The phylogenetic relationships of the Andean swamp rat genus <Emphasis Type="Italic">Neotomys</Emphasis> (Rodentia,Cricetidae, Sigmodontinae) based on mitochondrial and nuclear markers

The aim of this study was to assess the phylogenetic position of the South American cricetid genus Neotomys using two molecular markers: one nuclear (Irbp) and one mitochondrial (mt-cyb). This genus is currently considered as incertae sedis in the Sigmodontinae radiation. The phylogenetic relationships were estimated using three approaches: Bayesian inference, maximum likelihood and parsimony. We found the genus Neotomys closely related to the genera Euneomys and Irenomys, which are also considered incertae sedis. Our results suggest a common origin for this group of genera; this fact should be reflected in the taxonomy as a supra generic group with a tribal level. However, further and deeper analysis of both molecular and morphological data are needed to diagnose and formalize the proposed tribe. The relationships of this clade to the other members of Sigmodontinae were not clear as assessed by these data sets. The three genera are distributed around the Central and Southern Andes in South America evidencing that the Andes have played an important role in the diversification of several tribes of sigmodontine rodents.     

Phylogenetic reassessment of the five forewing radial-veined tribes of Riodininae (Lepidoptera: Riodinidae)

The relationships among the genera and tribal groupings of Riodininae with five forewing radial veins, and between these and tribes with four forewing radial veins, were examined using a phylogenetic analysis. Using the type species from all sixteen genera in the tribal groupings Eurybiini, Mesosemiini and incertae sedis (a presumed paraphyletic group of loosely related genera), and representatives from the four forewing radial‐veined riodinine tribes, thirty‐five new and traditional characters were coded from adult ecology, wing venation and pattern, the adult head and body, male and female genitalia, and early stage ecology and morphology. The majority of characters are illustrated. Phylogenetic analysis of these data produced five equally most parsimonious cladograms using equal weights and after successive weighting. The strict consensus of these confirms the monophyly of Eurybiini and Mesosemiini as currently conceived, but also indicates several higher‐level relationships not previously hypothesized. Mesosemiini is here more broadly defined to also include the entire incertae sedis section, and the tribe is divided into Mesosemiina, for the previously delimited Mesosemiini plus Eunogyra and Teratophthalma, and Napaeina, subtr.n. for the incertae sedis section minus these two genera. The following hypothesis of relationships is tentatively proposed for the basal clades of Riodininae: Mesosemiini + (Eurybiini + remainder of Riodininae). These new hypotheses, and the characters supporting them, are discussed and compared with those previously proposed.     

Dating an impressive Neotropical radiation: Molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography

With about 400 living species and 82 genera, rodents of the subfamily Sigmodontinae comprise one of the most diverse and more broadly distributed Neotropical mammalian clades. There has been much debate on the origin of the lineage or the lineages of sigmodontines that entered South America, the timing of entrance and different aspects of further diversification within South America. The ages of divergence of the main lineages and the crown age of the subfamily were estimated by using sequences of the interphotoreceptor retinoid binding protein and cytochrome b genes for a dense sigmodontine and muroid sampling. Bayesian inference using three fossil calibration points and a relaxed molecular clock estimated a middle Miocene origin for Sigmodontinae (～12 Ma), with most tribes diversifying throughout the Late Miocene (6.9–9.4 Ma). These estimates together results of analyses of ancestral area reconstructions suggest a distribution for the most recent common ancestor of Sigmodontinae in Central-South America and a South American distribution for the most recent common ancestor of Oryzomyalia.     

An Assessment of the Systematics of Arvicanthine Rodents Using Mitochondrial DNA Sequences: Evolutionary and Biogeographical Implications

Mitochondrial DNA sequences of cytochrome b (1140-bp), 12S (375-bp) and 16S (475-bp) ribosomal RNA gene fragments were used to investigate the phylogenetic relationships of a group of African rodents referred as the arvicanthines (Family Muridae, Subfamily Murinae). A total of 49 specimens including all seven genera and 15 of the 24 arvicanthine species currently recognized as well as outgroups from the subfamily Acomyinae, Arvicolinae, Gerbillinae, Murinae and Otomyinae were examined. Our molecular data support the monophyly of the African arvicanthine genera and their partition into three distinct lineages: one composed of Arvicanthis, Mylomys and Pelomys, one composed of Desmomys and Rhabdomys, and one represented by Lemniscomys. The Indian arvicanthine Golunda is external to this clade and is part of a larger clade, together with the African arvicanthines and other African Murinae such as Aethomys, Dasymys, Grammomys, and Hybomys, for which we propose the use of the tribal name Arvicanthini. The basal relationships within this set of species are poorly resolved, suggesting the possibility of a rapid radiation. Calibration based on the fossil record suggests that this radiative event would have taken place at about 8.0 Mya (Million years ago). The identification of the Otomyinae as the sister-taxon to Arvicanthini implies that the former are true murines and should therefore be given only tribal rank within the Murinae.     

Phylogeny of the subfamily Larentiinae (Lepidoptera: Geometridae): integrating molecular data and traditional classifications

Larentiinae are the second largest subfamily of Geometridae, with more than 6200 described species. Despite recent advances in molecular systematics of geometrid moths, phylogenetic relationships between the numerous subgroups of Larentiinae are poorly known. In this study we present the most comprehensive attempt to date to resolve the phylogeny of Larentiinae, having sampled at least one species from all currently recognized 23 tribes. Fragments of one mitochondrial (COI) and eight nuclear (EF‐1α, WGL, GAPDH, RPS5, IDH, MDH, CAD and 28S) genes were sequenced, for a total of 6939 bp. Maximum likelihood and Bayesian analyses resulted in identical well‐resolved phylogenetic trees, which had maximum or near‐maximum support values at most nodes. Almost all conventionally recognized tribes represented by more than one genus were found to be monophyletic. Close to the root of Larentiinae, six tribes branch off the main lineage one after another, with Dyspteridini being sister to all other members of the subfamily. The rest of larentiines are divided into two very diverse lineages, comprising eight and at least ten tribes, respectively. There were just three findings incongruent with the conventional tribal subdivision of the subfamily. First, the genera Collix Guenée and Anticollix Prout formed a separate, previously unrecognized but well‐supported clade at the tribe level. Second, the Palaearctic genus Pelurga Hübner was placed apart from Larentia Treitschke and Mesoleuca Hübner, which were the other members of Larentiini in this analysis. Third, Cataclysmini appeared together with genera belonging to Xanthorhoini, leaving the latter paraphyletic. The Neotropic genus Oligopleura Herrich‐Schäffer is shown to belong to the tribe Euphyiini ( comb.n. ) according to both molecular data and male genital morphology. The results and the tribal classification of Larentiinae are discussed with reference to the principal publications since the end of the 19th Century. We conclude that the current tribal classification of Larentiinae is not controversial from the phylogenetic point of view and that its increasing complexity has merely reflected the accumulation of information, mainly through different methods of biosystematic study having become available for researchers. Our results indicate that diurnal lifestyle, accompanied by conspicuous coloration, has evolved independently in several subgroups of Larentiinae.     

Ribosomal DNA ITS-1 Intergenic Spacer Polymorphism in Triatomines (Triatominae, Heteroptera)

The length polymorphism of ribosomal DNA ITS-1 intergenic spacer was analyzed in eight species of triatomines belonging to Triatoma, Rhodnius, and Panstrongylus genera. The analyzed species were Rhodnius domesticus, R. neivai, R. robustus, Triatoma brasiliensis, T. infestans, T. vitticeps, Panstrongylus megistus, and P. herreri. These insects are vectors of Chagas' disease, one of the most prominent public health problems among South American countries. This work allowed the differentiation between species of the Triatomini and Rhodniini tribes through the analysis of ITS-1 length polymorphism by PCR and RFLP techniques. The species of the Triatoma and Panstrongylus genera presented an amplified ITS-1 fragment between 600 and 1000 bp, whereas Rhodnius presented a less variable ITS-1 length fragment, around 300 bp, which could reflect the monophyletic origin of the Rhodniini tribe. Species belonging to this genus were further differentiated by RFLP with HaeIII and AluI endonucleases. Our results corroborate the hypothesis of polyphyletic origin in this group of insects and contribute to knowledge about evolutionary relationships in triatomines.     

Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents

LINE-1 transposable elements (L1s) are ubiquitous in mammals and are thought to have remained active since before the mammalian radiation. Only one L1 extinction event, in South American rodents in the genus Oryzomys, has been convincingly demonstrated. Here we examine the phylogenetic limits and evolutionary tempo of that extinction event by characterizing L1s in related rodents. Fourteen genera from five tribes within the Sigmodontinae subfamily were examined. Only the Sigmodontini, the most basal tribe in this group, demonstrate recent L1 activity. The Oryzomyini, Akodontini, Phyllotini, and Thomasomyini contain only L1s that appear to have inserted long ago; their L1s lack open reading frames, have mutations at conserved amino acid residues, and show numerous private mutations. They also lack restriction site-defined L1 subfamilies specific to any species, genus or tribe examined, and fail to form monophyletic species, genus or tribal L1 clusters. We determine here that this L1 extinction event occurred roughly 8.8 million years ago, near the divergence of Sigmodon from the remaining Sigmodontinae species. These species appear to be ideal model organisms for studying the impact of L1 inactivity on mammalian genomes.     

Phylogenetic relationships of New Zealand Asteraceae inferred from ITS sequences

Forty-five sequences from members of all genera of Asteraceae indigenous to New Zealand and 50 published sequences representing the tribal diversity in the family were analyzed to assess the utility of ITS sequences to resolve phylogenetic relationships. Previous studies using chloroplast DNA sequences and morphology provided support for several clades in the Asteraceae, yet the relationships among some of these were uncertain. The results from ITS analysis were largely consistent with these earlier studies. The New Zealand species are included in at least six clades, most of these corresponding to recognized tribes. Our results have also clarified the tribal affinities of a few anomalous genera. Haastia, previously aligned with the Gnaphalieae or the Astereae, is nested in the Senecioneae. Centipeda, previously included in the Astereae or Anthemideae, emerges near the Heliantheae. The relationships of Abrotanella remain unresolved. Received August 8, 2001 Accepted November 6, 2001     

Sigmodontine rodents diversified in South America prior to the complete rise of the Panamanian Isthmus

The extant distribution of sigmodontine rodents encompasses most of the New World, and the majority of the species in this subfamily inhabit South America. Nevertheless, the basal lineages of the Sigmodontinae are distributed in North and Central America, and the fossil record indicates a North American origin. This evidence has produced contentious theories concerning the evolution of these rodents. The dispute usually stems from a disagreement about the way in which sigmodontines reached South America, which was an isolated landmass during most of the Cenozoic. Fundamentally, the debate is associated with the role of Panamanian Isthmus formation and the Great American Biotic Interchange (GABI) in the diversification of the clade. An early hypothesis implies that sigmodontines arrived in South America before the complete rise of the Panamanian Isthmus, whereas a late hypothesis directly correlates the diversification of the lineage with this event. To address this question, we have sequenced nuclear and mitochondrial sequences, as well as the first Sigmodontinae mitochondrial genomes (Akodon montensis and Wiedomys cerradensis) and performed a Bayesian dating analysis. Our results showed that the most recent common ancestor of the subfamily lived at approximately 15 Ma. Although the diversification of sigmodontines was not associated with the complete rise of the Panamanian Isthmus, we cannot exclude the hypothesis that this event played a relevant role in the evolution of the lineage during the Miocene.     

Closing the gaps: phylogenetic relationships in the Brassicaceae based on DNA sequence data of nuclear ribosomal ITS region

Sequence data from the nuclear encoded ribosomal internal transcribed spacer (ITS) region were used to determine monophyly of tribes, tribal limits, and tribal relationships of 96 so far unassigned or tentatively assigned genera (represented by 101 taxa/accessions) within the Brassicaceae. Maximum-parsimony and maximum-likelihood analyses of 185 ITS Brassicaceae sequences, which also included representatives of each of the 34 currently recognized tribes, supported the separate phylogenetic distinctness of these tribes and permitted the tribal assignment of all but 12 of the unassigned genera into tribal clades. The data support the recognition of eight new, well-resolved, uni- or oligogeneric tribes recognized herein as the Alyssopsideae [96% bootstrap support (BS); including the central and southwestern Asian Alyssopsis and Calymmatium], Asteae (100% BS; including the Mexican Asta), Eudemeae (97% BS; South American Brayopsis, Eudema, and Xerodraba), Kernereae (96% BS; European Kernera and Rhizobotrya), Notothlaspideae (100% BS; New Zealandic Notothlaspi), Oreophytoneae (100% BS; eastern African Oreophyton and southern European Murbeckiella), and Yinshanieae (100% BS; Chinese Yinshania), as well as the moderately supported Microlepidieae (75% BS; Australian Microlepidium and Carinavalva). Furthermore, the results fully support the recent findings that the tribes Schizopetaleae and Thelypodieae ought to be recognized as two distinct tribes instead of a single tribe, as well as provide some support for the re-establishment of the tribe Cremolobeae, bringing the total number to 44 tribes in the family. Nearly 92% (308) of the 336 genera in the family have been assigned to a tribe. The earlier-published Anastaticeae is taken here to replace the Malcolmieae.     

Molecular systematics and paleobiogeography of the South American sigmodontine rodents [published erratum appears in Mol Biol Evol 1998 Feb;15(2):224]

The murid rodent subfamily Sigmodontinae contains 79 genera which are distributed throughout the New World. The time of arrival of the first sigmodontines in South America and the estimated divergence time(s) of the different lineages of South American sigmodontines have been controversial due to the lack of a good fossil record and the immense number of extant species. The "early-arrival hypothesis" states that the sigmodontines must have arrived in South America no later than the early Miocene, at least 20 MYA, in order to account for their vast present-day diversity, whereas the "late-arrival hypothesis" includes the sigmodontines as part of the Plio-Pleistocene Great American Interchange, which occurred approximately 3.5 MYA. The phylogenetic relationships among 33 of these genera were reconstructed using mitochondrial DNA (mtDNA) sequence data from the ND3, ND4L, arginine tRNA, and ND4 genes, which we show to be evolving at the same rate. A molecular clock was calibrated for these genes using published fossil dates, and the genetic distances were estimated from the DNA sequences in this study. The molecular clock was used to estimate the dates of the South American sigmodontine origin and the main sigmodontine radiation in order to evaluate the "early-" and "late-arrival" scenarios. We estimate the time of the sigmodontine invasion of South America as between approximately 5 and 9 MYA, supporting neither of the scenarios but suggesting two possible models in which the invading lineage was either (1) ancestral to the oryzomyines, akodonts, and phyllotines or (2) ancestral to the akodonts and phyllotines and accompanied by the oryzomyines. The sigmodontine invasion of South America provides an example of the advantage afforded to a lineage by the fortuitous invasion of a previously unexploited habitat, in this case an entire continent.      

Tracing the diversification history of a Neogene rodent invasion into South America

We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals a pattern of species co‐occurrence in which assemblages of closely related species are also the fastest diversifying ones. Subregions of the Neotropics occupied by distantly related species that are on average more slowly diversifying include Central America, northern South America, and the Atlantic forest. In southern South America, recent species turnover appears to have been higher. Ancestral locations for the main tribes of sigmodontines were also estimated, suggesting eastern South America and the Amazonian lowlands were colonized before some central Andean regions, even though the latter are now centers of species richness for these rodents. Moreover, a past connection between the tropical Andes and the Atlantic Forest is suggested by our results, highlighting a role for a hypothetical arc connecting the two biomes, which would have impacted many other groups of organisms. Whether rapid, recent speciation in some regions is related to Quaternary climatic fluctuations and the young age of sigmodontines (~12.7 Ma crown age) or instead to intrinsic traits of these rodents remains an open question. If the former is true, we hypothesize that contrasting trends will characterize older Neotropical clades.     

Molecular phylogeny of the Acre clade (Crassulaceae): Dealing with the lack of definitions for Echeveria and Sedum

The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the “Acre clade”, a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European–Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera – Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.     

The immunoglobulin allotypes (Gm and Km) of twelve Indian Tribes of Central and South America

The Gm and Km immunoglobulin allotypes are presented, for the first time, for six South American Indian tribes (Baniwa, Kanamari, Kraho, Makiritare, Panoa, and Ticuna) and one Central American tribe (Guaymi). Additional allotype information is presented for five previously reported South American tribes (Cayapo, Piaroa, Trio, Xavante and Yanomama). The distributions of the Gm and Km allotypes among all the tribal populations tested to date are reviewed and evidence is presented for the presence of a north (high) -south (low) cline in Km frequency. The wave theory of the populating of the South American continent was tested by an examination of the distribution of six alleles (Gm^ax;g, Gm^a;b0,3,t, Di^a, R^z, TF^D Chi, and 6PGD^C), absent in some populations but with polymorphic proportions in others. The present, limited, data failed to confirm the theory.     

A new record and an evaluation of the phylogenetic relationships of Abrothrix olivaceus markhami (Rodentia: Sigmodontinae)

Recent phylogenetic studies of the subfamily of cricetid rodents (Sigmodntinae) have validated the taxonomic classification at the tribal level of the Andean Clade. It is possible that some endemic species from Patagonian South America are part of this new tribe, but previous studies have not evaluated this hypothesis due to the difficulty of obtaining samples. In this study, we evaluate the phylogenetic relationships of Akodon markhami (Pine, 1973), a species endemic to the Chilean Patagonia, using individuals recently captured at the type locality of this taxon. Our results indicate that this form of Akodon corresponds to a subspecies of Abrothrix olivaceus, and should be incorporated into the Andean Clade as a geographic race of this widely distributed species on the South American continent. Based on a molecular clock calibration, we dated the origin of this geographic race during the last glacial cycles of the Quaternary, as the result of a vicariant process.     

Phylogeny of the bee family Megachilidae (Hymenoptera: Apoidea) based on adult morphology

Phylogenetic relationships within the bee family Megachilidae are poorly understood. The monophyly of the subfamily Fideliinae is questionable, the relationships among the tribes and subtribes in the subfamily Megachilinae are unknown, and some extant genera cannot be placed with certainty at the tribal level. Using a cladistic analysis of adult external morphological characters, we explore the relationships of the eight tribes and two subtribes currently recognised in Megachilidae. Our dataset included 80% of the extant generic‐level diversity, representatives of all fossil taxa, and was analysed using parsimony. We employed 200 characters and selected 7 outgroups and 72 ingroup species of 60 genera, plus 7 species of 4 extinct genera from Baltic amber. Our analysis shows that Fideliinae and the tribes Anthidiini and Osmiini of Megachilinae are paraphyletic; it supports the monophyly of Megachilinae, including the extinct taxa, and the sister group relationship of Lithurgini to the remaining megachilines. The Sub‐Saharan genus Aspidosmia, a rare group with a mixture of osmiine and anthidiine features, is herein removed from Anthidiini and placed in its own tribe, Aspidosmiini, new tribe . Protolithurgini is the sister of Lithurgini, both placed herein in the subfamily Lithurginae; the other extinct taxa, Glyptapina and Ctenoplectrellina, are more basally related among Megachilinae than Osmiini, near Aspidosmia, and are herein treated at the tribal level. Noteriades, a genus presently in the Osmiini, is herein transferred to the Megachilini. Thus, we recognise four subfamilies (Fideliinae, Pararhophitinae, Lithurginae and Megachilinae) and nine tribes in Megachilidae. We briefly discuss the evolutionary history and biogeography of the family, present alternative classifications, and provide a revised key to the extant tribes of Megachilinae.     

Improved tribal delimitation of the subfamily Dictyopharinae and description of new genera and new species (Homoptera,Fulgoroidea, Dictyopharidae)

Ten new genera, five new subgenera, and five new species are described in the family Dictyopharidae. Three generic names are synonymized. A new name is proposed for the generic homonym. Dictyophara kazeruna Dlabola is transferred to the genus Callodictya Melichar. The genus Sinodictya Matsumura, with the type species Sinodictya tukana Matsumura, is redescribed. A new key to the tribes of the subfamily Dictyopharinae is given. The composition and characters of the tribes Taosini and Lappidini are revised. All the genera of the subfamily Dictyopharinae are listed according to their tribal position. New records are given for some interesting species.     

Implications of morphological phylogenetics for the placement of the generaAdenocaulon andEriachaenium (Asteraceae)

Adenocaulon andEriachaenium are two problematic genera because their tribal and subfamilial placement in Asteraceae is uncertain. Previous cladistic analyses based on molecular data undertaken to analyze the relationships within Asteraceae, placeAdenocaulon in the tribe Mutisieae (Cichorioideae). This paper investigates cladistic relationships amongAdenocaulon andEriachaenium and tribes of subfamilies Cichorioideae and Asteroideae using morphological data. Thirty-eight characters were scored across 52 genera selected as exemplar taxa to represent the current classification system. In the analysis (one tree, length = 86, c.i. = 0.55, r.i. = 0.64)Adenocaulon andEriachaenium are sister taxa and appear as an isolated clade nested in Cichorioideae. A new, tentative position among the tribes of the paraphyletic Cichorioideae is proposed for these two isolated genera.     

Host range and geographical distribution of <Emphasis Type="Italic">Ixodes sigelos</Emphasis> (Acari: Ixodidae)

Larvae, nymphs and females of Ixodes sigelos Keirans, Clifford and Corwin (Ixodidae) were collected in 13 localities of the Patagonian region of Argentina parasitizing eight species of sigmodontine rodents. We report for the first time adults of I. sigelos for Argentina. Besides, we extend the southern limit of its geographical distribution, and six species of sigmodontines are added as new host species of I. sigelos (Phyllotis xanthopygus, Euneomys chinchilloides, Calomys musculinus, Reithrodon auritus, Loxodontomys micropus and Eligmodontia morgani). The presence of larvae, nymphs and females on sigmodontines, as well as more than 50% of the individuals engorged, indicate that I. sigelos can develop the complete parasitic phase of its life cycle on these small mammals. The geographical distribution of I. sigelos is restricted to the biogeographical Andean Region in Argentina and Chile.