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Fig 5 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library

Fig 5. Neighbour-joining tree showing all available DNA barcodes for species in family Rhinolophidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, JV = Java Indonesia, IND = India, CH = China, CM = Cambodia, MN = Myanmar. https://doi.org/10.1371/journal.pone.0179555.g005

Fig 4 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library

Fig 4. Neighbour-joining tree showing all available DNA barcodes for species in family Hipposideridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China, CM = Cambodia. https://doi.org/10.1371/journal.pone.0179555.g004

Fig 2 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library

Fig 2. Neighbour-joining tree showing all available DNA barcodes for species in family Pteropodidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, JV = Java, Indonesia, BN = Borneo (including Sabah, Sarawak, Brunei and Kalimantan), TH = Thailand, LA = Laos. https://doi.org/10.1371/journal.pone.0179555.g002

Fig 3 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library

Fig 3. Neighbour-joining tree showing all available DNA barcodes for species in families Emballonuridae, Megadermatidae, Molossidae and Nycteridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China. https://doi.org/10.1371/journal.pone.0179555.g003

opencc-by-4.0Nov 2024View details →

Reference Sequence Library Resources - Maine-eDNA

The following files and resources are associated with the Maine-eDNA Reference Library Research Group - aiming to create reference sequence library resources for researchers part of Maine-eDNA or otherwise interested in leveraging eDNA tools for research in the Gulf of Maine. These include: <ul> <li> RoughWorkflow.zip </li> <ul> <li> contains a NCBI scraping script to build reference databases based on an input species list, a configuration file for the script, and genbankr version - most useful for shorter species lists (time-intensive) </li> </ul> <li> 12S_REFDB.fasta </li> <ul> <li> A DADA2-compliant reference library for 12S sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list </li> </ul> <li> COI_REFDB.fasta </li> <ul> <li> A DADA2-compliant reference library for COI sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list </li> </ul> <li> GitHub Repo - referee - <a href="https://github.com/BigelowLab/referee">https://github.com/BigelowLab/referee</a> </li> <ul> <li> Scripts for building reference databases for the Maine-eDNA project through downloading GenBank - this workflow is suggested especially for large species lists </li> </ul> <li> GitHub Repo - refdbtools - <a href="https://github.com/BigelowLab/refdbtools">https://github.com/BigelowLab/refdbtools</a>  </li> <ul> <li> R language package to assist in making eDNA reference databases </li> </ul> <li> SpeciesListMeta_Shareable.xlsx </li> <ul> <li> Describes the sources from which the GNRMaineSpecies_May2024.csv and GNRMaineTaxonomiedSpecies_May2024.csv species lists were compiled - sources not associated with a link were found as separate files and are hosted elsewhere. Species list sources are courtesy of public datasets, Maine-eDNA researchers, and collaborators </li> </ul> <li> GNRMaineSpecies_May2024.csv </li> <ul> <li> A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (full results) </li> </ul> <li> GNRMaineTaxonomiedSpecies_May2024.csv </li> <ul> <li> A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (only species results that could be resolved with taxonomy) </li> </ul> </ul>   Contact Beth Y. Davis - bethy.davis4@gmail.com for questions   ### Changelog: May 16, 2023 (Version 1.0) - Initial upload July 11, 2023 (Version 1.1) - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList May 20, 2024 (Version v3) -  Additional cleaning to correct deduplication errors and ran taxize's gnr_resolve to resolve names and fill out taxonomy. The version update adds two files, GNRMaineSpecies_May2024.csv containing the full result of gnr_resolve, and GNRMaineTaxonomiedSpecies_May2024.csv contains only those species from the original list that could be resolved with taxonomy. The SpeciesListMeta_Shareable.csv has not been updated but is still an accurate tracker of the sources from which the species names were gained from. November 27, 2024 (Version 4.0) - Updated Zenodo description and added the RoughWorkflow R files, 12S and COI files

opencc-by-4.0Dec 2020View details →

InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning

LTR retrotransposons are mobile elements that make up the major part of most plant genomes. Their identification and annotation via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their involvement in the variation in genome size, these elements are also associated in the function and structure of different chromosomal regions and in the alteration of the function of coding regions, among others. Several plant retrotransposon sequence databases of LTR retrotransposons are available with public access such as PGSB, RepetDB or restricted access such as Repbase. Although they are useful for approaches to identify LTR-RTs in new genomes by similarity, the elements of these databases are not classified down to the lineage/family level. with great depth.  Here, we present InpactorDB a semi-curated dataset composed of 130,511 elements from 195 plant genomes (belonging to 108 plant species), classified down to the lineage level. This data set has been used to train two deep neural networks (one fully connected and one convolutional) for fast classification of elements. Used in lineage-level classification approaches, we obtain a score above 98% of F1-score, precision and recall.  In order to classify elements of the ‘LTR_STRUC’ and ‘EDTA’ datasets, we used the methodology proposed by Inpactor, which uses homology-based strategy with known coding domains belonging to LTR-RTs. We utilized the RexDB  domain library as reference. LTR-RTs were classified into superfamilies, Gypsy (RLG) or Copia (RLC) and sub-classified into lineages according to the similarities of five different amino acid reference domains (GAG, AP, RT, RNAseH, and INT domains). In addition, we applied filters to remove keep only intact elements: 1) to remove predicted elements with domains from two different superfamilies (i.e. Gypsy and Copia), 2) or elements with domains belonging to two or more different lineages, 3) to remove elements with lengths different than those reported by Gypsy Database (GyDB) with a tolerance of 20%, 4) to delete incomplete elements which has less than three identified domains, and 5) to remove elements with insertions of TE class II (reported in Repbase).  The final non-redundant version of InpactorDB consists of 67,305 LTR retrotransposons. Both redundant and non-redundant versions of InpactorDB are available in Fasta format in which sequences have identifiers with the following general Identification code: >Superfamily-Lineage-plant_family-specie-source-length-ID, Where Superfamily can is either RLC (for Copia) or RLG (for Gypsy), Lineage/family follows following the RexDB nomenclature, source (can be Repbase, RepetDB, PGSB, LTR_STRUC or EDTA datasets), length, and ID, is a unique number which identify each element inside the InpactorDB.

Figure 3 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library

Figure 3. Mounted specimens illustrating the species of Microgastrinae recovered in this study. A, Cotesia glabrata Telenga ex Carcharodus alceae, Italy. Adult plus cocoons. Gregarious parasitoid; brood sizes vary considerably, host usually well grown or prepupal when killed. The other Cotesia species (near glabrata) look similar and behave in the same way. B, Dolichogenidea sp. near sicaria Marshall, ex Carcharodus alceae, Spain. Adult plus cocoon. Solitary parasitoid, killing the host while still quite young. C, Microgaster australis Thomson, ex Muschampia stauderi, Greece. Adult plus cocoon. Solitary parasitoid, usually killing the host as a prepupa. D, Microgaster nobilis Reinhard, ex Carcharodus alceae, Spain. Adult plus cocoon. Solitary parasitoid, usually killing the host as a prepupa. All specimens are in the collection of the National Museums of Scotland.

Figure 4 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library

Figure 4. Interaction matrices showing the recorded interactions of Hesperiidae and their hostplants (A), Hesperiidae and their parasitoids (B) and parasitoids and hostplants of Hesperiidae (C). White squares indicate recorded interactions between the taxa in the corresponding row and column, while blue squares indicate lack of interaction.

Figure 2 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library

Figure 2. Circular cladogram showing ecological interactions among European and North African Hesperiidae, their hostplants, and their microgastrine parasitoids, recovered through DNA barcoding for Hesperiidae and/or parasitoids. Hesperiid, parasitoid and plant cladograms are coloured in orange, blue and green, respectively. Lines representing interactions with parasitoids are coloured in blue, while lines involving hostplant interactions are coloured in green.

Figure 1 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library

Figure 1. Representation of the study system. Hesperiid larvae feeding on their hostplants can be attacked by a number of parasitoids, which can in turn be attacked by various hyperparasitoids. A, Spialia rosae on its hostplant Rosa sicula. B, third instar larva of Sp. rosae on a silk shelter. C, Microgaster australis parasitizing an L3 Sp. rosae larva. D, Gelis sp. parasitizing M. australis on its cocoon after emerging from the Sp. rosae larva. Drawings by Martí Franch.

opencc-by-4.0May 2024View details →

Public reference library for edible dormouse calls

The acoustics of small mammals, particularly dormice species, are generally understudied. We explored the vocalisations and acoustic behaviour of the edible dormouse (Glis glis) in various environments in Catalonia (northern Iberian Peninsula) using ultrasound recorders between 2022 and 2023. Up to five different types of calls were identified in various environmental conditions (captivity and free-ranging animals) and developmental stages, from pups to adults. Additionally, one new call type was described, highlighting the plasticity of their vocalisations, and ultrasonic sound production was discovered in pups, suggesting ontogenetic changes in the vocal repertoire. With this project, we emphasise the potential of the acoustic method as a non-invasive tool for studying ecological behaviours and interactions, or early detection of the species in the natural environment. We, hereby, provide an open reference library for edible dormouse calls, laying the groundwork for a better understanding of its acoustics, behaviour and conservation. The compilation provides five clean sequences of high quality for each of the five call types recorded under different environmental conditions (totalling 35 recordings). This includes the chirp (captivity and wild), blow (captivity), aggressive call (captivity and wild), pups during manipulation (wild) and free-ranging pups (wild). The collection of sounds was prepared under the Dormouse Project (<a href="http://www.dormice.org/" target="_blank" rel="noopener">www.dormice.org</a>) This work was supported by the Barcelona Zoo Fundation under the Research and Conservation Program Grant; Generalitat de Catalunya under Grant number ARD264/23/000001; and Diputació de Barcelona under Grant number 2023/0005732.