Population genetics of Galápagos land iguana (genus Conolophus) remnant populations

The Galápagos land iguanas (genus Conolophus) have faced significant anthropogenic disturbances since the 17th century, leading to severe reduction of some populations and the extinction of others. Conservation activities, including the repatriation of captive‐bred animals to depleted areas, have been ongoing since the late 1970s, but genetic information has not been extensively incorporated. Here we use nine species‐specific microsatellite loci of 703 land iguanas from the six islands where the species occur today to characterize the genetic diversity within, and the levels of genetic differentiation among, current populations as well as test previous hypotheses about accidental translocations associated with early conservation efforts. Our analyses indicate that (i) five populations of iguanas represent distinct conservation units (one of them being the recently discovered rosada form) and could warrant species status, (ii) some individuals from North Seymour previously assumed to be from the natural Baltra population appear related to both Isabela and Santa Cruz populations, and (iii) the five different management units exhibit considerably different levels of intrapopulation genetic diversity, with the Plaza Sur and Santa Fe populations particularly low. Although the initial captive breeding programmes, coupled with intensive efforts to eradicate introduced species, saved several land iguana populations from extinction, our molecular results provide objective data for improving continuing in situ species survival plans and population management for this spectacular and emblematic reptile.     

Feeding range studies of Rodolia cardinalis (Mulsant), a candidate biological control agent of Icerya purchasi Maskell in the Galápagos islands

The immediate threat of the cottony cushion scale, Icerya purchasi Maskell (Homoptera: Margarodidae), to the conservation of endangered flora in the Galápagos islands prompted conservation groups to assess the risks associated with the introduction of its natural enemy, Rodolia cardinalis (Mulsant) (Coleoptera: Coccinellidae). Although R. cardinalis has been widely used for controlling this exotic pest, little information was found to confirm its presumed narrow feeding range. Consequently, studies were deemed necessary to determine whether the introduction of R. cardinalis would harm the island’s native invertebrate fauna, in particular rare or threatened species. Using no-choice trials, we tested neonate and third instar larvae of R. cardinalis against 16 and 11 potential prey species, respectively. Adults with prior feeding experience on I. purchasi were tested against eight non-target species and naïve adults (those that had not fed on I. purchasi) were tested against six. These trials included up to 35% of the Homoptera species of conservation value presumed to have the highest risk of being preyed upon by R. cardinalis. To maximize the range of species exposed to R. cardinalis, feeding trials were also carried out with some introduced species representative of groups containing potential non-target species that were not located for testing. R. cardinalis was unable to complete its life cycle on any of the test prey species and only fed on Margarodes similis Morrison (Homoptera: Margarodidae), a species closely related to the cottony cushion scale. M. similis, however, is subterranean and in its natural habitat is not at risk from foraging by R. cardinalis. Based on these trials, we believe that immature stages of R. cardinalis will have no impact on the non-target invertebrate fauna of the Galápagos islands because they specialize on Margarodidae. Although the limited nature of our testing prevents us from reaching a definitive conclusion about the prey range of R. cardinalis adults, our results indicate that it is also narrow. According to our field and laboratory studies, niche overlap with native predators of Homoptera will be minimal and intraguild predation should not occur.     

A set of highly discriminating microsatellite loci for the Galápagos marine iguana Amblyrhynchus cristatus

We describe here the cloning of 12 (7 dinucleotide, 1 trinucleotide and 4 tetranucleotide) microsatellite loci for the Galápagos marine iguana Amblyrhynchus cristatus. When tested for individuals from five different island populations on the Galápagos archipelago, high genetic diversities (9–20 alleles per locus) and heterozygosities (0.200–0.944) were observed. All loci showed no obvious deviations from Hardy–Weinberg equilibrium. The new set of microsatellite loci was able to assign individuals reliably to their island of origin, thus being able to discriminate between residents and migrants between islands.     

The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited

Results of molecular studies regarding the phylogenetic placement of the order Ostropales and related taxa within Lecanoromycetes were thus far inconclusive. Some analyses placed the order as sister to the rest of Lecanoromycetes, while others inferred a position nested within Lecanoromycetes. We assembled a data set of 101 species including sequences from nuLSU rDNA, mtSSU rDNA, and the nuclear protein-coding RPB1 for each species to examine the cause of incongruencies in previously published phylogenies. MP, minimum evolution, and Bayesian analyses were performed using the combined three-region data set and the single-gene data sets. The position of Ostropales nested in Lecanoromycetes is confirmed in all single-gene and concatenated analyses, and a placement as sister to the rest of Lecanoromycetes is significantly rejected using two independent methods of alternative topology testing. Acarosporales and related taxa (Acarosporaceae group) are basal in Lecanoromycetes. However, if the these basal taxa are excluded from the analyses, Ostropales appear to be sister to the rest of Lecanoromycetes, suggesting different ingroup rooting as the cause for deviating topologies in previously published phylogenies.     

Malate dehydrogenase: a useful phylogenetic marker for the genus Aeromonas

The reconstruction of correct genealogies among biological entities, the estimation of the divergence time between organisms or the study of the different events that occur along evolutionary lineages are not always based on suitable genes. For reliable results, it is necessary to look at full-length sequences of genes under stabilizing selection (neutral or purifying) and behaving as good molecular clocks. In bacteria it has been proved that the malate dehydrogenase gene (mdh) can be used to determine the inter- and intraspecies divergence, and hence this gene constitutes a potential marker for phylogeny and bacterial population genetics. We have sequenced the full-length mdh gene in 36 type and reference strains of Aeromonas. The species grouping obtained in the phylogenetic tree derived from mdh sequences was in agreement with that currently accepted for the genus Aeromonas. The maximum likelihood models applied to our sequences indicated that the mdh gene is highly conserved among the Aeromonas species and the main evolutionary force acting on it is purifying selection. Only two sites under potential diversifying selection were identified (T 108 and S 193). In order to determine if these two residues could have an influence on the MDH structure, we mapped them in a three-dimensional model constructed from the sequence of A. hydrophila using the human mitochondrial MDH as a template. The presence of purifying selection together with the linear relationship between substitutions and gene divergence makes the mdh an excellent candidate gene for a phylogeny of Aeromonas and probably for other bacterial groups.     

On the phylogenetic position of the Okinawa woodpecker (Sapheopipo noguchii)

The Okinawa woodpecker Sapheopipo noguchii is the rarest extant woodpecker species. The monotypic genus Sapheopipo was considered to be a representative of an old lineage of woodpeckers that led to the Eurasian genera Picus and the Blythipicus–Gecinulus species. This view, based on similarities in color patterns, external morphology and foraging behavior, has been adopted in all major accounts of the family. The alternative view, that this woodpecker may be related to the widespread white-backed woodpecker Dendrocopos leucotos, which evolved distinctive subspecies on other East Asian islands, has not been generally accepted. We analyzed partial sequences of the mitochondrial cytochrome b (cyt b) gene to test these hypotheses. The data suggest that the Okinawa woodpecker is a member of the genus Dendrocopos, with white-backed woodpecker and great spotted woodpecker D. major as close relatives. Color patterns support the genetic results and indicate a closer relationship with the white-backed woodpecker. Consequently, the correct taxonomic designation of the Okinawa woodpecker would be Dendrocopos noguchii (Seebohm in Ibis 5(5):173–182, 1887) in the tribe Campetherini rather than Picini.This revised version was published online in February 2005 with corrections to tables 1 and 2.     

Evolution of the biochemical pathway for aromatic amino acid biosynthesis in Serpens flexibilis in relationship to its phylogenetic position

Given the availability of a reasonably complete phylogenetic tree constructed by means of modern nucleic acid sequencing techniques, it is sometimes possible to use biochemical-pathway characteristics as a basis to fine-tune the phylogenetic position of certain organisms making up the tree. A case in point in Serpens flexibilis, a helical bacterium shown by oligonucleotide cataloging to belong to the group Ia cluster of pseudomonads. The results show that within the group Ia pseudomonad cluster, S. flexibilis clusters with the Pseudomonas stutzeri/P. mendocina/P. alcaligenes/P. pseudoalcaligenes assemblage, which diverges from a lineage leading to P. aeruginosa and from yet another lineage leading to species of Azomonas and Azotobacter.     

The mitochondrial genome of the spinyhead croaker Collichthys lucida: genome organization and phylogenetic consideration

The complete mitochondrial genome of the spiny head croaker Collichthys lucida was determined in the present study. The mitochondrial DNA was 16,442 base pairs in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major non-coding control region, with the content and order of genes being similar to those in typical teleosts. Most of the genes of C. lucida were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pairs of genes overlapped: ATPase 8 and 6 and ND4L and ND4 by ten and seven nucleotides, respectively. The control region was unusually short at only 768bp, and absence of typical conserved blocks (CSB-D, CSB-E, and CSB-F). Phylogenetic analyses indicated that C. lucida was located in the cluster of fish species from the family Sciaenidae, supporting the traditional taxonomic classification of fish, and in the cluster of Serranidae, the divergence time in Plectropomus leopardus is longer than that among its coordinal species. On the other hand, phylogenetic analyses do not support the monophyletic of family Centracanthidae and genera Larimichthys and Collichthys, which is against the morphological results.     

The antennae of neopseustid moths: Morphology and phylogenetic implications, with special reference to the sensilla (Insecta, Lepidoptera, Neopseustidae)

The antennae of Lepidoptera Neopseustidae were examined with the scanning electron microscope. The studied species, Nematocentropus cfr. omeiensis, Neopseustis meyricki, Synempora andesae, Apoplania valdiviana and Apoplania penai possess nine types of antennal flagellum sensilla: multiporous large sensilla basiconica, multiporous thin sensilla basiconica, multiporous small sensilla basiconica, multiporous sensilla trichodea, multiporous sensilla coeloconica; uniporous sensilla chaetica; aporous sensilla chaetica, aporous stylus-shaped sensilla chaetica, aporous sensilla styloconica.The multiporous sensillum type here termed “multiporous large sensillum basiconicum” is unknown from other Lepidoptera and probably constitutes an autapomorphy of the family Neopseustidae. This sensillum type is remarkable by having a single base in female Apoplania and Synempora while in male Apoplania it has a bifid or trifid base, and in male Synempora it is composed of two or three incompletely separated hairs. This may be the first recorded example of a sexually dimorphic lepidopteran sensillum type. The stylus-shaped sensillum chaeticum is a primitive type which occurs only in some lower Lepidoptera.     

The celC gene, a new phylogenetic marker useful for taxonomic studies in Rhizobium

The celC gene codifies for a cellulase that fulfils a very significant role in the infection process of clover by Rhizobium leguminosarum. This gene is located in the celABC operon present in the chromosome of strains representing R. leguminosarum, Rhizobium etli and Rhizobium radiobacter whose genomes have been completely sequenced. Nevertheless, the existence of this gene in other species of the genus Rhizobium had not been investigated to date. In this study, the celC gene was analysed for the first time in several species of this genus isolated from legume nodules and plant tumours, in order to compare the celC phylogeny to those of other chromosomal and plasmidic genes. The results obtained showed that phylogenies of celC and chromosomal genes, such as rrs, recA and atpD, were completely congruent, whereas no relation was found with symbiotic or virulence genes. Therefore, the suitability and usefulness of the celC gene to differentiate species of the genus Rhizobium, especially those with closely related rrs genes, was highlighted. Consequently, the taxonomic status of several strains of the genus Rhizobium with completely sequenced genomes is also discussed.     

The phylogenetic position of the endemic flat-needle pinePinus krempfii (Pinaceae) from Vietnam, based on PCR-RFLP analysis of chloroplast DNA

Pinus krempfii is morphologically very unique as compared to otherPinus species by having flat leaf-like needles. Its taxonomic position has been problematic ever since its discovery. In this study, an attempt was made to infer the taxonomic status ofP. krempfii through restriction fragment length polymorphism analysis of 12 PCR amplified chloroplast (cp) DNA regions. Phylogenetic analysis was conducted using 10 representatives of the twoPinus subgenera:Strobus andPinus. In addition, to infer the position ofP. krempfii in Pinaceae in relation with other genera, 14 representatives of eight additional genera were included in the analysis. Our cpDNA-based results indicate that: 1)P. krempfii clearly belongs to the genusPinus. This result does not favour the creation of a new genusDucampopinus in Pinaceae for this taxon. 2) Within the genusPinus, P. krempfii is more allied with species in subgenusStrobus and differs distinctly from species in subgenusPinus. 3) Despite the similarity in certain morphological and anatomical leaf and wood characters toKeteleeria andPseudolarix, the cpDNA data do not support the hypothesis for close relationship betweenP. krempfii and these two genera.     

The phylogenetic position of Ovavesicula popilliae (Microsporidia) and its relationship to Antonospora and Paranosema based on small subunit rDNA analysis

Comparative small subunit rDNA sequence analyses, indicate that Ovavesicula popilliae, a microsporidian parasite of the Japanese beetle, Popillia japonica, represents a distant sister group to Paranosema and Antonospora. These three genera represent a second major group (the Nosema/Vairimorpha clade representing the first) of Microsopridia which infect terrestrial insects, suggesting independent origins for both groups. Phylogenetic analyses of Ovavesicula and other Microsporidia having a multi-sporous sporogony reveal that this condition is found in several unrelated taxa implying either that multi-sporous sporogony is the ancestral condition for Microsporidia or that it has multiple origins.     

The Lipomycetaceae,a model family for phylogenetic studies

The Lipomycetaceae (Endomycetales) are known from the generaDipodascopsis, Lipomyces andZygozyma with budding anamorphic states inMyxozyma. The family is easily recognized culturally and physiologically but is phenotypically and ecologically extremely diverse. This natural taxon is phylogenetically distinct from the Saccharomycetaceae, but probably related to the Dipodascaceae. The possible evolution of the lipomycetaceous anamorphs is discussed.     

Genetic diversity and phylogenetic position of the subclass Astomatia (Ciliophora) based on a sampling of six genera from West African oligochaetes (Glossoscolecidae, Megascolecidae), including description of the new genus Paraclausilocola n. gen

To more confidently assess phylogenetic relationships among astome ciliates, we obtained small subunit (SSU) rRNA sequences from nine species distributed in six genera and three families: Almophrya bivacuolata, Eudrilophrya complanata, Metaracoelophrya sp. 1, Metaracoelophrya sp. 2, Metaracoelophrya intermedia, Metaradiophrya sp., Njinella prolifera, Paraclausilocola constricta n. gen., n. sp., and Paraclausilocola elongata n. sp. The two new species in the proposed new clausilocolid genus Paraclausilocola n. gen. are astomes with no attachment apparatus, two files of contractile vacuoles, and an arc-like anterior suture that has differentiations of thigmotactic ciliature on the anterior ends of the left kineties of the upper surface. Phylogenetic analyses were undertaken using neighbor-joining, Bayesian inference, maximum likelihood, and maximum parsimony. The nine species of astomes formed a strongly supported clade, showing the subclass Astomatia to be monophyletic and a weakly supported sister clade to the scuticociliates. There were two strongly supported clades within the astomes. However, genera assigned to the same family were found in different clades, and genera assigned to the same order were found in both clades. Thus, astome taxa appear to be paraphyletic when morphology is used to assign species to genera.     

Head morphology of Caurinus (Boreidae, Mecoptera) and its phylogenetic implications

External and internal head structures of Caurinus dectes were examined and described in detail. The features are compared to conditions found in other groups of Antliophora. Caurinus is obviously crucial for the reconstruction of the mecopteran and antliophoran groundplan. It displays a remarkable series of plesiomorphic character states such as a complete clypeolabral suture, the presence of M. hypopharyngomandibularis (M. 13) and M. frontohypopharyngalis (M. 41), a subdivided clypeus, a short head without rostrum, a dorsal tentorial arm attached to the head capsule, the absence of a cranial dilator of the antenna, and large mandibles with a well developed apical tooth, two distinct subapical teeth, and a basal molar part. The first three plesiomorphic features render potential autapomorphies of Mecoptera in the traditional sense invalid. Autapomorphies of Caurinus are the distinctly flattened labrum, the absence of the labroepipharyngeal muscle, the very large size of M. 13, the strongly enlarged penultimate palpomeres, the partition of M. 41, the very strongly developed precerebral sucking chamber, strongly curved optic lobes, the presence of a large protocerebral extension in the genal region and deep posterior excavations of the protocerebrum. The maxillolabial plate, the absence of cardines as separate structures, the reduction of ocelli, and the origin of maxillary palp muscles on a median ridge or area of the maxillolabial plate are likely autapomorphies of Boreidae. Another potential autapomorphy of the family is the presence of longitudinal furrows on the mandibles. However, they are absent in Boreus. The thick strongly sclerotised, median ridge of the maxillolabial plate, the missing retractibility of the prementum, the absence of extrinsic labial muscles, and the presence of a median ridge on the prepharyngeal roof suggest a clade Boreus + Hesperoboreus. The origin of extrinsic maxillary muscles from the clypeus has probably evolved independently in Boreus and Hesperoboreus, and in Panorpa, respectively. The absence of M. craniolacinialis and the presence of a row of several subapical mandibular teeth are autapomorphies of Boreus. The presence of a specific intrinsic muscle of the salivary duct and a membranous galea enclosing the labrum and mandibular base are derived features shared by Boreidae and Pistillifera (galea absent in Nannochorista, Siphonaptera and Diptera). The loss of M. frontolabralis (M. 8) is a potential apomorphy of Mecoptera incl. Siphonaptera. A sister group relationship between Boreidae and Siphonaptera is not supported by characters of the adult head. Head structures of Siphonaptera are extremely modified in correlation with ectoparasitic habits.