A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.     

From near extinction to diversification by means of a shift in pollination mechanism in the gymnosperm relict Ephedra (Ephedraceae,Gnetales)

Pollination in gymnosperms is usually accomplished by means of wind, but some groups are insect‐pollinated. We show that wind and insect pollination occur in the morphologically uniform genus Ephedra (Gnetales). Based on field experiments over several years, we demonstrate distinct differences between two Ephedra species that grow in sympatry in Greece in pollen dispersal and clump formation, insect visitations and embryo formation when insects are denied access to cones. Ephedra distachya, nested in the core clade of Ephedra, is anemophilous, which is probably the prevailing state in Ephedra. Ephedra foeminea, sister to the remaining species of the genus, is entomophilous and pollinated by a range of diurnal and nocturnal insects. The generalist entomophilous system of E. foeminea, with distinct but infrequent insect visitations, is in many respects similar to that reported for Gnetum and Welwitschia and appears ancestral in Gnetales. The Ephedra lineage is well documented already from the Early Cretaceous, but the diversity declined dramatically during the Late Cretaceous, possibly to near extinction around the Cretaceous–Palaeogene boundary. The clade imbalance between insect‐ and wind‐pollinated lineages is larger than expected by chance and the shift in pollination mode may explain why Ephedra escaped extinction and began to diversify again.     

Sorting out the Snakebirds: The species status,phylogeny, and biogeography of the Darters (Aves: Anhingidae)

Although the avian family Anhingidae is unequivocally monophyletic, the number and relationships of the component species within the single genus (Anhinga) have long remained unclear. Here, we use extensive mitochondrial and nuclear DNA sequence data (8,878 bp) to show that four species should be recognized. Our fully resolved and well‐supported tree shows that the American Anhinga (Anhinga anhinga) is sister to the three Old World species, with the Oriental (A. melanogaster) and African (A. rufa) Darters sister within the Old World clade, which also includes the Australian Darter (A. novaehollandiae). We estimate that the divergence between the New World and Old World branches occurred 19–22 mya, with the Australian Darter separating from its Old World congeners 14–16 mya and the Oriental and African species splitting ~10 mya. The genus is yet another example of osteological conservatism in the Suliformes, which is comparable to that shown by the cormorants and shags. Nevertheless, the relationships we infer are congruent with recent plumage studies and are biogeographically plausible. We suggest that further investigation of the variation within the African and Australian Darters would be of interest.     

Repeated trans-Atlantic dispersal catalysed a global songbird radiation

Aim Turdus thrushes are one of the most speciose and widespread songbird genera, comprising nearly 70 species that combined have a near‐global distribution. Herein, we use molecular phylogenetic, molecular clock and behavioural evidence to examine the historical biogeography of the genus. Ancestral area reconstructions in conjunction with divergence estimates and palaeoclimatogical data are used to test whether the long‐standing paradigm of Beringian colonization or trans‐Atlantic dispersal best explains modern distributions in the New and Old Worlds. Location Worldwide, with emphasis on New World–Old World biotic interchange. Methods Using a molecular phylogenetic hypothesis of Turdus thrushes, we reconstructed ancestral area relationships utilizing the five major continental or regional areas occupied by species in the genus. We also examined the evolution of behaviours on the phylogeny, and estimated the timing of major lineage divergences via a molecular clock. Results Turdus originated in Eurasia, and following the colonization of Africa underwent a series of five trans‐Atlantic sweepstake dispersals. The data reject the alternative hypothesis that connections between Old and New World Turdus species can be attributed to movement through Beringia with subsequent extinction. Divergence estimates indicate that these dispersals all occurred near the Miocene–Pliocene boundary, 5 Ma. A significant phylogenetic correlation between migratory and flocking behaviour is evident in the genus. Main conclusions The initial divergence of Turdus in the Old World was followed by a series of trans‐Atlantic sweepstake dispersal events. These dispersals are temporally correlated with a specific palaeoclimatic system, which would have facilitated transport of Turdus from the Caribbean to the Old World across the Atlantic. Uplift of the Central American Seaway 4.7 Ma effectively shut down the palaeoclimatic system, and no additional trans‐Atlantic dispersals are evident in Turdus after this time. Migratory movements by ancestral lineages in flocks, rather than as single individuals, suggest an increased likelihood of successfully colonizing new areas, post‐dispersal.     

Around the world in 10 million years: biogeography of the nearly cosmopolitan true toads (Anura: Bufonidae)

Aim The species‐rich family of true toads (Anura: Bufonidae) has been the focus of several earlier studies investigating the biogeography of geographically widespread taxa. Herein, we employ newly developed Bayesian divergence estimate methods to investigate the biogeographical history of this group. Resulting age estimates are used to test several key temporal hypotheses including that the origin of the bufonid clade pre‐dates Gondwanan vicariance (~105 million years ago, Ma). Area cladograms are also invoked to investigate the geographical origin of the family. Location Worldwide, except the Australia–New Guinea plate, Madagascar and the Antarctic. Methods A phylogenetic hypothesis of the relationships among true toads was derived from analysis of 2521 bp of DNA data including fragments from three mitochondrial (12S, tRNA^val, 16S) and two nuclear (RAG‐1, CXCR‐4) genes. Analysis of multiple, unlinked loci with a Bayesian method for estimating divergence times allowed us to address the timing and biogeographical history of Bufonidae. Resulting divergence estimates permitted the investigation of alternative vicariance/dispersal scenarios that have been proposed for true toads. Results Our area cladogram resulting from phylogenetic analysis of DNA data supports a South American origin for Bufonidae. Divergence estimates indicate that the family originated earlier than had been suggested previously (78–99 Ma). The age of the enigmatic Caribbean clade was dated to the late Palaeocene–early Eocene. A return of bufonids to the New World in the Eocene was followed by rapid diversification and secondary expansion into South America by the early Oligocene (Rupelian). Main conclusions The South American origin of Bufonidae in the Upper Cretaceous was followed by relatively rapid expansion and radiation around the globe, ending with a return to the Americas via a Eurasian/North American land bridge in the Eocene. Though the exact route of this dispersal (Beringia or North Atlantic) remains unclear, an argument is made for the less frequently invoked North Atlantic connection. The origin of the enigmatic Caribbean lineage was found to be consistent with colonization following the bolide impact at the K/T boundary. These findings provide the first, firm foundation for understanding true toad divergence times and their truly remarkable and global radiation.     

Ecological consequences of contrasting dispersal syndromes in New World Ephedra: higher rates of niche evolution related to dispersal ability

In this study we selected the New World species of Ephedra to understand the ecological consequences of different dispersal syndromes. The twenty‐three species of Ephedra in the New World have a disjunct distribution in North and South American arid and semi‐arid habitats, exhibiting three dispersal syndromes related to dispersal by birds, wind and rodents. Using DNA sequence data we inferred phylogenetic relationships and lineage divergence times, and used these estimates to test different ecological assumptions. Using comparative methods we tested for correlations between dispersal syndromes and a set of ecological variables (niche breadth, niche evolution, distributional ranges and niche position). We found that speciation events in the New World coincided with the expansion of arid habitats in this region. We suggest that the bird dispersal syndrome is related with higher rates of climatic niche evolution for all variables used, including aridity index, mean annual temperature and mean annual precipitation. Distribution ranges were correlated with niche breadth, they were however not significantly different between dispersal syndromes. Species inhabiting the extremely arid regions on niche axes had narrower niche breadths. We conclude that species whose seeds are dispersed by birds have colonized a broader set of habitats and that those with wind and rodent dispersal syndromes might have promoted the colonization of more arid environments.     

Phylogenetic relationships of Amazonetta,Speculanas, Lophonetta,and Tachyeres: four morphologically divergent duck genera endemic to South America

We studied the phylogenetic relationships of four duck genera endemic to South America: Brazilian teal Amazonetta brasiliensis, spectacled duck Speculanas specularis, crested duck Lophonetta specularioides, and four species of steamer ducks Tachyerespatachonicus, T. leucocephalus, T. pteneres, T. brachypterus. Genetic divergence within and among species was compared using population‐level sampling of the mitochondrial DNA (mtDNA) control region, supplemented with three additional mtDNA genes and six independent nuclear loci from one individual of each species and a variety of outgroup taxa. The monophyly of these four morphologically divergent South American genera was strongly supported. Within this clade, Amazonetta and Speculanas were supported as sister species in all analyses, but different gene regions yielded conflicting or ambiguous results for Lophonetta and Tachyeres. This lack of resolution resulted from little informative variation in nuclear loci and high levels of homoplasy in the mtDNA control region. Control region sequences from the four Tachyeres species fell into two distinct clades. In one clade, T. patachonicus and T. leucocephalus share a set of closely related haplotypes (≤0.6% sequence divergence); while no identical haplotypes were shared between species, the control region phylogeny was insufficiently resolved to either support or reject reciprocal monophyly. The second clade, ~1.7% divergent from the first, comprised haplotypes of the Falkland Islands species T. brachypterus and a captive individual of T. pteneres. These distinctive South American ducks likely experienced two bouts of rapid diversification, thus making analysis of their phylogenetic relationships difficult. Incomplete lineage sorting, founder effects, and perhaps introgression likely have contributed to obscuring the relationships among steamer ducks.     

The female reproductive unit of Ephedra (Gnetales): comparative morphology and evolutionary perspectives

Morphological variation in Ephedra (Gnetales) is limited and confusing from an evolutionary perspective, with parallelisms and intraspecific variation. However, recent analyses of molecular data provide a phylogenetic framework for investigations of morphological traits, albeit with few informative characters in the investigated gene regions. We document morphological, anatomical and histological variation patterns in the female reproductive unit and test the hypothesis that some Early Cretaceous fossils, which share synapomorphies with Ephedra, are members of the extant clade. Results indicate that some morphological features are evolutionarily informative although intraspecific variation is evident. Histology and anatomy of cone bracts and seed envelopes show clade‐specific variation patterns. There is little evidence for an inclusion of the Cretaceous fossils in the extant clade. Rather, a hypothesized general pattern of reduction of the vasculature in the ephedran seed envelope, probably from four vascular bundles in the fossils, to ancestrally three in the living clade, and later to two, is consistent with phylogenetic and temporal analyses, which indicate that extant diversity evolved after the Cretaceous–Tertiary boundary. Notwithstanding striking similarities between living and Cretaceous Ephedra, available data indicate that the Mesozoic diversity went almost entirely extinct in the late Cretaceous causing a bottleneck effect in Ephedra, still reflected today by an extraordinarily low level of genetic and structural diversity. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 387–430.     

A complete molecular phylogeny of Claravis confirms its paraphyly within small New World ground‐doves (Aves: Peristerinae) and implies multiple plumage state transitions

The three species in the genus Claravis (Aves: Peristerinae) are unique among members of the small New World ground‐dove clade. All three species inhabit forested areas rather than open scrubby habitat, and exhibit obvious sexual dichromatism. However, the phylogenetic relationships within Claravis remain unknown. The only molecular phylogenetic study to include more than one species of Claravis indicated the genus is paraphyletic. Here we include molecular data from all three Claravis species, including sequences from a museum skin of the previously unsampled Claravis geoffroyi (purple‐winged ground‐dove). Using both mitochondrial and nuclear loci, we estimate phylogenies and divergence times for the small New World ground‐dove clade. We also use ancestral state reconstruction methods to infer the evolution of male blue plumage (and thus sexual dimorphism) in the clade. As in the previous study we recover Claravis as a paraphyletic group, but with Claravis geoffroyi as the sister species to Claravis mondetoura (maroon‐chested ground‐dove). This result has important implications for the evolutionary history of the small New World ground‐dove clade. In particular, we recover multiple independent transitions between the monomorphic and dimorphic plumage states, which perhaps indicates sexual dimorphism arose twice in the group.     

'Andean-centred' genera in the short-branch clade of Annonaceae: testing biogeographical hypotheses using phylogeny reconstruction and molecular dating

Aim We test biogeographical hypotheses regarding the origin of Andean‐centred plant groups by reconstructing phylogeny in the short‐branch clade (SBC) of Annonaceae, and estimating the timing of diversifications in four apparently Andean‐centred genera: Cremastosperma R.E.Fr., Klarobelia Chatrou, Malmea R.E.Fr. and Mosannona Chatrou. The SBC includes species distributed in both the Old and New World tropics. A number of the Neotropical genera display ‘Andean‐centred’ distribution patterns, with high species richness on both sides of the Andes mountain range. In particular, we test whether these groups could have originated on the South American continent during the time frame of the Andean orogeny [from c. 23 Ma (Miocene) to the present]. Methods Chloroplast DNA sequences were used to reconstruct phylogeny in related Annonaceae taxa plus outgroups, under maximum parsimony and Bayesian inference. The markers rbcL, trnL‐trnF and psbA‐trnH were sampled for 96 accessions to test the monophyly of each of the genera, and thus whether they might be para‐ or polyphyletic with respect to related groups distributed across Amazonia. To determine the sister groups of the four genera, the additional markers matK, ndhF, trnT‐trnL, trnS‐trnG and atpB‐rbcL were sampled for 23 of the 96 accessions. Molecular dating techniques (nonparametric rate‐smoothing; penalized likelihood; Bayesian inference) were then applied to estimate the age of the crown group of each genus and the age of their sister groups. Results Monophyly was confirmed in Cremastosperma, Malmea and Mosannona. The monotypic genus Pseudephedranthus Aristeg. was found to be nested within Klarobelia, the species of which otherwise formed a monophyletic group, and a South American‐centred (SAC) clade was identified. The SAC clade comprises all the SBC genera distributed in South America and generally to a limited extent into Central America, but not those endemic to Africa, Asia and Central America. Age estimations for clades within the SBC were no older than around 60 Myr; those for the crown groups of Cremastosperma, Klarobelia, Malmea and Mosannona fell largely within the last 10–20 Myr. Main conclusions The distribution patterns of Cremastosperma, Klarobelia, Malmea and Mosannona are not the arbitrary result of the definition of para‐ or polyphyletic groups. We infer the presence of a common ancestor of the four genera in South America, but not by vicariance of an ancestral population on Gondwana. The age estimations, instead, may suggest that the SAC clade originated in South America by dispersal across the Boreotropics. Although the strength of this test was limited by imprecision in the molecular dating results, the ages of crown groups of the four genera suggest that diversifications occurred within the time frame of the orogeny of the Northern Andes.     

From East Gondwana to Central America: historical biogeography of the Alstroemeriaceae

Aim The Alstroemeriaceae is among 28 angiosperm families shared between South America, New Zealand and/or Australia; here, we examine the biogeography of Alstroemeriaceae to better understand the climatic and geological settings for its diversification in the Neotropics. We also compare Alstroemeriaceae with the four other Southern Hemisphere families that expanded from Patagonia to the equator, to infer what factors may have permitted such expansions across biomes. Location South America, Central America, Australia and New Zealand. Methods Three chloroplast genes, one mitochondrial gene and one nuclear DNA region were sequenced for 153 accessions representing 125 of the 200 species of Alstroemeriaceae from throughout the distribution range; 25 outgroup taxa were included to securely infer evolutionary directions and be able to use both ingroup and outgroup fossil constraints. A relaxed‐clock model relied on up to three fossil calibrations, and ancestral ranges were inferred using statistical dispersal–vicariance analysis (S‐DIVA). Southern Hemisphere disjunctions in the flowering plants were reviewed for key biological traits, divergence times, migration directions and habitats occupied. Results The obtained chronogram and ancestral area reconstruction imply that the most recent common ancestor of Colchicaceae and Alstroemeriaceae lived in the Late Cretaceous in southern South America/Australasia, the ancestral region of Alstroemeriaceae may have been South America/Antarctica, and a single New Zealand species is due to recent dispersal from South America. Chilean Alstroemeria diversified with the uplift of the Patagonian Andes c. 18 Ma, and a hummingbird‐pollinated clade (Bomarea) reached the northern Andes at 11–13 Ma. The South American Arid Diagonal (SAAD), a belt of arid vegetation caused by the onset of the Andean rain shadow 14–15 Ma, isolated a Brazilian clade of Alstroemeria from a basal Chilean/Argentinean grade. Main conclusions Only Alstroemeriaceae, Calceolariaceae, Cunoniaceae, Escalloniaceae and Proteaceae have expanded and diversified from Patagonia far into tropical latitudes. All migrated northwards along the Andes, but also reached south‐eastern Brazil, in most cases after the origin of the SAAD. Our results from Alstroemeria now suggest that the SAAD may have been a major ecological barrier in southern South America.     

The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea)

The Lanceocercata are a clade of stick insects (Phasmatodea) that have undergone an impressive evolutionary radiation in Australia, New Caledonia, the Mascarene Islands and areas of the Pacific. Previous research showed that this clade also contained at least two of the nine New Zealand stick insect genera. We have constructed a phylogeny of the Lanceocercata using 2277 bp of mitochondrial and nuclear DNA sequence data to determine whether all nine New Zealand genera are indeed Lanceocercata and whether the New Zealand fauna is monophyletic. DNA sequence data were obtained from mitochondrial cytochrome oxidase subunits I and II and the nuclear large subunit ribosomal RNA and histone subunit 3. These data were subjected to Bayesian phylogenetic inference under a partitioned model and maximum parsimony. The resulting trees show that all the New Zealand genera are nested within a large New Caledonian radiation. The New Zealand genera do not form a monophyletic group, with the genus Spinotectarchus Salmon forming an independent lineage from the remaining eight genera. We analysed Lanceocercata apomorphies to confirm the molecular placement of the New Zealand genera and to identify characters that confirm the polyphyly of the fauna. Molecular dating analyses under a relaxed clock coupled with a Bayesian extension to dispersal‐vicariance analysis was used to reconstruct the biogeographical history for the Lanceocercata. These analyses show that Lanceocercata and their sister group, the Stephanacridini, probably diverged from their South American relatives, the Cladomorphinae, as a result of the separation of Australia, Antarctica and South America. The radiation of the New Caledonian and New Zealand clade began 41.06 million years ago (mya, 29.05–55.40 mya), which corresponds to a period of uplift in New Caledonia. The main New Zealand lineage and Spinotectarchus split from their New Caledonian sister groups 33.72 (23.9–45.62 mya) and 29.9 mya (19.79–41.16 mya) and began to radiate during the late Oligocene and early Miocene, probably in response to a reduction in land area and subsequent uplift in the late Oligocene and early Miocene. We discuss briefly shared host plant patterns between New Zealand and New Caledonia. Because Acrophylla sensu Brock & Hasenpusch is polyphyletic, we have removed Vetilia Stål from synonymy with Acrophylla Gray.     

Biogeography of the Monimiaceae (Laurales): a role for East Gondwana and long‐distance dispersal,but not West Gondwana

Aim The biogeography of the tropical plant family Monimiaceae has long been thought to reflect the break‐up of West and East Gondwana, followed by limited transoceanic dispersal. Location Southern Hemisphere, with fossils in East and West Gondwana. Methods We use phylogenetic analysis of DNA sequences from 67 of the c. 200 species, representing 26 of the 28 genera of Monimiaceae, and a Bayesian relaxed clock model with fossil prior constraints to estimate species relationships and divergence times. Likelihood optimization is used to infer switches between biogeographical regions on the highest likelihood tree. Results Peumus from Chile, Monimia from the Mascarenes and Palmeria from eastern Australia/New Guinea form a clade that is sister to all other Monimiaceae. The next‐deepest split is between the Sri Lankan Hortonia and the remaining genera. The African Monimiaceae, Xymalos monospora, then forms the sister clade to a polytomy of five clades: (I) Mollinedia and allies from South America; (II) Tambourissa and allies from Madagascar and the Mascarenes; (III) Hedycarya, Kibariopsis and Leviera from New Zealand, New Caledonia and Australia; (IV) Wilkiea, Kibara, Kairoa; and (V) Steganthera and allies, all from tropical Australasia. Main conclusions Tree topology, fossils, inferred divergence times and ances‐tral area reconstruction fit with the break‐up of East Gondwana having left a still discernible signature consisting of sister clades in Chile and Australia. There is no support for previous hypotheses that the break‐up of West Gondwana (Africa/South America) explains disjunctions in the Monimiaceae. The South American Mollinedia clade is only 28–16 Myr old, and appears to have arrived via trans‐Pacific dispersal from Australasia. The clade apparently spread in southern South America prior to the Andean orogeny, fitting with its first‐diverging lineage (Hennecartia) having a southern‐temperate range. The crown ages of the other major clades (II–V) range from 20 to 29 Ma, implying over‐water dispersal between Australia, New Caledonia, New Zealand, and across the Indian Ocean to Madagascar and the Mascarenes. The endemic genus Monimia on the Mascarenes provides an interesting example of an island lineage being much older than the islands on which it presently occurs.     

The genus Artemisia (Asteraceae: Anthemideae) at a continental crossroads: molecular insights into migrations, disjunctions, and reticulations among Old and New World species from a Beringian perspective

Artemisia is the largest genus (ca. 350-500+ spp.) in the tribe Anthemideae and is composed of ecologically, morphologically, and chemically diverse species that are found primarily throughout the Northern Hemisphere. Two major centers of diversity for the genus are located in Eurasia and western North America, but phytogeographic links connecting these two regions are observed all across the North Pacific Rim and adjacent areas in the Arctic, including many islands and archipelagos. Previous phylogenetic studies have helped to clarify major lineages and identify likely sister relationships, but many questions remain unanswered regarding the relationships and migration history of New and Old World species. Here we investigate the phylogenetics of Artemisia within a biogeographic context centered in the Beringian Region and offer new hypotheses concerning species relationships, migration history, and the likely role of reticulate evolution in the genus. Our sampling included many new taxa and emphasized multiple accessions of widespread species, species from proposed refugia, and species with disjunct/vicariant distributions. The ITS phylogeny contained 173 accessions (94 new and 79 from GenBank) and indicated that Artemisia is paraphyletic by the exclusion of several small Asian genera and the North American genus Sphaeromeria. Following a survey of thirteen chloroplast loci, phylogenies based on two plastid markers (psbA-trnH and rpl32-trnL spacers) were constructed with a reduced data set, and though largely consistent with the ITS topology, revealed several cases of possible introgression among New World and Beringian species. Our analysis reveals that North American Artemisia species have multiple origins, and that western North America has served as a source for some colonizing elements in eastern Asia and South America.     

Phylogeny of the large extinct South American Canids (Mammalia,Carnivora, Canidae) using a “total evidence” approach

South America currently possesses a high diversity of canids, comprising mainly small to medium‐sized omnivorous species, but in the Pleistocene there were large hypercarnivorous taxa that were assigned to Protocyon spp., Theriodictis spp., Canis gezi, Canis nehringi and Canis dirus. These fossils have never been included in phylogenies based on quantitative cladistics, but hand‐constructed cladograms published in the 1980s included some of them in the South American canine clade and others in the Canis clade. In this work, the phylogenetic position of the large extinct South American canids was studied using a large sample of living and extinct canids, as well as different sources of characters (e.g. DNA and 133 osteological characters). The phylogenetic analysis corroborates the inclusion of Theriodictis and Protocyon in the “South American clade”, where C. gezi is also included. In addition, the position of C. dirus as a highly derived Canis species is confirmed. The simultaneous analysis supports hypercarnivory having arisen at least three times in Caninae and once in the “South American clade”. The combination of the phylogenetic analyses, the fossil record and divergence dates estimated in previous works suggests that at least three or four independent lineages of the “South American clade” invaded South America after the establishment of the Panama bridge around 3 million years ago, plus other events corresponding to the immigration of Urocyon and Canis dirus.
© The Willi Hennig Society 2009.     

Molecular clocks keep dispersal hypotheses afloat: evidence for trans‐Atlantic rafting by rodents

Aim In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time‐frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the African and South American continents has been an irreconcilable controversy for evolutionary biologists, presenting enigmas for both Gondwanan vicariance and Late Eocene dispersal hypotheses. In an attempt to resolve this discordance, we aim to provide a more robust phylogenetic hypothesis and improve divergence‐date estimates, which are essential to assessing the null hypothesis of vicariance biogeography. Location The primary centres of distribution are in Africa and South America. Methods We implemented parsimony, maximum‐likelihood and Bayesian methods to generate a phylogeny of 37 hystricognath taxa, the most comprehensive taxonomic sampling of this group to date, on the basis of two nuclear gene regions. To increase phylogenetic resolution at the basal nodes, these data were combined with previously published data for six additional nuclear gene regions. Divergence dates were estimated using two relaxed‐molecular‐clock methods, Bayesian multidivtime and nonparametric rate smoothing. Results Our data do not support reciprocal monophyly of African and South American lineages. Indeed, Old World porcupines (i.e. Hystricomorpha) appear to be more closely related to New World lineages (i.e. Caviomorpha) than to other Old World families (i.e. Bathyergidae, Petromuridae and Thryonomyidae). The divergence between the monophyletic assemblage of South American lineages and its Old World ancestor was estimated to have occurred c. 50 Ma. Main conclusions Our phylogenetic hypothesis and divergence‐date estimates are strongly at odds with Gondwanan‐vicariance isolating mechanisms. In contrast, our data suggest that transoceanic dispersal has played a significant role in governing the contemporary distribution of hystricognath rodents. Molecular‐clock analyses imply a trans‐Tethys dispersal event, broadly confined to the Late Cretaceous, and trans‐Atlantic dispersal within the Early Eocene. Our analyses also imply that the use of the oldest known South American rodent fossil as a calibration point has biased molecular‐clock inferences.     

Evolution of seed dispersal in North American <Emphasis Type="Italic">Ephedra</Emphasis>

Related plants often produce seeds that are dispersed in very different ways, raising questions of how and why plants undergo adaptive shifts in key aspects of their reproductive ecology. Here we analyze the evolution of seed dispersal syndromes in an ancient group of plants. Ephedra (Gymnospermae; Gnetales; Ephedraceae) is a genus containing ≈50 species in semiarid ecosystems worldwide and with three distinct types of cones. We collected mature cones and seeds of ten species of Ephedra in southwestern United States and measured nine morphological traits for each species. Principal component analysis and other data characterized three types of Ephedra cones and seeds. Species with dry, winged cone bracts are dispersed by wind (i.e., E. torreyana and E. trifurca), those with succulent, brightly-colored cone bracts are dispersed by frugivorous birds (i.e., E. antisyphilitica), and those with small, dry cone bracts and large seeds are dispersed by seed-caching rodents (e.g., E. viridis and E. californica). Two species (E. funerea and E. nevadensis) have cone and seed morphologies intermediate between two seed dispersal syndromes. Seed and cones traits were mapped onto two recent phylogenies to help reveal the evolutionary history of seed dispersal syndromes. Bird dispersal is thought to be the ancestral form of seed dispersal in ephedras as it is common in the Old World where Ephedra originated, but the three North American species dispersed by birds are not monophyletic. The two wind dispersed species in North America also do not cluster together, suggesting separate origins. Seed dispersal by seed-caching rodents is common in North America and appears to have evolved several times, but this syndrome is absent form other continents. The evolutionary history of Ephedra in North America suggests that the means of seed dispersal has been malleable. Evolutionary shifts were likely linked to changes in ecological conditions.     

Trachemys medemi n. sp. from northwestern Colombia turns the biogeography of South American slider turtles upside down

South America was invaded by slider turtles (Trachemys spp.) twice, with one immigration wave estimated to have reached South America 8.6–7.1 million years ago (mya) and a second wave, 2.5–2.2 mya. The two widely disjunct South American subspecies of Trachemys dorbigni (northeastern and southern Brazil, Río de la Plata region of Argentina and Uruguay) are derived from the first dispersal pulse, while the two South American subspecies of Trachemys venusta (Colombia, Venezuela) originated from the second immigration event. We describe a new species of slider turtle from the lower Atrato river basin of Antioquia and Chocó departments, northwestern Colombia. This new species, the Atrato slider (Trachemys medemi n. sp.), is the first representative of the older immigration wave inhabiting northern South America. Using phylogenetic analyses of 3,242 bp of mitochondrial and 3,396 bp of nuclear DNA, we show that T. medemi is more closely related to T. dorbigni than to the geographically neighboring subspecies of Trachemys grayi and T. venusta from Central America and northern South America. The two subspecies of T. dorbigni are separated from the Atrato slider by the Andes and the Amazon Basin, and occur approximately 4,600 km and 3,700 km distant from T. medemi. According to molecular clock calculations, T. medemi diverged from the last common ancestor of the two subspecies of T. dorbigni during the Pliocene (4.1–2.8 mya), with T. dorbigni diversifying later (2.3–1.9 mya) in eastern South America beyond the Amazon basin. The divergence of the T. dorbigni subspecies overlaps with the estimated arrival of T. venusta in South America (2.5–2.2 mya). This time is characterized by massive climatic and environmental fluctuations with intermittent dispersal corridors in South America. According to their distribution, it seems likely that the ancestors of the extant subspecies of T. dorbigni dispersed along the eastern corridor, leaving a relict population northwest of the Andes with T. medemi. The distribution range of T. medemi is surrounded by taxa derived from the second southern range expansion of slider turtles, so that it can be concluded that T. venusta circumvented the habitats occupied by the ancestors of the Atrato slider when entering South America.     

Phylogenetic status and historical origins of the oviparous and viviparous gyrodactylids (Monogenoidea,Gyrodactylidea)

Phylogenetic analyses of sequences of the 18S rDNA and MT‐CO2 gene fragments indicated that the oviparous and viviparous gyrodactylid‐like monogenoids formed independent monophyletic clades within the Order Gyrodactylidea, supporting the reinstatement of the Oogyrodactylidae and limiting the Gyrodactylidae to the viviparous species. Analyses further indicated that the clade comprising the two families shared a common ancestor with the Udonellidae. Two clades, that of Aglaiogyrodactylus and that of Phanerothecium, were identified within the Oogyrodactylidae, while Onychogyrodactylus was shown to be polyphyletic and Oogyrodactylus basal within the family. One putative synapomorphy was identified for the Oogyrodactylidae, that is presence of a massive Mehlis’ gland. The Gyrodactylidae was limited to species having a viviparous mode of reproduction, although relationships within the family were generally poorly resolved. Several putative synapomorphies were found for the Gyrodactylidae, including viviparity and protogyny, a bulbous and armed MCO, absence of a vitellarium, and presence of a knob‐like deep anchor root (Fig. 3e). Ultrametric analyses suggested that the initial divergence of the clade of the gyrodactylid‐like monogenoids and Udonellidae occurred about 335 mya (based on the 18S rDNA fragment) and about 400 mya (based on the MT‐CO2 gene fragment). Using the 18S rDNA fragment and three calibration points, ultrametric analyses indicated that the Gyrodactylidae and Oogyrodactylidae diverged at approximately 278 mya, with initial diversification within the Gyrodactylidae (about 211 mya) occurring earlier than that of the Oogyrodactylidae (about 133 mya), the latter coinciding with the breakup of Gondwana and the initial diversification of the armoured catfishes (Loricariidae). Finally, diagnoses were provided for the Gyrodactylidae and Oogyrodactylidae along with a list of genera assigned to each family.