The Fleas of Endemic and Introduced Small Mammals in Central Highland Forests of Madagascar: Faunistics, Species Diversity, and Absence of Host Specificity
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Evoregions: Mapping Shifts in Phylogenetic Turnover Across Biogeographic
bioRxiv preprint doi: https://doi.org/10.1101/650713; this version posted May 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Evoregions: Mapping Shifts in Phylogenetic Turnover Across Biogeographic 2 Regions 3 Running head: Mapping evolutionary important regions 4 Renan Maestri1,* & Leandro Duarte1,* 5 1Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, 6 Av. Bento Gonçalves 9500, CP 15007, Porto Alegre RS 91501-970, Brazil 7 *Correspondence be sent to: Departamento de Ecologia, Universidade Federal do Rio 8 Grande do Sul, Av. Bento Gonçalves 9500, CP 15007, Porto Alegre RS 91501-970, 9 Brazil; E-mail: [email protected]; [email protected] 10 ABSTRACT: Biogeographic regionalization offers context to the geographical 11 evolution of clades. The positions of bioregions inform both the spatial location of 12 clusters in species distribution and where their most important boundaries are. 13 Nevertheless, defining bioregions based on species distribution alone only incidentally 14 recovers regions that are important during the evolution of the focal group. The extent 15 to which bioregions correspond to centers of independent diversification depends on 16 how clusters of species composition naturally reflect the radiation of single clades, 17 which is not the case when mixed colonization occurred. Here, we showed that using 18 phylogenetic turnover based on fuzzy sets, instead of species composition, led to more 19 adequate detection of evolutionary important bioregions, that is, regions that truly 20 account for the independent diversification of lineages. -
Subfamily Nesomyinae)
bs_bs_banner Biological Journal of the Linnean Society, 2013, ••, ••–••. With 5 figures Latitude drives diversification in Madagascar’s endemic dry forest rodent Eliurus myoxinus (subfamily Nesomyinae) JEFF J. SHI1†, LAUREN M. CHAN1*‡, ZAFIMAHERY RAKOTOMALALA2,3, AMY M. HEILMAN1, STEVEN M. GOODMAN3,4 and ANNE D. YODER1 1Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA 2Département de Biologie Animale, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar 3Association Vahatra, BP 3972, Antananarivo 101, Madagascar 4Department of Zoology, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA Received 29 March 2013; revised 14 May 2013; accepted for publication 14 May 2013 Numerous hypotheses have been proposed for the historical processes governing the rich endemism of Madagas- car’s biodiversity. The ‘watershed model’ suggests that drier climates in the recent geological past have resulted in the contraction of forests around major watersheds, thereby defining areas of endemism. We test whether this hypothesis explains phylogeographical patterns in a dry forest-dependent rodent, Eliurus myoxinus, an endemic species widely distributed through western Madagascar. We sequenced the mitochondrial cytochrome b locus and nuclear introns of the β-fibrinogen and the growth hormone receptor genes for E. myoxinus. Using a parametric bootstrapping approach, we tested whether the mitochondrial gene tree data fit expectations of local differentiation given the watershed model. We additionally estimated population differentiation and historical demographic parameters, and reconstructed the spatial history of E. myoxinus to highlight spatial and temporal patterns of differentiation. The data do not support the watershed model as a clear explanation for the genetic patterns of diversity within extant E. -
Rodent Assemblages in the Mosaic of Habitat Types in the Zambezian Bioregion
diversity Article Rodent Assemblages in the Mosaic of Habitat Types in the Zambezian Bioregion Vincent R. Nyirenda 1,* , Ngawo Namukonde 1 , Matamyo Simwanda 2 , Darius Phiri 2, Yuji Murayama 3 , Manjula Ranagalage 3,4 and Kaula Milimo 5 1 Department of Zoology and Aquatic Sciences, School of Natural Resources, Copperbelt University, P.O. Box 21692, Kitwe 10101, Zambia; [email protected] 2 Department of Plant and Environmental Sciences, School of Natural Resources, Copperbelt University, P.O. Box 21692, Kitwe 10101, Zambia; [email protected] (M.S.); [email protected] (D.P.) 3 Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, Ibaraki 305-8572, Japan; [email protected] (Y.M.); [email protected] (M.R.) 4 Department of Environmental Management, Faculty of Social Sciences and Humanities, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka 5 Department of National Parks and Wildlife, Ministry of Tourism and Arts, Private Bag 1, Chilanga 10100, Zambia; [email protected] * Correspondence: [email protected]; Tel.: +260-977-352035 Received: 12 July 2020; Accepted: 21 September 2020; Published: 23 September 2020 Abstract: Rodent assemblages have ecological importance in ecosystem functioning and protected area management. Our study examines the patterns of assemblages of rodents across four habitat types (i.e., Miombo woodland, Acacia woodland, grasslands and farmlands) in the savanna environment. Capture-mark-recapture (CMR) methods were applied for data collection across the Chembe Bird Sanctuary (CBS) landscape. The Non-metric Multi-Dimensional Scaling (NMDS) was used for exploratory data analysis, followed by Analysis of Variance (ANOVA) and Tukey–Kramer’s Honestly Significant Difference (HSD) post-hoc tests. -
Mystromys Albicaudatus – White-Tailed Rat
Mystromys albicaudatus – White-tailed Rat Fynbos biomes; Dean 1978) and is endemic to South Africa and Lesotho. Although it occurs widely across the assessment region, it has an extremely patchy and fragmented area of occupancy due to its preference for microhabitats within vegetation types and transitory habitats created after fire. Out of a total area of 417,452 km2 broadly available to the species, we inferred an effective occupancy of only 3,719–12,061 km2. They are one of the rarest species in the small mammal community, as demonstrated by consistently low trapping records. Given estimated densities ranging from 0.9– 37 colonies (breeding pairs) / km2, the most likely mature population size is 6,997–13,648 individuals. Using Patrick O’Farrell grassland vegetation type as a proxy for subpopulation delineation, subpopulation size averages 178 ± 177 colonies and ranges from 1–760 colonies, which means Red List status (2016) Vulnerable C2a(i)*† the largest subpopulation is likely to be 712–1,521 mature Red List status (2008) Endangered A3c individuals. There is an inferred continuing decline from grassland habitat loss (due to expansion in crop Reasons for change Non-genuine change: agriculture, urban and industrial development, and climate New information change) and grassland habitat degradation, primarily from Red List status (2004) Endangered A3c suppression of natural fire regimens. This may represent an emerging threat to this species if fire is increasingly TOPS listing (NEMBA) (2007) None suppressed or controlled with the rise of intensive wildlife CITES listing None breeding. Grasslands are the most threatened biome in the assessment region with at least 33% transformed Endemic No already. -
Dendromus Nyikae – Nyika African Climbing Mouse
Dendromus nyikae – Nyika African Climbing Mouse records have been misidentified with other Dendromus species. Further molecular work is required to confirm the taxonomic status of the species within the assessment region. For this reason, we list this species as Data Deficient until new evidence is available for reassessment. Photograph Regional population effects: No dispersal is suspected, thus this is suspected to be an isolated population wanted (Skinner & Chimimba 2005). Distribution This species occurs widely but patchily throughout southern Africa, extending into the Eastern Arc mountains of Tanzania in the north (Monadjem et al. 2015). It is found only in natural moist savannah habitat. Although Regional Red List status (2016) Data Deficient* widespread throughout Zimbabwe, within the assessment National Red List status (2004) Near Threatened B1 region it has only been collected from the Tzaneen district of Limpopo (Rautenbach 1982). While recent specimens Reasons for change Non-genuine change: from Phinda Private Game Reserve in KwaZulu-Natal were New information provisionally assigned to D. nyikae (Rautenbach et al. 2014), subsequent genetic analyses revealed the Global Red List status (2016) Least Concern specimens to be D. melanotis sensu lato (Solano et al. TOPS listing (NEMBA) (2007) None 2014). It has not been recorded in Mozambique (Monadjem et al. 2015). CITES listing None Endemic Edge of range Population *Watch-list Data It is generally uncommon but can be locally abundant This species was first described from the (Happold 2013). It is a common species in Zimbabwe, but Nyika Plateau in Malawi. has not been recently recorded within the assessment region. The presence and taxonomic status of this species in South Africa needs further investigation. -
IRBP) in Ground Squirrels and Blind Mole Rats
Molecular Evolution of the Interphotoreceptor Retinoid Binding Protein (IRBP) in Ground Squirrels and Blind Mole Rats Research Thesis Presented in partial fulfillment of the requirements for graduation with Research Distinction in Biology in the Undergraduate Colleges of The Ohio State University by Bethany N. Army The Ohio State University December 2015 Project Advisor: Dr. Ryan W. Norris, Department of Evolution, Ecology and Organismal Biology Abstract Blind mole rats are subterranean rodents and spend most of their lifetime underground. Because these mammals live in a dark environment, their eyes have physically changed and even the role played by their eyes has changed. The processing of visual information begins in the retina, with the detection of light by photoreceptor cells. Interphotoreceptor retinoid binding protein (IRBP) is a transport protein, which facilitates exchange between photoreceptors and retinal-pigmented epithelium. The IRBP gene has been commonly used in rodent phylogenetic analyses, so I analyzed IRBP in blind mole rats to interpret its evolution and to see if there were any changes among the amino acids in the protein. To do this I used molecular data (cytochrome b and IRBP) from two groups of rodents, the muroids and the marmotines. I constructed phylogenetic trees and interpreted the amino acid sequence of IRBP. Blind mole rats had a slower rate of evolution than expected, but there were changes along the amino acid sequence of IRBP, which may indicate that the IRBP gene is functioning in a specialized way to meet the needs of the particular lifestyle of this mammal. Introduction: Blind mole rats, subfamily Spalacinae, are burrowing mammals that spend most of their life underground. -
Steatomys Krebsii – Krebs's Fat Mouse
Steatomys krebsii – Krebs’s Fat Mouse usually 35–60% of their head and body length (Monadjem et al. 2015). In parts of its range, S. krebsii overlaps with S. pratensis and these species are not easily distinguished, although S. krebsii has eight nipples, while S. pratensis has 10–14 (Monadjem et al. 2015). Photograph Assessment Rationale wanted This species is currently listed as Least Concern due to its wide distribution within the assessment region and its potential ability to survive in modified landscapes, such as fallow fields. However, it is naturally rare and trap-shy and thus population size may be fairly small. Further taxonomic resolution is required as this species, due to its disjunct distribution within the assessment region, may represent several endemic species, some of which may Regional Red List status (2016) Least Concern* potentially be threatened. For example, S. krebsii was not National Red List status (2004) Least Concern recorded during a recent survey in North West Province. Reassessment should follow once molecular and Reasons for change No change additional field data are available. Density and occupancy Global Red List status (2016) Least Concern should also be calculated to facilitate more accurate future revision. It is uncertain whether there are any threats to TOPS listing (NEMBA) (2007) None this species but presumably habitat loss is causing local CITES listing None and regional declines. Endemic No Regional population effects: This species has a scattered, disjunct distribution through southern Africa. *Watch-list Data Limited dispersal may be possible between South Africa There is a substantial degree of colour variation in and Botswana across the Molopo River, although the this species based on its geographic distribution, species was not recorded in North West Province during a ranging from an orange colouration in the recent survey (Power 2014). -
Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils Ryan Norris University of Vermont
University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2009 Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils Ryan Norris University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Recommended Citation Norris, Ryan, "Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils" (2009). Graduate College Dissertations and Theses. 164. https://scholarworks.uvm.edu/graddis/164 This Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. PHYLOGENETIC RELATIONSHIPS AND DIVERGENCE TIMES IN RODENTS BASED ON BOTH GENES AND FOSSILS A Dissertation Presented by Ryan W. Norris to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Specializing in Biology February, 2009 Accepted by the Faculty of the Graduate College, The University of Vermont, in partial fulfillment of the requirements for the degree of Doctor of Philosophy, specializing in Biology. Dissertation ~xaminationCommittee: w %amB( Advisor 6.William ~il~atrickph.~. Duane A. Schlitter, Ph.D. Chairperson Vice President for Research and Dean of Graduate Studies Date: October 24, 2008 Abstract Molecular and paleontological approaches have produced extremely different estimates for divergence times among orders of placental mammals and within rodents with molecular studies suggesting a much older date than fossils. We evaluated the conflict between the fossil record and molecular data and find a significant correlation between dates estimated by fossils and relative branch lengths, suggesting that molecular data agree with the fossil record regarding divergence times in rodents. -
The Input of DNA Sequences to Animal Systematics: Rodents As Study Cases
6 The Input of DNA Sequences to Animal Systematics: Rodents as Study Cases Laurent Granjon1 and Claudine Montgelard2 1Institut de Recherche Pour le Développement (IRD), CBGP(UMRIRD/INRA/CIRAD/MontpellierSupAgro), Campus de Bel-Air, Dakar, 2Biogéographie et Ecologie des Vertébrés (EPHE), Centre d’Ecologie Fonctionnelle et Evolutive (UMR 5175 CNRS), Montpellier, Cedex 5 1Senegal 2France 1. Introduction 1.1 General context The advent of molecular techniques, and especially the possibility to get DNA sequences that can then be compared between individuals of any taxon using more and more powerful algorithms of analysis, has represented a kind of revolution in systematics (Lecointre et al., 2006; Giribet et al., 2007). As in other groups, mammalian systematics was for long only based on morphological and anatomical characters. A brief history of Mammal taxonomy has been provided by Wilson & Reeder (2005: xxiii), starting by early works of Trouessart (1898-99, 1904-5) and ending by the compilation by Mc Kenna & Bell (1997). Since the latter, a huge quantity of data including a significant proportion of molecular ones has accumulated, that have greatly improved our view of the relationships between main mammalian groups (Springer et al., 2004), and increased the number of individual species in each of them (Wilson & Reeder, 2005). Rodents represent the most diverse order of Mammals, comprising around 40% of both generic and specific mammalian diversity (Wilson & Reeder, 2005). In one of the first significant contribution to the study of their classification, Tullberg (1899) subdivided them into two suborders, the Sciurognathi and Hystricognathi (see Hautier et al., 2011), based on morpho-anatomical characteristics of their skull. -
Saccostomus Campestris – Pouched Mouse
Saccostomus campestris – Pouched Mouse rural gardens, and there is no identified threat that could cause widespread population decline. Its wide habitat use allows this species to inhabit semi-deserts, grasslands, savannahs and forests and it has also been recorded on the edges of marshes and vleis. Regional population effects: It is distributed widely in the sub-region, and there is possible movement from Mozambique, Zimbabwe, Botswana and Namibia into South Africa. The ability of this species to utilise transformed habitats, including degraded grassland and agricultural land, increases the rescue effect of this species. Tim Jackson Distribution Regional Red List status (2016) Least Concern This species occurs extensively across the savannahs of National Red List status (2004) Least Concern southern Africa (Monadjem et al. 2015), and is present within southwestern Tanzania, Angola (Crawford-Cabral Reasons for change No change 1998), Zambia, Malawi, Zambia, Zimbabwe, Mozambique, Botswana, Namibia (although they are absent along the Global Red List status (2016) Least Concern coast and in the south), Swaziland and South Africa. TOPS listing (NEMBA) (2007) None Generally, their range extends from 50 m to about 2,000 m asl. CITES listing None Within the assessment region, the Pouched Mouse occurs Endemic No in all provinces. This species occurs in high numbers on the northern plains of the Kruger National Park The Pouched Mouse is so named (MacFadyen 2007) in the Limpopo Province, Tswalu from the large cheek pouches in which the animal Kalahari Reserve in the Northern Cape, and Venetia temporarily stores large quantities of food while Limpopo Nature Reserve in the Limpopo Province foraging; and occasionally females will carry their (MacFadyen pers. -
Perception of Predation Risk by African Giant Pouched Rats (Cricetomys Sp
Behavioural Processes 168 (2019) 103953 Contents lists available at ScienceDirect Behavioural Processes journal homepage: www.elsevier.com/locate/behavproc Perception of predation risk by African giant pouched rats (Cricetomys sp. nov) is higher in forest-edge microhabitats T ⁎ Biplang G. Yadoka,b, , Roger Pechc, Hazel Chapmana,b a School of Biological Sciences, University of Canterbury, PB 4800, Christchurch, New Zealand b Nigerian Montane Forest Project, Yelwa village, Taraba State, Nigeria c Landcare Research, Lincoln, P. O. Box 69040, Christchurch, New Zealand ARTICLE INFO ABSTRACT Keywords: How rodents perceive predation risk may alter their seed foraging behaviour and therefore potentially influence Predation risk the recruitment of tree species. In this study we used two methods to investigate the effect of predation risk on Giving up density habitat use by the African giant pouched rat (Cricetomys sp. nov) in Ngel Nyaki forest reserve, Nigeria. The first African giant pouched rat method was ‘giving up density’ (GUD), an index of perceived risk of predation at an artificial food patch, and the Afrotropical forests second was the ‘spool-and-line’ approach, whereby unravelling spools attached to rodent bodies are used to trace Foraging their tracks. For our GUD experiment, we chose four major sites in the forest; two representative of core habitat and two at the forest edge. Additionally, three characteristic microsites were used in the GUD experiment: dense understory, open understory and near-burrows. We hypothesised that GUDs would be lower on every succeeding observation day as rats learn to use the food patches, higher GUDs would be observed in the forest edges and open microsites, and rats would show preference for the microhabitats with least exposure to potential pre- dators. -
New Findings at Andrahomana Cave, Southeastern Madagascar
Portland State University PDXScholar Anthropology Faculty Publications and Presentations Anthropology 4-1-2008 New Findings at Andrahomana Cave, Southeastern Madagascar David A. Burney National Tropical Botanical Garden Natalie Vasey Portland State University, [email protected] Laurie R. Godfrey University of Massachusetts William L. Jungers Stony Brook University Ramilisonina Musée d'Art et d'Archéologie See next page for additional authors Follow this and additional works at: https://pdxscholar.library.pdx.edu/anth_fac Part of the Anthropology Commons Let us know how access to this document benefits ou.y Citation Details D.A. Burney, N. Vasey, L.R. Godfrey, Ramilisonina, W.L. Jungers, M. Ramarolahy, and L. Raharivony – New Findings at Andrahomana Cave, Southeastern Madagascar. Journal of Cave and Karst Studies, v. 70, no. 1, p. 13–24. This Article is brought to you for free and open access. It has been accepted for inclusion in Anthropology Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Authors David A. Burney, Natalie Vasey, Laurie R. Godfrey, William L. Jungers, Ramilisonina, M. F. Ramarolahy, and L. L. Raharivony This article is available at PDXScholar: https://pdxscholar.library.pdx.edu/anth_fac/47 D.A. Burney, N. Vasey, L.R. Godfrey, Ramilisonina, W.L. Jungers, M. Ramarolahy, and L. Raharivony – New Findings at Andrahomana Cave, Southeastern Madagascar. Journal of Cave and Karst Studies, v. 70, no. 1, p. 13–24. NEW FINDINGS AT ANDRAHOMANA CAVE, SOUTHEASTERN MADAGASCAR D.A. BURNEY1,*,N.VASEY2, L.R. GODFREY3,RAMILISONINA4, W.L. JUNGERS5,M.RAMAROLAHY6, AND L.