Time-dependent rates of molecular evolution

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.

Anomalous capitulum structure and monoecy may confer flexibility in sex allocation and life history evolution in the Ifloga lineage of paper daisies (Compositae: Gnaphalieae)

PREMISE OF THE STUDY

Evolutionary significance of the Compositae capitulum and variation in its structure is poorly understood, although it may permit flexibility in sexual expression. Optimal sex ratio differs with life-history and reproductive strategy. We explore how the genus Ifloga and related members of southern African Gnaphalieae achieved different sex ratios, and the associations of these ratios with annual and perennial life history.

METHODS

Sex allocation was measured using the male to female ratio (M/F), a novel approximator of the pollen to ovule ratio (P/O). Life-history (annuality/perenniality), capitulum structure, capitular sexual system, and M/F were reconstructed on time-proportional phylogenies. Trait associations were examined using phylogenetically independent contrasts (PICs).

KEY RESULTS

Annual taxa have strongly female-biased capitula, as measured by M/F, and either gynomonoecious or monoecious sexual systems, while perennials have equal or male-biased capitula that are hermaphroditic or monoecious. These results are largely supported by PIC analysis. Different sexual systems afford differing flexibility in sex allocation, with hermaphrodites having the least, and monoecious taxa the greatest, range in M/F. Within Ifloga, the anomalous capitulum evolved in an annual, gynomonoecious ancestor, followed by two independent gains of monoecy. Two subsequent gains of perenniality occurred within a monoecious sublineage.

CONCLUSIONS

Different life histories have divergent sex allocation optima and are strongly associated with different sexual systems in gnaphalioid daisies. An anomalous capitulum structure in Ifloga may have facilitated the evolution of monoecy, which in turn may be linked to the evolution of life-history diversity in the genus.

Systematics and biogeography of the Gondwanan Orthocladiinae (Diptera: Chironomidae)

Restrictions to effective dispersal and gene flow caused by the fragmentation of ancient supercontinents are considered to have driven diversification and speciation on disjunct landmasses globally. Investigating the role that these processes have played in the development of diversity within and among taxa is crucial to understanding the origins and evolution of regional biotas. Within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae), a group of genera that are distributed across the austral continents (Australia, New Zealand, South America) have been proposed to represent a relict Gondwanan clade. We used a molecular approach to resolve relationships among taxa with the aim to determine the relative roles that vicariance and dispersal may have played in the evolution of this group. Continental biotas did not form monophyletic groups, in accordance with expectations given existing morphological evidence. Patterns of phylogenetic relationships among taxa did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent. Likewise, divergence time estimates, particularly for New Zealand taxa, largely post-dated continental fragmentation and implied instead that several transoceanic dispersal events may have occurred post-vicariance. Passive dispersal of gravid female chironomid adults is the most likely mechanism for transoceanic movement, potentially facilitated by West Wind Drift or anti-cyclone fronts. Estimated timings of divergence among Australian and South American Botryocladius, on the other hand, were congruent with the proposed ages of separation of the two continents from Antarctica. Taken together, these data suggest that a complex relationship between both vicariance and dispersal may explain the evolution of this group. The sampling regime we implemented here was the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly revealed several novel taxa that will require formal description.

Molecular phylogenetics of suborder Cactineae (Caryophyllales), including insights into photosynthetic diversification and historical biogeography

PREMISE OF THE STUDY

Phylogenetic relationships were investigated among the eight families (Anacampserotaceae, Basellaceae, Cactaceae, Didiereaceae, Halophytaceae, Montiaceae, Portulacaceae, Talinaceae) that form suborder Cactineae (= Portulacineae) of the Caryophyllales. In addition, photosynthesis diversification and historical biogeography were addressed. •

METHODS

Chloroplast DNA sequences, mostly noncoding, were used to estimate the phylogeny. Divergence times were calibrated using two Hawaiian Portulaca species, due to the lack of an unequivocal fossil record for Cactineae. Photosynthetic pathways were determined from carbon isotope ratios (δ(13)C) and leaf anatomy. •

KEY RESULTS

Maximum likelihood and Bayesian analyses were consistent with previous studies in that the suborder, almost all families, and the ACPT clade (Anacampserotaceae, Cactaceae, Portulacaceae, Talinaceae) were strongly supported as monophyletic; however, relationships among families remain uncertain. The age of Cactineae was estimated to be 18.8 Myr. Leaf anatomy and δ(13)C and were congruent in most cases, and inconsistencies between these pointed to photosynthetic intermediates. Reconstruction of photosynthesis diversification showed C(3) to be the ancestral pathway, a shift to C(4) in Portulacaceae, and five independent origins of Crassulacean acid metabolism (CAM). Cactineae were inferred to have originated in the New World. •

CONCLUSIONS

Although the C(3) pathway is inferred as the ancestral state in Cactineae, some CAM activity has been reported in the literature in almost every family of the suborder, leaving open the possibility that CAM may have one origin in the group. Incongruence among loci could be due to internal short branches, which possibly represent rapid radiations in response to increasing aridity in the Miocene.

Tracing the temporal and spatial origins of island endemics in the Mediterranean region: a case study from the citrus family (Ruta L., Rutaceae)

Understanding the origin of island endemics is a central task of historical biogeography. Recent methodological advances provide a rigorous framework to determine the relative contribution of different biogeographic processes (e.g., vicariance, land migration, long-distance dispersal) to the origin of island endemics. With its complex but well-known history of microplate movements and climatic oscillations, the Mediterranean region (including the Mediterranean basin and Macaronesia) provides the geographic backdrop for the diversification of Ruta L., the type genus of Rutaceae (citrus family). Phylogenetic, molecular dating, and ancestral range reconstruction analyses were carried out to investigate the extent to which past geological connections and climatic history of the Mediterranean region explain the current distribution of species in Ruta, with emphasis on its island endemics. The analyses showed that Ruta invaded the region from the north well before the onset of the Mediterranean climate and diversified in situ as the climate became Mediterranean. The continental fragment island endemics of the genus originated via processes of land migration/vicariance driven by connections/disconnections between microplates, whereas the oceanic island endemics were the product of a single colonization event from the mainland followed by in situ diversification. This study emphasizes the need for an integrative, hypothesis-based approach to historical biogeography and stresses the importance of temporary land connections and colonization opportunity in the biotic assembly of continental fragment and oceanic islands, respectively.

Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration

Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.

Molecular systematics and global phylogeography of angel sharks (genus Squatina)

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe-North Africa-Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events.

Insights into the evolutionary history of Indo-Pacific bloodfeeding terrestrial leeches (Hirudinida:Arhynchobdellida:Haemadipisdae)

Haemadipsidae is a clade of notorious bloodfeeding annelids adapted to tropical and sub-tropical rainforests found throughout the Indo-Pacific. This family traditionally includes duognathous (two-jawed) endemics, each placed in their own genus, from continental and volcanic islands including: Australia, Indonesia, Madagascar, Papua New Guinea, Philippines, Seychelles, and South Pacific islands, while trignathous (three-jawed) Tritetrabdella species and the speciose Haemadipsa are exclusive to the Indian subcontinent ranging into east and south-east Asia. One of the more compelling aspects of haemadipsids is their distribution on post-Gondwanan landmasses. In this study, the phylogenetic relationships, taxonomy and biogeographic patterns of Haemadipsidae were examined. Over 5 kb of sequence data from three genes (nuclear 18S rDNA and 28S rDNA and mitochondrial COI) for 37 haemadipsid exemplars, representing 12 of the 15 recognised genera, were analysed under the criteria of maximum parsimony and Bayesian inference. The results show that widespread duognathous species form a monophyletic group derived from trignathous ancestry and are sister to a new trignathous clade for Haemadipsidae. This phylogenetic hypothesis rejected Gondwanan vicariance as an explanation for the diversification of haemadipsids. Haemadipsidae is accepted as the formal name for these Indo-Pacific leeches. Whereas the subdivisions Haemadipsinae and Domanibdellinae are clarified, there is a need to establish a new subfamily, Tritetrabdellinae, for the newly identified trignathous clade that is sister to Domanibdellinae. This study provides a basis for continued elucidation of the evolutionary relationships and classification of these terrestrial annelids.

Out of Antarctica?--new insights into the phylogeny and biogeography of the Pleurobranchomorpha (Mollusca, Gastropoda)

The aim of the current study was to gain new insights into the phylogeny, biogeography and evolution of the opisthobranch clade Pleurobranchomorpha. We focused on testing the hypothesis of an Antarctic origin of this clade. The combination of four gene markers (18S rDNA, 28S rDNA, 16S rDNA and CO1) was used to infer a phylogenetic hypothesis of the Pleurobranchomorpha employing Maximum likelihood and Bayesian inference methods. Four methodologically distinct approaches were applied to reconstruct the historical biogeography and dating of the tree was performed via relaxed molecular clock analysis. Phylogenetic analyses supported the monophyly of the Pleurobranchomorpha and their sister group relationship to the Nudibranchia. Monophyly of the main subgroups Pleurobranchaeinae and Pleurobranchinae could not be revealed. Reconstruction of the ancestral area of the Pleurobranchomorpha yielded different possibilities in the diverse analyses. However, the Pleurobranchinae most probably derived from an Antarctic origin. Estimation of divergence times revealed a long credible interval for the Pleurobranchomorpha, whereas the Pleurobranchinae diverged in Early Oligocene and underwent rapid radiation during Oligocene and Early Miocene. Divergence of the Pleurobranchinae into the Antarctic Tomthompsonia and the remaining species in Early Oligocene coincides with two major geological events; namely the onset of glaciation in Antarctica and the opening of the Drake Passage with following formation of the Antarctic Circumpolar Current (ACC). These sudden and dramatic changes in climate probably led to subsequent migration of the last common ancestor of the remaining Pleurobranchinae into warmer regions, while the ACC may have accounted for larval dispersal to the Eastern Atlantic.

Evolutionary pattern and process within the Vertigo gouldii (Mollusca: Pulmonata, Pupillidae) group of minute North American land snails

A phylogenetic analysis of 19 sibling taxa in the Vertigo gouldii group was conducted on 73 individuals sampled across North America using DNA sequence data of the mitochondrial genes cytochrome oxidase subunit 1 (CO1) and 16S ribosomal RNA (16S), and the internal transcribed spacer-2 of the nuclear ribosomal RNA (ITS-2) gene. The results of these analyses were found incongruent with previous taxonomic concepts used to define the V. gouldii group and its composite taxa that were based entirely on conchological features. The mtDNA sequence data suggest that some previous members of the traditional V. gouldii group may be more closely related to V. modesta. They also suggest that V. gouldii may itself consist of seven species-level branches spread across two deeply rooted clades. Revision of geographical distributions on the basis of these analyses suggests that these Vertigo species may commonly possess continental-sized ranges in spite of their minute size and limited active dispersal ability. High levels of sympatry within the group are also confirmed, with up to four species being known to co-occur within single microsites. These data also suggest that rates of diversification have been non-constant. Assuming a 1%/my rate of base pair substitution, a 10-fold diversification pulse is indicated from 6.7-7.0 myBP, which would be co-incident with known mid-late Miocene global climate changes.

A watershed study on genetic diversity: phylogenetic analysis of the Platypleura plumosa (Hemiptera: Cicadidae) complex reveals catchment-specific lineages

Historical biogeography studies have at their disposal a small suite of vicariance models to explain genetic differentiation within and between species. One of these processes involves the role of river catchments and their associated watersheds, in driving diversification and is applicable to both aquatic and terrestrial organisms. Although the idea of catchments structuring the genetic history of aquatic organisms is reasonably well understood, their effect on terrestrial organisms has largely been overlooked, with relevant studies being limited in scope. South Africa presents a perfect test-bed for elucidating this mechanism of diversification due to its rich biodiversity, range of climatic environments and many large river catchments. Here we use the cicadas of the Platypleura plumosa complex to highlight the importance of catchments and their associated watersheds in driving diversification of terrestrial invertebrates that lack an aquatic life-stage. Population structure was found to correspond to primary and in some cases secondary catchments; highlighting the need to include information on catchment structure when formulating hypotheses of population diversification. Recognizing that climate change in the near future is likely to alter the environment, and particularly precipitation patterns, insight into recent patterns of population change related to catchments may be useful in a conservation context.

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

BACKGROUND

Molecular dating has gained ever-increasing interest since the molecular clock hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees, allowing diverse evolutionary questions to be addressed. The key aspect of the molecular clock hypothesis, namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged, was soon shown to be untenable. Other approaches were proposed to take into account rate heterogeneity among lineages, but the calibration process, by which relative times are transformed into absolute ages, has received little attention until recently. New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record.

SCOPE AND CONCLUSIONS

The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper; other sources of calibration information are also discussed. Particularly error-prone aspects of fossil calibration are identified, such as fossil dating, the phylogenetic placement of the fossil and the incompleteness of the fossil record. Methods proposed to tackle one or more of these potential error sources are discussed (e.g. fossil cross-validation, prior distribution of calibration points and confidence intervals on the fossil record). In conclusion, the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.

Evolution of mimicry patterns in Metriorrhynchus (Coleoptera: Lycidae): the history of dispersal and speciation in southeast Asia

The concept of Müllerian mimicry suggests convergent evolution to an intermediate pattern and does not predict polymorphism in mimicry rings. We examined the evolution of mimicry patterns and the order of divergence of various factors, including the role of aposematic patterns in speciation, in a clade of net-winged beetles with a robust phylogeny that suggests that they dispersed from the Australian to Asian plate. We found strong evidence for the evolution of mimicry via advergence in Metriorrhynchus because older patterns are represented in the Oriental region within more than 100 species of lycids from several lineages. Advergence was likely the cause of the observed intraspecific polymorphism in contrast to the predicted universal monomorphism. Polymorphism was found in populations of two species in Sumatra and Borneo and in populations fine-tuned to subtle variants in various habitats. The advergence is likely to be based on the small population sizes of immigrants. The differences in population sizes result in much higher benefits for dispersing species than native populations. Speciation was trigged by the divergence in aposematic coloration, and the genetic differences accumulated slowly during incomplete isolation. We assumed that the differentiation in genitalia through sexual selection ultimately reinforced speciation initiated by the shift between mimicry patterns.

Island biogeography of Galápagos lava lizards (Tropiduridae: Microlophus): species diversity and colonization of the archipelago

The "lava lizards" (Microlophus) are distributed throughout the Galápagos Archipelago, and consist of radiations derived from two independent colonizations. The "Eastern Radiation" includes M. bivittatus and M. habeli endemic to San Cristobal and Marchena Islands. The "Western Radiation" includes five to seven historically recognized species distributed across almost the entire Archipelago. We combine dense geographic sampling and multilocus sequence data to estimate a phylogenetic hypothesis for the Western Radiation, to delimit species boundaries in this radiation, and to estimate a time frame for colonization events. Our phylogenetic hypothesis rejects two earlier topologies for the Western Radiation and paraphyly of M. albemarlensis, while providing strong support for single colonizations on each island. The colonization history implied by our phylogeny is consistent with general expectations of an east-to-west route predicted by the putative age of island groups, and prevailing ocean currents in the Archipelago. Additionally, combined evidence suggests that M. indefatigabilis from Santa Fe should be recognized as a full species. Finally, molecular divergence estimates suggest that the two colonization events likely occurred on the oldest existing islands, and the Western Radiation represents a recent radiation that, in most cases, has produced species that are considerably younger than the islands they inhabit.

Biogeography and the molecular dating game: a futile revival of phenetics?

In molecular dating, branch lengths are considered parameters that may be estimated by counting similarities and differences in DNA sequences. Long and short branches imply long and short time spans, which might appear informative additions when imposed on a tree that is otherwise cladistic. Recent attempts to apply molecular dating to southern hemisphere biogeography (Nothofagus, Adansonia) seem only another “excursion into futility,” as was the fate of phenetic systematics [H.H. Ross, 1964]. Some conceptual matters are clarified with reference to the experimental approach of Claude Bernard (1813–1878).

Origin and diversification of the clawed lobster genus Metanephrops (Crustacea: Decapoda: Nephropidae)

A phylogenetic analysis of all 17 extant species of the clawed lobster genus Metanephrops based on mitochondrial 12S rRNA, 16S rRNA and cytochrome c oxidase I, and nuclear histone H3 gene sequences supports the morphological groupings of two of the traditional groups of the genus (the binghami and japonicus groups) but refutes monophyly of the other two groups (the arafurensis and thomsoni groups). The results in general support a recent morphology-based cladistic analysis of this genus except that this study suggests M. neptunus to be a basal rather than a derived species as indicated in the morphological analysis. This species is genetically diverse over its geographical range. Moreover, the two color forms of M. thomsoni are genetically distinct, most likely representing different species. The molecular phylogeny and current distribution pattern of the extant species, together with the fossil record, suggest that the genus originated in the Antarctica in the Cretaceous, followed by diversification and dispersal along the continental shelf of different continents as a result of the vicariant events associated with the breakup of the Southern Temperate Gondwana since Late Cretaceous.

The age and biogeography of Citrus and the orange subfamily (Rutaceae: Aurantioideae) in Australasia and New Caledonia

The geological history of Australasia, New Caledonia, and Southeast Asia, has been complex, resulting in competing biogeographic hypotheses for taxa found here. Alternative hypotheses-Gondwanan vicariance, rafting terranes, long-distance dispersal-may be distinguished by different predicted divergence times between disjunct sister taxa. Taxa within Rutaceae subfamily Aurantioideae are ideal for testing these hypotheses because of their distributions. Therefore, the ages of Rutaceae and Aurantioideae were estimated using molecular dating. One data set comprised 51 sequences of rbcL and atpB with sampling across rosids and three fossil calibrations: crown Fabales+Fagales+Rosales (>94 Ma), Fabaceae (>51 Ma) and stem Ailanthus, Simaroubaceae (>52 Ma). Another data set comprised 81 Aurantioideae using >8 kb of chloroplast sequence and secondary calibration. Confidence in estimated divergence times was explored by varying the root age, dating method (strict, local, and relaxed clocks), and inclusion of internal calibrations. We conclude that the Rutaceae crown diverged in the Eocene (36.4-56.8 Ma, mean 47.6), whereas the Aurantioideae crown originated in the early Miocene (12.1-28.2 Ma, mean 19.8). This young age suggests that Gondwanan vicariance does not explain the distributions of extant Aurantioideae. Taxa found in New Caledonia may have arrived by separate transoceanic dispersal events.

New Caledonia: a very old Darwinian island?

New Caledonia has generally been considered a continental island, the biota of which largely dates back to Gondwanan times owing to its geological origin and the presence of phylogenetic relicts. This view is contradicted by geological evidence indicating long Palaeocene and Eocene submersions and by recent biogeographic and phylogenetic studies, with molecular or geophysical dating placing the biota no older than the Oligocene. Phylogenetic relicts do not provide conclusive information in this respect, as their presence cannot be explained by simple hypotheses but requires assumption of many ad hoc extinction events. The implication of this new scenario is that all the New Caledonian biota colonized the island since 37 Ma Local richness can be explained by local radiation and adaptation after colonization but also by many dispersal events, often repeated within the same groups of organisms. Local microendemism is another remarkable feature of the biota. It seems to be related to recent speciation mediated by climate, orography, soil type and perhaps unbalanced biotic interactions created by colonization disharmonies. New Caledonia must be considered as a very old Darwinian island, a concept that offers many more fascinating opportunities of study.

Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regions

From a phylogenetic perspective, the genus Manihot can be considered as an orphan group of plants, and the scientific knowledge acquired has been mainly related to cassava, one of the most important crops in poor tropical countries. The goal of the majority of evolutionary studies in the genus has been to decipher the domestication process and identify the closest relatives of cassava. Few investigations have focused on wild Manihot species, and the phylogeny of the genus is still unclear. In this study the DNA sequence variation from two chloroplast regions, the nuclear DNA gene G3pdh and two nuclear sequences derived from the 3'-end of two cassava ESTs, were used in order to infer the phylogenetic relationships among a subset of wild Manihot species, including two species from Cnidoscolus as out-groups. Maximum parsimony and Bayesian analyses were conducted for each data set and for a combined matrix due to the low variation of each region when analyzed independently. A penalized likelihood analysis of the chloroplast region trnL-trnF, calibrated with various age estimates for genera in the Euphorbiaceae extracted from the literature was used to determine the ages of origin and diversification of the genus. The two Mesoamerican species sampled form a well-defined clade. The South American species can be grouped into clades of varying size, but the relationships amongst them cannot be established with the data available. The age of the crown node of Manihot was estimated at 6.6 million years ago. Manihot esculenta varieties do not form a monophyletic group that is consistent with the possibility of multiple introgressions of genes from other wild species. The low levels of variation observed in the DNA regions sampled suggest a recent and explosive diversification of the genus, which is confirmed by our age estimates.

Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa

Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host-plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near-simultaneous radiation events, coupled with shifts in host-plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene - early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation-associated changes in climate and sea level.

The effect of inappropriate calibration: three case studies in molecular ecology

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.

Gondwanan break-up: legacies of a lost world?

Fierce debate surrounds the history of organisms in the southern hemisphere; did Gondwanan break-up produce ocean barriers that imposed distribution patterns on phylogenies (vicariance)? Or have organisms modified their distributions through trans-oceanic dispersal? Recent advances in biogeographical theory suggest that the current focus on vicariance versus dispersal is too narrow because it ignores 'geodispersal' (i.e. expansion of species into areas when geographical barriers disappear), extinction and sampling errors. Geodispersal produces multiple, conflicting vicariance patterns, and extinction and sampling errors destroy vicariance patterns. This perspective suggests that it is more difficult to detect vicariance than trans-oceanic dispersal and that specialized methods must be applied if an unbiased understanding of southern hemisphere biogeography is to be achieved.

THE ROLE OF BIOTIC AND ABIOTIC FACTORS IN EVOLUTION OF ANT DISPERSAL IN THE MILKWORT FAMILY (POLYGALACEAE)

A phylogenetic approach was taken to investigate the evolutionary history of seed appendages in the plant family Polygalaceae (Fabales) and determine which factors might be associated with evolution of elaiosomes through comparisons to abiotic (climate) and biotic (ant species number and abundance) timelines. Molecular datasets from three plastid regions representing 160 species were used to reconstruct a phylogenetic tree of the order Fabales, focusing on Polygalaceae. Bayesian dating methods were used to estimate the age of the appearance of ant-dispersed elaiosomes in Polygalaceae, shown by likelihood optimizations to have a single origin in the family. Topology-based tests indicated a diversification rate shift associated with appearance of caruncular elaiosomes. We show that evolution of the caruncular elaiosome type currently associated with ant dispersal occurred 54.0-50.5 million year ago. This is long after an estimated increase in ant lineages in the Late Cretaceous based on molecular studies, but broadly concomitant with increasing global temperatures culminating in the Late Paleocene-Early Eocene thermal maxima. These results suggest that although most major ant clades were present when elaiosomes appeared, the environmental significance of elaiosomes may have been an important factor in success of elaiosome-bearing lineages. Ecological abundance of ants is perhaps more important than lineage numbers in determining significance of ant dispersal. Thus, our observation that elaiosomes predate increased ecological abundance of ants inferred from amber deposits could be indicative of an initial abiotic environmental function.

Partitioned Bayesian analyses, dispersal-vicariance analysis, and the biogeography of Chinese toad-headed lizards (Agamidae: Phrynocephalus): a re-evaluation

The toad-headed lizards of genus Phrynocephalus are distributed from northwestern China to Turkey and are one of the major components of the central Asian desert fauna. To date, published morphological and molecular phylogenetic hypotheses of Phrynocephalus are only partially congruent, and the relationships within the genus are still far from clear. We re-analyzed published mitochondrial gene sequence data (12S, 16S, cyt b, ND4-tRNA(Leu)) by employing partition-specific modeling in a combined DNA analysis to clarify existing gaps in the phylogeny of Chinese Phrynocephalus. Using this phylogenetic framework, we inferred the genus' historical biogeography by using weighted ancestral-area analysis and dispersal-vicariance analysis in combination with a Bayesian relaxed molecular-clock approach and paleogeographical data. The partitioned Bayesian analyses support the monophyly of Phrynocephalus and its sister-group relationship with Laudakia. An earlier finding demonstrating the monophyly of the viviparous group is corroborated. However, our hypothesis of internal relationships of the oviparous group differs from a previous hypothesis as our results do not support monophyly of the oviparous taxa. Instead, the viviparous taxa form a clade with many oviparous taxa exclusive of P. helioscopus and P. mystaceus. Our results also suggest that: (1) P. putjatia is a valid species, comprising populations from Guide, Qinghai Province and Tianzhu, Gansu Province; (2) P. hongyuanensis is not a valid species, synonymized instead with P. vlangalii; (3) P. zetangensis is not a valid species and should be included in P. theobaldi; (4) the population occurring in Kuytun, Xinjiang Uygur Autonomous Region is recognized as P. guttatus instead of P. versicolor; and (5) the Lanzhou population of P. frontalis is part of P. przewalskii. Congruent with previous hypotheses, the uplift of the Tibetan Plateau played a fundamental role in the diversification of Phrynocephalus. An evolutionary scenario combining aspects of vicariance and dispersal is necessary to explain the distribution of Phrynocephalus. Bayesian divergence-time estimation suggests that Phrynocephalus originated at the Middle-Late Miocene boundary (15.16-10.4 Ma), and diversified from Late Miocene to Pleistocene from a center of origin in Central Asia, Tarim Basin, and Junggar Basin temperate desert, followed by several rapid speciation events in a relatively short time. The proposed biogeographic scenarios also indicate that the Tarim Basin desert may be the secondary diversification center, followed by Junggar Basin temperate desert and Alashan Plateau temperate desert. In the viviparous group, the allopatric speciation of P. theobaldi and P. vlangalii may have been caused by the uplifting of Tanggula Mountain Ranges. In addition, the results of this study make an important contribution to understanding the uplift of the Tibetan Plateau and Tian Shan Mountains and the biogeography of the entire region.

Recalibrated tree of leaf beetles (Chrysomelidae) indicates independent diversification of angiosperms and their insect herbivores

BACKGROUND

The great diversity of the "Phytophaga" (weevils, longhorn beetles and leaf beetles) has been attributed to their co-radiation with the angiosperms based on matching age estimates for both groups, but phylogenetic information and molecular clock calibrations remain insufficient for this conclusion.

METHODOLOGY

A phylogenetic analysis of the leaf beetles (Chrysomelidae) was conducted based on three partial ribosomal gene markers (mitochondrial rrnL, nuclear small and large subunit rRNA) including over 3000 bp for 167 taxa representing most major chrysomelid lineages and outgroups. Molecular clock calibrations and confidence intervals were based on paleontological data from the oldest (K-T boundary) leaf beetle fossil, ancient feeding traces ascribed to hispoid Cassidinae, and the vicariant split of Nearctic and Palearctic members of the Timarchini.

PRINCIPAL FINDINGS

The origin of the Chrysomelidae was dated to 73-79 Mya (confidence interval 63-86 Mya), and most subfamilies were post-Cretaceous, consistent with the ages of all confirmed body fossils. Two major monocot feeding chrysomelid lineages formed widely separated clades, demonstrating independent colonization of this ancient (early Cretaceous) angiosperm lineage.

CONCLUSIONS

Previous calibrations proposing a much older origin of Chrysomelidae were not supported. Therefore, chrysomelid beetles likely radiated long after the origin of their host lineages and their diversification was driven by repeated radiaton on a pre-existing diverse resource, rather than ancient host associations.

Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae)

New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data.

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.

A method for constraining the age of origination of derived characters

Fossils are the physical records of the history of morphological character evolution on Earth and can provide valuable information concerning the sequence and timing of origination of derived characters. Knowledge of the timing of origination of synapomorphies makes it possible to estimate when unobserved character changes occurred in the geological past. Here we present a method for estimating the temporal interval during which synapomorphies evolved. The method requires either direct inclusion of fossil taxa (with or without extant taxa) in cladistic analyses based on morphological or combined data, or indirectly using the "molecular scaffold approach." Second, characters of interest are mapped on a most parsimonious tree and "minimum age node mapping" is used to place minimum ages on the nodes of the tree. Finally, characters of interest are evaluated for younger and/or older temporal constraints on the time of their origination; application of the older bound assumes ancestry of fossil terminals included in the tree. A key is provided herein describing the method. Among other applications, this approach has the potential to provide a powerful test of purported evolutionary cause-effect relationships. For example, the method has the ability to discover that derived characters of suggested adaptational significance may considerably pre-date the cause(s) that are hypothesized to have favored their establishment.

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

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

Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea

We present a molecular phylogenetic analysis of 2808 aligned bp of rrnL, cox1, cob, H3 and 18S rRNA of all major morphological groups of Papuadytes diving beetles (Coleoptera: Dytiscidae) which are diverse in running water habitats throughout the Australian region. We focus on the origin of the fauna of the megadiverse islands of New Guinea and New Caledonia. Parsimony as well as Bayesian analyses suggest a basal position of Australian species in a paraphyletic series, with more recent nested radiations in New Caledonia and New Guinea. According to molecular clock analyses, both landmasses were colonized during the Miocene, which matches geological data and corroborates similar findings in other taxonomic groups. Our analyses suggest that dispersal played an important role in the formation of these large insular faunas, although successful colonization appears to be a rare event, and, in this case, is unidirectional. Whether or not a lineage is present on an island is due to chance: Papuadytes are absent from Fiji, where related Copelatus have radiated extensively in the same habitats occupied by Papuadytes in New Caledonia and New Guinea, while Copelatus are absent from New Caledonia. Lineages of Papuadytes apparently colonized New Caledonia twice, around 14 and 9 MYA according to the molecular calibration, and both lineages are derived from an Australian ancestor. The older clade is represented only by two apparently relictual mountain species (one morphologically strongly adapted to highly ephemeral habitats), while the younger clade contains at least 18 species exhibiting a great morphological diversity. The 150+ species in New Guinea are monophyletic, apparently derived from an Australian ancestor, and constitute a morphologically rather homogenous group. The tree backbone remains insufficiently supported under parsimony and Bayesian analyses, where shorter branches suggest a rapid sequence of major branching events.