Revisiting the Great American Biotic Interchange through analyses of amphitropical bees

The Great American Biotic Interchange (GABI) is zoogeographic event characterized by the exchange of taxa between North and South America, typically associated with the rise of the Isthmus of Panama in the late Pliocene. Recent geologic evidence suggests the connections between North and South America may be much older, and that the interchange of organisms between the two continents could have therefore happened much earlier than 3 Ma. Most of the research investigating the GABI has come from tropical vertebrate taxa; little work has been done on invertebrates or on non‐tropical species. To investigate how the GABI shaped the distribution of arid‐adapted species, particularly those with amphitropical distributions (i.e. taxa found in South and North American xeric regions yet absent from the tropics), we examine the historical biogeography of the bee genus Diadasia using a hypothesis of Diadasia phylogenetic relationships. Nuclear and mitochondrial genetic loci are used to reconstruct a phylogeny of Diadasia, which is then used to estimate divergence dates and reconstruct ancestral area relationships. Our analyses suggest the divergence between North and South American Diadasia species occurred between 20.5 and 15 Ma, long before the formation of the Isthmus of Panama. This study is the first to show a Miocene connection for an amphitropically‐distributed insect group. It suggests that the biotic connection between continents is more complicated than previously thought and may have initiated long before the late Pliocene.     

Domestication of the neotropical tree Chrysophyllum cainito from a geographically limited yet genetically diverse gene pool in Panama

Species in the early stages of domestication, in which wild and cultivated forms co‐occur, provide important opportunities to develop and test hypotheses about the origins of crop species. Chrysophyllum cainito (Sapotaceae), the star apple or caimito, is a semidomesticated tree widely cultivated for its edible fruits; it is known to be native to the neotropics, but its precise geographic origins have not been firmly established. Here, we report results of microsatellite marker analyses supporting the hypothesis that the center of domestication for caimito was the Isthmus of Panama, a region in which few crop species are believed to have originated, despite its importance as a crossroads for the dispersal of domesticated plants between North and South America. Our data suggest that caimito was domesticated in a geographically restricted area while incorporating a diverse gene pool. These results refute the generally accepted Antillean origin of caimito, as well as alternative hypotheses that the species was domesticated independently in the two areas or over a broad geographic range including both. Human‐mediated dispersal from Panama to the north and east was accompanied by strong reductions in both genotypic and phenotypic diversity. Within Panama, cultivated and wild trees show little neutral genetic divergence, in contrast to striking phenotypic differentiation in fruit and seed traits. In addition to providing a rare example of data that support the hypothesis of a narrow geographic origin on the Isthmus of Panama for a now widespread cultivated plant species, this study is one of the first investigations of the origins of an edible species of the large pantropical family Sapotaceae.     

The Great American Biotic Interchange in frogs: multiple and early colonization of Central America by the South American genus Pristimantis (Anura: Craugastoridae)

The completion of the land bridge between North and South America approximately 3.5-3.1 million years ago (Ma) initiated a tremendous biogeographic event called the Great American Biotic Interchange (GABI), described principally from the mammalian fossil record. The history of biotic interchange between continents for taxonomic groups with poor fossil records, however, is not well understood. Molecular and fossil data suggest that a number of plant and animal lineages crossed the Isthmus of Panama well before 3.5 Ma, leading biologists to speculate about trans-oceanic dispersal mechanisms. Here we present a molecular phylogenetic analysis of the frog genus Pristimantis based on 189 individuals of 137 species, including 71 individuals of 31 species from Panama and Colombia. DNA sequence data were obtained from three mitochondrial (COI, 12S, 16S) and two nuclear (RAG-1 and Tyr) genes, for a total of 4074 base pairs. The resulting phylogenetic hypothesis showed statistically significant conflict with most recognized taxonomic groups within Pristimantis, supporting only the rubicundus Species Series, and the Pristimantis myersi and Pristimantis pardalis Species Groups as monophyletic. Inference of ancestral areas based on a likelihood model of geographic range evolution via dispersal, local extinction, and cladogenesis (DEC) suggested that the colonization of Central America by South American Pristimantis involved at least 11 independent events. Relaxed-clock analyses of divergence times suggested that at least eight of these invasions into Central America took place prior to 4 Ma, mainly in the Miocene. These findings contribute to a growing list of molecular-based biogeographic studies presenting apparent temporal conflicts with the traditional GABI model.     

A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America

Several recent studies have suggested that a substantial portion of today's plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than vicariance, but more data are needed to substantiate this claim. Guatteria (Annonaceae) is, with 265 species, the third largest genus of Neotropical trees after Inga (Fabaceae) and Ocotea (Lauraceae), and its widespread distribution and frequent occurrence makes the genus an excellent model taxon to study diversification patterns. This study reconstructed the phylogeny of Guatteria and inferred three major biogeographical events in the history of the genus: (1) a trans-oceanic Miocene migration from Central into South America before the closing of the Isthmus of Panama; (2) a major diversification of the lineage within South America; and (3) several migrations of South American lineages back into Central America via the closed Panamanian land bridge. Therefore, Guatteria is not an Amazonian centred-genus sensu Gentry but a major Miocene diversification that followed its dispersal into South America. This study provides further evidence that migration into the Neotropics was an important factor in the historical assembly of its biodiversity. Furthermore, it is shown that phylogenetic patterns are comparable to those found in Ocotea and Inga and that a closer comparison of these genera is desirable.     

The Central American Isthmus: Implications for Intraspecific Phylogeny and Biogeography of a Pantropical Green Alga

An intraspecific phylogenetic study was undertaken to resolve the evolutionary relationship of isolates of the green alga Phyllodictyon anastomosans (Harv.) Kraft et Wynne that occur on Atlantic and Pacific coasts of the Central American Isthmus. Patterns of vicariance related to the emergence of the Central American Isthmus were evident, but numerous examples of recent trans‐oceanic and trans‐isthmian dispersal obscured the underlying pattern. This study, one of the first studies to assess the impact of the emergence of the Central American Isthmus in seaweed phylogeography, provided an ideal opportunity to estimate the rate of sequence evolution using a single time point. Using this newly calibrated molecular clock the timing of an historical introduction across the isthmus is shown to be concordant with a shallow water breach of the isthmus dated at approximately 2.3–2.0 million years ago. This work contributes to a growing body of literature that suggests marine algae are fairly successful at dispersing over long distances in recent times.     

Early and dynamic colonization of Central America drives speciation in Neotropical army ants

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.     

Phytogeography of the trees of the Osa Peninsula,Costa Rica

A phytogeographic analysis of the distributions of 454 species of trees native to the Osa Peninsula in 22 families revealed that 4.8% of the species are endemic to the Osa Peninsula and the adjacent mainland of Costa Rica. However, nearly one-fourth of the species might be regionally endemic to Central-South Mesoamerica (Costa Rica, Nicaragua, and Panama). Our sample suggests that 53.6% of the species occur in some part of Mesoamerica and sometimes range into northwestern South America, and that 44.5% of the species have wide distributions throughout tropical America. There is a strong affinity with the flora of northwestern South America, with 46.2% of the species on the Osa also found there. In addition, 50.6% of the tree species on the Osa occur on both the Atlantic and Pacific slopes of Central America or, if they reach South America, are sometimes found on both sides of the Andes. Major contributions to the tree flora of the Osa have been made by species arriving in the Osa by 1) dispersal from South and North America to islands in proto Central America before the formation of a dry-land connection between the two continents, and 2) migration from South America and North America after the closure of the Panamanian isthmus was made. This analysis demonstrates the importance of the Osa as a regional refuge for protecting species with distributions limited to the Osa and parts of Panama, Costa Rica, or Nicaragua. The Osa is also important because it harbors the last expanse of tropical wet forest on the Pacific slope of Central America large enough to ensure the survival of the Central American populations of widely distributed plants and animals.     

Neogene sloth assemblages (Mammalia,Pilosa) of the Cocinetas Basin (La Guajira,Colombia): implications for the Great American Biotic Interchange

We describe sloth assemblages from the Cocinetas Basin (La Guajira peninsula, Colombia), found in the Neogene Castilletes and Ware formations, located in northernmost South America, documenting otherwise poorly known biotas. The tentative referral of a specimen to a small megatherioid sloth, Hyperleptus?, from the early–middle Miocene Castilletes Formation, suggests affinities of this fauna with the distant Santa Cruz Formation and documents a large latitudinal distribution for this taxon. The late Pliocene Ware Formation is much more diverse, with five distinct taxa representing every family of ‘ground sloths’. This diversity is also remarkable at the ecological level, with sloths spanning over two orders of magnitude of body mass and probably having different feeding strategies. Being only a few hundred kilometres away from the Isthmus of Panama, and a few hundred thousand years older than the classically recognized first main pulse of the Great American Biotic interchange (GABI 1), the Ware Formation furthermore documents an important fauna for the understanding of this major event in Neogene palaeobiogeography. The sloths for which unambiguous affinities were recovered are not closely related to the early immigrants found in North America before GABI 1.     

Biogeographically dynamic genetic structure bridging two continents in the monotypic Central American rodent Ototylomys phyllotis

Central America is an ideal region in which to study patterns of historical divergence and population genetic differentiation, because of its extraordinarily dynamic biogeographical, tectonic, and climatic history. The rodent Ototylomys phyllotis is the only extant species of the genus Ototylomys and is distributed within this region from the Isthmus of Tehuantepec, Mexico, to central Costa Rica, offering an excellent opportunity to study spatial and temporal patterns of population structure of the species and to explain the ecological and evolutionary processes responsible for those patterns. We estimated the genetic diversity and structure within and between populations of O. phyllotis, times of divergence, and migration patterns using mitochondrial DNA and a comprehensive combination of phylogenetic and phylogeographical computational analyses. Our results support monophyly of the genus Ototylomys. We identified three major phylogeographical lineages within O. phyllotis that are linked to its diversification and coincide with the main geological features that shaped Middle America. The origin of the genus was before 3.35 Mya, prior to the Great American Biotic Interchange (GABI), and its initial occurrence was near the centre of its current distribution (Honduras/El Salvador), from which it later spread (3.20–2.84 Mya) following a series of GABI pulses. The species showed an initial northward dispersal to the Chiapas and Guatemala highlands (2.27 Mya) followed by diversification. A later dispersal (1.82 Mya) occurred toward both the south (Nicaragua, Costa Rica) and the north (Belize). The Yucatan peninsula was colonized (0.8 Mya) by individuals from Belize. Extremely high radiation and range expansion occurred throughout the entire range, the highest of which was in the Yucatan peninsula (0.125 Mya). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 593–610.     

Chloroplast DNA phylogeography of a distylous shrub (Palicourea padifolia, Rubiaceae) reveals past fragmentation and demographic expansion in Mexican cloud forests

Several phylogeographic studies in northern Mesoamerica have examined the influence of Pleistocene glaciations on the genetic structure of temperate tree species with their southern limit by the contact zone between species otherwise characteristic of North or South America, but few have featured plant species that presumably colonized northern Mesoamerica from South America. A phylogeographical study of Palicourea padifolia, a fleshy-fruited, bird dispersed distylous shrub, was conducted to investigate genetic variation at two chloroplast regions (trnS-trnG and rpl32-trnL) across cloud forest areas to determine if such patterns are consistent with the presence of Pleistocene refugia and/or with the historical fragmentation of the Mexican cloud forests. We conducted population and spatial genetic analyses as well as phylogenetic and isolation with migration analyses on 122 individuals from 22 populations comprising the distribution of P. padifolia in Mexico to gain insight of the evolutionary history of these populations. Twenty-six haplotypes were identified after sequencing 1389 bp of chloroplast DNA. These haplotypes showed phylogeographic structure (N(ST) = 0.508, G(ST) = 0.337, N(ST) > G(ST), P < 0.05), including a phylogeographic break at the Isthmus of Tehuantepec, with private haplotypes at either side of the isthmus, and a divergence time of the split in the absence of gene flow dating back c. 309,000-103,000 years ago. The patterns of geographic structure found in this study are consistent with past fragmentation and demographic range expansion, supporting the role of the Isthmus of Tehuantepec as a biogeographical barrier in the dispersal of P. padifolia. Our data suggest that P. padifolia populations were isolated throughout glacial cycles by the Isthmus of Tehuantepec, accumulating genetic differences due to the lack of migration across the isthmus in either direction, but the results of our study are not consistent with the existence of the previously proposed Pleistocene refugia for rain forest plant species in the region.     

Phylogeny of species of Sciadicleithrum (Monogenoidea: Ancyrocephalinae), and their historical biogeography in the neotropics

The phylogenetic relationships and historical biogeography of species of Sciadicleithrum parasitizing Neotropical cichlid fishes were studied. Hypotheses were: Did the presence of Sciadicleithrum species in southeast Mexico (SM) and Central America (CA) result from early dispersal of cichlid species from South America (SA) to the north via the Antilles during the Tertiary (24 million years ago [mya]), or did it occur after emergence of the Panama Isthmus in the Pleistocene (2-5 mya)? The Sciadicleithrum phylogeny was based on 19 morphological transformation series, with species of Gussevia and Cichlidogyrus as outgroups. The most parsimonious cladogram had a 40% consistency index, with one clade including all the species of Sciadicleithrum from SA and all but one of those from CA and another with all the Sciadicleithrum species from SM and S. maculicaudae from CA. Results support the late dispersal hypothesis following emergence of the Panama Isthmus. Fifteen species of Sciadicleithrum parasitize 13 cichlid species from SA and CA. In contrast, only 4 species of Sciadicleithrum infect 14 cichlid species from SM. Parasite speciation appears to lag behind host speciation, with 2 equally possible explanations: loss of parasite species and host switching.     

The profound influence of the Late Pliocene Panamanian uplift on the exchange,diversification, and distribution of New World birds

Separated throughout most of the Cenozoic era, North and South America were joined during the mid‐Pliocene when the uplift of Panama formed a land bridge between these two continents. The fossil record indicates that this connection allowed an unprecedented degree of inter‐continental exchange to occur between unique, previously isolated biotic assemblages, a phenomenon now recognized as the “Great American Biotic Interchange”. However, a relatively poor avian fossil record has prevented our understanding the role of the land bridge in shaping New World avian communities. To address the question of avian participation in the GABI, we compiled 64 avian phylogenetic studies and applied a relaxed molecular clock to estimate the timing of trans‐isthmus diversification events. Here, we show that a significant pulse of avian interchange occurred in concert with the isthmus uplift. The avian exchange was temporally consistent with the well understood mammalian interchange, despite the presumed greater vagility of birds. Birds inhabiting a variety of habitats and elevational zones responded to the newly available corridor. Within the tropics, exchange was equal in both directions although between extratropical and tropical regions it was not. Avian lineages with Nearctic origins have repeatedly invaded the tropics and radiated throughout South America; whereas, lineages with South American tropical origins remain largely restricted to the confines of the Neotropical region. This previously unrecognized pattern of asymmetric niche conservatism may represent an important and underappreciated contributor to the latitude diversity gradient.     

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi‐taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional‐scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low‐structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long‐distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene–Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in‐depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.     

Historical and present distribution of coyote (Canis latrans) in Mexico and Central America

Aim Coyote (Canis latrans) distribution in Mexico and Central America has expanded recently reaching the Yucatan peninsula, Belize and Panama, probably promoted by deforestation of tropical areas. Historically, the southern distribution of coyotes prior to European settlement in America was described as reaching only as far south as central Mexico and that introduction of livestock favoured migration of coyotes to southern Mexico and Central America. However, coyote fossil records in Central America and Yucatan, as well as observational records of travellers during the sixteenth century suggest that the coyote's arrival to the region was earlier. Because of the uncertainty of past coyote distribution and the possible economic and ecological impacts due to recent range expansion, the objectives of this study were to confirm if paleontological and historical evidence support the hypothesis that the southernmost limit of coyote distribution before the arrival of European settlers was the centre of Mexico, to discuss the possible factors that have influenced historical shifts in coyote distribution, and to model the present distribution of the coyote in Mexico and Central America, determining the areas where they could invade in the near future. Location The research area comprises continental Mexico and the Central American Isthmus countries: Guatemala, Belize, El Salvador, Honduras, Nicaragua, Costa Rica and Panama. Methods The historical distribution (Pleistocene–Early Holocene, Pre‐Columbian, sixteenth to nineteenth centuries and twentieth century) was established from coyote records obtained from museum collections and specialized literature. Present coyote distribution for Mexico and Central America was modelled using the Genetic Algorithms for Rule‐set Prediction (GARP). Results Historical coyote records show that this species was distributed in southern Mexico and Central America during the Pleistocene–Early Holocene, the Pre‐Columbian period, and during the arrival of Europeans in the sixteenth century. Coyote records indicate a continuous range expansion during the twentieth century. Historical advance and regression of tropical forests in southern Mexico and Central America produced by natural and human events such as climatic changes and variation in human densities could help us understand the historical coyote distribution. The modelled present‐day coyote distribution included the north of Belize, the north of Panama, the north of the Yucatan Peninsula and a corridor on the Gulf costal plain of Campeche in Mexico. Also, the model predicted a region north of the Darien in southern Panama as appropriate for the presence of coyotes, although they have not been detected there so far. Main conclusion Coyote records in southern Mexico and Central America during the Pleistocene–Early Holocene, the Pre‐Columbian period, and early arrival of European settlers to the area indicated that coyotes were probably already present there and did not recently disperse from the north of Mexico to the south due to livestock introduction.     

Dispersal of Pleistocene Equus (Family Equidae) into South America and Calibration of GABI 3 Based on Evidence from Tarija,Bolivia

The dispersal of Equus into South America during the Great American Biotic Interchange (GABI) represented a major event for Pleistocene land-mammal age chronology on that continent. It has been argued that this dispersal occurred during the late Pleistocene, ∼0.125 Ma, and it defines the base of the Lujanian South American Land Mammal Age (SALMA). In this scenario, Equus dispersed during the fourth and latest recognized phase of the interchange, i.e., GABI 4. Although Equus was widely distributed in South America during the Pleistocene, only a few localities are calibrated by independent chronostratigraphic data. In this paper, new biostratigraphic evidence documents that Equus occurs from 15 superposed faunal horizons or zones throughout the Tolomosa Formation at Tarija, Bolivia. This biostratigraphic sequence is independently calibrated to occur between ∼0.99 to <0.76 Ma during the middle Pleistocene Ensenadan SALMA and coincident with GABI 3, not GABI 4. Tarija remains the only well calibrated Ensenadan locality at which Equus is found. The new biostratigraphic data presented here are unambiguous and document the earlier (pre-Lujanian) occurrence of this genus in South America. The hypothesized dispersal of the genus Equus into South America at ∼0.125 Ma is no longer supportable in light of the new biostratigraphic evidence presented here. The new data from Tarija thus have continent-wide implications for the origins and biogeography of Equus in South America as well as the calibration of GABI 3.     

Microsatellite DNA and behavioural studies provide evidence of host-mediated speciation in Myzus persicae (Hemiptera: Aphididae)

The fossil record of mammals records a major interchange of northern and southern faunas in the New World, upon closure of the Panamanian isthmus approximately 3 Mya, termed the Great American Biotic Interchange (GABI). Due to their poor preservation in the fossil record, the degree of participation of birds in this interchange remains largely unknown. A phylogeny for wrens of the genus Campylorhynchus (Aves: Passeriformes) was reconstructed using DNA sequences from the mitochondrial control region and cytochrome b gene. This phylogeny, in combination with biogeographical inference and molecular clock methods, allows estimates of the importance of Late Pliocene interchange to the history of the group. Biogeographical reconstructions and divergence date estimates suggest that the genus began diversification in North America prior to closure of the Panamanian isthmus, consistent with a hypothesized North American origin for the family Troglodytidae. These reconstructions are consistent with pre-GABI dispersal of at most a single Campylorhynchus lineage into South America, with subsequent dispersal of additional lineages, probably across the fully formed isthmus. Increased sampling of avian taxa with widespread New World distributions will continue to clarify the timing and direction of continental interchange.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 687–702.     

Biogeographical,ecological and morphological structure in a phylogenetic analysis of Ateleia (Swartzieae,Fabaceae) derived from combined molecular,morphological and chemical data

A phylogenetic analysis of combined morphological, chemical and ITS/5.8S sequence data reveals that species of Ateleia are often more genetically than morphologically divergent, and that species thought to be most closely related morphologically are distant relatives within the genus. Ateleia shows niche conservatism, with most species confined to seasonally dry tropical forest in Central America and the Caribbean, and fewer species in the same biome in South America. Four independent transitions to wet forests may have occurred in the genus. The estimated ages of Ateleia lineages spanning Central and South America are either older or younger than the estimated age of closure of the Isthmus of Panama. The older dates clearly suggest that over‐water dispersal is responsible for the distribution of Ateleia that includes the Caribbean Islands. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 39–53.     

Historical biogeography of lowland species of toads (Bufo) across the Trans-Mexican Neovolcanic Belt and the Isthmus of Tehuantepec

Aim In this study, we investigate phylogeographic structure in two different species groups of lowland toads. First, we further investigate strict parapatry of the Pliocene‐vicariant Bufo valliceps/B. nebulifer species pair. Secondly, we test for similar phylogeographic structure in the distantly related toad B. marinus, a species we hypothesize will show a Pleistocene dispersal across the same area. Location The eastern extension of the Trans‐Mexican Neovolcanic Belt (TMNB) contacts the Atlantic Coast in central Veracruz, Mexico. Although it is not a massive structure at this eastern terminus, the TMNB has nonetheless effected vicariance and subsequent speciation in several groups of animals. The Isthmus of Tehuantepec unites the North American continent with Nuclear Central America and is also known to be a biogeographic barrier for many taxa. Methods We use sequence data from two mitochondrial DNA genes (c. 550 base‐pairs (bp) of 16S and c. 420 bp of cyt b) from 58 individuals of the B. valliceps/nebulifer complex, collected from 24 localities. We also present homologous sequence data from 23 individuals of B. marinus, collected from 12 localities. We conduct maximum‐parsimony, maximum‐likelihood and Bayesian analyses to investigate phylogeographic structure. We then use parsimony‐ and likelihood‐based topology tests to assess alternative phylogenetic hypotheses and use a previously calibrated molecular rate of evolution to estimate dates of divergence. Results Our results further define the parapatric contact zone across the TMNB between the Pliocene‐vicariant sister species B. valliceps and B. nebulifer. In contrast, phylogenetic structure among populations of B. marinus across the TMNB is much shallower, suggesting a more recent Pleistocene dispersal in this species. In addition, we found phylogeographic structure associated with the Isthmus of Tehuantepec in both species groups. Main conclusions The existence of a Pliocene–Pleistocene seaway across the Isthmus of Tehuantepec has been controversial. Our data depict clades on either side of the isthmus within two distinct species (B. valliceps and B. marinus), although none of the clades associated with the isthmus, for either species, are reciprocally monophyletic. In the B. valliceps/B. nebulifer complex, the TMNB separation appears to predate the isthmian break, whereas in B. marinus dispersal across the TMNB has occurred subsequent to the presence of a barrier at the Isthmus of Tehuantepec.     

Sigmodontine rodents diversified in South America prior to the complete rise of the Panamanian Isthmus

The extant distribution of sigmodontine rodents encompasses most of the New World, and the majority of the species in this subfamily inhabit South America. Nevertheless, the basal lineages of the Sigmodontinae are distributed in North and Central America, and the fossil record indicates a North American origin. This evidence has produced contentious theories concerning the evolution of these rodents. The dispute usually stems from a disagreement about the way in which sigmodontines reached South America, which was an isolated landmass during most of the Cenozoic. Fundamentally, the debate is associated with the role of Panamanian Isthmus formation and the Great American Biotic Interchange (GABI) in the diversification of the clade. An early hypothesis implies that sigmodontines arrived in South America before the complete rise of the Panamanian Isthmus, whereas a late hypothesis directly correlates the diversification of the lineage with this event. To address this question, we have sequenced nuclear and mitochondrial sequences, as well as the first Sigmodontinae mitochondrial genomes (Akodon montensis and Wiedomys cerradensis) and performed a Bayesian dating analysis. Our results showed that the most recent common ancestor of the subfamily lived at approximately 15 Ma. Although the diversification of sigmodontines was not associated with the complete rise of the Panamanian Isthmus, we cannot exclude the hypothesis that this event played a relevant role in the evolution of the lineage during the Miocene.     

Phylogeographic analysis of the chloroplast DNA variation in wild common bean (Phaseolus vulgaris L.) in the Americas

The wild common bean (Phaseolus vulgaris) is widely but discontinuously distributed from northern Mexico to northern Argentina on both sides of the Isthmus of Panama. Little is known on how the species has reached its current disjunct distribution. In this research, chloroplast DNA polymorphisms in seven non-coding regions were used to study the history of migration of wild P. vulgaris between Mesoamerica and South America. A penalized likelihood analysis was applied to previously published Leguminosae ITS data to estimate divergence times between P. vulgaris and its sister taxa from Mesoamerica, and divergence times of populations within P. vulgaris. Fourteen chloroplast haplotypes were identified by PCR-RFLP and their geographical associations were studied by means of a Nested Clade Analysis and Mantel Tests. The results suggest that the haplotypes are not randomly distributed but occupy discrete parts of the geographic range of the species. The current distribution of haplotypes may be explained by isolation by distance and by at least two migration events between Mesoamerica and South America: one from Mesoamerica to South America and another one from northern South America to Mesoamerica. Age estimates place the divergence of P. vulgaris from its sister taxa from Mesoamerica at or before 1.3 Ma, and divergence of populations from Ecuador-northern Peru at or before 0.6 Ma. As these ages are taken as minimum divergence times, the influence of past events, such as the closure of the Isthmus of Panama and the final uplift of the Andes, on the migration history and population structure of this species cannot be disregarded.