252 results found
Ge X, Peng L, Vogler AP, et al., 2022, Massive gene rearrangements of mitochondrial genomes and implications for the phylogeny of Trichoptera (Insecta), SYSTEMATIC ENTOMOLOGY, ISSN: 0307-6970
Overcast I, Achaz G, Aguilee R, et al., 2022, Towards a genetic theory of island biogeography: Inferring processes from multidimensional community-scale data, GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 32, Pages: 4-23, ISSN: 1466-822X
Li Z, Linard B, Vogler AP, et al., 2022, Phylogenetic diversity only weakly mitigates climate-change-driven biodiversity loss in insect communities, MOLECULAR ECOLOGY, ISSN: 0962-1083
Emerson BC, Borges PAV, Cardoso P, et al., 2022, Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands, MOLECULAR ECOLOGY, ISSN: 0962-1083
Arias MB, Hartle-Mougiou K, Taboada S, et al., 2022, Unveiling biogeographical patterns in the worldwide distributed Ceratitis capitata (medfly) using population genomics and microbiome composition., Mol Ecol, Vol: 31, Pages: 4866-4883
Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographical history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographical regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonized environments.
Paula DP, Timbo RV, Togawa RC, et al., 2022, Quantitative prey species detection in predator guts across multiple trophic levels by mapping unassembled shotgun reads, MOLECULAR ECOLOGY RESOURCES, Vol: 23, Pages: 64-80, ISSN: 1755-098X
Arribas P, Andujar C, Bohmann K, et al., 2022, Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods, GIGASCIENCE, Vol: 11, ISSN: 2047-217X
Andujar C, Arribas P, Lopez H, et al., 2022, Community assembly and metaphylogeography of soil biodiversity: Insights from haplotype-level community DNA metabarcoding within an oceanic island, MOLECULAR ECOLOGY, Vol: 31, Pages: 4078-4094, ISSN: 0962-1083
Baselga A, Gomez-Rodriguez C, Araujo MB, et al., 2022, Joint analysis of species and genetic variation to quantify the role of dispersal and environmental constraints in community turnover, Ecography: pattern and diversity in ecology, Vol: 2022, Pages: 1-13, ISSN: 0906-7590
Spatial turnover of biological communities is determined by both dispersal and environmental constraints. However, we lack quantitative predictions about how these factors interact and influence turnover across genealogical scales. In this study, we have implemented a predictive framework based on approximate Bayesian computation (ABC) to quantify the signature of dispersal and environmental constraints in community turnover. First, we simulated the distribution of haplotypes, intra-specific lineages and species in biological communities under different strengths of dispersal and environmental constraints. Our simulations show that spatial turnover rate is invariant across genealogical scales when dispersal limitation determines the species ranges. However, when environmental constraint limits species ranges, spatial turnover rates vary across genealogical scales. These simulations were used in an ABC framework to quantify the role of dispersal and environmental constraints in 16 empirical biological communities sampled from local to continental scales, including several groups of insects (both aquatic and terrestrial), molluscs and bats. In seven datasets, the observed genealogical invariance of spatial turnover, assessed with distance–decay curves, suggests a dispersal-limited scenario. In the remaining datasets, the variance in distance–decay curves across genealogical scales was best explained by various combinations of dispersal and environmental constraints. Our study illustrates how modelling spatial turnover at multiple genealogical scales (species and intraspecific lineages) provides relevant insights into the relative role of dispersal and environmental constraints in community turnover.
Rahman MM, Burian A, Creedy TJ, et al., 2022, DNA-based assessment of environmental degradation in an unknown fauna: The freshwater macroinvertebrates of the Indo-Burmese hotspot, JOURNAL OF APPLIED ECOLOGY, Vol: 59, Pages: 1644-1658, ISSN: 0021-8901
Bian X, Garner B, Liu H, et al., 2022, The SITE-100 project: site-based biodiversity genomics for species discovery, community ecology, and a global tree-of-life, Frontiers in Ecology and Evolution, Vol: 10, ISSN: 2296-701X
Most insect communities are composed of evolutionary diverse lineages, but detailed phylogenetic analyses of whole communities are lacking, in particular in species-rich tropical faunas. Likewise, our knowledge of the Tree-of-Life to document life’s evolutionary diversity remains highly incomplete and especially requires the inclusion of unstudied lineages from species-rich ecosystems. Here we present the SITE-100 program, which is an attempt at building the Tree-of-Life from whole-community sampling of high-biodiversity sites around the globe. Combining the local data sets into a global tree produces an increasingly comprehensive tree, while also re-tracing evolutionary history of lineages constituting the local community. Local sets are collected in bulk in standardised passive traps and imaged with a large-scale high-resolution camera, which is followed by a parataxonomy step for the preliminary separation of morphospecies and selection of specimens for phylogenetic analysis. Selected specimens are used for individual DNA extraction and sequencing, usually to sequence mitochondrial genomes. All remaining specimens are bulk extracted and subjected to metabarcoding. Phylogenetic analysis on the mitogenomes produces a reference tree to which short barcode sequences are added in a secondary analysis using phylogenetic placement or backbone constrainedtree searches. However, the approach may be hampered by the fact that (1) mitogenomes are limited in phylogeneticinformativeness, and (2) site-based sampling may produce poor taxon coverage and cause a suite of challenges for phylogenetic inference. To mitigate problems of phylogenetic reconstruction at deep levels, we follow a hierarchical way of gathering molecular information, where nuclear genome and mitogenome data from taxonomically chosen specimens consolidate the base and middle portion of the tree, respectively, and adding species-resolution contributed by DNA barcode data. We posit that site-based samplin
Creedy TJ, Andújar C, Meramveliotakis E, et al., 2022, Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation, Molecular Ecology Resources, Vol: 22, Pages: 847-861, ISSN: 1471-8278
Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.
Ceballos Escalera Fernandez A, Richards J, Arias MB, et al., 2022, Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers, MycoKeys, Vol: 88, Pages: 1-33, ISSN: 1314-4057
Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.
Huang J, Miao X, Wang Q, et al., 2022, Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem, Ecology and Evolution, Vol: 12, Pages: 1-13, ISSN: 2045-7758
Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species’ geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.
Noguerales V, Meramveliotakis E, Castro-Insua A, et al., 2021, Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests, MOLECULAR ECOLOGY, ISSN: 0962-1083
Motyka M, Kusy D, Hava J, et al., 2021, Mitogenomic data elucidate the phylogeny and evolution of life strategies in Dermestidae (Coleoptera), SYSTEMATIC ENTOMOLOGY, Vol: 47, Pages: 82-93, ISSN: 0307-6970
Huang K, Wang J, Huang J, et al., 2021, Host phylogeny and diet shape gut microbial communities within bamboo-feeding insects, Frontiers in Microbiology, Vol: 12, Pages: 1-13, ISSN: 1664-302X
The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.
Wei Q, Yin R, Huang J, et al., 2021, The diversity of soil mesofauna declines after bamboo invasion in subtropical China, SCIENCE OF THE TOTAL ENVIRONMENT, Vol: 789, ISSN: 0048-9697
Ge D, Feijó A, Wen Z, et al., 2021, Demographic history and genomic response to environmental changes in a rapid radiation of wild rats, Molecular Biology and Evolution, Vol: 38, Pages: 1905-1923, ISSN: 0737-4038
For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau (QHTP) was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.
Arribas P, Andujar C, Bidartondo MI, et al., 2021, Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis, Molecular Ecology, Vol: 30, Pages: 1120-1135, ISSN: 0962-1083
High‐throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site‐based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled “Next Generation Biodiversity Monitoring” was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3‐day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS‐based strategy to collectively build an integrative framework for site‐based biodiversity data generation.
Andujar C, Creedy TJ, Arribas P, et al., 2021, Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data, MOLECULAR ECOLOGY RESOURCES, Vol: 21, Pages: 1772-1787, ISSN: 1755-098X
Arribas P, Andujar C, Salces-Castellano A, et al., 2020, The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding, MOLECULAR ECOLOGY, Vol: 30, Pages: 48-61, ISSN: 0962-1083
Nie R, Vogler AP, Yang X-K, et al., 2020, Higher-level phylogeny of longhorn beetles (Coleoptera: Chrysomeloidea) inferred from mitochondrial genomes, SYSTEMATIC ENTOMOLOGY, Vol: 46, Pages: 56-70, ISSN: 0307-6970
Timmermans MJTN, Srivathsan A, Collins S, et al., 2020, Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed-invected, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 287, ISSN: 0962-8452
Arribas P, Andujar C, Lourdes Moraza M, et al., 2020, Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 37, Pages: 683-694, ISSN: 0737-4038
Creedy TJ, Norman H, Tang CQ, et al., 2020, A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding, MOLECULAR ECOLOGY RESOURCES, Vol: 20, Pages: 40-53, ISSN: 1755-098X
Miller KE, Inward DJG, Gomez-Rodriguez C, et al., 2019, Predicting the unpredictable: How host specific is the mycobiota of bark and ambrosia beetles?, FUNGAL ECOLOGY, Vol: 42, ISSN: 1754-5048
Murria C, Sainz-Bariain M, Vogler AP, et al., 2019, Vulnerability to climate change for two endemic high-elevation, low-dispersive Annitella species (Trichoptera) in Sierra Nevada, the southernmost high mountain in Europe, INSECT CONSERVATION AND DIVERSITY, Vol: 13, Pages: 283-295, ISSN: 1752-458X
Nie R-E, Andujar C, Gomez-Rodriguez C, et al., 2019, The phylogeny of leaf beetles (Chrysomelidae) inferred from mitochondrial genomes, SYSTEMATIC ENTOMOLOGY, Vol: 45, Pages: 188-204, ISSN: 0307-6970
Ge D, Lu L, Abramov AV, et al., 2019, Coalescence Models Reveal the Rise of the White-Bellied Rat (Niviventer confucianus) Following the Loss of Asian Megafauna, JOURNAL OF MAMMALIAN EVOLUTION, Vol: 26, Pages: 423-434, ISSN: 1064-7554
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