Phylogeny of North American fireflies (Coleoptera: Lampyridae): implications for the evolution of light signals

Representatives of the beetle family Lampyridae ("fireflies", "lightningbugs") are well known for their use of light signals for species recognition during mate search. However, not all species in this family use light for mate attraction, but use chemical signals instead. The lampyrids have a worldwide distribution with more than 2000 described species, but very little is known about their phylogenetic relationships. Within North America, some lampyrids use pheromones as the major mating signal whereas others use visual signals such as extended glows or short light flashes. Here, we use a phylogenetic approach to illuminate the relationships of North American lampyrids and the evolution of their mating signals. Specifically, to establish the first phylogeny of all North American lampyrid genera, we sequenced nuclear (18S) and mitochondrial (16S and COI) genes to investigate the phylogenetic relationships of 26 species from 16 North American (NA) genera and one species from the genus Pterotus that was removed recently from the Lampyridae. To test the monophyly of the NA firefly fauna we sequenced the same genes from three European lampyrids and three Asian lampyrids, and included all available Genbank data (27 additional Asian lampyrids and a former lampyrid from Asia, Rhagophthalmus). Our results show that the North American lampyrids are not monophyletic. Different subgroups are closely related to species from Europe, Asia and tropical America, respectively. The present classification of fireflies into subfamilies and tribes is not, for the most part, supported by our phylogenetic analysis. Two former lampyrid genera, Pterotus and Rhagophthalmus, which have recently been removed from this family, are in fact nested within the Lampyridae. Further, we found that the use of light as a sexual signal may have originated one or four times among lampyrids, followed by nine or four losses, respectively. Short flashes originated at least twice and possibly three times independently among our study taxa. The use of short flashes as a mating signal was replaced at least once by the use of long glows, and light signals as mating signals were lost at least three times in our study group and replaced by pheromones as the main signal mode.     

Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium l., malvaceae)

The 13 "D-genome"cotton species are a monophyletic assemblage of morphologically diverse diploids that inhabit arid to semiarid regions in Mexico, with 1 disjunct species each in Peru and the Galapagos Islands and 1 species whose range extends northward into Arizona. While these species lack commercially significant fiber (i. e., cotton), they are important in that they represent one of the parental genomes of the cultivated tetraploid cottons. To assess phylogenetic relationships among these species, we sequenced and analyzed a region of a nuclear-encoded alcohol dehydrogenase gene (AdhA). Phylogenetic analysis resulted in a topology that is generally consistent with current taxonomic alignment of the species, although the phylogeny based on AdhA sequences conflicts with those inferred from cpDNA and ITS data sets, most notably in the position of the anomalous species Gossypium gossypioides. In one lineage, we detected both gene duplication and sequence polymorphisms that transcend species boundaries; sequences in this lineage formed a monophyletic clade, yet no taxon within the clade contained a monophyletic collection of sequences. Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed.     

Genetic diversity, reproductive biology, and speciation in the entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin.

Beauveria bassiana, a mitosporic fungus used for the biological control of many insect species, is recognized as a "species complex" comprising genetically diverse lineages. Being predominantly asexual, mating tests cannot be applied to delimit species in this species complex. Genetic tests offer an indirect means of identifying species among isolates. To this end, molecular genetic analysis of a sample of B. bassiana isolates with 2 subsamples, 1 representing a worldwide collection and another from a localized epizootic population was carried out. DNA markers generated through AFLPs (amplified fragment length polymorphisms) and SSCPs (single-strand conformation poly morphisms) and nucleotide sequence data of different allelic forms of 3 genes (large and small subunits of rRNA and beta-tubulin) were evaluated. The B. bassiana isolates from the worldwide sample showed 11% overall similarity and no closely clustered groups. Phylogenetic trees generated from the AFLP and SSCP data of this sample resolved the different isolates into distinct phylogenetic lineages. In the epizootic B. bassiana population, prevalence of recombination was evident from random association of alleles in multilocus tests and lack of phylogenetic concordance among 3 gene genealogies. Thus, the worldwide sample of B. bassiana exhibits a predominantly clonal structure, hinting at species divergence leading to cryptic speciation with recombination being customary among isolates sharing a close ecological niche.     

Evolution, mitochondrial DNA phylogeny and systematic position of the Macaronesian endemic Hydrotarsus Falkenström (Coleoptera: Dytiscidae)

Abstract.  Hydrotarsus Falkenström (Coleoptera, Dytiscidae) is the only genus of aquatic beetle considered to be endemic to the Atlantic islands of Macaronesia. Its three known species ( H. lundbladi Falkenström from Madeira, and H. compunctus (Wollaston) and H. pilosus Guignot from the Canary Islands) are revised, and their phylogenetic position studied based on sequences of the 16S rRNA and Cytochrome Oxidase I genes of mitochondrial DNA. Our results clearly indicate that the species of Hydrotarsus fall deep within the genus Hydroporus Clairville, in a clade formed by (in addition to Hydrotarsus ) species currently included in the H. fuscipennis , marginatus , nigrita and tessellatus groups, and in consequence a new synonymy is proposed: Hydrotarsus Falkenström =  Hydroporus Clairville syn.n. The origin of the species of ' Hydrotarsus ', based on molecular clock estimations, is late Miocene, relatively recent in the history of the Atlantic islands. They are therefore not palaeoendemics but highly derived, recently evolved elements in the Macaronesian fauna. The estimated ages of divergence among species are much more recent than the emergence of any of the islands on which they are found, suggesting rare long-range dispersal as the mechanism driving the diversification of the lineage. Morphological modifications of the species of ' Hydrotarsus ' are discussed, as well as those of other dytiscids from hygropetric habitats.     

Mitogenome of Coprophanaeus ensifer and phylogenetic analysis of the Scarabaeidae family (Coleoptera)

Several studies about the phylogenetic relationships of the Scarabaeinae subfamily (Coleoptera: Scarabaeidae) have been performed, but some phylogenetic uncertainties persist including the relationship and monophyly of different tribes and some genera. The aim of this study was to characterize the mitogenome of Coprophanaeus ensifer in order to establish its position within the Scarabaeidae family and to contribute to the resolution of some phylogenetic uncertainties. The mitogenome was sequenced on the Illumina HiSeq 4000, assembled using the Mitobim software and annotated in MITOS WebServer. The phylogenetic trees were reconstructed by Bayesian inference. The C. ensifer mitogenome is a molecule of 14,964 bp that contains the number and organization of the genes similar to those of most Coleoptera species. Phylogenetic reconstruction suggests monophyly of the tribe Phanaeini and supports the hypothesis that Coprini is a sister group of Phanaeini. The results also revealed the position of the tribe Oniticellini which is grouped with Onthophagini and Onitini. The geographic distribution of these species that form the most ancestral clade suggests with Scarabaeinae originated in Africa. Keywords: Dung beetle, mitochondrial genome, phylogenomics     

Effects of delayed mating on reproductive output of female oriental beetle Anomala orientalis (Coleoptera: Scarabaeidae)

1 Although management of the oriental beetle Anomala orientalis (Waterhouse) by mating disruption shows promise across a range of agricultural systems, relatively little is known about aspects of the reproductive biology of this species relevant to its management. We studied the effects of delayed mating on several aspects of the oviposition behaviour and biology of the oriental beetle using females mated in the laboratory at 4–13 days posteclosion. 2 Females exhibited a gradual decline in fecundity with increased age at mating that was largely a function of a decline in duration of the oviposition period, as well as lower female fertility: females mated at 11 days were less likely to lay any fertile eggs. However, egg fertility did not vary with female age at mating. 3 Because mating delay did not affect longevity, females mated at older ages experienced decreased oviposition periods; however, females laid more eggs per day with increased age at mating, which partially offset shorter oviposition periods. 4 A mating delay of ≥ 6 days relative to females mated within the first day of reaching sexual maturity resulted in an approximately 35–50% lower mean fecundity. 5 These results suggest that, for mating disruption to be a successful management tool for the oriental beetle, mating must be prevented rather than delayed. We compare the findings of the present study with the published research on delayed mating in moths and discuss the importance of these results in relation to management of the oriental beetle using female sex pheromones.     

The phylogenetic position of the East Asian freshwater crayfish Cambaroides within the Northern Hemisphere Astacoidea (Crustacea, Decapoda, Astacida) based on molecular data

The phylogenetic position of the four East Asian freshwater crayfish species of the genus Cambaroides is not settled. Morphological phylogenetic analyses suggest close affinities of Cambaroides with North American Cambaridae. This view is based mainly on characters of the male and female reproductive organs. In contrast, the only molecular phylogenetic analysis so far available leaves the phylogenetic position of Cambaroides unresolved. The question of whether Cambaroides is monophyletic or paraphyletic has so far been neither addressed morphologically nor with molecular data sets. Here we present the first comprehensive phylogenetic analysis of all four currently described species of Cambaroides in the framework of Northern Hemisphere freshwater crayfish (Astacoidea) relationships based on partial sequences of two mitochondrial genes ( CO1 and 12S rRNA). Despite some evidence in favour of a monophyletic Cambaroides more data is needed to resolve this question. Our analyses suggest a close relationship of the North American Cambaridae and the European Astacidae, leaving the Asian Cambaroides basal to them. If these results hold true the similar reproductive organs of Cambaroides and American Cambaridae must be either homoplastic or ancestral for Northern Hemisphere Astacoidea.     

Reinstatement of Rhodotorula colostri (Castelli) Lodder and Rhodotorula crocea Shifrine & Phaff, former synonyms of Rhodotorula aurantiaca (Saito) Lodder

Rhodotorula aurantiaca (Saito) Lodder is an anamorphic basidiomycetous yeast species that belongs to the so-called "Erythrobasidium lineage" of the Urediniomycetes, according to molecular phylogenetic studies based on nucleotide sequence analyses of different ribosomal DNA regions. In the most recent editions of the yeast taxonomy treatises the species Rhodotorula colostri (Castelli) Lodder and Rhodotorula crocea Shifrine & Phaff were listed as synonyms of R. aurantiaca. Taxonomic heterogeneity within R. aurantiaca was demonstrated in a study based on whole-cell protein profiles and is also hinted at by the observed differences in physiological and biochemical characteristics among the different strains under that species name. We determined partial nucleotide sequences of the 26S rRNA gene (D1/D2 domains) of strains maintained in the CBS culture collection under R. aurantiaca, including the type strains of its synonyms. The results showed that R. colostri and R. crocea are clearly distinct from R. aurantiaca and from any other currently recognised basidiomycetous yeast species. Furthermore, phylogenetic analysis of the sequence data placed the former two species in separate lineages of the Microbotryomycetidae: R. colostri in the "ruineniae clade" (Sporidiobolus lineage or Sporidiobolales) and R. crocea loosely linked to Rhodotorula javanica (Microbotryum lineage).     

The testate lobose amoebae (order Arcellinida Kent, 1880) finally find their home within Amoebozoa

Testate lobose amoebae (order Arcellinida Kent, 1880) are common in all aquatic and terrestrial habitats, yet they are one of the last higher taxa of unicellular eukaryotes that has not found its place in the tree of life. The morphological approach did not allow to ascertain the evolutionary origin of the group or to prove its monophyly. To solve these challenging problems, we analyzed partial small-subunit ribosomal RNA (SSU rRNA) genes of seven testate lobose amoebae from two out of the three suborders and seven out of the 13 families belonging to the Arcellinida. Our data support the monophyly of the order and clearly establish its position among Amoebozoa, as a sister-group to the clade comprising families Amoebidae and Hartmannellidae. Complete SSU rRNA gene sequences from two species and a partial actin sequence from one species confirm this position. Our phylogenetic analyses including representatives of all sequenced lineages of lobose amoebae suggest that a rigid test appeared only once during the evolution of the Amoebozoa, and allow reinterpretation of some morphological characters used in the systematics of Arcellinida.     

Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches

Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer confidence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the efficiency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wide-ranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required approximately 80% less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and the paraphyly of "S. undulatus" with respect to S. belli, S. cautus, and S. woodi. Parallel evolution of ecomorphs within "S. undulatus" has masked the actual number of species within this group. This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species.     

Morphology, molecular characteristics and prevalence of a Cystosporogenes species (Microsporidia) isolated from Agrilus anxius (Coleoptera: Buprestidae)

A microsporidium was isolated from the bronze birch borer, Agrilus anxius Gory (Coleoptera: Buprestidae), collected near Sudbury and Sault Ste Marie, Canada. Light and electron microscopic investigations showed that gross pathology and ultrastructure of the investigated Cystosporogenes species was similar to those characterized and described for other Cystosporogenes species. Small subunit rRNA gene sequence data and comparative phylogenetic analysis confirmed that the microsporidian species from A. anxius is most closely related to the genus Cystosporogenes clade of microsporidia. Infection average in the Sudbury and Sault Ste Marie beetle populations was >80% and relatively stable in 2006-2007 but declined in 2008. Field prevalence of the A. anxius isolate, mechanisms that may potentially be involved in its horizontal (autoinfection) and vertical (transovarial) transmission, and disease dynamics are discussed. The congeneric relationship between Agrilus planipennis and A. anxius makes it imperative to study the virulence of this Cystosporogenes species in A. planipennis.     

Togninia (Calosphaeriales) is confirmed as teleomorph of Phaeoacremonium by means of morphology, sexual compatibility and DNA phylogeny

Petri disease, or black goo, is a serious disease of vines in most areas where grapevines are cultivated. The predominant associated fungus is Phaeomoniella chlamydospora (Chaetothyriales). Several species of Phaeoacremonium (Pm.) also are associated, of which Pm. aleophilum is the most common. Although no teleomorph is known for Phaeoacremonium, the genus Togninia previously has been linked to phaeoacremonium-like anamorphs. To investigate the possible anamorph-teleomorph connection of Phaeoacremonium to Togninia, anamorphs of Togninia minima, T. fraxinopennsylvanica and T. novae-zealandiae morphologically were compared with Pm. aleophilum and some representative cultures were mated in all combinations. Although no interspecies mating proved fertile, matings between isolates of Pm. aleophilum produced a Togninia teleomorph within 3-4 weeks. Certain field isolates of Pm. aleophilum commonly produced the teleomorph, demonstrating that both mating types can occur in the same vine and thus also explaining the genetic diversity observed for this fungus in some vineyards. To elucidate the phylogenetic relationships among these taxa, isolates were subjected to sequence analysis of the nuclear ribosomal internal transcribed spacers (ITS1, ITS2) and the 5.8S rRNA gene, as well as portions of the translation elongation factor 1 alpha (EF-1α) gene. The generic placement of teleomorphs within Togninia (Calosphaeriales) further was confirmed via phylogenetic analyses of 18S small subunit (SSU) DNA. From these sequences, morphological and mating data, we conclude that T. minima is the teleomorph of Pm. aleophilum, and that it has a biallelic heterothallic mating system. An epitype and mating type tester strains also are designated for T. minima.     

Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei)

Labyrinth fishes (Perciformes: Anabantoidei) are primary freshwater fishes with a disjunct African-Asian distribution that exhibit a wide variety of morphological and behavioral traits. These intrinsic features make them particularly well suited for studying patterns and processes of evolutionary diversification. We reconstructed the first molecular-based phylogenetic hypothesis of anabantoid intrarelationships using both mitochondrial and nuclear nucleotide sequence data to address anabantoid evolution. The mitochondrial data set included the complete cytochrome b, partial 12S rRNA, complete tRNA Val, and partial 16S rRNA genes (3332 bp) of 57 species representing all 19 anabantoid genera. The nuclear data set included the partial RAG1 gene (1494 bp) of 21 representative species. The phylogenetic analyses of a combined (mitochondrial+nuclear) data set recovered almost fully resolved trees at the intrafamily level with different methods of phylogenetic inference. Phylogenetic relationships at this taxonomic level were compared with previous morphology-based hypotheses. In particular, the enigmatic pike-head (Luciocephalus) was confidently placed within the "spiral egg" clade, thus resolving the long-standing controversy on its relative phylogenetic position. The molecular phylogeny was used to study the evolution of the different forms of parental care within the suborder. Our results suggest that the evolution of breeding behavior in anabantoids is highly correlated with phylogeny, and that brood care evolved three times independently from an ancestral free spawning condition without parental care. Ancestral character state reconstructions under maximum parsimony and maximum likelihood further indicated that both bubble nesting and mouthbrooding have evolved recurrently during anabantoid evolution. The new phylogenetic framework was also used to test alternative biogeographic hypotheses that account for the disjunct African-Asian distribution. Molecular divergence time estimates support either a drift vicariance linked to the breakup of Gondwana or Late Mesozoic Early Tertiary dispersal from Africa to Asia or vice versa.     

The mitochondrial genome of red-necked phalarope <Emphasis Type="Italic">Phalaropus lobatus</Emphasis> (Charadriiformes: Scolopacidae) and phylogeny analysis among Scolopacidae

The red-necked phalarope is a wonderful species with specific morphological characters and lifestyles. Mitochondrial genomes, encoding necessary proteins involved in the system of energy metabolism, are important for the evolution and adaption of species. In this study, we determined the complete mitogenome sequence of Phalaropus lobatus (Charadriiformes: Scolopacidae). The circular genome is 16714 bp in size, containing 13 PCGs, two ribosomal RNAs and 22 tRNAs and a high AT-rich control region. The AT skew and GC skew of major strand is positive and negative respectively. Most of PCGs are biased towards A-rich except ND1. A codon usage analysis shows that 3 start codons (ATG, GTG and ATA), 4 stop codons (TAA, TAG, AGG, AGA) and two incomplete terminate codons (T–). Twenty two transfer RNAs have the typical cloverleaf structure, and a total of ten base pairs are mismatched throughout the nine tRNA genes. The phylogenetic tree based on 13 PCGs and 2 rRNA genes indicates that monophyly of the family and genus Phalaropus is close to genus Xenus plus Tringa. The analysis of selective pressure shows 13 protein-coding genes are evolving under the purifying selection and P. lobatus is different from other Scolopacidae species on the selective pressure of gene ND4. This study helps us know the inherent mechanism of mitochondrial structure and natural selection.     

The Effect of Single, Double, and Triple Matings on the Lifetime Fecundity of Callosobruchus analis and Callosobruchus maculatus (Coleoptera: Bruchidae)

This study examined the effect of single, double, and triple matings on female lifetime fecundity in two closely related species of beetle, Callosobruchus analis and C. maculatus. Multiple mating resulted in elevated lifetime fecundities in both species, although the pattern of elevation differed between the two species. When oviposition resource was plentiful the elevation was apparent after a second but not a third copulation for C. maculatus and after a second and after a third for C. analis. By altering the availability of oviposition sites to C. maculatus females, we were able to alter the pattern of fecundity elevation between matings. When oviposition sites were limited, fecundity increased after a third mating but not a second mating. We suggest that the pattern of fecundity elevation associated with multiple mating in these species is primarily the result of oviposition stimulants delivered by males, rather than a nutritional donation brought about by the metabolism of ejaculates. We also suggest that the intra- and interspecific differences in the relationship between mating frequency and fecundity are the result of differences in egg maturation rates.     

The first complete mitogenome of Picumnus innominatus (Aves,Piciformes, Picidae) and phylogenetic inference within the Picidae

The avian family Picidae, which is nearly global in distribution, contains the piculets (Picumninae and Nesoctitinae), the woodpeckers (Picinae), and the wrynecks (Jynginae). However, the phylogenetic relationships within the Picidae remain obscure for most genera. In the present study, the complete mitochondrial genome of Picumnus innominatus was determined and described, which was the first complete mitogenome reported in the Picumnus. The circular mitogenome of P. innominatus was 17,180 bp in size and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNA genes, a control region (CR), and a noncoding region. The gene order and arrangement of the P. innominatus mitogenome were identical to other mitogenomes of the Picidae. Moreover, strikingly large tandem repeats were found in the noncoding region of the P. innominatus mitogenome, which have not yet been covered in other picid species to date. At the family level (Picidae), the highest dN/dS ratio was detected for the ND1 gene (1.38726) among 13 PCGs, indicating that positive selection was powerful for this gene. Bayesian and Maximum Likelihood phylogenetic analyses based on the combination of 12S rRNA and CYTB gene supported strongly that the Picumninae is monophyletic.     

Phylogenetic position of the marine ciliate, Certesia quadrinucleata (Ciliophora; Hypotrichia; Hypotrichida) inferred from the complete small subunit ribosomal RNA gene sequence

The complete small subunit rRNA (SSrRNA) gene sequence of the rare marine hypotrich, Certesia quadrinucleata Fabre-Domergue, 1885, was determined, and found to be 1752 nucleotides long. The phylogenetic position of this species was deduced using distance matrix, maximum parsimony and maximum likelihood methods. Certesia was consistently demonstrated to be a member of the Aspidisca-Euplotes group and clearly exhibits a very close relationship to the well-known genus Euplotes (99% Bay, 99% LS, 99% NJ, 99% MP). The phylogenetic trees further suggest that: (1) Uronychia and Diophrys, traditionally placed in the family Uronychiidae, branch earlier and share a closer relationship to each other than to other hypotrichs; (2) taxa in Gastrocirrhidae, represented by Euplotidium arenarium, might be an "ancestral" group among "traditional" hypotrichs.     

Evolutionary constraints in hind wing shape in Chinese dung beetles (Coleoptera: Scarabaeinae)

This study examines the evolution hindwing shape in Chinese dung beetle species using morphometric and phylogenetic analyses. Previous studies have analyzed the evolution of wing shape within a single or very few species, or by comparing only a few wing traits. No study has analyzed wing shape evolution of a large number of species, or quantitatively compared morphological variation of wings with proposed phylogenetic relationships. This study examines the morphological variation of hindwings based on 19 landmarks, 119 morphological characters, and 81 beetle species. Only one most parsimonious tree (MPT) was found based on 119 wing and body characters. To better understand the possible role of the hindwing in the evolution of Scarabaeinae, additional phylogenetic analyses were proposed based on the only body features (106 characters, wing characters excluded). Two MPT were found based on 106 body characters, and five nodes were collapsed in a strict consensus. There was a strong correlation between the morphometric tree and all phylogenetic trees (r>0.5). Reconstructions of the ancestral wing forms suggest that Scarabaeinae hindwing morphology has not changed substantially over time, but the morphological changes that do occur are focused at the base of the wing. These results suggest that flight has been important since the origin of Scarabaeinae, and that variation in hindwing morphology has been limited by functional constraints. Comparison of metric disparity values and relative evolutionary sequences among Scarabaeinae tribes suggest that the primitive dung beetles had relatively diverse hindwing morphologies, while advanced dung beetles have relatively similar wing morphologies. The strong correlation between the morphometric tree and phylogenetic trees suggest that hindwing features reflect the evolution of whole body morphology and that wing characters are suitable for the phylogenetic analyses. By integrating morphometric and cladistic approaches, this paper sheds new light on the evolution of dung beetle hind wings.     

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus)

Background

The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats.

Methodology/Principal Findings

We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general “3 clade” structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism.

Conclusions/Significance

This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to lead to additional species diversity. These dispersal-limited taxa provide novel insight into the biogeography and Earth history processes of California.     

Gluconobacter sphaericus (Ameyama 1975) comb. nov., a brown pigment-producing acetic acid bacterium in the Alphaproteobacteria

Strain NBRC 12467(T )was examined genetically, phylogenetically, phenotypically, and chemotaxonomically. The DNA G+C content of the strain was 59.5 mol%. The strain represented low levels of DNA-DNA hybridization of 49-9% to the type strains of eight Gluconobacter species. The strain formed a cluster along with the type strains of G. albidus and G. kondonii in phylogenetic trees based on 16S rRNA gene sequences. In a phylogenetic tree based on 16S-23S rRNA gene ITS sequences, however, the strain formed an independent cluster from the type strains of the eight Gluconobacter species. Such phylogenetic relationships were supported by the calculated pair-wise 16S rRNA gene and 16S-23S rRNA gene ITS sequence similarities. The strain was distinguished from the type strains of the eight Gluconobacter species by 16S-23S rRNA gene ITS restriction analysis using five restriction endonucleases. The strain produced a water-soluble brown pigment and 2,5-diketo-D-gluconate from D-glucose, differing from the type strains of the eight Gluconobacter species, and acid from meso-erythritol very weakly, differing from the type strains of the remaining seven Gluconobacter species except for the type strain of G. roseus, but not from maltose, differing from the type strain of G. oxydans, and had Q-10. For the strain, which was once classified as G. oxydans subsp. sphaericus, Gluconobacter sphaericus (Ameyama 1975) comb. nov. is proposed. The type strain is NBRC 12467(T), which is also deposited as BCC 14448(T).