NMNS Avian DNA Barcode Project

Данные в формате DwC-A	Скачать 191 Записи в English (29 KB) - Частота обновления: as needed
Метаданные в формате EML	Скачать в English (33 KB)
Метаданные в формате RTF	Скачать в English (17 KB)

Описание

This project documents bird specimens collected across Taiwan from 1991 to 2012, as part of an effort to preserve avian genetic resources and contribute to the knowledge of biodiversity in Taiwan and globally. Specimens were obtained from naturally deceased individuals and non-lethal sources such as window collisions, banding mortality, and rescue center mortalities. These were donated by a range of contributors, including private individuals, ornithological societies, universities, conservation agencies, wildlife rescue centers and others. From 2012 to 2013, specimens underwent wet lab procedures at the National Museum of Natural Science (NMNS), Taichung. Muscle tissue was sampled under sterile conditions, and DNA was extracted and sequenced targeting the mitochondrial cytochrome c oxidase subunit I (COI) gene, a widely used barcode marker for avian species identification. The dataset comprises 191 records, covering a diverse range of bird species from multiple orders and families, aligned with the 2023 TWBF Checklist of the Birds of Taiwan (Link to checklist: https://www.bird.org.tw/sites/default/files/field/file/download/The%202023%20TWBF%20Checklist%20of%20the%20Birds%20of%20Taiwan%2020240624ed.pdf). Most records are georeferenced to sites across Taiwan. Sequencing data are publicly available via NCBI GenBank, with accession numbers ranging from PV770366 to PV770556. This dataset contributes both morphological and molecular resources to the scientific community, supporting avian taxonomy, DNA barcoding, and long-term conservation research. All bird specimens were collected under the Ornithology Collection of the National Museum of Natural Science (NMNS) and are curated to ensure high standards of preservation, data quality, and accessibility for future research.

Записи данных

Данные этого occurrence ресурса были опубликованы в виде Darwin Core Archive (DwC-A), который является стандартным форматом для обмена данными о биоразнообразии в виде набора из одной или нескольких таблиц. Основная таблица данных содержит 191 записей.

Данный экземпляр IPT архивирует данные и таким образом служит хранилищем данных. Данные и метаданные ресурсов доступны для скачивания в разделе Загрузки. В таблице версий перечислены другие версии ресурса, которые были доступны публично, что позволяет отслеживать изменения, внесенные в ресурс с течением времени.

Версии

В таблице ниже указаны только опубликованные версии ресурса, которые доступны для свободного скачивания.

Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

Hoh D, Yao C (2026). NMNS Avian DNA Barcode Project. Version 1.1. National Museum of Natural Science. Occurrence dataset. https://ipt.taibif.tw/resource?r=nmns_avian_dna_barcode_project&v=1.1

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является National Museum of Natural Science. Эта работа находится под лицензией Creative Commons Attribution (CC-BY 4.0).

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 586c3f2c-4bb4-4581-b33e-5bfc9a9c9bd5. National Museum of Natural Science отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке Taiwan Biodiversity Information Facility.

Ключевые слова

Occurrence; Specimen

Контакты

Daphne Hoh

Originator

Postdoctoral Researcher

Taiwan Biodiversity Information Facility

Taipei

daphnehohzhiwei@gmail.com

https://orcid.org/0000-0002-7810-1034

Chiou-Ju Yao

Metadata Provider ●
Point Of Contact

Associate Research Fellow

National Museum of Natural Science

No.1, Guanqian Rd., North Dist.

404023 Taichung

yaocj@nmns.edu.tw

Географический охват

Taiwan

Ограничивающие координаты	Юг Запад [21,952, 118,367], Север Восток [25,485, 122,106]

Таксономический охват

Описание отсутсвует

Kingdom	Animalia
Phylum	Chordata
Class	Aves
Order	Suliformes, Cuculiformes, Anseriformes, Galliformes, Passeriformes, Pelecaniformes, Falconiformes, Accipitriformes, Gruiformes, Columbiformes, Apodiformes, Charadriiformes, Bucerotiformes, Podicipediformes, Strigiformes, Coraciiformes, Piciformes
Family	Laridae, Corvidae, Upupidae, Phylloscopidae, Columbidae, Motacillidae, Muscicapidae, Cuculidae, Podicipedidae, Pycnonotidae, Glareolidae, Picidae, Sturnidae, Alcedinidae, Scolopacidae, Sterna, Reguliidae, Charadriidae, Threskiornithidae, Accipitridae, Campephagidae, Hirundinidae, Strigidae, Phasianidae, Falconidae, Timaliidae, Apodidae, Turdidae, Rallidae, Tytonidae, Sulidae, Turnicidae, Laniidae, Paridae, Ardeidae, Locustellidae, Oriolidae, Dicruridae, Anatidae, Pittidae

Временной охват

Дата начала / Дата окончания	0029-09-12 / 0028-04-03

Данные проекта

Описание отсутсвует

Название	NMNS Avian DNA Barcode Project
Финансирование	This project is supported by subsidies from the Ministry of Agriculture, Forestry, and the Nature Conservation Agency, Taiwan, for the projects titled "Operation of the Cryopreservation Genetic Material Repository and Utilization of Genetic Material" (Part 2 of 3) in 2012 and (Part 3 of 3) in 2013.

Методы сбора

Bird specimens were primarily obtained from dead individuals found in the field across Taiwan. These specimens were donated by a variety of sources, including private individuals, ornithological societies, airport authorities, universities, government conservation and research agencies, national parks, and bird conservation organizations. A smaller proportion originated from window collisions, mortalities during bird banding research, or birds that did not survive rescue efforts at wildlife rescue and rehabilitation centers.

Охват исследования	This study focuses on avian specimens collected across Taiwan. The majority of specimens were sourced from naturally deceased individuals found in the field, with additional contributions from bird collisions, banding mortalities, and unsuccessful wildlife rescue cases. Sampling and genetic analysis were performed at the National Museum of Natural Science (NMNS), Taichung. The dataset encompasses a temporal span of collections work from 1991 to 2012, and molecular work from 2012 to 2013, primarily focusing on the mitochondrial COI region for species identification and genetic resource preservation.
Контроль качества	The occurrence data of the bird specimens collected was formatted into the Darwin Core format (Darwin Core Maintenance Group, 2023) and validated using GBIF's Data Validator tool (https://www.gbif.org/tools/data-validator).

Охват исследования

This study focuses on avian specimens collected across Taiwan. The majority of specimens were sourced from naturally deceased individuals found in the field, with additional contributions from bird collisions, banding mortalities, and unsuccessful wildlife rescue cases. Sampling and genetic analysis were performed at the National Museum of Natural Science (NMNS), Taichung. The dataset encompasses a temporal span of collections work from 1991 to 2012, and molecular work from 2012 to 2013, primarily focusing on the mitochondrial COI region for species identification and genetic resource preservation.

Контроль качества

The occurrence data of the bird specimens collected was formatted into the Darwin Core format (Darwin Core Maintenance Group, 2023) and validated using GBIF's Data Validator tool (https://www.gbif.org/tools/data-validator).

Описание этапа методики:

Sample collection: Each specimen was sampled individually, with all procedures conducted by personnel wearing masks and freshly disinfected rubber gloves. Prior to sampling, the workbench, all equipment (including gloves and the drill machine), and the bone sampling area were thoroughly cleaned using a 10% bleach solution. A sterile stainless steel instrument, autoclaved prior to use, was employed to collect muscle samples weighing between 10 and 25 mg. To minimize the risk of cross-contamination, each drill bit was used only once. Following collection, all samples were promptly stored at –20 °C until further processing.
DNA Extraction: DNA extraction of the muscle samples was performed at a dedicated workbench in the National Museum of Natural Science, Taichung. Prior to use, the bench surface was thoroughly sterilized using 75% alcohol followed by a 10% bleach solution. DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, 19300 Germantown Rd., Germantown, MD 20874, United States), following the manufacturer’s recommended protocol.
Polymerase Chain Reaction (PCR) and DNA Sequencing: The extracted DNA was subsequently amplified using PCR to target specific regions of mitochondrial DNA, including the control region and the cytochrome c oxidase subunit I (COI) gene. Because the specimens were aged and had been stored under conditions of elevated temperature and humidity, the DNA was expected to be significantly degraded. To accommodate this, primers were designed to amplify short fragments ranging from 200 to 300 base pairs. PCR was conducted in a 20 μL reaction mixture containing 10–80 ng of template DNA, 0.2 mM of dNTPs, 0.1 μM of each primer, 0.5 units of Ex Taq DNA Polymerase (TaKaRa), and 1× PCR buffer. Amplification was carried out using a Biometra TProfessional thermocycler with the following thermal profile: an initial denaturation at 95 °C for 5 minutes; 40 cycles of 30 seconds at 94 °C, 30 seconds at the primer-specific annealing temperature, and 30 seconds at 72 °C; followed by a final extension at 72 °C for 5 minutes. PCR products were visualized by electrophoresis on a 2% agarose gel to confirm amplification success. Positive amplicons were purified using the QIAquick PCR Purification Kit (Qiagen), and direct sequencing was performed following the PRISM™ Ready Reaction Dye Deoxy Terminator Protocol. Sequencing was conducted on an ABI 3730XL Genetic Analyzer (Applied Biosystems Inc., Foster City, CA, USA).

Данные коллекции

Название коллекции	Ornithology Collection

Дополнительные метаданные

Альтернативные идентификаторы	586c3f2c-4bb4-4581-b33e-5bfc9a9c9bd5
	https://ipt.taibif.tw/resource?r=nmns_avian_dna_barcode_project