The geography of diversification in the mormoopids (Chiroptera: Mormoopidae)

The traditional explanation of the distribution of the Mormoopidae is that this family originated in southern Central America or northern South America, later expanding its range north to Mexico and the West Indies, and differentiating into eight species. An alternative fossil-based hypothesis argues that the family originated in the northern Neotropics, reached the Caribbean early in its history, and dispersed to South America after the completion of the Isthmus of Panama. The present study analyses new and previously published sequence data from the mitochondrial 12S, tRNA^val, 16S, and cytochrome b , and the nuclear Rag 2, to evaluate species boundaries and infer relationships among extant taxa. Fixed differences in cytochrome b often coincide with published morphological characters and show that the family contains at least 13 species. Two additional, morphologically indistinct, lineages are restricted to Suriname and French Guiana. Phylogeny-based inferences of ancestral area are equivocal on the geographical origin of mormoopids, in part because several internal nodes are not resolved with the available data. Divergences between Middle American and Antillean populations are greater than those between Mexico/Central America and South America. This suggests that mormoopids diversified in northern Neotropics before entering South America. A northern neotropical origin for mormoopids is congruent with both the Tertiary fossil record and recent phylogenetic hypotheses for the sister family to the Mormoopidae, the Phyllostomidae.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 101–118.     

Evolution of the gibbon subgenera inferred from cytochrome b DNA sequence data

DNA sequences for the mitochondrial cytochrome b gene from the four extant gibbon subgenera are described. The data confirm that the gibbon subgenera evolved from a common hylobatid ancestor and suggest that they diverged from each other after the divergence of the extant African great ape species. The cytochrome b gene does not resolve the evolutionary relationships between the gibbon subgenera themselves.     

On the origin of Darwin's finches

Darwin's finches comprise a group of 15 species endemic to the Galápagos (14 species) and Cocos (1 species) Islands in the Pacific Ocean. The group is monophyletic and originated from an ancestral species that reached the Galápagos Archipelago from Central or South America. Descendants of this ancestor on the Archipelago then colonized Cocos Island. In the present study, we used sequences of two mitochondrial (mt) DNA segments (922 bp of the cytochrome b gene and 1,082 bp of the control region), as well as two nuclear markers (830 bp of numt2, consisting of 140 bp of mtDNA control region and 690 bp of flanking nuclear DNA; and 740 bp of numt3, consisting of 420 bp of mt cytochrome b sequence flanked by 320 bp of nuclear DNA) to identify the species group most closely related to the Darwin's finches. To this end, we analyzed the sequences of 28 species representing the main groups (tribes) of the family Fringillidae, as well as 2 outgroup species and 13 species of Darwin's finches. In addition, we used mtDNA cytochrome b sequences of some 180 additional Fringillidae species from the database for phylogeny reconstruction by maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods. The study identifies the grassquit genus Tiaris, and specifically the species Tiaris obscura, as the nearest living relative of Darwin's finches among the species surveyed. Darwin's finches diverged from the Tiaris group shortly after the various extant species of Tiaris diverged from one another. The initial adaptive radiation of the Tiaris group apparently occurred on the Caribbean islands and then spread to Central and South America, from where the ancestors of Darwin's finches departed for the Galápagos Islands approximately 2.3 MYA, at the time of the dramatic climatic changes associated with the closure of the Panamanian isthmus and the onset of Pleistocene glaciation.     

Cytochrome b sequence data suggest rapid speciation within the Paramecium aurelia species complex

We investigated mitochondrial Cytochrome b sequences from all 15 members of the enigmatic Paramecium aurelia species complex (Ciliophora). The analysis revealed high genetic distances between the different P. aurelia species (6.1-19.8%) and a largely unresolved, star-like phylogenetic tree. This result strongly supports a rapid radiation in the evolutionary history of this species complex and it correlates well with the hypothesis that the extant species diversity may have originated from the neutral consequences of a whole genome duplication in the common ancestor of P. aurelia.     

Phylogenetic relationships of the sea eagles (genus Haliaeetus): reconstructions based on morphology, allozymes and mitochondrial DNA sequences

The relationships of eight extant species of sea eagles (genus Haliaeetus ) and some potentially related Accipitrid genera were investigated. A phylogenetic hypothesis is developed based on morphological characters and allozyme data, which is then contrasted with a reconstruction based on 1071 nucleotides of mitochondrial DNA (cytochrome b and part of one tRNA gene). Phylogenies derived from the three data sets are largely congruent, although several aspects are supported by only one kind of evidence (but not contradicted by the others). Only with regard to the position of south-east Asian H. leucogaster and its closely related sister species H. sanfordi was there conflict between allozyme and mtDNA data. The position of H. pelagicus relative to H. leucoryphus or H. albicilla/leucocephalus could not be resolved with the mtDNA sequence data, suggesting that some speciation events occurred in relatively quick succession during the early Pliocene or late Miocene periods. Available evidence suggests that extant sea eagles originated at tropical latitudes, the northernmost species appearing most derived.     

Molecular phylogeny of Megaloceros giganteus--the giant deer or just a giant red deer?

Two fragments of mitochondrial DNA (mtDNA) of the cytochrome b gene (137 bp and 167 bp) were successfully isolated and sequenced from antlers and bones of five specimens of the Giant Deer (Megaloceros giganteus) to examine the phylogenetic position of Megaloceros giganteus within the family Cervidae. This is the first report on ancient DNA (aDNA) sequences from Megaloceros giganteus. A phylogenetic analysis based on parameter-rich models describes the evolutionary relationships between five individuals of fossil Megaloceros giganteus and 37 individuals of 11 extant species of the family Cervidae. The results support a "Cervus-Megaloceros" clade. The phylogenetic positions of sympatric Megaloceros and Cervus elaphus specimens in particular indicate either that the Megaloceros mtDNA gene pool did not evolve for a substantial time period as an entity distinct from Cervus elaphus until its extinction, or that Megaloceros contributed mtDNA to Cervus elaphus or vice versa. The results of this study allow the conclusion that the European Megaloceros giganteus is more related to its modern regional counterparts of the species of Cervus elaphus than recent claims have suggested.     

Molecular phylogeny of the blind cavefish <Emphasis Type="Italic">Phreatichthys andruzzii</Emphasis> and <Emphasis Type="Italic">Garra barreimiae</Emphasis> within the family Cyprinidae

The phylogenetic relationships of two cavefish, Phreatichthys andruzzii and Garra barreimiae, belonging to the family Cyprinidae, were investigated by sequencing the mitochondrial cytochrome b gene. These cavefish species are native to Somalia (eastern Africa) and Oman (southeastern Arabian peninsula), respectively, and so far no molecular support to their taxonomy and phylogenetic position was ever provided. The analysis of cytochrome b sequences showed that the species are monophyletic taxa, closely related to each other and to other species of the genus Garra. Molecular clock calculations allowed to date the origin of these hypogaean species back to the Plio-Pleistocene and support the hypothesis that African cyprinids originated from Miocenic immigrations of Asian ancestors.     

Phylogeny of the Acipenseriformes: cytogenetic and molecular approaches

The review of the data on karyology and DNA content in Acipenseriformes shows that both extant families, the Polyodontidae and Acipenseridae, originated from a tetraploid ancestor which probably had a karyotype consisting of 120 macro- and microchromosomes and DNA content of about 3.2–3.8 pg per nucleus. The tetraploidization of the presumed 60-chromosome ancestor seems to have occurred at an early time of evolution of the group. The divergence of the Acipenseridae into Scaphirhyninae and Acipenserinae occurred without polyploidization. Within the genus Acipenser, polyploidization was one of the main genetic mechanisms of speciation by which 8n and 16n-ploid species were formed. Individual gene trees constructed for sequenced partial fragments of the 18S rRNA (230 base pairs, bp), 12S rRNA (185 bp), 16S rRNA (316 bp), and cytochrome b (270 bp) genes of two Eurasian (A. baerii and A. ruthenus) and two American (A. transmontanus and A. medirostris) species of Acipenser, Huso dauricus, Pseudoscaphirhynchus kaufmanni, Scaphirhynchus albus, and Polyodon spathula showed a low level of resolution; the analysis of a combined set of data for the four genes, however, gave better resolution. Our phylogeny based on molecular analysis had two major departures from existing morphological hypotheses: Huso dauricus is a sister-species to Acipenser instead of being basal to all acipenseriforms, and Scaphirhynchus and Pseudoscaphirhynchus do not form a monophyletic group. The phylogenetic tree constructed for the cytochrome b gene fragments (with inclusion of 7 additional species of Acipenser) supported the conclusion that octoploid species appeared at least three times within Acipenser.     

Molecular Phylogeny of Mitochondrial Cytochrome b and 12S rRNA Sequences in the Felidae: Ocelot and Domestic Cat Lineages

Molecular phylogeny of the cat family Felidae is derived using two mitochondrial genes, cytochrome b and 12S rRNA. Phylogenetic methods of weighted maximum parsimony and minimum evolution estimated by neighbor-joining are employed to reconstruct topologies among 20 extant felid species. Sequence analyses of 363 bp of cytochrome b and 376 bp of the 12S rRNA genes yielded average pair-wise similarity values between felids ranging from 94 to 99% and from 85 to 99%, respectively. Phylogenetic reconstruction supports more recent, intralineage associations but fails to completely resolve interlineage relationships. Both genes produce a monophyletic group ofFelisspecies but vary in the placement of the pallas cat. The ocelot lineage represents an early divergence within the Felidae, with strong associations between ocelot and margay, Geoffroy's cat and kodkod, and pampas cat and tigrina. Implications of the relative recency of felid evolution, presence of ancestral polymorphisms, and influence of outgroups in placement of the topological root are discussed.     

The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes)

The relationships among families of catfishes are poorly understood and have yet to be the subject of a comprehensive investigation with molecular data. Existing phylogenetic hypotheses are based on morphological data and incompletely resolved. This study analyzed complete sequences of mitochondrial gene cytochrome b for 170 species from 29 of 33 extant families, and focused on the relationships of Ictaluridae to other catfishes. In addition to previous phylogenetic studies, the fossil record, paleogeography, biogeography, and distribution of extant catfish families collectively suggest the location (if extant) of the ictalurid sister taxon to be Northern or Eastern Asia. Of the extant catfishes currently native to this area and included in this analysis, parsimony and Bayesian likelihood analyses recovered Cranoglanis bouderius as the most proximal sister taxon of Ictaluridae. Seemingly, ictalurids and cranoglanidids represent another biogeographic component linking freshwater fishes of North America and eastern Asia, e.g., catostomids and paddlefishes. The results coupled with present-day catfish distributions and inferences from the fossil record collectively suggest the ancestor of Ictaluridae to have invaded freshwaters of North America at the close of the Cretaceous through northeastern Asia and northwestern North America. Other superfamilial nodes supported the results of previous phylogenetic studies of narrower taxonomic scope. Several novel relationships were recovered (including a clade composed of Pimelodidae, Pseudopimelodidae, and Heptapteridae) and these along with sources of systematic error are discussed. A broad sampling of Bagridae permitted an examination of intergeneric relationships within this family and in light of recent morphological and molecular studies.     

Xantusiid "night" lizards: a puzzling phylogenetic problem revisited using likelihood-based Bayesian methods on mtDNA sequences

Contentious issues in Night Lizard (Xantusiidae) evolution are revisited using Maximum Likelihood-based Bayesian methods and compared with results from Neighbor-Joining and Maximum Parsimony analyses. Fragments of three mitochondrial genes, the 12S and 16S ribosomal genes, and the cytochrome b gene, are sampled across an ingroup composed of seven xantusiid species and a 12-species outgroup chosen to bracket ancestral states for six additional clades of scleroglossan lizards. Our phylogenetic analyses afford robust support for the following conclusions: Xantusiidae is part of Scincomorpha, rather than being allied with Gekkota; Lepidophyma is sister to Xantusia, rather than to Cricosaura; Xantusia riversiana is imbedded within, rather than being sister to, other Xantusia species; and rock-morph Xantusia are not closely related to one another. Convergence related to retarded rates of growth and development, or to physical constraints imposed by living in rock crevices, may be responsible for much of the character discordance underlying conflicts in xantusiid phylogeny. Fossil-calibrated Maximum Likelihood-based divergence time estimates suggest that although the xantusiid stem may have originated in the Mesozoic, the crown clade is exclusively Tertiary in age. Thus, the clade including extant Cricosaura does not appear to have been extant during the K-T boundary bolide impact, as has been suggested. Moreover, our divergence-time estimates indicate that the xantusiid island endemics, Cricosaura typica on Cuba and Xantusia riversiana on the California Channel Islands, arrived via dispersal rather than vicariance, as previously proposed.     

Mass extinction, gradual cooling, or rapid radiation? Reconstructing the spatiotemporal evolution of the ancient angiosperm genus Hedyosmum (Chloranthaceae) using empirical and simulated approaches

Chloranthaceae is a small family of flowering plants (65 species) with an extensive fossil record extending back to the Early Cretaceous. Within Chloranthaceae, Hedyosmum is remarkable because of its disjunct distribution--1 species in the Paleotropics and 44 confined to the Neotropics--and a long "temporal gap" between its stem age (Early Cretaceous) and the beginning of the extant radiation (late Cenozoic). Is this gap real, reflecting low diversification and a recent radiation, or the signature of extinction? Here we use paleontological data, relaxed-clock molecular dating, diversification analyses, and parametric ancestral area reconstruction to investigate the timing, tempo, and mode of diversification in Hedyosmum. Our results, based on analyses of plastid and nuclear sequences for 40 species, suggest that the ancestor of Chloranthaceae and the Hedyosmum stem lineages were widespread in the Holarctic in the Late Cretaceous. High extinction rates, possibly associated with Cenozoic climatic fluctuations, may have been responsible for the low extant diversity of the family. Crown group Hedyosmum originated c. 36-43 Ma and colonized South America from the north during the Early-Middle Miocene (c. 20 Ma). This coincided with an increase in diversification rates, probably triggered by the uplift of the Northern Andes from the Mid-Miocene onward. This study illustrates the advantages of combining paleontological, phylogenetic, and biogeographic data to reconstruct the spatiotemporal evolution of an ancient lineage, for which the extant diversity is only a remnant of past radiations. It also shows the difficulties of inferring patterns of lineage diversification when incomplete taxon sampling is combined with high extinction rates.     

The Bathyclarias-Clarias species flock. A new model to understand rapid speciation in African great lakes

Phylogenetic relationships between seven species of the catfish species flock from Lake Malawi (genus Bathyclarias) and other Clariid catfish have been investigated using cytochrome b partial sequences. Here we demonstrate that this species flock originated from a widespread, generalist species, Clarias gariepinus, still occurring in the lake. Bathyclarias species and their ancestor C. gariepinus form a simple model that can be used to understand the mechanisms of adaptation and rapid speciation in African Great lakes.     

A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution

The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent rainforest refugia probably acted as "lifeboats" that preserved existing species, rather than "species pumps" where many new successful lineages originated. We estimate that polyploidization occurred at least six times in clawed frogs.     

Ancestral Sequence Reconstruction of a Cytochrome P450 Family Involved in Chemical Defense Reveals the Functional Evolution of a Promiscuous,Xenobiotic-Metabolizing Enzyme in Vertebrates

The cytochrome P450 family 1 enzymes (CYP1s) are a diverse family of hemoprotein monooxygenases, which metabolize many xenobiotics including numerous environmental carcinogens. However, their historical function and evolution remain largely unstudied. Here we investigate CYP1 evolution via the reconstruction and characterization of the vertebrate CYP1 ancestors. Younger ancestors and extant forms generally demonstrated higher activity toward typical CYP1 xenobiotic and steroid substrates than older ancestors, suggesting significant diversification away from the original CYP1 function. Caffeine metabolism appears to be a recently evolved trait of the CYP1A subfamily, observed in the mammalian CYP1A lineage, and may parallel the recent evolution of caffeine synthesis in multiple separate plant species. Likewise, the aryl hydrocarbon receptor agonist, 6-formylindolo[3,2-b]carbazole (FICZ) was metabolized to a greater extent by certain younger ancestors and extant forms, suggesting that activity toward FICZ increased in specific CYP1 evolutionary branches, a process that may have occurred in parallel to the exploitation of land where UV-exposure was higher than in aquatic environments. As observed with previous reconstructions of P450 enzymes, thermostability correlated with evolutionary age; the oldest ancestor was up to 35 °C more thermostable than the extant forms, with a ¹⁰T₅₀ (temperature at which 50% of the hemoprotein remains intact after 10 min) of 71 °C. This robustness may have facilitated evolutionary diversification of the CYP1s by buffering the destabilizing effects of mutations that conferred novel functions, a phenomenon which may also be useful in exploiting the catalytic versatility of these ancestral enzymes for commercial application as biocatalysts.     

Phylogenetic position of Platanista gangetica: insights from the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences

The evolutionary relationship of peculiar and poorly known Ganges River dolphin with extinct and extant cetaceans has been in the state of confusion for more than a century. The close resemblance of platanistidae with some of the extinct taxon viz., Dalpiaziniidae and Waipatiidae and their sister group relationship with many of the extant lineages of cetaceans has been reported but none of the alternative hypotheses provide an unambiguous placement for this species. The present study provides insights into the molecular relationships of Platanista with other cetaceans based on comprehensive analyses of the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences, obtained from 15 specimens of Ganges dolphin from India and Bangladesh. The mean substitution distance analysis of phylogenetically informative characters in the cytochrome b sequences suggested that Platanista gangetica is significantly closer (P<0.001) to Mysticeti than to any other group of toothed whales. However, the conventional methods of phylogenetic reconstruction supported this finding with low to moderate (41-69%) bootstrap values.     

A daphniid ephippium (Branchiopoda: Anomopoda) of Cretaceous age

An anomopod ephippium from the Lower Cretaceous of Australia, remarkably similar to that of Simocephalus , shows that daphniids whose ephippia at least were very similar to those of extant species, existed about 120 million years ago. The family clearly originated in pre-Cretaceous times, and the Anomopoda considerably early than this.     

The status of the Japanese and East Asian bats of the genus Myotis (Vespertilionidae) based on mitochondrial sequences

The genus Myotis includes the largest number of species in the family Vespertilionidae (Chiroptera), and its members are distributed throughout most of the world. To re-evaluate the phylogenetic position of East Asian Myotis species with respect to Myotis species worldwide, we analyzed mitochondrial gene sequences of NADH dehydrogenase subunit 1 and cytochrome b from 24 East Asian individuals as well as 42 vespertilionid bats determined previously. The results suggest that: (1) some individuals having the same species name in Europe and Japan do not form a monophyletic clade, indicating that some bat species exhibit morphological convergence, (2) Japanese Myotis mystacinus forms a sister relationship with Myotis brandtii (Palaearctic), and both species are included in the American clade implying that an ancestor of these species originated in North America, and (3) the Black whiskered bat, Myotis pruinosus, is endemic to Japan and forms sister relationships with Myotis yanbarensis and Myotis montivagus collected from Okinawa (Japan) and Selangor (Malaysia), respectively, implying that M. pruinosus originated from the south. The systematics of Japanese and East Asian Myotis bats were revisited by considering their phylogenetic relationships. Our study provides the first extensive phylogenetic hypothesis of the genus Myotis that includes East Asian and Japanese species.     

Geophilomorph centipedes from the Cretaceous amber of Burma

The only previously known Mesozoic fossils of the chilopod order Geophilomorpha are two species from the Late Jurassic and Late Cretaceous, both known from single specimens that cannot be assigned with precision to a family. Four specimens from the Late Cretaceous (earliest Cenomanian) amber of Burma include three that can be identified as conspecific, described here as Kachinophilus pereirai gen. nov. sp. nov. These specimens preserve greater morphological detail in comparison with other fossil geophilomorphs: the form and fine features of the head, the maxillary complex, the trunk sternites with associated glandular pores and the ultimate pair of legs defend the assignment of the species to the extant family Geophilidae, and most probably to a derived subgroup including well‐known extant genera such as Ribautia Brölemann, 1909. Confocal laser scanning microscopy supplements examination under incident and transmitted light to document details of high taxonomic relevance in the head and the forcipular segment. The modern appearance of this species and its membership among deeply nested extant clades are consistent with molecular estimates that most of the diversity of crown‐group Geophilomorpha originated before the Late Cretaceous.