Range extension of the endangered rodent Rhipidomys tribei (Cricetidae: Sigmodontinae) in Southeastern BrazilABSTRACT
The arboreal rodent Rhipidomys tribei Costa, Geise, Pereira & Costa, 2011, which is endemic to Southeast Brazil, is a sparsely documented species, with only five confirmed published records, mainly in the mountainous areas of the Atlantic Forest and the transitional semi-deciduous zones adjacent to the Cerrado biome. We report a new locality for R. tribei within the Itatiaia National Park, in the municipality of Itatiaia, state of Rio de Janeiro, Brazil, within the Mantiqueira Mountains range, where we captured six individuals. This discovery significantly expands the known geographic range of this rare and endangered species. Taxonomic identification was confirmed by cytogenetic and mitochondrial cytochrome b gene analyses. Our results support the Meridional Mantiqueira Mountains as a new habitat for R. tribei, extending its range approximately 300 km southward into Rio de Janeiro. This identification is significant because R. tribei remains unrecorded in the neighboring lowlands and Serra do Mar Mountains, where its sister species, Rhipidomys itoan Costa, Geise, Pereira & Costa, 2011, is found.
KEYWORDS:
Conservation; cytochrome b; geographic range; karyotype; Rodentia
INTRODUCTION
Rhipidomys Tschudi, 1845 encompasses arboreal sigmo dontine rodents commonly known as climbing mice. This genus belongs to Thomasomyini Steadman & Ray, 1982, and currently comprises 28 species distributed throughout forested habitats in the Neotropical region (Tribe 2015). Five species are recorded in the Atlantic Forest: R. mastacalis (Lund, 1840); R. macrurus (Gervais, 1855); R. itoan Costa, Geise, Pereira & Costa, 2011; R. tribei Costa, Geise, Pereira & Costa, 2011; and R. bezerrensis Campos, Percequillo & Langguth, 2022. The latter three species are endemic to this domain (Tribe 2005, Costa et al. 2011, Rocha et al. 2011, Tribe 2015, Brito et al. 2017, Campos et al. 2022, Lanes and Bonvicino 2023).
Rhipidomys tribei has a relatively limited known distribution, as there are few documented localities in published articles (Costa et al. 2011, Tribe 2015, Faria et al. 2020). Similarly, information on the natural history of R. tribei is scarce and comes from a few specimens collected from fragments of riparian semi-deciduous submontane forest, at mid-elevations up to 1,300 m (Tribe 2015). Currently, R. tribei is classified as Endangered (EN) in the official Brazilian Red List of Threatened Species (MMA 2022) and as Data Deficient (DD) in the IUCN Red List of Threatened Species (Roach 2017).
In contrast, the phylogenetic position of R. tribei is well established. Analyses of mitochondrial cytochrome b gene sequences (Costa 2003, Costa et al. 2011, Rocha et al. 2011, Brito et al. 2017, Lanes and Bonvicino 2023) recover R. tribei and R. itoan as sister species (with 8.3% genetic divergence; Costa et al. 2011) within the “R. leucodactylus” section of the genus (sensu Tribe 1996).
Regarding their chromosomal complement, Rhipidomys specimens from southern Espírito Santo have been reported with a karyotype of 2n = 44, FN = 50 (Zanchin et al. 1992, Thomazini 2009) and were later associated with R. tribei (Tribe 2015, Carvalho 2017, Paixão et al. 2021). The same karyotype (2n = 44 and FN = 50) was also reported for R. tribei in Santa Bárbara, Minas Gerais, at the type locality, and Alto Jequitibá and Viçosa (Carvalho 2009, Côrtes 2020, Faria et al. 2020).
Here, we report new data that significantly extend the known geographic distribution of R. tribei towards the state of Rio de Janeiro into the Meridional Mantiqueira Mountains. In addition, we provide new insights into the karyotype and genetic diversity of this species and discuss its known distribution.
MATERIAL AND METHODS
Sampling was conducted as part of a broader study on the small mammal fauna of the Itatiaia National Park (PNI - Parque Nacional do Itatiaia), in the municipality of Itatiaia, state of Rio de Janeiro, Brazil (Fig. 1), during ten consecutive nights, from May 26, 2022, to June 4, 2022, at the end of the rainy season. The study included six transects established at different elevations (approximately 800 to 1,600 m). Each transect had 15 trap stations with one Sherman (3” × 3.75” × 12”) and one Tomahawk (16” × 5” × 5”) live traps placed on the ground. In addition, where possible, we attached three Sherman and three Tomahawk traps to branches 5-6 feet above the ground in the understory at different locations along each transect. Traps were baited with a mixture of peanut butter, banana, rolled oats, and sardines and were checked daily. The sampling effort was 1260 trap nights for the campaign.
Map exhibiting the Mantiqueira and Serra do Mar mountain ranges, variation in altitude, collecting sites, and the type locality of Rhipidomys tribei. State of Minas Gerais: (1) Santa Bárbara, (2) Alto Jequitibá, (3) Fervedouro, (4) Viçosa, (5) Mariana. State of Espírito Santo: (6) Castelo, (7) Ibitirama, (8) Muqui, (9) Vargem Alta. Rio de Janeiro: (10) Itatiaia, Parque Nacional do Itatiaia (PNI).
All procedures related to the capture and handling of animals, as well as the collection of biological samples, received prior approval from the Ethics Committee on the Use of Animals (CEUA/IOC) under license L-036/2018-A1 and were carried out in accordance with the SISBIO authorization for activities with scientific purposes 74498-11, issued by the Chico Mendes Institute for Biodiversity Conservation (ICMBio). The specimens were deposited at the Integrated Collection of Wild Reservoir Mammals (COLMASTO), formerly the Laboratory of Biology and Control of Schistosomiasis (LBCE), of the Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), and at the Mammal Collection of the Museu Nacional/UFRJ.
We obtained standard external measurements from the original specimen tags: head-and-body length (HB), tail length (TL), hindfoot length with claws (HF), ear length (E), and body weight (W). Cranial measurements were performed using digital calipers with a precision of 0.01 mm. Thirty cranial measurements were recorded from the specimens, as described by Tribe (1996): occipito-nasal length (ONL), condylo-incisive length (CIL), palatal length (PL), post-palatal length (PPL), molar row crown length (MRC), molar row alveolar length (MRA), 1st molar breadth (M1B), palatal bridge length (PBL), temporal fossa length (TFL), diastema length (DL), incisive foramen length (IFL), incisive foramen breadth (IFB), palatal breadth at M1 (PB1), palatal breadth at M3 (PB3), mesopterygoid fossa breadth (MFB), breadth across incisor tips (BIT), bullar width (BW), bullar length (BL), braincase breadth (BCB), skull height (SH), rostral height (RH), rostral breadth (RB), rostral length (RL), nasal length (NL), zygomatic plate length (ZPL), interorbital breadth (IOB), zygomatic breadth (ZB), greatest length of mandible (GLM), mandibular molar row (MMR), depth of Ramus (DR). Furthermore, we analyzed external and cranial qualitative morphological characteristics, as described in Costa et al. (2011) and Tribe (2015). We contrasted R. tribei with R. itoan and R. mastacalis (see Supplementary material 1, Table S1 for a list of specimens examined).
We obtained cell suspensions of R. tribei from bone marrow cultures in vitro using RPMI medium supplemented with 10% fetal bovine serum and colchicine (Andrade and Bonvicino 2003). We transferred the resuspended cell pellet by dropping it onto microscope slides and used conventional Giemsa staining to visualize the metaphases to identify the diploid number (2n), the fundamental autosome number (FN, excluding sexual chromosomes), and the chromosome morphology.
We isolated DNA from liver samples stored in absolute ethanol from the six specimens collected in the PNI and from one specimen from Alto Jequitibá, state of Minas Gerais (MBF143, karyotyped by Faria et al. 2020), using two diffe rent methods: a Chelex 100 protocol (Walsh et al. 1991) and a phenol/chloroform protocol (Green and Sambrook 2012). We performed PCR amplifications of the cytochrome b gene (mt-Cytb - symbol for Mus musculus following Eppig et al. 2015) using two protocols with the following primer pairs and thermal conditions: i) MVZ 05 (Smith and Patton 1993) and CIT-REV (Casado et al. 2010) with pre-denaturation at 94 °C for 2 min; followed by 35 cycles of denaturation at 94 °C for 30 s, annealing at 48 °C for 30 s, and extension at 72 °C for 60 s; with a final extension at 72 °C for 5 min; and ii) MOD - L14724 (Ferracioli et al. 2023) and CIT-REV (Casado et al. 2010) with the same conditions, except for annealing at 54 °C. Amplicons were verified through 1.5% agarose gel electrophoresis with GelRed Nucleic Acid Stain (Biotium, Hayward, California, USA) and purified using the Illustra GFX PCR DNA and Gel Band Purification Kit (GE Health care, Little Chalfont, Bucks, UK), following the manufacturer’s protocol.
For sequencing, along with the previously mentioned external PCR primers, we used as internal primers: MVZ 16 (Smith and Patton 1993), CB-in1 (Cassens et al. 2000), MVZ 127 (Leite and Patton 2002), and MEU1 (Gonçalves et al. 2007). Sequencing reactions were conducted with BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Carlsbad, California, USA). Cycle sequencing products were precipitated, formamide resuspended, and sequenced using the ABI3730xl DNA Analyzer (Applied Biosystems) in the Fiocruz Platform for DNA Sequencing by Capillary Electrophoresis (P01-001-RPT/FIOCRUZ). The resulting electropherograms were verified, edited, and assembled into contigs using the Geneious Prime 2023 software platform (Kearse et al. 2012). The generated sequences were deposited in GenBank (accession numbers PQ626028-PQ626033 and PQ640353).
We built a dataset with our Rhipidomys sequences and sequences retrieved from the GenBank database for species-level identification. We added the GenBank sequences of R. tribei (HM594662, HM594663) and completed the dataset with sequences of all available Rhipidomys species: R. albujai (KY366342, KY366343); R. caracolensis (HM594667, HM594669); R. cariri (HM594666); R. gardneri (HM594673, U03550); R. ipukensis (HM594628, HM594632); R. itoan (AF108683, KY366336); R. latimanus (KY366338, KY366341); R. leucodactylus (HM594659, HQ634183); R. macconnelli (AF108681, AY275130); R. macrurus (HQ634180, HQ634181); R. mastacalis (HM594644, HM622063); R. nitela (HM594664, HM594665); R. tribei (HM594662, HM594663); R. wetzeli (AF108680, HQ634184); and R. ybyrae (HM594637, AF108682). We added sequences of Rhagomys longilingua (KX423691), R. septentrionalis (MT441549), Thomasomys andersoni (DQ914644), and T. notatus (AF108676) as outgroups.
The dataset was aligned in Geneious using Clustal Omega (Sievers et al. 2011). The aligned matrix was checked for stop codons and exported using the Mesquite 3.81 software package (Maddison and Maddison 2011). Pairwise uncorrected genetic distances (p-distances) within and between Rhipidomys species were calculated using PAUP* 4.0a169 (Swofford 2002). To accurately calculate genetic distances, the matrix was trimmed to remove non-matching ends resulting from incomplete sequences.
Maximum likelihood (ML) phylogenetic reconstruction was performed in the IQ-TREE web server (Trifinopoulos et al. 2016). The best-fit substitution model was selected under the Bayesian information criterion (BIC) using ModelFinder (Kalyaanamoorthy et al. 2017) with codon partitioning (Chernomor et al. 2016). Branch support was assessed using the nonparametric Shimodaira-Hasegawa-like approximate likelihood ratio test (SH-aLRT) (Guindon et al. 2010) and ultrafast bootstrap (UFBoot) (Hoang et al. 2018), each with 1,000 replicates, and the parametric Bayesian-like transformation of aLRT (aBayes) (Anisimova et al. 2011).
Bayesian inference (BI) phylogenetic reconstruction was performed in MrBayes 3.2.7 (Ronquist et al. 2012) on XSEDE via the CIPRES Science Gateway (Miller et al. 2010), with different GTR+I+Γ models for each codon position. Markov chain Monte Carlo (MCMC) sampling was set at intervals of 1,000 generations, for a total of 10,000,000 generations. Bayesian posterior probabilities (BPP) were calculated to assess branch support after burn-in removal of the first 25% generations. We evaluated the parameter convergence (ESS > 200) using Tracer 1.7.2 (Rambaut et al. 2018).
RESULTS
Six specimens of Rhipidomys were captured near the Abrigo Lamego location, all within the same transect extending from coordinates 22°25’36.48”S, 44°37’54.91”W, at an elevation of ca. 1,530 m, to 22°25’37.25”S, 44°37’58.53”W, at an elevation of ca. 1,590 m. The transect was in a sloped terrain, characterized by a closed canopy with a mean height of 11.9 ± 4.15 m. We observed the presence of bamboo stands, an intermediate (semi-open) understory, the absence of clearings in the vicinity, a substantial accumulation of leaf litter on the ground, fallen logs at numerous locations, and the pervasive presence of vines and lianas. The captures occurred between May 27 and June 4, 2022.
Specimens consisted of two females (LBCE 22996, 23031) and four males (LBCE 23030, 23068, 23081, 23121). The majority of the captures were made with Sherman traps, except for the specimen LBCE 23121, which was caught using a Tomahawk trap. Half of the specimens were captured at ground level (LBCE 22996, 23030, 23068), while the remaining were caught in the understory (LBCE 23031, 23081, 23121). Subsequent examination revealed that neither of the two females was found to be pregnant. The individual measurements of the adult specimens are documented in the supplementary material (Supplementary material 2, Table S2). The mean and extreme values (minimum and maximum, respectively) of the external measurements for the adult Rhipidomys were as follows: HB = 125 mm, 109-140 mm; TL = 152 mm, 128-165 mm; HF = 29 mm, 26-30 mm; E = 17 mm, 15-19 mm; and W = 55 g, 38-71 g.
Karyotype analyses revealed a chromosomal complement of 2n = 44 and FN = 50 (Fig. 2). The autosome complement consisted of four pairs of medium-small biarmed chromosomes and 17 pairs of acrocentric chromosomes varying in size from large to small. The sexual chromosomes comprised a medium-sized acrocentric X chromosome and a small-sized acrocentric Y chromosome.
Conventional Giemsa staining karyotype of a male R. tribei (LBCE 23068) with 2n = 44 and FN = 50. Both X and Y sexual chromosomes are acrocentric.
Complete mt-Cytb sequences (1,143 base pairs) were obtained for all six Itatiaia specimens. Three of them (LBCE 22996, 23030, 23031) had identical sequences, while the remaining three sequences constituted distinct haplotypes. The sequences from Fervedouro, Santa Barbara, and Alto Jequitibá were also different haplotypes. The resulting matrix included 40 taxa and 1,143 bp, with 650 constant base pairs and 405 parsimony-informative variable characters. The ML best-fit models selected through ModelFinder were TIM2e+G4, HKY+F+R2, and TN+F+I+G4 for the first, second, and third codon positions, respectively. The ML analysis yielded a best tree score of -7475.843. The BI analysis yielded a mean estimated marginal likelihood of -7523.825 (standard error of mean = 0.0977, median = -7523.392). The ESS indicated a robust sampling across all parameters.
The ML and BI phylogenetic reconstructions exhibited similar tree topologies, differing only in the arrangement of basal dichotomies within Rhipidomys (Fig. 3, Supplementary material 3). Rhipidomys wetzeli emerged as the first offshoot within the genus, followed by R. macconnelli in the ML topology, while their position was inverted in the BI tree. However, the support for these relationships was low in both analyses (SH-aLRT = 0.14, UFBoot = 0.47, aBayes = 0.59, BPP = 0.50). The species group “R. leucodactylus” included R. leucodactylus and a robustly supported clade (SH-aLRT = 0.99, UFBoot = 1.00, aBayes = 1.00, BPP = 1.00) with R. itoan and R. tribei. The R. tribei clade had strong support (SH-aLRT = 0.96, UFBoot = 0.98, aBayes = 1.00, BPP = 1.00) and included two subclades: the first with R. tribei sequences from the state of Minas Gerais and the second formed by the new mt-Cytb sequences from Rio de Janeiro (Itatiaia).
Bayesian phylogenetic tree reconstruction for Rhipidomys based on mt-Cytb sequences. Maximum likelihood analysis produced a similar topology, with the inversion of R. macconnelli and R. wetzeli positions (see results and sup. information). Symbols at nodes indicate branch supports given by Bayesian posterior probabilities (BPP) and bootstrap percentages (BS): black circles indicate high support (BPP > 0.95, BS > 90%), whereas white squares indicate low support (BPP > 0.95, BS > 90%). Brazilian states: Minas Gerais (MG), Rio de Janeiro (RJ).
For the calculation of genetic distances, the removal of unmatched ends resulted in a matrix comprising 40 taxa and 801 base pairs. Of these, 477 were constant and 278 were parsimony informative. Four sequences of R. tribei were identical (LBCE 22996, 23030, 23031, 23068) in this matrix. The interspecific p-distances of R. tribei (Table 1) ranged from 7.7%, with R. itoan to 15.6%, with R. macconnelli. The mean p-distance between R. tribei and other Rhipidomys species was 11.4%. The intraspecific distance of R. tribei ranged from zero to 1.4%. The mean intraspecific p-distance among R. tribei specimens was 0.6%. The genetic distances between R. tribei specimens from Rio de Janeiro and R. tribei specimens from Minas Gerais ranged from 0.5% to 1.4% (mean = 1.0%). The distance among our R. tribei specimens from Rio de Janeiro ranged from zero to 0.5% (mean = 0.2%). The distance among R. tribei specimens from Minas Gerais ranged from 0.4% to 0.6% (mean = 0.5%).
Examination of the qualitative morphological charac ters supports the distinction between R. tribei and its congeners R. itoan and R. mastacalis. All three species are small rodents with R. itoan being slightly larger. Rhipidomys tribei and R. mastacalis share similar tail-to-body length ratios, although R. mastacalis has a moderately longer tail. The tail-to-body length ratio is greater in R. itoan. Rhipidomys tribei has a small tail tuft, while R. itoan has small to medium tufts and R. mastacalis has medium tufts. All three species share a characteristic dark dorsal patch on the metatarsals, extending to the digits, with lighter sides.
Mean pairwise genetic uncorrected p-distance (%) estimates for the mt-Cytb among Rhipidomys species.
Cranially (Fig. 4), R. tribei has an anteriorly convergent interorbital region, with a rounded shape and no supraorbital crest. In contrast, R. itoan has an hourglass-shaped interorbital region with a slight supraorbital crest, while R. mastacalis has an anteriorly convergent interorbital region with a moderate to prominent supraorbital crest. The lacrimal projection is broad, elongated, and laterally expanded in R. tribei, whereas it is small and less prominent in R. itoan and R. mastacalis. The incisive foramina in R. tribei are diamond-shaped, with posterior and anterior portions of lateral margins converging toward the midline to form distinct angles; in R. itoan, the foramina have nearly parallel margins with slight posterior convergence, resulting in a bullet shape; while in R. mastacalis, they are elliptical, with gradual tapering at both posterior and anterior portions. Regarding dental morphology, R. tribei generally lacks or has a reduced protoflexus on the second upper molar (M2), whereas R. itoan and R. mastacalis have a well-developed M2 protoflexus.
Cranial characteristics that distinguish three species of Rhipidomys from the Eastern Brazilian Atlantic Forest, R. tribei, R. itoan, R. mastacalis. Examined specimens: Rhipidomys itoan (A, D, G: MN63618, from Angra dos Reis, state of Rio de Janeiro); R. mastacalis (B, E, H: MN75987 from Chapada Diamantina, state of Bahia); and R. tribei (C, F, I: LBCE 23031). (A, B, C): dorsal view of the interorbital region. (D, E, F): dorsal view of the dorsal projection of the lacrimal bone. (G, H, I): incisive foramina. Scale bars: 1 mm.
DISCUSSION
The identification of the Itatiaia specimens as R. tribei was confirmed through a combination of phylogenetic and karyotypic analyses, as well as morphological examination. The genetic distance found between specimens from Rio de Janeiro (Itatiaia) and Minas Gerais (three localities) was minimal despite the geographic distance, corroborating their classification as conspecifics. Phylogenetic reconstructions (Fig. 3) also revealed a well-supported sister species relationship between R. itoan and R. tribei in the “R. leucodactylus” section, thereby confirming prior analyses (Costa et al. 2011, Lanes and Bonvicino 2023). Furthermore, our phylogenetic reconstructions yielded similar tree topologies, albeit with minor differences in basal placements within Rhipidomys. In our ML tree, R. wetzeli emerged as the initial branch, followed by R. macconnelli, consistent with the findings of Brito et al. (2017) and Lanes and Bonvicino (2023). Conversely, this order was inverted in the BI topology. The two hypotheses received a low level of support. Consequently, the most accurate representation of these relationships is likely a polytomy connecting R. macconnelli, R. wetzeli, and a main clade containing the remaining Rhipidomys species, as depicted by Costa et al. (2011).
The karyotype of the Itatiaia specimens was consistent with those associated with R. tribei specimens from the type locality of Santa Bárbara and from other localities where karyological data are available, such as Alto Jequitibá, Lavras, and Viçosa, in Minas Gerais, and Ibitirama, Muqui, and Vargem Alta, in southern Espírito Santo (Table 2; Carvalho 2017, Tribe 2015, Côrtes 2020, Faria et al. 2020). Other Rhipidomys species - such as R. leucodactylus, R. gardneri, R. macrurus (see Lanes et al. 2024), R. caracolensis (see Campos et al. 2022), R. itoan (see Di-Nizo et al. 2014), and R. macconnelli (see Aguilera et al. 1994) - also have 2N = 44 / FN = 50 karyotypes, with four pairs of biarmed chromosomes and 17 pairs of acrocentric chromosomes. However, there is clear variation in the morphology of the largest biarmed pair and especially of the sex chromosomes. Rhipidomys tribei has a medium-sized acrocentric X chromosome (Lanes et al. 2024, Di-Nizo et al. 2014), while R. itoan has a large submetacentric X chromosome (Costa et al. 2011). Other species, such as R. leucodactylus, R. cariri, R. caracolensis, and R. gardneri, share the same submetacentric X chromosome morphology (Lanes et al. 2024, Campos et al. 2022, Carvalho 2017, Thomazini 2009). In contrast, R. macrurus has a sexual chromosome morphology similar to that of R. tribei, with a medium acrocentric X chromosome and a small acrocentric Y chromosome (Lanes et al. 2024, Thomazini 2009).
Documented localities of Rhipidomys tribei. Map numbers refer to localities in Fig. 1. References: 1. Carvalho (2009); 2. Costa et al. (2011); 3. Rocha et al. (2011); 4. Faria et al. (2020); 5. Côrtes (2020); 6. Carvalho (2017); 7. Thomazini (2009); 8. Zanchin et al. (1992); 9. Tribe (2015); 10. Campos et al. (2022); 11. Simões (2016); 12. Present work. Abbreviations: (BRA) Brazil, (ES) Espírito Santo, (LBCE) Coleção Integrada de Mamíferos Silvestres Reservatórios, (MG) Minas Gerais, (MZNB) Museu de Zoologia Newton Baião de Azevedo, (MZUFV) Museu de Zoologia da Universidade Federal de Viçosa, (RJ) Rio de Janeiro, (UFES) Universidade Federal do Espírito Santo, (UFMG) Universidade Federal de Minas Gerais, (UFPB) Universidade Federal da Paraíba.
The morphological examination of the Itatiaia specimens aligns with the species characterization of Costa et al. (2011), particularly in distinguishing R. tribei from its congeners R. itoan and R. mastacalis, both of which occur in the Serra do Mar region of the Atlantic Forest. Our findings have significantly extended the known geographic range of R. tribei by approximately 300 km to the southwest, firmly establishing this species as an inhabitant of the Meridional Mantiqueira Mountains. The Mantiqueira Mountains range spans the states of Espírito Santo, Minas Gerais, Rio de Janeiro, and São Paulo. Due to its extension, it is categorized into two main subdivisions: Meridional Mantiqueira to the south and Septentrional to the north, with most of its territory situated within Minas Gerais (Gonzaga and Menini Neto 2017). Concurrently, the Serra do Caraça, where the type locality of R. tribei is located, lies at the southern end of the Espinhaço Mountains range, in the center of the state of Minas Gerais (Costa et al. 2011).
The distribution of the species can be traced from the Septentrional Mantiqueira, stretching from Santa Bárbara (Minas Gerais) to Vargem Alta (Espírito Santo), and now we register further into the Meridional Mantiqueira, reaching its southern limit in Itatiaia (Rio de Janeiro). The collection localities of R. tribei are situated at an altitude range of approxi mately 500 m to 1,500 m above sea level and are characterized by montane forest vegetation. The vegetation of the Itatiaia collecting locality is that of the Transitional Montane Forest of Brade (1956) or Middle Montane Forest of Segadas-Viana (1965). The latter describes it as a spaced climax forest with trees ranging from 20 to 30 meters in height, with a mixture of tree and shrub species found at lower and upper elevations, a dense undergrowth, and significant increase in epiphytes, lianas, and mosses compared to lower levels. Our collecting site had a lower canopy, and a more open (intermediate) understory, probably due to the steepness of the terrain.
The six captures were concentrated within a single transect in the PNI, in a segment comprising eight traps positioned at ground level and in the lower understory (ca. 1-3 m). Rhipidomys tribei was not found in other transects situated at ca. 1,500 m, nor at elevations between 800-1,200 m. These other transects had higher moisture levels, a more pronounced canopy, a denser understory and a greater abundance of epiphytes, lianas, and mosses. R. tribei shared its habitat with the sigmodontine rodents Castoria angustidens, Delomys dorsalis, and Thaptomys nigrita, and the didelphid marsupials Gracilinanus microtarsus, Marmosops paulensis, and Monodelphis americana.
Previous accounts of Rhipidomys in the PNI and its vicinity were either categorized as R. mastacalis or lacked species-level identification. It is noteworthy that most records of rodent species in the PNI predate the formal description of R. tribei. An exception is a survey conducted in 2011 for the revision of the PNI Management Plan, published in 2013 (ICMBio 2013). In this survey, seven specimens, identified as R. mastacalis, were captured across three different locations surrounding the PNI. The specimens captured during the PNI management plan survey were found at elevations ranging from ca. 1,070 to 1,550 m (ICMBio 2013).
Barth (1957) included R. mastacalis in his compilation of the fauna within the PNI. Conversely, Ávila-Pires and Gouvêa (1999) did not include any Rhipidomys species in their records. Finally, Geise et al. (2004) mentioned Rhipi domys sp. at an altitude of appoximately 830 m in their study. However, it remains to be conclusively determined whether these records correspond to R. tribei or another Rhipidomys species occurring near the PNI, such as R. itoan, or even R. mastacalis.
Very few localities of R. tribei have been documented in published articles (Costa et al. 2011, Tribe 2015, Faria et al. 2020, Campos et al. 2022) and in unpublished theses (Thomazini 2009, Simões 2016, Carvalho 2017), and some of them are based on unsubstantiated IDs; we provide an overview of these localities below (see also Table 2). Four of the published records are situated in different municipalities within the state of Minas Gerais: the type-locality Reserva Particular do Patrimônio Natural (RPPN) Santuário do Caraça, municipality of Santa Bárbara; Mata do Paraíso, municipality of Viçosa; Parque Estadual da Serra do Brigadeiro, Fazenda Neblina, municipality of Fervedouro; Fazenda Harmonia, RPPN Mata dos Jacus, municipality of Alto Jequitibá (Costa et al. 2011, Faria et al. 2020). All these collection records are based on molecular, karyological, and/or morphological data (Table 2).
In the state of Espírito Santo, the taxon was recorded as Rhipidomys sp. by Zanchin, Langguth, and Mattevi (1992), in the Hotel Fazenda Monte Verde, municipality of Vargem Alta, 24 km SE of Venda Nova, and later identified as R. tribei by Tribe (2015). Campos et al. (2022) morphologically identified this specimen as R. mastacalis, but provided no evidence to support this identification. Although we did not examine the specimen, we follow Tribe (2015) in recognizing this locality (Table 2). Campos et al. (2022) also reported two additional localities for R. tribei in the state of Minas Gerais, namely the Reserva Peti, municipality of Catas Altas; and the Parque Estadual do Ibitipóca, municipality of Lima Duarte. These localities are listed in the appendix of their study with the corresponding specimens. However, the authors did not provide any evidence for the species identification (Table 2). Further analyses are needed to recognize these specimens as R. tribei.
At least six additional records of R. tribei are described in unpublished theses and dissertations (Thomazini 2009, Simões 2016, Carvalho 2017), including the municipalities of Castelo, Ibitirama, and Muqui, in Espírito Santo, and Mariana, Lavras, and Luminárias, in Minas Gerais. Records from the first four locations are reported with molecular data and associated voucher specimens (Thomazini 2009, Carvalho 2017), and they had already been documented in the literature (Table 2, see also Tribe, 2015, Paixão et al. 2021). In contrast, the latter two records, from Lavras and Luminárias, were based on unvouchered and non-sequenced data (Simões 2016) and were not considered here (Table 2). To corroborate these records, we advocate additional analyses adopting integrative approaches.
While R. tribei appears to thrive in the Mantiqueira Mountains, it is conspicuously absent from lowland areas and from the neighboring Serra do Mar Mountains range, which are habitats for its sibling species, R. itoan. The present study has two primary contributions. Firstly, it provides a more comprehensive understanding of biodiversity within the Mantiqueira Mountains and the PNI. Secondly, it expands the list of documented species within this region.
ACKNOWLEDGMENTS
We express our sincere gratitude to our funding agencies, CNPq and FAPERJ, for their generous financial support. We extend our heartfelt appreciation to the staff, fire brigade, and management personnel of PNI for granting the necessary permits and for their invaluable assistance during our fieldwork. We especially thank Gustavo Tomzhinski, Léo Nascimento, Leonardo Cândido, Luiz Aragão, Luiz Sergio Sarahyba, Marcelo Motta, Mário Pitombeira, and José Celso (Celsinho) for their exceptional support. We also extend our appreciation to the LABPMR, LABVET/UFRRJ, and MN/UFRJ field teams for their invaluable assistance during fieldwork. Lastly, our deepest thanks are owed to Cynthia Ito, who played an indispensable role in providing support in various aspects, including food, logistics, transportation, and much more.
LITERATURE CITED
- Aguilera M, Pérez-Zapata A, Martino A, Barros MA, Patton J (1994) Karyosystematics of Aepomys and Rhipidomys (Rodentia, Cricetidae). Acta Científica Venezolana 45: 247-248.
-
Andrade AFB, Bonvicino CR (2003) A new karyological variant of Oecomys (Rodentia: Sigmodontinae) and its phylogenetic relationships based on molecular data. Genome 46(2): 195-203. https://doi.org/10.1139/g02-123
» https://doi.org/10.1139/g02-123 -
Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O (2011) Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Systematic Biology 60(5): 685-699. https://doi.org/10.1093/sysbio/syr041
» https://doi.org/10.1093/sysbio/syr041 - Ávila-Pires FD, Gouvêa É (1999) Mamíferos do Parque Nacional do Itatiaia. Boletim de Pesquisa do Parque Nacional do Itatiaia 9: 1-29.
- Barth R (1957) A fauna do Parque Nacional do Itatiaia. Boletim de Pesquisa do Parque Nacional do Itatiaia 6: 1-149.
- Brade AC (1956) A flora do Parque Nacional do Itatiaia. Boletim do Parque Nacional do Itatiaia 5: 1-114.
-
Brito JM, Tinoco N, Chávez D, Moreno-Cárdenas P, Batallas D, Ojala-Barbour R (2017) New species of arboreal rat of the genus Rhipidomys (Cricetidae, Sigmodontinae) from Sangay National Park, Ecuador. Neotropical Biodiversity 3(1): 65-79. https://doi.org/10.1080/23766808.2017.1292755
» https://doi.org/10.1080/23766808.2017.1292755 -
Campos BATP, Percequillo AR, Miranda G, Langguth A (2022) Two new species of Rhipidomys (Rodentia: Sigmodontinae) from Eastern Brazil, with comments on the taxonomy of the genus. Hystrix, the Italian Journal of Mammalogy 33(2): 139-157. https://doi.org/10.4404/hystrix-00443-2021
» https://doi.org/10.4404/hystrix-00443-2021 -
Carvalho AH (2009) Caracterização citogenética de espécies de Rhipidomys (Cricetidae, Rodentia) de Minas Gerais. Master’s thesis, Universidade Federal de Minas Gerais Belo Horizonte, 56 pp. https://livros01.livrosgratis.com.br/cp091860.pdf
» https://livros01.livrosgratis.com.br/cp091860.pdf -
Carvalho AH (2017) Evolução molecular e cariotípica em Rhipidomys Tschudi, 1845 (Rodentia, Cricetidae). PhD Thesis, Universidade Federal do Espírito Santo, Vitória, 92 pp. http://repositorio.ufes.br/handle/10/9925
» http://repositorio.ufes.br/handle/10/9925 -
Casado F, Bonvicino CR, Nagle C, Comas B, Manzur TD, Lahoz MM, Seuánez HN (2010) Mitochondrial divergence between 2 populations of the hooded capuchin, Cebus (Sapajus) cay (Platyrrhini, Primates). Journal of Heredity 101(3): 261-269. https://doi.org/10.1093/jhered/esp119
» https://doi.org/10.1093/jhered/esp119 - Cassens I, Vicario S, Waddell VG, Balchowsky H, Van Belle D, Ding W, et al. (2000) Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proceedings of the National Academy of Sciences 97(21): 11343-11347.
-
Chernomor O, von Haeseler A, Minh BQ (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Systematic Biology 65(6): 997-1008. https://doi.org/10.1093/sysbio/syw037
» https://doi.org/10.1093/sysbio/syw037 -
Côrtes FM (2020) Variação morfológica de Rhipidomys Tschu di, 1845 (Rodentia, Cricetidae) no estado de Minas Gerais e descrição de novo cariótipo. Master’s thesis, Universidade Federal de Viçosa, Viçosa, 57 pp. https://locus.ufv.br//handle/123456789/27976
» https://locus.ufv.br//handle/123456789/27976 -
Costa BMA, Geise L, Pereira LG, Costa LP (2011) Phylogeography of Rhipidomys (Rodentia: Cricetidae: Sigmodontinae) and description of two new species from southeastern Brazil. Journal of Mammalogy 92(5): 945-962. https://doi.org/10.2307/23259930
» https://doi.org/10.2307/23259930 -
Costa LP (2003) The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals. Journal of Biogeography 30(1): 71-86. https://doi.org/10.1046/j.1365-2699.2003.00792.x
» https://doi.org/10.1046/j.1365-2699.2003.00792.x -
Di-Nizo CB, Neves CL, Vilela JJF, Silva MJDJ (2014) New karyologycal data and cytotaxonomic considerations on small mammals from Santa Virgínia (Parque Estadual da Serra do Mar, Atlantic Forest, Brazil). Comparative Cytogenetics 8: 11-30. https://doi.org/10.3897/CompCytogen.v8i1.6430
» https://doi.org/10.3897/CompCytogen.v8i1.6430 -
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE (2015) The Mouse Genome Database Group. The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Research 28(D1): D726-736. https://doi.org/10.1093/nar/gku967
» https://doi.org/10.1093/nar/gku967 - Faria MB, Lanes RDO, Bonvicino CR (2020) Non-volant small mammals (Rodentia and Didelphimorphia) diversity in an isolated area of the Serra da Mantiqueira, Minas Gerais state, Brazil. Boletim do Museu Paraense Emílio Goeldi, Ciências Naturais 15(3): 643-662.
-
Ferracioli P, de Oliveira MB, Cezar AM, Lazar A, Povill C, Laeta M, et al. (2023) A new mammalian universal primer for the mitochondrial cytochrome b locus. Brazilian Journal of Mammalogy e92: e922023102-e922023102 https://doi.org/10.32673/bjm.vie92.102
» https://doi.org/10.32673/bjm.vie92.102 -
Geise L, Pereira LG, Bossi DEP, Bergallo HG (2004) Pattern of elevational distribution and richness of non volant mammals in Itatiaia National Park and its surroundings, in southeastern Brazil. Brazilian Journal of Biology 64(3B): 599-612. https://doi.org/10.1590/S1519-69842004000400007
» https://doi.org/10.1590/S1519-69842004000400007 -
Gonçalves PR, Myers P, Vilela JF, de Oliveira JA (2007) Systematics of species of the genus Akodon (Rodentia: Sigmodontinae) in southeastern Brazil and implications for the biogeography of the Campos de Altitude. Miscellaneous Publications of the Museum of Zoology of Michigan 197: 1-24. https://hdl.handle.net/2027.42/102734
» https://hdl.handle.net/2027.42/102734 - Gonzaga DR, Menini Neto L (2017) Estado de conservação da Serra da Mantiqueira: ameaças, lacunas, avanços e perspectivas do conhecimento da flora. In: Barbosa BC, Resende LO, Prezoto F, Gonçalves EL (Eds) Tópicos em Sustentabilidade & Conservação. Authors’ Edition, Juiz de Fora, 77-86.
- Green MR, Sambrook J (2012) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 4th ed., vol. 1, 2028 pp.
-
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59(3): 307-321. https://doi.org/10.1093/sysbio/syq010
» https://doi.org/10.1093/sysbio/syq010 -
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35(2): 518-522. https://doi.org/10.1093/molbev/msx281
» https://doi.org/10.1093/molbev/msx281 - ICMBio (2013) Plano de Manejo do Parque Nacional do Itatiaia. ICMBio/MMA, Brasília, 132 pp.
-
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14(6): 587-589. https://doi.org/10.1038/nmeth.4285
» https://doi.org/10.1038/nmeth.4285 -
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12): 1647-1649. https://doi.org/10.1093/bioinformatics/bts199
» https://doi.org/10.1093/bioinformatics/bts199 -
Lanes RO, Pires C, Teixeira BR, Bonvicino CR (2024) New findings on the karyotype and distribution of two Rhipidomys Tschudi, 1845 species (Rodentia: Sigmodontinae) from Upper Purus River”. Mammalia 88(6): 580-584. https://doi.org/10.1515/mammalia-2024-0028
» https://doi.org/10.1515/mammalia-2024-0028 -
Lanes RDO, Bonvicino CR (2023) Reevaluation of Rhipidomys emiliae (JA Allen 1916) and description of a new Rhipidomys (Rodentia: Cricetidae) species from Amazonia and Cerrado. Zootaxa 5346: 581-597. https://doi.org/10.11646/zootaxa.5346.5.5
» https://doi.org/10.11646/zootaxa.5346.5.5 -
Leite YLR, Patton JL (2002) Evolution of South American spiny rats (Rodentia, Echimyidae): the star-phylogeny hypothesis revisited. Molecular Phylogenetics and Evolution 25(3): 455-464. https://doi.org/10.1016/S1055-7903(02)00279-8
» https://doi.org/10.1016/S1055-7903(02)00279-8 -
Maddison WP, Maddison DR (2023) Mesquite: a modular system for evolutionary analysis. Version 3.81 http://www.mesquiteproject.org
» http://www.mesquiteproject.org -
Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Gateway Computing Environments Workshop (GCE), New Orleans, 1-8. https://doi.org/10.1109/GCE.2010.5676129
» https://doi.org/10.1109/GCE.2010.5676129 -
MMA (2022) Portaria MMA nº 148, de 7 de junho de 2022. Diário Oficial da União, Brasília, vol. 108, Seção 1, p. 74. https://in.gov.br/en/web/dou/-/portaria-mma-n-148-de-7-de-junho-de-2022-406272733
» https://in.gov.br/en/web/dou/-/portaria-mma-n-148-de-7-de-junho-de-2022-406272733 - Paixão VS, Suárez P, Silva WO, Geise L, Ferguson-Smith MA, O’Brien PCM, et al. (2021) Comparative genomic mapping reveals mechanisms of chromosome diversification in Rhipidomys species (Rodentia, Thomasomyini) and syntenic relationship between species of Sigmodontinae. Plos One 16: e0258474. https://10.1371/journal.pone.0258474
-
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67(5): 901-904. https://doi.org/10.1093/sysbio/syy032
» https://doi.org/10.1093/sysbio/syy032 -
Roach N (2017) Rhipidomys tribei The IUCN Red List of Threatened Species 2017: e.T48297988A48297992. https://doi.org/10.2305/IUCN.UK.2017-2.RLTS.T48297988A48297992.en
» https://doi.org/10.2305/IUCN.UK.2017-2.RLTS.T48297988A48297992.en -
Rocha RG, Ferreira E, Costa BMA, Martins ICM, Leite YLR, Costa LP, Fonseca C (2011) Small mammals of the mid-Araguaia River in Central Brazil, with the description of a new species of climbing rat. Zootaxa 2789: 1-34. https://doi.org/10.11646/zootaxa.2789.1.1
» https://doi.org/10.11646/zootaxa.2789.1.1 -
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, et al. (2012) MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539-542. https://doi.org/10.1093/sysbio/sys029
» https://doi.org/10.1093/sysbio/sys029 - Segadas-Vianna F (1968) Ecology of the Itatiaia Range, southeastern Brazil. I. Altitudinal Zonation of the Vegetation. Arquivos do Museu Nacional 53: 7-30.
-
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7: 539. https://doi.org/10.1038/msb.2011.75
» https://doi.org/10.1038/msb.2011.75 -
Simões MB (2016) Pterygodermatites (Nematoda: Rictulariidae): revisão de literatura e identificação de espécies em quirópteros da Mata Atlântica, Sudeste brasileiro. Master’s thesis, Universidade Federal do Espírito Santo, Vitória, 72 pp. http://repositorio.ufes.br/handle/10/9426
» http://repositorio.ufes.br/handle/10/9426 -
Smith MF, Patton JL (1993) The diversification of South American murid rodents: evidence from mitochondrial DNA sequence data for the akodontine tribe. Biological Journal of the Linnean Society 50(3): 149-177. https://doi.org/10.1111/j.1095-8312.1993.tb00924.x
» https://doi.org/10.1111/j.1095-8312.1993.tb00924.x - Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland.
-
Thomazini NB (2009) Correlação entre estrutura cariotípica e filogenia molecular em Rhipidomys (Cricetidae, Rodentia) do leste do Brasil. Master’s thesis, Universidade Federal do Espírito Santo, Vitória, 99 pp. http://repositorio.ufes.br/handle/10/3815
» http://repositorio.ufes.br/handle/10/3815 -
Tribe CJ (1996) The Neotropical rodent genus Rhipidomys (Cricetidae, Sigmodontinae) - A taxonomic revision. PhD Thesis, University College London, London, 320 pp. https://discovery.ucl.ac.uk/id/eprint/10119506/
» https://discovery.ucl.ac.uk/id/eprint/10119506/ - Tribe CJ (2005) A new species of Rhipidomys (Rodentia, Muroidea) from North-Eastern Brazil. Arquivos do Museu Nacional 63(1): 131-146.
- Tribe CJ (2015) Genus Rhipidomys Tschudi, 1945. In: Patton JL, Pardiñas UFJ, D’Elía G (Eds) Mammal of South America 2 Rodents. The University of Chicago Press, Chicago, 583-617.
-
Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44(W1): W232-W235. https://doi.org/10.1093/nar/gkw256
» https://doi.org/10.1093/nar/gkw256 -
Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10(4): 506-513. https://doi.org/10.2144/000113897
» https://doi.org/10.2144/000113897 -
Zanchin NIT, Langguth A, Mattevi MS (1992) Karyotypes of Brazilian species of Rhipidomys (Rodentia, Cricetidae). Journal of Mammalogy 73(1): 120-122. https://doi.org/10.2307/1381872
» https://doi.org/10.2307/1381872
ADDITIONAL NOTES
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Funding
Conselho Nacional de Desenvolvimento Científico 311712/2021-5, 309654-2020-3, 305289/2023-3. Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro 26/210.925/2019, E-26/201.232/2022. Fieldwork and laboratory analyses were supported by grants to CR Bonvicino (Conselho Nacional de Desenvolvimento Científico-CNPq 311712/2021-5 and Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro-FAPERJ E-26/210.925/2019) and to M Weksler (CNPq 309654-2020-3 and 305289/2023-3 and FAPERJ E-26/201.232/2022).
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Data Availability
Sequences are deposited in the GenBank database (https://www.ncbi.nlm.nih.gov/genbank/) with accession numbers PQ626028-PQ626033 and PQ640353.
- ZooBank register
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How to cite this article
Vilela RV, Ribeiro MCS, Lanes RO, Teixeira BR, Freitas TPT, Weksler M, Bonvicino CR (2025) Range extension of the endangered rodent Rhipidomys tribei (Cricetidae: Sigmodontinae) in Southeastern Brazil. Zoologia 42: e24057. https://doi.org/10.1590/S1984-4689.v42.e24057
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Published by
Sociedade Brasileira de Zoologia at Scientific Electronic Library Online - https://www.scielo.br/zool
Supplementary material 1
Authors: Vilela RV, Ribeiro MCS, Lanes RO, Teixeira BR, Freitas TPT, Weksler M, Bonvicino CR
Data type: Specimens’ data.
Supplementary material 2
Authors: Vilela RV, Ribeiro MCS, Lanes RO, Teixeira BR, Freitas TPT, Weksler M, Bonvicino CR
Data type: Specimens’ data.
Supplementary material 3
Supplementary S3. Original trees from IQ-tree and Mrbayes in NEXUS format.
Authors: Vilela RV, Ribeiro MCS, Lanes RO, Teixeira BR, Freitas TPT, Weksler M, Bonvicino CR
Data type: Tree files.
Copyright notice: These datasets are made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Sequences are deposited in the GenBank database (https://www.ncbi.nlm.nih.gov/genbank/) with accession numbers PQ626028-PQ626033 and PQ640353.
