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Supplementary material 8 from: Thanoosing C, Orr MC, Warrit N, Vogler AP, Williams PH (2023) A taxonomic re-assessment of the widespread oriental bumblebee Bombus flavescens (Hymenoptera, Apidae). Journal of Hymenoptera Research 96: 507-541. https://doi.org/10.3897/jhr.96.104715

Thanoosing, Chawatat ; Orr, Michael C. ; Warrit, Natapot ; [et al.]

Pensoft Publishers ; 2023

In: Journal of Hymenoptera Research Vol. 96 ( 2023-06-22), p. 507-541

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In: Journal of Hymenoptera Research, Pensoft Publishers, Vol. 96 ( 2023-06-22), p. 507-541

Abstract: Bombus flavescens Smith is one of the most widespread bumblebee species in the Oriental region. Due to colour polymorphisms, this species or species-complex has been a challenge for taxonomy. This study aims to assess the taxonomic status of the flavescens -complex using evidence from COI barcodes and morphology. We then reconstruct its biogeographic history from a phylogenetic analysis of populations across the current range, combining COI with 16S and nuclear PEPCK data. Despite a large range of polymorphisms across its distribution, the results show that B. flavescens is a single species based on algorithmic species delimitation methods, and it is clearly separated from its sister species, B. rotundiceps Friese. We suggest that B. flavescens diverged from its sister lineage in the Himalaya and dispersed into Southeast Asia in the Pleistocene. Conservation of the widespread B. flavescens will need to consider its several unique island populations.

Type of Medium: Online Resource

ISSN: 1314-2607 , 1070-9428

URL: Article

DOI: 10.3897/jhr.96.104715

DOI: 10.3897/jhr.96.104715.figure1

DOI: 10.3897/jhr.96.104715.figure10

DOI: 10.3897/jhr.96.104715.figure11

DOI: 10.3897/jhr.96.104715.figure12

DOI: 10.3897/jhr.96.104715.figure2

DOI: 10.3897/jhr.96.104715.figure3

DOI: 10.3897/jhr.96.104715.figure4

DOI: 10.3897/jhr.96.104715.figure5

DOI: 10.3897/jhr.96.104715.figure6

DOI: 10.3897/jhr.96.104715.figure7

DOI: 10.3897/jhr.96.104715.figure8

DOI: 10.3897/jhr.96.104715.figure9

DOI: 10.3897/jhr.96.104715.suppl1

DOI: 10.3897/jhr.96.104715.suppl2

DOI: 10.3897/jhr.96.104715.suppl3

DOI: 10.3897/jhr.96.104715.suppl4

DOI: 10.3897/jhr.96.104715.suppl5

DOI: 10.3897/jhr.96.104715.suppl6

DOI: 10.3897/jhr.96.104715.suppl7

DOI: 10.3897/jhr.96.104715.suppl8

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2023

detail.hit.zdb_id: 2477175-2

SSG: 12

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Supplementary material 7 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106

Ceballos-Escalera, Angelina ; Richards, John ; Arias, Maria Belen ; [et al.]

Pensoft Publishers ; 2022

In: MycoKeys Vol. 88 ( 2022-03-08), p. 1-33

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In: MycoKeys, Pensoft Publishers, Vol. 88 ( 2022-03-08), p. 1-33

Abstract: 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.

Type of Medium: Online Resource

ISSN: 1314-4049 , 1314-4057

URL: Article

DOI: 10.3897/mycokeys.88.77106

DOI: 10.3897/mycokeys.88.77106.figure1

DOI: 10.3897/mycokeys.88.77106.figure2

DOI: 10.3897/mycokeys.88.77106.figure3

DOI: 10.3897/mycokeys.88.77106.figure4

DOI: 10.3897/mycokeys.88.77106.figure5

DOI: 10.3897/mycokeys.88.77106.figure6

DOI: 10.3897/mycokeys.88.77106.figure7

DOI: 10.3897/mycokeys.88.77106.figure8

DOI: 10.3897/mycokeys.88.77106.suppl1

DOI: 10.3897/mycokeys.88.77106.suppl2

DOI: 10.3897/mycokeys.88.77106.suppl3

DOI: 10.3897/mycokeys.88.77106.suppl4

DOI: 10.3897/mycokeys.88.77106.suppl5

DOI: 10.3897/mycokeys.88.77106.suppl6

DOI: 10.3897/mycokeys.88.77106.suppl7

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2022

detail.hit.zdb_id: 2630648-7

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Quantitative prey species detection in predator guts across multiple trophic levels by mapping unassembled shotgun reads

Paula, Débora P. ; Timbó, Renata V. ; Togawa, Roberto C. ; [et al.]

Wiley ; 2023

In: Molecular Ecology Resources Vol. 23, No. 1 ( 2023-01), p. 64-80

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In: Molecular Ecology Resources, Wiley, Vol. 23, No. 1 ( 2023-01), p. 64-80

Abstract: Quantifying species trophic interaction strengths is crucial for understanding community dynamics and has significant implications for pest management and species conservation. DNA‐based methods to identify species interactions have revolutionized these efforts, but a significant limitation is the poor ability to quantify the strength of trophic interactions, that is the biomass or number of prey consumed. We present an improved pipeline, called Lazaro, to map unassembled shotgun reads to a comprehensive arthropod mitogenome database and show that the number of prey reads detected is quantitatively predicted from the prey biomass consumed, even for indirect predation. Two feeding bioassays were performed: starved coccinellid larvae consuming different numbers of aphids (Prey Quantity bioassay), and starved coccinellid larvae consuming a chrysopid larvae that had consumed aphids (Direct and Indirect Predation bioassay). Prey taxonomic assignment against a mitochondrial genome database had high accuracy (99.8% positive predictive value) and the number of prey reads was directly related to the number of prey consumed and inversely related to the elapsed time since consumption with high significance ( r 2 = .932, p = 4.92E‐6). Aphids were detected up to 6 h after direct predation plus 3 h after indirect predation (9 h in total) and detection was related to the predator‐specific decay rates. Lazaro enabled quantitative predictions of prey consumption across multiple trophic levels with high taxonomic resolution while eliminating all false positives, except for a few confirmed contaminants, and may be valuable for characterizing prey consumed by field‐sampled predators. Moreover, Lazaro is readily applicable for species diversity determination from any degraded environmental DNA.

Type of Medium: Online Resource

ISSN: 1755-098X , 1755-0998

URL: Issue

URL: Article

DOI: 10.1111/men.v23.1

DOI: 10.1111/1755-0998.13690

Language: English

Publisher: Wiley

Publication Date: 2023

detail.hit.zdb_id: 2406833-0

SSG: 12

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Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

Arribas, Paula ; Andújar, Carmelo ; Bohmann, Kristine ; [et al.]

Oxford University Press (OUP) ; 2022

In: GigaScience Vol. 11 ( 2022-07-19)

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In: GigaScience, Oxford University Press (OUP), Vol. 11 ( 2022-07-19)

Abstract: Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

Type of Medium: Online Resource

ISSN: 2047-217X

URL: Article

DOI: 10.1093/gigascience/giac065

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2022

detail.hit.zdb_id: 2708999-X

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Towards a genetic theory of island biogeography: Inferring processes from multidimensional community‐scale data

Overcast, Isaac ; Achaz, Guillaume ; Aguilée, Robin ; [et al.]

Wiley ; 2023

In: Global Ecology and Biogeography Vol. 32, No. 1 ( 2023-01), p. 4-23

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In: Global Ecology and Biogeography, Wiley, Vol. 32, No. 1 ( 2023-01), p. 4-23

Abstract: MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography. Motivation/goal We aim to promote the development of process‐based biodiversity models that predict community genetic diversity patterns together with other community‐scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community‐scale data including a genetic component. Main conclusions Our review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top‐down or a bottom‐up approach. Finally, we highlight key ecological and evolutionary questions that might be addressed by unified models including a genetic component and establish hypotheses about how processes across scales might impact patterns of community genetic diversity.

Type of Medium: Online Resource

ISSN: 1466-822X , 1466-8238

URL: Issue

URL: Article

DOI: 10.1111/geb.v32.1

DOI: 10.1111/geb.13604

Language: English

Publisher: Wiley

Publication Date: 2023

detail.hit.zdb_id: 1479787-2

detail.hit.zdb_id: 2021283-5

SSG: 12

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New progress in exploring the mechanisms underlying extraordinarily high biodiversity in global hotspots and their implications for conservation

Ge, Deyan ; Qu, Yanhua ; Deng, Tao ; [et al.]

Wiley ; 2022

In: Diversity and Distributions Vol. 28, No. 12 ( 2022-12), p. 2448-2458

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In: Diversity and Distributions, Wiley, Vol. 28, No. 12 ( 2022-12), p. 2448-2458

Type of Medium: Online Resource

ISSN: 1366-9516 , 1472-4642

URL: Issue

URL: Article

DOI: 10.1111/ddi.v28.12

DOI: 10.1111/ddi.13657

Language: English

Publisher: Wiley

Publication Date: 2022

detail.hit.zdb_id: 2020139-4

detail.hit.zdb_id: 1443181-6

SSG: 12

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Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents

Paula, Débora P. ; Linard, Benjamin ; Crampton-Platt, Alex ; [et al.]

Public Library of Science (PLoS) ; 2016

In: PLOS ONE Vol. 11, No. 9 ( 2016-9-13), p. e0161841-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 9 ( 2016-9-13), p. e0161841-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0161841

DOI: 10.1371/journal.pone.0161841.g001

DOI: 10.1371/journal.pone.0161841.t001

DOI: 10.1371/journal.pone.0161841.t002

DOI: 10.1371/journal.pone.0161841.t003

DOI: 10.1371/journal.pone.0161841.s001

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2016

detail.hit.zdb_id: 2267670-3

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Connecting Earth observation to high-throughput biodiversity data

Bush, Alex ; Sollmann, Rahel ; Wilting, Andreas ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Nature Ecology & Evolution Vol. 1, No. 7 ( 2017-06-22)

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In: Nature Ecology & Evolution, Springer Science and Business Media LLC, Vol. 1, No. 7 ( 2017-06-22)

Type of Medium: Online Resource

ISSN: 2397-334X

URL: Article

DOI: 10.1038/s41559-017-0176

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2879715-2

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The founding charter of the Genomic Observatories Network

Davies, Neil ; GOs-COS ; Field, Dawn ; [et al.]

Oxford University Press (OUP) ; 2014

In: GigaScience Vol. 3, No. 1 ( 2014-12)

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In: GigaScience, Oxford University Press (OUP), Vol. 3, No. 1 ( 2014-12)

Type of Medium: Online Resource

ISSN: 2047-217X

URL: Article

DOI: 10.1186/2047-217X-3-2

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2014

detail.hit.zdb_id: 2708999-X

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Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles

Andújar, Carmelo ; Pérez‐González, Sergio ; Arribas, Paula ; [et al.]

Wiley ; 2017

In: Molecular Ecology Vol. 26, No. 21 ( 2017-11), p. 6053-6070

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In: Molecular Ecology, Wiley, Vol. 26, No. 21 ( 2017-11), p. 6053-6070

Abstract: Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species’ habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below‐ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement inside the soil. We studied a species‐rich endogean ground beetle lineage, Typhlocharina, including three genera and more than 60 species, as a model for the evolutionary biology of dispersal and speciation in the deep soil . A time‐calibrated molecular phylogeny generated from 〉 400 individuals was used to delimit candidate species, to study the accumulation of lineages through space and time by species–area–age relationships and to determine the geographical structure of the diversification using the relationship between phylogenetic and geographic distances across the phylogeny. Our results indicated a small spatial scale of speciation in Typhlocharina and low dispersal capacity combined with sporadic long distance, presumably passive dispersal events that fuelled the speciation process. Analysis of lineage growth within Typhlocharina revealed a richness plateau correlated with the range of distribution of lineages, suggesting a long‐term species richness equilibrium mediated by density dependence through limits of habitat availability. The interplay of area‐ and age‐dependent processes ruling the lineage diversification in Typhlocharina may serve as a general model for the evolution of high species diversity in endogean mesofauna.

Type of Medium: Online Resource

ISSN: 0962-1083 , 1365-294X

URL: Issue

URL: Article

DOI: 10.1111/mec.2017.26.issue-21

DOI: 10.1111/mec.14358

RVK:

WA 15000

Language: English

Publisher: Wiley

Publication Date: 2017

detail.hit.zdb_id: 2020749-9

detail.hit.zdb_id: 1126687-9

SSG: 12

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