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We report a chromosomal-level genome assembly of a male North American wolverine (Gulo gulo luscus) from the Kugluktuk region of Nunavut, Canada. The genome was assembled directly from long-reads, comprising: 758 contigs with a contig N50 of 36.6 Mb; contig L50 of 20; base count of 2.39 Gb; and a near complete representation (99.98%) of the BUSCO 5.2.2 set of 9,226 genes. A presumptive chromosomal-level assembly was generated by scaffolding against two chromosomal-level Mustelidae reference genomes, the ermine and the Eurasian river otter, to derive a final scaffold N50 of 144.0 Mb and a scaffold L50 of 7. We annotated a comprehensive set of genes that have been associated with models of aggressive behavior, a trait which the wolverine is purported to have in the popular literature. To support an integrated, genomics-based wildlife management strategy at a time of environmental disruption from climate change, we annotated the principal genes of the innate immune system to provide a resource to study the wolverine’s susceptibility to new infectious and parasitic diseases. As a resource, we annotated genes involved in the modality of infection by the coronaviruses, an important class of viral pathogens of growing concern as shown by the recent spillover infections by severe acute respiratory syndrome coronavirus-2 to naïve wildlife. Tabulation of heterozygous single nucleotide variants in our specimen revealed a heterozygosity level of 0.065%, indicating a relatively diverse genetic pool that would serve as a baseline for the genomics-based conservation of the wolverine, a rare cold-adapted carnivore now under threat.

We describe a new species of mastiff bat in the genus Molossus (Molossidae), which was previously confused with the common and widely distributed M. molossus, from Guyana and Ecuador based on morphological and molecular differences. It is diagnosed by the following set of morphological characteristics: bicolored dorsal pelage, rounded anterior arch of the atlas, triangular occipital bone, and smaller body and skull size. In a molecular phylogenetic analysis of mitochondrial and nuclear DNA, maximum likelihood and parsimony trees recovered eight clades in the genus and a polyphyletic relationship for the M. molossus species complex. The new species was recovered in a well-supported clade that can be genetically distinguished from other species in the genus by its high level of sequence divergence based on the mitochondrial CO1 gene (8.0–10.1%) and on the nuclear gene beta fibrinogen (1.0–3.1%). It is broadly sympatric with M. molossus sensu stricto in northern South America, but morphologically distinct and genetically divergent.

Molossus is one of the most diverse genera of free-tailed bats in the pantropical family Molossidae and occurs though all the Neotropics. Nevertheless, the taxonomy and phylogeny of this group is poorly understood. Here, we present the data on evolutionary relationships of Molossus based on DNA barcodes of COI gene from 346 specimens of Molossus and its sister genus Promops and another New World molossid Eumops. Of these specimens, 50 are new sequences and 296 were obtained from GenBank. In addition, the nuclear gene beta fibrinogen was sequenced from a subset of 35 specimens. These data provide the basis for further exploration and understanding of the phylogenetic relationships of the genus Molossus (Loureiro et al., 2018) [1]. Keywords: Molossidae, Phylogenetics, Neotropics, Evolution

The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 ×) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon–gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology.

Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype‐by‐sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes., In this manuscript, we use the genotype‐by‐sequencing approach on three species of Mastiff bats with different ecological histories and geographical distributions to explore population genetics parameters and better understand the role of geographic barriers in the dispersal and gene flow in bats. Our analyses show that the population structure of each species varies according to environmental factors, levels of population isolation, and demographic histories. We show that oceanic straights seem to pose a partial barrier for some species and that more isolated lineages on islands tend to undergo genetic bottlenecks more than connected lineages closer to the mainland.

Mammals are one of the better known groups of animals, and in the Neotropics bats typically comprise about half of the mammalian species diversity. But, well resolved species-level phylogenies are still lacking for most taxa of bats. One broadly distributed genus is the mastiff bats, Molossus. Species within this genus are morphologically very similar, which results in a confusing and unstable taxonomy. In addition, low levels of genetic divergence among some clades make resolution of phylogenetic relationships difficult. Most authors recognize Molossus as being monophyletic, however, phylogenetic relationships within the genus remain poorly understood based on traditional Sanger sequencing of individual genes. We propose a more comprehensive framework based on large-scale genomic data derived from Next Generation Sequencing techniques to better understand evolutionary relationships within a group of closely related species with a rich taxonomic history. In this study, we utilized the NGS method of Genotype by Sequencing (GBS) to test the monophyly of the genus, understand evolutionary relationships within Molossus and investigate the genetic integrity of currently recognized species. Given that both de novo and reference genome pipelines are often used in the assembly of Single Nucleotide Polymorphism data from GBS, and that several tree inference methodologies have been proposed for SNP data, we test whether different alignments and phylogenetic approaches produce similar results. We also examined how the process of SNP identification and mapping can affect the consistency of the analyses. Our data provide the first high resolution phylogeny for the genus Molossus, bringing new insights into recognition of species boundaries and relationships among taxa. This study clarifies the taxonomy of Molossus and elevates the number of species in the genus from 11 to 14. We suggest the revalidation of the names M. nigricans, and M. fluminensis, which were synonymized under the name M. rufus; and M. bondae, previously synonymized under the name M. currentium. Different alignments and phylogenetic inferences produce consistent results, supporting use of SNP approach in addressing evolutionary questions on a macroevolutionary scale where the genetic distance among clades is low.

• Herein we propose a framework for assembling and analyzing Genotype by Sequencing (GBS) data to better understand evolutionary relationships within a group of closely related species using the mastiff bats (Molossus) as our model system. Many species within this genus have low-levels of genetic variation within and between morphologically distinct species, and the relationships among them remain unresolved using traditional Sanger sequencing methods. Given that both de novo and reference genome pipelines can be used to assemble next generation sequences, and that several tree inference methodologies have been proposed for single nucleotide polymorphism (SNP) data, we test whether different alignments and phylogenetic approaches produce similar results. We also examined how the process of SNP identification and mapping can affect the consistency of the analyses. Different alignments and phylogenetic inferences produced consistent results, supporting the GBS approach for answering evolutionary questions on a macroevolutionary scale when the genetic distance among phenotypically identifiable clades is low. We highlight the importance of exploring the relationships among groups using different assembly assumptions and also distinct phylogenetic inference methods, particularly when addressing phylogenetic questions in genetic and morphologically conservative taxa. • The method uses the comparison of several filter settings, alignments, and tree inference approaches on Genotype by Sequencing data. • Consistent results were found among several approaches. • The methodology successfully recovered well supported species boundaries and phylogenetic relationships among species of mastiff bats not hypothesized by previous methods., Graphical abstract Image, graphical abstract

Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. Unfortunately, the region continues to experience some of the highest deforestation rates in the world. For mammals, the evolutionary relationships of many endemic taxa are controversial, as it is the case for members of the genus Handleyomys. Estimation of a time-calibrated hypothesis for the evolution of these six genera (Euryoryzomys, Handleyomys, Hylaeamys, Nephelomys, Oecomys and Transandinomys) supported a monophyletic Handleyomys sensu lato. Based on their distinctive morphology and the amount of inter-generic genetic divergence, Handleyomys sensu stricto, H. alfaroi, the H. chapmani, and the H. melanotis species groups warrant recognition as separate genera. In addition, species delimitation documents the existence of cryptic species-level lineages within H. alfaroi and H. rostratus. Cryptic lineages within H. rostratus exhibited significant niche differentiation, but this was not the pattern among species-level clades within H. alfaroi. Similarly, age–range correlations revealed that niche evolution within Handleyomys is not correlated with evolutionary time, instead, ancestral climate tolerance reconstructions show niche disparities at specific diversification events within the chapmani and melanotis species groups, while the climatic niche of the rest of species of Handleyomys tended to be conservative.

The genus Molossus of the free-tailed bat family Molossidae is morphologically conservative and the level of genetic divergence is also low among many species, which has masked the actual species diversity in the genus. We analyzed the evolutionary relationships among species within Molossus using three mitochondrial (COI, Cytb, and 16S RNA), and two nuclear genes (RAG2 and β-fib) from more than 400 specimens across the Neotropics. We also investigated the genetic integrity of currently recognized species, especially those with broad geographic distributions and controversial taxonomic arrangements. Maximum likelihood and Bayesian phylogenetic reconstructions show that some recognized species are not monophyletic. The use of combined mitochondrial and nuclear genes as well as the use of only mitochondrial markers revealed more robust phylogenies than those for individual data sets and those restricted to the two nuclear genes. We recovered the recently described M. fentoni and M. alvarezi, validated M. milleri and M. verrilli as distinct species relative to M. molossus, and confirmed that the name M. barnesi should be considered as a junior synonym of M. coibensis. Additionally, M. rufus appears to be a complex of cryptic species, showing that the broadly distributed genus Molossus is more diverse than previously reported.

Stereotypic behaviour, such as territorial calls and songs, is thought to be evolutionarily conserved, and therefore useful in discerning systematic relationships. We examined vocalizations of several species of Peromyscus and Onychomys, a monophyletic group of rodents (Peromyscini). We report stereotypic vocal signals occurring in both sexes of the deer mice Peromyscus californicus, P. eremicus, P. leucopus, P. melanophrys, P. polionotus, and the grasshopper mice Onychomys arenicola and O. leucogaster. The stereotypic vocalizations of P. eremicus, P. leucopus, and P. polionotus are confined to frequencies greater than 20 kHz, unlike those of Onychomys, which are clearly audible, or P. californicus and P. melanophrys, which generate lower frequency vocalizations than the other Peromyscus. We did not observe stereotypic vocalizations in P. aztecus. Intensity, context and consistency suggest that these vocalizations serve an announcement function. Distribution of spectral energy distinguishes genera and mos...

The mitochondrial cytochrome c oxidase subunit I gene is the standard DNA barcoding region used for species identification and discovery. We examined the variation of COI (454 bp) to discriminate 20 species of bats in the family Phyllostomidae that are found in the Yucatan Peninsula of southeastern Mexico and northern Guatemala and compared them genetically to other samples from Central America. The majority of these species had low intraspecific variation (mean = 0.75%), but some taxa had intraspecific variation ranging to 8.8%, suggesting the possibility of cryptic species (i.e. Desmodus rotundus and Artibeus jamaicensis). There was a recurring biogeographic pattern in eight species with a separation of northern and southern Middle American localities. The Yucatan Peninsula was a discrete area identified in four species, whereas Panama was recovered in five species of phyllostomid bats. Our study establishes a foundation for further molecular work incorporating broader taxonomic and geographic coverage to better understand the phylogeography and genetic diversity that have resulted from the ecological constraints in this region and the remarkable differentiation of bats in the Neotropics.

Reig's short-tailed opossum (Monodelphis reigi) was recently described morphologically, based on a single specimen from southeastern Venezuela. It was considered most similar to M. adusta, which is allopatrically distributed in the Andes and surrounding areas, but there has not been an explicit study of systematic relationships with other species of Monodelphis. We report the first occurrence from Guyana of this rare species that was previously known by only the holotype. In a molecular phylogenetic analysis of mitochondrial cytochrome b sequence variation, it groups within a well-supported monophyletic clade that includes M. adusta, M. handleyi, M. osgoodi, and M. peruviana. M. adusta was found to be the sister taxon to the rest of the adusta-complex. M. reigi is the basal taxon (sister species) of remaining adusta-complex forms. This corroborates earlier morphological studies suggesting close affinity of these taxa. As presently known, M. reigi is endemic to the highland regions (>1,000 m asl) of the Guiana Shield of northern South America, and is the only taxon within the M. adusta species complex that does not occur in the Andes or adjacent lowland regions. Based on previous molecular dating of Didelphidae, this suggests that there was a dispersal event from the Andes to the Guiana Highlands in the Miocene that gave rise to M. reigi.

We studied molecular and morphological variation in small fruit-eating bats (Artibeus) in northern South America to establish species boundaries, evolutionary relationships, and distributional limits. Although this is a speciose genus with some of the most common bats in Neotropical forests, resolution of taxonomy and their identification has been difficult. Our molecular phylogeny based on Bayesian and parsimony analyses of cytochrome b variation includes a well supported topology of A. glaucus glaucus sister to a clade of A. gnomus and A. glaucus bogotensis indicating that A. glaucus is a paraphyletic amalgam. A re-assessment of morphology corroborates differences between A. g. bogotensis from the Andean valleys of Colombia east into the Guianas and A. g. glaucus from western Amazonia. Thus, we recognize A. bogotensis and A. glaucus as distinct and allopatrically occurring species. Based on a Kimura-2 parameter model of substitution for cytochrome b, there was 1.2% sequence divergence within A....

Peromyscine mice of the cricetid subfamily Neotominae comprise the most common and speciose assemblage of North American rodents. The composition and phylogenetic relationships within this group have been addressed using multiple character systems but remain unresolved, particularly the branching pattern of deeply rooted lineages. The relationships and status of several taxa formerly included within Peromyscus also are controversial. We present a new phylogenetic hypothesis based on combined mitochondrial and nuclear sequences using cytochrome b, interphotoreceptor retinoid-binding protein, and growth hormone receptor gene sequences, and include all major peromyscine lineages. Bayesian and parsimony approaches recover a congruent, well-resolved phylogeny, wherein Peromyscus forms a monophyletic assemblage only if a number of putative genera are included within it. Onychomys rather than Reithrodontomys is the sister taxon to Peromyscus (within which are included Habromys, Osgoodomys, Megadontomys, Podomys, and Neotomodon). Reithrodontomys in turn is the sister taxon to Isthmomys, and these 2 genera are the nearest outlier to Onychomys plus an expanded concept of Peromyscus, consistent with the recent recognition of this entire group as the tribe Reithrodontomyini. The Baiomyini, Ochrotomyini, and Neotoma (Neotomini) appear as successive outgroups to this clade. Based on these results, we present a systematic review of higher-level relationships among peromyscine rodents.

Multiple unlinked loci are surveyed in a methodological approach for mammalian systematics that uses genes from the four pathways of genetic transmission: mitochondrial, autosomal, and X and Y sex chromosomes. Each of these components has different properties, such as effective population size, mutation rate, and recombination, that result in a robust hypothesis of evolutionary history. The utility of this experimental design is tested with bats in the family Emballonuridae and the hypothesis that the New World taxa are monophyletic. Parsimony and Bayesian analyses of the individual data sets give generally congruent topologies with high bootstrap proportions and posterior probabilities for monophyletic clades representing species and genera. The mitochondrial gene has significantly faster rates of substitution, higher levels of homoplasy, and a greater degree of saturation than the nuclear genes that contributed to the loss of phylogenetic signal at deeper branches of the tree. However, there is better resolution and support for the more slowly evolving nuclear introns including a New World clade, indicating a single origin of emballonurid bats in the Neotropics (tribe Diclidurini). One novel subtribe has a hard basal polytomy that is unresolved for all of the nuclear partitions, suggesting a rapid burst of evolution during the diversification of genera. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 189–209.

We examined spectral features that characterize the highly stereotyped, repetitive vocalizations of New World baiomyine rodents. Although stereotyped vocal signaling, described as “song,” has been documented in Scotinomys (singing or brown mice), its occurrence was unknown in the sister taxon Baiomys (pygmy mice). We also recorded vocalizations of females, about which little information was previously available. Although examination of morphological and molecular data supports a close relationship between the 2 baiomyine genera, we identified song as a complex behavior that further underpins the monophyly of the Baiomyini. Both spectral and temporal features render these songs highly localizable, a characteristic of possible utility for courtship and other social behavior. The song of Baiomys is confined entirely to the ultrasonic spectrum, unlike that of Scotinomys, which uses a broader range of frequencies. The intensity, identity, and predictability of vocalization suggest that these songs are...

One hundred DNA sequences from the mitochondrial cytochrome-b gene of 44 species of deer mice (Peromyscus (sensu stricto), 1 of Habromys, 1 of Isthmomys, 2 of Megadontomys, and the monotypic genera Neotomodon, Osgoodomys, and Podomys were used to develop a molecular phylogeny for Peromyscus. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were conducted to evaluate alternative hypotheses concerning taxonomic arrangements (sensu stricto versus sensu lato) of the genus. In all analyses, monophyletic clades were obtained that corresponded to species groups proposed by previous authors; however, relationships among species groups generally were poorly resolved. The concept of the genus Peromyscus based on molecular data differed significantly from the most current taxonomic arrangement. Maximum-likelihood and Bayesian trees depicted strong support for a clade placing Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys within Peromyscus. If Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are regarded as genera, then several species groups within Peromyscus (sensu stricto) should be elevated to generic rank. Isthmomys was associated with the genus Reithrodontomys; in turn this clade was sister to Baiomys, indicating a distant relationship of Isthmomys to Peromyscus. A formal taxonomic revision awaits synthesis of additional sequence data from nuclear markers together with inclusion of available allozymic and karyotypic data.

We examined genealogical relationships among six of seven species of crested-tailed mice (Habromys chinanteco, H. delicatulus, H. ixtlani, H. lepturus, H. lophurus, and H. simulatus) using DNA sequence data from the cytochrome-b gene. Gene trees based on maximum likelihood, Bayesian inference and maximum parsimony were largely congruent in that H. lepturus and H. ixtlani were closely related and formed the sister group to H. lophurus. All analyses also arranged H. chinanteco and H. simulatus as sister taxa. These results are concordant with the phenetic groupings of Carleton et al. (2002) based on morphology. Our unweighted maximum parsimony trees did not resolve placement of H. delicatulus relative to other taxa. However, analyses using weighted maximum parsimony, maximum likelihood and Bayesian inference optimality criteria recovered a sister group relationship between H. delicatulus and the clade comprised of ((H. lepturus H. ixtlani)(H. lophurus)). This relationship differs from the overall phenetic similarity of H. delicatulus with H. simulatus and H. chinanteco, influenced by the small size of these three taxa, but is consistent with some derived features of the phallus (Carleton et al., 2002). Based on our sequence data, a specimen from Michoacan, Mexico, recently assigned to Peromyscus sagax likely was inadvertently misidentified (Tiemann-Boege et al., 2000) and actually represents a new locality record for H. delicatulus. Finally, we comment on the conservation status of species of Habromys.

Sequence diversity in the cytochrome c oxidase subunit 1 gene has been shown to be an effective tool for species identification and discovery in various groups of animals, but has not been extensively tested in mammals. We address this gap by examining the performance of DNA barcodes in the discrimination of 87 species of bats from Guyana. Eighty-one of these species showed both low intraspecific variation (mean = 0.60%), and clear sequence divergence from their congeners (mean = 7.80%), while the other six showed deeply divergent intraspecific lineages suggesting that they represent species complexes. Although further work is needed to examine patterns of sequence diversity at a broader geographical scale, the present study validates the effectiveness of barcoding for the identification of regional bat assemblages, even highly diverse tropical faunas.

An inventory of mammals in the vicinity of Brownsberg Nature Park, Suriname, incorporated a number of different sampling methods including examining museum voucher specimens, an animal-rescue operation, transect surveys, camera photo-traps, and interviews with local inhabitants. We document a total of 125 mammal species present in the Park. These include ten opossums, five pilosans, four armadillos, 58 bats, eight monkeys, 13 carnivores, one tapir, four artiodactyls, and 22 rodents. Nine of these species are reported for the first time from Suriname: one mouse opossum (Marmosops pinheiroi); one naked-backed moustached bat (Pteronotus gymnonotus); four fruit-eating bats (Artibeus bogotensis, A. gnomus, A. obscurus, and A. planirostris); two evening bats (Eptesicus chiriquinus and Myotis riparius);and one arboreal rice rat (Oecomys auyantepui). There are 191 indigenous non-marine mammals presently known from Suriname.

As part of a larger project on biodiversity and conservation in Guyana, we documented 130 species of mammals from Iwokrama Forest. This included 7 marsupials, 4 xenarthrans, 86 bats, 5 primates, 8 carnivores, 1 perissodactyl, 4 artiodactyls, and 15 rodents. As is typical for most Neotropical sites, the 86 species of bats represent over half of the mammal diversity. Standardized collecting methods implemented in the 1997 faunal survey of Iwokrama Forest in central Guyana enabled us also to investigate species diversity and abundance resulting from the inventory of mammals. Four species of fruit-eating bats (Artibeus lituratus, A. obscurus, A. planirostris, and Carollia perspicillata) were the most abundant and accounted for 43% of the 2,097 total captures in mist nets and harp traps during 79 nights of sampling. For nonvolant mammals, terrestrial spiny rats (Proechimys spp.) represented over half (55%) of the 65 captures in primarily live box-style traps. We estimate that our inventory is approxim...

We analyzed the phylogenetic relationships of all eleven currently recognized species of large Artibeus using the cytochrome b mitochondrial gene. The topology from a maximum parsimony analysis included: (1) A. obscurus and A. planirostris as sister species with successively basal lineages of (2) A. amplus, (3) a clade with A. lituratus and A. intermedius, (4) A. jamaicensis, (5) a clade of A. inopinatus sister to A. hirsutus and A. fraterculus, (6) A. fimbriatus, and (7) the most basal lineage of A. concolor. The individual species were monophyletic and well supported by bootstrap and decay values. The monophyletic clade of ((((obscurus + planirostris) + amplus) + (lituratus + intermedius)) + jamaicensis) was also highly supported, although some of the interspecific relationships were less so. Contrary to previous hypotheses of species limits based on a presumed intergradation in body size, A. jamaicensis and A. planirostris do not form a monophyletic group, refuting their conspecificity and supporting a...

Summary A phylogeny of least sac-winged bats (Balantiopteryx) was constructed from morphological data, and molecular data derived from mapped restriction cleavage sites of the 2,400 base pair mtDNA gene region including ND3, ND4L, and ND4. Separate and combined phylogenetic analyses each gave single most-parsimonious solutions with a well supported topology of (B. plicata, (B. io, B. infusca)). Incorporating current distribution patterns and habitat preferences with our phylogeny and estimates of divergence suggests that speciation within Balantiopteryx occurred in the Late Miocene prior to the establishment of the Isthmian Link between South and North America. Based on the premise that the genus arose in insular South America, we hypothesize that ancestral Balantiopteryx dispersed overwater to Middle America and that B. plicata subsequently diverged in the dry Pacific versant of Middle America after tectonic uplifting. B. io and B. infusca subsequently speciated allopatrically in the wet Atlantic versant of southern Mexico and northern Central America, and in the Pacific versant of southwestern Colombia and northwestern Ecuador, respectively, prior to the present land connection between North and South America.

The Sunda region of south-east Asia comprises the Malay Peninsula and the islands of Java, Sumatra and Borneo, all of which lie on a shallow continental shelf projecting from Indochina. Pleistocene glacial cycles caused sea levels to drop repeatedly, exposing vast areas of the Sunda shelf and creating land bridges among the islands and mainland. These land bridges, the latest of which connected all three of the major Sunda islands to the Malay Peninsula as recently as 9500 years ago, may have enabled mammalian migrations across the Sunda shelf. Pleistocene land bridges on the Sunda shelf have been invoked to explain the current distributions of mammalian taxa occupying ranges corresponding with the Pleistocene limits of land and the appearance of new mammal species in the Pleistocene fossil record. The ability of mammals to move throughout the exposed shelf during periods of low sea level would, however, have been influenced by topographic and ecological features, which have been variously described as savanna-like or as moist tropical rain forest. Using a phylogeographical approach, we test the hypothesis that Pleistocene land bridges enabled widespread movements in three rain-forest-restricted murine rodents of the Sunda shelf: Maxomys surifer, Leopoldamys sabanus and Maxomys whiteheadi. Our results do not support the hypothesis of broad Pleistocene migrations in these taxa, but instead suggest a deep history of vicariant evolution that may correspond with the Pliocene fragmentation of the Sunda block. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 91–109.

Cynomops (dog-faced bat) generally is regarded as either a monophyletic genus or, in some cases, a subgenus of Molossops. Species limits and phylogenetic relationships within Cynomops, however, remain unresolved due primarily to subtle morphological differences and similarity in size of the small taxa. We used a combination of morphometric analyses for quantifying size variation and molecular data for reconstructing the evolutionary history within Cynomops. Rooting the tree with Eumops hansae produced a clade of Molossops neglectus and M. temminckii that was sister to a monophyletic Cynomops clade. The most parsimonious topology (in parenthetical notation) for Cynomops was (((paranus + planirostris) + (greenhalli + abrasus)) + mexicanus). Molecular analysis supports the autapomorphy of white venter as diagnostic for C. planirostris, although there was some overlap in size with the slightly larger, dark-venter C. paranus. Cynomops greenhalli was intermediate in size between C. paranus and C. mexic...

The genetic algorithm for rule-set prediction (GARP) has beensuccessfully used in modeling species' distributions with environmental data forwell-studied birds in the United States and elsewhere. GARP's efficiency hasbeen demonstrated to be robust even with incomplete occurrence and geographicdata. Thorough biological sampling in conjunction with comprehensive geographicinformation, however, is not the norm for many tropical areas where mostbiodiversity occurs. Mammals from Guyana were used as a test of the robustnessof these approaches in a worst-case scenario of uneven sampling combined withcoarse geographic data. The occurrence of species in poorly surveyed regions,such as the Pakaraima Highlands of west-central Guyana, was consistentlyunder-predicted, whereas presence in well-surveyed areas such as thesouthwestern Rupununi was usually correctly predicted. Comparisons of numbersof species and specimens collected also indicate that lowland forests in thesoutheast and coastal forests in the northwest are under-sampled. For robustdistributional predictions in Guyana, more thorough inventories are needed inthese diverse environments.

Previous studies on genetics of hoary bats produced differing conclusions on the timing of their colonization of the Hawaiian Islands and whether or not North American (Aeorestes cinereus) and Hawaiian (A. semotus) hoary bats are distinct species. One study, using mtDNA COI and nuclear Rag2 and CMA1, concluded that hoary bats colonized the Hawaiian Islands no more than 10,000 years ago based on indications of population expansion at that time using Extended Bayesian Skyline Plots. The other study, using 3 mtDNA and 1 Y-chromosome locus, concluded that the Hawaiian Islands were colonized about 1 million years ago. To address the marked inconsistencies between those studies, we examined DNA sequences from 4 mitochondrial and 2 nuclear loci in lasiurine bats to investigate the timing of colonization of the Hawaiian Islands by hoary bats, test the hypothesis that Hawaiian and North American hoary bats belong to different species, and further investigate the generic level taxonomy within the tribe. Phylogenetic analysis and dating of the nodes of mtDNA haplotypes and of nuclear CMA1 alleles show that A. semotus invaded the Hawaiian Islands approximately 1.35 Ma and that multiple arrivals of A. cinereus occurred much more recently. Extended Bayesian Skyline plots show population expansion at about 20,000 years ago in the Hawaiian Islands, which we conclude does not represent the timing of colonization of the Hawaiian Islands given the high degree of genetic differentiation among A. cinereus and A. semotus (4.2% divergence at mtDNA Cytb) and the high degree of genetic diversity within A. semotus. Rather, population expansion 20,000 years ago could have resulted from colonization of additional islands, expansion after a bottleneck, or other factors. New genetic data also support the recognition of A. semotus and A. cinereus as distinct species, a finding consistent with previous morphological and behavioral studies. The phylogenetic analysis of CMA1 alleles shows the presence of 2 clades that are primarily associated with A. semotus mtDNA haplotypes, and are unique to the Hawaiian Islands. There is evidence for low levels of hybridization between A. semotus and A. cinereus on the Hawaiian Islands, but it is not extensive (

With 86 species, Iwokrama Forest in central Guyana has the highest reported bat biodiversity for a protected area in the world. Using standardized capture data for 73 of these 86 species, we document community structure of bats in terms of species diversity, relative abundance, gross biomass, feeding guilds, vertical stratification and a trophic-size niche matrix. Based on faunal surveys in 1997, with similar amounts of effort in the forest canopy and at ground level, the greater fruit-eating bat (Artibeus lituratus) was by far the most ecologically dominant species in terms of frequency of capture and biomass. In total, frugivores comprised 70% of the species diversity and 78% of the biomass. The most common species of bat were fully partitioned in a resource niche matrix of size and trophic guild when vertical stratification was included as a variable. We conclude that resource partitioning and species packing differentially affect relative size in tropical bats, and are better summarized and analysed in three dimensions.

Fourteen species of bats are reported for the first time from Guyana (Saccopteryx gymnura, Micronycteris brachyotis, M. homezi, Lichonycteris obscura, Anoura latidens, Vampyressa pusilla, Vampyrodes caraccioli, Eptesicus chiriquinus, Cynomops paranus, Molossops neglectus, Molossus sp., Molossus coibensis, Molossus sinaloae, and Promops centralis) bringing the known bat diversity for the country to 121 species. Information including measurements, reproductive data, distribution, and taxonomy are provided for these species. Seven of these new records were collected in the Iwokrama International Rain Forest Programme site in central Guyana. Eighty-six bat species are now documented from Iwokrama Forest which is the highest species diversity for bats reported from any protected area in the world. There are, however, few tropical sites that have relatively complete inventories. A summary for bat species diversity in southern Venezuela, Guyana, Suriname, and French Guiana indicates that at least 146 species of bats are known from the Guianan subregion. Intense inventory surveys, especially in the often neglected subcanopy, suggest that species richness is probably underestimated in most Neotropical areas. Likewise, species-level diversity in the Guianan subregion is higher than previously suggested. Surveying and monitoring biodiversity are critical to developing a National Protected Areas System in Guyana.

Intrageneric relationships within Carollia and Rhinophylla (Phyllostomidae) are examined using the 1,140 base pairs of the mitochondrial cytochrome-b gene. We also examined the proposed sister relationship of Carollia and Rhinophylla by comparing the cytochrome-b gene from those two taxa to that of representatives of Phyllonycteris, Lonchophylla, Uroderma, Artibeus, Dermanura, Enchisthenes, and Chiroderma. Within Carollia, representatives of C. brevicauda and C. perspicillata are most closely related, whereas C. subrufa is more closely related to these two species than is C. castanea, which forms the basal divergence for the genus. Within Rhinophylla, data for relationships of species are equivocal and suggest a concomitant divergence for all three species. If the rate of evolution is the same for the cytochrome-b gene in the two genera, then species within Rhinophylla diverged earlier than did any of the species of Carollia. If those two genera shared a common ancestor to the exclusion of the remainder of the Phyllostomidae, common ancestry was of short duration. The alternative hypothesis, that Carollia and Rhinophylla are not sister taxa and shared morphological characteristics are convergent, remains viable based on our data.

Two taxa within the Oryzomys palustris species group, O. p. texensis and O. couesi aquaticus , occur sympatrically in southern Texas and northeastern Tamaulipas, Mexico. Tissues of 379 individuals from sympatric and allopatric populations within this area and allopatric populations outside the area were analyzed using starch-gel electrophoresis to describe genic variation in the contact zone within each taxon, determine the level of gene flow, if any, between the two taxa, and resolve the taxonomic status of the two rice rats. Populations of O. palustris in and near the contact zone have lower mean heterozygosity than populations from regions to the north and east, whereas O. couesi does not show lower heterozygosity within the contact zone relative to adjacent regions. Within the contact zone, O. palustris has a more linear (coastal) pattern of gene flow with greater differentiation among local populations than does O. couesi . Within and outside the zone of contact, the two taxa were fixed for alternate alleles at four loci, and unique alleles were expressed by one or the other of the two taxa at eight loci. Based on the lack of evidence of hybridization or introgression in sympatry, O. palustris and O. couesi are recognized as distinct species.

Chromosomal variation was examined in 10 populations of Dicrostonyx in the eastern and High Arctic of Canada to determine the extent and nature of chromosomal variation and to examine chromosomal differentiation within and among species and subspecies. Chromosomal data are presented for two species of collared lemmings, D. hudsonius and D. groenlandicus, including D. g. groenlandicus, D. g. clarus, and D. g. lentus. Standard, G-banded, and C-banded karyotypes revealed variation among populations of D. groenlandicus due to Robertsonian fusions and the addition of B chromosomes. G-banding revealed complete homologous banding patterns of autosomal arms between D. groenlandicus and D. hudsonius; however, sex chromosome constitution differed between the two species. Dicrostonyx groenlandicus possesses a neo-XY, formed by a Robertsonian fusion of the sex chromosomes and a pair of autosomes. The neo-XY does not occur in D. hudsonius, and this absence appears to be the primitive state for the genus.

Morphological analyses of 23 specimens of Rhogeessa from localities in the Yucatan Peninsula revealed significant sexual dimorphism in some characters. Although there was no significant sexual dimorphism in length of ear or length of tragus, males had conspicuous ear glands and females did not. Rhogeessa produced short, broad-band echolocation calls that showed significant inter-individual variation. Karyotypes of 16 Rhogeessa were similar to a karyotype reported from Belize and different than those of R. tumida from areas adjacent to the Yucatan Peninsula. Yucatan populations also are morphologically distinctive and we assign them to a separate species, R. aeneus Goodwin.

Genetic differentiation among populations and speciation in Dicrostonyx is hypothesized to have resulted from either allopatric divergence in glacial refugia during the Wisconsin or sympatric processes uncorrelated with refugial isolation. We examined chromosomal and mitochondrial DNA variation in four laboratory colonies, representing three species, in a preliminary evaluation of these hypotheses. Chromosomal variation is extensive among populations, diploid numbers ranging from 38 to 50. Autosomal variation appears to be due primarily to Robertsonian rearrangements and additions of supernumerary chromosomes, and is geographically unpatterned. Sex chromosome morphology is geographically structured and correlated with proposed southern and northern refugia. Restriction fragment analysis of mitochondrial DNA revealed two ancient, divergent genotypic assemblages, corresponding to geographic distributions of sex chromosomes. Autosomal variation, and any resulting reproductive isolation, probably is recent and uncorrelated with refugial history, whereas divergence of sex chromosomes and disparate mitochondrial assemblages likely predate the Wisconsin.

Reports of audible vocalizations are rare in adult muroid rodents, animals generally very small in body size and under strong predation pressure. By contrast, communication using high, often ultrasonic vocal frequencies is relatively common. There are anecdotal reports of audible vocalizations for some harvest mice (genus Reithrodontomys), however none have been recorded or analyzed. Several species of harvest mice are studied, representing the subgenera Reithrodontomys (R. fulvescens, R. sumichrasti) and Aporodon (R. creper, R. mexicanus, R. spp.), as part of a larger phylogenetic analysis of stereotypical vocal communication. Only R. mexicanus produced stereotyped vocalizations on a regular basis. Acoustic signals of R. mexicanus contain prominent harmonics bridging both the audible and ultrasonic range, with evidence of non-linear distribution of energy within and between notes of an individual call. Harmonic emphasis varies, making the carrier frequency difficult to locate. These Reithrodontomys vocalizations are compared with members of their phylogenetic sister group Onychomys+Peromyscus, genera whose stereotypic calls exclusively occupy the audible or ultrasonic spectrum, respectively. It is hypothesized that the stereotypic signals of harvest mice represent announcement calls. Given the number of anecdotal reports of stereotyped 1, 2, and 3-note calls among Reithrodontomys species, further interspecific comparisons are warranted.

We report the discovery of a new species of doglike bat (Peropteryx) from the lowland Amazonian forests of Ecuador and Peru. It has transparent wing membranes that are faintly tinged brown with pale-brown arms and digits; ears that are separated on the forehead; and a skull with small, shallow pterygoid pits that are anterolateral to an undivided basisphenoid pit and that are separated by a mesopterygoid extension. These characters distinguish the new species from morphologically similar species with which it was previously confused (P. leucoptera and P. macrotis). A molecular phylogenetic analysis of unlinked loci from each of the four genetic transmission systems of mammals (mitochondrial, nuclear-autosomal, X, and Y chromosomes) independently corroborated the placement of the new species as the sister taxon to a clade that includes P. kappleri, P. macrotis, and P. trinitatis; the basal lineage for the genus is P. leucoptera. This phylogeny suggests that transparent wings (sometimes described as ‘‘white’’ but actually lacking pigment), the traditional character used to diagnose Peronymus, is not a unique synapomorphy. Furthermore, based on a molecular dating analysis, the depth of divergence of Peropteryx is equivalent to that of another New World emballonurid genus (Balantiopteryx). Therefore, Peronymus does not warrant higher-level recognition as a subgenus or genus.

We examined allozymic exchange across a contact zone between Perognathus flavus and P. merriami in Texas and New Mexico by use of starch-gel electrophoresis. Frequency differences between the taxa were pronounced ; the overall Rogers' genetic similarity was 0.82. P. flavus and P. merriami were sympatric at six localities and, based on the electrophoretic data, introgression between them appeared limited. These results contrast with those of others who concluded that the two taxa intergraded in this zone of overlap, based on morphological analyis. In western Texas and eastern New Mexicon, P. flavus and P. merriami appear to interact as distinct biological species

Isothrix sinnamariensis was originally described and known only from French Guiana. We document the first occurence of this species from Guyana. A single sub-adult male was collected in lowland tropical rainforest near the headwaters of the Essequibo River. Although smaller in external and cranial size than the two adult females of the type description, our third known specimen represents the basal lineage to the type-series clade, with an average sequence difference of 1.72% based on cytochrome b mitochondrial DNA sequences. However, the degree of morphological and genetic divergence (2.67%) between I. sinnamariensis and its sister taxon I. pagurus is substantially less than the chromosomal differences originally used to distinguish them as two separate species. In contrast, distinctive karyotypes, morphological differences, and higher levels of mtDNA divergence (13.48%) between the other two species recognized, I. negrensis that was recently separated from I. bistriata , suggest an earlier and deeper diversification for these taxa.

The patterns of synapsis and chiasma formation of the B chromosomes of male collared lemmings (Dicrostonyx groenlandicus) were analyzed by light and electron microscopy and compared to expectations for various hypotheses for the intragenomic origin of supernumerary chromosomes. Pachytene analysis revealed a variety of synaptic configurations including B-chromosome univalents, bivalents and trivalents. In approximately one-half of the pachytene nuclei examined, B chromosomes were in synaptic associations with the normally unpaired portion of the Y chromosome. The B-chromosome configurations at pachynema, including those involving the Y chromosome, were maintained into diakinesis and metaphase I. The meiotic behavior of the B chromosomes was inconsistent with their derivation from centric-fusion products, isochromosome formation, small-autosome polysomy, or the X chromosome. However, the frequent synapsis and apparent recombination between B chromosomes and the Y chromosome implicate this sex chromosome as a possible source of the B chromosomes in collared lemmings.

Electron-microscopic analysis of surface-spread synaptonemal complexes at pachynema and light-microscopic analysis of chromosomal configurations at diakinesis/metaphase I corroborate the hypothesized neo-XY derivation of the sex chromosomes of Dicrostonyx groenlandicus. Although an intact neo-XY pairing configuration was observed in a relatively small percentage of the pachytene cells in each individual, the high incidence of neo-XY bivalents at diakinesis/metaphase I suggests that the other observed pachytene configurations were artifacts of the physical stresses of the surface-spreading procedure. The very low frequency (0.6 %) of univalent neo-X and neo-Y chromosomes at diakinesis and metaphase I is attributable to consistent synapsis and recombination between their homologous autosomally derived segments. The resultant stability of the sex bivalent through metaphase I may have increased the efficacy of sex-chromosome segregation, and thereby played a mechanistic role in the evolutionary incorporation of the neo-XY sex-chromosome constitution in D. groenlαndicus.