Metabarcoding of fecal DNA shows dietary diversification in wolves substitutes for ungulates in an island archipelago

Roffler, Gretchen H.; Allen, Jennifer M.; Massey, Aimee; Terborgh, John

doi:10.1002/ecs2.3297

Cited by 32 publications

(58 citation statements)

References 52 publications

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“…Our diagnostic method with species‐specific markers adds to the more frequent studies using DNA from carnivore scats to identify prey (Hacker et al., 2021 ; Quéméré et al., 2021 ; Roffler et al., 2021 ; Shi et al., 2021 ; Smith et al., 2018 ; Xiong et al., 2017 ). These studies primarily used DNA metabarcoding, which produces a vast amount of valuable information but sometimes also needs consideration of potential bias sources in key steps in the data handling process, lack of reference databases of barcodes for many prey species, but also intensive laboratory procedures and considerable bioinformatics training (Hacker et al., 2021 ; Tercel et al., 2021 ; Zinger et al., 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Bernardi

Wikenros

Hedmark

et al. 2021

Ecology and Evolution

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Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA‐based methods applied to detect prey in predators’ scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species‐specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high‐throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost‐efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.

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Section: Discussionmentioning

confidence: 99%

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Bernardi

Wikenros

Hedmark

et al. 2021

Ecology and Evolution

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“…Increased consumption of marine prey items (Giannico & Nagorsen, 1989), consistent with the more robust jaw cranial morphology of M. caurina (Colella, Johnson, et al, 2018), may have enabled the persistence of refugial, and later insular populations within relatively small coastal areas. A similar dietary shift toward increased consumption of marine food sources is also evident in insular NPC wolves (Darimont et al, 2009;Muñoz-Fuentes et al, 2010;Roffler et al, 2021). The insular-continental split within M. caurina is consistent with signatures from numerous other NPC paleoendemic mammals (bears, Heaton et al, 1996;wolves, Weckworth et al, 2005;deer, Latch et al, 2009;ermine, Colella, Lan, et al, 2018;shrews, Demboski & Cook, 2001;deer mice, Sawyer et al, 2019) and also evident in the few associated parasites examined to date (Soboliphyme baturini, Koehler et al, 2007Koehler et al, , 2009Hoberg et al, 2012).…”

Section: Evidence For a Cryptic Species Forested Refugia And Dynamic Contactmentioning

confidence: 78%

Whole‐genome resequencing reveals persistence of forest‐associated mammals in Late Pleistocene refugia along North America’s North Pacific Coast

Colella

Lan

Talbot

et al. 2021

Journal of Biogeography

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Aim: Numerous glacial refugia have been hypothesized along North America's North Pacific Coast that may have increased divergence of refugial taxa, leading to elevated endemism and subsequently clustered hybrid zones following deglaciation. The locations and community composition of these ice-free areas remains controversial, but whole-genome sequences now enable detailed analysis of the demographic and evolutionary histories of refugial taxa. Here, we use genomic data to test spatial and temporal processes of diversification among martens with respect to the Coastal Refugium Hypothesis, to understand the role of climate cycling in shaping diversity across complex landscapes.Location: North America and North Pacific Coast archipelagos. Taxon: North American martens (Martes).Methods: Short-read whole-genome resequencing data were generated for 11 martens: four M. americana, four M. caurina, two hybrids, and one outgroup (Martes zibellina). Sampling was representative of known genetic clades within New World martens, including sampling within insular and continental hybrid zones and along the North Pacific Coast (five island populations). ADMIXTURE, F-statistics, and Dstatistics (ABBA-BABA) were used to identify introgression and infer directionality.Heterozygosity densities, estimated via PSMC, were used to characterize historical demography at and below the species level to infer refugial and colonization processes. Results: Forest-associated Pacific martens (M. caurina) are divided into distinct insular and continental clades consistent with the Coastal Refugium Hypothesis. There was no evidence of introgression on islands that received historical translocations of American pine martens (M. americana), but introgression was detected in two active zones of secondary contact: one insular and one continental. Only early-generational hybrids were identified across multiple hybrid zones, a pattern consistent with potential genetic swamping of M. caurina by M. americana. Main conclusions: Despite an incomplete fossil record, genomic evidence supports the persistence of forest-associated martens, likely the insular Pacific marten lineage, along the western edges of the Alexander Archipelago during the Last Glacial Maximum. This discovery informs our understanding of refugial paleoenvironments,

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“…Moreover, metabarcoding has been performed on stomach contents and scat samples to study the diets of numerous taxa including birds (Jedlicka et al, 2013), marine fish and mammals (Leray and Knowlton, 2015;Berry et al, 2017;Jakubavièiûtë et al, 2017), freshwater fishes (Guillerault et al, 2017), terrestrial mammals (Shehzad et al, 2012;Srivathsan et al, 2015;Iwanowicz et al, 2016), and even highly cryptic species such as flying insects (Kaunisto et al, 2017) and insectivorous bats (Bohmann et al, 2011;Galan et al, 2018). As the cost of sequencing has declined, metabarcoding has been applied on massive spatial extents to study the biogeography of animal diets (Roffler et al, 2021). Some of the more interesting applications have taken diet analysis a step further and inferred resource partitioning among large-bodied African herbivores (Kartzinel et al, 2015) and population structure of vampire bats (Bohmann et al, 2018) from diet metabarcoding data (Figure 4G).…”

Section: Advances In Genetics: Describing Nature With Environmental Dna High-throughput Sequencing and Dna Metabarcodingmentioning

confidence: 99%

The Rapid Rise of Next-Generation Natural History

et al. 2021

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Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.

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Metabarcoding of fecal DNA shows dietary diversification in wolves substitutes for ungulates in an island archipelago

Abstract: of fecal DNA shows dietary diversification in wolves substitutes for ungulates in an island archipelago.

Cited by 32 publications

References 52 publications

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Whole‐genome resequencing reveals persistence of forest‐associated mammals in Late Pleistocene refugia along North America’s North Pacific Coast

The Rapid Rise of Next-Generation Natural History

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