DNA mini‐barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species

Rodrigues, Nayra T.; Saranholi, Bruno H.; Angeloni, Thais A.; Pasqualotto, Nielson; Chiarello, Adriano Garcia; Galetti, Pedro M.

doi:10.1002/ece3.5863

Cited by 12 publications

(6 citation statements)

References 48 publications

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“…We did attempt to identify seeds to as fine a level as possible where these had been preserved well, but neither invertebrates nor green plant tissues were identified further. It would be advantageous to conduct more detailed dietary analyses by scoring the relative abundance of each specific food item by estimating its percentage occurrence in fresher or better preserved samples [15], to explore the utility of DNA-based mini-or meta-barcoding techniques to identify the full range of dietary items, e.g., [62], or to run cafeteria-style trials in the field or laboratory [63]. Except for cafeteria trials, these latter techniques have the advantage that they can be used on faecal samples.…”

Section: Discussionmentioning

confidence: 99%

Foraging and Food Selection in a Desert Rodent: Diet Shifts of the Sandy Inland Mouse between Population Booms and Busts

Yip

Dickman

2023

Animals

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Seeds are commonly viewed as the mainstay of the diet of desert rodents. We describe the diet of a common Australian desert rodent, the sandy inland mouse Pseudomys hermannsburgensis, using direct observations of free-living animals and analysis of the stomach contents of preserved specimens. Direct observations showed that animals forage mostly on the ground surface and eat seeds from a wide range of plant species, as well as invertebrates and occasional green plant material. Stomach content analysis revealed no differences in the presence or absence of these three major food groups between seasons or the sexes. However, invertebrates were more prominent in the diet of mice during prolonged, dry, population ‘bust’ periods compared with post-rain population ‘boom’ periods, with this dietary shift probably reflecting a scarcity of seeds during the busts. The results confirm that seed is an important component of the diet of P. hermannsburgensis, with 92% of stomachs containing seed. The results also support the classification of the species as omnivorous rather than granivorous, with 70% of stomachs containing invertebrates and over half the specimens analysed containing both seeds and invertebrates. We suggest that dietary flexibility is important for rodent persistence in Australia’s climatically unpredictable arid regions.

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Section: Discussionmentioning

confidence: 99%

Foraging and Food Selection in a Desert Rodent: Diet Shifts of the Sandy Inland Mouse between Population Booms and Busts

Yip

Dickman

2023

Animals

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“…Although COI presents the most extensive reference database for barcode studies (Hebert, Ratnasingham, & de Waard, 2003), there is a challenge in the development of primers that amplify a small fragment capable of identifying a high proportion of taxa (Deagle et al, 2014), avoiding COI primer mismatch (Kocher, de Thoisy, Catzeflis, Huguin, et al, 2017). Mini-COI sequences are usually developed to identify species within vertebrate groups, as recently developed to leporids (Rodrigues et al, 2020) and elasmobranchs (Zahn, Silva, & Hellberg, 2020). Nevertheless, a substantial amplification bias towards non-metazoan taxa has been identified with COI, which can hinder the recovery of all vertebrate taxa in an environmental sample (Harper et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance

Carvalho

Oliveira

Rodriguez-Castro

et al. 2021

Preprint

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Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been increasingly recognized as a powerful tool for biodiversity assessment and conservation management. However, because of uncertainties on the efficiency of eDNA/iDNA approach in comparison to conventional methods, its use to assess the vertebrate diversity is still rare. Here we assessed the efficiency of eDNA/iDNA in comparison to conventional methods to survey vertebrate diversity across several type of samplers, vertebrate groups, and location (tropical vs temperate zones), as well as its efficiency to be used as a proxy for relative abundance or biomass across different molecular methods (qPCR and metabarcoding) and types of experiments (in the lab or in the field). The metanalysis showed that, in general, there is no difference in the number of species detected or number of sites that a target species was detected when using eDNA/iDNA or conventional methods, suggesting that eDNA/iDNA and conventional methods were equally efficient in characterizing the biodiversity. However, for water sampler and fish, separately, the risk of not finding a species was greater using conventional method than eDNA, suggesting that eDNA/iDNA was more efficient in finding the target species. Abundance and biomass showed similar correlation patterns, and there was a positive correlation between eDNA/iDNA and abundance/biomass data, suggesting that eDNA/iDNA can be used as a proxy for abundance and biomass. Therefore, eDNA/iDNA has proved to be an efficient tool to assess vertebrate diversity in terms of both diversity of species and abundance or biomass.

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“…In the agricultural matrix, the three transects were sampled on dirt roads located between crop/pasture fields or between crop fields and native vegetation areas, sampling a wide variety of agricultural land uses. Leporids ( Lepus europaeus and Sylvilagus minensis ) faecal samples were discerned using DNA mini‐barcoding (Rodrigues et al., 2020). In addition, we installed one camera trap (Reconyx, model HC500) in three native vegetation sites per landscape.…”

Section: Methodsmentioning

confidence: 99%

Landscape heterogeneity can partially offset negative effects of habitat loss on mammalian biodiversity in agroecosystems

do Carmo Pônzio,

Pasqualotto,

Zanin

et al. 2023

Journal of Applied Ecology

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Intensive, large‐scale agriculture promotes the conversion of natural habitats and diversified crops into monocultures, decreasing both native vegetation cover and landscape heterogeneity, leading to landscape simplification. Yet, a key knowledge gap persists on the relative impacts of the loss of native vegetation and landscape heterogeneity on biodiversity. Addressing this gap is pressing to support policies that conciliate agricultural production and biodiversity conservation and to move forward some scientific controversies, as the ‘land sharing versus land sparing’ and ‘habitat loss versus fragmentation’ debates. Through a hierarchical sampling design that maximised variation, while minimising correlation, between landscape heterogeneity and native vegetation cover, we recorded the occurrence of medium and large‐bodied mammals in native vegetation and agricultural areas of 55 landscapes in a global conservation hotspot and a key commodity production area—the Brazilian Savanna, Cerrado. We compared simple, additive and interactive models to investigate the effects of landscape heterogeneity and native vegetation cover on richness and composition of native and invasive mammals. Native and invasive mammal communities were affected by both native vegetation cover and landscape heterogeneity, although the effects of the first was stronger than the later. Both aspects had positive effects on native species richness and negative effects on invasive species richness, indicating that the loss of native vegetation and the reduction in landscape heterogeneity lead to biotic homogenisation. Yet, while landscape heterogeneity benefited most native species, the direction of its effect varied among invasive species and depended on native vegetation cover. Synthesis and applications. Besides reducing habitat loss, avoiding landscape homogenisation is key for conciliating agricultural production and biodiversity conservation, pointing to the relevance of policies encouraging crop diversification. As increasing landscape heterogeneity can in part compensate the negative effects of losing native habitat on biodiversity in agroecosystems, policies can gain feasibility by adjusting the balance between native vegetation cover and landscape heterogeneity according to what best suits local restraints and demands.

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DNA mini‐barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species

Cited by 12 publications

References 48 publications

Foraging and Food Selection in a Desert Rodent: Diet Shifts of the Sandy Inland Mouse between Population Booms and Busts

Foraging and Food Selection in a Desert Rodent: Diet Shifts of the Sandy Inland Mouse between Population Booms and Busts

Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance

Landscape heterogeneity can partially offset negative effects of habitat loss on mammalian biodiversity in agroecosystems

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