Discovery of facultative parthenogenesis in a New World crocodile

Over the past two decades, there has been an astounding growth in the documentation of vertebrate facultative parthenogenesis (FP). This unusual reproductive mode has been documented in birds, non-avian reptiles—specifically lizards and snakes—, and elasmobranch fishes. Part of this growth among vertebrate taxa is attributable to awareness of the phenomenon itself and advances in molecular genetics/genomics and bioinformatics, and as such our understanding has developed considerably. Nonetheless, questions remain as to its occurrence outside of these vertebrate lineages, most notably in Chelonia (turtles) and Crocodylia (crocodiles, alligators, and gharials). The latter group is particularly interesting because unlike all previously documented cases of FP in vertebrates, crocodilians lack sex chromosomes and sex determination is controlled by temperature. Here, using whole-genome sequencing data, we provide the first evidence of FP in a crocodilian, the American Crocodile, Crocodylus ac..., DNA extracted from the mother and fetus using a Qiagen DNeasy Blood & Tissue kit was sent to Novogene (Sacramento, CA) for whole genome sequencing on an Illumina platform (NovaSeq 6000 PE150). Raw sequences were mapped by Novogene to the Saltwater crocodile, Crocodylus porosus, reference genome with single nucleotide polymorphisms (SNPs) identified by Novogene using the following the command in SAMtools: mpileup -m 2 -F 0.002 -d 10.
Following the parameters used in Card et al. as a guideline, variants were filtered using VCFtools v. 0.1.16, the R package vcfR, and bedtools v2.30.0, with the following criteria: (1) indels were excluded; (2) individuals with a read depth of less than 5 were excluded; (3) variants with a Phred quality score below 30 were excluded; (4) non-biallelic SNPs were excluded; (5) SNPs with significant statistical biases were removed using the hard filter ‘MQ < 40.0’; (6) SNPs were thinned to avoid the potential effects of linkage by randomly selecting one v...,