Andrew T. Beckenbach

Episodic radiations in the fly tree of life

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.

Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata.

We report the complete mitochondrial DNA sequence of the spotted asparagus beetle, Crioceris duodecimpunctata. The genome complement, gene order, and nucleotide composition of this beetles mitochondrial genome were found to be typical of those reported for other insects. Unusual features of this genome include the substitution of UCU for GCU as the anticodon for tRNA(Ser), an unusual TpsiC loop for the tRNA(Ile) gene, and the identification of a putative ATT start codon for cox1. The utility of complete mitochondrial genome data for phylogenetic inference of the insect orders was tested, and compared to that of cox1 and combined mitochondrial ribosomal DNA sequences. Even though the number of insect orders represented by complete mitochondrial genomes is still limited, several well-established relationships are evident in the phylogenetic analysis of the complete sequences. Monophyly of the orders Diptera, Lepidoptera, and Coleoptera were consistently recovered. Monophyly of the Holometabola was also observed in some (though not all) analyses. The accumulation of complete mitochondrial sequences from a broader array of insect orders holds the promise of clarifying the early diversification of insects.

mtDNA Sequence Diversity of Orangutans from the Islands of Borneo and Sumatra

Abstract. A comparison of mitochondrial DNA sequences was undertaken for two genes among orangutans from Borneo and Sumatra. The distribution of haplotypes among 42 individuals for NADH dehydrogenease subunit 3 and 39 individuals for cytochrome B was used to infer population structure. The haplotypes among all Bornean orangutans form a cluster of closely related individuals for both genes, with two distinct haplotypes occupying different regions of the island. Sumatran haplotypes fall into three distinct, and highly diverged, groups. Strikingly, one of the Sumatran haplotypes shares sequence identity with the most widespread Bornean haplotype. This haplotype distribution is considered in the context of the highly complex geological history for the area around the Malay Archipelago. Alternating periods of geographic isolation and reunion, resulting from glacially induced land bridge formation, presented substantial opportunity for population dispersal between periodically isolated demes. We present a paleodispersal model that is consistent with genetic, geological, paleoecological, and fossil data. The disparity of sequences present in orangutan populations argues against a simple Sumatra–Borneo dichotomy. Our evidence, and that of others, suggests that the Sumatran population alone contains the remnants of at least three separate lineages.

Molecular analysis of the biting midges (Diptera: Ceratopogonidae), based on mitochondrial cytochrome oxidase subunit 2

Sequences from the mitochondrial cytochrome oxidase subunit 2 gene (cox2) were determined for 14 species from the family Ceratopogonidae, representing 12 genera and all five subfamilies, along with six representatives of other nematoceran families. The purpose was to develop a molecular phylogeny of the Ceratopogonidae, and interpret the phylogenetic position of the family within the infraorder Culicomorpha. These taxa have been analysed using cladistic methodology which, in combination with an excellent fossil record, provides a well established morphological phylogeny. Sequence analysis of cox2 revealed a high degree of sequence divergence among the species, reflecting in part the antiquity of the family, but also a significant acceleration of sequence evolution in the ceratopogonids compared to other nematoceran Diptera. Phylogenetic reconstruction by neighbor-joining and maximum parsimony gave strong support for an early separation of an ancient lineage that includes the two genera, Austroconops and Leptoconops, from the remainder of the family. The results support the existence of a clade that includes two subfamilies, Dasyheleinae and Forcipomyiinae, and this clade appears as sister to the remaining subfamily, Ceratopogoninae. The molecular phylogeny also supports monophyly of the Ceratopogonidae, and either a sister or paraphyletic relationship of this family with the Chironomidae.

Single Nucleotide +1 Frameshifts in an Apparently Functional Mitochondrial Cytochrome b Gene in Ants of the Genus Polyrhachis

Twelve of 30 species examined in the ant genus Polyrhachis carry single nucleotide insertions at one or two positions within the mitochondrial cytochrome b (cytb) gene. Two of the sites are present in more than one species. Nucleotide substitutions in taxa carrying insertions show the strong codon position bias expected of functional protein coding genes, with substitutions concentrated in the third positions of the original reading frame. This pattern of evolution of the sequences strongly suggests that they are functional cytb sequences. This result is not the first report of +1 frameshift insertions in animal mitochondrial genes. A similar site was discovered in vertebrates, where single nucleotide frameshift insertions in many birds and a turtle were reported by Mindell et al. (Mol Biol Evol 15:1568, 1998). They hypothesized that the genes are correctly decoded by a programmed frameshift during translation. The discovery of four additional sites gives us the opportunity to look for common features that may explain how programmed frameshifts can arise. The common feature appears to be the presence of two consecutive rare codons at the insertion site. We hypothesize that the second of these codons is not efficiently translated, causing a pause in the translation process. During the stall the weak wobble pairing of the tRNA bound in the peptidyl site of the ribosome, together with an exact Watson–Crick codon–anticodon pairing in the +1 position, allows translation to continue in the +1 reading frame. The result of these events is an adequate level of translation of a full-length and fully functional protein. A model is presented for decoding of these mitochondrial genes, consistent with known features of programmed translational frameshifting in the yeast TY1 and TY3 retrotransposons.

Mitochondrial Genome Sequences of Nematocera (Lower Diptera): Evidence of Rearrangement following a Complete Genome Duplication in a Winter Crane Fly

The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.

Partial sequence of a sponge mitochondrial genome reveals sequence similarity to Cnidaria in cytochrome oxidase subunit II and the large ribosomal RNA subunit.

Abstract. A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3′ end of the 16S rRNA gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5′ portion of ATPase subunit 6. The Porifera cluster distinctly within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII—tRNALys—ATP8—ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.

SELECTION AND THE "SEX-RATIO" POLYMORPHISM IN NATURAL POPULATIONS OF DROSOPHILA PSEUDOOBSCURA

“Sex‐ratio” (SR) is a naturally occurring X‐linked meiotic drive system, where the SR‐X chromosome is transmitted to nearly all progeny of SR males. It occurs at frequencies of up to 25% in some populations of Drosophila pseudoobscura. Because of the twofold drive advantage, SR should rapidly fix in populations, causing the extinction of the species, unless opposed by strong selection. I examine several of the adult components of fitness, including the frequencies of all genotypic mating combinations, fertilities, and fecundities of flies from two populations in southeastern Arizona. Significant reduction of fecundity of SR/SR females was observed in the Tucson population. No evidence was found for either lower fertility or reduced mating success of SR males, relative to standard males. Most selection opposing SR appears to be operating at the larval stages in nature.

Insect mitochondrial genomics 3: the complete mitochondrial genome sequences of representatives from two neuropteroid orders: a dobsonfly (order Megaloptera) and a giant lacewing and an owlfly (order Neuroptera)

We describe the complete mitochondrial genomes from representatives of two orders of the Neuropterida: a dobsonfly, Corydalus cornutus (Megaloptera: Corydalidae, GenBank Accession No. FJ171323), a giant lacewing Polystoechotes punctatus (Neuroptera: Polystoechotidae, FJ171325), and an owlfly, Ascaloptynx appendiculatus (Neuroptera: Ascalaphidae, FJ171324). The dobsonfly sequence is 15,687 base pairs with a major noncoding (A+T rich) region of approximately 967 bp. The gene content and organization of the dobsonfly is identical to that of most insects. The giant lacewing sequence is 16 036 bp with a major noncoding region of about 1123 bp, while the owlfly sequence is 15,877 bp with a major noncoding region of about 1066 bp. The two Neuroptera sequences include a transposition of two tRNA genes, tRNATrp and tRNACys. These tRNA genes are coded on opposite strands and overlap by seven residues in the standard insect mitochondrial gene arrangement. Thus, the transposition required a duplication of at least the region of overlap. It is likely that the transposition occurred by a duplication of both genes followed by deletion of one copy of each gene. Examination of this region in two other neuropteroid species, a snakefly, Agulla sp. (Raphidioptera: Raphidiidae), and an antlion, Myrmeleon immaculatus (Neuroptera: Myrmeleontidae), shows that the rearrangement is widespread in the order Neuroptera but not present in either of the other two orders of Neuropterida.

Evolutionary transitions of complex labile traits: Silk weaving and arboreal nesting in Polyrhachis ants

Understanding the maintenance and evolution of complex group behavioural systems has broad significance to our understanding of social evolution, yet we have little insight into how these systems have evolved. Nest-weaving, a rare group behaviour considered a pinnacle of cooperative action in social insects, involves the coordination of workers and larvae by incorporating larval silk into the nest structure. To investigate the evolution of this complex behaviour in the ant genus Polyrhachis, we used comparative analysis and an inferred molecular phylogeny based on three mitochondrial genes COI, COII and CytB, and three nuclear genes EF1 a-F2, Wg and Tf. Our results showed that arboreality and nest-weaving are closely associated, but in contrast to the previous hypotheses, represent the ancestral state in the monophyletic genus. Nest-weaving within the genus, moreover, is remarkably labile. Arboreality and nest-weaving have been lost and partially regained on at least two occasions: two non-weaving subterranean species (sister taxa likely reflecting a single evolutionary event) have reverted to arboreal nesting habits without regaining the use of silk nests, while a third subterranean species has transitioned to nesting in silk nests on the sides of rocks, obtaining silk from spiders and not their own larvae. The loss of larval cocoons, which is correlated with the most complex form of nest-weaving behavior as typified in Oecophylla, has occurred independently on at least two occasions within Polyrhachis. The repeated loss of nest-weaving behaviour and its partial regaining within the genus provides the first example of a complex group-level trait that did not arise through behavioural progression from simple to complex states. The evolution and loss of complex group-level traits may be more evolutionarily labile than previously appreciated.