A molecular phylogeny of minivets (Passeriformes: Campephagidae: Pericrocotus): implications for biogeography and convergent plumage evolution

Jønsson, K. A., Irestedt, M., Ericson, P. G. P. & Fjeldså, J. (2009). A molecular phylogeny of minivets (Passeriformes: Campephagidae: Pericrocotus ): implications for biogeography and convergent plumage evolution.— Zoologica Scripta, 39 , 1–8.
Minivets are conspicuous and mostly intensely colourful birds inhabiting wooded environments in tropical and subtropical South and Southeast Asia and temperate East Asia. We present a robust phylogeny of the group based on nuclear and mitochondrial DNA data including all 12 recognized species and also many subspecies representing disjunct populations in the Oriental mainland and in Indonesia. The study indicates that minivets radiated within mainland Asia and dispersed to the Indonesian archipelago. We also demonstrate that in accordance with studies on other bird groups, plumage characters are highly plastic and that the diversity of plumage patterns and colouration represents an example of convergent evolution.     

Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

Trogidae constitute a monophyletic and biologically unique family within Scarabaeoidea, being the only keratinophagous group in the superfamily. Traditionally, the family has been divided into three distinctive genera, Polynoncus Burmeister, Omorgus Erichson and Trox Fabricius. Although the taxonomy of the group is relatively well studied, changes to the existing classification have recently been proposed and the family as currently constituted has not been subjected to phylogenetic analyses. Here we present a molecular phylogeny for this cosmopolitan family based on three partially sequenced gene regions: 16S rRNA, 18S rRNA and 28S rRNA (domain 2). Included in the analyses are representatives belonging to four of the five extant genera (and three of the four subgenera) from all major zoogeographic regions, representing about 20% of the known trogid species diversity in the family. Phylogenetic analyses performed included parsimony and Bayesian inference. We deduce their historical biogeography by using trogid fossils as calibration points for divergence estimates. Our analyses resolved relationships between and within genera and subgenera that are largely congruent with existing phylogeny hypotheses based on morphological data. We recovered four well‐supported radiations: Polynoncus, Omorgus, Holarctic Trox and African Phoberus MacLeay. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. The subgenera Trox and Phoberus should be elevated to genera to include the Holarctic and all the Afrotropical species, respectively, and Afromorgus returned to subgeneric rank. Estimates of divergence time are consistent with a Pangaean origin of the family in the Early Jurassic. The subsequent diversification of the major lineages is largely attributed to the break‐up of Pangaea and Gondwana in the Middle Jurassic and early Late Cretaceous, respectively.     

Phylogeny and systematics of the Proterodiplostomidae Dubois, 1936 (Digenea: Diplostomoidea) reflect the complex evolutionary history of the ancient digenean group

The Proterodiplostomidae Dubois, 1936 is a relatively small family of diplostomoidean digeneans parasitising the intestines of reptilian hosts associated with freshwater environments in tropical and subtropical regions. The greatest diversity of proterodiplostomids is found in crocodilians, although some parasitise snakes and turtles. According to the most recent revision, the Proterodiplostomidae included 17 genera within 5 subfamilies. Despite the complex taxonomic structure of the family, availability of testable morphology-based phylogenetic hypotheses and ancient hosts, molecular phylogenetic analyses of the group were practically lacking. Herein, we use novel DNA sequence data of the nuclear lsrRNA gene and mitochondrial cox1 gene from a broad range of proterodiplostomid taxa obtained from crocodilian, fish, and snake hosts on four continents to test the monophyly of the family and evaluate the present morphology-based classification system of the Proterodiplostomidae in comparison with the molecular phylogeny. This first detailed phylogeny for the Proterodiplostomidae challenges the current systematic framework. Combination of molecular phylogenetic data with examination of freshly collected quality specimens and re-evaluation of morphological criteria resulted in a number of systematic and nomenclatural changes along with a new phylogeny-based classification of the Proterodiplostomidae. As the result of our molecular and morphological analyses: (i) the current subfamily structure of the Proterodiplostomidae is abolished; (ii) three new genera, Paraproterodiplostomum n. g., Neocrocodilicola n. g. and Proteroduboisia n. g., are described and Pseudoneodiplostomoides Yamaguti, 1954 is restored and elevated from subgenus to genus level; (iii) two new species, Paraproterodiplostomum currani n. g., n. sp. and Archaeodiplostomum overstreeti n. sp., are described from the American alligator in Mississippi, USA. Comparison of the structure of terminal ducts of the reproductive system in all proterodiplostomid genera did not support the use of these structures for differentiation among subfamilies (or major clades) within the family, although they proved to be useful for distinguishing among genera and species. Our study includes the first report of proterodiplostomids from Australia and the first evidence of a snake acting as a paratenic host for a proterodiplostomid. A key to proterodiplostomid genera is provided. Questions of proterodiplostomid-host associations parasitic in crocodilians are discussed in connection with their historical biogeography. Our molecular phylogeny of the Proterodiplostomidae closely matches the current molecular phylogeny of crocodilians. Directions for future studies of the Proterodiplostomidae are outlined.

     

Molecular Phylogeny of Nepenthaceae Based on Cladistic Analysis of Plastid trnK Intron Sequence Data

Abstract: Nepenthaceae are an exceptional family with regard to carnivory and the uniformity of characters. This makes it difficult to resolve phylogenetic relationships due to convergent evolution of morphological features. Using comparative sequencing of the chloroplast trnK intron, the monophyly of this complex family and hypotheses of infrageneric relationships were tested. Sequences from 71 Nepenthes taxa, representing all groups and two taxa of the closely related Ancistrocladaceae and Dioncophyllaceae as outgroup, were determined and analysed using maximum parsimony methods. Results of this analysis show that the isolated taxa N. distillatoria (Sri Lanka) and N. pervillei (Seychelles) are the most basal, clearly separated from the Madagascan taxa N. madagascariensis and N. masoalensis which are placed in a distinct subclade. This corresponds with some plesiomorphic characters shared by these taxa. N. khasiana (North India) has an intermediate position between these relic Western species and the remaining taxa. The species of the Malay Archipelago can be referred to three distinct lineages which indicate a correlation to biogeography. Thus the recent disjunct distribution of Nepenthes is interpreted as a result of an incisive extinction of progenitors, a process of migration and a subsequent diversification on the islands of Borneo, Sumatra, Sulawesi and New Guinea. Based on our molecular data, two interpretations concerning the origin of Nepenthes are possible: i) evolution in the Northern Tethys which is supported by fossil pollen records from the European Focene, or, ii) a Gondwanaland origin at a time when the Indian plate was separated from Madagascar. Molecular data indicate that colonization of SE Asia started from an ancient Indian stock. Subsequently, in the Malay Archipelago a new secondary centre of diversity developed. Madagascar, the Seychelles and New Caledonia were probably reached by migration via land bridges, starting from widespead common ancestors with subsequent extinction leaving the current taxa. There is no evidence for long‐distance dispersal. Current infragenic classification of Nepenthes is only partly in accordance with the phylogeny inferred from trnK intron data.     

Uncovering an overlooked radiation: molecular phylogeny and biogeography of Madagascar's endemic river snails (Caenogastropoda: Pachychilidae: Madagasikara gen. nov.)

By analysing key morphological characters (with emphasis on shell, radula and stomach anatomy) and a partial fragment of the mitochondrial 16S rRNA gene (alignment length 860 bp), we examined patterns of diversity and differentiation of a previously overlooked radiation of Madagascan pachychilid freshwater gastropods. These analyses resulted in the discovery of three new species in addition to the two species that were already recognized. The complex nomenclatural and taxonomic implications are discussed and the finding of a viviparous reproductive mode in at least one among otherwise oviparous species is reported. Using a mitochondrial phylogeny that includes all currently accepted pachychilid genera and a strict molecular clock approach, we address the historical biogeography of the Madagascan species with respect to vicariant versus dispersalist biogeographical models. Using two alternative calibrations that were previously suggested for other gastropods, the molecular clock tree suggested that the origin of the Pachychilidae dates back to no more than 50 Mya, whereas the origin of the Madagascan lineage is estimated to date to a period between 15.6–31.5 Mya. These estimates are approximately concurrent with the dating of colonization events in a number of other Madagascan animal taxa. The pachychilid radiation on Madagascar appears not to be older than 3–5 Mya. Thus, although the global patterns of pachychilid distribution have earlier been interpreted to suggest a Gondwanan origin of the family, the present study does not support this postulate. Neither the topology of the molecular phylogeny, nor the timing of events as suggested from a molecular clock were found to be congruent with a vicariance scenario within the framework of Gondwanan fragmentation during the Mesozoic but, instead, imply overseas dispersal during the Cenozoic. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 867–894.     

The collision of the Indian plate with Asia: molecular evidence for its impact on the phylogeny of freshwater crabs (Brachyura: Potamidae)

Aim We used molecular data to answer the following questions: (1) Is morphology‐based (and to some extent, geography‐based) classification of the freshwater crab family Potamidae congruent with a molecular phylogeny? (2) What historical biogeographical event could have shaped this phylogeny? Location Material from the entire geographical range of the family Potamidae was analysed, including specimens from East Asia (China, Taiwan, the Ryukyus), Southeast Asia, South Asia (northern India, the Middle East and Near East), North Africa, and southern Europe. Methods Mitochondrial DNA sequences encoding 503 base pairs (excluding the variable regions) of the large subunit rRNA (16S rRNA) gene were obtained from 72 species belonging to 49 potamid genera, representing 51% of all known genera in this species‐rich family. Sequences were compared by means of phylogenetic analyses (minimum evolution, Bayesian inference, maximum likelihood and maximum parsimony) and Bayesian relaxed molecular clock estimates. Results The family Potamidae was found to be monophyletic with two major lineages, and there was support for the recognition of two mostly allopatric subfamilies, Potaminae and Potamiscinae. This is largely consistent with the current classification proposed. The ‘Potamiscinae’ clade comprised three subclades: (1) a well‐supported ‘eastern Asia’ subclade that included species from the eastern part of the range (China, Taiwan, the Ryukyus, the Philippines, Indochina, Malay Peninsula, northern India and Myanmar/Burma); (2) a weakly supported ‘Sunda Shelf islands’ subclade that included species from the larger Southeast Asian islands on the Sunda Shelf (Borneo, Sumatra and Java); and (3) a ‘Socotra’ subclade that comprised only Socotrapotamon from Socotra Island, off the north‐east coast of Africa. Main conclusions The discrete distribution of the two subfamilies in Europe/Asia is hypothesized to be the result of vicariance due to the collision of the Indian tectonic plate with the Asian continent, and the orogeny that caused the separation of the two freshwater crab lineages around 22.8 Ma. Within the Potamiscinae, the ‘Sunda Shelf islands’ subclade separated from other potamiscines around 21.1 Ma; and the endemic fauna of the East Asian islands (Taiwan, the Ryukyus and mainland Japan) was isolated from the Asian continent c. 8.4 Ma, following the opening of the Okinawa Trough. The ‘Socotra’ subclade diverged from the ‘eastern Asia’ subclade at 19.1 Ma during the Miocene. Its taxonomic position, however, remains unclear as the members of this clade possess the key potamine character of a transverse ridge on thoracic sternite 8, suggesting that this may in fact be a relict potamid group.     

Historical biogeography of tamarins,genus Saguinus: the molecular phylogenetic evidence

Hypotheses of the historical biogeography of tamarins (genus Saguinus) based on variation in coat colors and body size are tested using phylogenetic relationships inferred from mitochondrial DNA (mtDNA) sequence data. Samples from all 12 species of Saguinus and several subspecies are included in the analysis. Approximately 1,200 bases of mtDNA sequence from the cytochrome b and D-loop regions are reported for the tamarins and several outgroup taxa. Parsimony analysis of the mtDNA sequence data reveals Saguinus to be a monophyletic taxon composed of two major clades: one, the Small-bodied clade, contains S. nigricollis, S. tripartitus, and S. fuscicollis, and the other, the Large-bodied clade, contains the other nine species. The phylogenetic relationships among tamarins inferred from the mtDNA sequence data reject previous hypotheses for the historical biogeography of tamarins and suggest different dispersal routes for this group of New World monkeys. The molecular data suggest that tamarins dispersed across South America in two major waves from an origin somewhere south of the Amazon. One wave moved in a westerly direction, whereas the other moved in a northeastern direction toward the Amazon delta and then west along the northern portion of the continent into northern Colombia and Panama. Am J Phys Anthropol 108:65–89, 1999. © 1999 Wiley-Liss, Inc.     

Historical biogeography, divergence times, and diversification patterns of bumble bees (Hymenoptera: Apidae: Bombus)

Bumble bees (Bombus) are a cold-adapted, largely alpine group that can elucidate patterns of Holarctic historical biogeography, particularly in comparison to the alpine plants with which they likely coevolved. A recently published molecular phylogeny of bumble bees provides uniquely comprehensive species sampling for exploring historical patterns of distribution and diversification. Using this phylogeny and detailed data on extant distributions, I reconstruct the historical distribution of bumble bees in a temporal framework, estimating divergence times using fossil data and molecular rates derived from the literature. The nearly comprehensive phylogeny allows assessment of the tempo of diversification within the bumble bees using lineage-through-time plots and diversification statistics, which have been performed with special consideration to confidence intervals. These analyses reveal movements of Bombus concordant with geographic and climatic events of the late Cenozoic. The initial diversification of extant bumble bee lineages was estimated at around 25 to 40 Ma, near the Eocene-Oligocene boundary 34 Ma, a period of dramatic global cooling. Dispersal-vicariance analysis (DIVA) predicted an Old World Bombus ancestor, with early diversification events largely restricted to the eastern Old World. The numerous intercontinental dispersal events occurred mostly in the direction of Old World to New World and North America to South America. Early movements from the Palearctic into the Nearctic most likely took place after 20 Ma and may have coincided with a period of Miocene cooling that gave rise to taiga habitat across Beringia. Subsequent dispersal between these regions is estimated to have occurred among boreal and tundra-adapted species mostly in the last 5 million years. Radiations are estimated in both Nearctic and Neotropical regions at approximately 6 to 8 Ma and after 3.5 Ma, concordant with the opening of land corridors between the continents.     

Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus)

The mygalomorph spider genera Antrodiaetus and Atypoides (Antrodiaetidae) belong to an ancient lineage that has persisted since at least the Cretaceous. These spiders display a classic disjunct Holarctic distribution with species in the eastern Palaearctic plus the western and eastern Nearctic. Prior phylogenetic analyses of this group have been proposed on the basis of morphology, but lack strong support and independent corroboration. Here we present the first phylogenetic analysis of species-level relationships based on molecular data obtained from the mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S and 28S rRNA) genomes. Analyses corroborate earlier findings that Atypoides forms a paraphyletic grade with respect to Antrodiaetus, and consequently, that genus is formally synonymized under Antrodiaetus. In addition, our results support the relatively early divergence of Antrodiaetus roretzi. Antrodiaetus pacificus is "paraphyletic" with respect to the A. lincolnianus group and is likely an assemblage of numerous species. The final topology based on a combined molecular dataset, in conjunction with two different molecular dating techniques (penalized likelihood plus a Bayesian approach) and ancestral distribution reconstructions, was used to infer the historical biogeography of these spiders. Trans-Beringian and trans-Atlantic routes appear to account for the present-day distribution of Antrodiaetus in Japan and North America. Future studies on Antrodiaetus phylogeny will be used to address questions regarding morphological stasis and the evolution of quantitative morphological characters.     

Cladistic and phylogenetic biogeography: the art and the science of discovery

All methods used in historical biogeographical analysis aim to obtain resolved area cladograms that represent historical relationships among areas in which monophyletic groups of taxa are distributed. When neither widespread nor sympatric taxa are present in the distribution of a monophyletic group, all methods obtain the same resolved area cladogram that conforms to a simple vicariance scenario. In most cases, however, the distribution of monophyletic groups of taxa is not that simple. A priori and a posteriori methods of historical biogeography differ in the way in which they deal with widespread and sympatric taxa. A posteriori methods are empirically superior to a priori methods, as they provide a more parsimonious accounting of the input data, do not eliminate or modify input data, and do not suffer from internal inconsistencies in implementation. When factual errors are corrected, the exemplar presented by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) purporting to show inconsistencies in implementation by a posteriori methods actually corroborates the opposite. The rationale for preferring a priori methods thus corresponds to ontological rather than to epistemological considerations. We herein identify two different research programmes, cladistic biogeography (associated with a priori methods) and phylogenetic biogeography (associated with a posteriori methods). The aim of cladistic biogeography is to fit all elements of all taxon–area cladograms to a single set of area relationships, maintaining historical singularity of areas. The aim of phylogenetic biogeography is to document, most parsimoniously, the geographical context of speciation events. The recent contribution by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) makes it clear that cladistic biogeography using a priori methods is an inductivist/verificationist research programme, whereas phylogenetic biogeography is hypothetico‐deductivist/falsificationist. Cladistic biogeography can become hypothetic‐deductive by using a posteriori methods of analysis.     

Molecular phylogeography of Troglophilus cave crickets (Orthoptera,Rhaphidophoridae): A combination of vicariance and dispersal drove diversification in the East Mediterranean region

In this study, we investigated the molecular phylogenetic divergence and historical biogeography of cave crickets belonging to the genus Troglophilus (Orthoptera, Rhaphidophoridae) from caves in eastern Mediterranean and Anatolia regions. Three mitochondrial DNA genes (COI, 12S rDNA, and 16S rDNA) and two nuclear ones (18S rDNA and 28S rDNA) were amplified and partially sequenced to reconstruct phylogenetic relationships among most of the known Troglophilus species. Results showed a well‐resolved phylogeny with three main clades representing the Balkan, the Anatolian, and the Cycladian–Cretan lineages. Based on Bayesian analyses, we applied a relaxed molecular clock model to estimate the divergence times between these three lineages. Dating estimates indicate that radiation of the ingroup might have been triggered by the opening of the Mid‐Aegean trench, while the uplift of the Anatolian Plateau in Turkey and the changes of relief, emergence, and disappearance of orographic and hydrographical barriers in the Balkan Peninsula are potential paleogeographic events responsible for the initial diversification of the genus Troglophilus. A possible biogeographic scenario, reconstructed using S‐DIVA with RASP software, suggested that the current distribution of Troglophilus species can be explained by a combination of both dispersal and vicariance events that occurred in particular in the ancestral populations. The radiation of Troglophilus species likely started from the Aegean and proceeded eastward to Anatolia and westward to the Balkan region. Results are additionally compared to those available for Dolichopoda, the only other representative genus of Rhaphidophoridae present in the Mediterranean area.     

Phylogeography of the Namib Desert dung beetles Scarabaeus (Pachysoma) MacLeay (Coleoptera: Scarabaeidae)

Aim Namib biogeography in many instances remains reliant on advanced and detailed systematic studies. This study attempts to combine molecular phylogenetic data, geology and palaeo‐climatic data to (i) resolve the relationships of the 13 morphological species of Scarabaeus (Pachysoma) and (ii) relate their evolution to past climatic and geological events. Location South Africa and Namibia. Methods Sequencing of a 1197 bp segment of the mitochondrial cytochrome oxidase I (COI) gene of the 13 species within Scarabaeus (Pachysoma) was undertaken. Analyses performed included Parsimony and Maximum Likelihood as well as imposing a molecular clock. Results The molecular phylogeny showed strong support for 11 of the 13 morphological species. The remaining two species, S. (P.) glentoni and S. (P.) hippocrates, formed a complex and could not be assigned specific status on the basis of the COI gene phylogeny. Strong support for the three species formerly classified within the genus Neopachysoma was consistently obtained. The subgenus appears to have arisen c. 2.9 Ma. Species within the subgenus arose at different times, with the common ancestor to Neopachysoma and the hippocrates complex having evolved 2.65 and 2.4 Ma, respectively. Scarabaeus (P.) denticollis, S. (P.) rotundigenus, S. (P.) rodriguesi and S. (P.) schinzi are some of the youngest species, having diverged between 2 million and 600,000 years ago. Main conclusions Scarabaeus (Pachysoma) is a derived monophyletic clade within the Scarabaeini. The subgenus appears to be young in comparison with the age of the Namib Desert, which dates back to the Miocene (c. 15 Ma). The psammophilous taxa are shown to disperse with their substratum and habitat, barchan dunes. Clear south/north evolutionary gradients can be seen within the species of this subgenus, which are consistent with the unidirectional wind regime. Species with a suite of mostly plesiomorphic characters have a southerly distribution while their derived psammophilous relatives have central to northern Namib distributions. Major rivers such as the Orange, Buffels and Holgat appear to be gene barriers to certain species as well as areas of origin of speciation events.     

Phylogeny of European Pyrochroa (Coleoptera,Pyrochroidae) reveals cryptic taxa and different glacial histories

Only three saproxylic species of Pyrochroinae (Coleoptera: Pyrochroidae) are distributed in Europe, two of which belonging to Pyrochroa: P. coccinea and P. serraticornis. However, P. serraticornis is polytypic, for the presence of the endemic subspecies P. s. kiesenwetteri in southern Italy. Using both molecular and morphological data, we explored the phylogeny of the European Pyrochroa species. A multilocus (COI, CAD, 28S) phylogenetic analysis helped highlight different evolutionary histories for the two examined species. First, P. coccinea, distributed throughout Europe, showed a high differentiation among Italian and European populations. Furthermore, three different taxonomic entities were identified within P. serraticornis, among which the cryptic species Pyrochroa bifoveata sp. n. from central Europe is described and illustrated. A comprehensive identification key to the European Pyrochroinae is also provided. Our results also suggested an historical survival of P. coccinea and P. s. kiesenwetteri in glacial refugia in Italy, and a subsequent post-glacial spread of the former species throughout the Peninsula. In contrast, the current distribution of P. s. serraticornis likely originated from a post-glacial colonization of western European relict populations, while the survival of P. bifoveata plausibly occurred in more eastern glacial refugia (e.g. Carpathian or Balkan regions). Similarly, the European populations of P. coccinea could have originated from relict populations in glacial refugia out from the Italian Peninsula. More comprehensive data on the taxonomy, ecology and biogeography of Pyrochroa are needed to learn more about these species and to help preserve the European saproxylic fauna.     

Remarkable ancient divergences amongst neglected lorisiform primates

Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub‐Saharan Africa and South/South‐East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ～80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group. © 2015 The Linnean Society of London     

A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984)

The phylogenetic relationships and historical biogeography of 10 currently described rainforest skinks in the genus Saproscincus were investigated using mitochondrial protein-coding ND4 and ribosomal RNA 16S genes. A robust phylogeny is inferred using both maximum likelihood and Bayesian analysis, with all inter-specific nodes strongly supported when datasets are combined. The phylogeny supports the recognition of two major lineages (northern and southern), each of which comprises two divergent clades. Both northern and southern lineages have comparably divergent representatives in mid-east Queensland (MEQ), providing further molecular evidence for the importance of two major biogeographic breaks, the St. Lawrence gap and Burdekin gap separating MEQ from southern and northern counterparts respectively. Vicariance associated with the fragmentation and contraction of temperate rainforest during the mid-late Miocene epoch underpins the deep divergence between morphologically conservative lineages in at least three instances. In contrast, one species, Saproscincus oriarus, shows very low sequence divergence but distinct morphological and ecological differentiation from its allopatric sister clade within Saproscincus mustelinus. These results suggest that while vicariance has played a prominent role in diversification and historical biogeography of Saproscincus, divergent selection may also be important.     

Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-fingered frogs (Cardioglossa) estimated from mitochondrial data

The evolutionary history of living African amphibians remains poorly understood. This study estimates the phylogeny within the frog genera Arthroleptis and Cardioglossa using approximately 2400 bases of mtDNA sequence data (12S, tRNA-Valine, and 16S genes) from half of the described species. Analyses are conducted using parsimony, maximum likelihood, and Bayesian methods. The effect of alignment on phylogeny estimation is explored by separately analyzing alignments generated with different gap costs and a consensus alignment. The consensus alignment results in species paraphyly, low nodal support, and incongruence with the results based on other alignments, which produced largely similar results. Most nodes in the phylogeny are highly supported, yet several topologies are inconsistent with previous hypotheses. The monophyly of Cardioglossa and of miniature species previously assigned to Schoutedenella was further examined using Templeton and Shimodaira–Hasegawa tests. Cardioglossa monophyly is rejected and C. aureoli is transferred to Arthroleptis. These tests do not reject Schoutedenella monophyly, but this hypothesis receives no support from non-parametric bootstrapping or Bayesian posterior probabilities. This phylogeny provides a framework for reconstructing historical biogeography and analyzing the evolution of body size and life history. Direct development and miniaturization appear at the base of Arthroleptis phylogeny concomitant with a range expansion from Central Africa to throughout most of sub-Saharan Africa.     

Nothofagus Biogeography Revisited with Special Emphasis on the Enigmatic Distribution of Subgenus Brassospora in New Caledonia

Dispersals versus vicariance events and the presence of subgenus Brassospora in New Caledonia are two riddles of Nothofagus biogeography, a genus also distributed in New Guinea, New Zealand, South America, Southeast Australia, and Tasmania. Within a cladistic framework using the software COMPONENT 2.0, we demonstrate that most parsimonious area cladograms (areagrams) sensu cladistic biogeography need not always be the most plausible explanation nor reflect alternative geological hypotheses. The most parsimonious Nothofagus history sensu historical biogeography is reconstructed where a minimum of dispersed taxa is hypothesized and vicariance events are identified. A fully resolved well-established Nothofagus phylogeny was reconciled with three geological hypotheses (geograms) of East Gondwana break-up: (a) the conventional view, (b) an Australian—New Caledonian relationship, and (c) a biotic interchange between New Guinea and New Caledonia. Fossils determined to subgenus were optimized to the predicted lineages in the reconciled tree. Due to extensive extinctions, a maximum of three vicariance events are inferred, all being basal in the subgenera, an indication of subgeneric diversification prior to the break-up of Gondwana. Two taxa, N. gunnii and N. menziesii, are hypothesized as being long-distance dispersed. The most parsimonious solution suggests a close relationship between New Guinea and New Caledonia, supporting a Brassospora colonization route, but this hypothesis fails to predict numerous extinct lineages observed in the fossil record and thus must be rejected. The traditional break-up sequence of Gondwana is not the most parsimonious solution, indicating one incongruent node, but causes no overall incongruence with the fossil record. Considering all parameters, the occurrence of Brassospora in New Caledonia is most parsimoniously explained as a single colonization event from New Zealand where the subgenus subsequently went extinct in the Pliocene.     

Neogene diversification in the temperate lichen-forming fungal genus Parmelia (Parmeliaceae,Ascomycota)

The lichen-forming genus Parmelia Acharius occurs worldwide but its centre of distribution is in the northern hemisphere and it is widespread in boreal-temperate Eurasia and North America. Recent molecular work on Parmelia has identified phylogenetic relationships within two major groups of the genus: P. saxatilis s. lat. and P. sulcata s. lat. However, little is known about the diversification and historical biogeography of these groups. Here we have used a dataset of two genetic markers and 64 samples to estimate phylogenetic relationships within Parmelia. The dated phylogeny provides evidence for major diversification during the Neogene and Pleistocene. These diversification events are probably correlated with climatic changes during these periods. Evidence of gene flow within species between populations from North America and Europe has been found in three species: P. sulcata Taylor, P. saxatilis (L.) Acharius and P. barrenoae Divakar, M.C. Molina & A. Crespo. Cryptic species recently segregated on the basis of molecular differences (P. encryptata A. Crespo, Divakar & M.C. Molina vs. P. sulcata and P. saxatilis vs. P. mayi Divakar, A. Crespo & M.C. Molina) do not share a common ancestor. Moreover, the P. saxatilis complex is remarkably diverse. Two morphotypes of P. saxatilis s. lat. were shown to represent independent monophyletic lineages. Consequently, two species (P. sulymae Goward, Divakar, & M.C. Molina & A. Crespo and P. imbricaria Goward, Divakar, M.C. Molina & A. Crespo) are newly described here.     

How cold‐adapted flightless flies dispersed over the northern hemisphere: phylogeny and biogeography of the snow fly genus Chionea Dalman (Diptera: Limoniidae)

A phylogeny of the 37 known species and subspecies of the micropterous snow fly genus Chionea Dalman is presented using adult morphological characters. The genus contains two major clades: a strictly Palaearctic clade, and a combined Nearctic‐Palaearctic clade with representatives in the Nearctic and Western Palaearctic regions. As there is little congruence between the recovered phylogeny of Chionea and the currently used subgeneric division in Chionea s.s. and Sphaeconophilus Becker, we propose to abandon the use of subgeneric taxa in Chionea. A strictly morphological analysis appears to be insufficient to fully resolve the phylogeny of the genus at the species level, and future molecular work should provide additional evidence for the establishment of relationships among the members of Chionea. The large‐scale historical biogeography of Chionea was analysed using dispersal‐vicariance analysis. The initial distribution area of the genus probably extended in the Eastern Palaearctic, and the Nearctic and the origin of Chionea could be dated in the Late Cretaceous. The various dispersal and vicariance events that led to the major speciation events in the genus are set against major paleogeographic developments. The ancestor of the Western Palaearctic group in the second major clade originated from the Nearctic. The presence of the cold‐adapted Chionea in currently temperate to warm climatic zones in the southern parts of its distribution was analysed using ecological niche modelling. It appears that prolonged periods of climate cooling, as occurred during the Last Glacial Maximum, enabled Chionea to cover large parts of central and southern Europe and reach the southern distribution areas where the genus is present today. A similar biogeographic pattern was less evident in the Nearctic region.     

Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes

Of the 5000 fish species on coral reefs, corals dominate the diet of just 41 species. Most (61%) belong to a single family, the butterflyfishes (Chaetodontidae). We examine the evolutionary origins of chaetodontid corallivory using a new molecular phylogeny incorporating all 11 genera. A 1759‐bp sequence of nuclear (S7I1 and ETS2) and mitochondrial (cytochrome b) data yielded a fully resolved tree with strong support for all major nodes. A chronogram, constructed using Bayesian inference with multiple parametric priors, and recent ecological data reveal that corallivory has arisen at least five times over a period of 12 Ma, from 15.7 to 3 Ma. A move onto coral reefs in the Miocene foreshadowed rapid cladogenesis within Chaetodon and the origins of corallivory, coinciding with a global reorganization of coral reefs and the expansion of fast‐growing corals. This historical association underpins the sensitivity of specific butterflyfish clades to global coral decline.