Display omitted
•Dated phylogeny of family Muridae using a multilocus dataset.•Thorough review of the fossil record and their cross-validation.•Implementation of multiple fossil constrains within the ...Muridae.•Origin of the family Muridae during Early Miocene.•Dynamic biogeographic scenario with repeated colonisation events in Paleotropics.
Murid rodents (Rodentia: Muridae) represent the most diverse and abundant mammalian family. In this study, we provide a refined set of fossil calibrations which is used to reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 161 species representing 82 murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of nine robust fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 22.0–17.0 million years ago (Ma), and that most major lineages (i.e. tribes) started diversifying ca. 10 Ma. Historical biogeography analyses support the tropical origin for the family, with an initial internal split (vicariance event) between Afrotropical and Oriental (Indomalaya and Philippines) lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.
Aim
Assessment of phylogenetic diversity and biogeographical affinities of the rodent fauna from one of the most neglected areas in Africa.
Location
Angola (with biogeographical implications in ...adjacent areas).
Methods
Inference of mitochondrial phylogenies for rodent genera occurring in Angola, delimitation of molecular operational taxonomic units (MOTUs), assessment and comparative analysis of their geographical distribution.
Results
We provide the first genetic evidence for the presence of 44 rodent taxa from 19 genera and 5 families in Angola, including twelve MOTUs endemic to Angola, and 12 candidate new species, pending integrative taxonomic revisions. The endemic MOTUs were found almost exclusively in the Angolan Miombo Woodlands and in Angolan montane forest−grassland mosaic.
Main conclusions
The highly diverse Angolan rodent fauna is mostly composed of and shows affinities with taxa originating from three major biogeographical regions of sub‐Saharan Africa (Zambezian, South African and Congolian). It is also composed of a unique fauna comprising palaeoendemics from the Angolan Highlands. The species richness and the endemism detected in the Angolan montane forest−grassland mosaic and in the Angolan escarpment forests suggest that these are relevant for conservation, but more studies including other biological groups are needed to fundament this.
Resumo
Objetivo
Avaliação da diversidade filogenética e das afinidades biogeográficas da fauna de roedores de uma das áreas mais negligenciadas de África.
Localização
Angola (com implicações biogeográficas para as áreas adjacentes).
Métodos
Inferência de filogenias mitocondriais para géneros de roedores presentes em Angola, delimitação de unidades taxonómicas operacionais moleculares (MOTUs), avaliação e análise comparativa da sua distribuição geográfica.
Resultados
Aqui fornecemos evidências genéticas para a presença de 44 taxa de roedores de 19 géneros e 5 famílias em Angola, incluindo 12 MOTUs endémicas de Angola, e 12 espécies potencialmente novas, dependentes de revisões taxonómicas integrativas. As MOTUs endémicas foram encontradas quase exclusivamente em Mata de Miombo Angolana e no Mosaico de Floresta‑Prado de Montanha de Angola.
Conclusões principais
A fauna de roedores angolana é diversa, e composta por taxa originários de três regiões biogeográficas da África Subsaariana (Zambezíaca, da África Austral e Congolesa), com as quais tem afinidades biogeográficas. Esta fauna contém também elementos únicos, que consistem em paleoendemismos das Terras Altas de Angola. A riqueza específica e os endemismos detetados no Mosaico de Floresta‑Prado de Montanha de Angola e nas florestas da escarpa angolana sugerem que estas áreas são relevantes para a conservação, mas são necessários mais estudos em outros grupos biológicos para fundamentar esta tese.
Palavras‐chave
barcoding de DNA, endemismo, filogeografia, Muridae, ratazanas, ratos, região da África Austral, região Zambezíaca, unidades taxonómicas operacionais moleculares.
Aim
Deserts are generally perceived as areas of low diversity, and hence receive little attention from researchers and conservationists. Squamates are the dominant group of vertebrates in arid ...regions, and as such represent an ideal model to study biodiversity patterns in these areas. We examine spatial patterns of diversity, evolutionary history and endemism of terrestrial squamates of the Arabian Peninsula and test hypotheses on the role of topography and history of isolation so as to identify possible environmental drivers of diversification.
Location
The Arabian Peninsula.
Taxon
Squamate reptiles (Squamata; lizards and snakes).
Methods
We generated distribution maps for all Arabian squamate species (including yet undescribed) and reconstructed their phylogenetic relationships using existing and newly produced genetic data for nearly all the species. We assessed patterns of the distribution of species richness, phylogenetic diversity and phylogenetic endemism across the peninsula to identify areas that could be considered evolutionary or endemicity hotspots for squamates. We evaluated community turnover across the peninsula and assessed the possible environmental drivers affecting the diversity of Arabian squamates in a regression framework.
Results
The main hotspots of Arabian squamate diversity are mostly along the mountains that rim the peninsula while the most arid, central regions support a low diversity of species. The distribution of the phylogenetic diversity mirrors that of the species richness. Phylogenetic endemism is also highest in the mountains, especially when only endemic species are analysed. The deserts of northern Arabia are poor in terms of species richness and they show low connectivity to the peninsular communities. Topographic heterogeneity is the strongest predictor for Arabian squamates, followed by elevation. There is no correlation between richness and temperature.
Main conclusions
The mountains of Arabia support rich and unique squamate communities that are dominated by local radiations of closely related and narrow‐ranging species. In particular, the Asir Mountains of SW Arabia, Dhofar Province of Oman and the Hajar Mountains of northern Oman and UAE show unprecedented levels of squamate endemism and phylogenetic endemism. While many generalist species range across Arabia, a low number of species is shared between the peninsula and mainland Asia, indicating an effective isolation of the Arabian fauna. Squamate richness is highest in heterogeneous, topographically complex habitats.
Small terrestrial mammals and their biogeographical affinities were studied on Mount Kitumbeine, one of the little known volcanoes in the Gregory Rift Valley (northern Tanzania). In June, 2015, a ...total of 10 species, two insectivores and eight rodents, were recorded during a short-time sampling in two high altitude habitats. Taxonomic identification was based on genetic data allowing zoogeographic interpretations. For most of the taxa, there was a clear link with fauna of the northern part of the Eastern Arc Mountains, but there were also species with their core distributions in the Albertine Rift Mountains (
) as well as taxa endemic to the volcanic Northern Highlands (e.g. Hanang or Ngorongoro), such as
and probably
. Comparison of genotyped small mammals from Kitumbeine and neighboring hills with previously collected data revealed the first genetically confirmed Tanzanian records of two species (
and
) and one species (
) is reported for the first time from Zambia. The present study thus showed that, even in such well-studied areas like northern Tanzania, a basic faunistic survey of mammals can still bring interesting results stressing the need to study biota in small and poorly known areas.
Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, ...including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete.
We performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene.
We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.
Abstract
The geological and geographical settings of the Eastern Mediterranean have resulted in complex patterns of intraspecific diversifications and phylogeographical histories that can be observed ...in squamates. In this study, we examined genetic differentiation of the Collared dwarf racer (Platyceps collaris) using a multilocus genetic dataset with a sampling that covered the entire range of the species. We developed distribution models in current and past climatic conditions to assess the dynamics of the species distribution through time. We sequenced a fragment of the cytochrome b mitochondrial gene of the holotype and eight paratypes of Coluber rubriceps thracius, which is considered a synonym of Platyceps collaris. Our results show that there are two distinct clades within P. collaris, one occupying the Balkans and western and southern Anatolia (termed the Balkan–Anatolian clade), the other in the Levant (termed the Levantine clade). All type specimens of C. r. thracius are genetically identical and cluster within the Balkan–Anatolian clade. Distribution models indicate the presence of two refugia during climatically challenging periods. One was in western Anatolia and served as a source for the colonization of the Balkans and southern Anatolia, and the other was in the northern Levant, from where P. collaris dispersed further south. According to our results, we revise the subspecific taxonomy of P. collaris.
In this study we report findings in roosting ecology, ectoparasites, echolocation characteristics and the phylogenetic position of Cardioderma cor, an impressive bat species that is distributed ...throughout the savannas and woodlands of eastern Africa. For individuals caught in Mago National Park, Ethiopia, we recorded broadband frequency-modulated ultrasound signals having very short duration (2 ms) with three harmonic components. The mean peak frequency of the first harmonic was 50.4 kHz and the mean inter-signal interval was 186 ms. Phylogenetic reconstructions of all known species from the family Megadermatidae based on DNA sequences of two mitochondrial and four nuclear genes yielded incongruent topologies (both Bayesian inference and maximum likelihood analysis) with only weak support for nodes. The phylogeny that combined all six loci into a species tree was not congruent with any previous inference based on dental or cranial characteristics, but it suggested separate generic status of two Megaderma species. However, additional genetic data are necessary to resolve the phylogeny of Megadermatidae, a group that probably evolved by simultaneous divergence of all five extant lineages.
Aim: Grammomys are mostly arboreal rodents occurring in forests, woodlands and thickets throughout sub-Saharan Africa. We investigated whether the divergence events within the genus follow the ...existing evolutionary scenario for the development of African forests since the late Miocene. Location: Sub-Saharan African forests and woodlands. Methods: We inferred the molecular phylogeny of Grammomys using Bayesian and maximum likelihood methods and DNA sequences of 351 specimens collected from across the distribution of the genus. We mapped the genetic diversity, estimated the divergence times by a relaxed clock model and compared evolution of the genus with forest history. Results: Phylogenetic analysis confirms the monophyly of Grammomys and reveals five main Grammomys lineages with mainly parapatric distributions: (1) the poensis group in Guineo-Congolese forests; (2) the selousi group with a distribution mainly in coastal forests of southern and eastern Africa; (3) the dolichurus group restricted to the easternmost part of South Africa; (4) the macmillani group in the northern part of eastern and Central Africa with one isolated species in Guiñean forests; and (5) the surdaster group, widely distributed in eastern Africa south of the equator. Every group contains well supported sublineages suggesting the existence of undescribed species. The earliest split within the genus (groups 1 vs. 2-5) occurred in the late Miocene and coincides with the formation of the Rift Valley which resulted in the east-west division of the initially pan-African forest. The subsequent separation between groups (2 vs. 3-5) also dates to the end of the Miocene and suggests the split between Grammomys from coastal to upland forests in eastern Africa followed by a single dispersal event into western Africa during the Pleistocene. Conclusions: The evolutionary history of the genus Grammomys closely reflects the accepted scenario of major historical changes in the distribution of tropical African forests since the late Miocene.
e14042
Background: Diffuse gliomas are highly heterogenous tumors with variable biological behaviors, including high intratumor and extratumor heterogeneity, and with occurrence of recurrent lesions ...in majority of patients. During disease progression, gliomas undergo cellular and genomic evolution with newly acquired genetic properties. However, the mechanism of this complicated process associated with treatment failure is poorly understood. In this retrospective study, we performed cytogenomic analyses of primary and recurrent tumors in five patients with diffuse glioma who underwent surgical resections or biopsies of multiple recurrences. Methods: One primary and at least two recurrent freshly resected tumor tissues from each patient were analyzed using combination of cytogenomic methods. To assess specific and random copy number alterations (CNAs), I-FISH (Abbott Molecular, MetaSystems), array CGH/SNP (Agilent) and MLPA (MRC Holland) were performed. Methylation of MGMT promoter was investigated by methylation-specific MLPA (MRC Holland) and mutations of 67 genes associated with solid tumors were assessed by target NGS (Archer VariantPlex Solid Tumor, Invitae). Results: All five patients (three men and two women) experienced recurrence with newly acquired genetic or epigenetic changes. We observed a higher frequency of CNAs in recurrent gliomas than in primary tumors. Moreover, several aberrations were not detected in recurrence despite being found in earlier samples. As a primary event we proved mutation R132H of IDH1 gene. In addition, we detected methylation of the MGMT promoter, CDKN2A/B homozygous deletion, and RB1 deletion as later events that were probably associated with higher tumor grades. Besides the typical genomic changes, we detected many aberrations with unknown or unclear prognostic relevance (e.g. inframe deletion in TP53, p.Met243_Asn247del, etc.). The progression to a higher grade of glioma occurred in four patients. Conclusions: The evolutional patterns in glioma depend on clonal selection caused by CNAs, mutations, genetic drift, intratumor heterogeneity and/or the patient’s treatment. Recurrence may arise from one major tumor clone or from one or more subclones within the primary tumor through. Integrated cytogenomic analyses of genetic/epigenetic profiles of primary and all recurrent tissues can contribute to a better understanding of mechanisms responsible for these processes and to identification of new alterations related to gliomas progression and/or resistance to treatment. These biomarkers could subsequently serve as new therapeutic targets for personalized treatment.
We explore diversity of African pouched mice, genus Saccostomus (Rodentia, Nesomyidae), by sampling molecular and morphological variation across their continental‐scale distribution in southern and ...eastern African savannahs and woodlands. Both mitochondrial (cytochrome b) and nuclear DNA (IRBP, RAG1) as well as skull morphology confirm the distinction between two recognized species, S. campestris and S. mearnsi, with disjunct distribution in the Zambezian and Somali–Maasai bioregions, respectively. Molecular dating suggests the divergence of these taxa occurred in the Early Pliocene, 3.9 Ma before present, whereas the deepest divergences within each of them are only as old as 2.0 Ma for S. mearnsi and 1.4 Ma for S. campestris. Based on cytochrome b phylogeny, we defined five clades (three within S. campestris, two in S. mearnsi) whose species status was considered in the light of nuclear DNA markers and morphology. We conclude that S. campestris group consists of two subspecies S. campestris campestris (Peters, 1846; comprising two cytochrome b clades) and S. campestris mashonae (de Winton, 1897) that are moderately differentiated, albeit distinct in IRBP and skull form. They likely hybridize to a limited extent along the Kafue–Zambezi Rivers. Saccostomus mearnsi group consists of two species, S. mearnsi (Heller, 1910) and S. umbriventer (Miller, 1910), that are markedly differentiated in both nuclear markers and skull form and may possibly co‐occur in south‐western Kenya and north‐eastern Tanzania. Analysis of historical demography suggests both subspecies of S. campestris experienced population expansion dated to the Last Glacial. In the present range of S. campestris group, the distribution modelling suggests a moderate fragmentation of suitable habitats during the last glacial cycle, whereas in the range of S. mearnsi group it predicts substantial shifts of its occurrence in the same period.
PDF
