Ecological analyses of the R. mexicanus species complex.
The partial ROC tests showed a significant predictive ability of the models for all delimited species (p < 0.05; Appendix 7). ENMs predicted high-suitability areas for each of the delimited species (Fig. 6). The R. mexicanus clade IIA had the largest suitability areas, mainly distributed in the Sierra Madre Oriental, northern Oaxaca, and the Central Highlands of Chiapas and Guatemala. For the R. mexicanus clade I, suitability areas were found mostly in the Sierra Madre Oriental and northern Oaxaca. The suitability areas ofR. mexicanus clade IIIA were restricted to the northern region of the western and central Cordillera of the Colombian Andes, while theR. mexicanus clade IIIB occurs from the southwestern region of the Colombian Andes to the northern Ecuadorian Andes.
There were significant pairwise differences between the delimited species for all environmental variables except for Bio1 and Bio5 (Fig. 7a-g). The environmental niche of the R. mexicanus clade I presented the lowest temperature values for the coldest month (Bio6, mean of 6.5 °C). The R. mexicanus clade IIIA presented on average the highest values of annual precipitation (Bio12, mean of 2483 mm) and precipitation of the driest month (Bio14, mean of 95.2 mm) but showed similar average values of precipitation of the wettest month, together with the R. mexicanus clade IIA (Bio13, mean of 340.3 y 345.9 mm, respectively). The CVA completely segregated the environmental niches ofR. mexicanus clade IIIA – R. mexicanus clade IIIB from those of R. mexicanus clade I – R. mexicanus clade IIA, but there was still a small region of overlap in their environmental space (Fig 7h).
DISCUSSION
Reithrodontomys mexicanus cryptic species complex .
Reithrodontomys mexicanus originally comprised 13 subspecies (Hooper 1952; Hooper 1955), though 10 are currently recognized (Bradley 2017). Our phylogenies included samples of the formerly subspecies R. garichensis for the first time. We confirmed that it is distinct from R. mexicanus but belongs to the R. mexicanus group (Gardner and Carleton 2009). Surprisingly, the Costa Rican specimens considered to beReithrodontomys sp. by Miller and Engstrom (2008) showed a close relationship with R. garichensis . These authors suggested that the two specimens from Volcan Poas, Costa Rica represent a new species based on their morphological and genetic differences with respect toR. mexicanus . The three species delimitation methods implemented here supported their proposal. On the other hand, these methods failed to differentiate the specimen from La Carpentera, Costa Rica from that of R. garichensis . Therefore, both were identified as the same species, and the specimen from La Carpentera, Costa Rica is proposed to be reclassified as R. garichensis .
In this study, R. mexicanus was recovered as a polyphyletic taxon formed by three clades (I, II, III), highly divergent from each other, which agrees with Arellano et al. (2003; 2005). Within clade II, all delimitation methods demarcated individuals from Parque Nacional Montecristo, El Salvador (clade IIB) to the species level. The cytb genetic distance between this group and clade IIA was 4.96%, slightly lower than the 5 % limit estimated by Baker and Bradley (2006) to recognize sister mammal species. Specimens from El Salvador could not be examined morphologically. Nonetheless, we had access to 5 individuals from Los Esesmiles (Cerro El Pital); not included in the molecular or morphometric analyses. Compared to individuals of R. mexicanusclade I distributed in Mexico and Guatemala, these specimens from Los Esesmiles differ morphologically by their relatively shorter nasal bones, broader palatal, and rounded braincase. The pelage exhibits a cinnamon coloration, and the tail tends to be not much longer than the head and body together. Parque Nacional Montecristo and Los Esesmiles are only separated by ca. 30 km, so individuals from both localities could be assumed to have the same genetic identity. Thus, populations from El Salvador could be assumed to be a divergent lineage from the remaining members of R. mexicanus clade I, but more evidence is needed, such as molecular analyses that include an additional sampling of individuals from this region, to reach a conclusion regarding their taxonomic status.
The strongest morphometric similarities were found between the putative species R. mexicanus clade IIA and R. mexicanus clade IIIB, which showed no significant differences in the ventral skull shape. It has been reported that the ventral view of the skull is the one with a better phylogenetic signal (Camul and Polly 2005). Consequently, our morphometric results are consistent with the molecular data, which showed that these clades are more closely related to each other than to the R. mexicanus clade I. In mammals, it has been reported that the environment can influence the development of bone structures such as the skull and jaw (Camul and Polly 2005). The few morphometric differences found between these putative species (clades IIA and IIIB) could be due to the fact that, in general, they share similar habitat characteristics (Hooper 1952). However, the ecological analyses allowed us to clearly segregate their environmental space, based mainly on precipitation and VCF variables. Although their separation was weakly supported by geometric morphometrics, the genetic and environmental differentiation of these clades strongly support their demarcation as distinct species.
The bGMYC delimitation method proved to be the most conservative for proposing putative species within the clade that grouped the R. mexicanus specimens from South America. Despite the number of species proposed by the different methods, most pairwise comparisons did not exceed cytb genetic distance values of 5% (K2P distances range from 1.50 to 4.20%, Supplementary material 2). Low levels of genetic differentiation reported for South American rodents have been explained as a consequence of recent speciation processes (Patton and Smith 1992). Such would be the case in the genus Reithrodontomys , whose diversification processes began ca. 6.83 mya according to our results, expanding from North America to South America, of which only subspecies of R. mexicanus are known (Hooper 1952).
Arellano et al. (2005) analyzed a specimen from Colombia but retained it as part of R. mexicanus sensu stricto. In their analyses,R. darienensis from Panama was not included. Our phylogenetic analyses included R. darienensis and a good representation of specimens from Colombia and Ecuador that had been classified a priori asR. mexicanus . Our evidence supported the conclusion that South American specimens form a distinct clade from R. mexicanus which is sister to R. darienensis . Within this clade, delimitation methods and cytb genetic distances suggested that the Colombian specimens (R. mexicanus clade IIIA) from Risaralda (ICN16579) and Antioquia (FMNH78179) constitute a distinct species from the other South American individuals. Although it was not possible to corroborate the species-level distinction with morphological evidence, the ENM delimited its distribution to the northwestern region of the western and central Cordilleras of Colombia, with a habitat characterized mainly by high precipitation values. These individuals could be considered a divergent lineage that is already distinct from the rest of the South American populations in at least three species properties (reciprocal monophyly, genetic differentiation, and ecological niche distinctiveness; de Queiroz 2007).
The remaining individuals from Colombia and Ecuador (R. mexicanusclade IIIB) were validated at the species level by genetic and ecological data, and to a lesser extent with morphometric evidence. Hooper (1952) reported three subspecies of R. mexicanus in South America: R. m. milleri , R. m. soederstroemi , and R. m. eremiscus . The known distribution of R. m. milleri ranges from Colombia to northern Ecuador, including the suitability areas found for the two candidate species (R. mexicanus clade IIIA andR. mexicanus clade IIIB). However, the distribution of R. mexicanus clade IIIA was restricted to a small region of the western and central Cordillera, while R. mexicanus clade IIIB was distributed mainly in the Cordillera Oriental, a region not reported forR. m. milleri (Hooper 1952). In addition, the suitability areas of R. mexicanus clade IIIB included localities recognized for the other two subspecies (R. m. soederstroemi and R. m. eremiscus ), distributed only in Ecuador (Hooper 1952; Arellano et al. 2015). Therefore, an analysis focused on the harvest mice populations of South America is essential to correctly establish the taxonomic designation of the Reithrodontomys species that inhabit this region, since they undoubtedly do not belong to R. mexicanus .
Even though R. mexicanus clade I had already been considered a candidate species using allozymes (Arellano et al. 2003), cytb sequences (Arellano et al. 2005), and chromosomal data (Urbina et al. 2006), in our analyses, we were able to include a wide sampling that allowed us to support this new species not only with molecular data but also with morphological and ecological data. The phylogenetic position of this putative species in the trees confirms that it is a much older lineage (divergence time estimates ranging from 4.53 to 6.84 mya) and has a different evolutionary history from the rest of the clades within the subgenus Aporodon . Although representatives of the R. mexicanus clade I have historically been classified as R. mexicanus , they are genetically very distant from this species, even those that coexist in sympatry in the localities of La Esperanza and Puerto de la Soledad in Oaxaca, Mexico. Specimens of this clade could be discriminated correctly by morphology, especially by ventral skull shape. The phylogenetic signal that structures located on the ventral side of the skull exhibit (Lockwood et al. 2004; Macholán 2008) could explain the marked morphometric differentiation that this clade presented in accordance with its position in the phylogenetic trees. The environmental characteristics of this candidate species, partially overlap with those of R. mexicanus clade II. This is expected, given that they share part of their distribution in the Mexican cloud forests (Gual-Díaz and Rendón-Correa 2014). However, comparisons of most environmental variables were significantly different, with R. mexicanus clade I occupying a geographic area characterized by low values of temperatures and annual precipitation, and high forest cover (VCF). The congruence between the independent datasets is essential for the delimitation of this clade as a new species since until now, only molecular data had been used to differentiate it.
Taxonomy of the R. mexicanus species group .
Within the subgenus Aporodon , the R. mexicanus group currently comprises the species R. mexicanus , R. brevirostris , R. paradoxus , R. gracilis, R. spectabilis ,R. darienensis , and R. garichensis . The overall distribution of this group ranges from Mexico to South America, although most species are concentrated in Central America (Hall 1981). Here, all the members of this group, but R. paradoxus , were analyzed using molecular data, which allowed us to clarify the evolutionary relationships between them and make taxonomic considerations within the species group.
Reithrodontomys brevirostris was recovered as the sister group of the R. mexicanus clade II and confirmed as a valid species by all molecular delimitation methods. However, populations of this species have tended to be confused with those of R. mexicanus from Central America. Indeed, most of the individuals that exemplified theR. brevirostris clade in this study had originally been identified by their collectors as R. mexicanus (and another two as R. gracilis by Miller and Engstrom 2008). Similarly, in the phylogeny of Arellano et al. (2005) one individual from Costa Rica, grouped in their Clade I, was later reclassified as R. brevirostris by Gardner and Carleton (2009). Furthermore, these later authors assigned R. m. potrerograndei , a former R. mexicanus subspecies, as part of R. brevirostris “because of their comparably small size and other morphological resemblances” (Gardner and Carleton 2009: 172). Hooper (1952) noted that many of the morphological and cranial features of R. brevirostris were reminiscent of R. mexicanus , but the absence of evidence of interbreeding allowed them to be maintained as species. The separation between R. brevirostris and R. mexicanus clade I occurred at approximately 1.49 mya, and its genetic divergence for cytb was 5.68%, slightly higher than 5%, a generally observed distance between sister species in mammals (Baker and Bradley 2006). The relatively low genetic differentiation could account for the strong morphological similarity historically reported between these clades. They also share similar habitat characteristics, being distributed mainly in the cloud forest (Hooper 1952, Gual-Díaz and Rendón-Correa 2014). Both clades would fall within the gray zone described by de Queiroz (2007), in which the decision as to whether they constitute one or two taxonomic entities depends on the species criteria used. Based on our results, we propose that they remain distinct entities, under the assumption that they have been evolving as divergent lineages for sufficient time to separate but continue to maintain many of the common ancestral characteristics they share (de Queiroz 1998).
Hooper (1952) considered R. darienensis and R. gracilis to be superspecies because they did not show major differences in morphological traits, pelage coloration, or cranial or body size. The term superspecies was proposed by B. Rensch and later by E. Mayr to refer to monophyletic and allopatric taxa that formed a single entity and later evolved to the species level (Amadon 1966). However, our phylogenetic results did not recover R. darienensis and R. gracilis as a monophyletic group, and the genetic distances between them reached values of almost 14%. Furthermore, R. darienensiswas more closely related to the clade containing R. mexicanusspecimens from South America (although they were genetically well-differentiated) than to R. gracilis . This is consistent with its restricted distribution in eastern Panama (Bradley 2017). TheR. gracilis specimens from Yucatan and Campeche, Mexico were unequivocally delimited as the same entity as R. spectabilis , while those from El Salvador were recognized at the species level. According to their geographical distribution, these two specimens correspond to the subspecies R. g. anthonyi (Hall, 1981), but the genetic distances of almost 8% between these and the R. gracilis+ R. spectabilis clade suggest that it is necessary to reevaluate the Central American populations of R. gracilis , to assess if they completed speciation processes (Futuyma 2013).
Reithrodontomys spectabilis , whose distribution is restricted to Cozumel Island, Mexico, was described as one of the largest species of the genus (Jones and Lawor 1965). Although many aspects of its morphology were reminiscent of R. gracilis from Yucatan, marked differences in body size, darker coloration, and broader and heavier zygomatic arches prompted its recognition at the species level. Jones and Lawlor (1965) suggested that the precursor of R. spectabilisarrived from the Yucatan Peninsula during the Late Pleistocene, which assumes a relatively long period of isolation between these two species. Our results suggest that the divergence between these species (95% HPD = 0.19-0.47) occurred at some point in the Middle Pleistocene (from 0.781 to 0.126 Mya, Walker et al. 2018), indicating a very recent separation between their populations compared to those reported for other species of the subgenusAporodon (Martínez et al. 2022a; this study). This recent separation is also consistent with the low cytb genetic differentiation between these species (0.7 %), which fall within the intraspecific range values proposed for Reithrodontomys (Baker and Bradley 2006). The phylogenetic relationships between R. spectabilis andR. gracilis have been analyzed in the past with allozymes and the cytb gene, arriving at similar results to ours and suggesting an island effect as a possible cause of their morphological differences (Arellano et al. 2003; 2005). Rodents frequently exhibit island gigantism with respect to conspecific populations on the mainland (Lomolino 1985). This phenomenon is known as the Island rule (Foster 1964) and is affected by different factors including resources availability and the absence of natural predators (Lomolino 2005). We agree with Arellano et al. (2005) that this phenomenon could explain why the harvest mice populations of Isla Cozumel differ, mainly in body size, from the R. gracilis populations of Yucatan. Recognizing R. spectabilis as a conspecific of R. gracilisentails reevaluating its populations in many ways, considering that it is an endemic species classified as Critically Endangered by the IUCN Red List of Threatened Species (Vázquez et al. 2018). Additional comparative studies of both species employing different sources of evidence such as geometric morphometric, ecological niche, population genetics, among others, are necessary to reach a conclusion about their taxonomic status.
Species delimitation and its taxonomic implications .
Establishing species boundaries is difficult when dealing with taxonomically complex groups whose descriptions have been based primarily on their morphology (Dayrat 2005). Many of these species exhibit such a pronounced morphological resemblance to each other that they are recognized as cryptic species (Bickford et al. 2007). This is the case of R. mexicanus , where molecular (Arellano et al. 2003, 2005; Mill4er Engstrom 2008) and craniodental (Gardner and Carleton 2009) data have revealed broad cryptic variation leading to its recognition as a species complex. Integrating multiple approaches to delimit species has been strongly recommended to better confirm the species hypothesis (Dayrat 2005; Will et al. 2005). In this study, we implemented an integrative taxonomy approach to test if there are cryptic lineages within R. mexicanus that are evolving separately. We employed different criteria in accordance with the GLC (de Queiroz 1998; 2007), seeking as much evidence as possible to support the recognition of identified candidate species (Sangster 2018).
Species proposals were not always congruent among the delimitation methods. The limitations of methods based on DNA data have been discussed previously (see Luo et al. 2018), mainly those related to non-compliance with the assumptions of the method (Carsten et al. 2013). However, in Reithrodontomys , the efficacy of the delimitation methods used here (mPTP, bGMYC, and STACEY) to demarcate cryptic lineages at the species-level has been demonstrated (Martínez-Borrego et al. 2022a. The use of different molecular markers showed conflicting results among the phylogenies, with a high discordance between the topology of the cytb and those of the Fgb-I7 and IRBP, respectively. This mito-nuclear discordance has been suggested to be a consequence of introgression or incomplete lineage sorting (Toews and Brelsford 2012; Firneno et al. 2020). Although including more genetic markers can help to elucidate species limits, sometimes the use of multiple loci has complicated this purpose for taxonomists (Firneno et al. 2021). Therefore, in our study, the recognition of taxonomic entities was based primarily on molecular species delimitation methods, including the cytb genetic distances, traditionally used in mammal genetic studies (Bradley and Baker 2001; Baker and Bradley 2006), but other evidence such as skull morphometry and ecological niche were also used.
Geometric morphometrics and niche modeling have shown great applicability in taxonomic studies in mammals (Barčiová 2009; Martínez Gordillo et al. 2010) and have allowed the corroboration of species limits hypotheses derived from phylogenetic studies (e.g., Camul and Polly 2005; Rivera et al. 2018). However, the species-level clades proposed here by the three delimitation methods and genetic distances were not always strongly supported by ecological and/or morphological data. Under the GLC, failure to meet any of the species criteria does not necessarily mean that the candidate species does not correspond to a divergent lineage (de Queiroz 2007). Rather, GLC recognizes that species properties may evolve at different times during divergence (Sangster 2018), hence the importance of integrating multiple data sources to support or reject the species hypothesis (Padial et al. 2010).
CONCLUSIONS
This work confirms that R. mexicanus sensu lato is a cryptic species complex composed of at least four putative species: R. mexicanus clade I, R. mexicanus clade IIA (R. mexicanussensu stricto), R. mexicanus clade IIIA, and R. mexicanusclade IIIB. In addition, specimens from El Salvador (R. mexicanusclade IIB) should be reevaluated taxonomically including a better sampling of multiple lines of evidence. For R. mexicanus sensu stricto, additional analyses are necessary to estimate its phylogenetic relationship with respect to the subspecies R. mexicanus riparius , which was not included in our analyses but has evident geographic isolation from the other Mexican populations (Hooper 1955; Hall 1981). Finally, R. mexicanus clade I constitute a new species, pending formal description and assignment of a scientific name according to the International Code of Zoological Nomenclature rules.
AUTHOR CONTRIBUTIONS
Daily Martínez-Borrego: Conceptualization (equal), investigation (lead), data curation (lead), formal analysis (lead), methodology (lead), writing original draft (lead), review and editing (equal), visualization (lead). Elizabeth Arellano:Conceptualization (equal), methodology (supporting), writing – review and editing (supporting), resources (lead), supervision (lead).Francisco X. González-Cozátl: Conceptualization (equal), methodology (supporting), writing – review and editing (supporting), supervision (supporting). Sandra M. Ospina-Garcés:Conceptualization (equal), methodology (supporting), writing – review and editing (supporting). Duke S. Rogers: Conceptualization (equal), methodology (supporting), writing – review and editing (supporting), resources (supporting).
ACKNOWLEDGMENTS
We thank the following collections for providing samples (tissue or destructive sample or specimens loans): Department of Mammalogy, American Museum of Natural History (R. Voss); Colección Nacional de Mamíferos, UNAM (F. A. Cervantes); Colección de Mamíferos de El Colegio de la Frontera Sur, San Cristóbal (C. Lorenzo); Division of Mammals, National Museum of Natural History (D. Lunde). The Field Museum of Natural History (L. Heaney and A. W. Ferguson); Collection of Genetic Resources, Genetic Resources Collection, Museum of Texas Tech University (C. D. Phillips); Mammalogy, Royal Ontario Museum (M. D. Engstrom); Museum of Zoology, Louisiana State University (D. Dittmann); Museum of Zoology, University of Michigan (P. Tucker and C. Thompson); Museum of Southwestern Biology (J. Cook and M. Campbell); Museo de Zoología Alfonso L. Herrera, Facultad de Ciencias, UNAM (L. León-Paniagua); Colección Mastozoológica del Instituto de Investigaciones Biológicas, Universidad Veracruzana (A. González). Permits for fieldwork in Mexico were issued by the Secretaría de Medio Ambiente y Recursos Naturales. We thank the American Society of Mammologists, Consejo Nacional de Ciencia y Tecnología (CONACYT), and Universidad Autónoma del Estado de Morelos for the funding provided. We thank D. Cruz for his help with the map drawing and N. Lewis-Rogers for her support in the laboratory work.
FUNDING INFORMATION
DM-B was supported by a Ph.D. Scholarship Program 2018-000012 01NACF-11852LANC from Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico. Fieldwork season 2019-2020 was carried out thanks to the Latin American Field Research Award 2019 from the American Society of Mammologists.
CONFLICT OF INTEREST
The authors declare no competing interests.
DATA AVAILABILITY STATEMENT
REFERENCES
Adams D., M. Collyer, A. Kaliontzopoulou, and E. Baken. 2022. Geomorph: Software for geometric morphometric analyses. R package version 4.0.4. https://cran.rproject.org/package=geomorph
Aiello–Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B., and Anderson, R. P. 2015. spThin: An R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38:541–545. https://doi.org/10.1111/ecog.01132
Almendra, A. L., González–Cózatl, F. X., Engstrom, M. D., and Rogers, D. S. 2018. Evolutionary relationships and climatic niche evolution in the genus Handleyomys (Sigmodontinae: Oryzomyini). Molecular Phylogenetics and Evolution 128:12–25.
Amadon, D. 1966. The superspecies concept. Systematic Zoology 15(3):245–249.
Arellano, E. 2015. Genus Reithrodontomys Giglioli, 1874. Pp. 61–63 in Mammals of South America, vol. 2: Rodents (Patton, J. L., U. F. Pardiñas, and G. D’Elía, eds.). University of Chicago Press, Illinois, EE.UU.
Arellano, E., D. S. Rogers, and F. A. Cervantes. 2003. Genic differentiation and phylogenetic relationships among tropical harvest mice (Reithrodontomys : subgenus Aporodon ). Journal of Mammalogy 84:129–143.
Arellano, E., F. X. González–Cozátl, and D. S. Rogers. 2005. Molecular systematics of Middle American harvest mice Reithrodontomys(Muridae), estimated from mitochondrial cytochrome b gene sequences. Molecular Phylogenetics and Evolution 37:529–540.
Arellano, E., J. A. Guerrero, and D. S. Rogers. 2012. Variación morfométrica y alometría del crecimiento de Reithrodontomysmexicanus (Rodentia: Muridae) de Oaxaca, México. Pp. 35–45 in Estudio Sobre la Biología de Roedores Silvestres Mexicanos (Cervantes, F. A., and C. Ballesteros–Barrera, eds.). Creativa Impresores S.A., Mexico City, Mexico.
Baker, R. J., and R. D. Bradley. 2006. Speciation in mammals and the Genetic Species Concept. Journal of Mammalogy 87:643–662.
Barčiová, L. 2009. Advances in insectivore and rodent systematics due to geometric morphometrics. Mammal Review 39:80–91.
Bickford, D., Lohman, D. J., Sodhi, N. S., Ng, P. K. L., Meier, R., Winker, K., Ingram, K. K., and Das, I. 2007. Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution 22:148–155.
Bookstein, F. L. 1997. Landmark methods for forms without landmarks: Morphometrics of group differences in outline shape. Medical Image Analysis 1:225–43.
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.–H., Xie, D., Suchard, M. A., Rambaut, A., and Drummond, A. J. 2014. BEAST2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10:1–6.
Bradley, R. D. 2017. Genus Reithrodontomys . Pp. 367–383 in Handbook of the Mammals of the World: Rodents II (Wilson, D. E., T. E. Lacher, and R. A. Mittermeier, eds.). Lynx Edicions, Barcelona, Spain.
Bradley, R. D., and R. J. Baker. 2001. A test of the Genetic Species Concept: Cytochrome b sequences and mammals. Journal of Mammalogy 82:960–973.
Camul, R., and P. D. Polly. 2005. Phylogenetic and environmental components of morphological variation: skull, mandible, and molar shape in Marmots (Marmota, Rodentia). Evolution 59:2460–2472.
Carstens, B. C., T. A. Pelletier, N. M. Reid, and J. D. Satler. 2013. How to fail at species delimitation. Molecular Ecology 22:4369–4383.
Collyer, M. L., and D. C. Adams. 2018. RRPP: An r package for fitting linear models to high‐dimensional data using residual randomization. Methods in Ecology and Evolution 9:1772–1779.
Cracraft, J. 1989. Speciation and its ontology: the empirical consequences of alternative species concepts for understanding patterns and processes of differentiation. En: Speciation and its consequences (D. Otte y J.A. Endler, eds.). pp. 28–59. Sunderland, MA: Sinauer Associates.
Dayrat, B. 2005. Towards integrative taxonomy. Biological Journal of Linnean Society 85:407–415
D’Elía, G., Fabre, P. H., and Lessa, E. P. 2019. Rodent systematics in an age of discovery: recent advances and prospects. Journal of Mammalogy 100(3):852–871.
de Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of speciation: A conceptual unification and terminological recommendations. In D. J. Howard, and S. H. Berlocher (Eds.), Endless forms: Species and speciation (pp. 57–75). Oxford University Press.
de Queiroz, K. 2005. Ernst Mayr and the modern concept of species. Proceedings of the National Academy of Sciences of the United States of America 102:6600–6607.
de Queiroz, K. 2007. Species concepts and species delimitation. Systematic Biology 56:879–886.
ESRI. 2020. ArcGIS Desktop Release 10.8. Environmental System Research Institute, Inc. Redlands, California, EE.UU.
Fick, S. E., and R. J. Hijmans. 2017. WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37:4302–4315.
Firneno, T. J. Jr., O’Neill, J. R., Portik, D. M., Emery, A. H., Townsend, J. H., and Fujita, M. K. 2020. Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Molecular Ecology 29:3543–3559.
Firneno, T. J. Jr., O’Neill, J. R., Itgen, M. W., Kihneman, T. A., Townsend, J. H., and Fujita, M. K. 2021. Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance. Ecology and Evolution 00:1–15.
Foster, J.B. 1964. The evolution of mammals on islands. Nature 202:234–235.
Futuyma, D. J. 2013. Evolution. 3rd ed. Sinauer Associates Inc. Sunderland, Massachusetts.
Gardner A. L., and M. D. Carleton. 2009. A New Species ofReithrodontomys , Subgenus Aporodon (Cricetidae: Neotominae), from the Highlands of Costa Rica, with Comments on Costa Rican and Panamanian Reithrodontomys . Bulletin of the American Museum of Natural History 15:157–82.
González–Cozátl, F. X., and E. Arellano. 2015. Notes on the ecology ofReithrodontomys microdon based on new records in the Eje Neovolcánico, México. Western North Naturalist 75:377–379.
Gual–Díaz, M., and A. Rendón–Correa (Eds.). 2014. Bosques mesófilos de montaña de México: diversidad, ecología y manejo. Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Mexico City, Mexico 352 pp.
Guevara, L., B. E. Gerstner, J. M. Kass, and R. P. Anderson. 2018. Toward ecologically realistic predictions of species distributions: A cross‐time example from tropical montane cloud forests. Global Change Biology 24:1511–1522.
Hall, E. R. 1981. The Mammals of North America 2nd ed. John Wiley and Sons, Inc., New York, EE.UU.
Hansen, M. C., DeFries, J. R. S., Townshend, R. R., Sohlberg, G., Dimiceli C. and Carroll, M. 2002. Towards an operational MODIS continuous field of percent tree cover algorithm: examples using AVHRR and MODIS data. Remote Sensing of Environment 83:303–319.
Hooper, E. T. 1952. A systematic review of harvest mice (GenusReithrodontomys ) of Latin America. Miscellaneous Publications of the Museum of Zoology, University of Michigan 77:1–255.
Hooper, E. T. 1955. Notes of Mammals of Western Mexico. Occasional Papers of the Museum of Zoology, University of Michigan 565: 1–26.
Irwin, D. M., T. D. Kocher, and A. C. Wilson. 1991. Evolution of the cytochrome b gene of mammals. Journal Molecular and Evolution 32:128–144.
Jones, G. 2017. Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology 74:447–467.
Jones, J. K., Jr., and T. E. Lawlor. 1965. Mammals from Isla Cozumel, Mexico, with description of a new species of harvest mouse. University of Kansas publications, Museum of Natural History. 16:409–419.
Jörger, K. M., and M. Schrödl. 2013. How to describe a cryptic species? Practical challenges of molecular taxonomy. Frontiers in Zoology 10:59.
Kalyaanamoorthy S., B. Q. Minh, T. K. Wong, A. Von Haeseler, and L. S. Jermiin. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14:587–589.
Kapli T., S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis, and T. Flouri. 2017. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11):1630–1638.
Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Pääbo, F. X. Villablanca, and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences 86(16): 6196–6200.
Kovarovic, K., Aiello, L. C., Cardini, A., and Lockwood, C. A. 2011. Discriminant function analyses in archaeology: are classification rates too good to be true? Journal of Archaeological Science 38(11):3006–3018.
Kumar, S., G. Stecher, M. Li, C. Knyaz, and K. Tamura. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35:1547–1549.
Lockwood, C.A., W.H. Kimbel, and J.M. Lynch. 2004. Morphometrics and hominoid phylogeny: support for a chimpanzee–human clade and differentiation among great ape subspecies. Proceedings of the National Academy of Sciences of the United State of America 101:4356–4360.
Lomolino, M. V. 1985. Body size of mammals on islands: the island rule reexamined. The American Naturalist 125(2):310–316.
Lomolino, M. V. 2005. Body size evolution in insular vertebrates: generality of the island rule. Journal of Biogeography 32(10):1683–1699.
Luo, A., C. Ling, S. Y. Ho, and C. D Zhu. 2018. Comparison of methods for molecular species delimitation across a range of speciation scenarios. Systematic Biology 67:830–846.
Macholán, M. 2008. The mouse skull as a source of morphometric data for phylogeny inference. Zoologischer Anzeiger 247:315–327.
Martínez-Gordillo, D., O. Rojas-Soto, and A. Espinosa-De Los Monteros. 2010. Ecological niche modelling as an exploratory tool for identifying species limits: an example based on Mexican muroid rodents. Journal of Evolutionary Biology 23:259–270.
Martínez-Borrego, D., E. Arellano, F. X. González-Cozátl, and D. S. Rogers. 2020. Reithrodontomys mexicanus (Rodentia: Cricetidae). Mammalian Species 52:114–124.
Martínez-Borrego, D., E. Arellano, F. X. González-Cózatl, I. Castro-Arellano, L. León-Paniagua, and D. S. Rogers. 2022a. Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomysmicrodon species complex. Journal of Mammalogy 103(1):29–44.
Martínez-Borrego, D., E. Arellano, D. D. Cruz, F. X. González-Cózatl, E. Nava-García, and D. S Rogers. 2022b. Morphological and ecological data confirm Reithrodontomys cherrii as a distinct species fromReithrodontomys mexicanus . THERYA 13(1):115.
Mayden, R. L. 1997. A hierarchy of species concepts: the denouement in the saga of the species problem. Pp 381–423 in Species: The Units of Biodiversity (Claridge, M. F. H. A. Dawah, and M. R. Wilson, eds.). Chapman and Hall CRC Press, London, United Kingdom.
Mayr, E. 1942. Systematics and the Origin of Species. Columbia Univ. Press, New York.
Miller, J. R., and M. D. Engstrom. 2008. The relationships of major lineages within peromyscine rodents: a molecular phylogenetic hypothesis and systematic reappraisal. Journal of Mammalogy 89:1279–1295.
Miller, M. A., W. Pfeiffer, and T. Schwartz. 2012. The CIPRES science gateway: enabling high–impact science for phylogenetics researchers with limited resources. Pp. 1–8 in Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the extreme to the campus and beyond (C. Stewart, General Chair). Association for Computing Machinery. New York, New York.
Minh, B. Q., M. A. T. Nguyen, and A. Von Haeseler. 2013. Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30:1188–1195.
Muscarella, R., P. J. Galante, M. Soley‐Guardia, R. A. Boria, J. M. Kass, M. Uriarte, and R. P. Anderson. 2014. ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution 5: 1198–1205.
Nguyen, L. T., H. A Schmidt, A. Von Haeseler, and B. Q. Minh. 2015. IQ–TREE: a fast and effective stochastic algorithm for estimating maximum–likelihood phylogenies. Molecular Biology and Evolution 32:268–274.
Okonechnikov K., O. Golosova, M. Fursov, The Ugene Team. 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167.
Onditi, K. O., Demos, T. C., Peterhans, J. K., Chen, Z. Z., Bryja, J., Lavrenchenko, L. A., Musila, S., Verheyen E., Van de Perre, F., Akaibe, B. D.,de la Sancha, N. U., and Jiang, X. L. 2021. Historical biogeography, systematics, and integrative taxonomy of the non–Ethiopian speckled pelage brush–furred rats (Lophuromysflavopunctatus group). BMC ecology and evolution 21(1):1–27.
Padial, J., A. Miralles, I. De La Riva, and M. Vences. 2010. The integrative future of taxonomy. Frontiers in Zoology 7:16.
Patton, J. L., and Smith, M. F. 1992. MtDNA phylogeny of Andean mice: a test of diversification across ecological gradients. Evolution 46(1):174–183.
Pavan, A. C, and G. Marroig. 2016. Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus). Molecular Phylogenetics and Evolution 103:184–198.
Phillips, S. J., R. P. Anderson, and R. E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modeling 190: 231–259.
R Development Core Team. 2018. R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. www.R–project.org/
Rambaut, A., A. J. Drummond, D. Xie, G. Baele, and M. A. Suchard. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67:901–904.
Reid, N. M., and B. C. Carstens. 2012. Phylogenetic estimation error can decrease the accuracy species delimitation: a Bayesian implementation of the General Mixed Yule Coalescent model. BMC Evolutionary Biology 12:196.
Ripley, B., B. Venables, D.M. Bates, K. Hornik, A. Gebhardt, D. Firth, y M.B. Ripley. 2013. Package ‘mass’. Cran R. 538.
Rivera, P. C., R. E. González-Ittig, A. R. Barcia, L. I. Trimarchi, S. Levis, G. E. Calderón, and C. N. Gardenal. 2018. Molecular phylogenetics and environmental niche modeling reveal a cryptic species in theOligoryzomys flavescens complex (Rodentia, Cricetidae). Journal of Mammalogy 99:363–376.
Rogers, D. S., R. N. Leite, and R. J. Reed. 2011. Molecular phylogenetics of an endangered species: the Tamaulipan woodrat (Neotoma angustapalata ). Conservation Genetics 12(4):1035–1048.
Rohlf, F. J. 2015. The tps series of software. Hystrix – Italian Journal of Mammalogy 26:9–12.
Rohlf, F. J., and D. Slice. 1990. Extensions of the Procrustes method for the optimal superimposition of landmarks. Systematic Zoology 39:40–21.
Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics Applications Note 19:1572–1574.
Sangster, G. 2018. Integrative taxonomy of birds: the nature and delimitation of species. Pp. 9–37 in Bird species. Fascinating Life Sciences (Tietze, D.T., ed.). Springer, Cham, New York, EE.UU.
Santos, M. J., A. B. Smith, J. H. Thorne, and C. Moritz. 2017. The relative influence of change in habitat and climate on elevation range limits in small mammals in Yosemite National Park, California, USA. Climate Change Responses 4:1–12.
Saussure De, H. 1860. Note sur quelques mammifères du Mexique. Revue et Magasin de Zoologie Serie 2 12:97–110.
Schlager, S. 2016. Morpho: calculations and visualisations related to geometric morphometrics. R package version 2.3.1.1. Freiburg, Germany, Stefan Schlager, https://CRAN.R–project.org/package=Morpho.
Sikes, R. S., and The Animal Care And Use Committee Of The American Society Of Mammalogists. 2016. 2016 Guidelines of the American Society of Mammalogists for the use of wild animals in research and education. Journal of Mammalogy 97:663–688.
Stanchak, K. E., and S. E. Santana. 2018. Do ecogeographical rules explain morphological variation in a diverse, Holarctic genus of small mammals? Journal of Biogeography 46:110–122.
Stanhope, M. J., Czelusniak, J., Si, J. S., Nickerson, J., and Goodman, M. 1992. A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly. Molecular Phylogenetics and Evolution 1(2):148–160.
Toews, D. P., and Brelsford, A. 2012. The biogeography of mitochondrial and nuclear discordance in animals. Molecular ecology 21(16):3907–3930.
Urbina, S. I., M. A. Aguilar, E. Arellano, F. X. González–Cózatl, and D. S. Rogers. 2006. Karyotypes of three species of harvest mice (genusReithrodontomys ). The Southwestern Naturalist 51(4):564–568.
Van Valen, L. 1976. Ecological species, multispecies, and oaks. Taxon, pp.233–239.
Vázquez, E., de Grammont, P.C. and Cuarón, A.D. 2018.Reithrodontomys spectabilis . The IUCN Red List of Threatened Species 2018: e.T19416A22386261. Accessed Feb 25 2022.
Walker, J.D., Geissman, J.W., Bowring, S.A., and Babcock, L.E., compilers. 2018. Geologic Time Scale v. 5.0: Geological Society of America https://doi.org/10.1130/2018.CTS005R3C.
Warren, D. L., and Seifert, S. N. 2011. Ecological niche modeling in Maxent: The importance of model complexity and the performance of model selection criteria. Ecological Applications 21:335–342. https://doi.org/10.1890/10–1171.1
Wickliffe, J. K., F. G. Hoffmann, D. S. Carroll, Y. V. Dunina–Barkovskaya, R. D. Bradley, And R. J. Baker. 2003. PCR and sequencing primers for intron 7 (Fgb–I7) of the fibrinogen, B beta polypeptide (Fgb) in mammals: a novel nuclear DNA marker. Occasional Papers of the Museum at Texas Tech University 219:1–8.
Will, K. W., Mishler, B. D., and Wheeler, Q. D. 2005. The perils of DNA barcoding and the need for integrative taxonomy. Systematic biology 54(5):844–851.
Zelditch, M. L., D. L. Swiderski, H. D. Sheets, And W. L. Fink. 2004. Geometric morphometrics for biologists: A primer. Elsevier Academic Press, New York, EE.UU.
Table 1. Partition schemes and evolutionary models used in the phylogenetic analyses of the Reithrodontomys mexicanus species complex.