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. 2017 Jun 12;7(14):5435-5453.
doi: 10.1002/ece3.3123. eCollection 2017 Jul.

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)

Tina E Berry  1 , Sylvia K Osterrieder  2 , Dáithí C Murray  1 , Megan L Coghlan  1 , Anthony J Richardson  3 , Alicia K Grealy  1 , Michael Stat  1 , Lars Bejder  4 , Michael Bunce  1
Affiliations

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)

Tina E Berry et al. Ecol Evol. .

Abstract

The analysis of apex predator diet has the ability to deliver valuable insights into ecosystem health, and the potential impacts a predator might have on commercially relevant species. The Australian sea lion (Neophoca cinerea) is an endemic apex predator and one of the world's most endangered pinnipeds. Given that prey availability is vital to the survival of top predators, this study set out to understand what dietary information DNA metabarcoding could yield from 36 sea lion scats collected across 1,500 km of its distribution in southwest Western Australia. A combination of PCR assays were designed to target a variety of potential sea lion prey, including mammals, fish, crustaceans, cephalopods, and birds. Over 1.2 million metabarcodes identified six classes from three phyla, together representing over 80 taxa. The results confirm that the Australian sea lion is a wide-ranging opportunistic predator that consumes an array of mainly demersal fauna. Further, the important commercial species Sepioteuthis australis (southern calamari squid) and Panulirus cygnus (western rock lobster) were detected, but were present in <25% of samples. Some of the taxa identified, such as fish, sharks and rays, clarify previous knowledge of sea lion prey, and some, such as eel taxa and two gastropod species, represent new dietary insights. Even with modest sample sizes, a spatial analysis of taxa and operational taxonomic units found within the scat shows significant differences in diet between many of the sample locations and identifies the primary taxa that are driving this variance. This study provides new insights into the diet of this endangered predator and confirms the efficacy of DNA metabarcoding of scat as a noninvasive tool to more broadly define regional biodiversity.

Keywords: DNA metabarcoding; Neophoca cinerea; apex predator; dietary scat analysis; next generation sequencing.

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Figures

Figure 1
Figure 1
The Australian sea lion (Neophoca cinerea) at Seal Island, Shoalwater Bay, Western Australia
Figure 2
Figure 2
Sampling sites for metabarcoding study; Map of Australia, with inset showing southern Western Australian sampling sites (number of scats in brackets). The shaded areas denote the range of the Australian sea lion across Australia and within Western Australia
Figure 3
Figure 3
Sea lion diet: Classes of Taxa detected across the five WA study sites. The frequency a class of prey taxa was identified at each site using metabarcoding
Figure 4
Figure 4
Metabarcoding of sea lion diet analyzed using ordinal and operational taxonomic unit (OTU) assignments. The number of times an order within (a) Actinopterygii and (b) Chondrichthyes was detected at each site as a proportion of the number of scat samples taken from each sample location. The OTU analysis of the Fish16S assay (c) demonstrates clear divisions between the genetic diversity of fish in the sample sites and between those samples sourced in the Indian Ocean compared with those from the Southern Ocean. The data used for (c) can be found in Table A9
Figure 5
Figure 5
Sea lion diet: Orders of Cephalopod detected. The number of times an order within Cephalopoda was detected at each site as a proportion of the scat samples taken from each area. Data were obtained using the Ceph 16S, S_Ceph 16S, and Plank COI assays
Figure 6
Figure 6
Multivariate analysis of all metabarcoding data assigned a taxonomic rank. (a) metaMDS plot comparing A taxa from the different sites of collection, and (b) the dietary differences between the sea lions of the Southern and Indian Oceans, centroids are marked with a triangles
Figure 7
Figure 7
Indicator species analysis. Indval results from the total metabarcoding dataset showing the taxa characterizing each area and thus driving variations in sea lion diet between (a) sites, (b) oceans (all p values <.05)
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