Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)

CITATION: Dumbacher, J. P., Rathbun, G. B., Smit, H. A. & Eiseb, S. J. 2012. Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea). PLoS ONE, 7(3):e32410, doi:10.1371/journal.pone.0032410.The original publication is available at http://journals.plos.org/plosoneThe round-eared sengis or elephant-shrews (genus Macroscelides) exhibit striking pelage variation throughout their ranges. Over ten taxonomic names have been proposed to describe this variation, but currently only two taxa are recognized (M. proboscideus proboscideus and M. p. flavicaudatus). Here, we review the taxonomic history of Macroscelides, and we use data on the geographic distribution, morphology, and mitochondrial DNA sequence to evaluate the current taxonomy. Our data support only two taxa that correspond to the currently recognized subspecies M. p. proboscideus and M. p. flavicaudatus. Mitochondrial haplotypes of these two taxa are reciprocally monophyletic with over 13% uncorrected sequence divergence between them. PCA analysis of 14 morphological characters (mostly cranial) grouped the two taxa into non-overlapping clusters, and body mass alone is a relatively reliable distinguishing character throughout much of Macroscelides range. Although fieldworkers were unable to find sympatric populations, the two taxa were found within 50 km of each other, and genetic analysis showed no evidence of gene flow. Based upon corroborating genetic data, morphological data, near sympatry with no evidence of gene flow, and differences in habitat use, we elevate these two forms to full species. © 2012 Dumbacher et al.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032410Publisher's versio

Impact of crop cycle on movement patterns of pest rodent species between fields and houses in Africa

Abstract Context. Rodent pests can have severe impacts on crop production in sub-Saharan Africa. In particular, the multimammate mouse Mastomys natalensis severely damages agricultural crops in southern and eastern Africa, leading to significant losses. Both its population ecology and breeding biology have been studied in agricultural and natural habitats. Population numbers erupt depending on the timing and amount of rainfall and may reach plague proportions, especially in agricultural settings, where it may become a serious pest. However, the ecology of this species, in particular its interactions with other species within the context of human settlement, is poorly understood. It may occasionally enter houses, but the degree to which it does so and the factors influencing this movement are not known. Aims. We investigated the relationship between Rattus spp. and M. natalensis entering buildings in an agro-ecological setting. We predicted that M. natalensis would enter houses more readily when food availability was lowest in the surrounding fields, and when the larger Rattus spp. were absent. Methods. We followed 40 individuals of M. natalensis in Swaziland and Namibia by radio-telemetry. Mice were captured in maize fields within 50 m of a homestead and fitted with radio-transmitters at three different times corresponding to different stages of crop development: pre-harvest, post-harvest and pre-planting. To corroborate the findings of the telemetry study, a non-toxic marker, rhodamine B, was mixed with standard bait and left at bait stations inside houses in 10 homesteads in Swaziland and Tanzania. Key results. Mice remained in the fields during the entire period of study in Swaziland, but entered buildings in Namibia during the post-harvest stage, which may represent a period of food shortage for these mice in the field. Rodents captured after baiting with rhodamine B demonstrated that Rattus spp. predominated within the houses. A small number of rhodamine B-marked M. natalensis were captured outside the houses, the proportion declining with distance away from the houses. Conclusions. These results suggest that in a typical rural African setting dominated by subsistence agriculture, Rattus spp. (when present) competitively exclude the smaller M. natalensis from entering houses. Implications. Interactions between rodent pest species may be important in determining which rodent species enter houses in rural African landscapes. Consideration of such interactions may play an important role when developing pest management strategies

A systematic review of rodent pest research in Afro-Malagasy small-holder farming systems : are we asking the right questions

Rodent pests are especially problematic in terms of agriculture and public health since they can inflict considerable economic damage associated with their abundance, diversity, generalist feeding habits and high reproductive rates. To quantify rodent pest impacts and identify trends in rodent pest research impacting on small-holder agriculture in the Afro- Malagasy region we did a systematic review of research outputs from 1910 to 2015, by developing an a priori defined set of criteria to allow for replication of the review process. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We reviewed 162 publications, and while rodent pest research was spatially distributed across Africa (32 countries, including Madagascar), there was a disparity in number of studies per country with research biased towards four countries (Tanzania [25%], Nigeria [9%], Ethiopia [9%], Kenya [8%]) accounting for 51% of all rodent pest research in the Afro- Malagasy region. There was a disparity in the research themes addressed by Tanzanian publications compared to publications from the rest of the Afro-Malagasy region where research in Tanzania had a much more applied focus (50%) compared to a more basic research approach (92%) in the rest of the Afro-Malagasy region. We found that pest rodents have a significant negative effect on the Afro-Malagasy small-holder farming communities. Crop losses varied between cropping stages, storage and crops and the highest losses occurred during early cropping stages (46% median loss during seedling stage) and the mature stage (15% median loss). There was a scarcity of studies investigating the effectiveness of various management actions on rodent pest damage and population abundance. Our analysis highlights that there are inadequate empirical studies focused on developing sustainable control methods for rodent pests and rodent pests in the Africa-Malagasy context is generally ignored as a research topic.S1 Table. PRISMA checklist.S2 Table. List of rodent genera detected in rodent pest research in African agricultural systems from 1960±2015.S3 Table. List of different crops and cropping system as impacted by rodent pests in African agriculture (1960±2015).S1 List. Complete list of all publications used in the review±Publications in bold did not have full texts available at time of review.S2 List. Web of Science TM search history±.S1 Web of ScienceTM saved search.A European Union 9th European Development Fund grant from the African Caribbean and Pacific Science and Technology Programme (FED/2013/330-223), a grant from the United Kingdom's Department for International Development (AgriTT/894), a grant from the Sasol Agriculture Trust (South Africa), and International Foundation for Science (SE)-D/4984-2 to LHS.http://www.plosone.orgam2017Animal and Wildlife Science

Phylogeny and Taxonomy of the Round-Eared Sengis or Elephant-Shrews, Genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)

The round-eared sengis or elephant-shrews (genus Macroscelides) exhibit striking pelage variation throughout their ranges. Over ten taxonomic names have been proposed to describe this variation, but currently only two taxa are recognized (M. proboscideus proboscideus and M. p. flavicaudatus). Here, we review the taxonomic history of Macroscelides, and we use data on the geographic distribution, morphology, and mitochondrial DNA sequence to evaluate the current taxonomy. Our data support only two taxa that correspond to the currently recognized subspecies M. p. proboscideus and M. p. flavicaudatus. Mitochondrial haplotypes of these two taxa are reciprocally monophyletic with over 13% uncorrected sequence divergence between them. PCA analysis of 14 morphological characters (mostly cranial) grouped the two taxa into non-overlapping clusters, and body mass alone is a relatively reliable distinguishing character throughout much of Macroscelides range. Although fieldworkers were unable to find sympatric populations, the two taxa were found within 50 km of each other, and genetic analysis showed no evidence of gene flow. Based upon corroborating genetic data, morphological data, near sympatry with no evidence of gene flow, and differences in habitat use, we elevate these two forms to full species

A systematic review of rodent pest research in Afro-Malagasy small-holder farming systems: Are we asking the right questions?

Rodent pests are especially problematic in terms of agriculture and public health since they can inflict considerable economic damage associated with their abundance, diversity, generalist feeding habits and high reproductive rates. To quantify rodent pest impacts and identify trends in rodent pest research impacting on small-holder agriculture in the Afro-Malagasy region we did a systematic review of research outputs from 1910 to 2015, by developing an a priori defined set of criteria to allow for replication of the review process. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We reviewed 162 publications, and while rodent pest research was spatially distributed across Africa (32 countries, including Madagascar), there was a disparity in number of studies per country with research biased towards four countries (Tanzania [25%], Nigeria [9%], Ethiopia [9%], Kenya [8%]) accounting for 51% of all rodent pest research in the Afro-Malagasy region. There was a disparity in the research themes addressed by Tanzanian publications compared to publications from the rest of the Afro-Malagasy region where research in Tanzania had a much more applied focus (50%) compared to a more basic research approach (92%) in the rest of the Afro-Malagasy region. We found that pest rodents have a significant negative effect on the Afro-Malagasy small-holder farming communities. Crop losses varied between cropping stages, storage and crops and the highest losses occurred during early cropping stages (46% median loss during seedling stage) and the mature stage (15% median loss). There was a scarcity of studies investigating the effectiveness of various management actions on rodent pest damage and population abundance. Our analysis highlights that there are inadequate empirical studies focused on developing sustainable control methods for rodent pests and rodent pests in the Africa-Malagasy context is generally ignored as a research topic

The bii4africa dataset of faunal and floral population intactness estimates across Africa’s major land uses

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species’ population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate ‘intactness scores’: the remaining proportion of an ‘intact’ reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region’s major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/ taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems

Systematics and biogeography of the genus Mastomys (Rodentia: Muridae) occurring in Namibia and adjacent countries

Das Ziel dieser Studie war, die Anzahl der Mastomys-Arten und ihrer geographischen Verbreitung in Namibia und Teilen von Botswana und Angola zu bestimmen. Der methodische Ansatz umfasst Schädel-Morphometrie, Karyotypisierung und Cytochrom-b-Gen-Sequenzierung. Traditionellen Morphometrie-Studie lieferten keine klaren morphologischen, wohingegen die geometrische Morphometrie-Analyse erfolgreicher war. Hier zeigten die Ergebnisse bei drei Spezies deutliche dorsale und ventrale Unterschiede in der Schädelform. Die Resultate der zytogenetischen und molekularen Methoden ergaben drei Formen von Mastomys mit unterschiedlichen Karyotypen und mtDNA. Diese wurden M. coucha (2n = 36, aFN = 60/60), M. natalensis (2n = 32, aFN = 57/58) und M. shortridgei (2n = 36, aFN = 51/52) zugeordnet. Die mtDNA Divergenz zwischen der Art M. coucha und M. shortridgei war relativ gering (1.3%), außerdem legte die „Moleküluhr“ (molecular clock) nahe, dass M. shortridgei ein aktueller Ableger von M. coucha (0.71 Mya) ist. Man nimmt an, dass der Paläo-Makgadikgadi See, im heutigen Botswana einen Großteil des östlichen Kalahari-Beckens bedeckte. Es könnte sein, dass Ausläufer früherer Populationen von M. shortridgei in Kontakt mit dem Paläo-Makgadikgadi See kammen und während des End-Pleistozäns bis zum frühen Holozän durch das Schrumpfen des Sees isoliert wurden. Im Laufe der Zeit haben sich die frühen Populationen von M. shortridgei an die lokalen sumpfigen Umweltbedingungen angepasst. M. coucha und M. natalensis haben eine klar begrenzte geografischen Verteilung in Namibia, dies scheint durch Niederschlag beeinflusst zu sein: M. coucha tritt vor allem in den niederschlagsarmen Gebieten von Zentral-Namibia auf, M. natalensis dagegen in den niederschlagsreichen Gebieten im nördlich-zentralen und nordöstlichen Namibia und erstreckt sich bis nach Angola und in das nördliche Botswana hinein. Die M. shortridgei-Proben wurden nur in den Okavango-Sümpfen gefunden.Study aims to summarise the patterns of morphological, cytogenetic and genetic variation of genus Mastomys across the south-west arid region of southern Africa. The methodological approach included skull morphometrics, karyotyping and cytochrome-b gene sequencing. Traditional morphometrics study did not yield clear morphological differences between the three species. Geometric morphometrics analysis was more successful with clear differences, in the shape of the skulls based on landmarks from both the dorsal and ventral views. Results obtained with cytogenetical and molecular methods revealed three forms of Mastomys with different karyotypes and mtDNA clades. These were assigned to M. coucha (2n = 36, aFN = 60/60), M. natalensis (2n = 32, aFN = 57/58) and M. shortridgei (2n = 36, aFN = 51/52). The mtDNA divergence between the species M. coucha and M. shortridgei was relatively low (1.3%), additionally the molecular clock estimated M. shortridgei to be a recent off-shoot of M. coucha (0.71 Mya). It is estimated that the lake Palaeo-Makgadikgadi, in present day Botswana, covered much of the eastern Kalahari basin. It could be that the peripheral ancestral population of M. shortridgei came in contact with the lake Palaeo-Makgadikgadi and was isolated with the shrinking lake Palaeo-Makgadikgadi during the End-Pleistocene to Early Holocene. Over time ancestral populations of M. shortridgei became adapted to the local swampy environmental conditions. M. coucha and M. natalensis have distinct geographical distribution influenced by precipitation. M. coucha mainly occurs in the low rainfall areas of central Namibia, whereas M. natalensis occurs in higher rainfall areas of north-central and north-eastern Namibia, extending into Angola and northern Botswana. The M. shortridgei specimens were only trapped along the Okavango River swamps in northern Botswana and south-eastern Angola

Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)

CITATION: Dumbacher, J. P., Rathbun, G. B., Smit, H. A. & Eiseb, S. J. 2012. Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea). PLoS ONE, 7(3):e32410, doi:10.1371/journal.pone.0032410.The original publication is available at http://journals.plos.org/plosoneThe round-eared sengis or elephant-shrews (genus Macroscelides) exhibit striking pelage variation throughout their ranges. Over ten taxonomic names have been proposed to describe this variation, but currently only two taxa are recognized (M. proboscideus proboscideus and M. p. flavicaudatus). Here, we review the taxonomic history of Macroscelides, and we use data on the geographic distribution, morphology, and mitochondrial DNA sequence to evaluate the current taxonomy. Our data support only two taxa that correspond to the currently recognized subspecies M. p. proboscideus and M. p. flavicaudatus. Mitochondrial haplotypes of these two taxa are reciprocally monophyletic with over 13% uncorrected sequence divergence between them. PCA analysis of 14 morphological characters (mostly cranial) grouped the two taxa into non-overlapping clusters, and body mass alone is a relatively reliable distinguishing character throughout much of Macroscelides range. Although fieldworkers were unable to find sympatric populations, the two taxa were found within 50 km of each other, and genetic analysis showed no evidence of gene flow. Based upon corroborating genetic data, morphological data, near sympatry with no evidence of gene flow, and differences in habitat use, we elevate these two forms to full species. © 2012 Dumbacher et al.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032410Publisher's versio

<i>Macroscelides</i> from Namibia and South Africa.

<p>A (top). <i>Macroscelides proboscideus flavicaudatus</i> captured in the Namib Desert at Wlotzkasbaken, Namibia, on 25 May 2000 (photo by GBR). B (bottom). <i>M. p. proboscideus</i> captured in the Nama-Karoo at Loxton Commonage, Northern Cape, South Africa, on 21 March 2007 (Photo courtesy of Chris and Mathilde Stuart). Note the light coloration of the animal from the Namib Desert compared to the specimen from the Nama-Karoo.</p