Morphological Characters Are Compatible with Mitogenomic Data in Resolving the Phylogeny of Nymphalid Butterflies (Lepidoptera: Papilionoidea: Nymphalidae)

Nymphalidae is the largest family of butterflies with their phylogenetic relationships not adequately approached to date. The mitochondrial genomes (mitogenomes) of 11 new nymphalid species were reported and a comparative mitogenomic analysis was conducted together with other 22 available nymphalid mitogenomes. A phylogenetic analysis of the 33 species from all 13 currently recognized nymphalid subfamilies was done based on the mitogenomic data set with three Lycaenidae species as the outgroups. The mitogenome comparison showed that the eleven new mitogenomes were similar with those of other butterflies in gene content and order. The reconstructed phylogenetic trees reveal that the nymphalids are made up of five major clades (the nymphaline, heliconiine, satyrine, danaine and libytheine clades), with sister relationship between subfamilies Cyrestinae and Biblidinae, and most likely between subfamilies Morphinae and Satyrinae. This whole mitogenome-based phylogeny is generally congruent with those of former studies based on nuclear-gene and mitogenomic analyses, but differs considerably from the result of morphological cladistic analysis, such as the basal position of Libytheinae in morpho-phylogeny is not confirmed in molecular studies. However, we found that the mitogenomic phylogeny established herein is compatible with selected morphological characters (including developmental and adult morpho-characters).     

Phylogenetic relationships and historical biogeography of tribes and genera in the subfamily Nymphalinae (Lepidoptera: Nymphalidae)

We infer for the first time the phylogenetic relationships of genera and tribes in the ecologically and evolutionarily well‐studied subfamily Nymphalinae using DNA sequence data from three genes: 1450 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 1077 bp of elongation factor 1‐alpha (EF1‐α) and 400–403 bp of wingless (both in the nuclear genome). We explore the influence of each gene region on the support given to each node of the most parsimonious tree derived from a combined analysis of all three genes using Partitioned Bremer Support. We also explore the influence of assuming equal weights for all characters in the combined analysis by investigating the stability of clades to different transition/transversion weighting schemes. We find many strongly supported and stable clades in the Nymphalinae. We are also able to identify ‘rogue’ taxa whose positions are weakly supported (the different gene regions are in conflict with each other) and unstable. Our main conclusions are: (1) the tribe Coeini as currently constituted is untenable, and Smyrna, Colobura and Tigridia are part of Nymphalini; (2) ‘Kallimini’ is paraphyletic with regard to Melitaeini and should be split into three tribes: Kallimini s.s., Junoniini and Victorinini; (3) Junoniini, Victorinini, Melitaeini and the newly circumscribed Nymphalini are strongly supported monophyletic groups, and (4) Precis and Junonia are not synonymous or even sister groups. The species Junonia coenia, a model system in developmental biology, clearly belongs in the genus Junonia. A dispersal‐vicariance analysis suggests that dispersal has had a major effect on the distributions of extant species, and three biotic regions are identified as being centres of diversification of three major clades: the Palaearctic for the Nymphalis‐group, the Afrotropics for Junoniini and the Nearctic for Melitaeini. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86 , 227–251.     

Phylogenetic study of heliconiine butterflies based on morphology and restriction analysis of ribosomal RNA genes

Relationships of ten heliconiine butterflies (genera Dryas and Heliconius , family Nymphalidae) were elucidated by phylogenetic analysis of characters based on ribosomal DNA restriction site variation and morphology. Agraulis vanillae , also a heliconiine, was used as the outgroup species. Although neither the morphological nor the molecular data unambiguously resolve relationships among the heliconiines, a combined analysis of both data sets results in a tree that is similar to traditional systematic arrangements and previous views of radiation in the group. Both pupal-mating and nonpupal-mating species group as clades in the combined analysis. However, the restriction site data alone do not support the monophyly of the pupal-mating clade, and the morphological data alone do not support the monophyly of the non-pupal-mating clade. Furthermore, relationships of H. melpomene, H. cydno and the silvaniform species depart from traditional arrangements based on morphology and reproductive compatibility experiments. All trees support the independent evolution of similar wing patterns of species previously suggested to be members of mimicry complexes. Several mimicry complexes appear to have a member in each of the two major monophyletic groups (pupal-mating and non-pupal-mating clades).     

Chromosomal evolution in the South American Nymphalidae

We give the chromosome numbers of about 80 species or subspecies of Biblidinae as well as of numbers of neotropical Libytheinae (one species), Cyrestinae (4) Apaturinae (7), Nymphalinae (about 40), Limenitidinae (16) and Heliconiinae (11). Libytheana has about n=32, the Biblidinae, Apaturinae and Nymphalinae have in general n=31, the Limenitidinae have n=30, the few Argynnini n=31 and the few species of Acraeni studied have also mostly n=31. The results agree with earlier data from the Afrotropical species of these taxa. We supplement these data with our earlier observations on Heliconiini, Danainae and the Neotropical Satyroid taxa. The lepidopteran modal n=29-31 represents clearly the ancestral condition among the Nymphalidae, from which taxa with various chromosome numbers have differentiated. The overall results show that Neotropical taxa have a tendency to evolve karyotype instability, which is in stark contrast to the otherwise stable chromosome numbers that characterize both Lepidoptera and Trichoptera.     

基于线粒体16S rDNA序列探讨蛱蝶科(鳞翅目, 蝶亚目)主要分类群的系统发生关系

本文测定了蛱蝶科7亚科27种蛱蝶和斑蝶科2种蝴蝶的线粒体16S rRNA基因部分序列,并从GenBank中下载了6种蛱蝶的同源序列。以斑蝶科的幻紫斑蝶和绢斑蝶作外群,通过遗传分析软件对这些序列进行了比较分析,用邻接法和贝叶斯法重建了蛱蝶科的系统发育树,探讨了蛱蝶科主要类群间的系统发育关系。序列分析的结果显示:经比对处理后获得494bp长度序列,其中有可变位点206个,简约信息位点145个;A T平均含量78.4%,C G平均含量为21.6%,具A、T偏倚性。分子系统树显示:蛱蝶亚科并非单系群;蛱蝶族中眼蛱蝶属应移入斑蛱蝶族;闪蛱蝶和蛱蝶亚科与蛱蝶亚科具有较近的系统关系;结果支持豹蛱蝶和釉蛱蝶合为一亚科即釉蛱蝶亚科;支持将秀蛱蝶和蛱蝶亚科从线蛱蝶亚科中分离出来。     

Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions (COI, EF-1alpha and wingless). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1alpha data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.     

Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences

The rodent family Muridae is the single most diverse family of mammals with over 1300 recognized species. We used DNA sequences from the first exon ( approximately 1200bp) of the IRBP gene to infer phylogenetic relationships within and among the major lineages of muroid rodents. We included sequences from every recognized muroid subfamily except Platacanthomyinae and from all genera within the endemic Malagasy subfamily Nesomyinae, all recognized tribes of Sigmodontinae, and a broad sample of genera in Murinae. Phylogenetic analysis of the IRBP data suggest that muroid rodents can be sorted into five major lineages: (1) a basal clade containing the fossorial rodents in the subfamilies Spalacinae, Myospalacinae, and Rhizomyinae, (2) a clade of African and Malagasy genera comprising the subfamilies Petromyscinae, Mystromyinae, Cricetomyinae, Nesomyinae, and core dendromurines, (3) a clade of Old World taxa belonging to Murinae, Otomyinae, Gerbillinae, Acomyinae, and Lophiomyinae, (4) a clade uniting the subfamilies Sigmodontinae, Arvicolinae, and Cricetinae, and (5) a unique lineage containing the monotypic Calomyscinae. Although relationships among the latter four clades cannot be resolved, several well-supported supergeneric groupings within each are identified. A preliminary examination of molar tooth morphology on the resulting phylogeny suggests the triserial murid molar pattern as conceived by evolved at least three times during the course of muroid evolution.     

Multilocus ribosomal RNA phylogeny of the leaf beetles (Chrysomelidae)

Basal relationships in the Chrysomelidae (leaf beetles) were investigated using two nuclear (small and partial large subunits) and mitochondrial (partial large subunit) rRNA (≈ 3000 bp total) for 167 taxa covering most major lineages and relevant outgroups. Separate and combined data analyses were performed under parsimony and model‐based tree building algorithms from dynamic (direct optimization) and static (Clustal and BLAST) sequence alignments. The performance of methods differed widely and recovery of well established nodes was erratic, in particular when using single gene partitions, but showed a slight advantage for Bayesian inferences and one of the fast likelihood algorithms (PHYML) over others. Direct optimization greatly gained from simultaneous analysis and provided a valuable hypothesis of chrysomelid relationships. The BLAST‐based alignment, which removes poorly aligned sequence segments, in combination with likelihood and Bayesian analyses, resulted in highly defensible trees obtained in much shorter time than direct optimization, and hence is a viable alternative when data sets grow. The main taxonomic findings include the recognition of three major lineages of Chrysomelidae, including a basal “sagrine” clade (Criocerinae, Donaciinae, Bruchinae), which was sister to the “eumolpine” (Spilopyrinae, Eumolpinae, Cryptocephalinae, Cassidinae) plus “chrysomeline” (Chrysomelinae, Galerucinae) clades. The analyses support a broad definition of subfamilies (i.e., merging previously separated subfamilies) in the case of Cassidinae (cassidines + hispines) and Cryptocephalinae (chlamisines + cryptocephalines + clytrines), whereas two subfamilies, Chrysomelinae and Eumolpinae, were paraphyletic. The surprising separation of monocot feeding Cassidinae (associated with the eumolpine clade) from the other major monocot feeding groups in the sagrine clade was well supported. The study highlights the need for thorough taxon sampling, and reveals that morphological data affected by convergence had a great impact when combined with molecular data in previous phylogenetic analyses of Chrysomelidae. © The Willi Hennig Society 2007.     

Mitogenomic Evolution and Interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The First Evidence Toward Resolution of Higher-Level Relationships of the World’s Largest Freshwater Fish Clade Based on 59 Whole Mitogenome Sequences

Fishes of the order Cypriniformes are almost completely restricted to freshwater bodies and number > 3400 species placed in 5 families, each with poorly defined subfamilies and/or tribes. The present study represents the first attempt toward resolution of the higher-level relationships of the world’s largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from 53 cypriniforms (including 46 newly determined sequences) plus 6 outgroups. Unambiguously aligned, concatenated mt genome sequences (14,563 bp) were divided into 5 partitions (first, second, and third codon positions of the protein-coding genes, rRNA genes, and tRNA genes), and partitioned Bayesian analyses were conducted, with protein-coding genes being treated in 3 different manners (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]; third codon positions excluded). The resultant phylogenies strongly supported monophyly of the Cypriniformes as well as that of the families Cyprinidae, Catostomidae, and a clade comprising Balitoridae + Cobitidae, with the 2 latter loach families being reciprocally paraphyletic. Although all of the data sets yielded nearly identical tree topologies with regard to the shallower relationships, deeper relationships among the 4 major clades (the above 3 major clades plus Gyrinocheilidae, represented by a single species Gyrinocheilus aymonieri in this study), were incongruent depending on the data sets. Treatment of the rapidly saturated third codon–position transitions appeared to be a source of such incongruities, and we advocate that RY-coding, which takes only transversions into account, effectively removes this likely “noise” from the data set and avoids the apparent lack of signal by retaining all available positions in the data set. [Reviewing Editor: Rafael Zardoya]     

Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data

Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto . The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.     

The phylogeny of leaf beetles (Chrysomelidae) inferred from mitochondrial genomes

The high-level classification of Chrysomelidae (leaf beetles) currently recognizes 12 or 13 well-established subfamilies, but the phylogenetic relationships among them remain ambiguous. Full mitochondrial genomes were newly generated for 27 taxa and combined with existing GenBank data to provide a dataset of 108 mitochondrial genomes covering all subfamilies. Phylogenetic analysis under maximum likelihood and Bayesian inference recovered the monophyly of all subfamilies, except that Timarcha was split from Chrysomelinae in some analyses. Three previously recognized major clades of Chrysomelidae were broadly supported: the ‘chrysomeline’ clade consisting of (Chrysomelinae (Galerucinae + Alticinae)); the ‘sagrine’ clade with internal relationships of ((Bruchinae + Sagrinae) + (Criocerinae + Donaciinae)), and the ‘eumolpine’ clade comprising (Spilopyrinae (Cassidinae (Eumolpinae (Cryptocephalinae + Lamprosomatinae)))). Relationships among these clades differed between data treatments and phylogenetic algorithms, and were complicated by two additional deep lineages, Timarcha and Synetinae. Various topological tests favoured the PhyloBayes software as the preferred inference method, resulting in the arrangement of (chrysomelines (eumolpines + sagrines)), with Timarcha placed as sister to the chrysomeline clade and Synetinae as a deep lineage splitting near the base. Whereas mitogenomes provide a solid framework for the phylogeny of Chrysomelidae, the basal relationships do not agree with the topology of existing molecular studies and remain one of the most difficult problems of Chrysomelidae phylogenetics.     

Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B

Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous "bambusoid" lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhF trees and is nonexistent in rbcL and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae.     

Phylogeny of the Geometridae and the evolution of winter moths inferred from a simultaneous analysis of mitochondrial and nuclear genes

Geometridae is one of the most diverse families within the Lepidoptera, comprising nine subfamilies. Winter moths, which have a unique life history, are found in three subfamilies. To examine the phylogeny of the Geometridae at the subfamily level and determine the evolutionary history of winter moths, we constructed phylogenetic trees for all nine geometrid subfamilies using two mitochondrial and two nuclear gene sequences. Specimens of all subfamilies were sampled from Japan. Simultaneous analyses of the combined data from all genes revealed that the Geometridae comprised two major clades: one with subfamilies Larentiinae and Sterrhinae, and the other with the remaining seven subfamilies. The second clade included the largest subfamily, Ennominae, and the subfamily Archiearinae, which is traditionally considered to be an ancestral lineage of the Geometridae. The Larentiinae+Sterrhinae clade contained one winter moth lineage, and the second major clade consisted of three winter moth lineages, including Alsophilinae, which contains winter moths exclusively. Using a Bayesian inference of divergence times, we estimated that geometrids began to diverge 54 Mya (62-48 Mya), whereas winter moth lineages differentiated from non-winter moth lineages 34-12 Mya, during the global cooling events in the Oligocene and the early Miocene. The adaptation to cool climates may have been a preadaptation that facilitated the winter moth life cycle.     

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.     

Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii"

Higher-level relationships of the basal Euteleostei (=Protacanthopterygii) are so complex and controversial that at least nine different morphology-based phylogenetic hypotheses have been proposed during the last 30 years. Relationships of the Protacanthopterygii were investigated using mitochondrial genomic (mitogenomic) data from 34 purposefully chosen species (data for 12 species being newly determined during the study) that fully represented major basal euteleostean lineages and some basal teleosts plus neoteleosts as outgroups. Unweighted and weighted maximum parsimony (MP) and maximum likelihood (ML) analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and 3rd codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) from the 34 species. The resultant trees were well resolved and largely congruent, with most internal branches being supported by high statistical values. Monophyly of the protacanthopterygians was confidently rejected by the mitogenomic data. Of the five major monophyletic groups that received high statistical support within the protacanthopterygians, a clade comprising members of the alepocephaloids was unexpectedly nested within the Otocephala, sister-group of the euteleosts. The remaining four major monophyletic groups, on the other hand, occupied phylogenetic positions intermediate between the otocephalans and neoteleosts, with a clade comprising esociforms + salmoniforms being more basal to the argentinoids and osmeroids. Although interrelationships of the latter two clades (argentinoids and osmeroids) with the neoteleosts remained ambiguous, the present results indicated explicitly that the protacanthopterygians as currently defined merely represent a collective, polyphyletic group of the basal euteleosts, located between the basal teleosts (elopomorphs and below) and neoteleosts (stomiiforms and above).     

Phylogeny of the Nymphalidae (Lepidoptera)

A generic-level phylogeny for the butterfly family Nymphalidae was produced by cladistic analysis of 234 characters from all life stages. The 95 species in the matrix (selected from the 213 studied) represent all important recognized lineages within this family. The analysis showed the taxa grouping into six main lineages. The basal branch is the Libytheinae, with the Danainae and Ithomiinae on the next branch. The remaining lineages are grouped into two main branches: the Heliconiinae-Nymphalinae, primarily flower-visitors (but including the fruit-attracted Coeini); and the Limenitidinae (sensu strictu), Biblidinae, and the satyroid lineage (Apaturinae, Charaxinae, Biinae, Calinaginae, Morphinae, Brassolinae, and Satyrinae), primarily fruit-attracted. Data partitions showed that the two data sets (immatures and adults) are very different, and a partitioned Bremer support analysis showed that the adult characters are the main source of conflict in the nodes of the combined analysis tree. This phylogeny includes the widest taxon coverage of any morphological study on Nymphalid butterflies to date, and supports the monophyly and relationships of most presently recognized subgroups, providing strong evidence for the presently accepted phylogenetic scheme.     

Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei)

The phylogeny of groups within Gobioidei is examined with molecular sequence data. Gobioidei is a speciose, morphologically diverse group of teleost fishes, most of which are small, benthic, and marine. Efforts to hypothesize relationships among the gobioid groups have been hampered by the prevalence of reductive evolution among goby species; such reduction can make identification of informative morphological characters particularly difficult. Gobies have been variously grouped into two to nine families, several with included subfamilies, but most existing taxonomies are not phylogenetic and few cladistic hypotheses of relationships among goby groups have been advanced. In this study, representatives of eight of the nine gobioid familes (Eleotridae, Odontobutidae, Xenisthmidae, Gobiidae, Kraemeriidae, Schindleriidae, Microdesmidae, and Ptereleotridae), selected to sample broadly from the range of goby diversity, were examined. Complete sequence from the mitochondrial ND1, ND2, and COI genes (3573 bp) was used in a cladistic parsimony analysis to hypothesize relationships among the gobioid groups. A single most parsimonious topology was obtained, with decay indices indicating strong support for most nodes. Major phylogenetic conclusions include that Xenisthmidae is part of Eleotridae, and Eleotridae is paraphyletic with respect to a clade composed of Gobiidae, Microdesmidae, Ptereleotridae, Kraemeriidae, and Schindleriidae. Within this five-family clade, two clades are recovered. One includes Gobionellinae, which is paraphyletic with respect to Kraemeriidae, Sicydiinae, Oxudercinae, and Amblyopinae. The other contains Gobiinae, also paraphyletic, and including Microdesmidae, Ptereleotridae, and Schindleriidae. Previous morphological evidence for goby groupings is discussed; the phylogenetic hypothesis indicates that the morphological reduction observed in many goby species has been derived several times independently.     

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

Extant xenarthrans (armadillos, anteaters and sloths) are among the most derived placental mammals ever evolved. South America was the cradle of their evolutionary history. During the Tertiary, xenarthrans experienced an extraordinary radiation, whereas South America remained isolated from other continents. The 13 living genera are relics of this earlier diversification and represent one of the four major clades of placental mammals. Sequences of the three independent protein-coding nuclear markers alpha2B adrenergic receptor (ADRA2B), breast cancer susceptibility (BRCA1), and von Willebrand Factor (VWF) were determined for 12 of the 13 living xenarthran genera. Comparative evolutionary dynamics of these nuclear exons using a likelihood framework revealed contrasting patterns of molecular evolution. All codon positions of BRCA1 were shown to evolve in a strikingly similar manner, and third codon positions appeared less saturated within placentals than those of ADRA2B and VWF. Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set rooted by three marsupial outgroups resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships. This topology was fully compatible with recent studies, dividing placentals into the Southern Hemisphere clades Afrotheria and Xenarthra and a monophyletic Northern Hemisphere clade (Boreoeutheria) composed of Laurasiatheria and Euarchontoglires. Partitioned likelihood statistical tests of the position of the root, under different character partition schemes, identified three almost equally likely hypotheses for early placental divergences: a basal Afrotheria, an Afrotheria + Xenarthra clade, or a basal Xenarthra (Epitheria hypothesis). We took advantage of the extensive sampling realized within Xenarthra to assess its impact on the location of the root on the placental tree. By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling.     

Evolution of heteroneuran Lepidoptera (Insecta) and the utility of dopa decarboxylase for Cretaceous-age phylogenetics

This study tests the utility of the nuclear gene encoding dopa decarboxylase (DDC) for recovering Cretaceous‐age divergences within the lepidopteran clade Heteroneura, which contains 98% of lepidopteran species. A 709‐bp fragment of DDC has been sequenced in 32 species, including representatives of all major lineages of Heteroneura plus outgroups from more basal lepidopteran groups and the related order Trichoptera. Pairwise divergences across the first and second codon positions and amino acids increase with depth throughout the taxonomic hierarchy, indicating that non‐synonymous substitutions are not fully saturated; whereas, divergences across the third codon position level off at the family to superfamily level. Inclusion of non‐neolepidopteran outgroups results in phylogeny estimates that contradict well established groups, almost surely due to sparse taxon sampling and high character divergence. When these taxa and an equivalently divergent basal ditrysian are excluded, DDC trees show nearly complete recovery of ten uncontroversial basal heteroneuran ‘test clades’ of family rank and higher, about half with strong bootstrap support. Thus, DDC clearly carries phylogenetic signal at these levels. Bootstrap support for resolution of the controversial relationships among the five main heteroneuran groups (four monotrysian superfamilies plus Ditrysia) is individually low, but two of three previous hypotheses were statistically rejected overall by DDC. DDC trees within the primitive heteroneuran superfamily Incurvarioidea, though modestly supported, closely resemble a previous morphological hypothesis, while removing the requirement for reversal in a possible ‘key adaptation’, the larval case. Taxon overlap with a previous mtDNA study of Prodoxidae (Incurvarioidea), which includes much‐ studied mutualist pollinators, permits a comparison of substitution rates with the conservative mitochondrial COI+COII region, as well as combined‐data re‐examination of generic reltionships. Non‐synonymous substitution is about 25% slower in DDC than in COI+COII, though synonymous substitution is faster. With additional taxon sampling, and in combination with other genes, DDC promises to be a powerful tool for reconstructing among‐superfamily relationships within Lepidoptera and probably other insect groups.     

Phylogeny of Neotropical oryzomyine rodents (Muridae: Sigmodontinae) based on the nuclear IRBP exon

Sigmodontine rodents are the most diverse family-level mammalian clade in the Neotropical region, with about 70 genera and 320 recognized species. Partial sequences (1266 bp) from the first exon of the nuclear gene encoding the Interphotoreceptor Retinoid Binding Protein (IRBP) were used to infer the phylogenetic relationships among 44 species representing all 16 currently recognized genera of the largest sigmodontine tribe, the Oryzomyini. Monophyly of the tribe was assessed relative to 15 non-oryzomyine sigmodontine taxa representing all major sigmodontine lineages. Twelve taxa from seven muroid subfamilies were used as outgroups. The resulting matrix included 71 taxa and 386 parsimony-informative characters. Phylogenetic analysis of this matrix resulted in 16 equally parsimonious cladograms, which contained the following well-supported groups: (i). a monophyletic Oryzomyini, (ii). a clade containing all oryzomyines except Scolomys and Zygodontomys, (iii). a clade containing Oecomys, Handleyomys, and several species of forest-dwelling Oryzomys, and (iv). a clade containing the remaining oryzomyine taxa. The last clade is composed of two large subclades, each with lower nodal support, containing the following taxa: (i). Microryzomys, Oligoryzomys, Neacomys, and Oryzomys balneator; (ii). Holochilus, Lundomys, Pseudoryzomys, Nectomys, Amphinectomys, Sigmodontomys, and several species of open-vegetation or semiaquatic Oryzomys. Regarding relationships among non-oryzomyine taxa, sigmodontines, neotomines, and tylomyines do not form a monophyletic group; a clade containing Rheomys and Sigmodon is basal relative to all other sigmodontines; and the remaining sigmodontines are grouped in three clades: the first containing Thomasomyini, Akodontini, and Reithrodon; the second containing Abrothrichini, and Phyllotini, plus Wiedomys, Juliomys, Irenomys, and Delomys; and the third containing the oryzomyines. No conflict is observed between IRBP results and previous robust hypotheses from mitochondrial data, while a single case of incongruence is present between the IRBP topology and robust hypothesis from morphological studies.