DNA-Based Diet Analysis for Any Predator

Background: Prey DNA from diet samples can be used as a dietary marker; yet current methods for prey detection require a priori diet knowledge and/or are designed ad hoc, limiting their scope. I present a general approach to detect diverse prey in the feces or gut contents of predators. Methodology/Principal Findings: In the example outlined, I take advantage of the restriction site for the endonuclease Pac I which is present in 16S mtDNA of most Odontoceti mammals, but absent from most other relevant non-mammalian chordates and invertebrates. Thus in DNA extracted from feces of these mammalian predators Pac I will cleave and exclude predator DNA from a small region targeted by novel universal primers, while most prey DNA remain intact allowing prey selective PCR. The method was optimized using scat samples from captive bottlenose dolphins (Tursiops truncatus) fed a diet of 6–10 prey species from three phlya. Up to five prey from two phyla were detected in a single scat and all but one minor prey item (2% of the overall diet) were detected across all samples. The same method was applied to scat samples from free-ranging bottlenose dolphins; up to seven prey taxa were detected in a single scat and 13 prey taxa from eight teleost families were identified in total. Conclusions/Significance: Data and further examples are provided to facilitate rapid transfer of this approach to any predator. This methodology should prove useful to zoologists using DNA-based diet techniques in a wide variety of study systems

Macroalgal browsing on a heavily degraded, urbanized equatorial reef system

The removal of macroalgal biomass is critical to the health of coral reef ecosystems. Previous studies on relatively intact reefs with diverse and abundant fish communities have quantified rapid removal of macroalgae by herbivorous fishes, yet how these findings rel ate to degraded reef systems where fish diversity and abundance are markedly lower and algal biomass substantially higher, is unclear. We surveyed roving herbivorous fish communities and quantified their capacity to remove the dominant macroalga Sargassum ilicifolium on seven reefs in Singapore; a heavily degraded urbanized reef system. The diversity and abundance of herbivorous fishes was extremely low, with eight species and a mean abundance ~1.1 individuals 60 m -2 recorded across reefs. Consumption of S. ilicifolium varied with distance from Singapore's main port with consumption being 3- to 17-fold higher on reefs furthest from the port (Pulau Satumu: 4.18 g h -1 ; Kusu Island: 2.38 g h -1 ) than reefs closer to the port (0.35-0.78 g h -1 ). Video observations revealed a single species, Siganus virgatus, was almost solely responsible for removing S. ilicifolium biomass, accounting for 83% of the mass-standardized bites. Despite low herbivore diversity and intense urbanization, macroalgal removal by fishes on some Singaporean reefs was directly comparable to rates reported for other inshore Indo-Pacific reefs

Fear effects and group size interact to shape herbivory on coral reefs

Fear of predators (‘fear effects’) is an important determinant of foraging decisions by consumers across a range of ecosystems. Group size is one of the main behavioural mechanisms for mitigating fear effects while also providing foraging benefits to group members. Within coral reef ecosystems, fear effects have been shown to influence the feeding rates of herbivorous fishes, a key functional group that prevents macroalgal overgrowth. Yet, how fear effects and group size interact to shape macroalgal removal on coral reefs remains unclear. Here, we conducted field-based experiments using models of a common piscivorous fish, the leopard coral grouper Plectropomus leopardus and a series of macroalgal Sargassum ilicifolium assays positioned at increasing distances from the models (1, 2, 3 and 4 m) on two coral reefs in Singapore to investigate how acute fear effects shape the intensity of herbivory, and whether these effects were influenced by variation in the group size of herbivorous fishes feeding on the assays. We found acute fear effects strongly influenced the foraging behaviour of herbivorous fishes over small spatial scales. Rates of Sargassum biomass removal, feeding rates and the total number of individual feeding events were all lower near the predator model. These effects dissipated rapidly with increasing distance from the predator model and were undetectable at a distance of 4 m. We also found generally larger group sizes of herbivorous fishes further from the predator model, presumably reflecting decreased risk. Furthermore, the number of individual bites/event increased significantly with increasing group size for two common browsing fishes, Siganus virgatus and Siganus javus. Our findings highlight that acute fear effects influence the distribution and intensity of herbivory over small spatial scales. Fear effects also interacted with herbivore group size resulting in changes in the number of individual feeding events and bite rates that collectively shape the realized ecosystem function of macroalgal removal on coral reefs. Group size is an important context-dependent factor that should be considered when examining fear effects on coral reefs. A free Plain Language Summary can be found within the Supporting Information of this article

Fear effects and group size interact to shape herbivory on coral reefs

Fear of predators (‘fear effects’) is an important determinant of foraging decisions by consumers across a range of ecosystems. Group size is one of the main behavioural mechanisms for mitigating fear effects while also providing foraging benefits to group members. Within coral reef ecosystems, fear effects have been shown to influence the feeding rates of herbivorous fishes, a key functional group that prevents macroalgal overgrowth. Yet, how fear effects and group size interact to shape macroalgal removal on coral reefs remains unclear. Here, we conducted field-based experiments using models of a common piscivorous fish, the leopard coral grouper Plectropomus leopardus and a series of macroalgal Sargassum ilicifolium assays positioned at increasing distances from the models (1, 2, 3 and 4 m) on two coral reefs in Singapore to investigate how acute fear effects shape the intensity of herbivory, and whether these effects were influenced by variation in the group size of herbivorous fishes feeding on the assays. We found acute fear effects strongly influenced the foraging behaviour of herbivorous fishes over small spatial scales. Rates of Sargassum biomass removal, feeding rates and the total number of individual feeding events were all lower near the predator model. These effects dissipated rapidly with increasing distance from the predator model and were undetectable at a distance of 4 m. We also found generally larger group sizes of herbivorous fishes further from the predator model, presumably reflecting decreased risk. Furthermore, the number of individual bites/event increased significantly with increasing group size for two common browsing fishes, Siganus virgatus and Siganus javus. Our findings highlight that acute fear effects influence the distribution and intensity of herbivory over small spatial scales. Fear effects also interacted with herbivore group size resulting in changes in the number of individual feeding events and bite rates that collectively shape the realized ecosystem function of macroalgal removal on coral reefs. Group size is an important context-dependent factor that should be considered when examining fear effects on coral reefs

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology

A regionally coherent ecological fingerprint of climate change, evidenced from natural history collections

publishedVersio

Kunnskapsstatus for bruk av molekylære verktøy i kartlegging og overvåkning av biologisk mangfold i marine miljø

Source at https://www.miljodirektoratet.no/publikasjoner/2021/juni-2021/kunnskapsstatus-for-bruk-av-molekylare-verktoy-i-kartlegging-og-overvakning-av-biologisk-mangfold-i-marine-miljo/Denne rapporten er bestilt av Miljødirektoratet fra NorBOL (Norwegian Barcode of Life), et nasjonalt nettverk av forskningsinstitusjoner som koordineres av NTNU Vitenskapsmuseet. Universitetsmuseet i Bergen har hatt prosjektledelsen. Rapporten gir en oppsummering av dagens status på DNA-basert metodikk som verktøy i kartlegging og overvåking av biologisk mangfold i det marine miljø. Fokus har vært på innsamlingsmetodikk og protokoller for DNA-analyser av arter og artsgrupper. Metodikken er evaluert opp mot kartleggings- og overvåkingsaktivitet i regi av Miljødirektoratet, og kommer med anbefalinger for videre framdrift for å ta metodikken i bruk i nasjonal kartlegging og overvåking. Rapporten har også en gjennomgang og evaluering av eksisterende referansemateriale og referansesekvenser for relevante arter og artsgrupper som inngår i Miljødirektoratets kartleggings- og overvåkingsaktivitet

Isolation and characterization of microsatellite loci from\ud the Australasian sea snake, Aipysurus laevis

We developed 13 microsatellite loci for the olive sea snake, Aipysurus laevis, using both enriched and unenriched genomic DNA libraries. Eleven codominant loci, that reliably amplified, were used to screen 32 individuals across the geographic range of A. laevis. Four loci had four or more alleles (maximum 12), whereas the other seven had either two or three. All but one locus was in Hardy–Weinberg equilibrium. These loci will provide useful markers to investigate population genetic structure for the olive sea snake