Early Oligocene chinchilloid caviomorphs from Puerto Rico and the initial rodent colonization of the West Indies

Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses

In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes.

Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses

Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches

There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.

Late middle Miocene caviomorph rodents from Tarapoto, Peruvian Amazonia

Miocene deposits of South America have yielded several species-rich assemblages of caviomorph rodents. They are mostly situated at high and mid- latitudes of the continent, except for the exceptional Honda Group of La Venta, Colombia, the faunal composition of which allowed to describe the late middle Miocene Laventan South American Land Mammal Age (SALMA). In this paper, we describe a new caviomorph assemblage from TAR-31 locality, recently discovered near Tarapoto in Peruvian Amazonia (San Martín Department). Based on mammalian biostratigraphy, this single-phased locality is unambiguously considered to fall within the Laventan SALMA. TAR-31 yielded rodent species found in La Venta, such as the octodontoid Ricardomys longidens Walton, 1990 (nom. nud.), the chinchilloids Microscleromys paradoxalis Walton, 1990 (nom. nud.) and M. cribriphilus Walton, 1990 (nom. nud.), or closely-related taxa. Given these strong taxonomic affinities, we further seize the opportunity to review the rodent dental material from La Venta described in the Ph.D. volume of Walton in 1990 but referred to as nomina nuda. Here we validate the recognition of these former taxa and provide their formal description. TAR-31 documents nine distinct rodent species documenting the four extant superfamilies of Caviomorpha, including a new erethizontoid: Nuyuyomys chinqaska gen. et sp. nov. These fossils document the most diverse caviomorph fauna for the middle Miocene interval of Peruvian Amazonia to date. This rodent discovery from Peru extends the geographical ranges of Ricardomys longidens, Microscleromys paradoxalis, and M. cribriphilus, 1,100 km to the south. Only one postcranial element of rodent was unearthed in TAR-31 (astragalus). This tiny tarsal bone most likely documents one of the two species of Microscleromys and its morphology indicates terrestrial generalist adaptations for this minute chinchilloid.

An Early Oligocene age for the oldest known monkeys and rodents of South America

The Santa Rosa fossil locality in eastern Perú produced the first Paleogene vertebrate fauna from the Amazon Basin, including the oldest known monkeys from South America. This diverse paleofauna was originally assigned an Eocene age based largely on the stage of evolution of the site's caviomorph rodents and marsupials. Here, we present detrital zircon dates that indicate that the maximum composite age of Santa Rosa is 29.6 ± 0.08 Ma (Lower Oligocene), although several zircons from Santa Rosa date to the Upper Oligocene. The first appearance datum for Caviomorpha in South America is purported to be the CTA-27 site in the Contamana region of Perú, which is hypothesized to be ∼41 Ma (Middle Eocene) in age. However, the presence of the same caviomorph species and/or genera at both CTA-27 and at Santa Rosa is now difficult to reconcile with a >11-My age difference. To further test the Middle Eocene age estimate for CTA-27, we ran multiple Bayesian tip-dating analyses of Caviomorpha, treating the ages of all Paleogene species from Perú as unknown. These analyses produced mean age estimates for Santa Rosa that closely approximate the maximum 29.6 ± 0.08 Ma composite date provided by detrital zircons, but predict that CTA-27 is much younger than currently thought (∼30 Ma). We conclude that the ∼41 Ma age proposed for CTA-27 is incorrect, and that there are currently no compelling Eocene records of either rodents or primates in the known fossil record of South America.

Comprehensive total evidence phylogeny of chinchillids (Rodentia, Caviomorpha): Cheek teeth anatomy and evolution

Rodents are the most diverse order of extant mammals, and caviomorph rodents, or New World hystricognaths, have a remarkable morphological disparity and a long fossil record that begins in the Eocene. Chinchilloidea is a poorly understood clade within Caviomorpha, from an evolutionary and phylogenetic perspective. It includes the extant families Chinchillidae and Dinomyidae, the extinct Neoepiblemidae and Cephalomyidae, and several extinct chinchilloids without a clear phylogenetic position, like Eoincamys, Borikenomys, Chambiramys, Ucayalimys, Incamys, Saremmys, Garridomys and Scotamys. The family Chinchillidae includes the extant Chinchilla and Lagidium, grouped in Chinchillinae, and the only living Lagostominae, Lagostomus maximus. Among extinct chinchillids, Eoviscaccia (early Oligocene-early Miocene of Argentina, Bolivia and Chile), Prolagostomus (early-middle Miocene of Argentina, Bolivia and Chile) and Pliolagostomus (early-middle Miocene of Argentina) are the only genera originally described as members of the family. Based on the study of specimens with unworn or little-worn cheek teeth, belonging to extinct and extant taxa, we propose homologies of the cheek teeth structures and perform a combined molecular and morphological phylogenetic analysis including extinct and extant taxa of all families of Chinchilloidea and all genera of Chinchillidae. Our phylogenetic analysis recovered three major lineages in the evolutionary history of Chinchilloidea. The first major lineage is composed of the extant taxa Chinchilla, Lagidium and Lagostomus, and the extinct genera Eoviscaccia, Prolagostomus, Pliolagostomus, Garridomys, Incamys, Loncolicu and Saremmys. Cephalomyid (Banderomys, Cephalomys, Litodontomys, Soriamys) and neoepiblemid (Neoepiblema, Perimys, Phoberomys, Scotamys) genera are part of the second major lineage, while dinomyids such as Dinomys, Drytomomys, Scleromys, 'Scleromys' and Tetrastylus constitute the third major lineage within Chinchilloidea. The phylogenetic position of some taxa previously considered as incertae sedis chinchilloids or without a clear suprageneric group (i.e. Incamys, Saremmys, Garridomys and Loncolicu) show that they belong to pan-Chinchillidae and conform the stem Chinchillidae along with Eoviscaccia. The euhypsodont crown Chinchillidae includes the living subfamilies Chinchillinae and Lagostominae. Dinomyidae and Eoincamys pascuali are recovered as the sisters of a major clade composed by 'Cephalomyidae'+Neopiblemidae and pan-Chinchillidae, and Chambiramys sylvaticus occupies a basal position to the same clade. Four major radiation events are identified in the evolutionary history of Chinchilloidea. The analysis of new morphological characters linked with molecular evidence as well as the addition of taxa of uncertain or unstable phylogenetic position or not considered in previous studies allowed us resolve part of the relationships within Chinchilloidea, particularly that of Chinchillidae, supporting preceding morphological hypotheses.

Eocene intra-plate shortening responsible for the rise of a faunal pathway in the northeastern Caribbean realm

Intriguing latest Eocene land-faunal dispersals between South America and the Greater Antilles (northern Caribbean) has inspired the hypothesis of the GAARlandia (Greater Antilles Aves Ridge) land bridge. This landbridge, however, should have crossed the Caribbean oceanic plate, and the geological evolution of its rise and demise, or its geodynamic forcing, remain unknown. Here we present the results of a land-sea survey from the northeast Caribbean plate, combined with chronostratigraphic data, revealing a regional episode of mid to late Eocene, trench-normal, E-W shortening and crustal thickening by ∼25%. This shortening led to a regional late Eocene–early Oligocene hiatus in the sedimentary record revealing the location of an emerged land (the Greater Antilles-Northern Lesser Antilles, or GrANoLA, landmass), consistent with the GAARlandia hypothesis. Subsequent submergence is explained by combined trench-parallel extension and thermal relaxation following a shift of arc magmatism, expressed by a regional early Miocene transgression. We tentatively link the NE Caribbean intra-plate shortening to a well-known absolute and relative North American and Caribbean plate motion change, which may provide focus for the search of the remaining connection between ‘GrANoLA’ land and South America, through the Aves Ridge or Lesser Antilles island arc. Our study highlights the how regional geodynamic evolution may have driven paleogeographic change that is still reflected in current biology.

The earliest record of Caribbean frogs: a fossil coquí from Puerto Rico

The nearly 200 species of direct-developing frogs in the genus Eleutherodactylus (the Caribbean landfrogs, which include the coquís) comprise an important lineage for understanding the evolution and historical biogeography of the Caribbean. Time-calibrated molecular phylogenies provide indirect evidence for the processes that shaped the modern anuran fauna, but there is little direct evidence from the fossil record of Caribbean frogs about their distributions in the past. We report a distal humerus of a frog from the Oligocene (approx. 29 Ma) of Puerto Rico that represents the earliest known fossil frog from any Caribbean island. Based on its prominent rounded distal humeral head, distally projecting entepicondyle, and reduced ectepicondyle, we refer it to the genus Eleutherodactylus. This fossil provides additional support for an early arrival of some groups of terrestrial vertebrates to the Greater Antilles and corroborates previous estimates based on molecular phylogenies suggesting that this diverse Caribbean lineage was present in the islands by the mid-Cenozoic.