Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA

Euastacus crayfish are endemic to freshwater ecosystems of the eastern coast of Australia. While recent evolutionary studies have focused on a few of these species, here we provide a comprehensive phylogenetic estimate of relationships among the species within the genus. We sequenced three mitochondrial gene regions (COI, 16S, and 12S) and one nuclear region (28S) from 40 species of the genus Euastacus, as well as one undescribed species. Using these data, we estimated the phylogenetic relationships within the genus using maximum-likelihood, parsimony, and Bayesian Markov Chain Monte Carlo analyses. Using Bayes factors to test different model hypotheses, we found that the best phylogeny supports monophyletic groupings of all but two recognized species and suggests a widespread ancestor that diverged by vicariance. We also show that Euastacus and Astacopsis are most likely monophyletic sister genera. We use the resulting phylogeny as a framework to test biogeographic hypotheses relating to the diversification of the genus.     

Phylogenetic relationships of South American alligatorids and the caiman of Madeira River

We analyzed DNA sequences of the mitochondrial cytochrome b gene (cyt b), the nuclear Recombination Activating Gene 1 (RAG1) and the myelocytomatosis oncogene (MYC) to infer the phylogenetic relationship of Caiman crocodilus and Caiman yacare, and other South American alligatorid crocodilian species. Phylogenetic relationships were robustly supported with Paleosuchus sister to Melanosuchus and Caiman. Phylogenetic relationships of C. crocodilus and C. yacare were unclear as these two species share mitochondrial and nuclear haplotypes. Specifically this sharing occurs among specimens of C. yacare and C. crocodilus from the Madeira River drainage. Two potential explanations stand out: secondary contact followed by hybridization, and differentiation along a cline. Current data cannot resolve between these two competing hypotheses. In comparison with C. yacare and C. crocodilus, Paleosuchus trigonatus and Paleosuchus palpebrosus are very well differentiated and also show surprising haplotypic diversity in spite of their phenotypic similarity.     

Temporal speciation pattern in the western Mediterranean genus Tudorella P. Fischer, 1885 (Gastropoda,Pomatiidae) supports the Tyrrhenian vicariance hypothesis

The land snail genus Tudorella shows a peculiar disjunct distribution around the western Mediterranean coasts. Despite high phenotypic plasticity, only two species with a disputed number of subspecific taxa are currently recognised. We delimited the species with mitochondrial (COI & 16S) and nuclear (ITS-1) markers based on the unified species concept and suggested that there are eight species in the genus, two of them currently undescribed. Applying Bayesian phylogenetic model selection, we tested four different biogeographic hypotheses that could be causal for the current distribution pattern of extant Tudorella species. A scenario involving vicariance events resulting from the repeated splits of the Tyrrhenian plate with subsequent dispersal events over land bridges during the Pliocene received greatest support in the data.     

Phylogenetic analyses of band‐winged grasshoppers (Orthoptera,Acrididae, Oedipodinae) reveal convergence of wing morphology

Husemann, M., Namkung, S., Habel, J.C., Danley, P.D. & Hochkirch, A. (2012). Phylogenetic analyses of band‐winged grasshoppers (Orthoptera, Acrididae, Oedipodinae) reveal convergence of wing morphology. —Zoologica Scripta, 41, 515–526. Historically, morphological traits have been used to examine the relationships of distantly related taxa with global distributions. The use of such traits, however, may be misleading and may not provide the resolution needed to distinguish various hypotheses that may explain the distribution patterns of widely distributed taxa. One such taxon, the Oedipodine grasshoppers, contains two tribes principally defined by wing morphologies: the Bryodemini have broad wings whereas Sphingonotini are narrow‐winged. Through the use of morphological features alone, hypotheses concerning the evolution of these tribes cannot be distinguished. To differentiate hypotheses that may explain the distribution of Oedipodines, such as vicariance, natural dispersal and anthropogenic translocation, we used two mitochondrial and three nuclear gene fragments to reconstruct the phylogenetic relationships within and between the two tribes, and employed a molecular clock to evaluate the hypotheses of vicariance and dispersal. Our results clearly reject monophyly of the tribes and revealed monophyletic Old and New World clades, which is in agreement with previous molecular studies. The split between both clades was dated at 35 Ma (±12 Ma). This clearly rejects the vicariance hypothesis and supports a single invasion via the Beringian land bridge. In addition, our data clearly show that the similarities in wing morphology used for distinguishing both tribes are the result of at least one convergent event. Our study shows that interpretations of relationships based on the currently accepted taxonomy in the study groups will be error prone. We suggest that future revisions that consider our findings are required.     

Single origin and subsequent diversification of central Andean endemic Umbilicaria species

We studied an Andean endemic group of species of the lichen-forming fungal genus Umbilicaria from the subalpine and low-alpine zone, with their biogeographic center in Bolivia and Peru. A number of species and varieties have been described from this element, but apparent instability in several morphological traits has made it difficult to precisely delimit taxa. Based on DNA sequences of nuclear ITS, LSU and mitochondrial SSU from extensive collections from Argentina, Bolivia, Chile, Colombia, Ecuador and Peru, we present here a molecular phylogenetic analysis of this Andean endemic element within genus Umbilicaria. All analyses (MP, ML and Bayesian) support a single origin for the element and a division into two major groups characterized by different apothecium types: the Umbilicaria dichroa group and U. calvescens group. Taxa U. krempelhuberi, U. peruviana and U. subcalvescens are nested withinn U. calvescens and are treated as conspecific with the latter species. The endemic element shares a most recent common ancestor with the Umbilicaria vellea group, which has a worldwide distribution and contains several asexually reproducing (sorediate) species. Independent reversals to sexual reproduction might explain the evolution of two types of apothecia in this monophyletic endemic lineage. A number of cosmopolitan, mostly high-alpine, species of Umbilicaria also present in the central Andes are related only remotely to the endemic element and do not exhibit speciation into endemics. Because the An-dean element dominates the Umbilicaria habitats of the low- and subalpine zones we propose that the founder colonized the Andes at a time when the mountains had not yet reached their current elevation while the high-alpine species arrived more recently.     

Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei)

Labyrinth fishes (Perciformes: Anabantoidei) are primary freshwater fishes with a disjunct African-Asian distribution that exhibit a wide variety of morphological and behavioral traits. These intrinsic features make them particularly well suited for studying patterns and processes of evolutionary diversification. We reconstructed the first molecular-based phylogenetic hypothesis of anabantoid intrarelationships using both mitochondrial and nuclear nucleotide sequence data to address anabantoid evolution. The mitochondrial data set included the complete cytochrome b, partial 12S rRNA, complete tRNA Val, and partial 16S rRNA genes (3332 bp) of 57 species representing all 19 anabantoid genera. The nuclear data set included the partial RAG1 gene (1494 bp) of 21 representative species. The phylogenetic analyses of a combined (mitochondrial+nuclear) data set recovered almost fully resolved trees at the intrafamily level with different methods of phylogenetic inference. Phylogenetic relationships at this taxonomic level were compared with previous morphology-based hypotheses. In particular, the enigmatic pike-head (Luciocephalus) was confidently placed within the "spiral egg" clade, thus resolving the long-standing controversy on its relative phylogenetic position. The molecular phylogeny was used to study the evolution of the different forms of parental care within the suborder. Our results suggest that the evolution of breeding behavior in anabantoids is highly correlated with phylogeny, and that brood care evolved three times independently from an ancestral free spawning condition without parental care. Ancestral character state reconstructions under maximum parsimony and maximum likelihood further indicated that both bubble nesting and mouthbrooding have evolved recurrently during anabantoid evolution. The new phylogenetic framework was also used to test alternative biogeographic hypotheses that account for the disjunct African-Asian distribution. Molecular divergence time estimates support either a drift vicariance linked to the breakup of Gondwana or Late Mesozoic Early Tertiary dispersal from Africa to Asia or vice versa.     

Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini)

Aim We used mitochondrial DNA sequence data to reconstruct the phylogeny of a large clade of tanagers (Aves: Thraupini). We used the phylogeny of this Neotropical bird group to identify areas of vicariance, reconstruct ancestral zoogeographical areas and elevational distributions, and to investigate the correspondence of geological events to speciation events. Location The species investigated are found in 18 of the 22 zoogeographical regions of South America, Central America and the Caribbean islands; therefore, we were able to use the phylogeny to address the biogeographical history of the entire region. Methods Molecular sequence data were gathered from two mitochondrial markers (cytochrome b and ND2) and analysed using Bayesian and maximum‐likelihood approaches. Dispersal–vicariance analysis (DIVA) was used to reconstruct zoogeographical areas and elevational distributions. A Bayesian framework was also used to address changes in elevation during the evolutionary history of the group. Results Our phylogeny was similar to previous tanager phylogenies constructed using fewer species; however, we identified three genera that are not monophyletic and uncovered high levels of sequence divergence within some species. DIVA identified early diverging nodes as having a Northern Andean distribution, and the most recent common ancestor of the species included in this study occurred at high elevations. Most speciation events occurred either within highland areas or within lowland areas, with few exchanges occurring between the highlands and lowlands. The Northern Andes has been a source for lineages in other regions, with more dispersals out of this area relative to dispersals into this area. Most of the dispersals out of the Northern Andes were dispersals into the Central Andes; however, a few key dispersal events were identified out of the Andes and into other zoogeographical regions. Main conclusions The timing of diversification of these tanagers correlates well with the main uplift of the Northern Andes, with the highest rate of speciation occurring during this timeframe. Central American tanagers included in this study originated from South American lineages, and the timing of their dispersal into Central America coincides with or post‐dates the completion of the Panamanian isthmus.     

Gene flow and Andean uplift shape the diversification of Gasteracantha cancriformis (Araneae: Araneidae) in Northern South America

The Andean uplift has played a major role in shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here, we examined the phylogeography of the widespread color polymorphic spider Gasteracantha cancriformis to evaluate the effect of the northern Andean uplift on its divergence and assess whether its diversification occurred in the presence of gene flow. We inferred phylogenetic relationships and divergence times in G. cancriformis using mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence, and population structure were quantified. We also compared multiple demographic scenarios for this species using a model‐based approach (Phrapl ) to determine divergence with or without gene flow. At last, we evaluated the association between genetic variation and color polymorphism. Both nuclear and mitochondrial data supported two well‐differentiated clades, which correspond to populations occurring on opposite sides of the Eastern cordillera of the Colombian Andes. The final uplift of this cordillera was identified as the most likely force that shaped the diversification of G. cancriformis in northern South America, resulting in a cis‐ and trans‐Andean phylogeographic structure for the species. We also found shared genetic variation between the cis‐ and trans‐Andean clades, which is better explained by a scenario of historical divergence in the face of gene flow. This has been likely facilitated by the presence of low‐elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example in which the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.     

Molecular phylogeography of Jerdon’s pitviper (Protobothrops jerdonii): importance of the uplift of the Tibetan plateau

Aim To investigate the population history and demographics of Jerdon’s pitviper, Protobothrops jerdonii, and elucidate how the unique physical conditions and heterogeneous mountain environments resulting from the uplift of the Tibetan Plateau shaped the genetic diversity and evolutionary history of the species. Location China and Vietnam. Methods We sequenced and analysed a total of 1752 base pairs from two mitochondrial genes, cytochrome b (cyt b) and NADH dehydrogenase subunit (ND4), for 81 specimens sampled from 27 localities across the species’ range, and a total of 464 base pairs from two nuclear genes for 28 representative samples from all mitochondrial DNA lineages. Based on these data, we constructed the genealogical relationships and estimated the divergence times of the mitochondrial DNA clades. Results The mitochondrial DNA results revealed the existence of five distinct, strongly supported and geographically structured DNA lineages within populations of P. jerdonii that are paraphyletic with respect to Protobothrops xiangchengensis. Estimation of divergence dates suggested that P. jerdonii possibly evolved in the western Hengduan Mountains region c. 6.6 Ma in the late Miocene. Nuclear DNA data did not provide sufficient resolution to distinguish the mitochondrial DNA lineages. Main conclusions Based on the present‐day distribution and intraspecific genealogy, the evolutionary history of P. jerdonii can be explained by a pattern of dispersal followed by vicariance. All lines of evidence suggest that historical biogeographical factors, particularly the north–south orientation of the higher mountains, as well as low‐elevation areas in western China, had the greatest influence on the population structure, lineage formation and species distribution of this snake. However, highly heterogeneous habitats and glacial cycles appear to have affected patterns of intraspecific differentiation. While our mitochondrial data provide evidence for clear phylogeographical structure, our small sampling of nuclear genes does not, suggesting that nuclear markers may not have had sufficient time to coalesce to match patterns observed in the mitochondrial data.     

Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae)

The high biodiversity of tropical marine hotspots has long intrigued evolutionary biologists and biogeographers. The genus Haemulon (grunts) is one of the most important (numerically, ecologically, and economically) reef fish groups in the New World and an excellent candidate to test hypotheses of speciation and diversity generation in the Greater Caribbean, the richest Atlantic biodiversity hotspot, as well as the eastern Pacific. To elucidate the phylogenetic relationships among the species of Haemulon, we obtained a combined total of 2639 base pairs from two mitochondrial genes (cytochrome b and cytochrome oxidase I), and two nuclear genes (TMO-4C4 and RAG2) from all nominal species. Parsimony, Maximum likelihood, and Bayesian analyses resulted in a well-resolved phylogeny with almost identical topologies. Previous phylogenetic hypotheses based on adult morphology, such as the close relationship among H. aurolineatum, H. boschmae, and H. striatum were not supported, whereas others using developmental characters, such as the relationship between H. plumieri and H. sciurus, were confirmed. Our data also indicate that the populations of the nominal H. steindachneri from the two sides of the Isthmus of Panama are genetically divergent at the species level in each ocean, and that the boga, Inermia vittata (family Inermiidae), belongs in the genus Haemulon. This evidence implies that there are 21 valid species of Haemulon, two more than previously recognized. The Amazon barrier and the Isthmus of Panama seem to have played roles in allopatric speciation of Haemulon. However, the majority of sister species pairs have completely overlapping distributions, indicating that vicariance is not the only process driving speciation in this genus. We conclude that both vicariance between biogeographic provinces, and ecological mechanisms of speciation within provinces contribute to species richness in the genus Haemulon.     

Neotropical diversification: the effects of a complex history on diversity within the poison frog genus Dendrobates

Aim We study the Neotropical poison frogs of the genus Dendrobates Wagler, 1830 in order to clarify their phylogenetic relationships and biogeographical history. The genus Dendrobates is an excellent taxon for examining patterns of Neotropical diversification as the four major species groups appear to correspond roughly to distinct geographical regions: (1) trans‐Andean, (2) Andean foreland, (3) Brazilian Shield and (4) Guianan Shield/Central America. In order to test the agreement of five of the most prominent hypotheses of Amazonian diversification, phylogenetic patterns were examined for agreement with patterns predicted by these hypotheses. Location Central and South America Methods The phylogenetic relationships of the genus Dendrobates were examined from novel and existing (GenBank) sequences of four mitochondrial loci totalling c. 1400 bp from 40 specimens of 22 different species using maximum parsimony and Bayesian methods. Results were compared with traditional taxonomic arrangements by means of SH tests. Phylogenetic relationships and genetic distances were used to test the adequacy of various diversification hypotheses. Results Phylogenetic analyses support the restructuring of two species groups of Dendrobates and the creation of a new species group. Statistical tests of the traditional taxonomic arrangement indicate a significantly bad fit to the molecular data. This restructuring has important implications for the understanding of the historical biogeography of Dendrobates. Biogeographical patterns within this genus suggest that a complex interaction of biotic and abiotic factors since the Eocene have produced the diversity observed today. Main conclusions The current classification of Dendrobates into discrete species groups does not accurately reflect evolutionary history. Data presented here strongly support a monophyletic Brazilian Shield lineage whose members have previously been split among the quinquevittatus and tinctorius groups. Furthermore, previous attempts at elucidating the historical biogeography of this genus were compromised by incomplete sampling and conclusions drawn from a paraphyletic ingroup. Our findings demonstrate a role for numerous hypotheses of diversification (e.g. river, refuge, disturbance–vicariance) in the history of Dendrobates, supporting previous warnings about the dangers of over‐simplification in the study of Neotropical diversification.     

Phylogeography and speciation of the morphologically variable, widespread species Bufo valliceps, based on molecular evidence from mtDNA

The widespread, lowland toad Bufo valliceps has an unusual distribution in North and Middle America that straddles two major biogeographic areas; previous morphological studies of this species suggested the existence of two species. We used mitochondrial DNA sequences to examine the phylogeography of this species and discovered the existence of two distinct clades. We recognize these as two species: B. valliceps and B. nebulifer. These molecular data support morphological data from previous studies. Our results show low levels of molecular variation in a morphologically uniform temperate species (B. nebulifer) and high levels of molecular variation in a morphologically variable tropical species (B. valliceps), providing an example of molecules matching morphology. Two biogeographic hypotheses are tested to explain the current distribution of these species, based on a calibrated rate of evolution and the percent sequence divergence between the two species. A more recent Pleistocene dispersal event, followed by vicariance associated with rising sea level, is rejected in favor of an earlier Miocene-Pliocene vicariant hypothesis associated with the formation of the Trans-Mexican Neovolcanic Belt.     

Ecological and biogeographical inferences on two sympatric and enigmatic Andean cat species using genetic identification of faecal samples

The carnivore community of the altiplano ecosystem of the high Andes, including the Andean mountain cat (Leopardus jacobita) and pampas cat (Leopardus colocolo), is one of the least studied in the world. We determined the origin of 186 carnivore samples (184 faeces and two skulls) collected above 3000 m above sea level in northern Chile, including 33 from the Andean mountain cat and 75 from the pampas cat using diagnostic molecular genetic sequence variation. We determined for the first time food habits, habitat and physiographic associations, and general patterns of molecular genetic variation of the Andean mountain cat and the pampas cat in Chile. Both species had narrow dietary niches dominated by small rodents and there was a wide overlap in diet composition (0.82), suggesting low levels of prey partitioning between species. The mountain viscacha (Lagidium viscacia) made up a large proportion of the biomass of the diet of both species, especially for the Andean mountain cat (93.9% vs. 74.8% for the pampas cat), underscoring the importance of further research and conservation focus on this vanishing prey species. Although the probability of finding Andean mountain cat scats increased with altitude and slope, there was substantial geographical overlap in distribution between species, revealing that the pampas cat distribution includes high-altitude grassland habitats. The Andean mountain cat had relatively low levels of mitochondrial DNA (mtDNA) genetic variation (two mtDNA haplotypes) compared with the pampas cat (17 mtDNA haplotypes), suggestive of a distinct evolutionary history and relatively smaller historic populations. These insights will facilitate and provide tools and hypotheses for much-needed research and conservation efforts on these species and this ecosystem.     

Species trees for the tree swallows (Genus Tachycineta): An alternative phylogenetic hypothesis to the mitochondrial gene tree

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group.     

Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition

The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.     

Nuclear and mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus (Aves: Dendrocolaptidae): biogeography and systematics implications

We studied the intraspecific evolutionary history of the South American Atlantic forest endemic Xiphorhynchusfuscus (Aves: Dendrocolaptidae) to address questions such as: Was the diversification of this bird's populations associated to areas of avian endemism? Which models of speciation (i.e., refuges, river as barriers or geotectonism) explain the diversification within X. fuscus? Does the genetic data support subspecies as independent evolutionary units (species)? We used mitochondrial (n=34) and nuclear (n=68) DNA sequences of X. fuscus to study temporal and spatial relationships within and between populations. We described four main monophyletic lineages that diverged during the Pleistocene. The subspecies taxonomy did not match all the evolutionary lineages; subspecies atlanticus was the only one that represented a monophyletic and isolated lineage. The distribution of these lineages coincided with some areas of endemism for passerines, suggesting that those areas could be regions of biotic differentiation. The ancestor of X. fuscus diverged approximately 3 million years ago from Amazonian taxa and the phylogeographic pattern suggested that X. fuscus radiated from northeastern Brazil. Neither the riverine nor the geotectonic vicariance models are supported as the primary cause for diversification of geographic lineages, but rainforest contractions and expansions (ecological vicariance) can explain most of the spatial divergence observed in this species. Finally, analyses of gene flow and divergence time estimates suggest that the endangered subspecies atlanticus (from northeastern Brazil) can be considered a full species under the general lineage species concept.     

Trait differentiation and adaptation of plants along elevation gradients

Studies of genetic adaptation in plant populations along elevation gradients in mountains have a long history, but there has until now been neither a synthesis of how frequently plant populations exhibit adaptation to elevation nor an evaluation of how consistent underlying trait differences across species are. We reviewed studies of adaptation along elevation gradients (i) from a meta‐analysis of phenotypic differentiation of three traits (height, biomass and phenology) from plants growing in 70 common garden experiments; (ii) by testing elevation adaptation using three fitness proxies (survival, reproductive output and biomass) from 14 reciprocal transplant experiments; (iii) by qualitatively assessing information at the molecular level, from 10 genomewide surveys and candidate gene approaches. We found that plants originating from high elevations were generally shorter and produced less biomass, but phenology did not vary consistently. We found significant evidence for elevation adaptation in terms of survival and biomass, but not for reproductive output. Variation in phenotypic and fitness responses to elevation across species was not related to life history traits or to environmental conditions. Molecular studies, which have focussed mainly on loci related to plant physiology and phenology, also provide evidence for adaptation along elevation gradients. Together, these studies indicate that genetically based trait differentiation and adaptation to elevation are widespread in plants. We conclude that a better understanding of the mechanisms underlying adaptation, not only to elevation but also to environmental change, will require more studies combining the ecological and molecular approaches.     

A peninsula as an island: multiple forms of evidence for overwater colonization of Baja California by the gartersnake Thamnophis validus

The recent shift toward dispersal rather than vicariant explanations of disjunct distributions has been driven by the use of molecular data to estimate divergence dates between lineages. However, other kinds of evidence can also be critical in evaluating such biogeographic hypotheses. In the present study, we used a multifaceted approach employing diverse analyses of mitochondrial DNA sequences to assess explanations for the disjunct distribution of the gartersnake Thamnophis validus. The occurrence of this species in the Cape Region of the Baja California peninsula, isolated from mainland populations that occur along the west coast of Mexico, might be explained by: (1) separation of the peninsula from mainland Mexico through rifting 4–8 Mya (tectonic vicariance); (2) fragmentation of the range of this semi‐aquatic species because of post‐Pleistocene aridification (vicariance by aridification); (3) natural overwater dispersal across the Gulf of California; or (4) human introduction. Divergence dating indicates that peninsular and mainland T. validus separated from each other within the last 0.5 Myr, thus rejecting tectonic vicariance. In addition, the estimated closest mainland relatives of peninsular snakes are found farther north than expected under this hypothesis. Three findings argue against vicariance by aridification: (1) peninsular snakes and their closest mainland relatives are more genetically similar than predicted; (2) the location of closest mainland relatives is farther south than predicted; and (3) the species is absent from areas where one might expect to find relict populations. Taken together, refutation of the vicariance hypotheses and the fact that the estimated closest mainland relatives are found almost directly across the Gulf from the Cape Region supports some form of overwater colonization. Various additional arguments suggest that natural dispersal is more likely than human introduction. The present study emphasizes the need for multiple kinds of evidence, beyond divergence dates, to discriminate among hypotheses and to provide independent sources of corroboration or refutation in historical biogeography. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 409–424.     

Mid-Tertiary dispersal, not Gondwanan vicariance explains distribution patterns in the wax palm subfamily (Ceroxyloideae: Arecaceae)

The Ceroxyloideae is a small but heterogeneous subfamily of palms (Arecaceae, Palmae). It includes a Caribbean lineage (tribe Cyclospathae), a southern hemisphere disjunction (tribe Ceroxyleae), and an amphi-Andean element (tribe Phytelepheae), until recently considered a distinct subfamily (Phytelephantoideae) due to its highly derived morphology. A variety of hypotheses have been proposed to account for the biogeography of the subfamily, involving Gondwanan vicariance, austral interplate dispersal from South America to Australia via Antarctica, Andean orogeny, and Pleistocene refuges. We assessed the systematic classification and biogeography of the group based on a densely sampled phylogeny using >5.5kb of DNA sequences from three plastid and two nuclear genomic regions. The subfamily and each of its three tribes were resolved as monophyletic with high support. Divergence time estimates based on penalized likelihood and Bayesian dating methods indicate that Gondwanan vicariance is highly unlikely as an explanation for basic disjunctions in tribe Ceroxyleae. Alternative explanations include a mid-Tertiary trans-Atlantic/trans-African dispersal track and the "lemurian stepping stones" hypothesis. Austral interplate dispersal of Oraniopsis to Australia could have occurred, but apparently only in the mid-Eocene/early Oligocene interval after global cooling had begun. Our data do not support Pleistocene climatic changes as drivers for speciation in the Andean-centered Phytelepheae as previously proposed. Radiation in this tribe coincides largely with the major uplift of the Andes, favoring Andean orogeny over Pleistocene climatic changes as a possible speciation-promoting factor in this tribe.