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For faecal samples, mixed DNA from many organisms, low concentration, reaction inhibitors, and DNA degradation over time often hinder success. We aimed to develop a high\u2010throughput, cost\u2010effective faecal genotyping technique for monitoring invasive sambar deer (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Cervus unicolor<\/jats:italic>\n                    <\/jats:styled-content>\n                    ). We developed a multiplexed amplicon panel targeting 371 single nucleotide polymorphism (SNP) markers previously genotyped using restriction\u2010site associated DNA sequencing, and three sex markers. To evaluate panel performance in faecal samples, we undertook a degradation trial assessing the effects of time (0, 2, 4, 7, and 14\u2009days) on genotyping success under three conditions (outdoors on exposed ground, outdoors protected from rain and UV, and indoors). Fresh faecal samples performed equally to tissue, but environmental exposure rapidly degraded DNA. On average, exposed pellets were viable up to 4\u2009days, with ~200 SNPs successfully genotyped, while protected samples were still viable after 14\u2009days. In the field, we recommend sampling when there has been no rain for several days. We demonstrate that our method reliably ascertains individuals, sex, and species, with sufficient concordance among sample types and genotyping methods to support integration of faecal\u2010derived genotypes with existing datasets. Using existing reduced\u2010representation tissue sample data, we further demonstrate that the 200 SNPs reliably genotyped can resolve population structure and first\u2010order kinship, aiding informed management. More broadly, the insights for cost\u2010effective faecal DNA genotyping with optimised sample collection will benefit monitoring of both native wildlife and invasive species.\n                  <\/jats:p>","DOI":"10.1002\/ece3.74388","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T23:43:31Z","timestamp":1790034211000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development of a\n                    <scp>SNP<\/scp>\n                    Amplicon Panel for Invasive Deer Faecal Pellets and the Effects of Environmental Exposure on Genotyping Success"],"prefix":"10.1002","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5312-8647","authenticated-orcid":false,"given":"Tamandra H.","family":"D'Ombrain","sequence":"first","affiliation":[{"name":"Department of Ecological, Plant and Animal Sciences La Trobe University  Bundoora Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8070-8070","authenticated-orcid":false,"given":"Katherine A.","family":"Harrisson","sequence":"additional","affiliation":[{"name":"Department of Ecological, Plant and Animal Sciences La Trobe University  Bundoora Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5115-4120","authenticated-orcid":false,"given":"Carlo","family":"Pacioni","sequence":"additional","affiliation":[{"name":"Department of Energy, Environment and Climate Action Arthur Rylah Institute for Environmental Research  Heidelberg Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7642-696X","authenticated-orcid":false,"given":"Erin","family":"Hill","sequence":"additional","affiliation":[{"name":"Health and Biosecurity CSIRO  Canberra Australian Capital Territory Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0907-4642","authenticated-orcid":false,"given":"Nicholas P.","family":"Murphy","sequence":"additional","affiliation":[{"name":"Department of Ecological, Plant and Animal Sciences La Trobe University  Bundoora Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/s13364\u2010016\u20100305\u2010x"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12686\u2010024\u201001368\u20100"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13104\u2010021\u201005530\u2010x"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022\u20102836(05)80360\u20102"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.2981\/wlb.00080"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.10934"},{"key":"e_1_2_10_8_1","volume-title":"Monthly Climate Statistics: Viewbank (Station 086068)","author":"Australian Bureau of Meteorology","year":"2026"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1523\u20101739.2005.00549.x"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2014.04.003"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12686\u2010023\u201001310\u2010w"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10592\u2010009\u20109928\u20107"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1080\/10618600.1998.10474787"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.8993"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v080.i01"},{"key":"e_1_2_10_16_1","volume-title":"Abundance of Deer in Victoria: Regional and Statewide Estimates of Deer Density and Their Impact on Vegetation","author":"Cally J. 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