Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition
Our understanding of the biology of the extinct pig-footed bandicoots (<i>Chaeropus</i>) has been substantially revised over the past two decades by both molecular and morphological research. Resolving the systematic and temporal contexts of <i>Chaeropus</i> evolution has rel...
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MDPI AG
2022-04-01
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| Online Access: | https://www.mdpi.com/1424-2818/14/5/352 |
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| author | Matthew J. Phillips Manuela Cascini Mélina Celik |
| author_facet | Matthew J. Phillips Manuela Cascini Mélina Celik |
| author_sort | Matthew J. Phillips |
| collection | DOAJ |
| description | Our understanding of the biology of the extinct pig-footed bandicoots (<i>Chaeropus</i>) has been substantially revised over the past two decades by both molecular and morphological research. Resolving the systematic and temporal contexts of <i>Chaeropus</i> evolution has relied heavily on sequencing DNA from century-old specimens. We have used sliding window BLASTs and phylogeny reconstruction, as well as cumulative likelihood and apomorphy distributions, to identify contamination in sequences from both species of pig-footed bandicoot. The sources of non-target DNA that were identified range from other bandicoot species to a bird—emphasizing the importance of sequence authentication for historical museum specimens, as has become standard for ancient DNA studies. Upon excluding the putatively contaminated fragments, <i>Chaeropus</i> was resolved as the sister to all other bandicoots (Peramelidae), to the exclusion of bilbies (<i>Macrotis</i>). The estimated divergence time between the two <i>Chaeropus</i> species also decreases in better agreement with the fossil record. This study provides evolutionary context for testing hypotheses on the ecological transition of pig-footed bandicoots from semi-fossorial omnivores towards cursorial grazers, which in turn may represent the only breach of deeply conserved ecospace partitioning between modern Australo-Papuan marsupial orders. |
| first_indexed | 2024-03-10T03:02:09Z |
| format | Article |
| id | doaj.art-a9824f4009c748639adea2fb2fb57a02 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T03:02:09Z |
| publishDate | 2022-04-01 |
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| spelling | doaj.art-a9824f4009c748639adea2fb2fb57a022023-11-23T10:42:56ZengMDPI AGDiversity1424-28182022-04-0114535210.3390/d14050352Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological TransitionMatthew J. Phillips0Manuela Cascini1Mélina Celik2School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, AustraliaSchool of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, AustraliaSchool of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, AustraliaOur understanding of the biology of the extinct pig-footed bandicoots (<i>Chaeropus</i>) has been substantially revised over the past two decades by both molecular and morphological research. Resolving the systematic and temporal contexts of <i>Chaeropus</i> evolution has relied heavily on sequencing DNA from century-old specimens. We have used sliding window BLASTs and phylogeny reconstruction, as well as cumulative likelihood and apomorphy distributions, to identify contamination in sequences from both species of pig-footed bandicoot. The sources of non-target DNA that were identified range from other bandicoot species to a bird—emphasizing the importance of sequence authentication for historical museum specimens, as has become standard for ancient DNA studies. Upon excluding the putatively contaminated fragments, <i>Chaeropus</i> was resolved as the sister to all other bandicoots (Peramelidae), to the exclusion of bilbies (<i>Macrotis</i>). The estimated divergence time between the two <i>Chaeropus</i> species also decreases in better agreement with the fossil record. This study provides evolutionary context for testing hypotheses on the ecological transition of pig-footed bandicoots from semi-fossorial omnivores towards cursorial grazers, which in turn may represent the only breach of deeply conserved ecospace partitioning between modern Australo-Papuan marsupial orders.https://www.mdpi.com/1424-2818/14/5/352PeramelemorphiamarsupialsphylogenyecospaceDNA authentication |
| spellingShingle | Matthew J. Phillips Manuela Cascini Mélina Celik Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition Diversity Peramelemorphia marsupials phylogeny ecospace DNA authentication |
| title | Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition |
| title_full | Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition |
| title_fullStr | Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition |
| title_full_unstemmed | Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition |
| title_short | Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition |
| title_sort | identifying complex dna contamination in pig footed bandicoots helps to clarify an anomalous ecological transition |
| topic | Peramelemorphia marsupials phylogeny ecospace DNA authentication |
| url | https://www.mdpi.com/1424-2818/14/5/352 |
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