Neutral and functionally important genes shed light on phylogeography and the history of high‐altitude colonization in a widespread New World duck

Phylogeographic studies often infer historical demographic processes underlying species distributions based on patterns of neutral genetic variation, but spatial variation in functionally important genes can provide additional insights about biogeographic history allowing for inferences about the potential role of adaptation in geographic range evolution. Integrating data from neutral markers and genes involved in oxygen (O₂)‐transport physiology, we test historical hypotheses about colonization and gene flow across low‐ and high‐altitude regions in the Ruddy Duck (Oxyura jamaicensis), a widely distributed species in the New World. Using multilocus analyses that for the first time include populations from the Colombian Andes, we also examined the hypothesis that Ruddy Duck populations from northern South America are of hybrid origin. We found that neutral and functional genes appear to have moved into the Colombian Andes from both North America and southern South America, and that high‐altitude Colombian populations do not exhibit evidence of adaptation to hypoxia in hemoglobin genes. Therefore, the biogeographic history of Ruddy Ducks is likely more complex than previously inferred. Our new data raise questions about the hypothesis that adaptation via natural selection to high‐altitude conditions through amino acid replacements in the hemoglobin protein allowed Ruddy Ducks to disperse south along the high Andes into southern South America. The existence of shared genetic variation with populations from both North America and southern South America as well as private alleles suggests that the Colombian population of Ruddy Ducks may be of old hybrid origin. This study illustrates the breadth of inferences one can make by combining data from nuclear and functionally important loci in phylogeography, and underscores the importance of complete range‐wide sampling to study species history in complex landscapes.     

The Geographic Distribution of a Tropical Montane Bird Is Limited by a Tree: Acorn Woodpeckers (Melanerpes formicivorus) and Colombian Oaks (Quercus humboldtii) in the Northern Andes

Species distributions are limited by a complex array of abiotic and biotic factors. In general, abiotic (climatic) factors are thought to explain species’ broad geographic distributions, while biotic factors regulate species’ abundance patterns at local scales. We used species distribution models to test the hypothesis that a biotic interaction with a tree, the Colombian oak (Quercus humboldtii), limits the broad-scale distribution of the Acorn Woodpecker (Melanerpes formicivorus) in the Northern Andes of South America. North American populations of Acorn Woodpeckers consume acorns from Quercus oaks and are limited by the presence of Quercus oaks. However, Acorn Woodpeckers in the Northern Andes seldom consume Colombian oak acorns (though may regularly drink sap from oak trees) and have been observed at sites without Colombian oaks, the sole species of Quercus found in South America. We found that climate-only models overpredicted Acorn Woodpecker distribution, suggesting that suitable abiotic conditions (e.g. in northern Ecuador) exist beyond the woodpecker’s southern range margin. In contrast, models that incorporate Colombian oak presence outperformed climate-only models and more accurately predicted the location of the Acorn Woodpecker’s southern range margin in southern Colombia. These findings support the hypothesis that a biotic interaction with Colombian oaks sets Acorn Woodpecker’s broad-scale geographic limit in South America, probably because Acorn Woodpeckers rely on Colombian oaks as a food resource (possibly for the oak’s sap rather than for acorns). Although empirical examples of particular plants limiting tropical birds’ distributions are scarce, we predict that similar biotic interactions may play an important role in structuring the geographic distributions of many species of tropical montane birds with specialized foraging behavior.     

A south-to-north biogeographic hypothesis for Andean speciation: evidence from the lizard genus Proctoporus (Reptilia, Gymnophthalmidae)

Aim The lizard genus Proctoporus Tschudi, 1845 was used as a model to test the South‐to‐North Speciation Hypothesis (SNSH) for species groups occurring in the Andes Mountains of South America. This hypothesis proposes that speciation of high Andean taxa followed a south‐to‐north pattern, generally coinciding with the progression of final uplift of the Andes. According to SNSH, a phylogenetic hypothesis of relationships of a taxonomic group occurring in the high Andes would show a branching pattern in which the southernmost species diverged first, followed by the more northern species, and so on in a northerly pattern. Location The central and northern Andes Mountains in South America. Methods A phylogenetic hypothesis was reconstructed for all species of the lizard genus Proctoporus by examining the external morphology of 341 individuals. This phylogeny was then examined to determine monophyly of the genus, distribution patterns of species groups, and congruence with SNSH. Results The genus Proctoporus did appear to be monophyletic and, therefore, it was valid to use this group to assess SNSH. The southernmost species were found to be the most basal, which was consistent with SNSH. The species occurring in the northern Andes did not exactly match the SNSH prediction. The Venezuelan and Trinidadian species did appear to be highly derived, as predicted by the hypothesis, but the Ecuadorian and Colombian species did not form a particular pattern in relation to the hypothesis. Main conclusions The SNSH does appear to have predictive power with regard to large‐scale distribution patterns. The finer‐scale patterns of speciation in the Andes, however, appear to be a more complex phenomenon that cannot be fully explained by a simple hypothesis. It is important to have a testable hypothesis in hand with which to compare data from disparate species groups. The incorporation of phylogenetic data of other high Andean taxa with similar distribution patterns is necessary to determine the full utility of SNSH in explaining evolutionary patterns in the Andes of South America.     

Molecular systematics and historical biogeography of tree boas (Corallus spp.)

Inferring the evolutionary and biogeographic history of taxa occurring in a particular region is one way to determine the processes by which the biodiversity of that region originated. Tree boas of the genus Corallus are an ancient clade and occur throughout Central and South America and the Lesser Antilles, making it an excellent group for investigating Neotropical biogeography. Using sequenced portions of two mitochondrial and three nuclear loci for individuals of all recognized species of Corallus, we infer phylogenetic relationships, present the first molecular analysis of the phylogenetic placement of the enigmatic C. cropanii, develop a time-calibrated phylogeny, and explore the biogeographic history of the genus. We found that Corallus diversified within mainland South America, via over-water dispersals to the Lesser Antilles and Central America, and via the traditionally recognized Panamanian land bridge. Divergence time estimates reject the South American Caribbean-Track as a general biogeographic model for Corallus and implicate a role for events during the Oligocene and Miocene in diversification such as marine incursions and the uplift of the Andes. Our findings also suggest that recognition of the island endemic species, C. grenadensis and C. cookii, is questionable as they are nested within the widely distributed species, C. hortulanus. Our results highlight the importance of using widespread taxa when forming and testing biogeographic hypotheses in complex regions and further illustrate the difficulty of forming broadly applicable hypotheses regarding patterns of diversification in the Neotropical region.     

New Glyptodont from the Codore Formation (Pliocene), Falcón State, Venezuela, its relationship with theAsterostemma problem, and the paleobiogeography of the Glyptodontinae

One of the basal Glyptodontidae groups is represented by the Propalaehoplophorinae (late Oligocene — middle Miocene), whose genera (Propalaehoplophorus, Eucinepeltus, Metopotoxus, Cochlops, andAsterostemma) were initially recognized in Argentinian Patagonia. Among these,Asterostemma was characterized by its wide latitudinal distribution, ranging from southernmost (Patagonia) to northernmost (Colombia, Venezuela) South America. However, the generic assignation of the Miocene species from Colombia and Venezuela (A.? acostae, A. gigantea, andA. venezolensis) was contested by some authors, who explicitly accepted the possibility that these species could correspond to a new genus, different from those recognized in southern areas. A new comparative study of taxa from Argentinian Patagonia, Colombia and Venezuela (together with the recognition of a new genus and species for the Pliocene of the latter country) indicates that the species in northern South America are not Propalaehoplophorinae, but represent the first stages in the cladogenesis of the Glyptodontinae glyptodontids, the history of which was heretofore restricted to the late Miocene — early Holocene of southernmost South America. Accordingly, we propose the recognition of the new genusBoreostemma for the species from northern South America and the restriction ofAsterostemma to the Miocene of Patagonia. Thus, the available data indicate that the Glyptodontinae would in fact have arisen in the northernmost regions of this continent. Their arrival to more southerly areas coincides with the acme of the “Age of Southern Plains”. The Propalaehoplophorinae are geographically restricted to Patagonia.     

<Emphasis Type="Italic">Gryposuchus</Emphasis> (Crocodylia,Gavialoidea) from the early Miocene of Venezuela

Here, a fragment of a mandible recently discovered in the Cerro Zamuro site (Castillo Formation, Lara State, northwestern Venezuela) is assigned to the giant gavialoid Gryposuchus. This specimen, recovered from putative brackish environments of the early Miocene (~18 Ma) age, is unequivocally the earliest record of the genus in South America. Gryposuchus, together with the other gryposuchine previously recognized from the Castillo Formation, Siquisiquesuchus venezuelensis, increases the early Miocene taxonomic diversity of the group in the northern Neotropics. This new information from the Castillo Formation supports the conclusion that early gryposuchine evolutionary stages were in coastal, shallow marine or brackish environments, while the presence of some genera, such as Gryposuchus, in middle to late Miocene freshwater environments, is secondary habitat colonization late in the evolution of the clade. Freshwater colonization is probably the result of the gradual adaptation of early marine-adapted gryposuchines to the extensive estuarine-like environments of northern South America lowlands associated with marine transgressions that systematically occurred during the middle Eocene to early Oligocene. This new record is evidence of the wide chronological distribution of Gryposuchus in northern South America, highlighting the importance of this area as the center of origin and radiation of this successful Miocene gavialoid.     

Using Ecological Niche Models and Niche Analyses to Understand Speciation Patterns: The Case of Sister Neotropical Orchid Bees

The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species.     

Climatic niche evolution in the Andean genus <Emphasis Type="Italic">Menonvillea</Emphasis> (Cremolobeae: Brassicaceae)

The study of how climatic niches change over evolutionary time has recently attracted the interest of many researchers. Different methodologies have been employed principally to analyze the temporal dynamics of the niche and specially to test for the presence of phylogenetic niche conservatism. Menonvillea, a genus of Brassicaceae including 24 species, is distributed primarily along the Andes of Argentina and Chile, with some taxa growing in southern Patagonia and others in the Atacama Desert and the Chilean Matorral. The genus is highly diversified morphologically but also presents a remarkably wide ecological range, growing from the high Andean elevations, to the dry coastal deserts in Chile, or the Patagonia Steppe in Argentina. In this study, we used molecular phylogenies together with climatic data to study climatic niche evolution in the genus. The results show that the main climatic niche shifts in Menonvillea occurred between the sections Cuneata-Scapigera and sect. Menonvillea throughout the Mid-Late Miocene, and associated with the two main geographical distribution centers of the genus: the highlands of the central-southern Andes and the Atacama Desert-Chilean Matorral, respectively. Climatic niches in these lineages were mainly differentiated by the aridity and potential evapotranspiration, the minimum temperatures of the coldest month, and the temperature annual range and seasonality. Niche evolution in Menonvillea deviated from a Brownian motion process, with most of the climatic dimension best-fitting to an Ornstein-Uhlenbeck model of multiple adaptive peaks. Our results also indicated that higher aridity levels and lower annual temperature ranges were associated with the evolution of the annual habit, as exemplified by the distribution of sect. Menonvillea. Finally, the results suggested that climatic niche evolution in Menonvillea exhibited some degree of phylogenetic niche conservatism, fundamentally within the two main lineages (sect. Menonvillea and sects. Cuneata-Scapigera).     

The phylogeny and geography of Myrceugenia (Myrtaceae)

Myrceugenia is a mainly temperate South American genus with two species on the Juan Fernández Islands, 12 in central and southern Chile and adjacent Argentina, and 25 in the highlands of southeastern Brazil and adjacent regions. The continental populations are separated by about 1000 km. Numerical cladistic procedures based on the criteria of parsimony, compatible characters and a combination of compatible characters and character correlation are used to deduce hypothetical phylogenetic undirected trees. These indicate that 3–8 groups of species bridge the continent of South America. An explanation of how the distribution of the genus could have come about is given based on: 1) the above mentioned numerical analyses, 2) the ecology of the species, 3) the distribution of other plant genera, and 4) theories of the geologic and climatic history of southern South America. Myrceugenia is hypothesized to have grown continuously across South America during the early Tertiary and to have become divided into eastern and western populations probably during the Miocene.     

Systematics and biogeography of the Neotropical genus Mabuya,with special emphasis on the Amazonian skink Mabuya nigropunctata (Reptilia,Scincidae)

Phylogenetic analyses using up to 1532 base pairs (bp) of mitochondrial DNA from 106 specimens of Neotropical Mabuya, including 18 of the 19 recognized South American and Mesoamerican species, indicate that most species of the genus are monophyletic, including M. nigropunctata that had previously been reported to be paraphyletic. The present results shows that this species includes three highly divergent and largely allopatric lineages restricted to occidental, meridional, and oriental Amazonia. Our dataset demonstrates that previous claims regarding the paraphyletic status of M. nigropunctata and the phylogenetic relationships within this species complex based on the analysis of three mitochondrial and four nuclear genes (approx. 5000 bp) were erroneous and resulted from two contaminated cytochrome b sequences.The phylogenetic results indicate that diversification in the Neotropical genus Mabuya started approximately in the Middle Miocene (15.5–13.4 Ma). The divergence dates estimated for the Mabuya nigropunctata species complex suggest that the major cladogenetic events that produced the three main groups (occidental (oriental + meridional)) occurred during the Late Miocene. These estimations show that diversification within the M. nigropunctata species complex was not triggered by the climatic changes that occurred during the Pleistocene, as has been suggested by several authors. Rather, our data support the hypothesis that the late tertiary (essentially Miocene epoch) was a period that played a very important role in the generation of biological diversity in the Amazonian forests.Speciation between Mabuya carvalhoi, endemic to the coastal mountain range of Venezuela, and M. croizati, restricted to the Guiana Shield, occurred during the Middle Miocene and may have been as the result of a vicariant event produced by the formation of the present day Orinoco river drainage basin and the consequent appearance of the Llanos del Orinoco, which acted as a barrier to dispersal between these two species. The split between M. bistriata and M. altamazonica and between the occidental and (meridional + oriental) clades of M. nigropunctata fits very well with the biogeographic split between the eastern and western Amazon basins reported for several other taxa.     

Rarity up in the mountain: Ecological niche modeling,phenology, and reproductive biology of the most commercialized Masdevallia species

Knowledge of how natural and anthropogenic factors can limit the distribution of rare species is key to develop conservation strategies. We show data on how both factors potentially affect the distribution of a rare high Andean orchid. We chose Masdevallia coccinea as a model because it is endangered and the most commercialized species of the entire genus. Using ecological niche modeling, we confirm its rarity, with a restricted potential occurrence equivalent to only 0.00005 % of South America, 0.0003 % of the Andes, and 0.0009 % of Colombia. We projected the future potential occurrence of M. coccinea and found that it can have a reduction of 43.49 % in the best-case scenario and 89.06 % in the worst-case scenario in 2100. We describe the flowering and fruiting phenologies and demonstrate that the precipitation two months before may determine the first one. Masdevallia coccinea is a rewardless species and, unlike most Pleurothallidinae species, we show that it is self-compatible but non-autonomous selfer. Thus, it is dependent on biotic pollination, performed only by Leucophenga sp. (Drosophilidae: Diptera) which has low efficiency (8.6 % of fruit set). This is the first pollinator report for the genus. While self-compatibility may be related to reproductive assurance, apparently inbreeding depression may affect populations since selfed fruits had less viable seeds. Nevertheless, self-pollination can be avoided by the retention of the anther cap on pollinia, giving more time until the pollinator flies away to another flower. We consider that the rarity of M. coccinea may be a result of both anthropogenic (habitat loss, climate change, and overcollection) and natural factors (high elevation distribution, self-compatibility, rewardless strategy, pollinator specificity, and low fruit set). The several new facets investigated here can be used for future conservation strategies of this emblematic species as well as other high Andean threatened species.     

Molecular phylogenetics of Reig's short-tailed opossum (Monodelphis reigi) and its distributional range extension into Guyana

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

New species of the genus Cranichis (Orchidaceae, Cranichidinae) from Colombia

Two new species of the Neotropical genus Cranichis are described: Cranichis carlos-parrae Szlach. & Kolan. and Cranichis zarucchii Szlach. & Kolan. Both species are known exclusively from the Colombian Andes, where they were found growing in montane forests and paramo above 2,550 m of elevation. Each species is described and illustrated, and the habitat and distribution data are provided. A distribution map of the new species is presented. A dichotomous key for identification Colombian species of Cranichis is provided.     

A new species of Gaimanophis (Serpentes,Boidae) from the Miocene of northwestern Argentina with remarks on the Neogene boids of South America

Gaimanophis is an extinct boid genus represented so far by a single species (Gaimanophis tenuis) known by isolated vertebrae from the early Miocene of Patagonia. In this paper, a new species of Gaimanophis is described from the India Muerta Formation (late Miocene) of Tucumán province (Argentina). Gaimanophis powelli sp. nov. distinguishes itself from G. tenuis mainly in its larger size, prezygapophyses less slanting, neural spine shorter dorsally than ventrally, and zygosphene straight bearing an anteriorly protruding tongue. This record indicates a wider temporal and geographical distribution of the genus from the early Miocene of Patagonia to the late Miocene of northwestern Argentina. The recognition of a new species of boid in South America increases the known diversity of this group. Although boids have inhabited in this territory since the Paleocene, fossils belonging to the group only show a glimpse of the real past diversity in the continent.     

A Paleogeographic Overview of Tropical Fossil Sloths: Towards an Understanding of the Origin of Extant Suspensory Sloths?

Modern sloths are among the more characteristic mammals of South and Central American faunas. Recent discovery in four Paleogene, 22 Neogene, and dozens of Pleistocene fossiliferous localities in the tropics has revealed an unexpected paleobioversity constituted by some 81 fossil sloth species. Probably originating in southern South America near the Eocene/Oligocene transition, sloths were represented in the tropics during the late Oligocene by Pseudoglyptodon, Mylodontidae, and Megalonychidae. The latter occupied the West Indies between at least the late early Miocene and late Pleistocene, and two mylodontid clades, Octodontobradyinae and Urumacotheriinae, were characteristic of Amazonian localities from the Colhuehuapian and the Laventan periods, respectively, until the end of the Miocene. Megatheriinae and Nothrotheriidae appeared during the middle Miocene, colonizing the tropics and then North America, where Mylodontidae and Megalonychidae had already been present since the early late Miocene. Nothrotheriids are more abundant and diversified during the late Miocene in the tropics than in southern South America. Remains closely related to either of the modern sloths are absent from the fossil record, including those in the tropics. The characteristic suspensory posture of Bradypus and Choloepus appeared independently and likely after the Miocene epoch, and thus well after the hypothesized split suggested by molecular studies of the respective clades of these genera. Given their current widespread distribution in and reliance on the tropics, prospecting efforts for the direct fossil kin of suspensory sloths should concentrate on deposits in the Amazonian region, as this area has shown promise in producing fossil sloths.     

A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.     

Molecular phylogenetics of mouse opossums: new findings on the phylogeny of Thylamys (Didelphimorphia,Didelphidae)

The mouse opossums of the genus Thylamys constitute a group of species mainly adapted to open xeric‐like habitats and restricted to the southern portion of South America. We used molecular data (mitochondrial and nuclear sequences) to evaluate the phylogenetic and biogeographical relationships of all currently known living species of the genus, recognizing a new taxon from the middle and high elevations of the Peruvian Andes and evaluating the phylogenetic structuring within T. pallidior and T. elegans, as well as the validity of T. sponsorius, T. cinderella and T. tatei, and the haplogroups recognized within T. pusillus. Our results confirm the monophyly of the genus and that the Caatinga and the Cerrado inhabitants Thylamys karimii and T. velutinus are the most basal species in the radiation of Thylamys. We also calibrated a molecular clock which hypothesized a time of origin of the genus of about 24 My, with most species differentiating in middle and late Miocene and Plio‐Pleistocene times of South America.     

Mapping the observed and modelled intracontinental distribution of non-marine ostracods from South America

Ecological niche modelling (ENM) has been used to quantify the potential occurrence of species, by identifying the main environmental factors that determine the presence of species across geographical space. We provide a large-scale survey of the distribution of ostracod species in South America, by using the domains of 25 river basins. From 221 known ostracod species, we estimate the potential distribution of 61 species, using ENM. Ten clusters of potential distribution patterns were found. Clusters 8 and 9 grouped most of the species, which presented high similarity of niche between them. Heterocypris paningi Brehm, 1934 (group 1) obtained higher niche variability. The minimum temperatures of the coldest month and the mean elevation of the river basin were most important to predict the potential distribution of ostracods of most groups. South America has a complex pattern of elevation, which affects species distributions indirectly through changes in local factors. For instance, the Andes mountains might impose a barrier for ostracod distribution in the southern part of South America because of the low temperatures and precipitation. The ENM indicated that some regions and/or basins of South America might be susceptible to the entry of several ostracod species, presently absent, including non-native species.

     

Historical biogeography of the genus Rhadinaea (Squamata: Dipsadinae)

Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as “Eastern” and “Southern”. These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans‐Mexican Volcanic Belt and Chiapan–Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans‐Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time.