Evolutionary age of the Galápagos iguanas predates the age of the present Galápagos islands

New geological findings suggest that volcanoes existed over the Galápagos hotspot long before today's islands emerged less than 5 million years ago. The evolution of some of Galápagos' biota might have taken place on these former islands. This study investigates the evolutionary history of two of the archipelagos' older vertebrate taxa, the endemic Galápagos marine and land iguana (genera Amblyrhynchus and Conolophus). Mitochondrial rDNA sequences (in total about one kilobase of the 12S and 16S genes) were obtained from all extant genera of the family Iguanidae and the outgroup Oplurus. The phylogenetic analyses suggest that the Galápagos iguanas are sister taxa. Rate comparisons between the iguanid sequences and a corresponding set of sequences from ungulates with known fossil ages date their separation time at 10 million years, or more. The results strengthen the hypothesis that extended speciation times in the Galápagos are possible and provide an estimate of the minimum time inhabited islands of the archipelago may have existed.     

Phylogeny and rapid northern and southern hemisphere speciation of goldfinches during the Miocene and Pliocene epochs

Mitochondrial cytochrome b (cyt b) from 25 out of 31 extant goldfinches, siskins, greenfinches and redpolls (genus Carduelis) has been sequenced from living samples taken around the world, specimens have also been photographed. Phylogenetic analysis consistently gave the same groups of birds, and this grouping was generally related to geographical proximity. It has been supposed that Pleistocene glaciations played a crucial role in the origin of extant diversity and distribution of Northern Hemisphere vertebrates. Molecular comparison of most extant songbird species belonging to the genus Carduelis does not support this assertion. The fossil record of chicken and pheasant divergence time has been used to calibrate the molecular clock; cyt b DNA dendrograms suggest that speciation in Carduelinae birds occurred during the Miocene and Pliocene Epochs (9-2 million years ago) in both the Northern and Southern Hemispheres. Only about 4% average amount of nucleotide substitution per lineage is found between the most distant Carduelis species; this suggests a remarkably rapid radiation when compared with the radiation of other passerine songbird genera. In addition, a continuum of small songbird speciation may be found during the Miocene Epoch in parallel with speciation of other orders (i.e. Galliformes, chicken/pheasant). Pleistocene glaciations may have been important in subspeciation (i.e. Eastern European grey-headed goldfinches/Western European black-headed goldfinches) and also in ice-induced vicariance (isolation) (i.e. siskin in Western Europe vs. siskin in Far East Asia) around the world. European isolated Serinus citrinella (citril finch) is not a canary, but a true goldfinch. South American siskins have quickly radiated in the last 4 million years coinciding with the emergence of the Isthmus of Panama; probably, a North American siskin related to C. notata invaded a suitable and varied biotope (the South American island) for Carduelis birds. North American goldfinches may be renamed as siskins, because they have a distant genetic relationship with European goldfinches. Genus Acanthis could be dropped, and thus redpolls should be separated from twite and linnet, the latter (Europeans) probably being related to American goldfinches. Also, reproductive barriers are observed between closely related species and not between other more distant ones. Finally, a tentative classification for genus Carduelis species is suggested.     

The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery

The key protein of the signal recognition particle (termed SRP54 for Eucarya and Ffh for Bacteria) and the protein (termed SRalpha for Eucarya and Ftsy for bacteria) involved in the recognition and binding of the ribosome SRP nascent polypeptide complex are the products of an ancient gene duplication that appears to predate the divergence of all extant taxa. The paralogy of the genes encoding the two proteins (both of which are GTP triphosphatases) is argued by obvious sequence similarities between the N-terminal half of SRP54(Ffh) and the C-terminal half of SRalpha(Ftsy). This enables a universal phylogeny based on either protein to be rooted using the second protein as an outgroup. Phylogenetic trees inferred by various methods from an alignment (220 amino acid positions) of the shared SRP54(Ffh) and SRalpha(Ftsy) regions generate two reciprocally rooted universal trees corresponding to the two genes. The root of both trees is firmly positioned between Bacteria and Archaea/Eucarya, thus providing strong support for the notion (Iwabe et al. 1989; Gogarten et al. 1989) that the first bifurcation in the tree of life separated the lineage leading to Bacteria from a common ancestor to Archaea and Eucarya. None of the gene trees inferred from the two paralogues support a paraphyletic Archaea with the crenarchaeota as a sister group to Eucarya.     

Molecular phylogeography and the evolution and conservation of Amazonian mammals

The phylogeographic structure of 15 genera of Amazonian marsupials and rodents is summarized based on comparative sequence of the mitochondrial cytochrome b gene. The data are limited in geographical coverage, with samples widely scattered throughout Amazonia from the base of the Andes in Peru to the Guianan coast and eastern Brazil. We use this approach to define species boundaries, based minimally on the principle of reciprocal monophyly, in conjunction with morphological or other genetic discontinuities. The taxa so defined are older than previously appreciated, with many lineages dating from 1 to more than 3 Myr, and thus apparently predating the early Pleistocene. We relate patterns of concordant geographical shifts with underlying tectonic history and to current positions of major rivers. Finally, we provide comments on the utility of these data and patterns to conservation, articulating a need to incorporate phylogeographic information as part of the rationale in establishing conservation priorities at the organismal and geographical area levels.     

Archive contributions to a molecular phylogeography of the toad Bufo calamita in Britain

A complete phylogeographic analysis of any species requires sampling throughout its biogeographical range. In the case of the natterjack toad Bufo calamita in Britain, recent local extinctions have left substantial areas of its historical range without extant populations. We therefore obtained tissue samples of archived Bufo calamita from four museums in the United Kingdom. A range of tissues (tongue, liver, skin, lung, and larval tail) was sampled from a total of 33 individual animals. DNA was extracted and eight polymorphic microsatellite loci were scored. One or more loci were amplified successfully from 27 individuals, and sufficient data were obtained from regions with few or no surviving populations to supplement a phylogeographic analysis based on extant populations.     

Diploid hybrid speciation in Penstemon (Scrophulariaceae)

Hybrid speciation has played a significant role in the evolution of angiosperms at the polyploid level. However, relatively little is known about the importance of hybrid speciation at the diploid level. Two species of Penstemon have been proposed as diploid hybrid derivatives based on morphological data, artificial crossing studies, and pollinator behavior observations: Penstemon spectabilis (derived from hybridization between Penstemon centranthifolius and Penstemon grinnellii) and Penstemon clevelandii (derived from hybridization between P. centranthifolius and P. spectabilis). Previous studies were inconclusive regarding the purported hybrid nature of these species because of a lack of molecular markers sufficient to differentiate the parental taxa in the hybrid complex. We developed hypervariable nuclear markers using inter-simple sequence repeat banding patterns to test these classic hypotheses of diploid hybrid speciation in Penstemon. Each species in the hybrid complex was genetically distinct, separated by 10-42 species-specific inter-simple sequence repeat markers. Our data do not support the hybrid origin of P. spectabilis but clearly support the diploid hybrid origin of P. clevelandii. Our results further suggest that the primary reason diploid hybrid speciation is so difficult to detect is the lack of molecular markers able to differentiate parental taxa from one another, particularly with recently diverged species.     

Biogeographic origins of goannas (Varanidae): a molecular perspective

This project aims to clarify the phylogenetic relationships among the extant species of Varanus in order to elucidate the origins of Varanidae, using DNA sequences. Results obtained for a minimum of 662 nucleotides of 12S rRNA sequence data from each of 21 extant species of Varanus indicate that the Australian varanids form a single monophyletic clade and also suggest that within the Australian varanids, members of the subgenus Odatria (pygmy monitors) may from a clade separate from those in the subgenus Varanus (large monitors). The Asian species appear to be sister taxa to the Australian species, while the two African species investigated were most divergent, suggesting that the Varanidae are not Gondwanic in origin. Hypothesis testing analyses were performed and involved constraining the 12S sequence data according to previously described topologies and testing the difference using parametric and nonparametric statistics. The phylogeny generated using 12S sequence data was statistically different from previously described morphological trees, while there was some support for topologies based on chomosomal and immunological datasets. Overall, our results suggest that the Australian species may be derived from an Asian source and are, therefore, in agreement with the hypothesis based on the fossil record suggesting that Varanidae may be Asian in origin.     

Species realities and numbers in sexual vertebrates: perspectives from an asexually transmitted genome

A literature review is conducted on the phylogenetic discontinuities in mtDNA sequences of 252 taxonomic species of vertebrates. About 140 of these species (56%) were subdivided clearly into two or more highly distinctive matrilineal phylogroups, the vast majority of which were localized geographically. However, only a small number (two to six) of salient phylogeographic subdivisions (those that stand out against mean within-group divergences) characterized individual species. A previous literature summary showed that vertebrate sister species and other congeners also usually have pronounced phylogenetic distinctions in mtDNA sequence. These observations, taken together, suggest that current taxonomic species often agree reasonably well in number (certainly within an order-of-magnitude) and composition with biotic entities registered in mtDNA genealogies alone. In other words, mtDNA data and traditional taxonomic assignments tend to converge on what therefore may be "real" biotic units in nature. All branches in mtDNA phylogenies are nonanastomose, connected strictly via historical genealogy. Thus, patterns of historical phylogenetic connection may be at least as important as contemporary reproductive relationships per se in accounting for microevolutionary unities and discontinuities in sexually reproducing vertebrates. Findings are discussed in the context of the biological and phylogenetic species concepts.     

Phylogeography and pleistocene evolution in the North American black bear

To determine the extent of phylogeographic structuring in North American black bear (Ursus americanus) populations, we examined mitochondrial DNA sequences (n = 118) and restriction fragment length polymorphism profiles (n = 258) in individuals from 16 localities. Among the bears examined, 19 lineages falling into two highly divergent clades were identified. The clades differ at 5.0% of nucleotide positions, a distance consistent with an origin 1.8 MYA, and have different but overlapping geographical distributions. Areas of clade cooccurrence show that eastern and western populations are currently mixing, but regional differences in lineage distribution suggest that mixing has begun only recently. The long-term population history of black bears appears to be characterized predominantly by long-term regional isolation followed by recent contact and hybridization. Congruence between the pattern of diversity observed in black bears and patterns of forest refuge formation during the Pleistocene supports earlier speculation that Pleistocene forest fragmentations underlie a common pattern in the phylogeography of North American forest taxa.     

Molecular systematics of Phlebotominae: a pilot study. Paraphyly of the genus Phlebotomus

Phylogenetic relationships among Phlebotominae were inferred through a pilot study using parsimony analysis of the D2 domain of ribosomal DNA sequences: 455 pairs of bases were sequenced in nine species of Phlebotomine sandflies which belong to the genera Lutzomyia, Phlebotomus and Sergentomyia. Two taxa are used as outgroups: Psychoda sp. and Nemapalpus flavus which is the sister group of the Phlebotominae. The South American genus Lutzomyia appears to be monophyletic. The Mediterranean species Sergentomyia dentata is its sister group and is not clustered with the Old World genus Phlebotomus. The latter is a paraphyletic genus with an early individualization of the branch including the closely related subgenera Phlebotomus and Paraphlebotomus, and a late individualization of the subgenus Larroussius. These results have some consequences on the biogeography of the leishmaniasis in the Old World.     

Archetypal organization of the amphioxus Hox gene cluster

Organization into gene clusters is an essential and diagnostic feature of Hox genes. Insect and nematode genomes possess single Hox gene clusters (split in Drosophila); in mammals, there are 38 Hox genes in four clusters on different chromosomes. A collinear relationship between chromosomal position, activation time and anterior expression limit of vertebrate Hox genes suggests that clustering may be important for precise spatiotemporal gene regulation and hence embryonic patterning. Hox genes have a wide phylogenetic distribution within the metazoa, and are implicated in the control of regionalization along the anteroposterior body axis. It has been suggested that changes in Hox gene number and genomic organization played a role in metazoan body-plan evolution, but identifying significant changes is difficult because Hox gene organization is known from only very few and widely divergent taxa (principally insects, nematodes and vertebrates). Here we analyse the complexity and organization of Hox genes in a cephalochordate, amphioxus, the taxon thought to be the sister group of the vertebrates. We find that the amphioxus genome has only one Hox gene cluster. It has similar genomic organization to the four mammalian Hox clusters, and contains homologues of at least the first ten paralogous groups of vertebrate Hox genes in a collinear array. Remarkably, this organization is compatible with that inferred for a direct ancestor of the vertebrates; we conclude that amphioxus is a living representative of a critical intermediate stage in Hox cluster evolution.     

Comparative structure analysis of vertebrate ribonuclease P RNA

Ribonuclease P cleaves 5'-precursor sequences from pre-tRNAs. All cellular RNase P holoenzymes contain homologous RNA elements; the eucaryal RNase P RNA, in contrast to the bacterial RNA, is catalytically inactive in the absence of the protein component(s). To understand the function of eucaryal RNase P RNA, knowledge of its structure is needed. Considerable effort has been devoted to comparative studies of the structure of this RNA from diverse organisms, including eucaryotes, primarily fungi, but also a limited set of vertebrates. The substantial differences in the sequences and structures of the vertebrate RNAs from those of other organisms have made it difficult to align the vertebrate sequences, thus limiting comparative studies. To expand our understanding of the structure of diverse RNase P RNAs, we have isolated by PCR and sequenced 13 partial RNase P RNA genes from 11 additional vertebrate taxa representing most extant major vertebrate lineages. Based on a recently proposed structure of the core elements of RNase P RNA, we aligned the sequences and propose a minimum consensus secondary structure for the vertebrate RNase P RNA.     

Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data

Until a few decades ago, phylogenetic relationships among placental orders were ambiguous and usually depicted to radiate as an unresolved "bush." Resolution of this bush by various workers has been progressing slowly, but with promising results corroborated by nondental, dental, and molecular characters. In this study we continue to seek resolution. A total of 258 nondental and 2 dental characters was analyzed by PAUP and MacClade on 39 vertebrate taxa (3 reptiles, 1 nonmammalian therapsid, and 35 mammals; 20 of the mammals are extant and 15 are extinct) to study higher taxonomic relationships with emphasis on Placentalia (Eutheria). About two-thirds of the characters are osteological, the rest concern soft tissues, including myological but excluding molecular characters (most are our data, the rest are from the literature). Cladistic analysis included all 39 taxa (fossil taxa help to evaluate polarities of characters) and all characters were given equal weight. Extant Mammalia are divided into Prototheria and Theria, the latter into Marsupialia and Placentalia. Placentalia comprises Xenarthra and Epitheria. Within Epitheria, Lipotyphla and Preptotheria (emended) are sister-taxa. Preptotherian taxa group into: ungulate-related taxa and various nonungulates. The former include Carnivora, Pholidota, Tubulidentata, Artiodactyla, Cetacea, Perissodactyla, Hyracoidea, Proboscidea, and Sirenia. A possible association to embrace Lagomorpha, Rodentia, Macroscelidea, Scandentia, Primates, Chiroptera, and Dermoptera is suggested. Significant differences between our findings and those of recent investigators include the dissociation of Pholidota from Xenarthra and the plesiomorphous position of Lipotyphla within Epitheria. Congruence between morphological and molecular results is closer than previously reported.     

Intratumor pharmacokinetics, flow resistance, and metabolism during gemcitabine infusion in ex vivo perfused human small cell lung cancer

The Alcidae is a unique assemblage of Northern Hemisphere seabirds that forage by "flying" underwater. Despite obvious affinities among the species, their evolutionary relationships are unclear. We analyzed nucleotide sequences of 1,045 base pairs of the mitochondrial cytochrome b gene and allelic profiles for 37 allozyme loci in all 22 extant species. Trees were constructed on independent and combined data sets using maximum parsimony and distance methods that correct for superimposed changes. Alternative methods of analysis produced only minor differences in relationships that were supported strongly by bootstrapping or standard error tests. Combining sequence and allozyme data into a single analysis provided the greatest number of relationships receiving strong support. Addition of published morphological and ecological data did not improve support for any additional relationship. All analyses grouped species into six distinct lineages: (1) the dovekie (Alle alle) and auks, (2) guillemots, (3) brachyramphine murrelets, (4) synthliboramphine murrelets, (5) true auklets, and (6) the rhinoceros auklet (Cerorhinca monocerata) and puffins. The two murres (genus Uria) were sister taxa, and the black guillemot (Cepphus grylle) was basal to the other guillemots. The Asian subspecies of the marbled murrelet (Brachyramphus marmoratus perdix) was the most divergent brachyramphine murrelet, and two distinct lineages occurred within the synthliboramphine murrelets. Cassin's auklet (Ptychoramphus aleuticus) and the rhinoceros auklet were basal to the other auklets and puffins, respectively, and the Atlantic (Fratercula arctica) and horned (Fratercula corniculata) puffins were sister taxa. Several relationships among tribes, among the dovekie and auks, and among the auklets could not be resolved but resembled "star" phylogenies indicative of adaptive radiations at different depths within the trees.     

Sex differences in the sciatic notch of great apes and modern humans

The sciatic notch has been widely used as a sexing criterion in modern humans. In order to better understand the sex differences of this feature in modern humans and great apes, four measurements of the sciatic notch were taken on samples of modern humans and great apes of known sex. Univariate (ANOVA) analysis and discriminant function analysis were performed on the extant taxa to determine: (1) the discriminating power of each variable in these samples of known group membership; and (2) which of these extant taxa shows the best discrimination between the sexes for the sciatic notch. Of the four extant taxa, the sciatic notch of Homo sapiens is the most sexually dimorphic, followed by Gorilla gorilla, and more weakly by Pongo pygmaeus, while Pan troglodytes is the least dimorphic of these taxa. Since the presence of a well defined sciatic notch is a hominid trait resulting from the dorsal extension of the posterior ilium, the close approximation of the sacrum to the acetabulum, the shortened ischium, and the accentuation of the ischial spine as part of the bipedal adaptation, it seems likely that the configuration of the sciatic notch in hominids was initially related to bipedalism, not reproduction. The development of sex differences in the sciatic notch of modern humans is more likely to have occurred after the transition to bipedality.     

Dietary adaptations of Plio-Pleistocene Bovidae: implications for hominid habitat use

Detailed reconstructions of vegetation structure are critical to understanding morphological and behavioral adaptations of Plio-Pleistocene African hominids, Savanna grassland habitats are often postulated as being influential in the evolution of many hominid adaptations (e.g., bipedality, foraging behaviors), yet the existence of this habitat type throughout the African Plio-Pleistocene has not been clearly established. Broad-scale reconstructions of hominid habitats as "savanna-mosaic" do not account for the fact that African grasslands may be classified into at least two different types: edaphic grasslands, which include seasonally flooded valley grasslands; and secondary grasslands, which include vast, relatively dry savanna grasslands. Though edaphic grasslands have existed for millions of years, it is unknown when secondary grasslands became widespread. The presence of specific microhabitats, including secondary grasslands, at a number of hominid sites was investigated in this study through reconstruction of diet and habitat preference in five extinct bovid taxa that were contemporaneous with early hominids. To reconstruct diet in extinct taxa, morphological correlates of dietary preferences were identified through a comparative study of cranial form in extant bovids. Metric data from cranial material of the five African Plio-Pleistocene bovid taxa were compared with extant bovid results, which yielded information of specific feeding behaviors of the extinct taxa. Reconstructed diets suggest that the earliest taxa to inhabit secondary grasslands in East Africa were Connochaetes gentryi and Parmularius altidens at around 2 m.y.a. It may therefore be inferred that secondary grasslands became prevalent at this time. This inference of secondary grassland development suggests that adaptations to this habitat type were not related to the origin of the Hominidae or to the evolution of bipedality in hominids. However, evidence suggests that this habitat type was influential in the evolution of Homo erectus sensu lato just after 2 m.y.a. in East Africa.     

A reappraisal of early hominid phylogeny

We report here on the results of a new cladistic analysis of early hominid relationships. Ingroup taxa included Australopithecus afarensis, Australopithecus africanus, Australopithecus aethiopicus, Australopithecus robustus, Australopithecus boisei, Homo habilis, Homo rudolfensis, Homo ergaster and Homo sapiens. Outgroup taxa included Pan troglodytes and Gorilla gorilla. Sixty craniodental characters were selected for analysis. These were drawn from the trait lists of other studies and our own observations. Eight parsimony analyses were performed that differed with respect to the number of characters examined and the manner in which the characters were treated. Seven employed ordered characters, and included analyses in which (1) taxa that were variable with respect to a character were coded as having an intermediate state, (2) characters with variable states in any taxon were excluded; (3) a variable taxon was coded as having the state exhibited by the majority of its hypodigm, (4) variable taxa were coded as missing data for that character, (5) some characters were considered irreversible, (6) masticatory characters were excluded, and (7) characters whose states were unknown in some taxa were excluded. In the final analysis, (8) all characters were unordered. All analyses were performed using PAUP 3.0s. Despite the fact that the eight analyses differed with respect to methodology, they produced several consistent results. All agreed that the "robust" australopithecines form a clade, A. afarensis is the sister taxon of all other hominids, and the genus Australopithecus, as conventionally defined, is paraphyletic. All eight also supported trees in which A. africanus is the sister taxon of a joint Homo+ "robust" clade, although in one analysis an equally parsimonious topology found A. africanus to be the sister of the "robust" species. In most analyses, the relationships of A. africanus and H. habilis were unstable, in the sense that their positions vary in trees that are marginally less parsimonious than the favored one. Trees in which "robust" australopithecines are paraphyletic were found to be extremely unparsimonious.     

Trans-sialidase and sialidase activities discriminate between morphologically indistinguishable trypanosomatids

The expression of trans-sialidase and sialidase activities in the kinetoplastid protozoa was explored as a potential marker to discriminate between the morphologically indistinguishable flagellates isolated from human, insects and vertebrate reservoir hosts. By virtue of the differences observed in the ratios of these enzyme activities, a collection of 52 species and strains comprising the major taxa of these parasites could be separated into four expression types. Type-I parasites express comparable levels of both trans-sialidase and sialidase activities (Endotrypanum species and Trypanosoma lewisi). Type-II parasites express predominantly trans-sialidase activity (Trypanosoma cruzi and Trypanosoma conorhini). Type-III parasites express sialidase activity exclusively (Trypanosoma rangeli and Trypanosoma leeuwenhoeki). Type-IV parasites do not express either activity (Leishmania species and Trypanoplasma borreli). The measurement of trans-sialidase and sialidase activities thus permits the differentiation of parasites frequently found in the same insect vectors that are difficult to distinguish, such as T. cruzi and T. rangeli, or in the same sylvatic vertebrate and invertebrate hosts, such as Leishmania and Endotrypanum.     

Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses

Retroviruses are capable of infectious horizontal transmission between hosts, usually between individuals within a single species, although a number of probable zoonotic infections resulting from transmission between different species of placental mammals have also been reported. Despite these data, it remains unclear how often interspecies transmission events occur or whether their frequency is influenced by the evolutionary distance between host taxa. To address this problem we used PCR to amplify and characterize endogenous retroviruses related to the murine leukemia viruses. We show that members of this retroviral genus are harbored by considerably more organisms than previously thought and that phylogenetic analysis demonstrates that viruses isolated from a particular host class generally cluster together, suggesting that infectious virus horizontal transfer between vertebrate classes occurs only rarely. However, two recent instances of transmission of zoonotic infections between distantly related host organisms were identified. One, from mammals to birds, has led to a rapid adaptive radiation into other avian hosts. The other, between placental and marsupial mammals, involves viruses clustering with recently described porcine retroviruses, adding to concerns regarding the xenotransplantation of pig organs to humans.