Full text of DOI:10.1007/BF03192453

Acta Theriologica 47 (2): 125–135, 2002.
PL ISSN 0001–7051
Genetic studies in representatives of genus Rhipidomys
(Rodentia, Sigmodontinae) from Brazil
Jaqueline ANDRADES-MIRANDA, Luiz F. B. de OLIVEIRA,
C. André V. LIMA-ROSA, Denis A. SANA, Andrea P. NUNES
and Margarete S. MATTEVI*
Andrades-Miranda J., de Oliveira L. F. B., Lima-Rosa C. A. V., Sana D. A., Nunes A. P.
and Mattevi M. S. 2002. Genetic studies in representatives of genus Rhipidomys
(Rodentia, Sigmodontinae) from Brazil. Acta Theriologica 47: 125–135.
Karyotypic polymorphism of five taxa of the rodent genus Rhipidomys from the
Brazilian Amazon and Cerrado biomes was analysed. Rhipidomys nitela Thomas, 1901
from Amazon has 2n = 48, FN = 68. The other species, all have 2n = 44, but can be
separated into two groups, one with high FNs (76, 80) and the other with low FNs (48,
52). Two cytotypes of R. mastacalis (Lund, 1840) with high FNs were trapped in four
localities of the Cerrado, showing 19 and 17 biarmed autosomes, respectively. A low FN
(48) was observed in R. leucodactylus (Tschudi, 1844) in two localities of the Cerrado
and FN = 52 in one locality in the Cerrado and the Amazon. All taxa with 2n = 44 have
a medium-sized acrocentric X chromosome and a small Y. Rhipidomys nitela is
different from the species with 2n = 44 by presenting a heterochromatic short arm of
the X chromosome. In all karyotypes analysed, the nucleolus organizer regions were
located in the short arms of two to six pairs and the (T2AG3)n telomeric probes
hybridized in situ in both the short and long arms of all pairs of the karyotypes.
Departamento de Genética, Universidade Federal do Rio Grande do Sul, C.P. 15053,
91501-970, Porto Alegre, Rio Grande do Sul, Brazil, e-mail: mattevi@terra.com.br,
margarete.mattevi@ufrgs.br (JA-M, CAVL-R, DAS, MSM*); Museu Nacional, Setor de
Mastozoologia, Universidade Federal do Rio de Janeiro, 20940-040, Rio de Janeiro,
Brazil (LFBdO, APN)
Key words: Rhipidomys, Cerrado, Amazon, in situ hybridization, DNA microsatellite
Introduction
Rhipidomys is a widely distributed Neotropical tree rat, ranging from eastern
Panama, Guianas, Venezuela, Colombia, Ecuador, and Peru to southern Bolivia,
northwestern Argentina and north, central and eastern Brazil (Musser and
Carleton 1993). The majority of authors include Rhipidomys in the thomasomyine
group of the Sigmodontinae subfamily of the New World murids (Hershkovitz 1966,
Cerqueira 1982, Carleton and Musser 1989, Gardner 1989, Voss 1993, Steppan
1995). It is a speciose genus with a confused taxonomy, which was recently revised
* Corresponding author
[125]

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J. Andrades-Miranda et al.
by Tribe (1996). The proposed number of species ranges from 5 (Cabrera 1961), 7
(Honacki et al. 1982), 9 (Reig 1984), 14 (Musser and Carleton 1993), to 18 (Tribe
1996).
Cytogenetic studies performed in one species from Colombia (Gardner and
Patton 1976), 2 from Venezuela (Aguilera et al. 1994), and in 8 from Brazil
(Zanchin et al. 1992, Svartman and Almeida 1993, Silva and Yonenaga-Yassuda
1999), showed that, with the exception of one, all species of this genus have the
same diploid number (44), apparently differing among themselves only by the
number of biarmed elements they carry (autosomal arms numbers ranging from 48
to 74).
In this paper we report the 2n = 48 karyotype of R. nitela Thomas, 1901 from
Amazon, and 4 other Rhipidomys karyotypes with 2n = 44, 2 of them with high and
2 of them with low autosomal arm numbers, trapped in the Brazilian biomes of
Amazon and Cerrado. We are also describing the results of the in situ hybridization
analysis made in these 5 species with the telomeric probe (T2AG3)n.
Material and methods
Twenty-seven specimens (22 karyotyped) of 5 taxa trapped in 7 localities of the Brazilian territory
were examined (Fig. 1, Tables 1 and 2). Skins and skulls were deposited in the Mammals Collection of
the Museu Nacional, Rio de Janeiro. Voucher specimen numbers are in the Appendix.
Metaphase plates were obtained from bone marrow according to the technique of Baker et al.
(1982). C-banding, NOR and G-banding were performed employing the methods of Sumner (1972),
Howell and Black (1980) and Seabright (1971), respectively. In the case of the G-bands (data not
shown), due to a problem in preparing the cellular suspensions in the field, they were useful only to
detect the occurrence of pericentric inversions in the largest pairs of the karyotype. The hybridization
process of the telomeric sequence (T2AG3)n was done using the Oncor (Gaithersburg, MD) “all human
telomeres” probe stained with digoxigenin according to the manufacturer’s protocol, except for the
temperature of post-hybridization washing being lowered to 68°C. Detection was performed using
FITC anti-digoxigenin and propidium iodide as counterstaining. Kodak Ektachrome, ASA 400 film was
used in the photomicrographs.
Eleven sets of microsatellite DNA primers designed for Rattus (R12, R47, R65, R69, R75, and R97
designed by Serikawa et al. 1992) and Mus (M13, M23, and M49, and ATP, and KRT, according Love et
al. 1990 and Santos et al. 1995) were amplified by heterologous PCR in five species (four taxa as
described in Lima-Rosa et al. 2000, plus R. nitela of this work).
Results
The results of the analysis performed in the genus Rhipidomys in this study and
those described in the literature are presented in Table 2. Rhipidomys nitela was
the only species of the genus that did not present a diploid number of 44. Its 48
chromosomes include 11 and 12 biarmed and acrocentric autosomal pairs, respec-
tively. The X chromosome is a large submetacentric (size between pairs 1 and 2),
and the Y chromosome a small acrocentric (Fig. 2a). All the other species analysed
presented 2n = 44 and an acrocentric sexual pair, with the X chromosome being
medium sized and the Y chromosome small. They differ by their autosomal arms

Genetic studies in Rhipidomys
127
o
o
o
o
80
60
40
50
o
10
3
1
4
2
o
0
5
Amazon
6
16
7
8
CCeerrrraaddoo
9
15
10
11
14
13
o
20
forest
12
o
30
Fig. 1. Collection points: 1 – Surumú, Roraima state; 2 – Manaus, Amazon state; 3 – Venezuela; 4 –
Colombia; 5 – Caxiuanã, Pará state; 6 – River Jamari, Rondônia state; 7 – Aripuanã, and 8 – Vila Rica,
Mato Grosso state; 9 – Serra da Mesa (including the localities: a – 55 km N Niquelândia, b – 20 km NW
Colinas do Sul, c – 40 km SW Minaçú, and d – 40 km NE Uruaçú), Goiás state; 10 – Brasília, Distrito
Federal; 11 – Ipameri, Caldas Novas and Corumbaíba, Goiás state; 12 – Casa Grande, São Paulo state;
13 – Monte Verde, Espírito Santo state; 14 – Lagoa Santa, Minas Gerais state; 15 – Fazenda Unacau,
Bahia state; 16 – Serra dos Cavalos, Pernambuco state. Circles: Rhipidomys nitela; squares: R. leu-
codactylus cytotypes; lozenges: R. mastacalis cytotypes. Numbers 1, 5, 9 and 11 – this paper; 2, 7 and 8
– Silva and Yonenaga-Yassuda (1999); 3 – Aguilera et al. (1994); 4 – Gardner and Patton (1976); 6,
13–16 – Zanchin et al. (1992); 10 and 12 – Svartman and Almeida (1993).
Table 1. Number of specimens (n), localities and biomes analysed in this paper. Colection
points correspond to those in Fig. 1.
Species
n
Collection points
Biomes
Amazon
Rhipidomys nitela
2
2
1
R. mastacalis cytotype 1
R. mastacalis cytotype 2
R. leucodactylus
9
Cerrado
12
5
9
Cerrado
9, 11
5, 9
Cerrado
R. leucodactylus cytotype 1
6
Cerrado/Amazon

128
J. Andrades-Miranda et al.
Table 2. Species, collection points (numbers as in Fig. 1), diploid (2n) and autosomal arm numbers
(FN) and places of the signal of hybridization reported in this study and in the literature. p – short
arm, q – long arm.
Collec-
tion
points
(T2AG3)n
hybridized on:
Species
2n
FN
References
2n = 48–50
ends of p and q this paper
71,72 ends of p and q Silva and Yonenaga-Yassuda 1999
Rhipidomys nitela
1
2
48
50
68
R. nitela (sp. B)
2n = 44 / high FN cytotypes
R. mastacalis cytotype 1
R. mastacalis cytotype 2
R. mastacalis
9
44
44
44
44
80
ends of p and q this paper
ends of p and q this paper
9
76
14,15
16
74
–
–
Zanchin et al. 1992
R. cearanus
high
Zanchin et al. 1992
2n = 44 / low FN cytotypes
R. latimanus
4
44
44
44
44
44
44
44
44
44
48
48
48
48
48
49
50
52
52
–
Gardner and Patton 1976
R. sclateri
3
–
Aguilera et al. 1994
R. leucodactylus
R. leucodactylus
Rhipidomys sp.
Rhipidomys sp.
Rhipidomys sp.
9,11
6
ends of p and q this paper
–
–
–
–
Zanchin et al. 1992
10
Svartman and Almeida 1993
Svartman and Almeida 1993
Zanchin et al. 1992
10,12
13
R. leucodactylus cytotype 1 5,9
R. cf. mastacalis 7,8
ends of p and q this paper
ends of p and q Silva and Yonenaga-Yassuda 1999
number (FN), allowing us to separate them in two groups. One group included
species with high FNs and the other species with low FNs. The two taxa of
R. mastacalis (Lund, 1840) (R. m. cytotype 1, FN = 80, and R. m. cytotype 2, FN =
76) belonged to the first group. They were trapped in the same locality and
displayed, respectively, 19 and 17 biarmed autosomes (Fig. 2b and c, respectively).
Both taxa of R. leucodactylus (Tschudi, 1844) studied pertain to the species group
with low FNs. In the 2 localities where it was trapped, R. leucodactylus showed the
same FN = 48 karyotype (Fig. 2d), almost entirely consisting of acrocentrics (18
pairs). R. leucodactylus cytotype 1 (Fig. 2e), also in two localities, similarly to
R. leucodactylus, has a karyotype with a majority of acrocentrics (16 pairs,
FN = 52).
Rhipidomys nitela displayed C-bands in the centromeres of most autosomes and
in the centromere and short arm of the X chromosome (Fig. 3a). R. mastacalis
cytotype 1, R. m. cytotype 2 and R. leucodactylus showed similar patterns with
centromeric bands in the X chromosome and in 1, 2, and 4 pairs of acrocentrics,
respectively (Fig. 3b). In R. leucodactylus cytotype 1 the C-bands occurred in the

Genetic studies in Rhipidomys
129
Fig. 2. Karyotypes in conventional staining of (a) Rhipidomys nitela (2n = 48, FN = 68), (b) R.
mastacalis cytotype 1 (2n = 44, FN = 80), (c) R. mastacalis cytotype 2 (2n = 44, FN = 76), (d) R.
leucodactylus (2n = 44, FN = 48), and (e) R. leucodactylus cytotype 1 (2n = 44, FN = 52), female (in
the square the sex pair of a male).

130
J. Andrades-Miranda et al.

Genetic studies in Rhipidomys
131
Fig. 4. The NOR bearing pairs, Ag-staining of a – Rhipidomys nitela, b – R. mastacalis cytotype 2, c –
R. leucodactylus, and d – R. leucodactylus cytotype 1.
Fig. 5. Polyacrylamid-gel electrophoresis of the
microsatellite “alleles” from the Rhipidomys species
amplified with R47 and R65 primers. Lanes: a –
88–88bp; b – 88–91bp, and 101–103bp heteroduplex;
c – 88–94bp, and 138–140bp heteroduplex; d –
91–94bp, and 105–106 heteroduplex; e – 94–94bp;
(f) 97–97bp; g – molecular weight 100bp marker
(plus pBR 322 digested with MspI).

132
J. Andrades-Miranda et al.
centromeric region of most of the chromosomes (including the five biarmed pairs)
and of the X chromosome (Fig. 3c). In all 5 taxa the Y chromosome was entirely
heterochromatic. Three nucleolar organizer regions were observed in R. nitela,
located in the short arms of pairs 8, 17, and 22 (Fig. 4a). In both cytotypes of R.
mastacalis, 5 to 6 pairs (7, 9, 13, 15, 19, and 21) displayed NOR-bands, all in the
short arms (Fig. 4b). In R. leucodactylus only 2 pairs (8 and 11) showed nucleolar
organizers (Fig. 4c) and in R. leucodactylus cytotype 1 (Fig. 4d) this number rises to
5 pairs (3, 9, 12, 14, and 15).
The telomere (T2AG3)n probe hybridized both to short and long arms of all
chromosomes of R. nitela, R. mastacalis cytotypes 1 and 2, R. leucodactylus, and R.
l. cytotype 1 (Table 2). Of the 11 heterologous microsatellite DNA primers tested,
only two presented amplification products in Rhipidomys, both originally designed
for the Rattus species (R47 and R65, Fig. 5). R47 generated 4 “alleles” of 88bp,
91bp, 94bp, and 97bp size respectively, both in homozygous or heterozygous status.
“Alleles” 88bp and 91bp pertained exclusively to R. leucodactylus (FN = 48,
localities 9 and 11), the other 2 bands being found in the all taxa analysed. Two
“alleles” were originated by primer R65, 1 of 172bp seeing in the 5 species
investigated and the other (of 186bp) occurring in R. leucodactylus cytotype 1 only.
Discussion
Rhipidomys nitela is distributed throughout the Guianas, south of Venezuela to
the north and center of Brazil, and its type locality is described as occurring in
Guyana (Musser and Carleton 1993). We captured R. nitela in Surumú located in
the northern region of the Brazilian Amazon (state of Roraima). This site is within
the reported distribution area of the species. In specimens of this species collected
in Amazon, Silva and Yonenaga-Yassuda (1999) found 2n = 50 and a large
submetacentric X chromosome equal, apparently, to that we observed in Surumú.
The karyotypes with 2n = 48–50, however, are unique since all other karyotyped
species of Rhipidomys (see Table 2) showed diploid numbers of 44.
According to the number of pericentric inversions they carry (Zanchin et al.
1992, this paper), species with 2n = 44 may be joined into 2 groups, 1 with high FNs
(74, 76, 80), and the other with low FNs (48, 49, 50, 52). The former group would
include the mastacalis macrospecies described by Lund, 1840, whose type locality is
Rio das Velhas, Lagoa Santa, state of Minas Gerais, Brazil. It is distributed
throughout eastern and central Brazil, possibly in the Amazonian regions of
Venezuela, Colombia, Ecuador, and Peru (Musser and Carleton 1993). The speci-
mens reported by Zanchin et al. (1992), from the type locality (local 14, Table 2) and
from Unacau (local 15), state of Bahia, presented FN = 74 in both localities. The
specimens we analysed came from 4 localities (Fig. 1: collection points 9a–d) of
central Brazil, a territory which is also located inside the distribution area of
mastacalis. Because they have different numbers of biarmed elements (FN = 76, 80
vs 74) and are separated geographically, these cytotypes may be considered as

Genetic studies in Rhipidomys
133
subspecies of mastacalis. These 3 taxa exhibit the same morphology of the sex
chromosomes. Due to high FN, it is probable that R. cearanus, analysed by Zanchin
et al. (1992) in Pernambuco (ie, inside the distribution area of R. mastacalis) also
belongs to this group. Musser and Carleton (1993) classify cearanus as synonym of
R. mastacalis.
The group of species of Rhipidomys which showed low FNs is more chromo-
somally polymorphic than the group with high FN. It includes numerous taxa
which are subject to a great divergence in its classification and correspond to the
distinct cytotypes with FN = 48, 49, 50, and 52. Detailed comparisons of these
cytotypes indicated that all of them have the same basic karyotype, with observed
differences due to the numbers of biarmed elements they bear. These fundamental
numbers could correspond to taxonomic categories of species or subspecies grouped
under a large cytotaxonomic entity represented by the macrospecies R. leuco-
dactylus (Tschudi, 1844). This species has its type locality in eastern Peru, and
occupies the Guianas, southern Venezuela, northern Brazil, Ecuador, and Peru
(Musser and Carleton 1993). The cytotype representative of this macrospecies has
FN = 48 and inhabits the Jamari River, Amazon (Zanchin et al. 1992). The animals
we studied were collected at two localities (40 km SW Minaçú and Ipameri) of the
Cerrado biome.
Several other Rhipidomys taxa with karyotypes with low FNs (from 48 to 52)
were reported. R. latimanus, trapped by Gardner and Patton (1976) in Colombia
and R. sclateri from Venezuela (Aguilera et al. 1994), presented FN = 48. Musser
and Carleton (1993) relate that Thomas (1887) remarked that sclateri, named from
British Guiana, was the eastern counterpart of Peruvian R. leucodactylus. Svartman
and Almeida (1993) described specimens called Rhipidomys sp. with FN = 48 and
49 collected in São Paulo and in Brasilia with FN = 49, exclusively. Also in
Rhipidomys sp., Zanchin et al. (1992) report an animal trapped on the Brazilian
Atlantic coast (Monte Verde, see Fig. 1: collection point 13) presenting FN = 50. As
R. leucodactylus cytotype 1, we analysed specimens with FN = 52 from the Cerrado
biome (20 km NW Colinas do Sul) and from the Amazon biome (Caxiuanã). In two
localities of the Amazon, Silva and Yonenaga-Yassuda (1999) found this same
fundamental number (52).
In summary, the low FN species-group comprises the following taxa: R. leuco-
dactylus of Brazil (Amazon and Cerrado), R. latimanus of Colombia, and R. sclateri
of Venezuela, all with FN = 48; Rhipidomys sp. of São Paulo presenting FN = 48
and 49, and in Brasilia showing FN = 49; the FN = 50 cytotype of Monte Verde; and
the FN = 52 taxon seen at Cerrado and at 3 localities of the Amazon. This
species-group occupies a large part of the territory of South America, therefore
extending the limits of R. leucodactylus from northern South America (Venezuela)
to 25° South (state of São Paulo, Fig. 1).
Although the small sizes of some samples hinder definitive conclusions, micro-
satellite DNA data contributed in clarifying the relationships among some taxa.
The primer R65 amplified only in the species of Rhipidomys out of 11 species of

134
J. Andrades-Miranda et al.
thomasomyine and oryzomyine we previously investigated (Lima-Rosa et al. 2000).
In this case it can be considered as a marker of the genus. The species-group of
Rhipidomys with low FNs is unique because the bands of 88bp and 91bp (generated
by the R47 primer) and that of 186bp (R65 primer) were displayed exclusively in it.
In conclusion, we found that the genus Rhipidomys accepts three larger
species-groups. These are joined according to their diploid numbers (R. nitela with
2n = 48, 50 and the other species with 2n = 44), or by the numbers of their
autosomal arms (R. mastacalis and related taxa with high FN versus R. leuco-
dactylus and related taxa with low FN). The status of these species-groups is
reinforced, partly, by the existence of exclusive “alleles” of microsatellite DNA.
Acknowledgements: The authors are grateful to J. L. P. Cordeiro and J. R. Marinho for field work help;
and to L. S. Silva, and F. L. Hädrich for technical support. Conselho Nacional de Desenvolvimento
Científico e Tecnológico (CNPq), Financiadora de Estudos e Projetos (FINEP), Fundação de Amparo à
Pesquisa do Estado do Rio Grande do Sul (FAPERGS), and Organization of the American States (OAS)
have supported this study.
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Appendix. Collection numbers and localities of capturing of specimens studied.
Voucher specimens: Rhipidomys nitela: AN817, AN908 (Surumú, Roraima state, 60°47’W, 04°11’N).
R. mastacalis cytotype 1: MN36247 (20 km NW Colinas do Sul, Goiás state, 14°09’S, 48°04’W),
MN37350 (40 km NE Uruaçú, Goiás state, 14°31’S, 49°08’W). R. mastacalis cytotype 2: MN36058,
MN36196 (55 km N Niquelândia, Goiás state, 14°28’S, 48°27’W), MN36337*, MN36341, MN36358,
MN36425 (20 km NW Colinas do Sul, Goiás state, 14°09’S, 48°04’W), MN36681, MN36833 (40 km SW
Minaçú, Goiás state, 13°31’S, 48°13’W), MN37280*, MN37425, MN37438*, MN37439 (40 km NE
Uruaçú, Goiás state, 14°31’S, 49°08’W). R. leucodactylus: OT4709, OT5070, OT6926, OT7657
(Ipameri, Caldas Nova and Corumbaíba, Goiás state, between 17°41’–17°56’S and 48°28’–48°32’W),
MN36781* (40 km SW Minaçú, Goiás state, 13°31’S, 48°13’W). R. leucodactylus cytotype 1: AP111–115
(Caxiuanã, Pará state, 01°44’S, 51°23’W), MN36449 (20 km NW Colinas do Sul, Goiás state, 14°09’S,
48°04’W). *Specimens not karyotyped.