DOI: 10.5061/dryad.xgxd254fc
title: The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)

description: Model-based approaches that attempt to delimit species are hampered by
 computational limitations as well as the unfortunate tendency by users to
 disregard algorithmic assumptions. Alternatives are clearly needed, and
 machine-learning (M-L) is attractive in this regard as it functions
 without the need to explicitly define a species concept. Unfortunately,
 its performance will vary according to which (of several) bioinformatic
 parameters are invoked. Herein, we gauge the effectiveness of M-L-based
 species-delimitation algorithms by parsing 64 variably-filtered versions
 of a ddRAD-derived SNP dataset involving North American box turtles
 (Terrapene spp.). Our filtering strategies included: (A) minor allele
 frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing
 data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We
 found that species-delimitation via unsupervised M-L impacted the
 signal-to-noise ratio in our data, as well as the discordance among
 resolved clades. The latter may also reflect biogeographic history, gene
 flow, incomplete lineage sorting, or combinations thereof (as corroborated
 from previously observed patterns of differential introgression). Our
 results substantiate M-L as a viable species-delimitation method, but also
 demonstrate how commonly observed patterns of phylogenetic discord can
 seriously impact M-L-classification.
description: .<br> ├── depthPlot.tar.gz<br> ├──
 divergenceDating<br> │   ├── inputFiles.tar.gz<br> │   ├──
 outputFiles.tar.gz<br> │   └──
 run_dating_rooted_fixedDates_iqtree.sh<br> ├──
 speciesDelim<br> │   ├── BFD<br> │   │   ├──
 Rscripts<br> │   │   │   └── mle2bfd.Rmd<br> │   │   ├──
 inputFiles<br> │   │   │   ├── DIVEIN.tar.gz<br> │   │   │  
 └── bfd_xml_input.tar.gz<br> │   │   └── outputFiles<br> │  
 │       └── bfd_output.tar.gz<br> │   ├── Robjects<br> │   │  
 └── Robjects_missData_maf.tar.gz<br> │   ├── barplots<br> │  
 │   └── barplots_all.tar.gz<br> │   ├── cmds_isomds_tsne<br>
 │   │   ├── alignments<br> │   │   │   └──
 alignments_R.tar.gz<br> │   │   └── output<br> │   │       └──
 raw_txt_output<br> │   │           └──
 missData_maf_output_R.tar.gz<br> │   ├── delimitR<br> │   │  
 ├── Rscripts<br> │   │   │   ├── estimate_nm.R<br> │   │   │  
 ├── run_delimitR_linux.R<br> │   │   │   ├──
 run_delimitR_linux_2.R<br> │   │   │   ├──
 run_delimitR_linux_2_rf5K.R<br> │   │   │   └──
 writeTables_dr.R<br> │   │   ├── dr.pbs<br> │   │   ├──
 inputFiles<br> │   │   │   ├── alignments<br> │   │   │   │  
 └── delimitR_input.recode.vcf<br> │   │   │   ├── jSFS<br> │  
 │   │   │   └── delimitR_input_MSFS.obs<br> │   │   │   ├──
 popmap<br> │   │   │   │   └──
 popmap_final_delimitR_sorted.txt<br> │   │   │   └──
 traits<br> │   │   │       └── traits_dr_final.txt<br> │   │  
 └── outputFiles<br> │   │       ├── Prior<br> │   │       │  
 └── binned.tar.gz<br> │   │       ├── Robjects<br> │   │      
 │   ├── myRF_object_svdtree_5K.rds<br> │   │       │   ├──
 myobserved_object_svdtree_5K.rds<br> │   │       │   └──
 prediction_object_svdtree_5K.rds<br> │   │       └──
 tables<br> │   │           ├── myRF_errorRates_5K.csv<br> │  
 │           └── prediction_votes_5K.csv<br> │   └── vae<br>
 │       ├── alignments<br> │       │   └──
 alignments_vae.tar.gz<br> │       └── output<br> │          
 └── raw_txt_output<br> │               └──
 missData_maf_output_vae.tar.gz<br> ├── speciesTrees<br> │  
 ├── iqtree<br> │   │   ├── alignments<br> │   │   │   └──
 BOX_concat_goodOnly_N214.nex<br> │   │   ├──
 constraintTrees.tar.gz<br> │   │   ├──
 partitionTree.tar.gz<br> │   │   └── sCF<br> │   │       ├──
 inputFiles.tar.gz<br> │   │       ├── outputFiles.tar.gz<br>
 │   │       └── run_scf.sh<br> │   ├── pomo<br> │   │   ├──
 alignments<br> │   │   │   ├── BOX_pomo_FINAL.counts<br> │  
 │   │   └── BOX_pomo_FINAL.fasta<br> │   │   └──
 outputFiles.tar.gz<br> │   └── svdquartets<br> │       ├──
 alignments<br> │       │   └──
 BOX_svdq_run3_FINAL_filt.nex<br> │       └──
 outputFiles.tar.gz<br> └── treemix<br>     ├──
 inputFiles.tar.gz<br>     └── outputFiles.tar.gz
 36 directories, 43 files