The increasing affordability of whole genome resequencing in the past five years and numbers of published reference genomes have enabled multispecies population genomic and phylogenomic studies on non-model organisms, but they raise new questions: what reference genomes should be used for read mapping in comparative studies, and what mapping methods provide the greatest and least bias in comparative genomics? Focusing on Eastern North American white oaks (Quercus sect. Quercus), which have an estimated 36 Ma divergence, we compared the effects of mapping resequencing data to four Quercus reference genomes, using three read-mapping methods: Bowtie2 –end-to-end, Bowtie2 –local, and BWA mapping methods. We analyzed the reference genomes and read-mapping methods in a fully factorial design to call variants and invariants for nine Quercus genome resequencing samples, then used the resulting datasets to test how different combinations of reference genome and method influence genotyping accuracy and bias. We found that both the genetic distance of the reference genome to the ingroup samples and mapping method together impacted sample heterozygosity, tree topology, and tree branch lengths. Specifically, the heterozygosity of closely-related sample/reference genome pairs using Bowtie2 –end-to-end alone was not significantly different from the average heterozygosity of samples that match the reference species. The outgroup reference genome resulted in low base pair recovery, low heterozygosity, and unbalanced phylogenies. We concluded that using a closely related, but not conspecific reference is ideal to minimize bias from the reference and Bowtie2 –end-to-end minimizes mismapping enabling the most accurate calls.

Freezing tolerance plays a pivotal role in shaping the distribution and diversification of organisms. We investigated the dynamics of adaptation to climate and potential trade-offs between stem freezing tolerance and growth rate in 48 Quercus species. Species from colder regions exhibited higher freezing tolerance, lower growth rates and higher winter-acclimation potential than species from warmer climates. Despite an evolutionary lag, freezing tolerance in oaks is closely aligned with its optimal state. Deciduous species showed marked variability in freezing tolerance across their broad climatic range while evergreen species, confined to warm climates, displayed low freezing tolerance. Annual growth rates were constrained in all deciduous species but those that evolved in warm latitudes lost freezing tolerance precluding a trade-off between freezing tolerance and growth. We provide evidence that capacity to adapt to a wide range of thermal environments was critical to adaptive radiation and current dominance of the North American oaks.

Most foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of Molecular Ecology, Wagner et al. (2023) present the first nuclear genomes from ancient to subfossil oak wood, including two samples dated to the 15th century and one that dates to more than 3,500 years ago. These first assembled nuclear genomes from ancient trees open the possibility for investigating species adaptation, migration, divergence, and hybridization in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.

Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosomal rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for their extraordinary rates of chromosome evolution. Genome synteny has been reported to be conserved in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Comparing genomes of Carex species and a genome of a distantly related Cyperaceae we have characterised conserved vs. rearranged genome regions across pairs of species that range in time since divergence between 2 and 50 million years. We have compared a C. scoparia genome with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found a surprisingly conserved genome synteny even between very distantly related species and extraordinarily high rates of chromosome evolution in genus Carex. Comparing the distribution of repetitive DNA and gene density between conserved and rearranged genomic regions, we found repetitive DNA to be related to holocentromeres and as well as rearranged regions of the genome. This evidence of extremely conserved synteny in sedges and the massive events of chromosome fission and fusion found across the evolution of genus Carex suggests the presence of common genomic hotspots of chromosome evolution related to repetitive DNA.