Dual-locus DNA metabarcoding reveals southern hairy-nosed wombats (Lasiorhinus latifrons Owen) have a summer diet dominated by toxic invasive plants

Abstract

Habitat degradation and summer droughts severely restrict feeding options for the endangered southern hairy-nosed wombat (SHNW; Lasiorhinus latifrons). We reconstructed SHNW summer diets by DNA metabarcoding from feces. We initially validated rbcL and ndhJ diet reconstructions using autopsied and captive animals. Subsequent diet reconstructions of wild wombats broadly reflected vegetative ground cover, implying local rather than long-range foraging. Diets were all dominated by alien invasives. Chemical analysis of alien food revealed Carrichtera annua contains high levels of glucosinolates. Clinical examination (7 animals) and autopsy (12 animals) revealed that the most degraded site also contained most individuals showing signs of glucosinolate poisoning. We infer that dietary poisoning through the ingestion of alien invasives may have contributed to the recent population crashes in the region. In floristically diverse sites, individuals appear to be able to manage glucosinolate intake by avoidance or episodic feeding but this strategy is less tractable in the most degraded sites. We conclude that recovery of the most affected populations may require effective Carrichtera management and interim supplementary feeding. More generally, we argue that protection against population decline by poisoning in territorial herbivores requires knowledge of their diet and of those food plants containing toxic principles.

Fig 1. Diets of deceased southern hairy nosed wombats.

Diets reconstructed from three parts of the alimentary canal (stomach, long intestine and fecal [scat] samples) using ndhJ (panel A) and rbcL (panel B). Histograms represent percentage of ndhJ or rbcL barcodes matching one of the species shown in the margin. Codes on x-axis indicate the organ used, a numeric indication of year (12 = 2012), a numeric identifier of the animal. The final letter (A-C) indicates sample replicates, with technical replicates possessing identical letters.

Fig 2. Within-animal variation in reconstructed diets of deceased southern hairy nosed wombats.

Diets reconstructed using ndhJ sequences recovered from replicated stomach and fecal samples of three animals (A-C), with one animal yielding only fecal samples (D). Histograms represent percentage of reference ndhJ barcodes matching one of the species shown in the panel for: (A) stomach and fecal profiles from animal 282; (B) stomach and fecal profiles from animal 317; (C) stomach and fecal profiles from animal 646 and D technical replicates of a fecal profiles of animal 190.

Fig 3. Diets of captive southern hairy nosed wombats.

Diets reconstructed using ndhJ sequences from feces of three zoo animals (Zoo A-C) provided a semi-controlled diet. Histograms represent percentage of reference ndhJ barcodes matching species shown in the panel.

Fig 4. Summer diets of southern hairy nosed wombats in the Murraylands reconstructed from ndhJ sequences.

Panel A shows population-wide diets reconstructed using ndhJ sequences from all samples in Moorunde, Kooloola and Portee sites. Panel B shows diets of individual samples collected in each of the three sites. Diets are represented as the percentage of sequences matching to one of the species shown in the key.

Fig 5. Principal Component Analysis (PCA) of reconstructed diets from three locations.

PCA of ndhJ sequences from fresh feces of southern hairy nosed wombats collected in: Moorunde (red triangles); Kooloola (inverted blue triangles) and Portee (green circles) in the Murraylands, South Australia. The three axes represent 80% of total variation.

Fig 6. Summer diets of southern hairy nosed wombats in the Murraylands reconstructed using RbcL sequences.

Diets reconstructed using RbcL sequences recovered from southern hairy nosed wombat scats. Panel A shows the population-wide diets reconstructed using rbcL sequences from all samples collected in Moorunde, Kooloola and Portee sites. Panel B shows the diets of individual samples collected in each of the three sites. Diets are represented as the percentage of sequences matching to one of the species shown in the key.