Our account of the mammals of Honduras presents distribution based on verifiable data, with notes on natural history, ecology, and conservation. Notable additions include information from a recent checklist of bat ectoparasites for Honduras and basic acoustic descriptions of vocal signatures for some bat species. A total of 227 extant native mammalian species within 146 genera and 42 families, including three introduced rodent species, are verified to occur in Honduras. We anticipate that an additional 28 species could eventually be verified in Honduras, bringing the total to 255. A discussion of the importance of additional studies and the conservation of Honduran mammals is included. In closing, we discuss why some questionable records have persisted over time, with local and regional extinctions, and new threats. We hope this review will serve as a new baseline for the next generation to continue to study mammals systematically in the country.

The taxonomic status of Dasyprocta ruatanica Thomas, 1901, described as an endemic species from Roatán Island, Honduras, has remained controversial. Its diagnosis relied primarily on smaller body size and darker pelage compared to D. punctata Gray, 1842; traits later accepted by several authors. However, these characters are known to vary in insular mammals, where dwarfism and darker colorations are common ecological responses. Our morphometric analyses, based on multivariate approaches, demonstrate extensive overlap between D. ruatanica and D. punctata, with no statistically significant divergence in overall cranial and mandibular shape. Nonetheless, Roatán individuals show consistent reduction in size relative to both continental and other insular populations, confirming a strong pattern of island dwarfism. These results indicate that D. ruatanica does not warrant species-level recognition but rather represents a morphologically distinct insular lineage. Based on our findings, we propose treating D. ruatanica under the trinomial name of Dasyprocta punctata ruatanica. This reclassification maintains taxonomic stability while acknowledging its unique evolutionary trajectory. From a conservation perspective, the Roatán population remains highly vulnerable due to its restricted range, habitat loss, hunting, and possible introgression from introduced D. punctata. Effective management should prioritize habitat preservation, and invasive species control underscoring the need for tailored management to protect this insular lineage.

Myotis armiensis was recently described from specimens collected in the mountain ranges of Costa Rica, Panama, and Ecuador. During a systematic revision of Neotropical Myotis, we identified additional specimens from Venezuela and Colombia. Using an integrative approach that combined morphological traits, cytochrome b sequences, and ecological niche modeling, we assessed the geographic variation of M. armiensis. Our findings indicate that this species can be structured into two allopatric populations: one in the Talamanca Cordillera of Central America, and another restricted to the South American Andes and Cordillera de La Costa in Venezuela. These populations are reciprocally monophyletic, exhibiting genetic distances greater than 3

A range-wide morphological analysis of the Mexican cottontail (Sylvilagus cunicularius) has never been conducted using modern-day multivariate analyses. We took 26 craniodental measurements from the skulls of 155 adults. A discriminant function analysis identified four distinct morphological types. The four morphological types consist of two primary groups. The reddish-colored group occurs on the Pacific coastal plain from Sinaloa to Colima. The individuals from Sinaloa to northwestern Jalisco share various skull features, and those from southwestern Jalisco and Colima have other skull features in common. The constricted coastal plain in northwestern Jalisco appears to separate these two morphological types. The other primary group has a grayish dorsal pelage and occurs in the highlands (the Transvolcanic Belt and Sierra Madre del Sur) and Pacific coastal lowlands of Guerrero and Oaxaca. Within this group, the individuals from the highlands differ from those on the Pacific coastal plain of Guerrero and Oaxaca. Both morphological types have been collected along the western slopes of the Sierra Madre del Sur, one from sea level to 305 m and the other from 822 to 2,225 m. The red and gray cottontails might be distinct species, but we take a conservative approach, awaiting additional lines of evidence. Four distinct subspecies are recognized: Sylvilagus cunicularius cunicularius, Sylvilagus cunicularius insolitus, Sylvilagus cunicularius pacificus (here recognized), and Sylvilagus cunicularius new subspecies.

Myotis attenboroughi was recently described based on specimens from Tobago Island and considered an endemic species until now. Based on morphological and molecular data, we extended its occurrence to Grenada and Suriname. The presence of M. attenboroughi in Grenada, Tobago and mainland South America can be explained by the intermittent connections between these islands and the continent during the Plio-Pleistocene glaciations. However, our analyses recovered an Myotis individual from Grenada phylogenetically related to Myotis nyctor from Barbados, although it is morphologically like the other specimens of M. attenboroughi, revealing a surprising incongruence between genotype and phenotype. Barbados is a geologically recent island and historically unconnected with other Caribbean islands or with South America. We hypothesized that the invasion of the M. nyctor lineage from Barbados to Grenada was the result of an extreme overwater dispersal, perhaps driven by wind streams during tropical storms. Subsequently, introgression of lineages may have occurred through hybridization, which can explain the discordance between the phenotype (like M. attenboroughi) and the genotype (like M. nyctor) of this specimen. Additional comments on the formation of the Caribbean Myotis assemblage are presented from the perspective of new evolutionary discoveries for this genus.

Myotis is a diverse genus of vesper bats with a global distribution. Currently, over 35 Neotropical species are recognized, but molecular studies suggest the existence of a large number of distinct evolutionary lineages, revealing cryptic diversity. Thus, this genus poses a challenge for systematists since its high species diversity is not reflected in phenotypic differences. Using an integrative approach, we identified and described here a new species of Myotis. Ecological niche modeling indicates a strong association with the South American Chaco, Pantanal, and Cerrado ecoregions—spanning Argentina, Bolivia, Paraguay, and Brazil. Phylogenetic inference, genetic divergence, and morphological analyses support the recognition of the new species. Additionally, we present a set of external and skull diagnostic characters by comparing them with other Neotropical Myotis species. Specimens of this new species have been deposited in biological collections for more than 120 years. This discovery underscores the importance of systematic studies based on multiple lines of evidence and highlights the crucial role of natural history museums as biological repositories.

Accurate estimates of species diversity are essential for all biodiversity research. Delimiting species and understanding the underlying processes of speciation are also central components of systematic biology that frame our comprehension of the evolutionary mechanisms generating biodiversity. The South American tree squirrels (genus Guerlinguetus) are keystone mammals, widely distributed, that are critical in tree-seed predation and dispersal in one of the most fragile and threated ecosystems of the world, the tropical rainforests of South America. We obtained genomic data (ultraconserved elements and single nucleotide polymorphisms) to explore alternative hypotheses on species limits of this genus and to clarify recent and rapid speciation on continental-scale and dynamically evolving landscapes. Using a multilayered genomic approach that integrates fine-scale population genetic analyses with quantitative molecular species delimitation methods, we observed that (i) the most likely number of species within Guerlinguetus is six, contrasting with both classic morphological revision and mitochondrial species delimitation; (ii) incongruencies in species relationships still persist, which might be a response to population migration and gene flow taking place in the lowlands of eastern Amazonia and/or to the extremely rapid successive speciation events; and (iii) effective migration surfaces detected important geographic barriers associated with the major Amazonian riverine systems and the mountain ranges of the Guiana Shield. In conclusion, we uncovered unexpected and higher species diversity on Guerlinguetus and corroborate recent findings suggesting that much of the extant species-level diversity in Amazonia is young, dating back to the Quaternary. We also reinforce long-established hypotheses on the role of rivers and climate-driven forest dynamics in triggering Amazonian speciation.

Myotis riparius is an insectivorous bat species widely distributed in the Neotropics with evident geographical variation in morphological traits. We conducted an integrative study using mitochondrial DNA, qualitative and quantitative morphology, and current and past species distribution models to investigate the variation, population structure, and distributional limits within M. riparius populations. Phylogenetic inferences indicated that M. riparius is monophyletic, and populations are divided into geographically structured clades that split during the middle Pleistocene. There is no shared haplotype between geographical populations and strong evidence of partial restriction in gene flow. Morphological and morphometric variations revealed subtle distinctions among different populations, but little correspondence with molecular analysis. The distribution models indicated that M. riparius is associated with forest environments, with discontinuity between populations from South American ecoregions. Past distribution modelling, however, indicated that M. riparius had a larger distribution range in the Last Glacial Maximum than currently. Results of modelling and genetic analyses indicated that M. riparius consisted of a large, widespread, and panmictic (meta)population until the middle Pleistocene, when environmental changes driven by climatic dynamics fragmented and isolated the populations. Myotis riparius is here considered a complex of at least four allopatric and parapatric cryptic evolutionary units.

Accurate estimates of species diversity are essential for all biodiversity research. Delimiting species and understanding the underlaying processes of speciation are also central components of systematic biology that outline our comprehension of the evolutionary mechanisms generating biodiversity. We obtained genomic data (Ultraconserved Elements and single nucleotide polymorphisms) for a widespread genus of South American tree squirrels (genus Guerlinguetus ) to explore alternative hypotheses on species limits and to clarify recent and rapid speciation on continental-scale and dynamically evolving landscapes. Using a multilayered genomic approach that integrates fine-scale population genetic analyses with quantitative molecular species delimitation methods, we observed that (i) the most likely number of species within Guerlinguetus is six, contrasting with both classic morphological revision and mitochondrial species delimitation; (ii) incongruencies in species relationships still persist, which might be a response to population migration and gene flow taking place in lowlands of eastern Amazonia; and (iii) effective migration surfaces detected important geographic barriers associated with the major Amazonian riverine systems and the mountain ranges of the Guiana shield. In conclusion, we uncovered unexpected species diversity of keystone mammals that are critical in tree-seed predation and dispersal in one of the most fragile and threated ecosystems of the world, the tropical rainforests of South America. Our results corroborate recent findings suggesting that much of the extant species-level diversity in Amazonia is young, dating back to the Quaternary, while also reinforcing long-established hypotheses on the role of rivers and climate-driven forest dynamics triggering Amazonian speciation.### Competing Interest StatementThe authors have declared no competing interest.

Myotis nigricans was previously considered the most widely distributed Neotropical Myotis species, occurring from Mexico to northern Argentina, and several allopatric subspecies have been recognized, including M. n. extremus, from Mexico and Guatemala. However, recent studies have shown that M. nigricans is a species complex—many cryptic. Using molecular and morphological data, we assessed the taxonomic status of M. nigricans populations from Mexico, Guatemala, Paraguayan Chaco, and Brazilian Atlantic Forest. Our phylogenetic analysis indicated that M. nigricans is polyphyletic, and the populations classified as M. n. extremus were recovered in a clade composed of species from the ruber group. Populations from Paraguay and Brazil were recovered in distinct clades within the albescens group. Our morphological and morphometric analyzes corroborate the molecular findings, supporting the recognition of M. extremus as a full species. Furthermore, we propose that M. nigricans is a monotypic species occurring exclusively in the South American Atlantic Forest. Populations from other ecoregions should have their taxonomic status redefined in future studies.

AbstractInformation about opossums in Honduras has been scarce. Although there have been sporadic records of species, it was not clear which and how many species were occurring in the country because of taxonomic discussions and the group being understudied. Over the years, different authors studying mammals in Honduras have accepted or rejected the occurrence of some didelphid species. Herein we discuss the species of opossums occurring for Honduras based on taxonomic and distribution changes according to Voss, R.S. and Jansa, S.A. Opossums: an adaptive radiation of new world marsupials. Baltimore: Johns Hopkins University Press (2021) latest reviews for opossum species.

Eptesicus Rafinesque, 1820 is widely distributed in the Old and New World (26 species), and Histiotus Gervais, 1856 is a South American endemic (11 species). Molecular phylogenies have recovered Eptesicus (sensu lato) as polyphyletic, with New World Eptesicus and the sister genus Histiotus in a paraphyletic American clade sister to Old World Eptesicus. Based on these phylogenetic reconstructions, authors have treated Histiotus as either a subgenus of Eptesicus or restricted Eptesicus to the New World species, treating Histiotus as a full genus, and using the name Cnephaeus Kaup, 1829 at the generic rank to comprise Old World Eptesicus. Based on recently published molecular studies, and on novel qualitative and quantitative morphological comparisons of representatives of Histiotus and New and Old World Eptesicus, we provide evidence for restricting the name Eptesicus to the species E. fuscus (Palisot de Beauvois, 1796) and E. guadeloupensis Genoways & Baker, 1975, allocating the remaining New World species under a new genus, keeping Histiotus as a full genus, and raising Cnephaeus to generic rank to comprise all Old World taxa currently under Eptesicus. This arrangement resolves the paraphyly of New World Eptesicus, and promotes taxonomic stability for Histiotus, which is a well-established genus of easily recognizable Neotropical bats and treated separate from Eptesicus by most authorities.

Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences-performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria-resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.

Myotis is the most diverse genus of bats in the world, with more than 30 species recognized in the Neotropics. However, many of these species represent cryptic complexes and are evidence of the existence of hidden diversity in several regions. Using an integrative approach based on molecular, morphological, and bioacoustic data, we performed a systematic review of Myotis species from Chile. Phylogenetic inference using cytochrome-b indicated the existence of three monophyletic lineages, and qualitative and quantitative morphological analyses supported these lineages as distinct and morphologically diagnosable taxa. Analysis of discriminant functions using parameters of echolocation calls also indicates the existence of three distinct bioacoustic clusters. Thus, all lines of evidence congruently indicate the existence of three distinct taxa. As a result, we recognize Myotis arescens as a valid and distinct species and define its taxonomic limits from the other species from Chile, Myotis atacamensis and Myotis chiloensis.

Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Neotropical Myotis have an accentuated phenotypic conservatism, which makes species delimitation and identification difficult, hindering our understanding of the diversity, distribution, and phylogenetic relationships of taxa. To encourage new systematic reviews of the genus, a catalogue of the primary types and names is presented, current and in synonymy, for Neotropical Myotis. Currently 33 valid species (and three subspecies) are recognized, and their primary types are deposited in 12 scientific collections in the USA (30 types), Brazil (two types), England (two types), and France (one type). The names of 29 Neotropical Myotis species currently in synonymy were found. However, it is possible that some synonyms represent independent evolutionary lineages, considering recent results provided by taxonomic revisions.

Myotis is the most speciose genus of mammals in the world and recent taxonomic revisions have revealed an impressive diversity of species in South America. Even so, the phenotypic conservatism of some taxa makes taxonomic delimitation difficult. We perform a taxonomic review of Myotis from Argentina based on qualitative and quantitative morphological characters. Our results confirm the occurrence of 12 species (M. albescens, M. chiloensis, M. dinellii, M. izecksohni, M. keaysi, M. lavali, M. levis, M. nigricans, M. oxyotus, M. riparius, M. ruber, and M. cf. simus) and revealed an additional new species for the Yungas Forest. The new species is small to medium (forearm length ~ 35 mm) and can be distinguished from its congeners by a set of characters that includes forearm length, cranial measurements, discrete craniodental characters, and fur color. This review does not exhaust the need for new systematic studies with Argentinean Myotis, considering the possibility of occurrence of new species and the great morphological variation found for some complex taxa.

The genus Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Twenty-eight Neotropical species are currently recognized. In this study, we evaluate molecular and morphological variation in the M. keaysi complex, a high elevation clade of Neotropical myotine bats characterized by complex taxonomy and high morphological variation. A phylogeny inferred with cytochrome-b sequences recovered two clades composed of samples traditionally assigned to M. keaysi, with 9% of genetic divergence between them. These clades were also suggested as putative distinct species by molecular species delimitation methods. Qualitative and quantitative morphological analyses indicated a phenotypic discontinuity between specimens from central Andes (including the holotype of M. keaysi) and western lowlands of Ecuador, showing strong congruence between molecular and morphological approaches. We therefore describe a new species for the Tumbes-Choco-Magdalena region, documenting their external and cranial diagnostic characters by comparing them with other Neotropical species. In addition, we provide an emended diagnosis for our new concept of M. keaysi.

Aim:Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). Location:Global. Taxon:All extant mammal species. Methods:Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). Results:Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. Main conclusion:Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.