Exciting #ConSERTeam news! Our paper demonstrating the utility of closely-related reference genomes 🧬 for #conservation (Galla & Forsdick et al. 2019 @sgalla32 @NatForsdick @testeeves bit.ly/2Hj72z1) was published in @Genes_MDPI @MDPIOpenAccess. #ConGen 1/13
No longer just a promise (bit.ly/2SMXehV), the #ConservationGenomics revolution is here: #genomics is adding awesome tools to the #conservation tool box to inform the management of some of the world’s most threatened species. 2/13
One such tool is a reference #genome. Think of it as the picture of a completed puzzle on a puzzle box. Having a picture means genomic reads (puzzle pieces 🧩) can be placed correctly, allowing effective ID of SNPs (single nucleotide polymorphisms). 3/13
Good news 😃: more reference genomes are becoming available every day. Bad news 😔: they may not yet be available for many non-model species & generating them can be 💰💰💰 for budget-constrained #conservation projects. 4/13
With all the new genomes being produced every year, is it possible to use a reference #genome from a closely-related species and still find SNPs that are helpful for #conservation management 🤔? (thinking face emoji) Our research says yes 👍! 5/13
We mapped #NGS short-reads for the critically #endangered #kakī (black stilt, bit.ly/2RKcDCc) to 4 different reference genomes to ID SNPs: kakī, pied stilt (same genus), pied avocet (same family), and killdeer (same order). 6/13 
With the SNPs IDed, we estimated nucleotide diversity, individual heterozygosity (a proxy for inbreeding), and relatedness (used for pairing decisions to maximise diversity in captive #kakī, bit.ly/2SMXQ7d). 📸 @docgovtnz 7/13
This means that, in birds, SNPs discovered using closely related reference genomes can be used to estimate nucleotide diversity, individual heterozygosity and relatedness to inform #conservation. 9/13
Based on our combined results - including diminishing correlations, and a greater range of values, using more distantly related reference genomes - we recommend the most distant reference genome to use for birds is likely confamilial. 10/13
But if you grab a reference genome ‘off the shelf’, we recommend investigating the quality of the genome first. Looking at the raw reads with FastQC and SGA pre-QC is a great way to start. 11/13
With reference genomes costing min €6500 to produce, using available closely related genomes for SNP discovery will allow #conservation projects on a budget to adopt #genomics faster. Check out @B10K_Project @genomeark for birds & bit.ly/2Hj72z1 for more details. 12/13
We're grateful for the support of many incl the iwi & hapū that exercise kaitiakitanga for kakī & the #KakīRecoveryGroup. We thank @MBIEsci @royalsocietynz @docgovtnz (📸 ) @UCNZ @otago #BrianMasonTrust #MohuaTrust for funding. See ucconsert.org for data access. 13/13
