Constricted range and limited genetic variation in Reig's Grass Mouse Akodon reigi (Cricetidae: Sigmodontinae) in the Southern Campos

doi:10.21203/rs.3.rs-4947113/v1

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Constricted range and limited genetic variation in Reig's Grass Mouse Akodon reigi (Cricetidae: Sigmodontinae) in the Southern Campos

https://doi.org/10.21203/rs.3.rs-4947113/v1

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We present an updated distribution of Akodon reigi, a sigmodontine endemic to Campos in southern South America, and explore its habitat of occurrence and genetic diversity. Our findings reveal new occurrences of A. reigi extending approximately 110 km northwest and 120 km northeast beyond previously known limits. Contrary to previous assumptions of close association with forest formations, recent sightings suggest a degree of habitat plasticity within the species, with specimens found in shrubby/herbaceous phytophysiognomies. Fifty-three individuals sequenced for Cytochrome b (cyt b; 806 bp) and the first exon of Interphotoreceptor Retinoid Binding Protein (IRBP; 408 bp) showed low variability. Eleven distinct cyt b haplotypes were identified. The largest haplotype richness was observed in a locality in the Sul-Riograndense Shield, a region that could represent a center of the species' genetic diversification. No nucleotide variation was observed for IRBP. No significant indications of population expansion or contraction were detected. The relatively small range, the low genetic diversity, and the current condition of habitat stress due to floods related to global climate change draw attention to the species’ conservation.

Akodontini

Atlantic Forest

conservation

Pampa

small mammal

Wallacean shortfall

Akodon comprises a highly diverse genus of Sigmodontinae rodents, encompassing 42 extant species (Brandão et al. 2022) characterized by medium-sized cursorial forms. Its habitat spans from the southern Amazon Forest to central-southern Argentina, exhibiting varied geographical distribution patterns. These patterns imply expansive ranges across one or more biomes (e.g. Akodon cursor, A. montensis), restricted to specific physiognomies (e.g. A. pervalens, A. polopi, and A. reigi), and microendemisms (e.g. A. mystax, A. philipmyersi) (Gonçalves et al. 2007; Pardiñas et al. 2015).

A notable portion of Akodon diversity thrives within forests and open habitats in South America's subtropical and temperate zones (Pardiñas et al. 2015). Within this range, Reig’s Grass Mouse (Akodon reigi) was described based on specimens collected from the departments of Lavalleja and Durazno in central-western Uruguay, as well as the Taim Ecological Station, located in the coastal plain of Rio Grande do Sul state, southern Brazil (González et al. 1998). Following, additional localities of the species occurrence have been identified in Uruguay, and Rio Grande do Sul (Langone 2007; González and Martínez-Lanfranco 2010; Christoff et al. 2013; Luza et al. 2016; Queirolo 2016; Schott et al. 2020). These localities are situated within the inland steppes of Uruguay and Rio Grande do Sul, encompassing the Pampa biome and the Pioneer Formation of the southernmost Atlantic Forest biome (according to Fundação SOS Mata Atlântica/INPE, 2021). This territory, known as Campos (Overbeck et al. 2007), is predominantly characterized by grasslands and shrublands, occasionally interspersed with forest formations, typically associated with rivers and streams (riparian forests), hillside forests, and isolated “forest islands” along the coastal zone (restinga forests) (Alonso Paz and Bassagoda 2002; Bergamin et al. 2024; Müller et al. 2024).

The scarcity of specimens and confirmed records has significantly hampered the comprehension of fundamental aspects of A. reigi. Limited information about the species distribution, occurrence habitats, and genetic characteristics has been determined. Available data on trapping habitats suggest the species’ presence in gallery forests in Uruguay (González et al. 1998), Restinga forests (flooded and unflooded), and grassland-forest ecotones in Rio Grande do Sul (Langone 2007; Sponchiado et al. 2010; Luza et al. 2016). In examining microhabitat variables influencing small mammals' occurrence within the mosaic of open and forested environments at the Taim Ecological Station, Sponchiado et al. (2010) observed a positive correlation between A. reigi and forest habitats. Queirolo (2016) compiled the known distribution of the species up to that point (four localities in Uruguay and three in Rio Grande do Sul), a record later expanded upon by Luza et al. (2016). Genetic analyses investigating diversity and phylogenetic relationships within Akodon utilizing Cytochrome b sequences placed A. reigi either as a sister of A. paranaensis (e.g. Gonçalves et al. 2007; Brandão et al. 2021) or as a sister to a clade comprising A. paranaensis and A. mystax (D’Elía et al. 2003; Pardiñas et al. 2005; Abreu et al. 2014). However, data regarding intraspecific genetic diversity within Akodon reigi remain scarce.

Over the past decade, extensive sampling efforts targeting non-volant small mammals in Rio Grande do Sul have yielded new specimens of A. reigi, while simultaneously uncovering additional records of the species in Uruguay. These endeavors have facilitated a revision of our comprehension of A. reigi distribution and provided material for the inaugural exploration of its genetic diversity. In this study, we (1) updated the geographic distribution of A. reigi, providing insights into the habitats of collection sites, (2) conducted an analysis of intraspecific genetic diversity and population structure, and (3) inferred past demographic changes.

Specimens and data sampling

Specimens of Akodon exhibiting external morphology consistent with A. reigi (according to Gonzalez et al. 1998; Pardiñas et al. 2015) were collected by the first author (FMQ) from July 2011 to November 2012 in the state of Rio Grande do Sul, southern Brazil, during field surveys conducted for phylogeographic studies on akodontines including Scapteromys tumidus, Deltamys kempi, and Oxymycterus nasutus (Quintela et al. 2015, 2017; Peçanha et al. 2017). The geographic coordinates, elevation, and phytophysiognomic characteristics of the collecting sites were recorded. Tissue samples (liver and ear tips) were preserved in absolute alcohol and stored in a -20^o freezer. Skulls and skins are deposited at the Zoology Department of the Universidade Regional de Blumenau (FURB; Blumenau, Brazil).

Additional records and tissues were obtained from specimens deposited at the mammalian collection of the Museu de Ciências Naturais of the Universidade Luterana do Brasil (MCNU; Canoas, Brazil), Museo Nacional de Historia Natural (Montevideo, Uruguay), Universidade Federal de Santa Catarina (UFSC; Florianópolis, Brazil), and specimens donated by P. Q. Langone (Langone 2007), currently housed at FURB. When available, geographic coordinates and habitat characteristics of those specimens were recorded. The identity of specimens with available tissues was confirmed by molecular identification using the Basic Local Alignment Search Tool (BLAST) applied to Cytochrome B (cyt b) sequences (reference sequence: AY195865 [MNHN 3682, paratype]; D’Elía et al. 2003). We also compiled records obtained by Luza et al. (2016) from non-collected individuals whose identity was verified through BLAST analysis using the reference sequence AY195865.

Molecular DNA analysis

The DNA sequences analyzed for this study (excluding those from Uruguay) were obtained following this protocol. Genomic DNA was isolated using approximately 0.2 g of muscle tissue with a DNA PureLink Genomic kit. Fragments of the mitochondrial Cytochrome b gene (cyt b; 806 bp) and the first exon of the nuclear gene encoding Interphotoreceptor Retinoid Binding Protein (IRBP; 408 bp) were amplified by polymerase chain reaction (PCR) as described by Smith and Patton (1984) and Jansa and Voss (2000), respectively. PCR products were visualized using GelRed (Biotium) and analyzed on a 1% agarose gel, then purified enzymatically (Exonuclease and Alkaline Phosphatase; Amersham Biosciences, Piscataway, NJ), and sequenced using the Sanger method with forward primers. Sequences were visually inspected using Clustal X and aligned in MEGA 11 (Tamura et al. 2021) using full mode alignment without manual adjustment. The resulting nucleotide sequences were deposited in GenBank under accession numbers PQ150403-PQ150453.

To broaden our genetic approach, we incorporated two cyt b sequences of Akodon reigi from Uruguay available in GenBank (D’Elía et al., 2003, 2008), as well as 10 sequences generated by Luza et al. (2016) from unvouchered samples from Rio Grande do Sul stored in the database of the Departamento de Genética of Universidade Federal do Rio Grande do Sul (Porto Alegre, Brazil).

Statistical parameters of diversity, including the number of segregating sites (S), number of haplotypes (h), haplotype diversity (Hd), and nucleotide diversity (π) were calculated using DNASP 6.12 (Rozas et al. 2017). A median-joining haplotype network (Bandelt et al., 1999) was constructed in NETWORK 4.6 (http://www.fluxus-engineering.com/sharenet.htm). Levels of genetic structure among populations of A. reigi were characterized using ϕST based on haplotype distances and analyzed with Arlequin 3.5 (Excoffier and Lischer 2010). Bayesian phylogenetic analyses were performed using Markov chain Monte Carlo (MCMC) sampling as implemented in BEAST 1.7 (Drummond et al. 2012) using all haplotypes of A. reigi recovered in this study. Individuals of A. reigi. from previous studies (D’Elía et al. 2003, 2008; Luza et al. 2016) deposited in GenBank were also incorporated, as well as from its sister species A. paranaensis (EF101881-88, EF621302- 4, AY195866, EU251017, EU251019, EU579471). The congeners Akodon montensis (AY273906), A. azarae (AY702964), and A myxtax (AY273907) were also included due to either geographic or phylogenetic relatedness (based on Leite et al. 2014). Deltamys kempi (AY195861) was used to root the tree. We employed the GTR model of nucleotide substitution, which was estimated in jModelTest (Posada, 2008). Uniform interval priors were assumed for all parameters except base composition, for which we assumed a Dirichlet prior. We performed four independent runs of 25 million generations, each with a 5000-step thinning. All analyses were checked for convergence in Tracer 1.7 (Rambaut and Drummond 2007) by plotting the log-likelihood values against generation time for each run, and the first five million generations were discarded as burn-in. All posterior parameter estimates had effective sample sizes (ESS) above 200, and the remaining trees were used to calculate posterior probabilities for each node.

Finally, we examined the demographic history of Reigi’s Grass Mouse using a mismatch distribution analysis. While mismatch distributions from populations of constant size typically exhibit a ragged and erratic, they tend to be unimodal in populations that have recently undergone demographic expansion (Excoffier 2004). To access the goodness of fit of the observed mismatch distribution to that expected under the sudden expansion model, we employed parametric bootstrapping implemented in Arlequin version 3.0, using the sum of squared deviations (SSD) statistic. Additionally, we utilized the raggedness index defined by Harpending (1994), also implemented in Arlequin version 3.0, which yields lower values for unimodal and smoother distributions, indicative of expanding populations compared to multimodal distributions commonly found in a stationary population. The significance of the raggedness index was assessed in the same manner as that SSD. Tajima’s D (Tajima 1989) and Fu’s FS (Fu 1997) neutrality tests were conducted using 1,000 iterations, as implemented in Arlequin 3.0. Significant negative values of Tajima’s D and Fu’s FS suggest an excess of low-frequency mutations relative to expectations under the standard neutral model, indicating demographic expansion or purifying selection.

Our field sampling (material collected by the first author FMQ) yielded 79 Akodon specimens exhibiting morphology consistent with Akodon reigi (González et al. 1998; Pardiñas et al. 2015). In addition, 17 specimens identified as A. reigi were sourced from MCNU, eight from MNHN, and one from UFSC.

A subsample of 40 specimens representative of the six localities covered in our study and specimens from MCNU and UFSC were sequenced and confirmed as A. reigi through BLAST analysis. Additionally, three specimens collected by Langone (2007) displayed morphology consistent with A. reigi; however, attempts to sequence these specimens were unsuccessful, preventing BLAST identification.

Geographic Distribution and Habitat

Our sampling revealed eight new localities where A. reigi occurs (Rio Grande do Sul: São Sepé; Barra do Ribeiro, Camaquã, Cristal, São Lourenço do Sul, Pedras Altas, Pedro Osório; Uruguay: Department of Rivera). By combining these new findings with previous records (González et al. 1998; Langone 2007; González and Lanfranco 2010; Luza et al. 2016; Queirolo 2016), we compiled a total of 24 sites of the species’ occurrence, distributed in 22 localities. These localities are distributed across the geomorphological domains of Lagunar Plain, the southern Coastal Plain, and the Sul-Riograndense Plateau (sensu Dantas et al. 2010) in Rio Grande do Sul, and Gondwanic Sedimentary Basin, Western Sedimentary Basin, and Graben of Mirim Lagoon in Uruguay (Brazeiro et al. 2015). An updated map of A. reigi distribution is provided in Fig. 1.

Considering the northernmost known locality for the species occurrence, the municipality of Encruzilhada do Sul, Rio Grande do Sul (Luza et al. 2016), our examination of the species suggests that the range of A. reigi extends approximately 110 km northwest (to the municipality of São Sepé) and 120 km northeast (to the municipality of Barra do Ribeiro). The identities of specimens from these two localities were confirmed through BLAST. It should be noted that the geographic coordinates of the São Sepé specimen collection site (UFSC 6262) were not available; hence, central coordinates for the municipality were used for the estimative of the distribution extension for this locality and map indication.

Akodon reigi occurs in the vegetation units of Pioneer Formations, Semidecidual Seasonal Forest, and Steppes of Rio Grande do Sul, and ravine, mountain, and gallery forests of Uruguay (sensu FEPAM 2006; Alonso Paz and Bassagoda 2002). Data regarding the trapping habitats are available for seven sites in Rio Grande do Sul, distributed in the Pioneer Formations and Semidecidual Seasonal Forest vegetation units. In Barra do Ribeiro, Camaquã, Cristal, and São Lourenço do Sul, A. reigi specimens were obtained from shrubby/herbaceous formations with sparse arboreal individuals and soggy soil. In Pedro Osório, specimens were collected within a large stand of eryngo (Eryngium pandanifolium) located in a stream floodplain, characterized by waterlogged soil and lacking arboreal and shrubby vegetation. At Taim, specimens were found in grassland adjacent to restinga peat forest (sections with humid soils and shallow flooding depressions) with abundant E. pandanifolium and sparse cockspur coral tree (Erythrina crista-galli) (FMQ material). Within these herbaceous/shrubby patches, A. reigi coexisted with didelphid Monodelphis dimidiata, akodontines Deltamys kempi, Oxymycterus nasutus, and Scapteromys tumidus, as well as oryzomiynes Holochilus brasiliensis, Oligoryzomys flavescens, and O. nigripes. Sponchiado et al. (2010) recorded A. reigi in flooded and unflooded sections of the restinga forest in Taim. At Horto Botânico Irmão Teodoro Luis, Langone (2007) captured A. reigi at the sandy/peat restinga forest border adjacent to grassland and marsh. The author noted a higher number of captures in the grid segments located in the grassland and wetland areas. Other species captured in the same grids included didelphids Didelphis albiventris and Lutreolina crassicaudata, as well as akodontines D. kempi, O. nasutus, and S. tumidus, and oryzomyines O. flavescens, O. nigripes, and Sooretamys angouya. In Uruguay, A. reigi was observed in forest formations and landscape mosaics comprising various forest types and open phytophysiognomies. In the Rivera department, an individual was identified in the stomach contents of a rattlesnake (Crotalus durissus) collected in a ravine forest, locally known as ‘bosque de quebrada’. In the Maldonado department, A. reigi was found in a mosaic environment consisting of mountain forest, shrub patches, and grassland, coexisting with A. azarae, O. nigripes, and Oxymycterus josei. At Paso Centurión, within the Serranás del Este (Cerro Largo department), A. reigi was captured in gallery forest, alongside A. azarae and O. nigripes. At Paso Averías, in the floodplain of the Cebollatí river (Lavalleja department), type specimens of A. reigi were obtained in a gallery forest surrounded by grassland and lagoons, sharing habitat with A. azarae, D. kempi, and O. nigripes (González et al., 1998). In the Negro River floodplain, Durazno department, Ximénez and Langguth (1970) also collected A. reigi specimens in gallery forest.

Genetic Variability and Populational Analysis

Genetic variation was observed exclusively in the cyt b sequences, revealing 14 segregating sites that identified 11 haplotypes (Table 1). The Bayesian tree revealed a shallow structure of these haplotypes, which formed a sister cluster of A. paranaensis (Fig. 2). The median-joining network analysis did not reveal a clear structuring of haplogroups. One prevalent haplotype (H3) was widely distributed (Fig. 3), occurring in five populations along the north-south axis of the species’ distribution. Haplotype H1 was detected in samples from three localities in the northern part of the species’ range (Sul-Riograndense Plateau and Lagunar Plain of Rio Grande do Sul). Haplotype H5 was shared between two localities in the Sul-Riograndense Plateau. The remaining eight haplotypes were restricted to individual localities, with noteworthy occurrence in Santana da Boa Vista (Sul-Riograndense Plateau), where three exclusive haplotypes were identified. In contrast, the IRBP loci showed no nucleotide variation within A. reigi samples.

The results of the global Fu’s F_S-test of neutrality were negative (F_S: -0.95, p > 0.05), suggesting a potential demographic range expansion process, albeit non-significant. However, Tajima’s D-test did not reveal a signal of demographic range expansion at the global scale (D: 0.31, p > 0.05; Table 1). At the population level, Tajima’s D and Fu’s FS indicated variations in the demographic histories across different localities of the A. reigi distribution. The mismatch distribution appeared to be roughly multimodal (Fig. 4) and did not exhibit significant departures from an equilibrium model (SSD = 0.003, p = 0.61), implying constant population size, sustained subdivision, or both over an extended period. Furthermore, the Harpending raggedness index was not statistically significant (H = 0.008, p = 0.33). The average number of nucleotide differences across all populations was 2.99. Our analyses suggest that populations of A. reigi exhibit weak genetic structure, except for a notable differentiation observed between TAI and the other populations (Fig. 5).

The present study provides new insights into the distribution of Akodon reigi, a species that remains poorly understood and was previously known from very few localities. As demonstrated here, Akodon reigi is distributed across north-central and eastern Uruguay and within the territory of Rio Grande do Sul west of the Patos-Mirim Lagunar System, with a single locality east of this system (Taim Ecological Station). The known distribution of the species has been expanded to include the northern Lagunar Plain of Rio Grande do Sul and more inland areas of the Sul-Riograndense Plateau. Within this extended distribution, the identity of specimens from nine localities, including the new northern limit of the species distribution, was confirmed through BLAST comparisons, providing unequivocal identification. Additionally, sequences from our samples collected at Taim, a locality where specimens referenced in A. reigi description (González et al. 1998) were obtained, aligned with A. reigi sequences from Uruguay.

One of the key gaps in understanding Akodon species within the Southern Campos region relates to species delimitation. Akodon paranaensis was described subsequently to A. reigi (Christoff et al. 2000), and both have a diploid number of 2n = 44, differing only in fundamental number (FN = 42 in A. reigi and FN = 44 in A. paranaensis) (Pardinãs et al. 2015). The morphological similarity between these two taxa is notable (Pardinãs et al., 2015), yet surprisingly, A. paranaensis was not compared to A. reigi in its description. Gonçalves et al (2007) conducted maximum parsimony phylogenetic analyses of 28 Akodon species using cyt b sequences and recovered A. reigi as a sister to the clade composed of A. paranaensis sequences, albeit with low support (63%). Brandão et al. (2021) also obtained a similar topology of cyt b sequences for the two taxa, albeit with higher nodal support. While the validity of A. paranaensis is not questioned in our study, it is important to emphasize that the species boundary between A. paranaensis and A. reigi – both phylogenetically and geographically – is not well-established. In this regard, the indication of A. paranaensis in certain localities in Rio Grande do Sul, where the presence of A. reigi was confirmed through molecular identification in our study, warrants attention. Queirolo (2016) pointed out the occurrence of A. paranaensis in Camaquã based on Gonçalves et al. (2007), although such information was not found upon reviewing the work of Gonçalves et al. (2007). Queirolo (2016) also indicated the occurrence of A. paranaensis in Taim Ecological Station and Pelotas, based on karyotypic data obtained from specimens at those localities (Kasahara and Yonenaga-Yassuda 1984; Sbalqueiro 1989; Christoff 1997; Christoff et al. 2000). When considering these studies addressing A. paranaensis together with the confirmed occurrence of A. reigi on the latitudinal gradient between Taim and Camaqua (González et al. 1998; present study), it is assumed that the two species are sympatric in central-eastern and south-eastern Rio Grande do Sul. Specific identification of 53 ‘large-sized’ Akodon specimens with gray-olivaceous dorsal pelage – characteristics of both A. reigi and A. paranaensis – via BLAST, however, did not indicate the occurrence of any A. paranaensis samples from that region. Regarding A. paranaensis, Gonçalves et al. (2007) obtained sequences from two specimens from central-north and northeastern Rio Grande do Sul — Cambará do Sul (mixed ombrophilous forest) and Venâncio Aires (ecotone between deciduous seasonal forest and steppes) — which clustered with a sequence from a specimen from Piraquara, Paraná (the type locality of A. paranaensis [Christoff et al. 2000)]. Luza et al. (2016) identified 16 individuals as A. paranaensis via BLAST of cyt b sequences in northeastern Rio Grande do Sul (mixed ombrophilous forest), while 13 sequences assigned as A. reigi were found in individuals from Pampean domains of Rio Grande do Sul. Thus, it is possible that A. reigi and A. paranaensis, as currently recognized distinct species, exhibit allopatric distributions.

Akodon reigi appears restricted to Uruguay and regions in the Rio Grande do Sul encompassing the Pioneer Formations of Lagunar Plain and southern coastal plain, semideciduous decidual forest, and Pampean steppes. Conversely, Akodon paranaensis is distributed northwards in Rio Grande do Sul Atlantic Forest domains to Missiones, Argentina, and coastal southeastern Brazil (see Gonçalves et al. 2007; Pardiñas et al. 2015 in part). Data on the habitats of occurrence of A. reigi are available from Uruguay (González et al. 1998), Taim Ecological Station (González et al. 1998; Sponchiado et al. 2012), and Horto Botânico Irmão Teodoro Luis (HBITL; Langone 2007). The trapping habitats of the type series consisted of gallery forests in Uruguay and peat restinga forest in Taim. Additionally, efforts applied in open habitats (grasslands and wetlands) near forests where specimens were obtained in Uruguay were unsuccessful (González et al. 1998). These early findings led González et al. (1998) to presume that A. reigi exhibits a strong selection for forest habitats. Following, Langone (2007) sampled the small mammal assemblage occurring in a mosaic of restinga forest, wetland, and grassland in HBITL – Lagunar Plain of Rio Grande do Sul – and captured a total of 46 A. reigi individuals. Among these, 31 were captured in the open physiognomies of grassland and wetland. In contrast, Sponchiado et al. (2012) captured A. reigi (136 captures of 51 individuals) exclusively in forest habitats when sampling flooded and unflooded restinga forest and grassland, and dunes of Taim. The authors found A. reigi to be positively associated with environmental variables characterizing well-structured habitats, including tree and shrub density, canopy height, and environmental complexity (layers of vegetation). All 79 new specimens from Rio Grande do Sul presented herein were collected in sites characterized by shrubby/herbaceous phytophysiognomies with scattered or absent arboreal individuals. Among these, the most homogeneous habitat was observed in Pedro Osório, where four specimens were trapped in a large stand of Eryngium pandanifolium, an Apiacea herb with spiny leaves. Therefore, A. reigi appears to exhibit some habitat plasticity, not restricted solely to forest environments.

Sponchiado et al. (2012) identified a strong relationship between A. reigi and forest-associated variables; however, it should be noted that the shrubby grassland and herbaceous formations where the species occurs in Rio Grande do Sul also exhibit a degree of environmental complexity due to high plant density. Studies investigating the habitat by Akodon species in open formations (e.g. A. azarae, A. molina) have demonstrated a preference for habitat patches characterized by higher shrub and herbaceous coverage, litter depth and coverage, and stratum height (Busch et al. 2001; Corbalán and Ojeda 2004; Luza et al. 2018). According to Busch et al. (2001), the complexity of vegetation in open habitats is linked to productivity – availability of feeding resources – and protection against predation, particularly avian predation. In the mosaics of the Southern Campos, A. reigi may also select densely vegetated herbaceous/shrubby patches due to the provision of food resources and protection.

Our molecular analyses revealed low levels of genetic variation and differentiation within A. reigi. The conservative nature of IRBP was expected, given that this gene usually exhibits little variable in intraspecific and intrageneric lineages of sigmodontine rodents (e.g. Feijoo et al. 2008; Sierra et al. 2017; Laura-Alamendra et al. 2018). Nonetheless, the low variability of cyt b sequences was remarkable, with 11 haplotypes retrieved from 14 variable sites across 53 individuals sampled in 11 localities. In comparison, 23 individuals of A. cursor from 19 localities in southeastern Brazil presented 21 cyt b haplotypes (Geise et al. 2001), while a total of 86 A. montensis specimens from 36 localities along the species distribution (southeastern Brazil to northeastern Argentina and Rio Grande do Sul) generated 55 haplotypes (151 variable sites) (Valdez and D’Elía 2013). One factor possibly associated with this dissimilarity is the pattern of species distribution. It is hypothesized that mammal species living in tropical domains tend to exhibit higher intraspecific cyt b diversity compared to species from temperate domains as a coevolutionary response to the elevated mutational rates of local biota (Gillman et al. 2009). Another study demonstrated that mitochondrial sequences (cyt b and cytochrome oxidase I [COI] genes) are more variable in mammalian taxa from tropical due to more persistent populations throughout extended periods of climate stability (Theodoridis et al. 2020). The lower cyt b diversity detected in A. reigi could reflect comparatively lower evolutionary rates in subtropical biota and a few persistent populations. In addition to shallow divergences, our analyses revealed a pattern of sustained historical gene flow among A. reigi populations. A pronounced geographic structure was only evident concerning Taim and the remaining populations. Taim, situated in the southern coastal plain of Rio Grande do Sul (southern restinga), stands as the sole site east of the Patos-Mirim lagoons, while all other sampled sites are situated west of this system. This suggests that the Patos-Mirim system, encompassing the São Gonçalo channel, may serve as a geographic barrier hindering gene flow in A. reigi. The Patos Lagoon and its estuary, in particular, could pose a barrier to A. reigi dispersal toward the middle and northern segments of the Rio Grande do Sul coastal plain (northern restinga), as intensive sampling in that region failed to yield any records of the species. The Patos Lagoon estuary has also been identified as a potential geographic barrier to historical gene flow in sympatric/syntopic akodontines S. tumidus (Quintela et al. 2015), D. kempi (Quintela et al. 2017)d nasutus (Peçanha et al. 2017). In the case of O. nasutus, the population from Taim emerged as the most divergent, contributing to a phylogeographic break within the species (Peçanha et al. 2017).

The median-joining network revealed a pattern suggestive of population expansion, characterized by a central widespread haplotype giving rise to haplotypes of varying distribution, with some restricted to specific localities. A similar expansion pattern was observed in the akodont Scapteromys tumidus (Quintela et al. 2015), which shares a comparable geographic distribution and coexists with A. reigi in most sampled localities. However, mismatch analysis indicated a constant population size for A. reigi, and neutrality tests did not show significant indicators of population expansion. Past demography reconstructions have indicated population expansions during the Pleistocene climatic oscillations for some sigmodontines (Calomys musculinus, O. flavescens, O. nigripes, O. nasutus, and S. tumidus) from the southern Atlantic Forest and Pampas region, likely driven by the availability of suitable open habitats and expansion of continental area during colder and drier periods (Quintela et al. 2015; Peçanha et al. 2017; Ortiz et al. 2023). However, these past climatic events appear to have had no discernible effect on the historical demography of A. reigi.

The locality with the highest haplotype richness among the samples was Santana da Boa Vista, situated within the Sul-Riograndense Plateau, a geomorphological unit embedded by the Precambrian Sul-Riograndense Shield. This particular unit could serve as a core area for cyt b diversification, followed by subsequent expansion into new regions where local differentiations occurred. Interestingly, the highest cyt b haplotypic diversity in S. tumidus was discovered in the Uruguayan department of Flores (Quintela et al. 2015), which lies in the southern extension of the Sul-Riograndense Shield. In a study by Ortiz et al. (2023), a relaxed random walk analysis on cyt b sequences of S. tumidus and the southern clade of O. nasutus pinpointed the southeastern Uruguayan coast, at the southernmost part of the Rio-Grandense Shield, as the center of origin for these lineages. Thus, the Precambrian formations of Rio Grande do Sul and Uruguay could signify a region of diversification and initial dispersion for sigmodontine rodents and other animal groups originating from subtropical-temperate domains of South America. Nevertheless, to validate the hypothesis of A. reigi origin, more extensive sampling is required to explore genetic-based biogeographic models and establish a robust time-calibrated phylogeny of intraspecific lineages.

Our study revealed low genetic diversity and an extended but still restricted distribution of A. reigi, which covers a latitudinal range of about 500 km. In these aspects, A. reigi is a species of conservation interest, especially when considering its potential low resilience to environmental changes due to low genetic variability and the fragility of the area occupied by the species in front of climate change, currently subjected to severe flooding episodes. Another crucial issue to investigate is the species boundary between A. reigi and A. paranaensis, two morphologically and karyotypically very similar nominal forms with apparent parapatric distributions.

Acknowledgements

We are grateful to Michel A. P. Vale for the preparation of the map, Ana Carolina Canary for the collection license, and Patricia Langone for specimen donation.

Author contribution

Fernando M. Quintela and Gislene L. Gonçalves contributed to the study conception. Field sampling was performed by Fernando M. Quintela. Consultation to mammal collections was made by Jéssica B. Pereira. Laboratory procedures were performed by Jéssica B. Pereira, Gislene L. Gonçalves, and Victor H. Valiati. Data analyses were conducted by Gislene L. Gonçalves and Fernando M. Quintela. The first draft of the manuscript was written by Fernando M. Quintela, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Funding

This study was partially supported by the Fundação Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – CAPES (process number 88882-314620/2019-1).

Data availability

Sequences generated in this study are available in GenBank through accession numbers PQ150403-PQ150453.

Ethics approval

All procedures adopted in the study are in accordance with institutional protocols for the use of animals in scientific research.

Consent to participate

All authors agreed to participate in this study and co-authorship.

Consent for publication

All authors agreed with the content, and all gave explicit consent to submit.

Conflict of interest

The authors declare no competing interests.

Abreu MSL, Christoff AU, Valiati VH, Oliveira LR (2014) New distribution records of Serra do Mar Grass Mouse Akodon serrensis Thomas, 1902 (Mammalia: Rodentia: Sigmodontinae) in the southernmost Brazil. Check List 10:655–659. https://doi.org/10.15560/10.3.655
Alonso Paz E, Bassagoda MJ (2002) Aspectos fitogeofráficos y diversidade biológica de las formaciones boscosas del Uruguay. Ciência Ambiente 24:35–50
Bandelt HJ, Forster P, Ohl AR (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
Bergamin RS, Molz M, Rosenfield MF, Klipel J, Biasotto LD, Jarenkow JA (2024) Forests in the South Brazilian Grassland region. In: Overbeck GE, Pillar VP, Müller SC, Bencke GA (eds) South Brazilian Grasslands – Ecology and Conservation of the Campos Sulinos. Springer, Cham, pp 385–416
Brandão MV, Percequillo AR, D’Elía G, Paresque R, Carmignotto AP (2021) A new species of Akodon Meyen, 1833 (Rodentia: Cricetidae: Sigmodontinae) endemic from the Brazilian Cerrado. J Mammal 102:101–122. https://doi.org/10.1093/jmammal/gyaa126
Brandão MV, Carmignotto AP, Percequillo AR, Christoff AU, Mendes-Oliveira AC, Geise L (2022) A new species of Akodon Meyen, 1833 (Rodentia: Cricetidae) from dry forests of the Amazonia-Cerrado transition. Zootaxa 5205:401–435. https://doi.org/10.11646/zootaxa.5205.5.1
Brazeir A, Panario D, Soutullo A, Gutiérrez O, Segura A, Mai P (2015) Identificación y delimitación de eco-regiones de Uruguay. In: Brazeiro A (ed) Ecoregiones de Uruguay: Bbiodiversidad, presiones y conservación. Aportes a la estrategia nacional de Biodiversidad. Facutad de Ciencias, CIEDUR, VS Uruguay, SZU, Montevideo, pp 1–40
Busch M, Miño MH, Dadon JR, Hodara K (2001) Habitat selection by Akodon azarae and Calomys laucha (Rodentia, Muridae) in Pampean agroecosystem. Mammalia 65(1):29–48. https://doi.org/10.1515/mamm.2001.65.1.29
Christoff AU (1997) Contribuição à sistemática das espécies do gênero Akodon (Rodentia: Sigmodontinae) do leste do Brasil: estudos anatômicos, citogenéticos e de distribuição geográfica. Dissertation, Universidade de São Paulo
Christoff AU, Fagundes V, Sbalqueiro IJ, Mattevi MS, Yonenaga-Yassuda Y (2000) Description of a new species of Akodon (Rodentia: Sigmodontinae) from Southern Brazil. J Mammal 81:838–851. https://doi.org/10.1644/1545-1542(2000)081<0838:DOANSO>2.3.CO;2
Christoff AU, Peters FB, Roth PRO, Coelho EL, Jung DMH (2013) Myomorpha. In: Weber MM, Roman C, Cáceres NC (eds) Mamíferos do Rio Grande do Sul. UFSM, Santa Maria, pp 287–342
Corbalán V, Ojeda R (2004) Spatial and temporal organization of small mammal communities in the Monte Desert. Argentina Mammalia 68:5–14. https://doi.org/10.1515/mamm.2004.001
Dantas ME, Viero AC, Silva DRA (2010) Origem das paisagens. In: Viero AC, Silva DRA (eds) Geodiversidade do Rio Grande do Sul. CPRM, Porto Alegre, pp 35–35
D’Elía G, González EM, Pardiñas UFJ (2003) Phylogenetic analysis of Sigmodontinae rodents (Muroidea), with special reference to the akodont genus Deltamys. Mammal Biol 68:351–364. https://doi.org/10.1078/1616-5047-00104
D’Elía G, Mora I, Myers P, Owen RD (2008) New and noteworthy records of Rodentia (Erethizontidae, Sciuridae, and Cricetidae) from Paraguay. Zootaxa 1784:39–57. https://doi.org/10.5281/zenodo.182407
Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973. https://doi.org/10.1093/molbev/mss075
Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol 13:853–864. https://doi.org/10.1046/j.1365-294X.2003.02004.x
Excoffier L, Lischer HEL (2010) ARLEQUIN suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Feijoo M, D’Elía G, Pardiñas UFJ, Lessa EP (2008) Systematics of the southern Patagonian-Fueguian endemic Abrothrix lanosus (Rodentia: Sigmodontinae): Phylogenetic position, karyotypic and morphological data. Mammal Biol 75:122–137. https://doi.org/10.1016/j.mambio.2008.10.004
FEPAM – Fundação Estadual de Proteção ao Meio Ambiente (2006) Mapa de Unidades de Vegetação do Rio Grande do Sul. &id=26&submenu=14. http://www.biodiversidade.rs.gov.br:80/portal/index.php?acao=secoes_portal
Accessed (2024) 05 May
Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925. https://doi.org/10.1093/genetics/147.2.915
Fundação SOS Mata Atlântica/INPE (2021) Atlas dos remanescentes naturais da Mata Atlântica. Período 2019–2020. https://cms.sosma.org.br/wp-content/uploads/2021/05/SOSMA_Atlas-da-Mata-Atlantica_2019-2020.pdf. Accessed 16 May 2024
Geise L, Smith MF, Patton JL (2001) Diversification in the genus Akodon (Rodentia: Sigmodontinae) in southeastern South America: mitochondrial DNA sequence analysis. J Mammal 82:92–101. https://doi.org/10.1644/1545-1542(2001)082%3C0092:DITGAR%3E2.0.CO;2
Gillman LN, Keeling DJ, Ross HA, Wright SD (2009) Latitude, elevation, and the tempo of molecular evolution in mammals. Proc R Soc B 276:3353–3359. https://doi.org/10.1098/rspb.2009.0674
Gonçalves PR, Myers P, Vilela JF, 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. Misc Public - Mus Zool Univ Mich 197:1–24
González EM, Langguth A, Oliveira LFB (1998) A new species of Akodon from Uruguay and southern Brazil (Mammalia: Rodentia: Sigmodontinae). Com Zool Mus Hist Nat Montevideo 12:1–7
González EM, Martínez-Lanfranco JA (2010) Mamíferos de Uruguay – guia de campo e introducción a su estudio y conservación. Banda Oriental, Montevideo
Harpending HC (1994) Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66:591–600
Jansa SA, Voss RS (2000) Phylogenetic studies on didelphid marsupials I. Introduction and preliminary results from nuclear IRBP gene sequences. J Mammal Evol 7:43–77. https://doi.org/10.1023/A:1009465716811
Kasahara S, Yonenaga-Yassuda Y (1984) A progress report of cytogenetic data on Brazilian rodents. Rev Bras Gen 7:509–533
Langone PQ (2007) Importância da matriz e das características do habitat sobre a assembléia de pequenos mamíferos em fragmento de mata de restinga no Sul do Brasil. Dissertation, Universidade Federal de Pelotas
Laura Almendra A, González-Cózatl FX, Engstrom MD, Rogers DS (2018) Evolutionary relationships and climatic niche evolution in the genus Handleyomys (Sigmodontinae: Oryzomyini). Mol Phylogenetics Evol 128:12–25. https://doi.org/10.1016/j.ympev.2018.06.018
Leite RN, Kolokotronis S, Almeida FC, Werneck FP, Rogers DS, Weksler M (2014) In the Wake of Invasion: Tracing the historical biogeography of the South American cricetid radiation (Rodentia, Sigmodontinae). PLoS ONE 9:e100687. https://doi.org/10.1371/journal.pone.0100687
Luza AL, Gonçalves GL, Pillar VD, Hartz SM (2016) Processes related to habitat selection, diversity and niche similarity in assemblages of non-volant small mammals at grassland–forest ecotones. Nat Conserv 14:88–98. https://doi.org/10.1016/j.ncon.2016.09.003
Luza AL, Trindade JPP, Maestri R, Duarte LS, Hartz SM (2018) Rodent occupancy in grassland paddocks subjected to different grazing intensities in South Brazil. Perspect Ecol Conserv 16:151–157. https://doi.org/10.1016/j.pecon.2018.06.006
Müller SC, Bergamin RS, Duarte LS, Peroni N, Sühs RB, Carlucci MB (2024) Mechanisms and processes shaping patterns of forest-grassland mosaics in southern Brazil. In: Overbeck GE, Pillar VP, Müller SC, Bencke GA (eds) South Brazilian Grasslands – Ecology and Conservation of the Campos Sulinos. Springer, Cham, pp 417–446
Ortiz N, Pinotti JD, Trimarchi LI, Gardenal CN, González-Ittig RE, Rivera PC (2023) Demographic processes, refugia and dispersal routes during the Pleistocene in a sigmodontine rodent assemblage from the South American Pampas. Biol J Linn Soc 141(3):419–434. https://doi.org/10.1093/biolinnean/blad096
Overbeck GE, Müller SC, Fidelis A, Pfadenhauer J, Pillar VD, Blanco C, Boldrini II, Both R, Forneck ED (2007) Brazil’s neglected biome: the South Brazilian Campos. Perspect Plant Ecol Evol Syst 9:101–116. 10.1016/j.ppees.2007.07.005
Pardiñas UFJ, D’Elía G, Cirignoli S, Suarez P (2005) A new species of Akodon (Rodentia, Cricetidae) from the northern Campos grasslands of Argentina. J Mammal 86:462–74. https://doi.org/10.1644/1545-1542(2005)86[462:ANSOAR]2.0.CO;2
Pardiñas UFJ, Teta P, Alvarado-Serrano D, Geise L, Jayat JP, Ortiz PE, Gonçalves PR, D’Elía G (2015) Genus Akodon Meyen, 1833. In: Patton JL, Pardiñas UFJ, D’Elía G (eds) Mammals of South America – Volume 2: Rodents. The University of Chicago Press, Chicago and London, pp 144–120
Peçanha WT, Quintela FM, Ribas LEJ, Althoff SL, Maestri R, Gonçalves GL, Freitas TRO (2019) A new species of Oxymycterus (Rodentia: Cricetidae: Sigmodontinae) from a transitional area of Cerrado–Atlantic Forest in southeastern Brazil. J Mammal 100:578–598. https://doi.org/10.1093/jmammal/gyz060
Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 5:1253–1256. https://doi.org/10.1093/molbev/msn083
Queirolo D (2016) Diversidade e padrões de distribuição de mamíferos dos Campos do Uruguai e Sul do Brasil. Bol Soc Zool Uruguay 25:92–246
Quintela FM, Bertuol F, González EM, Cordeiro-Estrela P, Freitas TRO, Gonçalves GL (2017) A new species of Deltamys Thomas, 1917 (Rodentia: Cricetidae) endemic to the southern Brazilian Araucaria Forest and notes on the expanded phylogeographic scenario of D. kempi. Zootaxa 4294:71–92. https://doi.org/10.11646/zootaxa.4294.1.3
Quintela FM, Gonçalves GL, Bertuol F, González EM, Freitas TRO (2015) Genetic diversity of the swamp rat in South America: population expansion after transgressive-regressive marine events in the Late Quaternary. Mammal Biol 80:510–517. http://dx.doi.org/10.1016/j.mambio.2015.08.003
Rambaut A, Drummond AJ (2007) Tracer v1.4. http://tree.bio.ed.ac.uk/software/tracer/. Accessed 4 April 2024
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A (2018) DnaSP 6: DNASequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol 34:3299–3302. https://doi.org/10.1093/molbev/msx248
Sbalqueiro IJ (1989) Análises cromossômicas e filogenéticas em algumas espécies de roedores da região sul do Brasil [thesis]. Dissertation, Universidade Federal do Rio Grande do Sul
Schott D, Umeno K, Dall’Agnol B, Souza UA, Webster A, Michel T, Peters F, Christoff AU, André MR, Ott R, Jardim M, Reck J (2020) Detection of Bartonella sp. and a novel spotted fever group Rickettsia sp. in Neotropical fleas of wild rodents (Cricetidae) from Southern Brazil. Comp Immunol Microbiol Infect Dis 73:101568. https://doi.org/10.1016/j.cimid.2020.101568
Smith MF, Patton JL (1984) Dynamics of morphological differentiation: temporal impact of gene flow in pocket gopher populations. Evolution 38:1079–1087. https://doi.org/10.1111/j.1558-5646.1984.tb00377.x
Sierra ABA, Castillo ER, Labaroni C, Barrandeguy ME, Martí DA, Ojeda R, Lanzone C (2017) Genetic studies in the recently divergent Eligmodontia puerulus and E. moreni (Rodentia, Cricetidae, Sigmodontinae) from Puna and Monte deserts of South America. Mamm Biol 87:93–100. https://doi.org/10.1016/j.mambio.2017.06.001
Sponchiado J, Melo GL, Cáceres NC (2010) Habitat selection by small mammals in Brazilian Pampas biome. J Nat Hist 46:1321–1335. https://doi.org/10.1080/00222933.2012.655796
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595. https://doi.org/10.1093/genetics/123.3.585
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
Theodoridis S, Fordham DA, Brown SC, Li S, Rahbek C, Nogues-Bravo D (2020) Evolutionary history and past climate change shape the distribution of genetic diversity in terrestrial mammals. Nat Commun 11:2557. https://doi.org/10.1038/s41467-020-16449-5
Valdez L, D’Elía G (2013) Differentiation in the Atlantic Forest: phylogeography of Akodon montensis (Rodentia, Sigmodontinae) and the Carnaval-Moritz model of Pleistocene refugia. J Mammal 94:911–922. https://doi.org/10.1644/12-MAMM-A-227.1
Ximénez A, Langguth A (1970) Akodon cursor montensis en el Uruguay (Mammalia, Cricetinae). Com Zool Mus Hist Nat Montevideo 10:1–7

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Constricted range and limited genetic variation in Reig's Grass Mouse Akodon reigi (Cricetidae: Sigmodontinae) in the Southern Campos

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Introduction

Material and Methods

Specimens and data sampling

Molecular DNA analysis

Results

Geographic Distribution and Habitat

Genetic Variability and Populational Analysis

Discussion

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References

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Supplementary Files

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