TY - JOUR

T1 - Mammal mitogenomics from invertebrate-derived DNA

AU - Danabalan, Renita

AU - Merkel, Kevin

AU - Schnell, Ida Bærholm

AU - Arandjelovic, Mimi

AU - Boesch, Christophe

AU - Brazzola, Gregory

AU - Dieguez, Paula

AU - Dupain, Jef

AU - Kambale-Vyalengerera, Magloire

AU - Kühl, Hjalmar S.

AU - Hoffmann, Constanze

AU - Lapuente, Juan

AU - Thinh, Van Ngoc

AU - Zimmermann, Fee

AU - Leendertz, Fabian H.

AU - Gilbert, M. Thomas P.

AU - Roos, Christian

AU - Mazzoni, Camila

AU - Gogarten, Jan F.

AU - Calvignac-Spencer, Sébastien

N1 - Publisher Copyright: © 2023 The Authors. Environmental DNA published by John Wiley & Sons Ltd.

PY - 2023

Y1 - 2023

N2 - The metabarcoding of vertebrate DNA found in invertebrate-derived DNA (iDNA) has proven a powerful tool for monitoring biodiversity. To date, iDNA has primarily been used to detect the presence/absence of particular taxa using metabarcoding, though recent efforts demonstrated the potential utility of these data for estimating relative animal abundance. Here, we test whether iDNA can also be used to reconstruct complete mammalian mitogenomes and therefore bring the field closer to population-level analyses. Specifically, we used mitogenomic hybridization capture coupled with high-throughput sequencing to analyze individual (N = 7) or pooled (N = 5) fly-derived DNA extracts, and individual (N = 7) or pooled (N = 1) leech-derived DNA extracts, which were known a priori to contain primate DNA. All sources of iDNA showed their ability to generate large amounts of mammalian mitogenomic information and deeper sequencing of libraries is predicted to allow for even more complete recovery of primate mitogenomes from most samples (90%). Sixty percent of these iDNA extracts allowed for the recovery of (near) complete mammalian mitochondrial genomes (hereafter mitogenomes) that proved useable for phylogenomic analyses. These findings contribute to paving the way for iDNA-based population mitogenomic studies of terrestrial mammals.

AB - The metabarcoding of vertebrate DNA found in invertebrate-derived DNA (iDNA) has proven a powerful tool for monitoring biodiversity. To date, iDNA has primarily been used to detect the presence/absence of particular taxa using metabarcoding, though recent efforts demonstrated the potential utility of these data for estimating relative animal abundance. Here, we test whether iDNA can also be used to reconstruct complete mammalian mitogenomes and therefore bring the field closer to population-level analyses. Specifically, we used mitogenomic hybridization capture coupled with high-throughput sequencing to analyze individual (N = 7) or pooled (N = 5) fly-derived DNA extracts, and individual (N = 7) or pooled (N = 1) leech-derived DNA extracts, which were known a priori to contain primate DNA. All sources of iDNA showed their ability to generate large amounts of mammalian mitogenomic information and deeper sequencing of libraries is predicted to allow for even more complete recovery of primate mitogenomes from most samples (90%). Sixty percent of these iDNA extracts allowed for the recovery of (near) complete mammalian mitochondrial genomes (hereafter mitogenomes) that proved useable for phylogenomic analyses. These findings contribute to paving the way for iDNA-based population mitogenomic studies of terrestrial mammals.

KW - fly

KW - hybridization capture

KW - iDNA

KW - leech

KW - mitochondrial genome

KW - non-human primates

U2 - 10.1002/edn3.436

DO - 10.1002/edn3.436

M3 - Journal article

AN - SCOPUS:85162009266

VL - 5

SP - 1004

EP - 1015

JO - Environmental DNA

JF - Environmental DNA

SN - 2637-4943

IS - 5

ER -