Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.
We studied interspecific and ontogenetic relationships between the size of a leaf and the primary diameter of the internode bearing it. Although these two variables are known to be strongly correlated across species, the form of this relationship has not been studied. In a re‐analysis of published data on interspecific comparisons of 69 temperate tree species, we showed the existence of a strong relationship between twig cross‐sectional area (before secondary growth) and surface area of leaves borne by it, within each of three morphological groups, deciduous angiosperms, evergreen angiosperms, and gymnosperms. Within each of these groups, this relationship is isometric: across species, primary cross‐sectional area of the stem increases proportionally with leaf surface area. When we consider the relationship between the cross‐sectional area of a twig and the surface area of one leaf borne by it, the y‐intercepts for this relation are different for the three groups. However, when total leaf surface area per first‐year shoot is considered, no differences remained between gymnosperms and evergreen angiosperms, but deciduous angiosperms continued to be distinct. This difference between deciduous and evergreen groups could be due to differences in leaf volume (evergreen species have thicker leaves than deciduous) or in traits related to a trade‐off between life span of leaves and their physiological behaviour. We present results of the first quantitative study of the relationship between leaf size and primary diameter of the stem during ontogeny. Both these parameters increase during development of the plant from seedling to adult. For the four tree species examined, the relationship between primary cross‐sectional area of the stem and leaf surface area is also isometric. These results bear on a functional interpretation of the relationship between leaf and stem dimensions, suggesting that vascular supply is directly proportional to the requirements of leaves supported by the stem.
Aim To describe the phylogeographic patterns of the black rat, Rattus rattus, from islands in the western Indian Ocean where the species has been introduced (Madagascar and the neighbouring islands of Réunion, Mayotte and Grande Comore), in comparison with the postulated source area (India).Location Western Indian Ocean: India, Arabian Peninsula, East Africa and the islands of Madagascar, Réunion, Grande Comore and Mayotte.Methods Mitochondrial DNA (cytochrome b, tRNA and D-loop, 1762 bp) was sequenced for 71 individuals from 11 countries in the western Indian Ocean. A partial D-loop (419 bp) was also sequenced for eight populations from Madagascar (97 individuals), which were analysed in addition to six previously published populations from southern Madagascar. ResultsHaplotypes from India and the Arabian Peninsula occupied a basal position in the phylogenetic tree, whereas those from islands were distributed in different monophyletic clusters: Madagascar grouped with Mayotte, while Réunion and Grand Comore were present in two other separate groups. The only exception was one individual from Madagascar (out of 190) carrying a haplotype that clustered with those from Réunion and South Africa. 'Isolation with migration' simulations favoured a model with no recurrent migration between Oman and Madagascar. Mismatch distribution analyses dated the expansion of Malagasy populations on a time-scale compatible with human colonization history. Higher haplotype diversity and older expansion times were found on the east coast of Madagascar compared with the central highlands.Main conclusions Phylogeographic patterns supported the hypothesis of human-mediated colonization of R. rattus from source populations in either the native area (India) or anciently colonized regions (the Arabian Peninsula) to islands of the western Indian Ocean. Despite their proximity, each island has a distinct colonization history. Independent colonization events may have occurred simultaneously in Madagascar and Grande Comore, whereas Mayotte would have been colonized from Madagascar. Réunion was colonized independently, presumably from Europe. Malagasy populations may have originated from a single successful colonization event, followed by rapid expansion, first in coastal zones and then in the central highlands. The congruence of the observed phylogeographic pattern with human colonization events and pathways supports the potential relevance of the black rat in tracing human history.
The worldwide intensification of human‐associated exchanges favours the multiplication of biological invasions. Among mammals, rodent species, including the house mouse Mus musculus, are identified as major invaders with profound impacts on native biodiversity, human health and activities. Though contemporary rodent invasions are described on several islands, there are few data describing ongoing house mouse invasions in continental areas. We first outline the known picture of the distribution of the house mouse in Africa. We then describe the ongoing range expansion of the house mouse in Senegal, in order to update its distribution area, assess the location of the invasion front, describe the spatio‐temporal dynamics of the invasion at the country scale and evaluate its impact on native small mammal communities. We briefly review the worldwide status of the house mouse, with special focus on its situation in Africa. Focusing on Senegal, we then use historical records and a large body of spatio‐temporal indoor trapping data obtained from small mammal communities over the last 30 years to analyse the invasion dynamics of the subspecies at the scale of the country. The geographic range of the invasive house mouse is surprisingly poorly known in Africa. In Senegal, we document a large range expansion of the subspecies in human settlements over the whole country within the last 30 years. The invasion is still ongoing further east and south within the country, and has major consequences for small mammal communities and thus probably for risks associated with zoonotic diseases.
Using microsatellite markers, we compared the genetic structure of populations of two carabid species, one described as a generalist (commonly found in forest and in open habitats) and the other known as a forest specialist. Both species were sampled in the same forest plots, which were separated from each other by either open or forested areas. At the local scale considered (13.6 km separating the most distant plots), genetic differentiation was substantial for both species studied, but populations of the forest specialist Carabus punctatoauratus appeared to be more spatially structured than those of C. nemoralis. Isolation by distance analyses showed that nonforested areas are partial barriers to gene flow for both species studied, although more clearly for the forest specialist. Between and within forests, dispersal capacity of the generalist C. nemoralis was shown to be higher than that of the specialist C. punctatoauratus.
In order to evaluate the contribution of geological, environmental, and climatic changes to the spatial distribution of genetic variation of Mastomys natalensis, we analysed cytochrome b sequences from the whole distribution area of the species to infer its phylogeographic structure and historical demography. Six well‐supported phylogroups, differentiated during the Pleistocene, were evidenced. No significant correlation between genetic and geographic distances was found at the continental scale, and the geographic distributions of the observed phylogroups have resulted from extensive periods of isolation caused by the presence of putative geographic and ecological barriers. The diversification events were probably influenced by habitat contraction/expansion cycles that may have complemented topographic barriers to induce genetic drift and lineage sorting. According to our results, we propose a scenario where climate‐driven processes may have played a primary role in the differentiation among phylogroups. © 2013 The Linnean Society of London
Aim To investigate the phylogeographical structure of the Guinea multimammate mouse, Mastomys erythroleucus (Temminck, 1853), a widespread murid rodent in sub‐Saharan (Sahel and Sudan) savannas, for a better understanding of the impacts of geographical and historical factors on the evolutionary history of this species, in the context of the growing database of phylogeographical studies of African savanna mammal species. Location Sahel and Sudan savannas, Africa. Methods We sequenced the whole cytochrome b gene in 211 individuals from 59 localities distributed from Senegal to Ethiopia. Sequence data were analysed using both phylogenetic (several rooted tree‐construction methods, median‐joining networks) and population genetic methods (spatial analyses of molecular variance, mismatch distributions). Results Haplotypes were distributed into four major monophyletic groups corresponding to distinct geographical regions across a west–east axis. Diversification events were estimated to have occurred between 1.16 and 0.18 Ma. Main conclusions Vicariance events related to the fragmentation of savanna habitats during the Pleistocene era may explain the phylogeographical patterns observed. Genetic structure was consistent with a role of major Sahelian rivers as significant barriers to west–east dispersal. Recent demographic expansions probably occurred during arid phases of the Holocene with the southward expansion of savannas.
Although observations suggest pairwise coevolution in speci¢c ant^plant symbioses, coevolutionary processes have rarely been demonstrated. We report on, what is to the authors' knowledge, the strongest evidence yet for reciprocal adaptation of morphological characters in a species-speci¢c ant^plant mutualism. The plant character is the prostoma, which is a small unligni¢ed organ at the apex of the domatia in which symbiotic ants excavate an entrance hole. Each myrmecophyte in the genus Leonardoxa has evolved a prostoma with a di¡erent shape. By performing precise measurements on the prostomata of three related myrmecophytes, on their speci¢c associated ants and on the entrance holes excavated by symbiotic ants at the prostomata, we showed that correspondence of the plant and ant traits forms a morphological and behavioural ¢lter. We have strong evidence for coevolution between the dimensions and shape of the symbiotic ants and the prostoma in one of the three ant^Leonardoxa associations.
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