Karyotypic Reshuffling in the Genus Rhipidomys (Rodentia: Cricetidae: Sigmodontinae) Revealed by Zoo-FISH.

INTRODUCTION: Rhipidomys is the second most specious and the most widespread genus of the tribe Thomasomyini. Chromosomal data have been an important tool in the taxonomy of the group that presents low variability of diploid number (2n) and highly variable fundamental numbers (FNs). Despite such diversity, the genus has been studied mainly by classical and banding cytogenetic techniques. METHODS: This study performed a comparative study between R. emiliae (2n = 44, FN = 52), R. macrurus (2n = 44, FN = 49), R. nitela (2n = 50, FN = 71), and R. mastacalis (2n = 44, FN = 72) using chromosome painting probes of two Oryzomyini species. RESULTS: Our analysis revealed pericentric inversion as the main rearrangement involved in the karyotype evolution of the group, although tandem fusions/fissions were also detected. In addition, we detected eight syntenic associations exclusive of the genus Rhipidomys, and three syntenic associations shared between species of the tribe Thomasomyini and Oryzomyini. CONCLUSION: Comparative cytogenetic analysis by ZOO-FISH on genus Rhipidomys supports a pattern of chromosomal rearrangement already suggested by comparative G-banding. However, the results suggest that karyotype variability in the genus could also involve the occurrence of an evolutionary new centromere.

Chromosomal rearrangements played an important role in the speciation of rice rats of genus Cerradomys (Rodentia, Sigmodontinae, Oryzomyini).

Rodents of the genus Cerradomys belong to tribe Oryzomyini, one of the most diverse and speciose groups in Sigmodontinae (Rodentia, Cricetidae). The speciation process in Cerradomys is associated with chromosomal rearrangements and biogeographic dynamics in South America during the Pleistocene era. As the morphological, molecular and karyotypic aspects of Myomorpha rodents do not evolve at the same rate, we strategically employed karyotypic characters for the construction of chromosomal phylogeny to investigate whether phylogenetic relationships using chromosomal data corroborate the radiation of Cerradomys taxa recovered by molecular phylogeny. Comparative chromosome painting using Hylaeamys megacephalus (HME) whole chromosome probes in C. langguthi (CLA), Cerradomys scotii (CSC), C. subflavus (CSU) and C. vivoi (CVI) shows that karyotypic variability is due to 16 fusion events, 2 fission events, 10 pericentric inversions and 1 centromeric repositioning, plus amplification of constitutive heterochromatin in the short arms of the X chromosomes of CSC and CLA. The chromosomal phylogeny obtained by Maximum Parsimony analysis retrieved Cerradomys as a monophyletic group with 97% support (bootstrap), with CSC as the sister to the other species, followed by a ramification into two clades (69% of branch support), the first comprising CLA and the other branch including CVI and CSU. We integrated the chromosome painting analysis of Eumuroida rodents investigated by HME and Mus musculus (MMU) probes and identified several syntenic blocks shared among representatives of Cricetidae and Muridae. The Cerradomys genus underwent an extensive karyotypic evolutionary process, with multiple rearrangements that shaped extant karyotypes. The chromosomal phylogeny corroborates the phylogenetic relationships proposed by molecular analysis and indicates that karyotypic diversity is associated with species radiation. Three syntenic blocks were identified as part of the ancestral Eumuroida karyotype (AEK): MMU 7/19 (AEK 1), MMU 14 (AEK 10) and MMU 12 (AEK 11). Besides, MMU 5/10 (HME 18/2/24) and MMU 8/13 (HME 22/5/11) should be considered as signatures for Cricetidae, while MMU 5/9/14, 5/7/19, 5 and 8/17 for Sigmodontinae.

Characterization of repetitive DNA on the genome of the marsh rat Holochilus nanus (Cricetidae: Sigmodontinae).

Repetitive DNA are sequences repeated hundreds or thousands of times and an abundant part of eukaryotic genomes. SatDNA represents the majority of the repetitive sequences, followed by transposable elements. The species Holochilus nanus (HNA) belongs to the rodent tribe Oryzomyini, the most taxonomically diverse of Sigmodontinae subfamily. Cytogenetic studies on Oryzomyini reflect such diversity by revealing an exceptional range of karyotype variability. However, little is known about the repetitive DNA content and its involvement in chromosomal diversification of these species. In the search for a more detailed understanding about the composition of repetitive DNA on the genome of HNA and other species of Oryzomyini, we employed a combination of bioinformatic, cytogenetic and molecular techniques to characterize the repetitive DNA content of these species. RepeatExplorer analysis showed that almost half of repetitive content of HNA genome are composed by Long Terminal Repeats and a less significant portion are composed by Short Interspersed Nuclear Elements and Long Interspersed Nuclear Elements. RepeatMasker showed that more than 30% of HNA genome are composed by repetitive sequences, with two main waves of repetitive element insertion. It was also possible to identify a satellite DNA sequence present in the centromeric region of Oryzomyini species, and a repetitive sequence enriched on the long arm of HNA X chromosome. Also, comparative analysis between HNA genome with and without B chromosome did not evidence any repeat element enriched on the supernumerary, suggesting that B chromosome of HNA is composed by a fraction of repeats from all the genome.

Reevaluation of Rhipidomys emiliae (J.A. Allen 1916) and description of a new Rhipidomys (Rodentia: Cricetidae) species from Amazonia and Cerrado.

We present the revalidation of the sigmodontinae rodent species R. emiliae, as well as the description of a new species for the genus Rhipidomys. The maximum likelihood analysis recovers R. emiliae as sister species of the clade with Rhipidomys sp. nov. and R. ipukensis, with high bootstrap values. Comparisons between these species based on the external, cranial, and dental morphology identified several unique characters in Rhipidomys sp. nov., including more grayish brown color of the dorsal coat, subsquamosal fenestra wide and long, angular process ends in the same position of the end of condyloid process, conspicuous protostyle and enterostyle. We describe a new karyotype (2n = 44 and FN = 64) for the genus and, based on an integrative analysis together with morphology and molecular phylogeny, assign it to R. emiliae, and assign the karyotype with 2n = 44 and FN = 52 to Rhipidomys sp. nov.. The analysis integrating data indicated that R. emiliae has a geographic distribution restricted to the lowlands of eastern Amazonia, whereas Rhipidomys sp. nov. occurs in the central Amazonia and Cerrado. The data showed that some Rhipidomys species have its distribution currently limited by rivers, as Rhipidomys sp. nov. occurring west of the Araguaia-Tocantins interfluve, R. emiliae east of the Tocantins River, and R. ipukensis between the Tocantins and Araguaia rivers. This work, in addition to revealing a still unknown biodiversity describing a species, brings a new understanding to the genus, and shows how integrating different markers helps in the correct association between the nominal form and the karyotype.

The emergence of a new sex-system (XX/XY1Y2) suggests a species complex in the "monotypic" rodent Oecomys auyantepui (Rodentia, Sigmodontinae).

X-autosome translocation (XY1Y2) has been reported in distinct groups of vertebrates suggesting that the rise of a multiple sex system within a species may act as a reproductive barrier and lead to speciation. The viability of this system has been linked with repetitive sequences located between sex and autosomal portions of the translocation. Herein, we investigate Oecomys auyantepui, using chromosome banding and Fluorescence In Situ Hybridization with telomeric and Hylaeamys megacephalus whole-chromosome probes, and phylogenetic reconstruction using mtDNA and nuDNA sequences. We describe an amended karyotype for O. auyantepui (2n = 64♀65♂/FNa = 84) and report for the first time a multiple sex system (XX/XY1Y2) in Oryzomyini rodents. Molecular data recovered O. auyantepui as a monophyletic taxon with high support and cytogenetic data indicate that O. auyantepui may exist in two lineages recognized by distinct sex systems. The Neo-X exhibits repetitive sequences located between sex and autosomal portions, which would act as a boundary between these two segments. The G-banding comparisons of the Neo-X chromosomes of other Sigmodontinae taxa revealed a similar banding pattern, suggesting that the autosomal segment in the Neo-X can be shared among the Sigmodontinae lineages with a XY1Y2 sex system.

Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae).

Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 12 main groups of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of a rapid radiation upon the group entrance into South America. Here, we attempted to resolve phylogenetic relationships within Sigmodontinae using target capture and high-throughput sequencing of ultraconserved elements (UCEs). We enriched and sequenced UCEs for 56 individuals and collected data from four already available genomes. Analyses of distinct data sets, based on the capture of 4634 loci, resulted in a highly resolved phylogeny consistent across different methods. Coalescent species-tree-based approaches, concatenated matrices, and Bayesian analyses recovered similar topologies that were congruent at the resolution of difficult nodes. We recovered good support for the intertribal relationships within Oryzomyalia; for instance, the tribe Oryzomyini appears as the sister taxa of the remaining oryzomyalid tribes. The estimates of divergence times agree with the results of previous studies. We inferred the crown age of the sigmodontine rodents at the end of the Middle Miocene, while the main lineages of Oryzomyalia appear to have radiated in a short interval during the Late Miocene. Thus, the collection of a genomic-scale data set with a wide taxonomic sampling provided resolution for the first time of the relationships among the main lineages of Sigmodontinae. We expect the phylogeny presented here will become the backbone for future systematic and evolutionary studies of the group.[Coalescent; Muroidea; Oryzomyalia; phylogenomics; polytomy; Rodentia; Sigmodontalia; species tree; UCEs.].

A review on the cytogenetics of the tribe Oryzomyini (Rodentia: Cricetidae: Sigmodontinae), with the description of new karyotypes.

Oryzomyini represents the most diverse and speciose tribe of subfamily Sigmodontinae, with 29 genera and about 141 species. This great diversity of species is distributed from southeastern North to southern South America. Its systematics have passed through major changes in the last years due to the integration of molecular data with morphological characters in phylogenetic inferences. Unsurprisingly, cytogenetic studies on Oryzomyini reflect such diversity, with chromosome diploid number varying from 2n = 16 to 2n = 88. In addition, some species present autosomal and sex chromosome polymorphisms, besides the presence of B chromosomes. However, despite decades of cytogenetic studies, our knowledge about the karyotype variability in this group were still poorly known. Considering such deep and profound changes on the tribe, along with important new evidence that was continuously being produced associated to field work in several areas of Brazil and South America, we performed a cytogenetic review of the Oryzomyini group. We provide standardized descriptions summarizing all the knowledge associated to the known species of the tribe. We also describe seven new karyotypes for the tribe, Euryoryzomys sp., 2n = 58 and FN = 92; Neacomys sp. 1, 2n = 48 and FN = 54; Neacomys sp. 2, 2n = 54 and FN = 62; Oecomys sp. 1, 2n = 54 and FN = 84; Oecomys sp. 2, 2n = 64 and FN = 92; Oecomys sp. 3, 2n = 84 and FN = 110; and Scolomys sp., 2n = 62 and FN = 80.

Karyotypic divergence reveals that diversity in the Oecomys paricola complex (Rodentia, Sigmodontinae) from eastern Amazonia is higher than previously thought.

The genus Oecomys (Rodentia, Sigmodontinae) is distributed from southern Central America to southeastern Brazil in South America. It currently comprises 18 species, but multidisciplinary approaches such as karyotypic, morphological and molecular studies have shown that there is a greater diversity within some lineages than others. In particular, it has been proposed that O. paricola constitutes a species complex with three evolutionary units, which have been called the northern, eastern and western clades. Aiming to clarify the taxonomic status of O. paricola and determine the relevant chromosomal rearrangements, we investigated the karyotypes of samples from eastern Amazonia by chromosomal banding and FISH with Hylaeamys megacephalus (HME) whole-chromosome probes. We detected three cytotypes for O. paricola: A (OPA-A; 2n = 72, FN = 75), B (OPA-B; 2n = 70, FN = 75) and C (OPA-C; 2n = 70, FN = 72). Comparative chromosome painting showed that fusions/fissions, translocations and pericentric inversions or centromeric repositioning were responsible for the karyotypic divergence. We also detected exclusive chromosomal signatures that can be used as phylogenetic markers. Our analysis of karyotypic and distribution information indicates that OPA-A, OPA-B and OPA-C are three distinct species that belong to the eastern clade, with sympatry occurring between two of them, and that the "paricola group" is more diverse than was previously thought.

Chromosomal Signatures Corroborate the Phylogenetic Relationships within Akodontini (Rodentia, Sigmodontinae).

Comparative chromosome-painting analysis among highly rearranged karyotypes of Sigmodontinae rodents (Rodentia, Cricetidae) detects conserved syntenic blocks, which are proposed as chromosomal signatures and can be used as phylogenetic markers. In the Akodontini tribe, the molecular topology (Cytb and/or IRBP) shows five low-supported clades (divisions: "Akodon", "Bibimys", "Blarinomys", "Oxymycterus", and "Scapteromys") within two high-supported major clades (clade A: "Akodon", "Bibimys", and "Oxymycterus"; clade B: "Blarinomys" and "Scapteromys"). Here, we examine the chromosomal signatures of the Akodontini tribe by using Hylaeamys megacephalus (HME) probes to study the karyotypes of Oxymycterus amazonicus (2n = 54, FN = 64) and Blarinomys breviceps (2n = 28, FN = 50), and compare these data with those from other taxa investigated using the same set of probes. We strategically employ the chromosomal signatures to elucidate phylogenetic relationships among the Akodontini. When we follow the evolution of chromosomal signature states, we find that the cytogenetic data corroborate the current molecular relationships in clade A nodes. We discuss the distinct events that caused karyotypic variability in the Oxymycterus and Blarinomys genera. In addition, we propose that Blarinomys may constitute a species complex, and that the taxonomy should be revised to better delimit the geographical boundaries and their taxonomic status.

Chromosomal phylogeny and comparative chromosome painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia.

BACKGROUND: The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. RESULTS: The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. CONCLUSIONS: Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.

Does the widely distributed rodent Calomys tener (Cricetidae: Sigmodontinae) constitute a single evolutionary unit?

The nominal species Calomys tener (Winge, 1887) ranges broadly in open lands of the Caatinga, Cerrado, Pantanal and Mata Atlântica of Brazil, and was recently reported from the Pampas of southern Brazil, and in the Selva Paranaense of eastern Paraguay and northeastern Argentina. This rodent can be infected with the pathogenic Araraquara hantavirus in Brazil. Given that most epidemiological studies have not taken into account updated taxonomic findings of their rodent hosts, in this study, we obtained sequence data of the Cyt-b and COI genes of specimens of C. tener from 22 different geographical localities from throughout the currently known distribution of the species (including individuals from Argentina, Paraguay, Bolivia, and Brazil) to test if it constitutes a single genetic unit or if it presents genetic discontinuities that may represent different evolutionary lineages. Phylogenetic analyses including several species of Calomys recovered several clades with strong support. Regarding C. tener, it is recovered as sister to the node that cluster C. laucha (Fischer, 1814) sensu lato, C. expulsus (Lund, 1841) and species in the C. callosus (Rengger, 1830) species complex. At the intraspecific level there are no genetic gaps among haplotypes of C. tener that could suggest more than one species. The recent captures in the Pampas of southern Brazil and in the Selva Paranaense suggest that the species may be colonizing new geographic areas.(AU)

Does the widely distributed rodent Calomys tener (Cricetidae: Sigmodontinae) constitute a single evolutionary unit?

The nominal species Calomys tener (Winge, 1887) ranges broadly in open lands of the Caatinga, Cerrado, Pantanal and Mata Atlântica of Brazil, and was recently reported from the Pampas of southern Brazil, and in the Selva Paranaense of eastern Paraguay and northeastern Argentina. This rodent can be infected with the pathogenic Araraquara hantavirus in Brazil. Given that most epidemiological studies have not taken into account updated taxonomic findings of their rodent hosts, in this study, we obtained sequence data of the Cyt-b and COI genes of specimens of C. tener from 22 different geographical localities from throughout the currently known distribution of the species (including individuals from Argentina, Paraguay, Bolivia, and Brazil) to test if it constitutes a single genetic unit or if it presents genetic discontinuities that may represent different evolutionary lineages. Phylogenetic analyses including several species of Calomys recovered several clades with strong support. Regarding C. tener, it is recovered as sister to the node that cluster C. laucha (Fischer, 1814) sensu lato, C. expulsus (Lund, 1841) and species in the C. callosus (Rengger, 1830) species complex. At the intraspecific level there are no genetic gaps among haplotypes of C. tener that could suggest more than one species. The recent captures in the Pampas of southern Brazil and in the Selva Paranaense suggest that the species may be colonizing new geographic areas.

Effective Population Size Differences in Calomys musculinus, the Host of Junín Virus: Their Relationship with the Epidemiological History of Argentine Hemorrhagic Fever.

Argentine hemorrhagic fever (AHF) is a serious endemic disease in Argentina, produced by Junín virus, whose host is the Sigmodontinae rodent Calomys musculinus. Within the endemic area, human incidence and proportion of infected rodents remains high for 5-10 years after the first appearance of the disease (epidemic [E] zone) and then gradually declines to sporadic cases (historic [H] zone). We tested the hypothesis that host populations within the E zone are large and well connected by gene flow, facilitating the transmission and maintenance of the virus, whereas those in the H and nonendemic (NE) zones are small and isolated, with the opposite effect. We estimated parameters affected by levels of gene flow and population size in 14 populations of C. musculinus: population effective size (Ne), genetic variability, and mean relatedness. Our hypothesis was not supported: the lowest levels of variability and of Ne and the highest genetic relatedness among individuals were found in the H zone. Populations from the NE zone displayed opposite results, whereas those in the E zone showed intermediate values. If we consider that populations are first NE, then E, and finally H, a correlative decrease in Ne was observed. Chronically infected females have a low reproductive success. We propose that this would lower Ne because each cohort would originate from a fraction of females of the previous generation, and affect other factors such as proportion of individuals that develop acute infection, probability of viral transmission, and evolution of virulence, which would explain, at least partly, the changing incidence of AHF.

B Chromosome Diversity and Repetitive Sequence Distribution in an Isolated Population of Akodon montensis (Rodentia, Sigmodontinae).

B chromosomes are supernumerary chromosomes found in the karyotypes of approximately 15% of all eukaryotic species. They present parasitic behavior and do not follow the standard Mendelian pattern of inheritance, resulting in an imbalance in gametogenesis. The evolutionary dynamics of B chromosomes is still unknown for many species, but studies indicate that the accumulation of repetitive sequences plays an important role in the differentiation of these elements. We analyzed morphology, frequency, and possible homologies amongst different B chromosomes found in an isolated Akodon montensis population in southern Brazil. Repetitive sequences (18S, 5S rDNA and telomeric sequences) were used to test for their accumulation on the supernumerary chromosomes and describe their localization in the species. The results indicate 4 different B chromosome morphotypes, and DNA libraries were generated for 3 of them. 18S rDNA was labelled polymorphically, except in the B chromosomes, whereas the 5S rDNA was located exclusively in an interstitial position on the long arm of chromosome 5. Chromosome painting with the B probes based on FISH revealed a homologous composition for all B chromosome morphotypes and no homology with the chromosomes in the A complement. B chromosomes found in this population may have a common origin and subsequently diversified in size and morphology.

Oecomys catherinae (Sigmodontinae, Cricetidae): Evidence for chromosomal speciation?

Among the Oryzomyini (Sigmodontinae), Oecomys is the most speciose, with 17 species. This genus presents high karyotypic diversity (2n = 54 to 2n = 86) and many taxonomic issues at the species level because of the presence of cryptic species and the overlap of morphological characters. For these reasons the real number of species of Oecomys may be underestimated. With the aim of verifying if the taxon Oecomys catherinae is composed of more than one species, we made comparative studies on two populations from two regions of Brazil, one from the Amazon and another from the Atlantic Forest using both classical cytogenetics (G- and C-banding) and comparative genomic mapping with whole chromosome probes of Hylaeamys megacephalus (HME), molecular data (cytochrome b mitochondrial DNA) and morphology. Our results confirm that Oecomys catherinae occurs in the southeast Amazon, and reveal a new karyotype for the species (2n = 62, FNa = 62). The comparative genomic analysis with HME probes identified chromosomal homeologies between both populations and rearrangements that are responsible for the different karyotypes. We compared our results in Sigmodontinae genera with other studies that also used HME probes. These chromosomal differences together with the absence of consistent differentiation between the two populations on morphological and molecular analyses suggest that these populations may represent cryptic species.

Taxonomy of the Phyllotis osilae species group in Argentina; the status of the "Rata de los nogales" (Phyllotis nogalaris Thomas, 1921; Rodentia: Cricetidae).

The taxonomic status of populations of the genus Phyllotis from northwestern Argentina (NWA) has undergone recent changes, with the addition of two species (P. alisosiensis and P. anitae) to the traditionally recognized forms (P. caprinus, P. xanthopygus, and P. osilae). Three of these species (P. anitae, P. osilae, and P. alisosiensis) were included within the Phyllotis osilae species group. Most authors recognized three subspecies of P. osilae for NWA: P. osilae osilae, P. o. nogalaris, and P. o. tucumanus. Morphological, morphometric, and molecular studies based on recently collected specimens suggest that current classification does not reflect the diversity of this group in NWA, revealing the need of some taxonomic reallocations and new distributional delimitations. Here we propose that P. nogalaris must be recognized as a valid species and the restriction of P. osilae to southern Peru and central Bolivia. Following our results, we expect an outstanding improvement in the taxonomic knowledge of the Phyllotis osilae species group in the coming years.

Extensive Chromosomal Reorganization in the Evolution of New World Muroid Rodents (Cricetidae, Sigmodontinae): Searching for Ancestral Phylogenetic Traits.

Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus--HME (Oryzomyini, 2n = 54), Necromys lasiurus--NLA (Akodontini, 2n = 34) and Akodon sp.--ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome.

Clues on Syntenic Relationship among Some Species of Oryzomyini and Akodontini Tribes (Rodentia: Sigmodontinae).

Sigmodontinae rodents represent one of the most diverse and complex components of the mammalian fauna of South America. Among them most species belongs to Oryzomyini and Akodontini tribes. The highly specific diversification observed in both tribes is characterized by diploid complements, which vary from 2n = 10 to 86. Given this diversity, a consistent hypothesis about the origin and evolution of chromosomes depends on the correct establishment of synteny analyzed in a suitable phylogenetic framework. The chromosome painting technique has been particularly useful for identifying chromosomal synteny. In order to extend our knowledge of the homeological relationships between Akodontini and Oryzomyini species, we analyzed the species Akodon montensis (2n = 24) and Thaptomys nigrita (2n = 52) both from the tribe Akodontini, with chromosome probes of Hylaeamys megacephalus (2n = 54) of the tribe Oryzomyini. The results indicate that at least 12 of the 26 autosomes of H. megacephalus show conserved synteny in A. montensis and 14 in T. nigrita. The karyotype of Akodon montensis, as well as some species of the Akodon cursor species group, results from many chromosomal fusions and therefore the syntenic associations observed probably represent synapomorphies. Our finding of a set of such associations revealed by H. megacephalus chromosome probes (6/21; 3/25; 11/16/17; and, 14/19) provides phylogenetic information for both tribes. An extension of these observations to other members of Akodontini and Oryzomyini tribes should improve our knowledge about chromosome evolution in both these groups.

The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents.

BACKGROUND: Much debate has focused on how transitions in life history have influenced the proliferation of some clades. Rodents of the subfamily Sigmodontinae (family Cricetidae) comprise one of the most diverse clades of Neotropical mammals (~400 living species in 86 genera). These rodents occupy a wide range of habitats and lifestyles so that ecological context seems relevant to understand the evolution of this group. Several changes in the landscape of South America through the Neogene might have provided vast resources and opportunity to diversify. The aim of this study was to examine whether transitions between i) lowland and montane habitats, ii) open vegetation and forest, and iii) distinct molar architectures are correlated with shifts in diversification rates and to characterize the general pattern of diversification. RESULTS: Based on a dense taxon sampling of 269 species, we recovered a new phylogeny of Sigmodontinae that is topologically consistent with those of previous studies. It indicates that the subfamily and its major lineages appeared during the Late Miocene. Analyses suggest that vegetation type and elevational range are correlated with diversification rates, but not molar architecture. Tropical lowlands accumulated more lineage diversity than other areas and also supported high speciation rates. Across the radiation the subfamily Sigmodontinae appear to have experienced a decline in diversification rate through time. We detected mixed evidence for lineage-specific diversification rate shifts (e.g., leading to the clades of Akodon, Bibimys, Calomys and Thomasomys). CONCLUSION: We report that the evolution of habitat preference (considering vegetation type and elevational range) was associated with diversification rates among sigmodontine rodents. We propose that the observed diversification slowdown might be the result of ecological or geographical constraints. Our results also highlight the influence of the tropical lowlands -which might have acted as both "a cradle and a museum of species." The tropical lowlands accumulated greater diversity than the remainder of the group's range.

Characterization of the kidney transcriptome of the long-haired mouse Abrothrix hirta (Rodentia, Sigmodontinae) and comparison with that of the olive mouse A. olivacea.

To understand how small mammals cope with the challenge of water homeostasis is a matter of interest for ecologists and evolutionary biologists. Here we take a step towards the understanding of the transcriptomic functional response of kidney using as a model the long-haired mouse (Abrothrix hirta) a species that distributes across Patagonian steppes and Austral temperate rainforests in Argentina and Chile. Specifically, we i) characterize the renal transcriptome of A. hirta, and ii) compare it with that-already available-of the co-generic and co-distributed A. olivacea. Renal mRNA transcripts from 16 specimens of A. hirta from natural populations were analyzed. Over 500 million Illumina paired-end reads were assembled de novo under two approaches, an individual assembly for each specimen, and a single in-silico normalized joint assembly including all reads from all specimens. The total number of annotated genes was similar with both strategies: an average of 14,956 in individual assemblies and 14,410 in the joint assembly. Overall, 15,463 distinct genes express in the kidney of A. hirta. Transcriptomes of A. hirta and A. olivacea were similar in terms of gene abundance and composition: 95.6% of the genes of A. hirta were also found in A. olivacea making their functional profiles also similar. However, differences in the transcriptome of these two species were observed in the set of highly expressed genes, in terms of private genes for each species and the functional profiles of highly expressed genes. As part of the novel transcriptome characterization, we provide distinct gene lists with their functional annotation that would constitute the basis for further research on these or any other species of the subfamily Sigmodontinae, which includes about 400 living species distributed from Tierra del Fuego to southern United States.