Identification of CR1 retroposons in Arborophila rufipectus and their application to Phasianidae phylogeny

Chicken repeat 1 (CR1), a member of non‐LTR retroposon, is an important phylogenetic marker in avian systematics. In this study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254 966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined data set comprising of 22 CR1 loci, mitochondrial genomes and eight unlinked introns was analysed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.     

Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control-region genes

The taxonomic status of some genera within the Phasianidae remains controversial. To demonstrate the phylogenetic relationships of four endemic genera (Tetraophasis, Ithaginis, Crossoptilon and Chrysolophus) and other 11 genera of Phasianidae in China, a total of 1070 nucleotides of mitochondrial DNA (mtDNA) control-region genes were sequenced. There are 376 variable sites including 345 parsimony sites. The genetic distance ranged from 0.067 (Chrysolophus and Phasianus) to 0.181 (Perdix and Bambusicola) among the 15 genera. Maximum likelihood method was used to construct a phylogenetic tree, which grouped all the genera into two deeply divergent clades. Perdix was shown to be a non-partridge genus. Alternatively, it appears ancestral to either partridges or pheasants. The sibling taxa of the four endemic genera were Lophophorus, Tragopan, Lophura and Phasianus, respectively. Calibrated rates of molecular evolution suggested that the divergence time between the four genera and related taxa was 4.00–5.00 million years ago, corresponding to the Pliocene. Considering their molecular phylogenetics, fossil and geographical distribution patterns, the four endemic genera might have originated in the southwestern mountains in China.     

THE INTERFACE BETWEEN PHYLOGENETICS AND POPULATION GENETICS: INVESTIGATING GENE TREES,SPECIES TREES,AND POPULATION DYNAMICS IN THE PHYLLOPHAGA FRATERNA SPECIES GROUP

This study uses traditional and contemporary phylogenetic and population genetic analyses to assess the causes of discordance (i.e., lineage sorting and introgression) among mitochondrial and nuclear gene trees for a clade of eastern North American scarab beetles (fraterna species group, genus Phyllophaga). I estimated gene trees using individual and combined analysis of one mitochondrial and two nuclear loci in MrBayes , and inferred a species tree using a hierarchical coalescent approach based on all loci in the program Best . Because hybridization violates the assumptions of Best , I tested for introgression by comparing species monophyly between the mitochondrial and nuclear gene trees based on the prediction that cytoplasmic genomes introgress more readily than nuclear genomes. Haplotype exclusivity was identified using Bayesian tests of monophyly and the genealogical sorting index. I used the results of the phylogenetic analyses and monophyly tests to develop an explicit hypothesis of introgression that could be tested in the program IMa. Results from these analyses provided evidence for introgression across clades within the fraterna group. The tiered analytical approach used in this study demonstrated how the use of multiple methods can identify when assumptions are violated and methods are prone to yield misleading results.     

Phylogenetics and evolution of the Macaronesian members of the genus Aichryson (Crassulaceae) inferred from nuclear and chloroplast sequence data

Aichryson is a genus of annual or perennial herbs, comprising approximately 13 species. The genus is nearly endemic to Macaronesia, with the center of diversity on the Canary Islands. Previous studies indicate that Aichryson is monophyletic and sister to a clade comprising two other genera, Monanthes and Aeonium. However, phylogenetic relationships within the genus have yet to be investigated. Phylogenetic relationships were estimated for Aichryson using DNA sequence data from both the nuclear and chloroplast genome. Parsimony analyses were conducted using separate nuclear and chloroplast data sets, as well as a combined data set. These combined analyses provide a well-resolved topology that is used to investigate patterns of evolution within the genus. For example, although typically herbaceous in habit, two members display a woody growth form. Our analyses indicate that woodiness is a derived feature in Aichryson that has arisen once. Furthermore, the data presented suggest that the Aichryson pachycaulon group, a group of five subspecies, are in fact not monophyletic and that a reexamination of classification is necessary. The present study indicates that the biogeographical patterns exhibited by Aichryson appear to be rare, occurring in only one other known genus.The authors would like to thank Susana Fontinha of the Madeiran Botanical Garden for plant material of Madeiran Aichryson; Drs. D. Crawford and J. Archibald, as well as two anonymous reviewers for helpful comments; Eastern Illinois Undergraduate Honors Research Fund, and University of Kansas Plant Biology Research Award. Additional financial support for this work was provided by the Department of Ecology and Evolutionary Biology and the Museum of Natural History and Biodiversity Research Center, University of Kansas and a Kansas NSF EPSCoR First Award (NSF 32171) to MEM.     

Phylogenetics and biogeography of the broad-nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae)

The Neotropical broad-nosed bats, genus Platyrrhinus, represent a well-defined monophyletic group of 14 recognized species. A recent study of morphological characters confirmed Platyrrhinus monophyly and species diagnosis, but offered little support to their intra-specific relationships. We conducted phylogenetic analyses of the genus, using dense taxonomic sampling in combination with four gene sequences representing both mitochondrial and nuclear DNA transmission systems. Our aim was to elucidate the phylogenetic structure among species, using the resulting 3341 bp of DNA. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies that confirm the monophyly of the genus Platyrrhinus and strongly support many previously unrecognized groups. Paraphyly of Platyrrhinus helleri and the unclear position of P. brachycephalus in the clades were also apparent in the data. Our biogeographical analysis suggests a Brazilian Shield origin for Platyrrhinus, followed by subsequent radiations of lineages in the Amazon Basin and Andes. Secondary dispersal from Amazonian and Andean centers is responsible for the Platyrrhinus inhabiting the Guianan Shield and the Pacific lowlands and Central America, respectively.     

CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes)

Chicken repeat 1 (CR1) elements, a class of retroposons belonging to non-long-terminal repeats, have been recognized as powerful tools for phylogenetic studies. Here we examine the phylogenetic relationships of 11 Phasianidae species based on CR1 retroposons. Together with 19 loci reported previously, a total of 99 CR1 loci were identified from chicken genome and turkey BAC clone sequences. 75 insertion events were used to address the branching order of 11 species in Phasianidae. The topology of our tree suggests that: 1) Gallus gallus possessed a basal phylogenetic position within Phasianidae and was related to Bambusicola thoracica (BSP=100%); 2) After the split of G. gallus and B. thoracica, Arborophila rufipectus diverged from Phasianidae (BSP=100%). Nine unambiguous insertion events supported a phylogenetic position of A. rufipectus different to previous mitochondrial data suggesting a hybrid origin or an ancient introgression of A. rufipectus; and 3) 22 CR1 insertion events strongly supported the eight phasianids under investigation sharing a common ancestor. Our study has revisited the phylogenetic position of G. gallus and A. rufipectus and provided a new insight into the phylogeny of Phasianidae birds. It showed that a CR1-based methodology has a great potential to be informative within Phasianidae in resolving relationships of closely related species whose radiation and speciation have occurred very recently.     

<Emphasis Type="Italic">Gallus gallus</Emphasis> aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups

Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGC1) for phylogenetic analysis of the main groups of Galliformes including Phasianidae, Numididae, and Odontophoridae. We also included species from Cracidae and Megapodiidae which are considered by some as Craciformes and others, including here as Galliformes. The uncorrected sequence divergence of the G3 fragments ranges from 1 among the grouses to 36% between some of the distant groups within Galliformes. These sequences contain 39–48% AT nucleotides and the ratios of transition versus transversion are above 1.5 in majority of the comparisons. Using G3 sequences from an Anseriform, Oxyura jamaicensis, as out-groups, phylogenetic trees were obtained using maximum parsimony and distance algorithms and bootstrap analyses. These trees were consistent with those described using Avian sarcoma and leucosis virus gag genes and those from amino acid sequences of hemoglobin and lysozyme c. Our data also support relationships among Galliformes which were defined using mtDNA sequences. In addition to the general support of the five main families of Galliformes, our data are also consistent with previous work that showed Francolinus africanus and Gallus gallus are in the same clade and that Tetraoninae is a well-supported monophyletic subfamily within Phasianidae. The results presented here suggest that the AGC1 sequences meet the criterion of novel nuclear DNA sequences that can be used to help resolve the relationships among Galliformes.     

A new taxonomic status for Iberoformica (Hymenoptera,Formicidae) based on the use of molecular markers

The subgeneric subdivision of the genus Formica is still open. In this article, we make a phylogenetic study on several species of the genus Formica and of its closely related genera, Polyergus and Proformica, using sequences of nuclear satellite DNA (stDNA) and the mitochondrial rrnL as molecular markers. Our goal was to shed light on their phylogenetic relationships and particularly on the systematic position of F. subrufa. This species was first included in the subgenus Serviformica, but afterwards a new subgenus (Iberoformica) was established to include only this species. The results show that a stDNA family previously reported in Formica species, with a repetitive unit 129 bp long, is also found in Polyergus rufescens and P. samurai but not in Proformica longiseta. This is the first case of presence of a stDNA family in two different ant genera. In F. subrufa, this stDNA is very divergent relative to those isolated in the remaining Formica species and in the genus Polyergus. The Bayesian analysis of mitochondrial rrnL sequences shows three highly supported groups: F. subrufa, the remaining Formica species studied, and the genus Polyergus, suggesting that parasites (Polyergus species) and hosts (Formica species) are closely related but not sibling species. The combined analysis of nuclear stDNA sequences and mitochondrial rrnL showed their phylogenetic congruence despite their distinct evolutionary dynamics. This analysis did not discriminate between the remaining Formica species that were not grouped according to the subgeneric classification. According to these results, it can no longer be assumed that F. subrufa belongs to the subgenus Serviformica or of the fusca species group. This differentiation was also supported by previous studies based on the morphological characters, molecular and cytogenetic data. Therefore, taking into consideration these arguments and others explained in detail in this article, we propose that the taxon Iberoformica, formerly synonymized subgenus, be raised to a genus status. This genus would be monotypic and only composed, up to the moment, by Iberoformica subrufa (= F. subrufa Roger, 1859 ).     

Phylogenetic relationships within the genus Tetrahymena inferred from the cytochrome c oxidase subunit 1 and the small subunit ribosomal RNA genes

Details of the phylogenetic relationships among tetrahymenine ciliates remain unresolved despite a rich history of investigation with nuclear gene sequences and other characters. We examined all available species of Tetrahymena and three other tetrahymenine ciliates, and inferred their phylogenetic relationships using nearly complete mitochondrial cytochrome c oxidase subunit 1 (cox1) and small subunit (SSU) rRNA gene sequences. The inferred phylogenies showed the genus Tetrahymena to be monophyletic. The three “classical” morphology-and-ecology-based groupings are paraphyletic. The SSUrRNA phylogeny confirmed the previously established australis and borealis groupings, and nine ribosets. However, these nine ribosets were not well supported. Using cox1 gene, the deduced phylogenies based on this gene revealed 12 well supported groupings, called coxisets, which mostly corresponded to the nine ribosets. This study demonstrated the utility of cox1 for resolving the recent phylogeny of Tetrahymena, whereas the SSU rRNA gene provided resolution of deeper phylogenetic relationships within the genus.     

DNA barcoding,phylogenetic relationships and speciation of snappers (genus <Emphasis Type="Italic">Lutjanus</Emphasis>)

The phylogenetic relationships of 13 snapper species from the South China Sea have been established using the combined DNA sequences of three full-length mitochondrial genes (COI, COII and CYTB) and two partial nuclear genes (RAG1, RAG2). The 13 species (genus Lutjanus) were selected after DNA barcoding 72 individuals, representing 20 species. Our study suggests that although DNA barcoding aims to develop species identification systems, it may also be useful in the construction of phylogenies by aiding the selection of taxa. Combined mitochondrial and nuclear gene data has an advantage over an individual dataset because of its higher resolving power.     

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.     

蛹虫草线粒体DNA与细胞核DNA进化关系的比较

【目的】分析蛹虫草是否存在核内线粒体DNA片段,比较蛹虫草线粒体DNA与细胞核DNA的碱基变异程度及所反映的菌株间的系统发育关系。【方法】通过本地BLAST或LAST对蛹虫草线粒体基因组和核基因组进行序列相似性搜索;从10个已知线粒体基因组的蛹虫草菌株中分别扩增7个细胞核蛋白编码基因片段,并与其在14个线粒体蛋白编码基因上的碱基变异情况进行比较。【结果】蛹虫草核基因组中存在5处较短的核内线粒体DNA片段,总长只有278bp。蛹虫草核DNA的变异频率整体上高于线粒体DNA。核DNA和线粒体DNA所反映的蛹虫草菌株间的系统发育关系存在显著差异。【结论】蛹虫草线粒体DNA与核DNA间不存在长片段的基因交流,二者变异频率不同,所反映的蛹虫草菌株间的系统发育关系也有差异。本研究增加了对蛹虫草线粒体与细胞核DNA进化关系的认识。     

Phylogenetic Relationships among Holarctic Populations of Chironomus entis and Chironomus plumosus in View of Possible Horisontal Transfer of Mitochondrial Genes

In eight Holarctic populations of two typical chironomid sibling species of the plumosus group, Chironomus entisandChironomus plumosus, nucleotide sequences of mitochondrial (cytb) and nuclear (gb2b) gene regions were examined. The phylogenetic trees reflecting the evolutionary histories of the nuclear and mitochondrial markers exhibited significant differences. On the tree based on the nuclear gene sequences the populations clustered according to their species affiliation, whereas on the tree based on the mitochondrial gene sequences the populations were grouped according to their geographic position. This discrepancy is probably explained by mitochondrial gene flow between sympatric species with incomplete reproductive isolation (sibling species). Based on our results together with the earlier data on nuclear and mitochondrial gene sequences of some other species from the phylogenetic group plumosus, a scheme of phylogenetic relationships within this group is proposed. This scheme is in many ways different from the traditional view on the evolutionary relationships among species of the plumosus group.     

Molecular phylogeny of theChironomus genus deduced from nucleotide sequences of two nuclear genes,ssp 160 and the globin 2b gene

Two genes were employed to study phylogenetic relatedness of theChironomus species: the protein-coding, salivary gland-specificssp160 gene, and the globin 2b (gb2b) gene. By using PCR, it was demonstrated that all the 38Chironomus species analyzed possess thegb2b gene, while only 13 have thessp160 gene. Partial nucleotide sequences of the genes of 22 species were determined. The data obtained were employed to construct phylogenetic trees which appeared to be topologically similar and revealed five groups of phylogenetically closely related species. Combining the data obtained in the studies of nuclear and mitochondrial genes, a molecular-data-based scenario could be suggested for theChironomus genus evolution.     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

Biogeography and evolution of flower color in Veratrum (Melanthiaceae) through inference of a phylogeny based on multiple DNA markers

Veratrum (Melanthiaceae) comprises ca. 27 species with highly variable morphology. This study aims to construct the molecular phylogeny of this genus to infer its floral evolution and historical biogeography, which have not been examined in detail before. Maximum parsimony, maximum likelihood, and Bayesian analyses were performed on the separate and combined ITS, trnL-F, and atpB-rbcL sequences to reconstruct the phylogenetic tree of the genus. All Veratrum taxa formed a monophyletic group, within which two distinct clades were distinguished: species with white-to-green perianth formed one highly supported clade, and the species with black-purple perianth constituted another highly supported clade. Phylogenetic inference on flower color evolution suggested that white-to-green perianth was a plesiomorphic state and black-purple perianth was apomorphic for Veratrum. When species distribution areas were traced as a multi-state character, parsimonious optimization inferred that Veratrum possibly originated in East Asia. Our study confirmed previous phylogenetic and taxonomic suggestions on this genus and provided a typical example of plant radiation across the Northern Hemisphere.     

Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.     

Phylogenetic position of the monotypic Des Murs’ Wiretail ( Sylviorthorhynchus desmursii , Aves: Furnariidae) based on mitochondrial and nuclear DNA

Parallelisms and paraphyletic assemblages are common among ovenbirds. Molecular markers are therefore the best approach when studying the evolutionary relationships among the members of this unparalleled diversified family. We obtained nucleotide sequence data from mitochondrial (cytochrome b) and nuclear genes (myoglobin and glyceraldehyde-3-phosphodehydrogenase) and used these to deduce the phylogenetic position of a monotypic genus endemic to the austral temperate rainforests of southern South America, the Des Murs’ Wiretail (Sylviorthorhynchus desmursii Des Murs, 1847, Aves: Furnariidae). Phylogenetic analyses based on maximum parsimony, maximum likelihood and Bayesian inference all converged into a congruent topology, with a basal position of Des Murs’ Wiretail within Synallaxinae together with Tit–Spinetails (Leptasthenura). Our data reject the hypothesis of a phylogenetic relationship between Des Murs’ Wiretail and thistletails (Schizoeaca) which exhibit parallelisms in morphology, tail structure and nest architecture. Using a molecular clock based on the myoglobin intron 2 gene, we estimated a divergence time of Des Murs’ Wiretail from Tit-Spinetails of 14–15 Myr, which is associated with the appearance of sclerophyllous forest elements in Chile at the Middle–Upper Miocene. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

African Dacus (Diptera: Tephritidae: Molecular data and host plant associations do not corroborate morphology based classifications

The genus Dacus Fabricius includes economically important pest fruit flies distributed in the Afrotropical and Indo-Australian regions. Two recent revisions based on morphological characters proposed new and partially discordant classifications synonymizing/revalidating several subgeneric names and forming species groups. Regardless these efforts, the phylogenetic relationships among Dacus species remained largely unresolved mainly because of the difficulties in assigning homologous character states. Therefore we investigated the phylogeny of African Dacus by sequencing 71 representatives of 32 species at two mitochondrial (COI, 16S) and one nuclear (period) gene fragments. Phylogenetic relationships were inferred through Bayesian and Maximum Parsimony methods and hypotheses about the monophyly of Dacus subgenera were tested by Shimodaira–Hasegawa tests. The congruence tests and the analyses of the single gene fragments revealed that the nuclear gene supports similar conclusions as the two mitochondrial genes. Levels of intra- and inter-specific differentiation of Dacus species were highly variable and, in some cases, largely overlapping. The analyses of the concatenated dataset resolved two major bootstrap-supported groups as well as a number of well-supported clades and subclades that often comprised representatives of different subgenera. Additionally, specimens of Dacus humeralis from Eastern and Western African localities formed separate clades, suggesting cryptic differentiation within this taxon. The comparisons between the molecular phylogeny and the morphological classification revealed a number of discrepancies and, in the vast majority of cases, the molecular data were not compatible with the monophyly of the currently recognised subgenera. Conversely, the molecular data showed that Apocynaceae feeders are a monophyletic sister group of species feeding on both Cucurbitaceae and Passifloraceae (these latter being also monophyletic). These results show a clear association between the molecular phylogeny of African Dacus and the evolution of host plant choice and provide a basis towards a more congruent taxonomy of this genus.