Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Merging quantitative genetics and population genomics, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing QST -FST) using clustering of individuals by climate of origin. 29,354 SNPs were investigated employing three different outlier detection methods. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection, and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees. We highlight that important loci underlying adaptive trait variation also show relationship to climate of origin.

A fundamental consideration for the conservation of a species is the extent of its native range, however defining a native range is often challenging as changing environments drive shifts in species distributions over time. The crucian carp, Carassius carassius (L.) is a threatened freshwater fish native to much of Europe, however the extent of this range is ambiguous. One particularly contentious region is England, in which C. carassius is currently considered native on the basis of anecdotal evidence. Here, we use 13 microsatellite loci, population structure analyses and approximate bayesian computation (ABC), to empirically test the native status of C. carassius in England. Contrary to the current consensus, ABC yields strong support for introduced origins of C. carassius in England, with posterior distribution estimates placing their introduction in the 15th century, well after the loss of the doggerland landbridge. This result brings to light an interesting and timely debate surrounding our motivations for the conservation of species. We discuss this topic, and make arguments for the continued conservation of C. carassius in England, despite its non-native origins.

The conservation of threatened species must be underpinned by phylogeographic knowledge in order to be effective. This need is epitomised by the freshwater fish Carassius carassius, which has recently undergone drastic declines across much of its European range. Restriction Site Associated DNA sequencing (RADseq) is being increasingly used for such phylogeographic questions, however RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. Such tradeoffs have predominantly been addressed using simulated data. Here we compare the results generated from microsatellites and RADseq to the phylogeography of C. carassius, to add real-data-informed perspectives to this important debate. These datasets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns; showing the existence of two previously unidentified C. carassius lineages in Europe. These lineages have been isolated for approximately 2.2-2.3 M years, and should arguably be considered as separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with Approximate Bayesian Computation to show that the postglacial colonisation routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.

Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bt resistance. We developed 350 bp Double-Digest Restriction-site Associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection, and inbreeding in this non-model insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily due to the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, where more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated and Bt-selected lines, we generated a dense intraspecific linkage map containing 3 PCR-based, and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups. These markers are likely associated with genomic regions under balancing selection, thus preventing fixation of deleterious alleles.

The extent of within-species genetic variation across the diversity of animal life is a fundamental but largely unexplored problem in ecology and evolution. The neutral theory of molecular evolution predicts that genetic variation scales positively with population size. However, the genetic diversity of mitochondrial DNA, a prominent marker used in DNA barcoding studies, shows very little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial variation within natural populations of two species of chaetognaths (arrow worms). We determined that this diversity is composed of deep intraspecific mitochondrial lineages within single populations that could be as divergent as human and newt. This mitochondrial diversity is the highest ever reported in animals without evidence of cryptic speciation or allopatric divergence as supported by nuclear evidence. We sequenced 54 complete mitogenomes revealing gene order rearrangements between these intraspecific lineages. Such structural differences have never previously been reported within single species. We confirm that this divergence was not driven by positive selection, and conversely show that these lineages evolved under purifying selection, consistently with neutral expectations. Our findings question the generally accepted narrow range of genetic variation in animal mitochondria and argue for a reappraisal of DNA barcoding techniques. Furthermore, extreme levels of mitogenomic variation in chaetognaths challenge classical views regarding mitochondrial evolution and cyto-nuclear co-evolution.