Phylogeny of the Procyonidae (Mammalia: Carnivora): Molecules, morphology and the Great American Interchange

Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae)

Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.

Gongylonema sp. in the Tongue of a Brown-Nosed Coati (Nasua nasua) from the Brazilian Atlantic Forest

Two parasites were collected from the epithelial layer of the tongue mucosa of a brown-nosed coati (Nasua nasua) in an area of Atlantic Forest in Minas Gerais State, Brazil. These were identified as female Gongylonema sp. nematodes, not previously reported in Brazilian wild carnivores.

Functional and phylogenetic interpretation of the forelimb myology of two South American carnivorans, the ring-tailed coati (Nasua nasua) and crab-eating raccoon (Procyon cancrivorus)

A comparative analysis of the forelimb myology of two neotropical procyonids (Nasua nasua and Procyon cancrivorus) was performed to assess how observed differences in their myological configuration would be related to their diverse ecological behaviors and phylogeny. Although both species are associated with the arboreal substrate, N. nasua is a more agile climber that usually digs; whereas P. cancrivorus spends most of its time on the ground foraging, climbing on the trees as shelter and is a good swimmer. Here, myological descriptions, muscle maps, phylogenetic optimizations, and muscle mass data of the forelimb of these two procyonids are presented. The main functional muscular groups are discussed in a comparative framework with other carnivorans that present a wide ecological diversity. Also, muscular characters were mapped onto a phylogeny to explore their evolution and to obtain ancestral state reconstructions. Results indicate clear myological differences among the two neotropical procyonids associated with their ecological preferences. One of the most remarkable anatomical differences is the arrangement and relative mass of the extrinsic musculature, mainly the musculus rhomboideus and the delto-pectoral complexes. In Nasua nasua, these suggested a greater stability in their shoulder girdle for climbing and digging and probably would provide stronger neck and head movements when they use them for foraging on the ground. Conversely, P. cancrivorus has a different extrinsic muscular configuration, which would allow an increment on the stride length and faster movements of the forelimb associated with more frequent terrestrial gaits. Also, significant differences are observed in the distal musculature, associated with strong movements of forepaws when climbing and digging in N. nasua; whereas, P. cancrivorus configuration suggested precise forearm and digits movements, related to manipulation of food items when they are catching prey or feeding. Most of the codified features of P. cancrivorus would reflect retention of plesiomorphies acquired in the common ancestor of caniforms or arctoids, whereas N. nasua shows derived traits, particularly in the proximal forelimb region. The present work increases the information available on the myology of these particular taxa and extant generalized arctoid models in general. The analyses presented here will be useful both for other comparative myological studies (morpho-functional and phylogenetic) and for muscular reconstruction in extinct procyonids, as well as other carnivorans.

Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology

The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.

Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids

The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.

Comparative phylogeography among eight Neotropical wild cat species: no single evolutionary pattern

The felid species of South America are thought to have arrived on the continent during the Great American Biotic Interchange (GABI) in the Pleistocene. However, molecular and palaeontological data do not agree on how this event affected speciation in felids. Here, we determine both the number of colonization events and the period when felines first migrated from North America to South America. In addition, we evaluate whether similar evolutionary events could have affected the eight Neotropical cat species in their levels of genetic diversity, spatial genetic structure and demographic changes. We analysed four concatenated mitochondrial genes of the jaguar, ocelot, margay, tigrina, pampas cat, Andean cat, puma and jaguarundi. The samples were representative of a wide distribution of these species in Central and South America. Our analysis suggests either three or four colonization events from North America to South America over the past 3 Myr, followed by subsequent speciation events and the attainment of high or very high genetic diversity levels for seven of the species. No unique evolutionary process was detected for any of the current Neotropical cat species.

The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing Gavialis basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian Portugalosuchus azenhae was recently described as the oldest crown crocodilian, with affinities to Gavialis, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians, including Portugalosuchus. Our analyses incorporating DNA data robustly recovered Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids and Borealosuchus spp.), questioning the status of Portugalosuchus as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss the impact of ambiguous fossil calibration and how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.

Coronaviruses Associated with the Superfamily Musteloidea

Among the animal superfamily Musteloidea, which includes those commonly known as mustelids, naturally occurring and species-specific alphacoronavirus infections have been observed in both mink (Mustela vison/Neovison vison) and domestic ferrets (Mustela putorius furo). Ferret systemic coronavirus (FRSCV), in particular, has been associated with a rare but fatal systemic disease. In recent months, it has become apparent that both minks and ferrets are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus and the cause of the coronavirus disease 2019 (COVID-19) pandemic. Several mink farms have experienced SARS-CoV-2 outbreaks, and experimental models have demonstrated susceptibility of ferrets to SARS-CoV-2. The potential for pet ferrets to become infected with SARS-CoV-2, however, remains elusive. During the 2002-2003 SARS epidemic, it was also apparent that ferrets were susceptible to SARS-CoV and could be utilized in vaccine development. From a comparative standpoint, understanding the relationships between different infections and disease pathogenesis in the animal superfamily Musteloidea may help elucidate viral infection and transmission mechanisms, as well as treatment and prevention strategies for coronaviruses.

Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor)

Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes. We discovered significant variation in contig and scaffold N50 and L50 statistics and genome completeness depending on the de novo assembler used. We compared the performance of these three assembly algorithms in hopes that this study will aid others looking to improve the quality of existing draft genome assemblies even without additional sequence data. We also estimate the demographic histories of raccoons and kinkajous using the Pairwise Sequentially Markovian Coalescent and discuss the variation in population sizes with respect to climatic change during the Pleistocene, as well as aspects of their ecology and taxonomy. Our goal is to achieve a better understanding of the evolutionary history of procyonids and to create robust genomic resources for future studies regarding adaptive divergence and selection.

Proximal Humerus Morphology Indicates Divergent Patterns of Locomotion in Extinct Giant Kangaroos

Sthenurine kangaroos, extinct “giant kangaroos” known predominantly from the Plio-Pleistocene, have been proposed to have used bipedal striding as a mode of locomotion, based on the morphology of their hind limbs. However, sthenurine forelimb morphology has not been considered in this context, and has important bearing as to whether these kangaroos employed quadrupedal or pentapedal locomotion as a slow gait, as in extant kangaroos. Study of the correlation of morphology of the proximal humerus in a broad range of therian mammals shows that humeral morphology is indicative of the degree of weight-bearing on the forelimbs during locomotion, with terrestrial species being distinctly different from arboreal ones. Extant kangaroos have a proximal humeral morphology similar to extant scansorial (semi-arboreal) mammals, but sthenurine humeri resemble those of suspensory arboreal taxa, which rarely bear weight on their forelimbs, supporting the hypothesis that they used bipedal striding rather than quadrupedal locomotion at slow gaits. The humeral morphology of the enigmatic extinct “giant wallaby,” Protemnodon, may be indicative of a greater extent of quadrupedal locomotion than in extant kangaroos.

The earliest mustelid in North America

Until now, the pre-Miocene fossil record of mustelids in North America has been restricted to specimens attributable to oligobunine taxa and isolated remains tentatively allocated to the genus Plesictis. In the present study, we report on a nearly complete cranium and a referred dentary of a new genus and species of mustelid. The specimens were recovered from the Turtle Cove and Kimberly Members of the John Day Formation, Oregon, USA.

These excellently preserved specimens more confidently confirm the presence of mustelids in the Early and Late Oligocene (Early and Late Arikareean) of North America. Like the holotype specimen of ‘Plesictis’ julieni, the new species lacks an alisphenoid canal and a postprotocrista on the M1 (synapomorphies of Mustelidae), but retains a dorsally deep suprameatal fossa (a feature occasionally suggested to be unique to Procyonidae). Phylogenetic analyses, applying parsimony and Bayesian inference to combined molecular (five genes totalling 5490 bp) and morphological data, recover this new species of mustelid as sister-species to ‘Plesictis’ julieni. The results of these analyses reveal that the new genus is a close relative of other species of Plesictis and several taxa traditionally allied with Oligobuninae, thereby rendering Oligobuninae paraphyletic. We further discuss the significance of the relatively small size of this new mustelid as it relates to predictions based on increased aridification of the palaeoclimate and the expansion of open habitats in the Oligocene.

Comparative leucocyte populations between two sympatric carnivores (Nasua narica and Procyon lotor)

Coatis (Nasua narica) and raccoons (Procyon lotor) potentially play an important role in zoonotic diseases because they may carry pathogens and can transmit them to humans. To date, our understanding of the immune function of these two carnivores is deficient. The aim of this study was to compare the number of leucocyte subtypes and the phagocytic capacity between the coati and the raccoon. Blood samples were collected, and leucocyte subtypes were characterized and counted by flow cytometry and microscopy, respectively. Phagocytosis was analysed by kinetic assay. Differences in leucocytes between these two species were found; the total count of neutrophils was higher in raccoons than in coatis, but lymphocytes and eosinophils were higher in coatis than in raccoons. Antigen reduction was more rapid for the coatis. However, raccoons had a higher efficient endocytic process than coatis. This study provides the basis for understanding the procyonid immune system, which informs conservation, particularly since some procyonids are imperilled.

Mitochondrial phylogeography of kinkajous (Procyonidae, Carnivora): maybe not a single ESU

Knowledge of how a species is divided into different genetic units, and the structure among these units, is fundamental to the protection of biodiversity. Procyonidae was one of the families in the Order Carnivora with more success in the colonization of South America. The most divergent species in this family is the kinkajou (Potos flavus). However, knowledge of the genetics and evolution of this species is scarce. We analyzed five mitochondrial genes within 129 individuals of P. flavus from seven Neotropical countries (Mexico, Guatemala, Honduras, Colombia, Ecuador, Peru, and Bolivia). We detected eight different populations or haplogroups, although only three had highly significant bootstrap values (southern Mexico and Central America; northern Peruvian, Ecuadorian, and Colombian Amazon; and north-central Andes and the southern Amazon in Peru). Some analyses showed that the ancestor of the southern Mexico–Central America haplogroup was the first to appear. The youngest haplogroups were those at the most southern area analyzed in Peru and Bolivia. A “borrowed molecular clock” estimated the initial diversification to have occurred around 9.6 million years ago (MYA). All the spatial genetic analyses detected a very strong spatial structure with significant genetic patches (average diameter around 400–500 km) and a clinal isolation by distance among them. The overall sample and all of the haplogroups we detected had elevated levels of genetic diversity, which strongly indicates their long existence. A Bayesian Skyline Plot detected, for the overall sample and for the three most significant haplogroups, a decrease in the number of females within the last 30,000–50,000 years, with a strong decrease in the last 10,000–20,000 years. Our data supported an alignment of some but not all haplogroups with putative morphological subspecies. We have not discounted the possibility of a cryptic kinkajou species.

Phylogeographic and diversification patterns of the white-nosed coati (Nasua narica): Evidence for south-to-north colonization of North America

White-nosed coatis (Nasua narica) are widely distributed throughout North, Central, and South America, but the patterns of temporal and spatial diversification that have contributed to this distribution are unknown. In addition, the biogeographic history of procyonid species in the Americas remains contentious. Using sequences from three mitochondrial loci (Cytochrome b, NAHD5 and 16S rRNA; 2201 bp) and genotypes from 11 microsatellite loci, we analyzed genetic diversity to determine phylogeographic patterns, genetic structure, divergence times, and gene flow among Nasua narica populations throughout the majority of the species' range. We also estimated the ancestral geographic range of N. narica and other procyonid species. We found a high degree of genetic structure and divergence among populations that conform to five evolutionarily significant units. The most southerly distributed population (Panama) branched off much earlier (∼3.8 million years ago) than the northern populations (<1.2 million years ago). Estimated gene flow among populations was low and mostly northwards and westwards. The phylogeographic patterns within N. narica are associated with geographic barriers and habitat shifts likely caused by Pliocene-Pleistocene climate oscillations. Significantly, our findings suggest the dispersal of N. narica was south-to-north beginning in the Pliocene, not in the opposite direction during the Pleistocene as suggested by the fossil record, and that the most recent common ancestor for coati species was most likely distributed in South or Central America six million years ago. Our study implies the possibility that the diversification of Nasua species, and other extant procyonid lineages, may have occurred in South America.

Whence the beardogs? Reappraisal of the Middle to Late Eocene 'Miacis' from Texas, USA, and the origin of Amphicyonidae (Mammalia, Carnivora)

The Middle to Late Eocene sediments of Texas have yielded a wealth of fossil material that offers a rare window on a diverse and highly endemic mammalian fauna from that time in the southern part of North America. These faunal data are particularly significant because the narrative of mammalian evolution in the Paleogene of North America has traditionally been dominated by taxa that are known from higher latitudes, primarily in the Rocky Mountain and northern Great Plains regions. Here we report on the affinities of two peculiar carnivoraforms from the Chambers Tuff of Trans-Pecos, Texas, that were first described 30 years ago as Miacis cognitus and M. australis. Re-examination of previously described specimens and their inclusion in a cladistic analysis revealed the two taxa to be diminutive basal amphicyonids; as such, they are assigned to new genera Gustafsonia and Angelarctocyon, respectively. These two taxa fill in some of the morphological gaps between the earliest-known amphicyonid genus, Daphoenus, and other Middle-Eocene carnivoraforms, and lend additional support for a basal caniform position of the beardogs outside the Canoidea. The amphicyonid lineage had evidently given rise to at least five rather distinct forms by the end of the Middle Eocene. Their precise geographical origin remains uncertain, but it is plausible that southern North America served as an important stage for a very early phase of amphicyonid radiation.

ENDEMIC ORTHOPOXVIRUS CIRCULATING IN PROCYONIDS IN MEXICO

Limited serosurveillance studies suggested that orthopoxviruses (OPXV) are widespread in the US (e.g., Raccoonpox virus, Skunkpox virus, Volepox virus) and Brazil (Vaccinia virus); however, their animal reservoir(s) remain unconfirmed. Mexican mammal diversity includes several species related to those in which evidence for OPXV infections has been found (Oryzomys, Peromyscus, Microtus, and Procyonidae). The presence of these groups of mammals in Mexico and the evidence of their possible involvement in the maintenance of OPXV in nature suggest the same or similar OPXV are circulating in Mexico. We tested 201 sera from 129 procyonids via modified enzyme-linked immunosorbent assay (ELISA) and Western blot (WB) to estimate OPXV antibody prevalence in these animals. We detected a prevalence of 16.67% in Nasua narica (white-nosed coati), 35% in Procyon lotor (raccoon), and 30.4% in Bassariscus astutus (ring-tailed cat) when tested by either ELISA or WB. Western blot results presented protein bands consistent with the size of some OPXV immunodominant bands (14, 18, 32, 36, and 62 kDa). These results support the hypothesis that OPXV circulate in at least three genera of Procyonidae in Central and Southeast Mexico.

Bony labyrinth shape variation in extant Carnivora: a case study of Musteloidea

The bony labyrinth provides a proxy for the morphology of the inner ear, a primary cognitive organ involved in hearing, body perception in space, and balance in vertebrates. Bony labyrinth shape variations often are attributed to phylogenetic and ecological factors. Here we use three-dimensional (3D) geometric morphometrics to examine the phylogenetic and ecological patterns of variation in the bony labyrinth morphology of the most species-rich and ecologically diversified traditionally recognized superfamily of Carnivora, the Musteloidea (e.g. weasels, otters, badgers, red panda, skunks, raccoons, coatis). We scanned the basicrania of specimens belonging to 31 species using high-resolution X-ray computed micro-tomography (μCT) to virtually reconstruct 3D models of the bony labyrinths. Labyrinth morphology is captured by a set of six fixed landmarks on the vestibular and cochlear systems, and 120 sliding semilandmarks, slid at the center of the semicircular canals and the cochlea. We found that the morphology of this sensory structure is not significantly influenced by bony labyrinth size, in comparisons across all musteloids or in any of the individual traditionally recognized families (Mephitidae, Procyonidae, Mustelidae). PCA (principal components analysis) of shape data revealed that bony labyrinth morphology is clearly distinguishable between musteloid families, and permutation tests of the Kmult statistic confirmed that the bony labyrinth shows a phylogenetic signal in musteloids and in most mustelids. Both the vestibular and cochlear regions display morphological differences among the musteloids sampled, associated with the size and curvature of the semicircular canals, angles between canals, presence or absence of a secondary common crus, degree of lateral compression of the vestibule, orientation of the cochlea relative to the semicircular canals, proportions of the cochlea, and degree of curvature of its turns. We detected a significant ecological signal in the bony labyrinth shape of musteloids, differentiating semi-aquatic taxa from non-aquatic ones (the taxa assigned to terrestrial, arboreal, semi-arboreal, and semi-fossorial categories), and a significant signal for mustelids, differentiating the bony labyrinths of terrestrial, semi-arboreal, arboreal, semi-fossorial and semi-aquatic species from each other. Otters and minks are distinguished from non-aquatic musteloids by an oval rather than circular anterior canal, sinuous rather than straight lateral canal, and acute rather than straight angle between the posterior and lateral semicircular canals - each of these morphological characters has been related previously to animal sensitivity for detecting head motion in space.

Hind limb myology of the ringtail ( Bassariscus astutus ) and the myology of hind foot reversal

The ringtail ( Bassariscus astutus ) is a widely distributed small carnivorous mammal (Procyonidae) in Mexico and the southwestern United States. As in other procyonids, the ringtail is capable of rotating its hind foot to allow headfirst descent of vertical substrates. The osteological correlates of this process, termed hind foot reversal, are well documented, but potential myological correlates have never been investigated. We present the 1st detailed study of the muscular anatomy of the hind limb of B. astutus , including the 1st muscle maps of the pelvis and pes of any procyonid. Comparison of the hind limb myology of the ringtail with other arctoid carnivorans, including taxa incapable of hind foot reversal, indicates that the muscles responsible for the action of reversal do not differ significantly between nonreversing forms and taxa capable of partial or full reversal. This suggests that specific myological adaptations are not necessary to achieve hind foot reversal. However, increased development of the digital flexors, which maintain a grip while body mass is supported by the hind limb, may characterize taxa that make use of reversed postures. The hind limb myology of members of Procyonidae does not strongly support either morphological or molecular hypotheses of relationship, in part because relatively few differences among members of the family can be documented.

Do constraints associated with the locomotor habitat drive the evolution of forelimb shape? A case study in musteloid carnivorans

Convergence in morphology can result from evolutionary adaptations in species living in environments with similar selective pressures. Here, we investigate whether the shape of the forelimb long bones has converged in environments imposing similar functional constraints, using musteloid carnivores as a model. The limbs of quadrupeds are subjected to many factors that may influence their shape. They need to support body mass without collapsing or breaking, yet at the same time resist the stresses and strains induced by locomotion. This likely imposes strong constraints on their morphology. Our geometric morphometric analyses show that locomotion, body mass and phylogeny all influence the shape of the forelimb. Furthermore, we find a remarkable convergence between: (i) aquatic and semi-fossorial species, both displaying a robust forelimb, with a shape that improves stability and load transfer in response to the physical resistance imposed by the locomotor environment; and (ii) aquatic and arboreal/semi-arboreal species, with both groups displaying a broad capitulum. This augments the degree of pronation/supination, an important feature for climbing as well as grasping and manipulation ability, behaviors common to aquatic and arboreal species. In summary, our results highlight how musteloids with different locomotor ecologies show differences in the anatomy of their forelimb bones. Yet, functional demands for limb movement through dense media also result in convergence in forelimb long-bone shape between diverse groups, for example, otters and badgers.

Neotropical mammal diversity and the Great American Biotic Interchange: spatial and temporal variation in South America's fossil record

The vast mammal diversity of the Neotropics is the result of a long evolutionary history. During most of the Cenozoic, South America was an island continent with an endemic mammalian fauna. This isolation ceased during the late Neogene after the formation of the Isthmus of Panama, resulting in an event known as the Great American Biotic Interchange (GABI). In this study, we investigate biogeographic patterns in South America, just before or when the first immigrants are recorded and we review the temporal and geographical distribution of fossil mammals during the GABI. We performed a dissimilarity analysis which grouped the faunal assemblages according to their age and their geographic distribution. Our data support the differentiation between tropical and temperate assemblages in South America during the middle and late Miocene. The GABI begins during the late Miocene (~10-7 Ma) and the putative oldest migrations are recorded in the temperate region, where the number of GABI participants rapidly increases after ~5 Ma and this trend continues during the Pleistocene. A sampling bias toward higher latitudes and younger records challenges the study of the temporal and geographic patterns of the GABI.

Morphometric study of phylogenetic and ecologic signals in procyonid (mammalia: carnivora) endocasts

Endocasts provide a proxy for brain morphology but are rarely incorporated in phylogenetic analyses despite the potential for new suites of characters. The phylogeny of Procyonidae, a carnivoran family with relatively limited taxonomic diversity, is not well resolved because morphological and molecular data yield conflicting topologies. The presence of phylogenetic and ecologic signals in the endocasts of procyonids will be determined using three-dimensional geometric morphometrics. Endocasts of seven ingroup species and four outgroup species were digitally rendered and 21 landmarks were collected from the endocast surface. Two phylogenetic hypotheses of Procyonidae will be examined using methods testing for phylogenetic signal in morphometric data. In analyses of all taxa, there is significant phylogenetic signal in brain shape for both the morphological and molecular topologies. However, the analyses of ingroup taxa recover a significant phylogenetic signal for the morphological topology only. These results indicate support for the molecular outgroup topology, but not the ingroup topology given the brain shape data. Further examination of brain shape using principal components analysis and wireframe comparisons suggests procyonids possess more developed areas of the brain associated with motor control, spatial perception, and balance relative to the basal musteloid condition. Within Procyonidae, similar patterns of variation are present, and may be associated with increased arboreality in certain taxa. Thus, brain shape derived from endocasts may be used to test for phylogenetic signal and preliminary analyses suggest an association with behavior and ecology.

Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna

Background

Recent molecular hypotheses suggest that some traditional suprageneric taxa of Characiformes require revision, as they may not constitute monophyletic groups. This is the case for the Bryconidae. Various studies have proposed that this family (considered a subfamily by some authors) may be composed of different genera. However, until now, no phylogenetic study of all putative genera has been conducted.

Results

In the present study, we analyzed 27 species (46 specimens) of all currently recognized genera of the Bryconidae (ingroup) and 208 species representing all other families and most genera of the Characiformes (outgroup). Five genes were sequenced: 16SrRNA, Cytochrome b, recombination activating gene 1 and 2 and myosin heavy chain 6 cardiac muscle. The final matrix contained 4699 bp and was analyzed by maximum likelihood, maximum parsimony and Bayesian analyses. The results show that the Bryconidae, composed of Brycon, Chilobrycon, Henochilus and Salminus, is monophyletic and is the sister group of Gasteropelecidae + Triportheidae. However, the genus Brycon is polyphyletic. Fossil studies suggest that the family originated approximately 47 million years ago (Ma) and that one of the two main lineages persisted only in trans-Andean rivers, including Central American rivers, suggesting a much older origin of Mesoamerican ichthyofauna than previously accepted.

Conclusion

Bryconidae is composed by five main clades, including the genera Brycon, Chilobrycon, Henochilus and Salminus, but a taxonomic review of these groups is needed. Our results point to a possible ancient invasion of Central America, dating about 20.3 ± 5.0 Ma (late Oligocene - early Miocene), to explain the occurrence of Brycon in Central America.

A three-dimensional analysis of the morphological evolution and locomotor behaviour of the carnivoran hind limb

Background

The shape of the appendicular bones in mammals usually reflects adaptations towards different locomotor abilities. However, other aspects such as body size and phylogeny also play an important role in shaping bone design.

We used 3D landmark-based geometric morphometrics to analyse the shape of the hind limb bones (i.e., femur, tibia, and pelvic girdle bones) of living and extinct terrestrial carnivorans (Mammalia, Carnivora) to quantitatively investigate the influence of body size, phylogeny, and locomotor behaviour in shaping the morphology of these bones. We also investigated the main patterns of morphological variation within a phylogenetic context.

Results

Size and phylogeny strongly influence the shape of the hind limb bones. In contrast, adaptations towards different modes of locomotion seem to have little influence. Principal Components Analysis and the study of phylomorphospaces suggest that the main source of variation in bone shape is a gradient of slenderness-robustness.

Conclusion

The shape of the hind limb bones is strongly influenced by body size and phylogeny, but not to a similar degree by locomotor behaviour. The slender-robust “morphological bipolarity” found in bone shape variability is probably related to a trade-off between maintaining energetic efficiency and withstanding resistance to stresses. The balance involved in this trade-off impedes the evolution of high phenotypic variability. In fact, both morphological extremes (slender/robust) are adaptive in different selective contexts and lead to a convergence in shape among taxa with extremely different ecologies but with similar biomechanical demands. Strikingly, this “one-to-many mapping” pattern of evolution between morphology and ecology in hind limb bones is in complete contrast to the “many-to-one mapping” pattern found in the evolution of carnivoran skull shape. The results suggest that there are more constraints in the evolution of the shape of the appendicular skeleton than in that of skull shape because of the strong biomechanical constraints imposed by terrestrial locomotion.

A three-dimensional analysis of morphological evolution and locomotor performance of the carnivoran forelimb

In this study, three-dimensional landmark-based methods of geometric morphometrics are used for estimating the influence of phylogeny, allometry and locomotor performance on forelimb shape in living and extinct carnivorans (Mammalia, Carnivora). The main objective is to investigate morphological convergences towards similar locomotor strategies in the shape of the major forelimb bones. Results indicate that both size and phylogeny have strong effects on the anatomy of all forelimb bones. In contrast, bone shape does not correlate in the living taxa with maximum running speed or daily movement distance, two proxies closely related to locomotor performance. A phylomorphospace approach showed that shape variation in forelimb bones mainly relates to changes in bone robustness. This indicates the presence of biomechanical constraints resulting from opposite demands for energetic efficiency in locomotion -which would require a slender forelimb- and resistance to stress -which would be satisfied by a robust forelimb-. Thus, we interpret that the need of maintaining a trade-off between both functional demands would limit shape variability in forelimb bones. Given that different situations can lead to one or another morphological solution, depending on the specific ecology of taxa, the evolution of forelimb morphology represents a remarkable "one-to-many mapping" case between anatomy and ecology.

Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a "molecular scaffold" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a "Paraná Portal" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.

Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes.

Early Miocene origin and cryptic diversification of South American salamanders

Background

The currently recognized species richness of South American salamanders is surprisingly low compared to North and Central America. In part, this low richness may be due to the salamanders being a recent arrival to South America. Additionally, the number of South American salamander species may be underestimated because of cryptic diversity. The aims of our present study were to infer evolutionary relationships, lineage diversity, and timing of divergence of the South American Bolitoglossa using mitochondrial and nuclear sequence data from specimens primarily from localities in the Andes and upper Amazon Basin. We also estimated time of colonization of South America to test whether it is consistent with arrival via the Panamanian Isthmus, or land bridge connection, at its traditionally assumed age of 3 million years.

Results

Divergence time estimates suggest that Bolitoglossa arrived in South America from Central America by at least the Early Miocene, ca. 23.6 MYA (95% HPD 15.9-30.3 MYA), and subsequently diversified. South American salamanders of the genus Bolitoglossa show strong phylogeographic structure at fine geographic scales and deep divergences at the mitochondrial gene cytochrome b (Cytb) and high diversity at the nuclear recombination activating gene-1 (Rag1). Species often contain multiple genetically divergent lineages that are occasionally geographically overlapping. Single specimens from two southeastern localities in Ecuador are sister to the equatoriana-peruviana clade and genetically distinct from all other species investigated to date. Another single exemplar from the Andes of northwestern Ecuador is highly divergent from all other specimens and is sister to all newly studied samples. Nevertheless, all sampled species of South American Bolitoglossa are members of a single clade that is one of several constituting the subgenus Eladinea, one of seven subgenera in this large genus.

Conclusions

The ancestors of South American salamanders likely arrived at least by the Early Miocene, well before the completion of the Late Pliocene Panamanian land bridge (widely accepted as ca. 3 MYA). This date is in agreement with recent, controversial, arguments that an older, perhaps short-lived, land connection may have existed between South America and present-day Panama 23–25 MYA. Since its arrival in South America, Bolitoglossa has diversified more extensively than previously presumed and currently includes several cryptic species within a relatively small geographic area. Rather than two upper Amazonian species currently recorded for this region, we propose that at least eight should be recognized, although these additional lineages remain to be formally described.