@article {539,
	title = {Systematics of the cyclostome subfamilies of braconid parasitic wasps (Hymenoptera: Ichneumonoidea): A simultaneous molecular and morphological Bayesian},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {38},
	year = {2006},
	pages = {130-145},
	abstract = {Phylogenetic relationships among 95 genera collectively representing 17 of the 18 currently recognized cyclostome braconid wasp sub- families were investigated based on DNA sequence fragments of the mitochondrial COI and the nuclear 28S rDNA genes, in addition to morphological data. The treatment of sequence length variation of the 28S partition was explored by either excluding ambiguously aligned regions and indel information (28SN) or recoding them (28SA) using the {\textquoteleft}fragment-level{\textquoteright} alignment method with a modiWed cod- ing approach. Bayesian MCMC analyses were performed for the separate and combined data sets and a maximum parsimony analysis was also carried out for the simultaneous molecular and morphological data sets. There was a signiWcant incongruence between the two genes and between 28S and morphology, but not for morphology and COI. DiVerent analyses with the 28SA data matrix resulted in topologies that were generally similar to the ones from the 28SN matrix; however, the former topologies recovered a higher number of signiWcantly supported clades and had a higher mean Bayesian posterior probability, thus supporting the inclusion of information from ambiguously aligned regions and indel events in phylogenetic analyses where possible. Based on the signiWcantly supported clades obtained from the simultaneous molecular and morphological analyses, we propose that a total of 17 subfamilies should be recognized within the cyclostome group. The subfamilial placements of several problematic cyclostome genera were also established.},
	keywords = {ambiguously aligned regions, Braconidae, fragment-level alignment, phylogeny, simultaneous analysis},
	author = {Zaldivar-River{\'o}n, A. and Mori, M. and Quicke, D.L.J.}
}
@article {536,
	title = {A single origin of gall association in a group of parasitic wasps with disparate morphologies},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {44},
	year = {2007},
	pages = {981-992},
	abstract = {The braconid wasp subfamily Doryctinae mainly comprises idiobiont ectoparasitoids of other insect larvae. In recent years, however, members of a few genera have been discovered to be associated with galls from various unrelated host plant families, with some of these being gall inducers whereas others are suspected as being predators of gallers. Because of their considerable morphological differences, these gall-associated taxa traditionally have been placed in separate tribes or even in other subfamilies. In this study, we investigate the phylogenetic relationships among representatives of a number of different doryctine genera, including five of its seven gall-associated genera using two genetic markers. Here we analyzed the length-variable 28S sequence data based on secondary structure both excising the unalignable regions and recoding them according to indel length. In addition, multiple alignments were carried out with a range of gap-opening and extension parameters. The combined (28S + CO1) phylogenetic hypotheses obtained, both excluding and recoding the unalignable regions, recover a clade comprising the five gall-associated genera, and most of the analyses using multiple alignments also support this relationship. These results support a scenario in which secondary phytophagy evolves from initially attacking primary gall- forming hosts. The relationships recovered are also more congruent with a model that explains the macroevolution of insect plant asso- ciation in the Doryctinae as reflecting geographic proximity rather than host plant relationships. Further, our phylogenetic hypotheses consistently show that one of the main morphological features employed in the higher level classification of the Doryctinae is actually highly homoplastic.},
	keywords = {Braconidae, character evolution, cyclostomes, Doryctinae, molecular phylogeny, multiple alignment, secondary structure alignment},
	author = {Zaldivar-River{\'o}n, A. and Belokobylskij, S.A. and Leon-Regagnon, V. and Mart{\'\i}nez, J.J. and Briceno, G.R.A. and Quicke, D.L.J.}
}
@article {447,
	title = {Phylogenetic relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA, 28S rDNA D2, 18S rDNA gene sequences and morphological characters},
	journal = {Molecular phylogenetics and evolution},
	volume = {37},
	year = {2005},
	pages = {104-116},
	publisher = {Elsevier},
	abstract = {Phylogenetic relationships among the Braconidae were examined using homologous 16S rDNA, 28S rDNA D2 region, and 18S rDNA gene sequences and morphological data using both PAUP* 4.0 and MRBAYES 3.0B4 from 88 in-group taxa representing 35 subfamilies. The monophyletic nature of almost all subfamilies, of which multiple representatives are present in this study, is well- supported except for two subfamilies, Cenocoelinae and Neoneurinae that should probably be treated as tribal rank taxa in the sub- family Euphorinae. The topology of the trees generated in the present study supported the existence of three large generally accepted lineage or groupings of subfamilies: two main entirely endoparasitic lineages of this family, referred to as the {\textquotedblleft}helconoid complex{\textquotedblright} and the {\textquotedblleft}microgastroid complex,{\textquotedblright} and the third {\textquotedblleft}the cyclostome.{\textquotedblright} The Aphidiinae was recovered as a member of the non-cyclosto- mes, probably a sister group of Euphorinae or Euphorinae-complex. The basal position of the microgastroid complex among the non-cyclostomes has been found in all our analyses. The cyclostomes were resolved as a monophyletic group in all analyses if two putatively misplaced groups (Mesostoa and Aspilodemon) were excluded from them. Certain well-supported relationships evident in this family from the previous analyses were recovered, such as a sister-group relationships of Alysiinae+Opiinae, of Braconinae+Doryctinae, and a close relationship between Macrocentrinae, Xiphozelinae, Homolobinae, and Charmontinae. The relationships of {\textquotedblleft}Ichneutinae+((Adeliinae+Cheloninae)+(Miracinae+(Cardiochilinae+Microgastrinae))){\textquotedblright} was conWrmed within the microgastroid complex. The position of Acampsohelconinae, Blacinae, and Trachypetinae is problematic. {\textcopyright} 2005 Elsevier Inc. All rights reserved.},
	keywords = {16S rDNA, 18S rDNA, 28S rDNA, Braconidae, morphology, Phylogenetic relationships},
	author = {Shi, M. and Chen, X.-X. and Achterberg, C. van}
}
@article {422,
	title = {Phylogenetic relationships among the Braconidae (Hymenoptera: Ichneumonoidea): a reassessment of Shi et al. (2005).},
	journal = {Molecular phylogenetics and evolution},
	volume = {43},
	year = {2007},
	pages = {338-343},
	author = {Pitz, Kevin M and Dowling, A.P.G. and Sharanowski, B.J. and Boring, C Andrew and Seltmann, K.C. and Sharkey, M.J.}
}
@article {403,
	title = {Molecular systematics of basal subfamilies of ants using 28S rRNA (Hymenoptera: Formicidae).},
	journal = {Molecular phylogenetics and evolution},
	volume = {40},
	year = {2006},
	pages = {359-369},
	abstract = {For many years, the ant subfamily Ponerinae was hypothesized to contain the basal (early branching) lineages of ants. Recently the Ponerinae were reclassified into six poneromorph subfamilies based on morphological analysis. We evaluate this new poneromorph classification using 1240 base pairs of DNA sequence data obtained from 28S rRNA gene sequences of 68 terminal taxa. The molecular tree supported the monophyly of the ant family Formicidae, with 100\% parsimony bootstrap (PB) support and posterior probabilities (PP) of 1.00, with the ant subfamily Leptanillinae as a sister group to all other ants (PB=62, PP=93). However, our analyses strongly support the polyphyly of the Poneromorph subfamilies (sensu Bolton). The Ectatomminae and Heteroponerinae are more closely related to the Formicoid subfamilies than to the rest of the poneromophs (PB=96, PP=100). The Amblyoponinae (PB=52, PP=96), Paraponerinae (PB=100, PP=100), Ponerinae (PB<50, PP=71), and Proceratiinae (PB=98, PP=100) appear as distinct lineages at the base of the tree and are identified as a poneroid grade. Monophyletic origins for the poneroid subfamilies Amblyoponinae, Paraponerinae, Ponerinae and Proceratiinae are supported in our analysis. However, the genus Platythyrea forms a distinct sister group to the Ponerini within the Ponerinae. The Heteroponerinae, based on our sample of Heteroponera, are associated with the subfamily Ectatomminae (PB=98, PP=100). Furthermore, our data indicate the genus Probolomyrmex belongs to the Proceratiinae as suggested by recent morphological analysis (PB=98, PP=100).},
	keywords = {28S, 28S: genetics, Animals, Hymenoptera, Hymenoptera: classification, Hymenoptera: genetics, phylogeny, Ribosomal, RNA},
	author = {Ouellette, Gary D and Fisher, B.L. and Girman, Derek J}
}
@article {394,
	title = {Phylogeny of the parasitic microgastroid subfamilies (Hymenoptera: Braconidae) based on sequence data from seven genes, with an improved time estimate of the origin of the lineage.},
	journal = {Molecular phylogenetics and evolution},
	volume = {47},
	year = {2008},
	pages = {378-395},
	abstract = {The microgastroid complex of braconid wasps is a widely recognized and biologically coherent lineage of endoparasitoids of lepidopteran larvae (caterpillars). The complex has received significant phylogenetic attention in recent years due in part to the taxons{\textquoteright} association with mutualistic polydnaviruses, with which they compromise host immune systems. A number of previous attempts using a variety of morphological and molecular approaches have not unequivocally resolved relationships amongst the main subfamilies. This work represents a more extensive attempt to resolve the microgastroid relationships, using seven genes (16S rRNA, cytochrome oxidase I (CO1), 28S rRNA, arginine kinase (ArgK), long wavelength rhodopsin (Ops), elongation factor 1 alpha (EF1a) and wingless (Wg)) and a greater taxonomic representation. Bayesian, likelihood and parsimony phylogenetic reconstructions of this improved data set has determined that the chelonines diverged first from the remainder of the microgastroids, however the relationships amongst the other subfamilies are still unclear, suggesting a greater nucleotide sample is required to resolve them. Examination of the contribution of individual gene trees to the phylogeny demonstrates why the relationships between subfamilies are still unclear, with not all groups monophyletic for all trees. Filtered supernetworks demonstrate that monophyly of all subfamilies is only recovered when splits found in only one or two genes are excluded, but this also results in little remaining structure left in the deep nodes to resolve inter-subfamily relationships. By increasing the breadth of the study we were also able to re-evaluate previous attempts at dating the lineage and, therefore the origin of the polydnavirus association. Previous attempts used a much reduced data set and fewer fossil calibrations. Thorough literature searches have revealed a substantial increase in the fossil calibrations and these, combined with more sophisticated molecular dating analysis, have substantially increased the age of the microgastroid lineage from previous estimates of approximately 73MYA to approximately 100MYA. Examination of the resultant linearized clock tree also allows an insight into the evolution of the more species rich subfamilies. The chelonines appear to have had a steady rate of evolution, whilst the microgastrines and cardiochilines appear to have undergone a more significant "burst" of evolution. It is hypothesized that the different parasitism strategies of subfamilies (Chelonines are egg parasitoids and the remainder are larval parasitioids) may have influenced the evolutionary rates of the groups.},
	keywords = {Animals, Base Sequence, DNA Primers, Hymenoptera, Hymenoptera: classification, Hymenoptera: genetics, Likelihood Functions, phylogeny},
	author = {Murphy, Nicholas and Banks, J.C. and Whitfield, J.B. and Austin, A.D.}
}
@article {347,
	title = {Molecular phylogeny of Cotesia Cameron, 1891 (Insecta: Hymenoptera: Braconidae: Microgastrinae) parasitoids associated with Melitaeini butterflies (Insecta: Lepidoptera: Nymphalidae: Melitaeini)},
	journal = {Molecular phylogenetics and evolution},
	volume = {32},
	year = {2004},
	pages = {207-220},
	publisher = {Elsevier},
	abstract = {Phylogenetic relationships among Cotesia Cameron (Braconidae) species parasitising Melitaeini butterflies were examined using DNA sequence data (mitochondrial cytochrome oxidase subunit I and NADH1 dehydrogenase genes, nuclear ribosomal DNA internal transcribed spacer region) as well as 12 microsatellite loci. Molecular data were available from ostensibly six species of Cotesia from 16 host butterfly species in Europe, Asia, and North America. Analysis of the combined sequence data using both maximum parsimony and maximum likelihood revealed two distinct Cotesia clades. In one clade (C. acuminata (Reinhard); C. bignellii (Marshall)) host ranges are apparently narrow and, although Euphydryas (s. lato) is well-utilised, permeation of Melitaea (s. lato) has been slight. In the other clade (C. melitaearum (Wilkinson); C. lycophron (Nixon); C. cynthiae (Nixon)) host utilization across the Melitaeini as a whole is more extensive and the data are consistent with more recent, or active, speciation processes. Neighbour-joining trees calculated separately for the two main clades based on Cavalli-Sforza and Edwards (1967) chord distance (DCE) of microsatellite allele frequencies were consistent with phylogenetic trees obtained from the sequence data. Our analysis strongly suggests the presence of several additional, previously unrecognised, Cotesia species parasitising this group of butterflies},
	keywords = {cotesia, melitaeini, microsatellites, mtdna, parasitoids, phylogeny},
	author = {Kankare, Maaria and Shaw, M.R.}
}
@article {156,
	title = {Dissecting the ancient rapid radiation of microgastrine wasp genera using additional nuclear genes},
	journal = {Molecular phylogenetics and Evolution},
	volume = {41},
	year = {2006},
	pages = {690-703},
	publisher = {Elsevier},
	abstract = {Previous estimates of a generic level phylogeny for the ubiquitous parasitoid wasp subfamily Microgastrinae (Hymenoptera) have been problematic due to short internal branches deep in the phylogeny. These short branches might be attributed to a rapid radiation among the taxa, the use of genes that are unsuitable for the levels of divergence being examined, or insufficient quantity of data. We added over 1200 nucleotides from four nuclear genes to a data set derived from three genes to produce a data set of over 3000 nucleotides per taxon. While the number of well-supported short branches in the phylogeny increased, we still did not obtain strong bootstrap support for every node. Parametric and non-parametric bootstrap simulations projected that an enormous, and likely unobtainable, amount of data would be required to get bootstrap support greater than 50\% for every node. However, a marked increase in the number of well-supported nodes was seen when we conducted a Bayesian analysis of a combined data set generated from morphological characters added to the seven gene data set. Our results suggest that, in some cases, combining morphological and genetic characters may be the most practical way to increase support for short branches deep in a phylogeny.},
	keywords = {Bayesian, Braconidae, Hymenoptera, morphology, support},
	author = {Banks, J.C. and Whitfield, J.B.}
}
@article {162,
	title = {A new enigmatic apterous cyclostome genus (Hymenoptera: Braconidae) from the Greek Islands},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {45},
	year = {2009},
	pages = {77-82},
	abstract = {A new West Palaearctic genus Achaiabracon gen. n. with the type species A. aenigmatus sp. n. is described and illustrated from the Greek Islands Crete and Corfu. The position of this genus in the cyclostome group of subfamilies of Braconidae and its possible relation with rhyssaline genera are discussed. A new tribe Achaiabraconini trib. n. is proposed.},
	keywords = {Achaiabracon gen. n., Corfu, Crete, new tribe, Rhyssalinae},
	author = {Belokobylskij, S.A.}
}
