Table 2 COI haplotype frequencies for Rana temporaria populations in the Province of Trento detected by eDNA metabarcoding across temporal replicates. For each wetland site, haplotype frequencies (mean of spatial replicates S1-3) detected by eDNA metabarcoding at the different temporal points (T1, T2 and mean T1 + T2) are reported, together with available frequencies derived from traditional tissue-based genetic sampling (reference dataset: 41). nd = no data.

From: A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian

Site

Dataset

COI haplotypes (frequencies)

CA2_TN4

VC6

PR4

SA1_PR7

TN2

TN3

TN5

MT5

Amp

eDNA (T1)

0.644

0

0

0

0.74

0

0

0

eDNA (T2)

0.317

0

0

0

0.68

0

0

0

eDNA (T1 + T2)

0.2907

0

0

0

0.71

0

0

0

reference dataset

0.4

0

0

0

0.6

0

0

0

Bed

eDNA (T1)

0.2637

0.61

0.122

0

0

0

0

0

eDNA (T2)

0.2006

0.59

0.209

0

0

0

0

0

eDNA (T1 + T2)

0.2321

0.6

0.166

0

0

0

0

0

reference dataset

0.1

0.8

0.1

0

0

0

0

0

Fia

eDNA (T1)

0.3871

0

0

0

0.16

0.43

0.0196

0

eDNA (T2)

0.4415

0

0

0

0.06

0.49

0

0

eDNA (T1 + T2)

0.4089

0

0

0

0.12

0.46

0.0118

0

reference dataset

0.3

0

0

0

0.1

0.3

0.3

0

Ing

eDNA (T1)

0.9528

0.05

0

0

0

0

0

0

eDNA (T2)

0.2345

0.77

0

0

0

0

0

0

eDNA (T1 + T2)

0.7133

0.29

0

0

0

0

0

0

reference dataset

0.8

0.2

0

0

0

0

0

0

Lel

eDNA (T1)

0.2203

0.78

0

0

0

0

0

0

eDNA (T2)

nd

nd

nd

nd

nd

nd

nd

nd

eDNA (T1 + T2)

0.2203

0.78

0

0

0

0

0

0

reference dataset

0.5

0.4

0

0.1a

0

0

0

0

PLa

eDNA (T1)

0.8031

0

0.134b

0.0628

0

0

0

0

eDNA (T2)

nd

nd

nd

nd

nd

nd

nd

nd

eDNA (T1 + T2)

0.8031

0

0.134b

0.0628

0

0

0

0

reference dataset

0.8

0

0

0.2

0

0

0

0

PMa

eDNA (T1)

0.1754

0.82

0

0

0

0

0

0

eDNA (T2)

nd

nd

nd

nd

nd

nd

nd

nd

eDNA (T1 + T2)

0.1754

0.82

0

0

0

0

0

0

reference dataset

0.7

0.3

0

0

0

0

0

0

PS1

eDNA (T1)

0.3936

0.35

0.26

0

0

0

0

0

eDNA (T2)

0.7635

0

0.237

0

0

0

0

0

eDNA (T1 + T2)

0.5169

0.23

0.252

0

0

0

0

0

reference dataset

0.3

0.2

0.5

0

0

0

0

0

PS2

eDNA (T1)

0.6715

0.09

0.238

0

0

0

0

0

eDNA (T2)

nd

nd

nd

nd

nd

nd

nd

nd

eDNA (T1 + T2)

0.6715

0.09

0.238

0

0

0

0

0

reference dataset

0.5

0.1

0.4

0

0

0

0

0

Va1

eDNA (T1)

0.5235

0

0

0

0.24

0.19

0.0373b

0

eDNA (T2)

0.4887

0

0

0

0.1

0.25

0.1544b

0

eDNA (T1 + T2)

0.5061

0

0

0

0.17

0.22

0.0959b

0

reference dataset

0.4

0

0

0

0.1

0.2

0

0.3a

  1. aundetected by eDNA metabarcoding, but present in the reference dataset41; bDetected by eDNA metabarcoding but not in the reference dataset41.