New World porcupines (Erethizontinae) originated in South America and dispersed into North America as part of the Great American Biotic Interchange (GABI) 3-4 million years ago.1 Extant prehensile-tailed porcupines (Coendou) today live in tropical forests of Central and South America.2,3 In contrast, North American porcupines (Erethizon dorsatum) are thought to be ecologically adapted to higher-latitude temperate forests, with a larger body, shorter tail, and diet that includes bark.4,5,6,7 Limited fossils8,9,10,11,12,13 have hindered our understanding of the timing of this ecological differentiation relative to intercontinental dispersal during the GABI and expansion into temperate habitats.14,15,16,17,18 Here, we describe functionally important features of the skeleton of the extinct Erethizon poyeri, the oldest nearly complete porcupine skeleton documented from North America, found in the early Pleistocene of Florida. It differs from extant E. dorsatum in having a long, prehensile tail, grasping foot, and lacking dental specializations for bark gnawing, similar to tropical Coendou. Results from phylogenetic analysis suggest that the more arboreal characteristics found in E. poyeri are ancestral for erethizontines. Only after it expanded into temperate, Nearctic habitats did Erethizon acquire the characteristic features that it is known for today. When combined with molecular estimates of divergence times, results suggest that Erethizon was ecologically similar to a larger species of Coendou when it crossed the Isthmus of Panama by the early Pleistocene. It is likely that the range of this more tropically adapted form was limited to a continuous forested biome that extended from South America through the Gulf Coast.

Determining if ecological communities are saturated (have a limit to the number of species they can support) has important implications for understanding community assembly, species invasions, and climate change. However, previous studies have generally been limited to short time frames that overlook extinction debt and have not explicitly considered how functional trait diversity may mediate patterns of community saturation. Here, we combine data from biodiversity surveys with functional and phylogenetic data to explore if the colonisation events after the Great American Biotic Interchange (closure of the Panamanian Isthmus) resulted in increases in species richness of communities of the snake family Dipsadidae. We determined the number and the direction of dispersal events between Central and South America by estimating ancestral areas based on a Bayesian time-calibrated phylogenetic analysis. We then evaluated whether variation in community saturation was mediated by the functional similarity of six traits for the resident and colonizing snakes and/or local environmental conditions. We found that colonised communities did not support more species than those that were not colonised. Moreover, we did not find an association between the functional diversity across sites and whether they were colonised by members from the lineages dispersing across the Isthmus or not. Instead, variation in species richness was predicted best by covariates such as time since colonisation and local environment. Taken together, our results suggest that snake communities of the Dipsadidae across the neotropics are saturated. Moreover, our research highlights two important factors to consider in studies of community saturation: extinction debt and the functional differences and similarities in species\' ecological roles.
Determinar si las comunidades ecológicas están saturadas (si tienen un límite en el número de especies que pueden albergar) tiene importantes implicaciones para entender el ensamblaje de comunidades, las invasiones de especies y el cambio climático. Sin embargo, los estudios previos en esta área se han limitado generalmente a marcos temporales cortos, ignorando el concepto de deuda de extinción y no considerando explícitamente cómo la diversidad de rasgos funcionales puede mediar en los patrones de saturación de las comunidades. En este trabajo combinamos datos publicados de muestreos de campo con datos funcionales y filogenéticos para explorar si los eventos de colonización después del Gran Intercambio Biótico Americano (ocurrido con el cierre del istmo de Panamá) resultaron en aumentos en la riqueza de especies de las comunidades de la familia de serpientes Dipsadidae. Determinamos el número y la dirección de los eventos de dispersión entre América Central y América del Sur mediante la estimación de áreas ancestrales basada en un análisis filogenético Bayesiano calibrado en el tiempo. Luego evaluamos si la variación en la saturación de las comunidades estaba mediada por la similitud funcional de seis rasgos para las serpientes residentes y colonizadoras y/o por las condiciones ambientales locales. Encontramos que las comunidades colonizadas no contienen más especies que aquellas que no fueron colonizadas. Además, no encontramos ninguna relación entre la diversidad funcional de los sitios considerados y el hecho de que estuvieran colonizados o no por miembros de los linajes que se dispersaron a través del Istmo. En cambio, la variación en la riqueza de especies se predijo mejor por covariantes como el tiempo transcurrido desde la colonización y el clima local. En conjunto, nuestros resultados sugieren que las comunidades de Dipsadidae a lo largo del neotrópico están saturadas. Además, nuestra investigación destaca dos factores importantes a considerar en los estudios de saturación de comunidades: la existencia de una deuda de extinción y las diferencias y similitudes funcionales en los papeles ecológicos de las especies.

Although there is general consensus that sampling of multiple genetic loci is critical in accurate reconstruction of species trees, the exact numbers and the best types of molecular markers remain an open question. In particular, the phylogenetic utility of sex-linked loci is underexplored. Here, we sample all species and 70% of the named diversity of the New World wren genus Campylorhynchus using sequences from 23 loci, to evaluate the effects of linkage on efficiency in recovering a well-supported tree for the group. At a tree-wide level, we found that most loci supported fewer than half the possible clades and that sex-linked loci produced similar resolution to slower-coalescing autosomal markers, controlling for locus length. By contrast, we did find evidence that linkage affected the efficiency of recovery of individual relationships; as few as two sex-linked loci were necessary to resolve a selection of clades with long to medium subtending branches, whereas 4-6 autosomal loci were necessary to achieve comparable results. These results support an expanded role for sampling of the avian Z chromosome in phylogenetic studies, including target enrichment approaches. Our concatenated and species tree analyses represent significant improvements in our understanding of diversification in Campylorhynchus, and suggest a relatively complex scenario for its radiation across the Miocene/Pliocene boundary, with multiple invasions of South 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.

American amphitropical disjunction (AAD) is an important but understudied New World biogeographic pattern in which related plants occur in extratropical North America and South America, but are absent in the intervening tropics. Subtribe Amsinckiinae (Boraginaceae) is one of the richest groups of plants displaying the AAD pattern. Here, we infer a time-calibrated molecular phylogeny of the group to evaluate the number, timing, and directionality of AAD events, which yields generalizable insights into the mechanism of AAD.
We perform a phylogenomic analysis of 139 samples of subtribe Amsinckiinae and infer divergence times using two calibration schemes: with only fossil calibrations and with fossils plus a secondary calibration from a recent family level analysis. Biogeographic analysis was performed in the R package BioGeoBEARS.
We document 18 examples of AAD in the Amsinckiinae. Inferred divergence times of these AAD examples were strongly asynchronous, ranging from Miocene (17.1 million years ago [Ma]) to Pleistocene (0.33 Ma), with most (12) occurring <5 Ma. Four events occurred 10-5 Ma, during the second rise of the Andes. All AAD examples had a North America to South America directionality.
Second only to the hyperdiverse Poaceae in number of documented AAD examples, the Amsinckiinae is an ideal system for the study of AAD. Asynchronous divergence times support the hypothesis of long-distance dispersal by birds as the mechanism of AAD in the subtribe and more generally. Further comparative phylogenomic studies may permit biogeographic hypothesis testing and examination of the relationship between AAD and fruit morphology, reproductive biology, and ploidy.

O\'Dea et al. challenged the inference that the Isthmus of Panama has been in place for the last 10 million years or more and from \"an exhaustive review and reanalysis of geological, paleontological, and molecular records,\" they argued for a \"formation of the Isthmus of Panama sensu stricto around 2.8 Ma.\" I review environmental changes since ~5 Ma throughout Earth, and I argue that environmental changes in the Central American-Caribbean region have been part of a concurrent, worldwide phenomenon that requires a global, not local, explanation. Accordingly, evidence of environmental change from the Central American-Caribbean region does not implicate the emergence of the Isthmus of Panama.

Female army ants cannot fly, making them very poor dispersers across water barriers. This dependence on terrestrial corridors motivated the investigation by Winston et al. (), published in this issue of Molecular Ecology, into the role of Panamanian isthmus formation in the diversification of Eciton army ants. Complete closure of this isthmus occurred around three million years ago (3 Ma), but it has also been hypothesized that earlier, temporary land connections facilitated additional colonization events between South and Central America over the past 13 million years or more. The phylogenomic and population genomic analyses by Winston et al. () uncovered multiple incursions of Eciton lineages into Central America between 4 and 7 Ma. Their study contributes to a growing body of evidence arguing that transitory land bridges predating 3 Ma supported substantial intercontinental biotic exchange.

The emergence of the Isthmus of Panama is one of the most important events in recent geological history, yet its timing and role in fundamental evolutionary processes remain controversial. While the formation of the isthmus was complete around 3 million years ago (Ma), recent studies have suggested prior intercontinental biotic exchange. In particular, the possibility of early intermittent land bridges facilitating colonization constitutes a potential mechanism for speciation and colonization before full closure of the isthmus. To test this hypothesis, we employed genomic methods to study the biogeography of the army ant genus Eciton, a group of keystone arthropod predators in Neotropical rainforests. Army ant colonies are unable to disperse across water and are therefore ideally suited to study the biogeographic impact of land bridge formation. Using a reduced representation genome sequencing approach, we show that all strictly Central American lineages of Eciton diverged from their respective South American sister lineage between 4 and 7 Ma, significantly prior to the complete closure of the isthmus. Furthermore, three of the lineage pairs form extensive and coincident secondary contact zones in Costa Rica and Nicaragua, with no evidence of gene flow. Such a discrete and repeated biogeographic pattern indicates at least two waves of army ant dispersal into Central America that were separated by significant genetic divergence times. Thus, by integrating phylogenomic, population genomic and geographic evidence, we show that early colonization of Central America across the emerging Isthmus of Panamá drove parallel speciation in Eciton army ants.

The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos ornatus), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears (Tremarctos), South American short-faced bears (Arctotherium) and North American short-faced bears (Arctodus) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears (Arctodus and Arctotherium), potentially as an adaptation to dominate competition for megafaunal carcasses.

Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4-386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset reveals that the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6-6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.