Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana

Abstract

Increased human activity and climate change are driving numerous tree species to endangered status, and in the worst cases extinction. Here we examine the genomic signatures of the critically endangered ironwood tree Ostrya rehderiana and its widespread congener O. chinensis. Both species have similar demographic histories prior to the Last Glacial Maximum (LGM); however, the effective population size of O. rehderiana continued to decrease through the last 10,000 years, whereas O. chinensis recovered to Pre-LGM numbers. O. rehderiana accumulated more deleterious mutations, but purged more severely deleterious recessive variations than in O. chinensis. This purging and the gradually reduced inbreeding depression together may have mitigated extinction and contributed to the possible future survival of the outcrossing O. rehderiana. Our findings provide critical insights into the evolutionary history of population collapse and the potential for future recovery of the endangered trees.

A general model to explain repeated turnovers of sex determination in the Salicaceae

“…To prevent biases in SNP calling accuracy due to the difference of samples size between groups, single-sample SNP and genotype calling were first implemented using GATK (DePristo et al , 2011) with ‘HaplotypeCaller’, and then multi-sample SNPs were identified after merging the results of each individual by ‘GenotypeGVCFs’. A series of filtering steps were performed to reduce false positives (Yang et al , 2018), including removal of (1) indels with a quality scores < 30, (2) SNPs with more than two alleles, (3) SNPs at or within 5 bp from any indels, (4) SNPs with a genotyping quality scores (GQ) < 10, and (5) SNPs with extremely low (< one-third average depth) or extremely high (> threefold average depth) coverage. The identified SNPs were used for subsequent GWAS analysis.…”

The draft genome of the endangered, relictual plantKingdonia uniflora(Circaeasteraceae, Ranunculales) reveals potential mechanisms and perils of evolutionary specialization

“…Habitat destruction caused by changing climate and human activities has driven 59 numerous plant species to endangered status (Yang et al, 2018). Recently there has 60 been a push to establish natural reserves to reduce the chance of extinction in 61 vulnerable species.…”

Using Haplotype Information for Conservation Genomics

“…SMC approaches, that are typically implemented using a hidden Markov model, have provided invaluable insights into changes in population size through time in various taxonomic groups. For instance, using phased genome sequences, Yang et al [42] provided evidence for continuous decline in the critically endangered population of ironwood tree (Ostrya rehderiana), accompanied by an increased number of deleterious mutations. However, some SMC-based methods make several assumptions, including the absence of population structure, migration, or admixture, which may bias inferences [43,44].…”

“…However, some SMC-based methods make several assumptions, including the absence of population structure, migration, or admixture, which may bias inferences [43,44]. To circumvent those limitations, the most recent extensions of SMC-based methods, including the multiple sequential Markovian coalescent (MSMC), have the potential to handle larger sample sizes [30,41,42] as well as more complex demographic models (e.g., more than one population, asymmetric migration rates, variable N e along the genome, etc.) [26], without necessarily needing phased data [45].…”