The plethodontid genus Batrachoseps, the slender salamanders, is the most diverse clade of salamanders in western North America, but it has posed taxonomic difficulties because it contains many morphologically cryptic species. A segment of the mitochondrial DNA gene cytochrome b was studied for 278 individuals densely sampled from throughout the range of all 18 described species and several undescribed species. Phylogenetic analyses of the mtDNA data identify six major clades, one corresponding to the subgenus Plethopsis and five within a monophyletic subgenus Batrachoseps. All major clades and most species within these clades display strong phylogeographic structuring. Comparisons of mtDNA and allozyme data show that several allozymically cohesive groups are not monophyletic with respect to mtDNA. We suggest that this phenomenon results from fragmentation of populations, divergence in allopatry, and then recontact and gradual merging of units caused predominantly by male‐mediated gene flow. The mtDNA offers evidence that populations were once more isolated than they are now, while the patterns of allozyme variation reflect recent and current interactions among populations. The complex patterns of morphological, allozymic and mtDNA variation associated with the constantly changing geological landscape give insight into the nature of processes responsible for species formation in Batrachoseps. © 2002 The Linnean Society of London. Biological Journal of the Linnean Society, 2002, 76, 361–391.

Axis patterning and appendage development have been well studied in Drosophila melanogaster, a species in which both limb and segment morphogenesis are derived. In Drosophila, positional information from genes important in anteroposterior and dorsoventral axis formation, including wingless (wg) and decapentaplegic (dpp), is required for allocating and patterning the appendage primordia. We used RNA interference to characterize the functions of wg and dpp in the red flour beetle, Tribolium castaneum, which retains more ancestral modes of limb and segment morphogenesis. We also characterized the expression of potential targets of the WG and DPP signaling pathways in these embryos. Tribolium embryos in which dpp had been downregulated had defects in the dorsalmost body wall, but did not appear to have been globally repatterned and had normal appendages. Downregulation of wg led to the loss of segment boundaries, gnathal and thoracic appendages, and lateral head lobes, and to changes in the expression of dpp, Distal-less, and Engrailed. The functions of wg varied along both the anteroposterior and dorsoventral axes of the embryo. Phylogenetic comparisons indicate that the role of WNT signaling in segment boundary formation is evolutionarily old, but that its role in appendage allocation originated in the common ancestor of holometabolous insects.

The superphylum Panarthropoda (Arthropoda, Onychophora, and Tardigrada) exhibits a remarkable diversity of segment morphologies, enabling these animals to occupy diverse ecological niches. The molecular identities of these segments are specified by Hox genes and other axis patterning genes during development [1, 2]. Comparisons of molecular segment identities between arthropod and onychophoran species have yielded important insights into the origins and diversification of their body plans [3-9]. However, the relationship of the segments of tardigrades to those of arthropods and onychophorans has remained enigmatic [10, 11], limiting our understanding of early panarthropod body plan diversification. Here, we reveal molecular identities for all of the segments of a tardigrade. Based on our analysis, we conclude that tardigrades have lost a large intermediate region of the body axis-a region corresponding to the entire thorax and most of the abdomen of insects-and that they have lost the Hox genes that originally specified this region. Our data suggest that nearly the entire tardigrade body axis is homologous to just the head region of arthropods. Based on our results, we reconstruct a last common ancestor of Panarthropoda that had a relatively elongate body plan like most arthropods and onychophorans, rather than a compact, tardigrade-like body plan. These results demonstrate that the body plan of an animal phylum can originate by the loss of a large part of the body.

Serial homologs are similar structures that develop at different positions within a body plan. These structures share some, but not all, aspects of developmental patterning, and their evolution is thought to be constrained by shared, pleiotropic gene functions. Here we describe the functions of 17 developmental genes during metamorphic development of the legs in the red flour beetle, Tribolium castaneum. This study provides informative comparisons between appendage development in Drosophila melanogaster and T. castaneum, between embryonic and adult development in T. castaneum, and between the development of serially homologous appendages. The leg gap genes Distal-less and dachshund are conserved in function. Notch signaling, the zinc-finger transcription factors related to odd-skipped, and bric-à-brac have conserved functions in promoting joint development. homothorax knockdown alters the identity of proximal leg segments but does not reduce growth. Lim1 is required for intermediate leg development but not distal tarsus and pretarsus development as in D. melanogaster. Development of the tarsus requires decapentaplegic, rotund, spineless, abrupt, and bric-à-brac and the EGF ligand encoded by Keren. Metathoracic legs of T. castaneum have four tarsomeres, whereas other legs have five. Patterns of gene activity in the tarsus suggest that patterning in the middle of the tarsal region, not the proximal- or distal-most areas, is responsible for this difference in segment number. Through comparisons with other recent studies of T. castaneum appendage development, we test hypotheses for the modularity or interdependence of development during evolution of serial homologs.

Antenna structure varies widely among insects, in contrast to the well-conserved structure of legs. The adult capitate antenna of the red flour beetle, Tribolium castaneum, is composed of eleven articles, organized into four distinct morphological regions (scape, pedicel, funicle and club). Here, we report the use of RNA interference to examine the functions of 21 genes during antenna metamorphosis in T. castaneum. Genes with conserved functions relative to the developmental model species Drosophila melanogaster include Distal-less and EGF signaling (antennal growth), spineless (determination of antennal identity) and the Notch signaling pathway (antennal growth, joint formation, and sensory bristle development). However, the functions of many genes differed from those predicted from the Drosophila model. In addition to a conserved gap phenotype, depletion of dachshund transformed funicle articles toward club-like identity. Depletion of Distal-less or homothorax did not cause antenna-to-leg transformation. Lim1 was required only for development of the scape-pedicle joint. Depletion of odd-skipped-related genes led to the loss of the entire funicle, while spalt, rotund, spineless, and dachshund affected smaller regions. Growth and joint formation were linked developmentally in the funicle, but not in the club. Joint formation within the club required bric-a-brac, aristaless, apterous, and pdm. Gene functions are discussed in terms of a model of antenna development in T. castaneum. This model provides a contrast to knowledge of antenna development in D. melanogaster, insight into the likely ancestral mode of antenna development, and a framework for considering diverse antenna morphologies.

Low-vagility species with deep evolutionary histories are key to our understanding of the biogeographical history of geologically complex areas, such as the west coast of North America. We present a detailed study of the phylogeography of the salamander Batrachoseps attenuatus (Caudata: Plethodontidae) using sequences of the mitochondrial gene cob from 178 individuals sampled from throughout the species' range. Sequences of three other mitochondrial genes (16S, cox1, nad4) and a nuclear gene (RAG-1) were used to investigate the deeper evolutionary history of the species. We found high levels of genetic diversity and deep divergences within a mostly continuous distribution, with five genetically well-differentiated and geographically structured mitochondrial DNA clades. Significant association between geographical and genetic distances within these clades suggests demographic stability, whereas Fu's FS tests suggest demographic expansions in three of them. Mantel tests identify two biogeographical barriers, the San Andreas Fault and the Sacramento-San Joaquin Delta, as important in the diversification of lineages. The timing of the main splitting events between intraspecific lineages was estimated by applying relaxed molecular clock methods combining several mutation rates and a fossil calibration. The earliest splitting events are old (Pliocene/Miocene), with more recent (Pleistocene) subdivisions in some clades. Disjunct populations distributed along the western foothills of the Sierra Nevada colonized this area relatively recently from a single refugium east of San Francisco Bay. The combination of fine-scale, comprehensive sampling with phylogenetic, historical demographic and hypothesis-based tests allowed delineation of a complex biogeographical scenario with general implications for the study of codistributed taxa.

Variation in the amount of nuclear DNA, the C-value, does not correlate with differences in morphological complexity. There are two classes of explanations for this observation, which is known as the ' C-value paradox '. The quantity of DNA may serve a ' nucleotypic ' function that is positively selected. Alternatively, large genomes may consist of junk DNA, which increases until it negatively affects fitness. Attempts to resolve the C-value paradox focus on the link between genome size and fitness. This link is usually sought in life history traits, particularly developmental rates. I examined the relationship among two life history traits, egg size and embryonic developmental time and genome size, in 15 species of plethodontid salamanders. Surprisingly, there is no correlation between egg size and developmental time, a relationship included in models of life history evolution. However, genome size is positively correlated with embryonic developmental time, a result that is robust with respect to many sources of variation in the data. Without information on the targets of natural selection it is not possible with these data to distinguish between nucleotypic and junk DNA explanations for the C-value paradox.

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