Publications
252 results found
Bocak L, Kundrata R, Fernandez CA, et al., 2016, The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing, Proceedings of the Royal Society B: Biological Sciences, Vol: 283, ISSN: 0962-8452
The ongoing exploration of biodiversity and the implementation of new molecular tools continue to unveil hitherto unknown lineages. Here, we report the discovery of three species of neotenic beetles for which we propose the new family Iberobaeniidae. Complete mitochondrial genomes and rRNA genes recovered Iberobaeniidae as a deep branch in Elateroidea, as sister to Lycidae (net-winged beetles). Two species of the new genus Iberobaenia, Iberobaenia minuta sp. nov. and Iberobaenia lencinai sp. nov. were found in the adult stage. In a separate incidence, a related sequence was identified in bulk samples of soil invertebrates subjected to shotgun sequencing and mitogenome assembly, which was traced to a larval voucher specimen of a third species of Iberobaenia. Iberobaenia shows characters shared with other elateroid neotenic lineages, including soft-bodiedness, the hypognathous head, reduced mouthparts with reduced labial palpomeres, and extremely small-bodied males without strengthening structures due to miniaturization. Molecular dating shows that Iberobaeniidae represents an ancient relict lineage originating in the Lower Jurassic, which possibly indicates a long history of neoteny, usually considered to be evolutionarily short-lived. The apparent endemism of Iberobaeniidae in the Mediterranean region highlights the importance of this biodiversity hotspot and the need for further species exploration even in the well-studied European continent.
Ahrens D, Fujisawa T, Krammer H-J, et al., 2016, Rarity and incomplete sampling in DNA-based species delimitation, Systematic Biology, Vol: 65, Pages: 478-494, ISSN: 1076-836X
DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including “singleton” representatives of species, which hampers estimates of intra- versus interspecies evolutionary processes. In a case study of southern African chafers (beetles in the family Scarabaeidae), many species and subclades were poorly represented and 48.5% of species were singletons. Using cox1 sequences from >500 specimens and ∼100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various other approaches for DNA-based species delimitation (Automatic Barcode Gap Discovery (ABGD), Poisson tree processes (PTP), Species Identifier, Statistical Parsimony), frequently produced poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence, low sampling may be compensated for by “clade addition” of lineages outside of the focal group. Similar findings were obtained in reanalysis of published data sets of taxonomically poorly known species assemblages of insects from Madagascar. The low performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective population size (NeNe), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species affect the power of the GMYC method only if they reflect great differences in NeNe among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue about the variation in NeNe and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a limited study group can overcome poor sampling for the GMYC method in particular under variable NeNe. This effect was less pronounced for methods of species d
Song F, Li H, Jiang P, et al., 2016, Capturing the phylogeny of holometabola with mitochondrial genome data and bayesian site-heterogeneous mixture models, Genome Biology and Evolution, Vol: 8, Pages: 1411-1426, ISSN: 1759-6653
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
Srivathsan A, Ang A, Vogler AP, et al., 2016, Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate, Frontiers in Zoology, Vol: 13, ISSN: 1742-9994
BACKGROUND: Rapid habitat loss and degradation are responsible for population decline in a growing number of species. Understanding the natural history of these species is important for designing conservation strategies, such as habitat enhancements or ex-situ conservation. The acquisition of observational data may be difficult for rare and declining species, but metagenomics and metabarcoding can provide novel kinds of information. Here we use these methods for analysing fecal samples from an endangered population of a colobine primate, the banded leaf monkey (Presbytis femoralis). RESULTS: We conducted metagenomics via shotgun sequencing on six fecal samples obtained from a remnant population of P. femoralis in a species-rich rainforest patch in Singapore. Shotgun sequencing and identification against a plant barcode reference database reveals a broad dietary profile consisting of at least 53 plant species from 33 families. The diet includes exotic plant species and is broadly consistent with > 2 years of observational data. Metagenomics identified 15 of the 24 plant genera for which there is observational data, but also revealed at least 36 additional species. DNA traces for the diet species were recovered and identifiable in the feces despite long digestion times and a large number of potential food plants within the rainforest habitat (>700 species). We also demonstrate that metagenomics provides greater taxonomic resolution of food plant species by utilizing multiple genetic markers as compared to single-marker metabarcoding. In addition, full mitochondrial genomes of P. femoralis individuals were reconstructed from fecal metagenomic shotgun reads, showing very low levels of genetic diversity in the focal population, and the presence of gut parasites could also be confirmed. Metagenomics thus allows for the simultaneous assessment of diet, population genetics and gut parasites based on fecal samples. CONCLUSIONS: Our study demonstrates that met
Arribas P, Andujar C, Hopkins K, et al., 2016, Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil, Methods in Ecology and Evolution, Vol: 7, Pages: 1071-1081, ISSN: 2041-210X
Bidegaray-Batista L, Sanchez-Gracia A, Santulli G, et al., 2016, Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider, Molecular Ecology, Vol: 25, Pages: 2046-2064, ISSN: 1365-294X
Andujar C, Faille A, Perez-Gonzalez S, et al., 2016, Gondwanian relicts and oceanic dispersal in a cosmopolitan radiation of euedaphic ground beetles, Molecular Phylogenetics and Evolution, Vol: 99, Pages: 235-246, ISSN: 1095-9513
Anillini are a tribe of minute, euedaphic ground beetles (Carabidae) characterized by the loss of eyes, loss of wings and high levels of local endemism. Despite their presumed low dispersal, they have a nearly cosmopolitan distribution, including isolated islands such as New Zealand and New Caledonia. We used a time calibrated molecular phylogeny to test, first, if the tribe as currently understood is monophyletic and, second, whether the time of divergence is compatible with an early vicariant diversification after the breakup of Gondwana. We sequenced portions of 6 mitochondrial and 3 nuclear genes for 66 specimens in 17 genera of Anillini plus 39 outgroups. The resulting phylogenetic tree was used to estimate the time of diversification using two independent calibration schemes, by applying molecular rates for the related genus Carabus or by dating the tree with fossil and geological information. Rates of molecular evolution and lineage ages were mostly concordant between both calibration schemes. The monophyly of Anillini was well-supported, and its age was consistent with a Gondwanian origin of the main lineages and an initial diversification at ca. 100 Ma representing the split between the eyed Nesamblyops (New Zealand) and the remaining Anillini. The subsequent diversification, including the split of the Nearctic Anillinus and the subsequent splits of Palaearctic lineages, was dated to between 80 and 100 Ma and thus was also compatible with a tectonic vicariant origin. On the contrary, the estimated age of the New Caledonian blind Orthotyphlus at ca. 30 ± 20 Ma was incompatible with a vicariant origin, suggesting the possibility of trans-oceanic dispersal in these endogean beetles.
Crampton-Platt A, Yu DW, Zhou X, et al., 2016, Mitochondrial metagenomics: letting the genes out of the bottle, GigaScience, Vol: 5, ISSN: 2047-217X
'Mitochondrial metagenomics' (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.
Miller K, Vogler A, Hopkins K, et al., 2016, Metabarcoding of fungal communities associated with bark beetles, Ecology and Evolution, Vol: 6, Pages: 1590-1600, ISSN: 2045-7758
Many species of fungi are closely allied with bark beetles, including many treepathogens, but their species richness and patterns of distribution remain largelyunknown. We established a protocol for metabarcoding of fungal communitiesdirectly from total genomic DNA extracted from individual beetles, showingthat the ITS3/4 primer pair selectively amplifies the fungal ITS. Using threespecimens of bark beetle from different species, we assess the fungal diversityassociated with these specimens and the repeatability of these estimates in PCRsconducted with different primer tags. The combined replicates produced 727fungal Operational Taxonomic Units (OTUs) for the specimen of Hylastes ater,435 OTUs for Tomicus piniperda, and 294 OTUs for Trypodendron lineatum,while individual PCR reactions produced on average only 229, 54, and 31OTUs for the three specimens, respectively. Yet, communities from PCR replicateswere very similar in pairwise comparisons, in particular when consideringspecies abundance, but differed greatly among the three beetle specimens. Differentprimer tags or the inclusion of amplicons in separate libraries did notimpact the species composition. The ITS2 sequences were identified with theLowest Common Ancestor approach and correspond to diverse lineages offungi, including Ophiostomaceae and Leotiomycetes widely found to be treepathogens. We conclude that Illumina MiSeq metabarcoding reliably capturesfungal diversity associated with bark beetles, although numerous PCR replicatesare recommended for an exhaustive sample. Direct PCR from beetle DNAextractions provides a rapid method for future surveys of fungal species diversityand their associations with bark beetles and environmental variables.
Gill RJ, Baldock KCR, Brown MJF, et al., 2016, Protecting an Ecosystem Service: Approaches to Understanding and Mitigating Threats to Wild Insect Pollinators, Advances in Ecological Research, Vol: 54, Pages: 135-206, ISSN: 0065-2504
Insect pollination constitutes an ecosystem service of global importance, providing significant economic and aesthetic benefits as well as cultural value to human society, alongside vital ecological processes in terrestrial ecosystems. It is therefore important to understand how insect pollinator populations and communities respond to rapidly changing environments if we are to maintain healthy and effective pollinator services. This chapter considers the importance of conserving pollinator diversity to maintain a suite of functional traits and provide a diverse set of pollinator services. We explore how we can better understand and mitigate the factors that threaten insect pollinator richness, placing our discussion within the context of populations in predominantly agricultural landscapes in addition to urban environments. We highlight a selection of important evidence gaps, with a number of complementary research steps that can be taken to better understand: (i) the stability of pollinator communities in different landscapes in order to provide diverse pollinator services; (ii) how we can study the drivers of population change to mitigate the effects and support stable sources of pollinator services and (iii) how we can manage habitats in complex landscapes to support insect pollinators and provide sustainable pollinator services for the future. We advocate a collaborative effort to gain higher quality abundance data to understand the stability of pollinator populations and predict future trends. In addition, for effective mitigation strategies to be adopted, researchers need to conduct rigorous field testing of outcomes under different landscape settings, acknowledge the needs of end-users when developing research proposals and consider effective methods of knowledge transfer to ensure effective uptake of actions.
Timmermans MJTN, Viberg C, Martin G, et al., 2016, Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections, Biological Journal of the Linnean Society, Vol: 117, Pages: 83-95, ISSN: 1095-8312
Polymerase chain reaction approaches for DNA sequencing from dried collection specimens of insects usually suffer from contamination, short fragment length, and limited phylogenetic power. As an alternative, we use shotgun metagenomic sequencing from mixed pools of DNA, from which mitochondrial sequences are filtered in silico. We extracted DNA from a single leg of 35 species of British butterflies that had been stored in the Natural History Museum for between 9 and 35 years. Illumina MiSeq (1/3 of flow cell) produced mitogenome sequences of > 10 kb for ten species, of which six were (almost) complete. In addition, full or partial barcode sequences for 31 species were recovered, which, in almost all cases, showed perfect (100%) identity to sequences available in the BOLD database under the same taxon name. The mean length of sequence reads was 167 bp (putative mitochondrial reads) and 153 bp (all reads). Assembly of contigs > 10 kb from these short reads was apparently error free, except in the case of two closely-related species of Pieris that formed chimeras. Contiguous sequences are difficult to obtain from degraded DNA with Sanger technology but the Illumina short reads are a natural fit for dry-collection specimens. The obvious possibility for scaling up this protocol provides exciting prospects for the large-scale indexing of natural history collections using partial or full mitochondrial genomes.
Linard B, Arribas P, Andujar C, et al., 2015, The mitogenome of Hydropsyche pellucidula (Hydropsychidae): first gene arrangement in the insect order Trichoptera, MITOCHONDRIAL DNA PART A, Vol: 28, Pages: 71-72, ISSN: 2470-1394
Timmermans MJTN, Barton C, Haran J, et al., 2015, Family-level sampling of mitochondrial genomes in coleoptera: compositional heterogeneity and phylogenetics, Genome Biology and Evolution, Vol: 8, Pages: 161-175, ISSN: 1759-6653
Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5, and nad6 genes. Credible tree topologies were obtained with the nhPhyML (“nonhomogeneous”) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.
Elfekih S, Shannon M, Haran J, et al., 2015, Detection of the Acetylcholinesterase Insecticide Resistance Mutation (G328A) in Natural Populations of <i>Ceratitis capitata</i> (vol 107, pg 1965, 2014), JOURNAL OF ECONOMIC ENTOMOLOGY, Vol: 108, Pages: 2837-2837, ISSN: 0022-0493
Crampton-Platt A, Timmermans MJTN, Gimmel ML, et al., 2015, Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean Rainforest sample, Molecular Biology and Evolution, Vol: 32, Pages: 2302-2316, ISSN: 1537-1719
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis ofdiversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed toaccelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could beincorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrialgenomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstratehow the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgunsequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic treeobtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage ofmajor lineages of Coleoptera. When all sequences were combined only minor topological changes were induced againstthis reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sampleexpanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enablean evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidlyexpands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes fromshotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetictree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.
Bocakova M, Bocak L, Gimmel ML, et al., 2015, Aposematism and mimicry in soft-bodied beetles of the superfamily Cleroidea (Insecta), Zoologica Scripta, Vol: 45, Pages: 9-21, ISSN: 1463-6409
The evolution of animal life strategies is among the main themes of current evolutionary biology. Checkered beetles, soft-winged flower beetles and their allies (superfamily Cleroidea), exhibit well-known aposematic colour patterns, particularly in the family Cleridae, which participate in mimicry complexes mostly with unpalatable beetles, ants and velvet ants representing a Müllerian–Batesian continuum. Many cleroids also exhibit attenuated hardening of cuticular layers resulting in a soft-bodied appearance. Here, a molecular phylogenetic analysis of the entire Cleroidea was performed using sequences of two nuclear and two mitochondrial loci of ~4 kb total length. Inferred phylogenies were used to reconstruct ancestral colour patterns and involvement in mimicry complexes. The hypothesis of a soft-bodied ancestor of Cleridae and allies was tested. The phylogenetic analyses corroborated the expanded Cleroidea concept including Byturidae and Biphyllidae formerly classified as Cucujoidea. Character state optimization showed cryptic coloration was the ancestral state in Cleroidea, from which aposematic coloration originated several times in distant cleroid lineages. Within Cleridae, mimicry also arose from an ancestor that was cryptic, and multiple lineages that mimicked unpalatable beetles (Chrysomelidae, Meloidae, Lycidae) and stinging Hymenoptera evolved. Aposematic coloration was acquired in all major clerid lineages including Thanerocleridae, which are either the sister group of Chaetosomatidae or Cleridae. These findings suggest that mimetic traits in the clerid clade evolved at various times, possibly soon after the origin of soft-bodiedness. The adaptive value of aposematism in cleroids is likely to be enhanced in soft-bodied species, as this trait provides limited means of protection against predators, and therefore may promote the acquisition of aposematic and mimetic coloration in various ecological situations.
Murria C, Rugenski AT, Whiles MR, et al., 2015, Long-term isolation and endemicity of Neotropical aquatic insects limit the community responses to recent amphibian decline, DIVERSITY AND DISTRIBUTIONS, Vol: 21, Pages: 938-949, ISSN: 1366-9516
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- Citations: 26
Gomez-Rodriguez C, Crampton-Platt A, Timmermans MJTN, et al., 2015, Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages, METHODS IN ECOLOGY AND EVOLUTION, Vol: 6, Pages: 883-894, ISSN: 2041-210X
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- Citations: 74
Baselga A, Gomez-Rodriguez C, Vogler AP, 2015, Multi-hierarchical macroecology at species and genetic levels to discern neutral and non-neutral processes, GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 24, Pages: 873-882, ISSN: 1466-822X
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- Citations: 28
Paula DP, Linard B, Andow DA, et al., 2015, Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics, MOLECULAR ECOLOGY RESOURCES, Vol: 15, Pages: 880-892, ISSN: 1755-098X
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- Citations: 46
Andujar C, Arribas P, Ruzicka F, et al., 2015, Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics, MOLECULAR ECOLOGY, Vol: 24, Pages: 3603-3617, ISSN: 0962-1083
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- Citations: 65
Linard B, Crampton-Platt A, Gillett CPDT, et al., 2015, Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics, Genome Biology and Evolution, Vol: 7, Pages: 1474-1489, ISSN: 1759-6653
Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by “genome skimming,” which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous “clusters” of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The “metagenome skimming” approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
Srivathsan A, Sha JCM, Vogler AP, et al., 2015, Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (<i>Pygathrix nemaeus</i>), MOLECULAR ECOLOGY RESOURCES, Vol: 15, Pages: 250-261, ISSN: 1755-098X
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- Citations: 89
Fujisawa T, Vogler AP, Barraclough TG, 2015, Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles, Proceedings. Biological sciences / The Royal Society, Vol: 282
Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.
Fujisawa T, Vogler AP, Barraclough TG, 2015, Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 282, ISSN: 0962-8452
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- Citations: 23
Elfekih S, Shannon M, Haran J, et al., 2014, Detection of the Acetylcholinesterase Insecticide Resistance Mutation (G328A) in Natural Populations of <i>Ceratitis capitata</i>, JOURNAL OF ECONOMIC ENTOMOLOGY, Vol: 107, Pages: 1965-1968, ISSN: 0022-0493
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- Citations: 9
Ahrens D, Schwarzer J, Vogler AP, 2014, The evolution of scarab beetles tracks the sequential rise of angiosperms and mammals, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 281, ISSN: 0962-8452
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- Citations: 110
Thompson MJ, Timmermans MJTN, Jiggins CD, et al., 2014, The evolutionary genetics of highly divergent alleles of the mimicry locus in <i>Papilio dardanus</i>, BMC EVOLUTIONARY BIOLOGY, Vol: 14, ISSN: 1471-2148
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- Citations: 11
Gillett CPDT, Crampton-Platt A, Timmermans MJTN, et al., 2014, Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea), Molecular Biology and Evolution, Vol: 31, Pages: 2223-2237, ISSN: 0737-4038
Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge.
Timmermans MJTN, Baxter SW, Clark R, et al., 2014, Comparative genomics of the mimicry switch in <i>Papilio dardanus</i>, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 281, ISSN: 0962-8452
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- Citations: 34
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