Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.

Download Full-text

Mammal diversity among vertical strata and the evaluation of a survey technique in a central Amazonian forest

Papéis Avulsos de Zoologia ◽

10.11606/1807-0205/2021.61.33 ◽

2021 ◽

Vol 61 ◽

pp. e20216133

Author(s):

Alexander Roldán Arévalo-Sandi ◽

André Luis Sousa Gonçalves ◽

Kota Onizawa ◽

Tsuneaki Yabe ◽

Wilson Roberto Spironello

Keyword(s):

Camera Trap ◽

Camera Traps ◽

Sampling Effort ◽

Mammal Species ◽

Lowland Forest ◽

Survey Technique ◽

Terrestrial Habitats ◽

Common Technique ◽

The Difference ◽

Mammal Diversity

Mammal groups have a vast variety of habitats, which include aquatic, aerial, arboreal, and terrestrial. For terrestrial habitats, camera traps are used as a common technique to record mammals and other vertebrates and have been recently utilized to observe arboreal animals as well. Here, we compare the difference in mammal diversity between floor and canopy strata and evaluate the use of camera trapping in a lowland forest in central Amazon. We installed nine paired camera traps, one in the canopy stratum and other in the floor stratum, in the Alto Cuieiras Biological Reserve (Brazilian Amazon). With a sampling effort of 720 camera-days, we recorded 30 mammal species: nine in canopy strata, 14 in floor strata, and seven in scansorial strata (sharing both strata). On the forest floor, the species with the greatest abundance was Myoprocta acouchy; in the canopy, Isothrix paguros had the greatest abundance; and among the scansorial species, Proechymis sp. was the most abundant. Our results show the differences in mammal diversity between floor and canopy strata; canopy strata contained more small and frugivorous mammals. Although we obtained a relatively low sampling effort with the camera-trap method compared with other studies utilizing different techniques, our results were especially similar to those of previous studies that worked with canopy and floor strata. Thus, camera trap can be very effective for recording short periods of time, and this method is less physically exhaustive and expensive for researchers to study vertical strata.

Download Full-text

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

PLoS ONE ◽

10.1371/journal.pone.0179555 ◽

2017 ◽

Vol 12 (7) ◽

pp. e0179555 ◽

Cited By ~ 5

Author(s):

Voon-Ching Lim ◽

Rosli Ramli ◽

Subha Bhassu ◽

John-James Wilson

Keyword(s):

Dna Barcode ◽

Peninsular Malaysia ◽

Reference Library

Download Full-text

A camera trap record of Asiatic Golden Cat Catopuma temminckii (Vigors & Horsfield, 1827) (Mammalia: Carnivora: Felidae) in State Land Forest, Merapoh, Pahang, Malaysia

Journal of Threatened Taxa ◽

10.11609/jott.6492.13.6.18651-18654 ◽

2021 ◽

Vol 13 (6) ◽

pp. 18651-18654

Author(s):

Lukman Ismail ◽

Syafiq Sulaiman ◽

Muhammad Izzat Hakimi Mat Nafi ◽

Muhammad Syafiq Mohmad Nor ◽

Nur Izyan Fathiah Saimeh ◽

...

Keyword(s):

Protected Area ◽

National Park ◽

Camera Trap ◽

Peninsular Malaysia ◽

Camera Traps ◽

Area Network ◽

Single Camera ◽

Wildlife Corridors ◽

Forest Reserve ◽

Wildlife Corridor

The Asiatic Golden Cat Catopuma temminckii is poorly studied in Peninsular Malaysia. We deployed 12 camera traps to assess the wildlife diversity in the unprotected State Land Forest of Merapoh, Pahang State. During the period from August to October 2019, one Asiatic Golden Cat was photographed at a single camera trap station. This record outside the protected area network emphasizes the importance of wildlife corridors. This State Land Forest is located between Forest Reserve and Taman Negara National Park. Therefore, appropriate conservation measures must be taken in order to maintain this site as a wildlife corridor.

Download Full-text

Revisiting the Diversity of Barbonymus (Cypriniformes, Cyprinidae) in Sundaland Using DNA-Based Species Delimitation Methods

Diversity ◽

10.3390/d13070283 ◽

2021 ◽

Vol 13 (7) ◽

pp. 283

Author(s):

Hadi Dahruddin ◽

Arni Sholihah ◽

Tedjo Sukmono ◽

Sopian Sauri ◽

Ujang Nurhaman ◽

...

Keyword(s):

Species Delimitation ◽

Stock Assessment ◽

Dna Barcode ◽

Peninsular Malaysia ◽

Reference Library ◽

Tropical Regions ◽

Operational Taxonomic Units ◽

Inland Fisheries ◽

Large Size ◽

Species Groups

Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of medium- to large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java.

Download Full-text

Notes on the Hoya (Apocynaceae, Asclepiadoideae) from Pergau Forest Reserve, Kelantan, Peninsular Malaysia

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/549/1/012031 ◽

2020 ◽

Vol 549 ◽

pp. 012031

Author(s):

Rahmad Zakaria ◽

Azim Rabbani ◽

Syed Mohd Edhzam Syed Hamzah ◽

Zulhazman Hamzah ◽

Muhammad Faizal

Keyword(s):

Peninsular Malaysia ◽

Forest Reserve

Download Full-text

The wildcat Felis silvestris in northern Turkey: assessment of status using camera trapping

Oryx ◽

10.1017/s0030605310001328 ◽

2011 ◽

Vol 45 (1) ◽

pp. 112-118 ◽

Cited By ~ 11

Author(s):

Özgün Emre Can ◽

İrfan Kandemi̇r ◽

İnci̇ Togan

Keyword(s):

Population Size ◽

Camera Traps ◽

Sampling Effort ◽

Felis Silvestris ◽

Forest Patch ◽

Western Turkey ◽

Lack Of Information ◽

The Status ◽

Capture Recapture ◽

Estimate Population Size

AbstractThe wildcat Felis silvestris is a protected species in Turkey but the lack of information on its status is an obstacle to conservation initiatives. To assess the status of the species we interviewed local forestry and wildlife personnel and conducted field surveys in selected sites in northern, eastern and western Turkey during 2000–2007. In January–May 2006 we surveyed for the wildcat using 16 passive infrared-trigged camera traps in Yaylacı k Research Forest, a 50-km2 forest patch in Yenice Forest in northern Turkey. A total sampling effort of 1,200 camera trap days over 40 km2 yielded photo-captures of eight individual wildcats over five sampling occasions. Using the software MARK to estimate population size the closed capture–recapture model M0, which assumes a constant capture probability among all occasions and individuals, best fitted the capture history data. The wildcat population size in Yaylacı k Research Forest was estimated to be 11 (confidence interval 9–23). Yenice Forest is probably one of the most important areas for the long-term conservation of the wildcat as it is the largest intact forest habitat in Turkey with little human presence, and without human settlements, and with a high diversity of prey species. However, it has been a major logging area and is not protected. The future of Yenice Forest and its wildcat population could be secured by granting this region a protection status and enforcing environmental legislation.

Download Full-text

Small Mammals Diversity in Pasoh Forest Reserve, Negeri Sembilan, Peninsular Malaysia

Pasoh ◽

10.1007/978-4-431-67008-7_29 ◽

2003 ◽

pp. 403-411

Author(s):

Lim Boo Liat ◽

Louis Ratnam ◽

Nor Azman Hussein

Keyword(s):

Small Mammals ◽

Peninsular Malaysia ◽

Forest Reserve ◽

Pasoh Forest Reserve

Download Full-text

A DNA barcode reference library of the French Polynesian shore fishes

10.1101/595793 ◽

2019 ◽

Author(s):

Erwan Delrieu-Trottin ◽

Jeffrey T. Williams ◽

Diane Pitassy ◽

Amy Driskell ◽

Nicolas Hubert ◽

...

Keyword(s):

Dna Barcoding ◽

Biological Diversity ◽

Dna Barcode ◽

Reef Fishes ◽

French Polynesia ◽

Morphological Characters ◽

Reference Library ◽

Society Islands ◽

Extensive Collection ◽

I Gene

AbstractThe emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

Download Full-text