstruct the evolutionary history of Lassa virus, which appeared 750 to 900 years ago in Nigeria and only recently spread across western Africa (170 years ago). Bayesian demographic inferences revealed that both the host and the virus populations have gone recently through severe genetic bottlenecks. The timing of these events matches civil war-related mass movements of refugees and accompanying environmental degradation. Forest and habitat destruction and human predation of the natural reservoir are likely explanations for the sharp decline observed in the rodent populations, the consequent virus population decline, and the coincident increased incidence of Lassa fever in these regions. Interestingly, we were also able to detect a similar pattern in Nigeria coinciding with the Biafra war. Our findings show that anthropogenic factors may profoundly impact the population genetics of a virus and its reservoir within the context of an emerging infectious disease.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0037068PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352846PMC
January 2013

Assessment of three mitochondrial genes (16S, Cytb, CO1) for identifying species in the Praomyini tribe (Rodentia: Muridae).

PLoS One 2012 4;7(5):e36586. Epub 2012 May 4.

Muséum National d'Histoire Naturelle, Département de Systématique et Evolution UMR CNRS 7205, Paris, France.

The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0036586PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3344912PMC
September 2012

Multiple geographic origins of commensalism and complex dispersal history of Black Rats.

PLoS One 2011 2;6(11):e26357. Epub 2011 Nov 2.

Australian National Wildlife Collection, CSIRO Ecosystem Sciences, Canberra, Australia.

The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026357PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206810PMC
March 2012

Novel arenavirus sequences in Hylomyscus sp. and Mus (Nannomys) setulosus from Côte d'Ivoire: implications for evolution of arenaviruses in Africa.

PLoS One 2011 9;6(6):e20893. Epub 2011 Jun 9.

Laboratoire des Arbovirus/Entérovirus, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire.

This study aimed to identify new arenaviruses and gather insights in the evolution of arenaviruses in Africa. During 2003 through 2005, 1,228 small mammals representing 14 different genera were trapped in 9 villages in south, east, and middle west of Côte d'Ivoire. Specimens were screened by pan-Old World arenavirus RT-PCRs targeting S and L RNA segments as well as immunofluorescence assay. Sequences of two novel tentative species of the family Arenaviridae, Menekre and Gbagroube virus, were detected in Hylomyscus sp. and Mus (Nannomys) setulosus, respectively. Arenavirus infection of Mus (Nannomys) setulosus was also demonstrated by serological testing. Lassa virus was not found, although 60% of the captured animals were Mastomys natalensis. Complete S RNA and partial L RNA sequences of the novel viruses were recovered from the rodent specimens and subjected to phylogenetic analysis. Gbagroube virus is a closely related sister taxon of Lassa virus, while Menekre virus clusters with the Ippy/Mobala/Mopeia virus complex. Reconstruction of possible virus-host co-phylogeny scenarios suggests that, within the African continent, signatures of co-evolution might have been obliterated by multiple host-switching events.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020893PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111462PMC
October 2011

Taphonomy and palaeoecology of the late Pleistocene to middle Holocene small mammal succession of El Harhoura 2 cave (Rabat-Témara, Morocco).

J Hum Evol 2011 Jan 30;60(1):1-33. Epub 2010 Oct 30.

Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire de Zoologie des Mammifères et Oiseaux, 55 rue Buffon, 75005 Paris, France.

The relationship between local and global climatic variations and the origin and dispersal of Homo sapiens in Africa is complex, and North Africa may have played a major role in these events. In Morocco, very few studies are specifically dedicated to small fossil vertebrates, and neither taphonomic nor palaeoecological studies have been undertaken on these taxa, particularly in archaeological contexts. The late Pleistocene to middle Holocene succession of El Harhoura 2 cave, situated in the region of Témara, yields an exceptionally rich small vertebrate assemblage. We present the results of a first systematic, taphonomic, and palaeoecological study of the small mammals from Levels 1 to 8 of El Harhoura 2. The absence of bone sorting and polishing, as well as the presence of significant traces of digestion indicate that the small mammal bones were accumulated in the cave by predators and that no water transport occurred. Other traces observed on the surface of bones consist mainly of root marks and black traces (micro-organisms or more probably manganese) which affected the majority of the material. The percentage of fragmentation is very high in all stratigraphic levels, and the post-depositional breakage (geologic and anthropogenic phenomena) obscure the original breakage patterns of bones by predators. According to the ecology of the different species present in the levels of El Harhoura 2, and by taking into account possible biases highlighted by the taphonomic analysis, we reconstruct the palaeoenvironmental evolution in the region. For quantitative reconstructions we used two indices: the Taxonomic Habitat Index (THI) and the Gerbillinae/Murinae ratio. Late Pleistocene accumulations were characterised by a succession of humid (Levels 3, 4a, 6, and 8) and arid (Levels 2?, 5, and 7) periods, with more or less open landscapes, ending in an ultimate humid and wooded period during the middle Holocene (Level 1). We discuss particular limits of our results and interpretations, due to an important lack of taxonomic, ecological, and taphonomic knowledge in North Africa.
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http://dx.doi.org/10.1016/j.jhevol.2010.07.016DOI Listing
January 2011

Morphological identification of sibling species: the case of West African Mastomys (Rodentia: Muridae) in sympatry.

C R Biol 2009 May 9;332(5):480-8. Epub 2009 Jan 9.

UMR CNRS- USM, Département systématique et évolution, Muséum national d'histoire naturelle, Paris, France.

In this study, we investigate skull size and shape differentiation between sibling species of Mastomys with the aim to characterize and discriminate three sympatric species found in West Africa: M. huberti, M. erythroleucus and M. natalensis. A total of 133 genetically determined specimens were used for the morphometric analyses. Statistical analyses clearly demonstrated that the three species largely overlapped in centroid size (M. erythroleucus tends to be larger on average than the M. huberti and M. natalensis) but they exhibited large differences in skull shape. The current study focused on skull shape, and allowed us to discriminate three morphological groups that are congruent with the three species suggested by molecular identification (90% of the individuals are correctly assigned by cross-validated classifications). In the Mastomys, the evolution of cranial length and shape may be influenced by competitive pressure between closely related species separated by ecological segregation. This source of variability could possibly induce character displacement between species of Mastomys.
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http://dx.doi.org/10.1016/j.crvi.2008.11.004DOI Listing
May 2009

Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily.

BMC Evol Biol 2008 Jul 10;8:199. Epub 2008 Jul 10.

UMR CNRS 5202, Origine, Structure et Evolution de la Biodiversité, Département Systématique et Evolution, Muséum Nationald'Histoire Naturelle, 55 rue Buffon, 75005 Paris, France.

Background: Within the subfamily Murinae, African murines represent 25% of species biodiversity, making this group ideal for detailed studies of the patterns and timing of diversification of the African endemic fauna and its relationships with Asia. Here we report the results of phylogenetic analyses of the endemic African murines through a broad sampling of murine diversity from all their distribution area, based on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR).

Results: A combined analysis of one mitochondrial and two nuclear gene sequences consistently identified and robustly supported ten primary lineages within Murinae. We propose to formalize a new tribal arrangement within the Murinae that reflects this phylogeny. The diverse African murine assemblage includes members of five of the ten tribes and clearly derives from multiple faunal exchanges between Africa and Eurasia. Molecular dating analyses using a relaxed Bayesian molecular clock put the first colonization of Africa around 11 Mya, which is consistent with the fossil record. The main period of African murine diversification occurred later following disruption of the migration route between Africa and Asia about 7-9 Mya. A second period of interchange, dating to around 5-6.5 Mya, saw the arrival in Africa of Mus (leading to the speciose endemic Nannomys), and explains the appearance of several distinctive African lineages in the late Miocene and Pliocene fossil record of Eurasia.

Conclusion: Our molecular survey of Murinae, which includes the most complete sampling so far of African taxa, indicates that there were at least four separate radiations within the African region, as well as several phases of dispersal between Asia and Africa during the last 12 My. We also reconstruct the phylogenetic structure of the Murinae, and propose a new classification at tribal level for this traditionally problematic group.
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http://dx.doi.org/10.1186/1471-2148-8-199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2490707PMC
July 2008

Mastomys natalensis and Lassa fever, West Africa.

Emerg Infect Dis 2006 Dec;12(12):1971-4

Philipps University Institute of Virology, Marburg, Germany.

PCR screening of 1,482 murid rodents from 13 genera caught in 18 different localities of Guinea, West Africa, showed Lassa virus infection only in molecularly typed Mastomys natalensis. Distribution of this rodent and relative abundance compared with M. erythroleucus correlates geographically with Lassa virus seroprevalence in humans.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291371PMC
http://dx.doi.org/10.3201/eid1212.060812DOI Listing
December 2006

Use of phylogeny to resolve the taxonomy of the widespread and highly polymorphic African giant shrews (Crocidura olivieri group, Crocidurinae, Mammalia).

Zoology (Jena) 2007 13;110(1):48-57. Epub 2006 Dec 13.

Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.

The aim of this study is to provide a better understanding of the genetic relationships within the widespread and highly polymorphic group of African giant shrews (Crocidura olivieri group). We sequenced 769 base pairs (bp) of the mitochondrial cytochrome b gene and 472 bp of the mitochondrial control region over the entire geographic range from South Africa to Morocco. The analyses reveal four main clades associated with different biomes. The largest clade occurs over a range covering Northwest and Central Africa and includes samples of C. fulvastra, C. olivieri, and C. viaria. The second clade is composed of C. goliath from Gabon, while South African C. flavescens, and C. hirta form two additional clades. On the basis of these results, the validity of some taxa in the C. olivieri group should be re-evaluated.
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http://dx.doi.org/10.1016/j.zool.2006.05.003DOI Listing
March 2007

Hantavirus in African wood mouse, Guinea.

Emerg Infect Dis 2006 May;12(5):838-40

Institute of Virology, Charité Medical School, Campus Charité Mitte, Schumannstrasse 20-21, D-10117 Berlin, Germany.

Hantaviruses are rodent-borne, emerging viruses that cause life-threatening human diseases in Eurasia and the Americas. We detected hantavirus genome sequences in an African wood mouse (Hylomyscus simus) captured in Sangassou, Guinea. Sequence and phylogenetic analyses of the genetic material demonstrate a novel hantavirus species, which we propose to name "Sangassou virus."
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374458PMC
http://dx.doi.org/10.3201/eid1205.051487DOI Listing
May 2006

Molecular phylogeny of the African pygmy mice, subgenus Nannomys (Rodentia, Murinae, Mus): implications for chromosomal evolution.

Mol Phylogenet Evol 2005 Aug 23;36(2):358-69. Epub 2005 Mar 23.

Institut des Sciences de l'Evolution (UMR5554), Génétique and Environnement, Université Montpellier II, Montpellier, France.

Molecular phylogenies based on sequences of mitochondrial cytochrome b and nuclear IRBP genes are assessed on a comprehensive taxonomic sampling of African pygmy mice (subgenus Nannomys of the genus Mus). They represent a taxonomically diversified group of morphologically similar species, and exhibit an important chromosomal diversity, particularly involving sex-autosome translocations, one of the rarest and most deleterious chromosomal changes among mammals. The results show that the species sampled are genetically well differentiated, and that chromosomal rearrangements offer accurate diagnostic characters for discriminating most species. Furthermore, the species carrying different sex-autosome translocations appear monophyletic, suggesting that a genome modification allowing a higher rate of occurrence and/or fixation of such translocations took place, leading to the emergence of this lineage. In addition to taxonomic and biogeographical clarifications, we provide a temporal framework within which patterns of genic and chromosomal evolution are discussed.
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http://dx.doi.org/10.1016/j.ympev.2005.02.011DOI Listing
August 2005

Cytochrome b-based phylogeny of the Praomys group (Rodentia, Murinae): a new African radiation?

C R Biol 2002 Jul;325(7):827-40

Laboratoire Zoologie, Mammifères et Oiseaux, Muséum national d'histoire naturelle, 55, rue Buffon, 75005 Paris, France.

Complete cytochrome b gene sequences allows, for the first time, establishing a nearly complete phylogeny among the Praomys group sensu lato. The genera Praomys, Mastomys and Stenocephalemys appear paraphyletic. Myomys is polyphyletic and this genus name probably needs to be restricted to its type species, M. verreauxii. The genera Zelotomys and Colomys appear as sister groups. Mastomys pernanus and Malacomys verschureni nest within the Praomys group, but their generic assignation must be further clarified. The genus Heimyscus appears closest to Praomys than to Hylomyscus. The different lineages probably result from an adaptive radiation at the end of the Miocene.
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http://dx.doi.org/10.1016/s1631-0691(02)01488-9DOI Listing
July 2002

A new hominid from the Upper Miocene of Chad, Central Africa.

Nature 2002 Jul;418(6894):145-51

Faculté des Sciences et CNRS UMR 6046, Université de Poitiers, 40 Avenue du Recteur Pineau, 86022 Poitiers Cedex, France.

The search for the earliest fossil evidence of the human lineage has been concentrated in East Africa. Here we report the discovery of six hominid specimens from Chad, central Africa, 2,500 km from the East African Rift Valley. The fossils include a nearly complete cranium and fragmentary lower jaws. The associated fauna suggest the fossils are between 6 and 7 million years old. The fossils display a unique mosaic of primitive and derived characters, and constitute a new genus and species of hominid. The distance from the Rift Valley, and the great antiquity of the fossils, suggest that the earliest members of the hominid clade were more widely distributed than has been thought, and that the divergence between the human and chimpanzee lineages was earlier than indicated by most molecular studies.
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http://dx.doi.org/10.1038/nature00879DOI Listing
July 2002