Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data

Ecological Applications : a Publication of the Ecological Society of America
Andrew DopheideRichard D Newcomb

Abstract

Invertebrates are a major component of terrestrial ecosystems, however, estimating their biodiversity is challenging. We compiled an inventory of invertebrate biodiversity along an elevation gradient on the temperate forested island of Hauturu, New Zealand, by DNA barcoding of specimens obtained from leaf litter samples and pitfall traps. We compared the barcodes and biodiversity estimates from this data set with those from a parallel DNA metabarcoding analysis of soil from the same locations, and with pre-existing sequences in reference databases, before exploring the use of combined data sets as a basis for estimating total invertebrate biodiversity. We obtained 1,282 28S and 1,610 COI barcodes from a total of 1,947 invertebrate specimens, which were clustered into 247 (28S) and 366 (COI) OTUs, of which ≤ 10% were represented in GenBank. Coleoptera were most abundant (730 sequenced specimens), followed by Hymenoptera, Diptera, Lepidoptera, and Amphipoda. The most abundant OTU from both the 28S (153 sequences) and COI (140 sequences) data sets was an undescribed beetle from the family Salpingidae. Based on the occurrences of COI OTUs along the elevation gradient, we estimated there are ~1,000 arthropod species (excluding mites...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 1, 1995·Australian and New Zealand Journal of Medicine·M B JamesonV J Harvey
Feb 13, 2001·The Journal of Hand Surgery : Journal of the British Society for Surgery of the Hand·D SimpsonP Kumar
Mar 5, 2003·Proceedings. Biological Sciences·Paul D N HebertJeremy R deWaard
Oct 11, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·K F Armstrong, S L Ball
Oct 11, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·M Alex SmithPaul D N Hebert
Jan 9, 2007·Molecular Phylogenetics and Evolution·Torbjørn EkremElisabeth Stur
Apr 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·John M BurnsPaul D N Hebert
Sep 12, 2008·Molecular Ecology Notes·Sujeevan Ratnasingham, Paul D N Hebert
Feb 3, 2009·Environmental Monitoring and Assessment·D FamulariK J Weston
Aug 12, 2009·Nature Methods·Christopher QuinceWilliam T Sloan
May 12, 2010·The American Naturalist·Andrew J HamiltonJian D L Yen
Aug 17, 2010·Bioinformatics·Robert C Edgar
Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster
Sep 16, 2011·Molecular Ecology·Kenneth AndersenEske Willerslev
Jan 17, 2012·Trends in Ecology & Evolution·Holly M BikW Kelley Thomas
Apr 11, 2012·Molecular Ecology·Pierre TaberletEske Willerslev
May 1, 2012·Nature Methods·Lauren BraggGene W Tyson
Jul 13, 2012·Trends in Ecology & Evolution·Brett R ScheffersWilliam F Laurance
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Jul 19, 2013·PloS One·Sujeevan Ratnasingham, Paul D N Hebert
May 9, 2014·Proceedings of the National Academy of Sciences of the United States of America·Joel GibsonMehrdad Hajibabaei
Oct 9, 2015·GigaScience·Alexei J DrummondNicola Nelson
Jun 24, 2016·Genome Génome / Conseil National De Recherches Canada·Elizabeth L ClareMelania E Cristescu
May 11, 2017·Global Change Biology·Katariina E M VuorinenRisto Virtanen
Jul 1, 2017·Central European Journal of Public Health·Airi OksanenKristina Kunttu
Jul 27, 2017·European Journal of Clinical Nutrition·R Pawlak

❮ Previous
Next ❯

Citations

May 16, 2020·Genome Génome / Conseil National De Recherches Canada·Ben A ParslowMark I Stevens
Nov 12, 2020·Animals : an Open Access Journal From MDPI·Heather J WebsterBettine Jansen van Vuuren
Jan 9, 2021·Ecological Applications : a Publication of the Ecological Society of America·Frances C RatcliffeSofia Consuegra
May 5, 2021·Molecular Ecology Resources·Stephanie D JurburgJonathan M Chase

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.