Molecular phylogenies in Dolichopoda cave crickets and mtDNA rate calibration

Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs

Tribolium castaneum, the red flour beetle, is among the most well-studied eukaryotic genetic model organisms. Tribolium often serves as a comparative bridge from highly derived Drosophila traits to other organisms. Simultaneously, as a member of the most diverse order of metazoans, Coleoptera, Tribolium informs us about innovations that accompany hyper diversity. However, understanding the tempo and mode of evolutionary innovation requires well-resolved, time-calibrated phylogenies, which are not available for Tribolium. The most recent effort to understand Tribolium phylogenetics used two mitochondrial and three nuclear markers. The study concluded that the genus may be paraphyletic and reported a broad range for divergence time estimates. Here we employ recent advances in Bayesian methods to estimate the relationships and divergence times among Tribolium castaneum, T. brevicornis, T. confusum, T. freemani, and Gnatocerus cornutus using 1368 orthologs conserved across all five species and an independent substitution rate estimate. We find that the most basal split within Tribolium occurred ~86 Mya [95% HPD 85.90-87.04 Mya] and that the most recent split was between T. freemani and T. castaneum at ~14 Mya [95% HPD 13.55-14.00]. Our results are consistent with broader phylogenetic analyses of insects and suggest that Cenozoic climate changes played a role in the Tribolium diversification.

Molecular evolution of the pDo500 satellite DNA family in Dolichopoda cave crickets (Rhaphidophoridae)

BACKGROUND

Non-coding satellite DNA (satDNA) usually has a high turn-over rate frequently leading to species specific patterns. However, some satDNA families evolve more slowly and can be found in several related species. Here, we analyzed the mode of evolution of the pDo500 satDNA family of Dolichopoda cave crickets. In addition, we discuss the potential of slowly evolving satDNAs as phylogenetic markers.

RESULTS

We sequenced 199 genomic or PCR amplified satDNA repeats of the pDo500 family from 12 Dolichopoda species. For the 38 populations under study, 39 pDo500 consensus sequences were deduced. Phylogenetic analyses using Bayesian, Maximum Parsimony, and Maximum Likelihood approaches yielded largely congruent tree topologies. The vast majority of pDo500 sequences grouped according to species designation. Scatter plots and statistical tests revealed a significant correlation between genetic distances for satDNA and mitochondrial DNA. Sliding window analyses showed species specific patterns of variable and conserved regions. The evolutionary rate of the pDo500 satDNA was estimated to be 1.63-1.78% per lineage per million years.

CONCLUSIONS

The pDo500 satDNA evolves gradually at a rate that is only slightly faster than previously published rates of insect mitochondrial COI sequences. The pDo500 phylogeny was basically congruent with the previously published mtDNA phylogenies. Accordingly, the slowly evolving pDo500 satDNA family is indeed informative as a phylogenetic marker.

Relationships among pest flour beetles of the genus Tribolium (Tenebrionidae) inferred from multiple molecular markers

Model species often provide initial hypotheses and tools for studies of development, genetics and molecular evolution in closely related species. Flour beetles of the genus Tribolium Macleay (1825) are one group with potential for such comparative studies. Tribolium castaneum (Herbst 1797) is an increasingly useful developmental genetic system. The convenience with which congeneric and other species of tenebrionid flour beetles can be reared in the laboratory makes this group attractive for comparative studies on a small phylogenetic scale. Here we present the results of phylogenetic analyses of relationships among the major pest species of Tribolium based on two mitochondrial and three nuclear markers (cytochrome oxidase 1, 16S ribosomal DNA, wingless, 28S ribosomal DNA and histone H3). The utility of partitioning the dataset in a manner informed by biological structure and function is demonstrated by comparing various partitioning strategies. In parsimony and partitioned Bayesian analyses of the combined dataset, the castaneum and confusum species groups are supported as monophyletic and as each other's closest relatives. However, a sister group relationship between this clade and Tribolium brevicornis (Leconte 1859) is not supported. The inferred phylogeny provides an evolutionary framework for comparative studies using flour beetles.

Molecular phylogeography of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae): a scenario suggested by mitochondrial DNA

This study focuses on the phylogenetic relationships among a number of West-Mediterranean cave crickets species belonging to Dolichopoda; primarily a Mediterranean genus, distributed from eastern Pyrenees to Caucasus. In this paper, 11 Dolichopoda species from the French Pyrenees (D. linderi), the island of Corsica (D. bormansi and D. cyrnensis), and northern, central, and southern Italy (D. ligustica, D. schiavazzii, D. aegilion, D. baccettii, D. laetitiae, D. geniculata, D. capreensis, and D. palpata) were studied. Two more species, one from the Caucasus, D. euxina, and one from Greece, D. remyi, were also included in the analyses, together with more distant species within the same family to be used as outgroups. Fifteen hundred base pairs of mitochondrial DNA, corresponding to the small subunit of the ribosomal RNA (16S rRNA) and to the subunit I of the cytochrome oxidase I (COI), were sequenced in order to clarify the phylogenetic relationships and biogeography of this group of Mediterranean cave crickets. The molecular data are congruent with a phylogeographic pattern; with the geographically close species also the most related ones. Based on mtDNA divergence, the present-day distribution of genetic diversity seems to have been impacted by climatic events due to glacial and interglacial cycles that have characterized the Pleistocene era.

The internal transcribed spacers (ITS1 and ITS2) of the rDNA differentiates the bark beetle forest pests Tomicus destruens and T. piniperda

The bark beetles species Tomicus destruens and T. piniperda constitute one of the main pests of European and Asian forests. T. destruens has been thought to be the same species as T. piniperda by some authors. A rapid PCR-based method using internal transcribed spacers (ITS1 and ITS2) of the ribosomal DNA has been developed in order to identifying these two species. We have studied differences in the size of the ITS1, and differences in the sequence and restriction patterns of the ITS2 in 75 individuals of both species. The results indicate a size difference of about 100 bp in the ITS1 of T. destruens and T. piniperda. The size of the ITS2 spacer is similar in both species (approximately 600 bp). However, the sequence is consistently different between T. destruens and T. piniperda in all populations analysed, showing some characteristic indels. Differences in the restriction target in both species for the enzymes HincII and DraI produce different band patterns in agarose NuSieve 5% gel electrophoresis. These data suggest the validity of T. destruens as a phylogenetically differentiated entity from T. piniperda. The phylogenetic analysis of a 789 bp fragment of the 3' end of the cytochrome oxidase I gene (COI) agrees with the two groupings obtained with the ITS2, showing a phylogenetic clustering rather than a phylogeographic structure.

A molecular biogeographic analysis of the relationship between North American melanoploid grasshoppers and their Eurasian and South American relatives

The Melanoplinae constitute one of the two largest subfamilies of Acrididae. Distributed mainly throughout the New World and parts of Eurasia, this group of grasshoppers includes over 100 genera and 800 species. Over the past five decades there has been considerable speculation on the origins of North and South American taxa. The most favored hypothesis proposes an ancient division of Laurasian taxa accompanying the separation of North America and Eurasia, with subsequent radiations within those continents, followed by a recent incursion of Nearctic melanoplines into the southern hemisphere with the establishment of the Isthmus of Panama. This research tests that scenario by phylogenetic analysis using as characters portions of five mitochondrial gene sequences, totaling 2285 bp. Three tree-building methods, maximum-parsimony, neighbor-joining, and maximum-likelihood, strongly support the different view that melanopline grasshoppers originated somewhere in the Americas and spread to the Old World. The feasibility of these findings is discussed within a geological context.

Wolbachia infections in native and introduced populations of fire ants (Solenopsis spp.)

Wolbachia are cytoplasmically inherited bacteria that induce a variety of effects with fitness consequences on host arthropods, including cytoplasmic incompatibility, parthenogenesis, male-killing and feminization. We report here the presence of Wolbachia in native South American populations of the fire ant Solenopsis invicta, but the apparent absence of the bacteria in introduced populations of this pest species in the USA. The Wolbachia strains in native S. invicta are of two divergent types (A and B), and the frequency of infection varies dramatically between geographical regions and social forms of this host. Survey data reveal that Wolbachia also are found in other native fire ant species within the Solenopsis saevissima species complex from South America, including S. richteri. This latter species also has been introduced in the USA, where it lacks Wolbachia. Sequence data reveal complete phylogenetic concordance between mtDNA haplotype in S. invicta and Wolbachia infection type (A or B). In addition, the mtDNA and associated group A Wolbachia strain in S. invicta are more closely related to the mtDNA and Wolbachia strain found in S. richteri than they are to the mtDNA and associated group B Wolbachia in S. invicta. These data are consistent with historical introgression of S. richteri cytoplasmic elements into S. invicta populations, resulting in enhanced infection and mtDNA polymorphisms in S. invicta. Wolbachia may have significant fitness effects on these hosts (either directly or by cytoplasmic incompatibility) and therefore these microbes potentially could be used in biological control programmes to suppress introduced fire ant populations.

Hybrid origins of honeybees from italy (Apis mellifera ligustica) and sicily (A. m. sicula)

The genetic variability of honeybee populations Apis mellifera ligustica, in continental Italy, and of A. m. sicula, in Sicily, was investigated using nuclear (microsatellite) and mitochondrial markers. Six populations (236 individual bees) and 17 populations (664 colonies) were, respectively, analysed using eight microsatellite loci and DraI restriction fragment length polymorphism (RFLP) of the cytochrome oxidase I (COI)-cytochrome oxidase II (COII) region. Microsatellite loci globally confirmed the southeastern European heritage of both subspecies (evolutionary branch C). However, A. m. ligustica mitochondrial DNA (mtDNA) appeared to be a composite of the two European (M and C) lineages over most of the Italian peninsula, and only mitotypes from the African (A) lineage were found in A. m. sicula samples. This demonstrates a hybrid origin for both subspecies. For A. m. ligustica, the most widely exported subspecies, this hybrid origin has long been obscured by the fact that in the main area of queen production (from which most of the previous ligustica bee samples originated) the M mitochondrial lineage is absent, whereas it is present almost everywhere else in Italy. This presents a new view of the evolutionary history of European honeybees. For instance, the Iberian peninsula was considered as the unique refuge for the M branch during the quaternary ice periods. Our results show that the Apennine peninsula played a similar role. The differential distribution of nuclear and mitochondrial markers observed in Italy seems to be a general feature of introgressed honeybee populations. Presumably, it stems from the social nature of the species in which both genome compartments are differentially affected by the two (individual and colonial) reproduction levels.

Phylogenetics of social behavior in Australian gall-forming thrips: evidence from mitochondrial DNA sequence, adult morphology and behavior, and gall morphology

Six species of Australian gall-forming thrips (Insecta: Thysanoptera) on Acacia exhibit soldier castes, individuals with reduced wings and enlarged forelegs that defend their gall against interspecific invaders. We used data from two mitochondrial genes (cytochrome oxidase I and 16S rDNA), adult morphology and behavior, and gall morphology to infer a phylogeny for Acacia gall-forming thrips with and without soldiers, and we used this phylogeny to evaluate hypotheses concerning soldier evolution. Phylogenies inferred from each data set analyzed separately yielded large numbers of most-parsimonious trees and weak support for most nodes. However, when analyzed together the data sets complemented and reinforced one another in such a way as to yield a well-resolved phylogeny. Our phylogeny implies that soldiers originated once or twice early in the history of this clade, that soldiers were lost once or twice, and that soldiers evolved from winged dispersers rather than from nonsoldier within-gall reproductive offspring of foundresses. The phylogeny also provides evidence for long-term morphological stasis, an ancient split between eastern and western gall thrips species, and a high degree of conservatism in host-plant affiliations.

Contrasting levels of variability between cytoplasmic genomes and incompatibility types in the mosquito Culex pipiens

Reproductive incompatibilities called cytoplasmic incompatibilities are known to affect a large number of arthropod species and are mediated by Wolbachia, a maternally transmitted microorganism. The crossing relationships between strains of potential hosts define their incompatibility types and it is generally assumed that differences between strains of Wolbachia induce different crossing types. Among all the described host species, the mosquito, Culex pipiens, displays the greatest variability of cytoplasmic incompatibility crossing types. We analysed mitochondrial and bacterial DNA variability in Culex pipiens in order to investigate some possible causes of incompatibility crossing type variability. We sequenced fragments of the ftsZ gene, and the A + T-rich control region of the mtDNA. We also sequenced the second subunit of the mitochondrial cytochrome oxidase (COII) gene, in Culex pipiens and a closely related species, C. torrentium, in order to verify the usefulness of the A + T-rich region for the present purposes. No variability was found in the Wolbachia ftsZ gene fragment, and very limited variation of the mitochondrial marker whatever the compatibility type or the origin of the host. A low variability was found in the A + T-rich region and comparison of divergence of the A + T-rich region and COII gene between C. pipiens and C. torrentium did not reveal any special constraints affecting this region. In contrast to observations in other host species, variability of incompatibility crossing types is not due to multiple infections by distantly related Wolbachia strains.