Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy.

BACKGROUND: Signaling by cAMP is organized in multiple distinct subcellular nanodomains regulated by cAMP-hydrolyzing PDEs (phosphodiesterases). Cardiac ß-adrenergic signaling has served as the prototypical system to elucidate cAMP compartmentalization. Although studies in cardiac myocytes have provided an understanding of the location and properties of a handful of cAMP subcellular compartments, an overall view of the cellular landscape of cAMP nanodomains is missing. METHODS: Here, we combined an integrated phosphoproteomics approach that takes advantage of the unique role that individual PDEs play in the control of local cAMP, with network analysis to identify previously unrecognized cAMP nanodomains associated with ß-adrenergic stimulation. We then validated the composition and function of one of these nanodomains using biochemical, pharmacological, and genetic approaches and cardiac myocytes from both rodents and humans. RESULTS: We demonstrate the validity of the integrated phosphoproteomic strategy to pinpoint the location and provide critical cues to determine the function of previously unknown cAMP nanodomains. We characterize in detail one such compartment and demonstrate that the PDE3A2 isoform operates in a nuclear nanodomain that involves SMAD4 (SMAD family member 4) and HDAC-1 (histone deacetylase 1). Inhibition of PDE3 results in increased HDAC-1 phosphorylation, leading to inhibition of its deacetylase activity, derepression of gene transcription, and cardiac myocyte hypertrophic growth. CONCLUSIONS: We developed a strategy for detailed mapping of subcellular PDE-specific cAMP nanodomains. Our findings reveal a mechanism that explains the negative long-term clinical outcome observed in patients with heart failure treated with PDE3 inhibitors.

Prevalence and genetic diversity of Bartonella spp. in wild small mammals from South Africa.

Bartonella spp. are intracellular bacteria associated with several re-emerging human diseases. Small mammals play a significant role in the maintenance and spread of Bartonella spp. Despite the high small mammal biodiversity in South Africa, there is limited epidemiological information regarding Bartonella spp. in these mammals. The main aim of this study was to determine the prevalence and genetic diversity of Bartonella spp. from wild small mammals from 15 localities in 8 provinces of South Africa. Small mammals (n = 183) were trapped in the Eastern Cape, Free State, Gauteng, Limpopo, Mpumalanga, Northern Cape, North West, and Western Cape provinces of South Africa between 2010 and 2018. Heart, kidney, liver, lung, and spleen were harvested for Bartonella DNA screening, and prevalence was determined based on the PCR amplification of partial fragments of the 16S-23S rRNA intergenic spacer (ITS) region, gltA, and rpoB genes. Bartonella DNA was detected in Aethomys chrysophilus, Aethomys ineptus, Gerbillurus spp., Lemniscomys rosalia, Mastomys coucha, Micaelamys namaquensis, Rhabdomys pumilio, and Thallomys paedulcus. An overall prevalence of 16.9% (31/183, 95% CI: 12.2%-23%) was observed. Bartonella elizabethae, Bartonella grahamii, and Bartonella tribocorum were the zoonotic species identified, while the remaining sequences were aligned to uncultured Bartonella spp. with unknown zoonotic potential. Phylogenetic analyses confirmed five distinct Bartonella lineages (I-V), with lineage IV displaying strong M. coucha host specificity. Our results confirm that South African wild small mammals are natural reservoirs of a diverse assemblage of Bartonella spp., including some zoonotic species with high genetic diversity, although prevalence was relatively low.IMPORTANCESmall mammals play a significant role in the maintenance and spread of zoonotic pathogens such as Bartonella spp. Despite the high small mammal biodiversity in southern Africa including South Africa, there is limited epidemiological information regarding Bartonella spp. in these mammals across the country. Results from our study showed the liver and spleen had the highest positive cases for Bartonella spp. DNA among the tested organs. Bartonella elizabethae, B. grahamii, and B. tribocorum were the three zoonotic species identified and five distinct Bartonella lineages (I-V) were confirmed through phylogenetic analyses. To the best of our knowledge, this study presents the first extensive nuclear diversity investigation of Bartonella spp. in South African small mammals in South Africa.

Underground speciation: Unraveling the systematics and evolution of the highly diverse tuco-tucos (genus Ctenomys) with genomic data.

Subterranean rodents of the genus Ctenomys (tuco-tucos) are endemic to South America and have experienced relatively recent radiation. There are about 67 recognized species that originated in approximately 1-2 MY. They stand out for their species richness, extraordinary chromosomal diversity, and wide range of habitat they occupy in the continent. Phylogenetic relationships among species of tuco-tucos have been challenging to resolve. Groups of closely-related species have been suggested, but their relationships must be resolved. This study estimates the phylogeny of the genus using massive sequencing, generating thousands of independent molecular markers obtained by RADseq, with a taxonomic sampling that includes 66% of the recognized species. The sequences obtained were mapped against the C. sociabilis genome, recovering up to 1215 widely shared RAD loci with more than 19,000 polymorphic sites. Our new phylogenetic hypothesis corroborated the species groups previously proposed with cytochrome b gene sequences and provided a much greater resolution of the relationships among species groups. The frater group is sister to all other tuco-tucos, whereas some of the earlierliest proposals placed the sociabilis group as sister to all other tuco-tucos. Ctenomys leucodon, previously proposed as an independent lineage, is associated with the frater group with moderate statistical support. The magellanicus and mendocinus are sister groups in a major clade formed by the boliviensis, talarum, tucumanus, torquatus, and opimus groups. Ctenomys viperinus, included in the phylogeny for the first time, belongs to the tucumanus group. This multi-locus phylogenetic hypothesis provides insights into the historical biogeography of understanding this highly diverse genus.

Ticks infesting terrestrial small mammals in a rural settlement in the Amazonas state, Brazil.

There is limited knowledge about tick diversity in the Amazon region. Here, we survey small terrestrial mammals for tick infestation at the Rio Pardo settlement, Amazonas State, Brazil. Sampling included rainy and dry seasons and four ecotones (primary forest, forest in regeneration, field crops and households). Each animal was inspected for ticks, which, if present, were placed in 70% alcohol and identified. Parasitological indexes were calculated and the presence/absence of ticks on hosts was tested for possible associations with independent variables (ecotone, host sex, host order, host family, host age and season). A total of 208 small mammals were captured, 47 individuals (10 species) in the primary forest, 124 (15 species) in the forest in regeneration, 11 (7 species) in the field crops, and 26 (4 species) in the households. A total of 14 small mammals were infested by ticks (overall prevalence: 6.7%; 95% CI: 3.72 - 11.04%), which consisted of 51 specimens that were identified into four species, as follows: Amblyomma humerale (32 nymphs); Ixodes luciae (6 females); Amblyomma coelebs (1 nymph); and Ornithodoros mimon (1 larva). In addition, 11 larvae were retained as Amblyomma spp. Only host order showed association (P = 0.002) with tick infestation, with marsupials 5.5 times more infested than rodents. Our record of O. mimon on D. marsupialis is the first on this host species, and the first record of a Argasidae tick in the Brazilian state of Amazonas. To the best of our knowledge, this is the first study that actively screened free-living terrestrial small mammals and provided data on prevalence, mean intensity and mean abundance of tick infestations in the Brazilian Amazonas state.

Survey of Rickettsia spp. in ticks (Acari: Ixodidae) infesting opossums (Didelphis albiventris) and capybaras (Hydrochoerus hydrochaeris) from an urban park in southeastern Brazil.

Ticks are hematophagous arthropods and, during feeding, may transmit pathogens to vertebrate hosts, including humans. This study aimed to investigate the presence of Rickettsia spp. in ticks collected between 2010 and 2013 from free-ranging capybaras (Hydrochoerus hydrochaeris) and opossums (Didelphis albiventris) that inhabit Sabiá Park in Uberlândia, Brazil. Overall, 1,860 ticks were collected: 1,272 (68.4%) from capybaras (487 of the species Amblyomma sculptum, 475 adults and 12 nymphs; 778 Amblyomma dubitatum, 727 adults and 51 nymphs; and seven larva clusters of the genus Amblyomma); and 588 (31.6%) from opossums (21 A. sculptum, one adult and 20 nymphs; 79 A. dubitatum, all nymphs; 15 Ixodes loricatus, 12 adults and three nymphs; 457 Amblyomma sp. larva clusters; 15 Ixodes sp. larva clusters; and one Argasidae larva cluster). Out of 201 DNA samples tested for the presence of Rickettsia spp. DNA using polymerase chain reaction (PCR) 12 showed amplification of a gtlA gene segment that was specific to Rickettsia bellii, a bacterium non-pathogenic to humans. As there has been a report showing serological evidence of infections caused by Rickettsia species of the spotted fever group (SFG) in capybaras and opossums in the park, including Rickettsia rickettsii, the etiological agent of Brazilian spotted fever, and considering the presence of A. sculptum ticks, which are aggressive to humans, as well as these vertebrate hosts, which are amplifiers of R. rickettsii, it is important to monitor the presence of SFG rickettsiae in the Sabiá Park, which is visited daily by thousands of people.

Embracing Heterogeneity in The Multicenter Stroke Preclinical Assessment Network (SPAN) Trial.

The Stroke Preclinical Assessment Network (SPAN) is a multicenter preclinical trial platform using rodent models of transient focal cerebral ischemia to address translational failure in experimental stroke. In addition to centralized randomization and blinding and large samples, SPAN aimed to introduce heterogeneity to simulate the heterogeneity embodied in clinical trials for robust conclusions. Here, we report the heterogeneity introduced by allowing the 6 SPAN laboratories to vary most of the biological and experimental model variables and the impact of this heterogeneity on middle cerebral artery occlusion (MCAo) performance. We included the modified intention-to-treat population of the control mouse cohort of the first SPAN trial (n=421) and examined the biological and procedural independent variables and their covariance. We then determined their impact on the dependent variables cerebral blood flow drop during MCAo, time to achieve MCAo, and total anesthesia duration using multivariable analyses. We found heterogeneity in biological and procedural independent variables introduced mainly by the site. Consequently, all dependent variables also showed heterogeneity among the sites. Multivariable analyses with the site as a random effect variable revealed filament choice as an independent predictor of cerebral blood flow drop after MCAo. Comorbidity, sex, use of laser Doppler flow to monitor cerebral blood flow, days after trial onset, and maintaining anesthesia throughout the MCAo emerged as independent predictors of time to MCAo. Total anesthesia duration was predicted by most independent variables. We present with high granularity the heterogeneity introduced by the biological and model selections by the testing sites in the first trial of cerebroprotection in rodent transient filament MCAo by SPAN. Rather than trying to homogenize all variables across all sites, we embraced the heterogeneity to better approximate clinical trials. Awareness of the heterogeneity, its sources, and how it impacts the study performance may further improve the study design and statistical modeling for future multicenter preclinical trials.

Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data.

Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.

Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus.

BACKGROUND: Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus. METHODS AND RESULTS: PCR amplification of the putative mtDNA CytB-D-loop fragment using 'universal' primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, 'haplotype B' was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop. CONCLUSIONS: Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.

[Geometric Approach to Phylogeographic Analysis Molecular Genetic Sequences: Principal Components and Dendrograms].

Currently, the search for manifestations of selection under the influence of the environment in molecular sequences is usually carried out within closely related species or at the intraspecific level. It is believed that at high taxonomic levels this is unpromising due to phylogenetic relationship. Cytochrome b amino acid sequences of 67 rodent and lagomorph species with known geographic coordinates were digitized using the AAindex database. Based on more than 200 thousand characters, the principal components were obtained. A well-known statistical method, which has not been previously used for such problems, was used, which makes it possible to orthogonally decompose multidimensional variability into intra- and intertaxon variability and analyze them separately. The subfamily level was selected. For the second principal component (17.05% of intertaxon variability), a correlation with latitude was found (r = 0.561; n = 67; p < E-5). The clear division into two groups, revealed by the first principal component (39.48% of intertaxon variability), which does not coincide with the taxonomic one, indicates a possible physicochemical underlying cause for the differences between them. This requires further research.

Evolutionary and ecological patterns of scatter- and larder-hoarding behaviours in rodents.

Scatter- and larder hoarding are the primary strategies of food-hoarding animals and have important implications for plant-animal interactions and plant recruitment. However, their origins and influencing factors have not been fully investigated across a wide range of taxa. Our systematic literature search amassed data for 183 seed-hoarding rodent species worldwide and tested relationships of seed-hoarding behaviours with phylogenetic signal, functional traits and environmental factors. We found that the evolution of hoarding strategies was not random in phylogeny, and scatter hoarding originated independently multiple times from larder hoarding. Rodents with higher encephalisation quotient (relative brain size), omnivorous diet (related to dependence on seeds) and inhabiting lower latitudes were disproportionately likely to scatter hoard. Despite body mass's potential relationship with competition through food defence, it was associated with food-hoarding strategy only in a few families. Our results show the need to study the community and ecological context of food-hoarding behaviours.

Serologic Surveillance for SARS-CoV-2 Infection among Wild Rodents, Europe.

We report results from serologic surveillance for exposure to SARS-CoV-2 among 1,237 wild rodents and small mammals across Europe. All samples were negative, with the possible exception of 1. Despite suspected potential for human-to-rodent spillover, no evidence of widespread SARS-CoV-2 circulation in rodent populations has been reported to date.Esitämme tulokset serologisesta tutkimuksesta, jossa seulottiin SARS-CoV-2 tartuntojen varalta 1,237 luonnonvaraista jyrsijää ja piennisäkästä eri puolilta Eurooppaa. Kaikki näytteet olivat negatiivisia, yhtä näytettä lukuun ottamatta. SARS-CoV-2:n läikkymisen ihmisistä jyrsijöihin on arveltu olevan mahdollista, mutta todisteet viruksen laajamittaisesta leviämisestä jyrsijäpopulaatioissa puuttuvat.

Evaluation of sperm membrane functionality during epididymal transit in red-rumped agouti (Dasyprocta leporina).

We studied the sperm membrane functionality through the epididymal transit by comparing different hypoosmotic solutions and verifying possible associations among osmotic response and functional parameters of sperm in red-rumped agouti (Dasyprocta leporina). For this purpose, epididymal sperm from six sexually mature male agoutis were collected via flotation. Then, analyses of sperm parameters and hypoosmotic swelling test using different hypoosmotic solutions (0, 50 and 200 mOsm/L) in different regions of the epididymis (caput, corpus and cauda) were performed. There was an increase (p < .05) in the values for sperm concentration, the total number of sperm recovered, total and progressive motility, average path velocity, straight-line velocity, curvilinear velocity, and rapid and medium subpopulations following the caput-corpus-cauda direction. Regardless of the hypoosmotic solution, the agouti sperm membrane presented similar functional integrity in all the epididymal regions. Moreover, the highest (p < .05) osmotic responses were reached with the use of 50 mOsm/L solution in comparison to 0 and 200 mOsm/L for all the regions. Significant correlations among osmotic response and some sperm kinetic parameters were observed, especially in epididymal caput, while no correlations were found in the region of the cauda. In summary, red-rumped agouti sperm present similar membrane functionality during epididymal transit, but there are evident correlations among such functionality and sperm kinetic parameters, especially in the caput region. Moreover, we indicate the use of a 50 mOsm/L hypoosmotic solution for the analysis of this parameter through the hypoosmotic swelling test.

Zoonotic ecotype-I of Anaplasma phagocytophilum in sympatric wildcat, pine marten and red squirrel - Short communication.

Anaplasma phagocytophilum is the causative agent of granulocytic anaplasmosis in humans, dogs, cats, horses and tick-borne fever in ruminants. In Europe, its main vector is the tick species Ixodes ricinus. In this study, spleen and liver samples, as well as ticks from 18 wild-living mammals (belonging to seven species) were analysed for the presence of A. phagocytophilum with molecular methods. The zoonotic ecotype-I of A. phagocytophilum was identified in a European wildcat (Felis silvestris) and its tick, a European pine marten (Martes martes) and a Eurasian red squirrel (Sciurus vulgaris). All PCR-positive samples were collected in 2019 and originated in the same geographic area. These results indicate that taxonomically diverse mammalian species can maintain the local enzootic cycle of the same genotype of A. phagocytophilum. To the best of our knowledge, this is the first report of the zoonotic variant of A. phagocytophilum in the wildcat and in the European pine marten in a broad geographical context, as well as in the red squirrel in Hungary. Since all these host species are well known for their urban and peri-urban presence, the results of this study verify their role in the synanthropic enzootic cycle of granulocytic anaplasmosis and tick-borne fever.

Finding of Molars of the Archaic Vole Lasiopodomys (Stenocranius) Gregaloides (Hinton, 1923) (Mammalia, Rodentia, Cricetidae) in the Late Pleistocene of the Southern Urals.

A total of 1250 lower first molars (m1) of voles (Arvicolini) were studied from Late Pleistocene deposits (the radiocarbon dates from rodent bones: 17 100 ± 50 IGANAMS-9117; 13 255 ± 60 IGANAMS-9116) of the Imanay Cave (southern Urals, 53°02' N, 56°26' E). Of these, 24 m1 of voles of the subgenus Stenocranius were found to have broadly connected triangles T4 and T5 (Pitymys-Rhombus) at the base of the anteroconid. This structure is characteristic of lower m1 of Lasiopodomys (Stenocranius) gregaloides (Hinton, 1923) from faunas of the second half of the Early Pleistocene and the first half of the Middle Pleistocene. Molars with such morphology have not been found so far in the Late Pleistocene and Holocene locations of Europe and the Urals.

Complex reticulate evolution of speckled brush-furred rats (Lophuromys) in the Ethiopian centre of endemism.

The Ethiopian highlands represent a remarkable biodiversity 'hot spot' with a very high number of endemic species, even among vertebrates. Ethiopian representatives of a species complex of speckled brush-furred rats (Lophuromys flavopunctatus sensu lato) inhabit highland habitats ranging from low-elevation forests to Afroalpine grasslands. These may serve as a suitable model for understanding evolutionary processes leading to high genetic and ecological diversity in montane biodiversity hot spots. Here, we analyse the most comprehensive genetic data set of this group, comprising 315 specimens (all nine putative Ethiopian Lophuromys taxa sampled across most of their distribution ranges) genotyped at one mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD sequencing. We performed phylogenetic analyses, delimited species and mapped their distribution and estimated divergence time between species (under the species-tree framework) and mitochondrial lineages. We found significant incongruence between mitochondrial and nuclear phylogenies, most probably caused by multiple interspecific introgression events. We discuss alternative scenarios of Ethiopian Lophuromys evolution, from retention of ancestral polymorphism to hybridization upon secondary contact of partially reproductively isolated lineages leading to reticulate evolution. Finally, we use the diversity of the speckled brush-furred rats for the description of the main biogeographic patterns in the fauna of the Ethiopian highlands.

New species boundaries and the diversification history of marsh rat taxa clarify historical connections among ecologically and geographically distinct wetlands of South America.

Taxa with broad geographic ranges that occur in different biomes and exhibit plastic morphological traits and/or adaptations to particular habitats make inferences about species boundaries especially challenging. However, technological and conceptual advances in the generation and analysis of genomic data have advanced the description of biodiversity. Here we address the outstanding questions about the delimitation of species in the genus Holochilus, a rodent with morphological specializations to wetland habitats distributed throughoutthe South America, using genome-wide SNP and morphometric data. Specifically, we apply a Bayesian model-based species delimitation that revealed significant re-arrangements of species boundaries based on consideration of both morphometric and genomic data alone, or in combination. With these shifts in species boundaries, our results provide an insightful framework for inferring the group's biogeographic history and considering possible connections between disjoint biomes in South America. Because of the ecological constraints of the marsh rats, and with the proposed taxonomic re-arrangements, the significance of our findings extends beyond systematics and suggests how diversification might be associated with past ecological/environmental changes during the Pleistocene. Overall, this study highlights how genomic data can provide phylogenetic information for resolving relationships among species of Holochilus, but also the importance of integrative approaches to identify evolutionary independent species. For the relatively understudied vast wetlands of South America, a robust species delimitation framework therefore becomes a critical source of data relevant to hypotheses about the history of the biomes themselves.

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

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.

Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera.

The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.

Rodents as indicators of the climatic conditions during the Middle Pleistocene in the southwestern Mediterranean region: implications for the environment in which hominins lived.

Rodents are a very useful tool in reconstructing the environment of the past, especially owing to their rapid response to climate change, their small home range, and their restricted habitat requirements. They are a highly diverse group of mammals, which have high reproduction rates and as a result can evolve rapidly. The abundance of their microfossil remains in archaeological and paleontological sites permits robust statistical analyses to reconstruct the past climate and environment. Recently, a number of studies have affirmed the need to deepen the climatic characterization of the European Quaternary, the Middle Pleistocene being an important stage for ascertaining how our hominin ancestors lived. The aim of this study is to characterize the climatic conditions in which hominins lived in southwestern Mediterranean Europe during the Middle Pleistocene. To reconstruct these climatic conditions, we apply the bioclimatic model to rodent assemblages from Middle Pleistocene sites with human remains (Caune de l'Arago, Sima de los Huesos, Aroeira cave, Visogliano, Trinchera Galeria, and Mollet cave). Based on the percentage distribution of the species in different climate types and applying multiple linear regressions, we estimated the mean annual temperature, the mean temperature of the coldest month, and the mean temperature of the warmest month. We compared these estimates with data collected over the last 30 years from nearby meteorological stations to obtain the differences with current climate and observe the fluctuations. The climatic conditions obtained from the results of this study show that, while in Iberia mild climatic condition prevailed, in southern France and northeastern Italy harsher weather conditions were indicated.

Diversity, distribution and changes in communities of fleas on small mammals along the elevational gradient from the Pannonian Plain to the Carpathian Mountains.

The causal chain of parasite-host-environment interactions, the so-called 'dual parasite environment', makes studying parasites more complicated than other wild organisms. A sample of 65 282 fleas taken from 336 different locations were analysed for changes in the distribution, diversity and compensation of flea communities found on small mammals along an elevational diversity gradient ranging from the Pannonian Plain to the base of the Carpathian summits. The fleas were divided into four groups, which were derived from changes in abundance and occurrence determined from cluster analysis. They are (1) flea species whose range seems unrelated to any change in elevation; (2) species that avoid high altitudes; (3) a group that can be subdivided into two types: (i) host-specific fleas and (ii) mountains species and (4) species opting for high altitudes on the gradient or preferring lower to middle elevations below 1000 m. Our study showed a unimodal pattern of flea diversity along the elevational gradient. It indicated that seasonality significantly conditions changes in biodiversity and patterns of spatial change along the elevational gradient, with specific flea species influenced by their host, while the impact of environmental conditions is more pronounced in opportunistic flea species.