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1.
Genome Biol Evol ; 16(1)2024 Jan 05.
Article in English | MEDLINE | ID: mdl-38190231

ABSTRACT

We present a high-quality assembly and annotation of the periodical cicada species, Magicicada septendecula (Hemiptera: Auchenorrhyncha: Cicadidae). Periodical cicadas have a significant ecological impact, serving as a food source for many mammals, reptiles, and birds. Magicicada are well known for their massive emergences of 1 to 3 species that appear in different locations in the eastern United States nearly every year. These year classes ("broods") emerge dependably every 13 or 17 yr in a given location. Recently, it has become clear that 4-yr early or late emergences of a sizeable portion of a population are an important part of the history of brood formation; however, the biological mechanisms by which they track the passage of time remain a mystery. Using PacBio HiFi reads in conjunction with Hi-C proximity ligation data, we have assembled and annotated the first whole genome for a periodical cicada, an important resource for future phylogenetic and comparative genomic analysis. This also represents the first quality genome assembly and annotation for the Hemipteran superfamily Cicadoidea. With a scaffold N50 of 518.9 Mb and a complete BUSCO score of 96.7%, we are confident that this assembly will serve as a vital resource toward uncovering the genomic basis of periodical cicadas' long, synchronized life cycles and will provide a robust framework for further investigations into these insects.


Subject(s)
Hemiptera , Animals , United States , Phylogeny , Hemiptera/genetics , Life Cycle Stages , Genomics , Chromosomes , Mammals/genetics
2.
Sci Rep ; 12(1): 20559, 2022 11 29.
Article in English | MEDLINE | ID: mdl-36446872

ABSTRACT

Host-microbe interactions are intimately linked to eukaryotic evolution, particularly in sap-sucking insects that often rely on obligate microbial symbionts for nutrient provisioning. Cicadas (Cicadidae: Auchenorrhyncha) specialize on xylem fluid and derive many essential amino acids and vitamins from intracellular bacteria or fungi (Hodgkinia, Sulcia, and Ophiocordyceps) that are propagated via transmission from mothers to offspring. Despite the beneficial role of these non-gut symbionts in nutrient provisioning, the role of beneficial microbiota within the gut remains unclear. Here, we investigate the relative abundance and impact of host phylogeny and ecology on gut microbial diversity in cicadas using 16S ribosomal RNA gene amplicon sequencing data from 197 wild-collected cicadas and new mitochondrial genomes across 38 New Zealand cicada species, including natural hybrids between one pair of two species. We find low abundance and a lack of phylogenetic structure and hybrid effects but a significant role of elevation in explaining variation in gut microbiota.


Subject(s)
Alphaproteobacteria , Gastrointestinal Microbiome , Hemiptera , Animals , Hemiptera/genetics , Phylogeny , Gastrointestinal Microbiome/genetics , New Zealand
3.
Sci Rep ; 12(1): 16967, 2022 10 10.
Article in English | MEDLINE | ID: mdl-36217008

ABSTRACT

Periodical cicadas (Hemiptera: Magicicada) have coevolved with obligate bacteriome-inhabiting microbial symbionts, yet little is known about gut microbial symbiont composition or differences in composition among allochronic Magicicada broods (year classes) which emerge parapatrically or allopatrically in the eastern United States. Here, 16S rRNA amplicon sequencing was performed to determine gut bacterial community profiles of three periodical broods, including II (Connecticut and Virginia, 2013), VI (North Carolina, 2017), and X (Maryland, 2021, and an early emerging nymph collected in Ohio, 2017). Results showed similarities among all nymphal gut microbiomes and between morphologically distinct 17-year Magicicada, namely Magicicada septendecim (Broods II and VI) and 17-year Magicicada cassini (Brood X) providing evidence of a core microbiome, distinct from the microbiome of burrow soil inhabited by the nymphs. Generally, phyla Bacteroidetes [Bacteroidota] (> 50% relative abundance), Actinobacteria [Actinomycetota], or Proteobacteria [Pseudomonadota] represented the core. Acidobacteria and genera Cupriavidus, Mesorhizobium, and Delftia were prevalent in nymphs but less frequent in adults. The primary obligate endosymbiont, Sulcia (Bacteroidetes), was dominant amongst core genera detected. Chryseobacterium were common in Broods VI and X. Chitinophaga, Arthrobacter, and Renibacterium were common in Brood X, and Pedobacter were common to nymphs of Broods II and VI. Further taxonomic assignment of unclassified Alphaproteobacteria sequencing reads allowed for detection of multiple copies of the Hodgkinia 16S rRNA gene, distinguishable as separate operational taxonomic units present simultaneously. As major emergences of the broods examined here occur at 17-year intervals, this study will provide a valuable comparative baseline in this era of a changing climate.


Subject(s)
Gastrointestinal Microbiome , Hemiptera , Animals , Bacteria/genetics , Gastrointestinal Microbiome/genetics , Hemiptera/genetics , RNA, Ribosomal, 16S/genetics , Soil , United States
4.
Syst Biol ; 71(6): 1504-1523, 2022 10 12.
Article in English | MEDLINE | ID: mdl-35708660

ABSTRACT

Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the anchored hybrid enrichment markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned data set, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after the removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution. [Auchenorrhyncha; base-composition bias; Cicadidae; Cicadoidea; Hemiptera; phylogenetic conflict.].


Subject(s)
Hemiptera , Animals , Hemiptera/genetics , High-Throughput Nucleotide Sequencing , Insecta/genetics , Phylogeny
5.
Syst Biol ; 71(4): 921-928, 2022 06 16.
Article in English | MEDLINE | ID: mdl-32915964

ABSTRACT

If all nucleotide sites evolved at the same rate within molecules and throughout the history of lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved to any other with equal probability, if all taxa could be sampled, if diversification happened at well-spaced intervals, and if all gene segments had the same history, then tree building would be easy. But of course, none of those conditions are true. Hence, the need for evaluating the information content and accuracy of phylogenetic trees. The symposium for which this historical essay and presentation were developed focused on the importance of phylogenetic support, specifically branch support for individual clades. Here, I present a timeline and review significant events in the history of systematics that set the stage for the development of the sophisticated measures of branch support and examinations of the information content of data highlighted in this symposium. [Bayes factors; bootstrap; branch support; concordance factors; internode certainty; posterior probabilities; spectral analysis; transfer bootstrap expectation.].


Subject(s)
Nucleotides , Bayes Theorem , Phylogeny , Probability
6.
Annu Rev Entomol ; 67: 457-482, 2022 01 07.
Article in English | MEDLINE | ID: mdl-34623904

ABSTRACT

Apart from model organisms, 13- and 17-year periodical cicadas (Hemiptera: Cicadidae: Magicicada) are among the most studied insects in evolution and ecology. They are attractive subjects because they predictably emerge in large numbers; have a complex biogeography shaped by both spatial and temporal isolation; and include three largely sympatric, parallel species groups that are, in a sense, evolutionary replicates. Magicicada are also relatively easy to capture and manipulate, and their spectacular, synchronized mass emergences facilitate outreach and citizen science opportunities. Since the last major review, studies of Magicicada have revealed insights into reproductive character displacement and the nature of species boundaries, provided additional examples of allochronic speciation, found evidence for repeated and parallel (but noncontemporaneous) evolution of 13- and 17-year life cycles, quantified the amount and direction of gene flow through time, revealed phylogeographic patterning resulting from paleoclimate change, examined the timing of juvenile development, and created hypotheses for the evolution of life-cycle control and the future effects of climate changeon Magicicada life cycles. New ecological studies have supported and questioned the role of prime numbers in Magicicada ecology and evolution, found bidirectional shifts in population size over generations, quantified the contribution of Magicicada to nutrient flow in forest ecosystems, and examined behavioral and biochemical interactions between Magicicada and their fungal parasites and bacterial endosymbionts.


Subject(s)
Hemiptera , Animals , Ecology , Ecosystem , Hemiptera/genetics , Hemiptera/microbiology , Humans , Life Cycle Stages , Phylogeography
7.
Zootaxa ; 5078(1): 170, 2021 Dec 08.
Article in English | MEDLINE | ID: mdl-35390831

ABSTRACT

The genus Chilecicada Sanborn, 2014 is shown to be a complex of closely related species rather than a monospecific genus. Chilecicada citatatemporaria Sanborn Cole n. sp., C. culenesensis Sanborn Cole n. sp., C. curacaviensis Sanborn Cole n. sp., C. impartemporaria Sanborn Cole n. sp., C. magna Sanborn Cole n. sp., C. mapuchensis Sanborn n. sp., C. oraria Sanborn Cole n. sp., C. parrajaraorum Sanborn n. sp., C. partemporaria Sanborn Cole n. sp., C. pehuenchesensis Sanborn Cole n. sp., C. trifascia Sanborn n. sp., C. trifasciunca Sanborn Cole n. sp., and C. viridicitata Sanborn Cole n. sp. are described as new. Chilecicada occidentis Walker, 1850 is re-described to facilitate separation of the new species from the only previously known species. Song and cytochrome oxidase I analysis available for most species support the separation of the new taxa from the type species of the genus. Known species distributions and a key to the species of the genus are also provided. The new species increases the known cicada diversity 61.9% to 34 species, 91.2% of which are endemic to Chile.


Subject(s)
Hemiptera , Animals , Chile
8.
Zootaxa ; 4747(1): zootaxa.4747.1.5, 2020 Mar 02.
Article in English | MEDLINE | ID: mdl-32230121

ABSTRACT

A recent paper by Ruschel Campos (2019) on "leaf-winged" cicadas proposed a significant reorganization of the cicada tribe Hemidictyini Distant, 1905g, including synonymization of the monogeneric tribe Lacetasini Moulds Marshall, 2018 following the results of a cladistic parsimony analysis of morphological characters. In this study, we reconsider and revise the morphological analysis of Ruschel Campos and obtain new genetic data for Hemidictya. We find that their study suffers from a limited taxon sample, inappropriate outgroup selection, and misinterpretation of genitalic characters (uncus vs. claspers). We show that Hemidictyini sensu Ruschel Campos includes members of multiple tribes and subfamilies, and we conclude that some of the taxonomic transfers by Ruschel Campos are not supported. The two most similar and leaf-like cicadas, Hemidictya Burmeister, 1835 (South America) and Hovana Distant, 1905g (Madagascar), are probably not closely related but rather an excellent example of convergent evolution. Lacetasini is not a junior synonym of the Hemidictyini but a distinct part of the Tettigomyiinae Distant, 1905g as originally classified. We return or transfer the genera Lacetas Karsch, 1890, Iruana Distant, 1905g, Bafutalna Boulard, 1993, and Murphyalna Boulard, 2012 to the Lacetasini. With the transfer of all genera of Iruanina Boulard, 1993 and Bafutalnina Boulard, 1993 to Lacetasini and with Lacetas transferred to the Iruanina, Lacetasini n. syn. becomes a subjective junior synonym of Iruanini rev. stat. in the Tettigomyiinae. We assign Hovana to Hovanini n. tribe in the Tettigomyiinae and Sapantanga Distant, 1905g to Sapantangini n. tribe in the Tibicininae Distant, 1905b. We propose that Hemidictyini sensu novo contains only the genus Hemidictya and we assign the tribe to Tibicininae with a revised diagnosis.


Subject(s)
Hemiptera , Animals , Genitalia
9.
Fungal Ecol ; 41: 147-164, 2019 Oct.
Article in English | MEDLINE | ID: mdl-31768192

ABSTRACT

Entomopathogenic fungi routinely kill their hosts before releasing infectious spores, but a few species keep insects alive while sporulating, which enhances dispersal. Transcriptomics- and metabolomics-based studies of entomopathogens with post-mortem dissemination from their parasitized hosts have unraveled infection processes and host responses. However, the mechanisms underlying active spore transmission by Entomophthoralean fungi in living insects remain elusive. Here we report the discovery, through metabolomics, of the plant-associated amphetamine, cathinone, in four Massospora cicadina-infected periodical cicada populations, and the mushroom-associated tryptamine, psilocybin, in annual cicadas infected with Massospora platypediae or Massospora levispora, which likely represent a single fungal species. The absence of some fungal enzymes necessary for cathinone and psilocybin biosynthesis along with the inability to detect intermediate metabolites or gene orthologs are consistent with possibly novel biosynthesis pathways in Massospora. The neurogenic activities of these compounds suggest the extended phenotype of Massospora that modifies cicada behavior to maximize dissemination is chemically-induced.

10.
Mol Biol Evol ; 36(6): 1187-1200, 2019 06 01.
Article in English | MEDLINE | ID: mdl-30850829

ABSTRACT

The mass application of whole mitogenome (MG) sequencing has great potential for resolving complex phylogeographic patterns that cannot be resolved by partial mitogenomic sequences or nuclear markers. North American periodical cicadas (Magicicada) are well known for their periodical mass emergence at 17- and 13-year intervals in the north and south, respectively. Magicicada comprises three species groups, each containing one 17-year species and one or two 13-year species. Within each life cycle, single-aged cohorts, called broods, of periodical cicadas emerge in different years, and most broods contain members of all three species groups. There are 12 and three extant broods of 17- and 13-year cicadas, respectively. The phylogeographic relationships among the populations and broods within the species groups have not been clearly resolved. We analyzed 125 whole MG sequences from all broods and seven species within three species groups to ascertain the divergence history of the geographic and allochronic populations and their life cycles. Our mitogenomic phylogeny analysis clearly revealed that each of the three species groups had largely similar phylogeographic subdivisions (east, middle, and west) and demographic histories (rapid population expansion after the last glacial period). The mitogenomic phylogeny also partly resolved the brood diversification process, which could be explained by hypothetical temporary life cycle shifts, and showed that none of the 13- and 17-year species within the species groups was monophyletic, possibly due to gene flow between them. Our findings clearly reveal phylogeographic structures in the three Magicicada species groups, demonstrating the advantage of whole MG sequence data in phylogeographic studies.


Subject(s)
Biological Evolution , Genome, Mitochondrial , Hemiptera/genetics , Animals , Genetic Variation , Phylogeography , United States
11.
J Hered ; 110(2): 247-256, 2019 03 05.
Article in English | MEDLINE | ID: mdl-30590568

ABSTRACT

Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.


Subject(s)
Genome, Mitochondrial , Genomics , Hemiptera/genetics , Animals , Anticodon , DNA, Ribosomal Spacer , Gene Order , Genetic Variation , Genomics/methods , Genotype , Locus Control Region , Phylogeny , RNA, Transfer/genetics , Symbiosis
12.
mBio ; 9(6)2018 11 13.
Article in English | MEDLINE | ID: mdl-30425149

ABSTRACT

For insects that depend on one or more bacterial endosymbionts for survival, it is critical that these bacteria are faithfully transmitted between insect generations. Cicadas harbor two essential bacterial endosymbionts, "Candidatus Sulcia muelleri" and "Candidatus Hodgkinia cicadicola." In some cicada species, Hodgkinia has fragmented into multiple distinct but interdependent cellular and genomic lineages that can differ in abundance by more than two orders of magnitude. This complexity presents a potential problem for the host cicada, because low-abundance but essential Hodgkinia lineages risk being lost during the symbiont transmission bottleneck from mother to egg. Here we show that all cicada eggs seem to receive the full complement of Hodgkinia lineages, and that in cicadas with more complex Hodgkinia this outcome is achieved by increasing the number of Hodgkinia cells transmitted by up to 6-fold. We further show that cicada species with varying Hodgkinia complexity do not visibly alter their transmission mechanism at the resolution of cell biological structures. Together these data suggest that a major cicada adaptation to changes in endosymbiont complexity is an increase in the number of Hodgkinia cells transmitted to each egg. We hypothesize that the requirement to increase the symbiont titer is one of the costs associated with Hodgkinia fragmentation.IMPORTANCE Sap-feeding insects critically rely on one or more bacteria or fungi to provide essential nutrients that are not available at sufficient levels in their diets. These microbes are passed between insect generations when the mother places a small packet of microbes into each of her eggs before it is laid. We have previously described an unusual lineage fragmentation process in a nutritional endosymbiotic bacterium of cicadas called Hodgkinia In some cicadas, a single Hodgkinia lineage has split into numerous related lineages, each performing a subset of original function and therefore each required for normal host function. Here we test how this splitting process affects symbiont transmission to eggs. We find that cicadas dramatically increase the titer of Hodgkinia cells passed to each egg in response to lineage fragmentation, and we hypothesize that this increase in bacterial cell count is one of the major costs associated with endosymbiont fragmentation.


Subject(s)
Hemiptera/microbiology , Hemiptera/physiology , Host Microbial Interactions , Symbiosis , Alphaproteobacteria/genetics , Animals , Evolution, Molecular , Female , Genome, Bacterial , Ovum/microbiology , Phylogeny
13.
Zootaxa ; 4424(1): 1-64, 2018 May 28.
Article in English | MEDLINE | ID: mdl-30313477

ABSTRACT

A molecular phylogeny and a review of family-group classification are presented for 137 species (ca. 125 genera) of the insect family Cicadidae, the true cicadas, plus two species of hairy cicadas (Tettigarctidae) and two outgroup species from Cercopidae. Five genes, two of them mitochondrial, comprise the 4992 base-pair molecular dataset. Maximum-likelihood and Bayesian phylogenetic results are shown, including analyses to address potential base composition bias. Tettigarcta is confirmed as the sister-clade of the Cicadidae and support is found for three subfamilies identified in an earlier morphological cladistic analysis. A set of paraphyletic deep-level clades formed by African genera are together named as Tettigomyiinae n. stat. Taxonomic reassignments of genera and tribes are made where morphological examination confirms incorrect placements suggested by the molecular tree, and 11 new tribes are defined (Arenopsaltriini n. tribe, Durangonini n. tribe, Katoini n. tribe, Lacetasini n. tribe, Macrotristriini n. tribe, Malagasiini n. tribe, Nelcyndanini n. tribe, Pagiphorini n. tribe, Pictilini n. tribe, Psaltodini n. tribe, and Selymbriini n. tribe). Tribe Tacuini n. syn. is synonymized with Cryptotympanini, and Tryellina n. syn. is synonymized with an expanded Tribe Lamotialnini. Tribe Hyantiini n. syn. is synonymized with Fidicinini. Tribe Sinosenini is transferred to Cicadinae from Cicadettinae, Cicadatrini is moved to Cicadettinae from Cicadinae, and Ydiellini and Tettigomyiini are transferred to Tettigomyiinae n. stat from Cicadettinae. While the subfamily Cicadinae, historically defined by the presence of timbal covers, is weakly supported in the molecular tree, high taxonomic rank is not supported for several earlier clades based on unique morphology associated with sound production.


Subject(s)
Hemiptera , Phylogeny , Animals , Bayes Theorem , Insecta
14.
Commun Biol ; 1: 26, 2018.
Article in English | MEDLINE | ID: mdl-30271912

ABSTRACT

Periodical cicadas comprise three species groups containing three pairs of 13- and 17-year life cycle species showing parallel divergence, along with a more anciently diverged 13-year species (Magicicda tredecim). The mechanism and genetic basis of this parallel divergence is unknown. Here we use orthologous transcriptome sequences to explore the demographic processes and genomic evolution associated with parallel life cycle divergence. The three 13- and 17-year species pairs have similar demographic histories, and the two life cycles diverged 200,000-100,000 years ago. Interestingly, these life cycle differences have been maintained despite substantial gene flow between 13- and 17-year species within species groups, which is possible during co-emergences. Sequence divergence between 13- and 17-year species in each species group (excluding M. tredecim) is minimal, and we find no shared divergent single-nucleotide polymorphisms (SNPs) or loci associated with all instances of life cycle divergence. The two life cycles may be controlled by highly limited genomic differences.

15.
PeerJ ; 6: e5282, 2018.
Article in English | MEDLINE | ID: mdl-30083444

ABSTRACT

The periodical cicadas of North America (Magicicada spp.) are well-known for their long life cycles of 13 and 17 years and their mass synchronized emergences. Although periodical cicada life cycles are relatively strict, the biogeographic patterns of periodical cicada broods, or year-classes, indicate that they must undergo some degree of life cycle switching. We present a new map of periodical cicada Brood V, which emerged in 2016, and demonstrate that it consists of at least four distinct parts that span an area in the United States stretching from Ohio to Long Island. We discuss mtDNA haplotype variation in this brood in relation to other periodical cicada broods, noting that different parts of this brood appear to have different origins. We use this information to refine a hypothesis for the formation of periodical cicada broods by 1- and 4-year life cycle jumps.

16.
Proc Natl Acad Sci U S A ; 115(2): E226-E235, 2018 01 09.
Article in English | MEDLINE | ID: mdl-29279407

ABSTRACT

Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over the last 4 million years, resulting in complexes of between two and six distinct Hodgkinia lineages per host. Individual genomes in these symbiotic complexes differ dramatically in relative abundance, genome size, organization, and gene content. Each Hodgkinia lineage retains a small set of core genes involved in genetic information processing, but the high level of gene loss experienced by all genomes suggests that extensive sharing of gene products among symbiont cells must occur. In total, Hodgkinia complexes that consist of multiple lineages encode nearly complete sets of genes present on the ancestral single lineage and presumably perform the same functions as symbionts that have not undergone splitting. However, differences in the timing of the splits, along with dissimilar gene loss patterns on the resulting genomes, have led to very different outcomes of lineage splitting in extant cicadas.


Subject(s)
Bacteria/classification , Bacteria/genetics , Bacterial Physiological Phenomena/genetics , Hemiptera/microbiology , Symbiosis/physiology , Animals , Biological Evolution , Chile , Genetic Variation , Genome, Bacterial , Phylogeny
17.
Curr Biol ; 27(22): 3568-3575.e3, 2017 Nov 20.
Article in English | MEDLINE | ID: mdl-29129532

ABSTRACT

When a free-living bacterium transitions to a host-beneficial endosymbiotic lifestyle, it almost invariably loses a large fraction of its genome [1, 2]. The resulting small genomes often become stable in size, structure, and coding capacity [3-5], as exemplified by Sulcia muelleri, a nutritional endosymbiont of cicadas. Sulcia's partner endosymbiont, Hodgkinia cicadicola, similarly remains co-linear in some cicadas diverged by millions of years [6, 7]. But in the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has split into dozens of tiny, gene-sparse circles that sometimes reside in distinct Hodgkinia cells [8]. Previous data suggested that all other Magicicada species harbor complex Hodgkinia populations, but the timing, number of origins, and outcomes of the splitting process were unknown. Here, by sequencing Hodgkinia metagenomes from the remaining six Magicicada and two sister species, we show that each Magicicada species harbors Hodgkinia populations of at least 20 genomic circles. We find little synteny among the 256 Hodgkinia circles analyzed except between the most closely related cicada species. Gene phylogenies show multiple Hodgkinia lineages in the common ancestor of Magicicada and its closest known relatives but that most splitting has occurred within Magicicada and has given rise to highly variable Hodgkinia gene dosages among species. These data show that Hodgkinia genome degradation has proceeded down different paths in different Magicicada species and support a model of genomic degradation that is stochastic in outcome and nonadaptive for the host. These patterns mirror the genomic instability seen in some mitochondria.


Subject(s)
Hemiptera/genetics , Hemiptera/microbiology , Symbiosis/genetics , Animals , Bacteria/genetics , Biological Evolution , DNA, Circular/genetics , Genome, Bacterial , Genomics , Phylogeny , Sequence Analysis, DNA/methods
18.
Mol Phylogenet Evol ; 116: 172-181, 2017 11.
Article in English | MEDLINE | ID: mdl-28830831

ABSTRACT

Phylogenetic studies of multiple independently inherited nuclear genes considered in combination with patterns of inheritance of organelle DNA have provided considerable insight into the history of species evolution. In particular, investigations of cicadas in the New Zealand genus Kikihia have identified interesting cases where mitochondrial DNA (mtDNA) crosses species boundaries in some species pairs but not others. Previous phylogenetic studies focusing on mtDNA largely corroborated Kikihia species groups identified by song, morphology and ecology with the exception of a unique South Island mitochondrial haplotype clade-the Westlandica group. This newly identified group consists of diverse taxa previously classified as belonging to three different sub-generic clades. We sequenced five nuclear loci from multiple individuals from every species of Kikihia to assess the nuclear gene concordance for this newly-identified mtDNA lineage. Bayes Factor analysis of the constrained phylogeny suggests some support for the mtDNA-based hypotheses, despite the fact that neither concatenation nor multiple species tree methods resolve the Westlandica group as monophyletic. The nuclear analyses suggest a geographic distinction between clearly defined monophyletic North Island clades and unresolved South Island clades. We suggest that more extreme habitat modification on South Island during the Pliocene and Pleistocene resulted in secondary contact and hybridization between species pairs and a series of mitochondrial capture events followed by subsequent lineage evolution.


Subject(s)
Hemiptera/genetics , Hybridization, Genetic , Phylogeny , Animals , Base Sequence , Bayes Theorem , DNA, Mitochondrial/genetics , Haplotypes/genetics , Mitochondria/genetics , New Zealand , Species Specificity
19.
Syst Biol ; 66(4): 569-589, 2017 Jul 01.
Article in English | MEDLINE | ID: mdl-28123112

ABSTRACT

Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO$_{2}$ levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants. We studied 162 species of cicadas in the Australian Pauropsalta complex, a large generic lineage within the tribe Cicadettini. We asked whether there were changes in the diversification rate of Pauropsalta over time and if so: 1) which clades were associated with the rate change? 2) did timing of rate shifts correspond to known periods of dramatic historical climate change, 3) did increases in diversification rate along select lineages correspond to adaptive radiations with movement into the arid zone? To address these questions, we estimated a molecular phylogeny of the Pauropsalta complex using ${\sim}$5300 bp of nucleotide sequence data distributed among five loci (one mtDNA locus and four nDNA loci). We found that this large group of cicadas did not diversify at a constant rate as they spread through Australia; instead the signature of decreasing diversification rate changed roughly around the time of the expansion of the east Antarctic ice sheets ${\sim}$16 Ma and the glaciation of the northern hemisphere ${\sim}$3 Ma. Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate in response to an early invasion of the arid zone. Instead multiple groups invaded the arid zone and experienced rates of diversification similar to mesic-distributed taxa. We found evidence for relictual groups, located in pre-Mesozoic habitat, that have not diversified and continue to reside on mesic hosts in isolated "habitat islands". Future work should focus on groups of similar ages with similar distribution patterns to determine whether this tempo and pattern of diversification and biogeography is consistent with evidence from other phytophagous insects.


Subject(s)
Biodiversity , Hemiptera/classification , Phylogeny , Animals , Australia , Climate Change , Hemiptera/genetics , Phylogeography
20.
PLoS One ; 11(11): e0165562, 2016.
Article in English | MEDLINE | ID: mdl-27851754

ABSTRACT

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a "complex within the complex": the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive introgression and mitochondrial capture.


Subject(s)
Biodiversity , Hemiptera/classification , Phylogeny , Vocalization, Animal/physiology , Acoustics , Animals , DNA, Mitochondrial/genetics , Electron Transport Complex IV/genetics , Female , Hemiptera/anatomy & histology , Linear Models , Male , Pigmentation , Principal Component Analysis , Quantitative Trait, Heritable , Temperature , Wings, Animal/anatomy & histology
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