Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleocene

Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies. We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 genera plus 8 outgroup taxa, and, together with sequences from 5 other pigeon genera retrieved from GenBank, recovered a strong phylogenetic hypothesis for the Columbiformes. Three major clades were recovered with the combined data set, comprising the basally branching New World pigeons and allies (clade A) that are sister to Neotropical ground doves (clade B), and the Afro-Eurasian and Australasian taxa (clade C). None of these clades supports the monophyly of current families and subfamilies. The extinct, flightless dodo and solitaires (Raphidae) were embedded within pigeons and doves (Columbidae) in clade C, and monophyly of the subfamily Columbinae was refuted because the remaining subfamilies were nested within it. Divergence times estimated using a Bayesian framework suggest that Columbiformes diverged from outgroups such as Apodiformes and Caprimulgiformes in the Cretaceous before the mass extinction that marks the end of this period. Bayesian and maximum likelihood inferences of ancestral areas, accounting for phylogenetic uncertainty and divergence times, respectively, favor an ancient origin of Columbiformes in the Neotropical portion of what was then Gondwana. The radiation of modern genera of Columbiformes started in the Early Eocene to the Middle Miocene, as previously estimated for other avian groups such as ratites, tinamous, galliform birds, penguins, shorebirds, parrots, passerine birds, and toucans. Multiple dispersals of more derived Columbiformes between Australasian and Afro-Eurasian regions are required to explain current distributions.     

Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes

Phylogenetic relationships of members of the salamander family Salamandridae were examined using complete mitochondrial genomes collected from 42 species representing all 20 salamandrid genera and five outgroup taxa. Weighted maximum parsimony, partitioned maximum likelihood, and partitioned Bayesian approaches all produce an identical, well-resolved phylogeny; most branches are strongly supported with greater than 90% bootstrap values and 1.0 Bayesian posterior probabilities. Our results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages. We successfully resolved the current polytomy at the base of the salamandrid tree: the Italian newt genus Salamandrina is sister to all remaining salamandrids. Beyond Salamandrina, a clade comprising all remaining newts is separated from a clade containing the true salamanders. Among these newts, the branching orders of well-supported clades are: primitive newts (Echinotriton, Pleurodeles, and Tylototriton), New World newts (Notophthalmus-Taricha), Corsica-Sardinia newts (Euproctus), and modern European newts (Calotriton, Lissotriton, Mesotriton, Neurergus, Ommatotriton, and Triturus) plus modern Asian newts (Cynops, Pachytriton, and Paramesotriton).Two alternative sets of calibration points and two Bayesian dating methods (BEAST and MultiDivTime) were used to estimate timescales for salamandrid evolution. The estimation difference by dating methods is slight and we propose two sets of timescales based on different calibration choices. The two timescales suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma. North American salamandrids were derived from their European ancestors by dispersal through North Atlantic Land Bridges in the Late Cretaceous ( approximately 69Ma) or Middle Eocene ( approximately 43Ma). Ancestors of Asian salamandrids most probably dispersed to the eastern Asia from Europe, after withdrawal of the Turgai Sea ( approximately 29Ma).     

Phylogenetic relationships and historical biogeography of neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences

Previous hypotheses of phylogenetic relationships among Neotropical parrots were based on limited taxon sampling and lacked support for most internal nodes. In this study we increased the number of taxa (29 species belonging to 25 of the 30 genera) and gene sequences (6388 base pairs of RAG-1, cyt b, NADH2, ATPase 6, ATPase 8, COIII, 12S rDNA, and 16S rDNA) to obtain a stronger molecular phylogenetic hypothesis for this group of birds. Analyses of the combined gene sequences using maximum likelihood and Bayesian methods resulted in a well-supported phylogeny and indicated that amazons and allies are a sister clade to macaws, conures, and relatives, and these two clades are in turn a sister group to parrotlets. Key morphological and behavioral characters used in previous classifications were mapped on the molecular tree and were phylogenetically uninformative. We estimated divergence times of taxa using the molecular tree and Bayesian and penalized likelihood methods that allow for rate variation in DNA substitutions among sites and taxa. Our estimates suggest that the Neotropical parrots shared a common ancestor with Australian parrots 59 Mya (million of years ago; 95% credibility interval (CrI) 66, 51 Mya), well before Australia separated from Antarctica and South America, implying that ancestral parrots were widespread in Gondwanaland. Thus, the divergence of Australian and Neotropical parrots could be attributed to vicariance. The three major clades of Neotropical parrots originated about 50 Mya (95% CrI 57, 41 Mya), coinciding with periods of higher sea level when both Antarctica and South America were fragmented with transcontinental seaways, and likely isolated the ancestors of modern Neotropical parrots in different regions in these continents. The correspondence between major paleoenvironmental changes in South America and the diversification of genera in the clade of amazons and allies between 46 and 16 Mya suggests they diversified exclusively in South America. Conversely, ancestors of parrotlets and of macaws, conures, and allies may have been isolated in Antarctica and/or the southern cone of South America, and only dispersed out of these southern regions when climate cooled and Antarctica became ice-encrusted about 35 Mya. The subsequent radiation of macaws and their allies in South America beginning about 28 Mya (95% CrI 22, 35 Mya) coincides with the uplift of the Andes and the subsequent formation of dry, open grassland habitats that would have facilitated ecological speciation via niche expansion from forested habitats.     

On the osteology and phylogenetic affinities of the Pseudasturidae – Lower Eocene stem-group representatives of parrots (Aves, Psittaciformes)

The osteology of the early Eocene (about 50 mya) avian taxon Pseudasturidae Mayr, 1998 is revised and its phylogenetic affinities are analysed. Members of the Pseudasturidae are known from abundant and excellently preserved skeletal material, both complete skeletons on slabs as well as isolated, three-dimensional bones. Although this taxon is thus among the best represented of all small early Tertiary birds, its systematic affinities were unknown so far. Derived osteological characters which are visible in newly recognized specimens from the Lower Eocene London Clay of England most convincingly support classification of the Pseudasturidae into the Psittaciformes (parrots). Both, in overall morphology and in terms of derived characters, the tarsometatarsus of the Pseudasturidae closely resembles that of the Eocene Quercypsittidae, which were assigned to the Psittaciformes by Mourer-Chauviré (1992 ). The Pseudasturidae are considered to be stem-group representatives of the Psittaciformes and the sister taxon of all other known psittaciform birds. The Eocene taxon lacks the specialized bill morphology of crown-group Psittaciformes of the Psittacidae. Several other osteological differences between the Pseudasturidae and the Psittacidae probably are also functionally correlated with the specialized feeding technique of the latter.  © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 136 , 715–729.     

Piecing together the "new" Plantaginaceae

Scrophulariaceae is one of the families that has been divided extensively due to the results of DNA sequence studies. One of its segregates is a vastly enlarged Plantaginaceae. In a phylogenetic study of 47 members of Plantaginaceae and seven outgroups based on 3561 aligned characters from four DNA regions (the nuclear ribosomal ITS region and the plastid trnL-F, rps16 intron, and matK-trnK intron regions), the relationships within this clade were analyzed. The results from parsimony and Bayesian analyses support the removal of the Lindernieae from Gratioleae to a position outside Plantaginaceae. A group of mainly New World genera is paraphyletic with respect to a clade of Old World genera. Among the New World taxa, those offering oil as a pollinator reward cluster together. Ourisia is sister to this clade. Gratioleae consist of Gratiola, Otacanthus, Bacopa, Stemodia, Scoparia, and Mecardonia. Cheloneae plus Russelia and Tetranema together constitute the sister group to a clade predominantly composed of Old World taxa. Among the Old World clade, Ellisiophyllum and Lafuentea have been analyzed for the first time in a molecular phylogenetic analysis. The former genus is sister to Sibthorpia and the latter is surprisingly the sister to Antirrhineae.     

Age and historical biogeography of the pantropically distributed Spathelioideae (Rutaceae,Sapindales)

Aim The family Rutaceae (rue family) is the largest within the eudicot order Sapindales and is distributed mainly in the tropical and subtropical regions of both the New World and the Old World, with a few genera in temperate zones. The main objective of this study is to present molecular dating and biogeographical analyses of the subfamily Spathelioideae, the earliest branching clade (which includes eight extant genera), to interpret the temporal and spatial origins of this group, ascertaining possible vicariant patterns and dispersal routes and inferring diversification rates through time. Location Pantropics. Methods A dataset comprising a complete taxon sampling at generic level (83.3% at species level) of Spathelioideae was used for a Bayesian molecular dating analysis (beast ). Four fossil calibration points and an age constraint for Sapindales were applied. An ancestral area reconstruction analysis utilizing the dispersal–extinction–cladogenesis model and diversification rate analyses was conducted. Results Dating analyses indicate that Rutaceae and Spathelioideae are probably of Late Cretaceous origin, after which Spathelioideae split into a Neotropical and a Palaeotropical lineage. The Palaeotropical taxa have their origin inferred in Africa, with postulated dispersal events to the Mediterranean, the Canary Islands, Madagascar and Southeast Asia. The lineages within Spathelioideae evolved at a relatively constant diversification rate. However, abrupt changes in diversification rates are inferred from the beginning of the Miocene and during the Pliocene/Pleistocene. Main conclusions The geographical origin of Spathelioideae probably lies in Africa. The existence of a Neotropical lineage may be the result of a dispersal event at a time in the Late Cretaceous when South America and Africa were still quite close to each other (assuming that our age estimates are close to the actual ages), or by Gondwanan vicariance (assuming that our age estimates provide minimal ages only). Separation of land masses caused by sea level changes during the Pliocene and Pleistocene may have been triggers for speciation in the Caribbean genus Spathelia.     

Macroevolutionary patterns in the diversification of parrots: effects of climate change,geological events and key innovations

Aim Parrots are thought to have originated on Gondwana during the Cretaceous. The initial split within crown group parrots separated the New Zealand taxa from the remaining extant species and was considered to coincide with the separation of New Zealand from Gondwana 82–85 Ma, assuming that the diversification of parrots was mainly shaped by vicariance. However, the distribution patterns of several extant parrot groups cannot be explained without invoking transoceanic dispersal, challenging this assumption. Here, we present a temporal and spatial framework for the diversification of parrots using external avian fossils as calibration points in order to evaluate the relative importance of the influences of past climate change, plate tectonics and ecological opportunity. Location Australasian, African, Indo‐Malayan and Neotropical regions. Methods Phylogenetic relationships were investigated using partial sequences of the nuclear genes c‐mos, RAG‐1 and Zenk of 75 parrot and 21 other avian taxa. Divergence dates and confidence intervals were estimated using a Bayesian relaxed molecular clock approach. Biogeographic patterns were evaluated taking temporal connectivity between areas into account. We tested whether diversification remained constant over time and if some parrot groups were more species‐rich than expected given their age. Results Crown group diversification of parrots started only about 58 Ma, in the Palaeogene, significantly later than previously thought. The Australasian lories and possibly also the Neotropical Arini were found to be unexpectedly species‐rich. Diversification rates probably increased around the Eocene/Oligocene boundary and in the middle Miocene, during two periods of major global climatic aberrations characterized by global cooling. Main conclusions The diversification of parrots was shaped by climatic and geological events as well as by key innovations. Initial vicariance events caused by continental break‐up were followed by transoceanic dispersal and local radiations. Habitat shifts caused by climate change and mountain orogenesis may have acted as a catalyst to the diversification by providing new ecological opportunities and challenges as well as by causing isolation as a result of habitat fragmentation. The lories constitute the only highly nectarivorous parrot clade, and their diet shift, associated with morphological innovation, may have acted as an evolutionary key innovation, allowing them to explore underutilized niches and promoting their diversification.     

The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: a molecular phylogenetic perspective

Nucleotide sequence data from a mitochondrial gene (16S) and two nuclear genes (c-mos, RAG-1) were used to evaluate the monophyly of the genus Coleodactylus, to provide the first phylogenetic hypothesis of relationships among its species in a cladistic framework, and to estimate the relative timing of species divergences. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the combined data sets retrieved Coleodactylus as a monophyletic genus, although weakly supported. Species were recovered as two genetically and morphological distinct clades, with C. amazonicus populations forming the sister taxon to the meridionalis group (C. brachystoma, C. meridionalis, C. natalensis, and C. septentrionalis). Within this group, C. septentrionalis was placed as the sister taxon to a clade comprising the rest of the species, C. meridionalis was recovered as the sister species to C. brachystoma, and C. natalensis was found nested within C. meridionalis. Divergence time estimates based on penalized likelihood and Bayesian dating methods do not support the previous hypothesis based on the Quaternary rain forest fragmentation model proposed to explain the diversification of the genus. The basal cladogenic event between major lineages of Coleodactylus was estimated to have occurred in the late Cretaceous (72.6+/-1.77 Mya), approximately at the same point in time than the other genera of Sphaerodactylinae diverged from each other. Within the meridionalis group, the split between C. septentrionalis and C. brachystoma+C. meridionalis was placed in the Eocene (46.4+/-4.22 Mya), and the divergence between C. brachystoma and C. meridionalis was estimated to have occurred in the Oligocene (29.3+/-4.33 Mya). Most intraspecific cladogenesis occurred through Miocene to Pliocene, and only for two conspecific samples and for C. natalensis could a Quaternary differentiation be assumed (1.9+/-1.3 Mya).     

Phylogeny and character evolution in the Empidonax group of tyrant flycatchers (Aves: Tyrannidae): a test of W. E. Lanyon's hypothesis using mtDNA sequences

We sequenced mitochondrial DNA from four protein-coding genes for 26 taxa to test W. E. Lanyon's hypothesis of intergeneric relationships and character evolution in the Empidonax group of tyrant flycatchers. Three genera in this group (Empidonax, Contopus, and Sayornis) successfully occupy north temperate habitats for breeding, while the remaining genera (Mitrephanes, Cnemotriccus, Aphanotriccus, Lathrotriccus, and Xenotriccus) are restricted to neotropical latitudes. Lanyon hypothesized two major clades in the group based on differences in syringeal morphology and proposed relationships among genera using a combination of morphologic, behavioral, and allozymic characters. The mtDNA data strongly support Lanyon's division of genera into two clades. In addition, the molecular and nonmolecular data sets agree in uniting Aphanotriccus and Lathrotriccus as sister taxa, with Cnemotriccus as basal to these genera. Species of Aphanotriccus, Lathrotriccus, and Cnemotriccus form a clade that exploits a distinctive nesting niche relative to other members of the Empidonax group. Within the second major clade, mtDNA sequences support a reconstruction based on allozymes that places Contopus and Empidonax as sister taxa. This hypothesis contradicts that of Lanyon, who allied Contopus with Mitrephanes on the basis of similarity in foraging mode. Genera in the Empidonax group are members of a larger assemblage that radiated in South America. Occupancy of temperate habitats by certain genera in this group is coincident with their evolution of migratory behavior and with independent diversification in foraging modes that reduces potential competition in sympatry.     

Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange

The Procyonidae (Mammalia: Carnivora) have played a central role in resolving the controversial systematics of the giant and red pandas, but phylogenetic relationships of species within the family itself have received much less attention. Cladistic analyses of morphological characters conducted during the last two decades have resulted in topologies that group ecologically and morphologically similar taxa together. Specifically, the highly arboreal and frugivorous kinkajou (Potos flavus) and olingos (Bassaricyon) define one clade, whereas the more terrestrial and omnivorous coatis (Nasua), raccoons (Procyon), and ringtails (Bassariscus) define another clade, with the similar-sized Nasua and Procyon joined as sister taxa in this latter group. These relationships, however, have not been tested with molecular sequence data. We examined procyonid phylogenetics based on combined data from nine nuclear and two mitochondrial gene segments totaling 6534bp. We were able to fully resolve relationships within the family with strongly supported and congruent results from maximum parsimony, maximum likelihood, minimum evolution, and Bayesian analyses. We identified three distinct lineages within the family: a (Nasua, Bassaricyon) clade, a (Bassariscus, Procyon) clade, and a Potos lineage, the last of which is sister to the other two clades. These findings, which are in strong disagreement with prior fossil and morphology-based assessments of procyonid relationships, reemphasize the morphological and ecological flexibility of these taxa. In particular, morphological similarities between unrelated genera possibly reflect convergence associated with similar lifestyles and diets rather than ancestry. Furthermore, incongruence between the molecular supermatrix and a morphological character matrix comprised mostly of dental characters [Baskin, J.A., 2004. Bassariscus and Probassariscus (Mammalia, Carnivora, Procyonidae) from the early Barstovian (Middle Miocene). J. Vert. Paleo. 24, 709-720] may be due to non-independence among atomized dental characters that does not take into account the high developmental genetic correlation of these characters. Finally, molecular divergence dating analyses using a relaxed molecular clock approach suggest that intergeneric and intrageneric splits in the Procyonidae mostly occurred in the Miocene. The inferred divergence times for intrageneric splits for several genera whose ranges are bisected by the Panamanian Isthmus is significant because they suggest diversification well precedes the Great American Interchange, which has long been considered a primary underlying mechanism for procyonid evolution.     

Systematics and evolution of the Pan‐Alcidae (Aves,Charadriiformes)

Puffins, auks and their allies in the wing‐propelled diving seabird clade Pan‐Alcidae (Charadriiformes) have been proposed to be key pelagic indicators of faunal shifts in Northern Hemisphere oceans. However, most previous phylogenetic analyses of the clade have focused only on the 23 extant alcid species. Here we undertake a combined phylogenetic analysis of all previously published molecular sequence data (～ 12 kb) and morphological data (n = 353 characters) with dense species level sampling that also includes 28 extinct taxa. We present a new estimate of the patterns of diversification in the clade based on divergence time estimates that include a previously vetted set of twelve fossil calibrations. The resultant time trees are also used in the evaluation of previously hypothesized paleoclimatic drivers of pan‐alcid evolution. Our divergence dating results estimate the split of Alcidae from its sister taxon Stercorariidae during the late Eocene (～ 35 Ma), an evolutionary hypothesis for clade origination that agrees with the fossil record and that does not require the inference of extensive ghost lineages. The extant dovekie Alle alle is identified as the sole extant member of a clade including four extinct Miocene species. Furthermore, whereas an Uria + Alle clade has been previously recovered from molecular analyses, the extinct diversity of closely related Miocepphus species yields morphological support for this clade. Our results suggest that extant alcid diversity is a function of Miocene diversification and differential extinction at the Pliocene–Pleistocene boundary. The relative timing of the Middle Miocene climatic optimum and the Pliocene–Pleistocene climatic transition and major diversification and extinction events in Pan‐Alcidae, respectively, are consistent with a potential link between major paleoclimatic events and pan‐alcid cladogenesis.     

A reassessment of Eocene parrotlike fossils indicates a previously undetected radiation of zygodactyl stem group representatives of passerines (Passeriformes)

In the past years, various Eocene fossil birds were described as stem group representatives of the zygodactyl Psittaciformes (parrots). These birds show quite disparate morphologies, which cast some doubt on the correct assignment of all of them to the psittaciform stem group. A reassessment of their affinities is further needed, because it was recently proposed that among extant birds, Psittaciformes and Passeriformes (passerines) form a clade and that passerines possibly derived from a zygodactyl ancestor. Here, phylogenetic analyses are performed, which for the first time also include representatives of the Zygodactylidae, the extinct zygodactyl sister taxon of the Passeriformes. The early Eocene Psittacopes was originally described as a stem group representative of Psittaciformes. However, none of the present analyses supported psittaciform affinities for Psittacopes and instead recovered this taxon in a clade together with zygodactylids and passerines. Also part of this clade are the early Eocene taxa Pumiliornis and Morsoravis, and it is detailed that Psittacopes and the long‐beaked and presumably nectarivorous Pumiliornis, with which it has not yet been compared, are very similar in their postcranial osteology. The present analysis corroborates the hypothesis of a zygodactyl stem species of passerines. To account for these results, Psittacopes is here assigned to a new higher‐level taxon and a new name is also introduced for the clade including Zygodactylidae and Passeriformes.     

Eastward from Africa: palaeocurrent-mediated chameleon dispersal to the Seychelles islands

Madagascar and the Seychelles are Gondwanan remnants currently isolated in the Indian Ocean. In the Late Cretaceous, these islands were joined with India to form the Indigascar landmass, which itself then split into its three component parts around the start of the Tertiary. This history is reflected in the biota of the Seychelles, which appears to contain examples of both vicariance- and dispersal-mediated divergence from Malagasy or Indian sister taxa. One lineage for which this has been assumed but never thoroughly tested is the Seychellean tiger chameleon, a species assigned to the otherwise Madagascar-endemic genus Calumma. We present a multi-locus phylogenetic study of chameleons, and find that the Seychellean species is actually the sister taxon of a southern African clade and requires accomodation in its own genus as Archaius tigris. Divergence dating and biogeographic analyses indicate an origin by transoceanic dispersal from Africa to the Seychelles in the Eocene–Oligocene, providing, to our knowledge, the first such well-documented example and supporting novel palaeocurrent reconstructions.     

A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family

Phylogenetic analysis of 330 plastid matK gene sequences, representing 235 genera from 37 of 39 tribes, and four outgroup taxa from eurosids I supports many well-resolved subclades within the Leguminosae. These results are generally consistent with those derived from other plastid sequence data (rbcL and trnL), but show greater resolution and clade support overall. In particular, the monophyly of subfamily Papilionoideae and at least seven major subclades are well-supported by bootstrap and Bayesian credibility values. These subclades are informally recognized as the Cladrastis clade, genistoid sensu lato, dalbergioid sensu lato, mirbelioid, millettioid, and robinioid clades, and the inverted-repeat-lacking clade (IRLC). The genistoid clade is expanded to include genera such as Poecilanthe, Cyclolobium, Bowdichia, and Diplotropis and thus contains the vast majority of papilionoids known to produce quinolizidine alkaloids. The dalbergioid clade is expanded to include the tribe Amorpheae. The mirbelioids include the tribes Bossiaeeae and Mirbelieae, with Hypocalypteae as its sister group. The millettioids comprise two major subclades that roughly correspond to the tribes Millettieae and Phaseoleae and represent the only major papilionoid clade marked by a macromorphological apomorphy, pseudoracemose inflorescences. The robinioids are expanded to include Sesbania and members of the tribe Loteae. The IRLC, the most species-rich subclade, is sister to the robinioids. Analysis of the matK data consistently resolves but modestly supports a clade comprising papilionoid taxa that accumulate canavanine in the seeds. This suggests a single origin for the biosynthesis of this most commonly produced of the nonprotein amino acids in legumes.     

On the systematic position of the Early Cretaceous fern genus “Athyrium”

The oldest fossils assigned to Athyrium (mostly based on the sorus morphology) comprise fronds and spores from the Lower Cretaceous of Northeast Asia. However, most molecular dating suggests that extant Athyrium diverged from its sister genus during the Eocene or later, implying that the Cretaceous fossils probably belong to another polypodiaceous taxon. By examining the sorus morphology of extant genera related to the family Athyriaceae, we found that the primary diagnostic feature for assigning the Cretaceous fossils to Athyrium, i.e., the sorus shape, is common to the entire extant family, or plesiomorphic for the genus. As the fronds are more commonly preserved than the reproductive parts, we compared the fossil frond morphology with those of living taxa of the family that is divided into two types. The Cretaceous fossil we examined here bears the frond’s costal groove characters on adaxial side, which is more closely related to that of the Deparia-clade instead of the clade including Athyrium and other genera of the family. The observation is further confirmed by the cladistic analysis using morphological characters. The systematic position of the Early Cretaceous “Athyrium” was resolved as a stem member of the total Athyriaceae using a tip-dating approach with the Fossilized Birth-Death model in a Bayesian framework. Our study suggests that Early Cretaceous fossils previously assigned to Athyrium require taxonomic revision.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

Nymphalid butterflies diversify following near demise at the Cretaceous/Tertiary boundary

The butterfly family Nymphalidae contains some of the most important non-drosophilid insect model systems for evolutionary and ecological studies, yet the evolutionary history of the group has remained shrouded in mystery. We have inferred a robust phylogenetic hypothesis based on sequences of 10 genes and 235 morphological characters for exemplars of 400 of the 540 valid nymphalid genera representing all major lineages of the family. By dating the branching events, we infer that Nymphalidae originated in the Cretaceous at 90 Ma, but that the ancestors of 10–12 lineages survived the end-Cretaceous catastrophe in the Neotropical and Oriental regions. Patterns of diversification suggest extinction of lineages at the Cretaceous/Tertiary boundary (65 Ma) and subsequent elevated speciation rates in the Tertiary.     

A new psittaciform bird from the London Clay (Lower Eocene) of England

A new psittaciform bird from the Lower Eocene (Ypresian) London Clay of England is described. This taxon, Pulchrapollia gracilis gen. et sp. nov., is assigned to the order Psittaciformes (parrots) on the basis of several distinctive structures of the tarsometatarsus, namely the trochlea for metatarsal III (trochlea metatarsi III) bearing a tubercle on its lateral side and the trochlea for metatarsal IV (trochlea metatarsi IV) completely retroverted (fully zygodactyl foot). Comparisons with other fossil and Recent taxa further support this conclusion. Cladistic analysis shows that Pulchrapollia is the sister-taxon of the single extant family within Psittaciformes, the Psittacidae. Palaeopsittacus georgei, a taxon previously described from the London Clay, is most likely based on some unassociated material and is regarded here as incertae sedis.