No abstract

We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi‐gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi‐gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases (“Ns”), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re‐split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near‐identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java‐based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.

The extraordinary species richness and endemism of the Indo-AustralianArchipelago (IAA) exists in one of the most geologically dynamic regions ofthe planet. The provenance of its biota has been debated, particularly in thearea known asWallacea. Application of molecular genetic approaches and abetter understanding of the region’s complex geology have stimulated muchrecent biogeographic work in the IAA. We review molecular phylogeneticand phylogeographic studies in light of current geological evidence. Presentdistribution patterns of species have been shaped largely by pre-Pleistocenedispersal and vicariance events, whereas more recent changes in the connectivityof islands within the Archipelago have influenced the partitioning ofintraspecific variation. Many genetic studies have uncovered cryptic specieswith restricted distributions. We discuss the conservation significance ofthe region and highlight the need for cross-taxon comparative studies usingnewly developed analytical approaches well suited to the challenges ofhistorical inference in this region

Ants are a dominant feature of terrestrial ecosystems, yet we know little about the forces that drive their evolution. Recent findings illustrate that their diets range from herbivorous to predaceous, with ''herbivores'' feeding primarily on exudates from plants and sap-feeding insects. Persistence on these nitrogen-poor food sources raises the question of how ants obtain sufficient nutrition. To investigate the potential role of symbiotic microbes, we have surveyed 283 species from 18 of the 21 ant subfamilies using molecular techniques. Our findings uncovered a wealth of bacteria from across the ants. Notable among the surveyed hosts were herbivorous ''turtle ants'' from the related genera Cephalotes and Procryptocerus (tribe Cephalotini). These commonly harbored bacteria from ant-specific clades within the Burkholderiales, Pseudomonadales, Rhizobiales, Verrucomicrobiales, and Xanthomonadales, and studies of lab-reared Cephalotes varians characterized these microbes as symbiotic residents of ant guts. Although most of these symbionts were confined to turtle ants, bacteria from an ant-specific clade of Rhizobiales were more broadly distributed. Statistical analyses revealed a strong relationship between herbivory and the prevalence of Rhizobiales gut symbionts within ant genera. Furthermore, a consideration of the ant phylogeny identified at least five independent origins of symbioses between herbivorous ants and related Rhizobiales. Combined with previous findings and the potential for symbiotic nitrogen fixation, our results strongly support the hypothesis that bacteria have facilitated convergent evolution of herbivory across the ants, further implicating symbiosis as a major force in ant evolution. diversification ͉ Formicidae ͉ Rhizobiales ͉ symbiosis ͉ trophic level I dentifying the mechanisms underlying adaptation and diversification is a central goal of evolutionary biology. Great strides have been made toward this end through the development of fast and affordable molecular tools, and the joint application of molecular phylogenetics and comparative methods (1-3). One unanticipated theme that has emerged from this work is that bacterial symbionts have played key roles in the evolution and diversification of eukaryotes, starting with endosymbiotic origins of mitochondria and chloroplasts (4). Bacterial symbionts are also prevalent among insects that feed on inaccessible or nutritionally marginal diets such as blood, wood, xylem, and phloem (5). Given the demonstrated nutritional roles of these bacteria, their near-ubiquity in insects that specialize on nutrient-poor diets, their long histories of coevolution, and the diversity of the many groups that harbor nutritional symbionts, it is clear that bacteria have had a strong impact on the dietary evolution and diversification of their insect hosts (6).Symbiosis has played an integral role in the evolution of the ants (Hymenoptera: Formicidae). Throughout the course of their 115-168 million year history (7,8), these diverse and ecologically dominant insects...

The estimated 6000 species of Lycaenidae account for about one third of all Papilionoidea. The majority of lycaenids have associations with ants that can be facultative or obligate and range from mutualism to parasitism. Lycaenid larvae and pupae employ complex chemical and acoustical signals to manipulate ants. Cost/benefit analyses have demonstrated multiple trade-offs involved in myrmecophily. Both demographic and phylogenetic evidence indicate that ant association has shaped the evolution of obligately associated groups. Parasitism typically arises from mutualism with ants, and entomophagous species are disproportionately common in the Lycaenidae compared with other Lepidoptera. Obligate associations are more common in the Southern Hemisphere, in part because highly ant-associated lineages make up a larger proportion of the fauna in these regions. Further research on phylogeny and natural history, particularly of the Neotropical fauna, will be necessary to understand the role ant association has played in the evolution of the Lycaenidae.