High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

Recombination is critical both for accelerating adaptation and for the purging of deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination and, thus, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Moreover, there was little evidence of phenotypic overdominance in inversion heterozygotes, consistent with observations of minimal deleterious load. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the geographic structuring and consequent excess homozygosity of inversions in wild sunflowers. Inversions contributing to local adaptation often exhibit geographic structure; such inversions represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely averting the accumulation of deleterious mutations due to recombination suppression.

BESFA: Bioinformatics based Evolutionary, Structural & Functional Analysis of Prostrate, Placenta, Ovary, Testis, and Embryo (POTE) Paralogs

The POTE family comprises 14 paralogues and is primarily expressed in Prostrate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins' structure, function, and Adaptive Divergence. Our result discerns that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this study's outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.

Adaptation Insights from Comparative Transcriptome Analysis of Two Opisthopappus Species in the Taihang Mountains

Opisthopappus is a major wild source of Asteraceae with good cold and drought resistance. Two species of this genus (Opisthopappus taihangensis and Opisthopappus longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus revealed a higher expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly regarding monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus, 1203 genes were found that related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Different PSG expressions occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Two PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights as to how the two species adapted to different environments, characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species of Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.

Genome-wide SNP analysis reveals patterns of population differentiation and adaptation of red rock lobster Jasus edwardsii

<p>Declines in global marine finfish catches, which accounts for ~15% of the animal protein consumed by humans, has caused a 6-fold increase in total reported catch of invertebrates since 1950. This has led to the over-exploitation and decline of many marine invertebrate fisheries. The red rock lobster (Jasus edwardsii) fishery is New Zealand’s most economically valuable inshore fishery. The current management strategy relies on the assumption that the stock is comprised of a single panmictic population. However, more recent studies have challenged the genetic homogeneity of Jasus edwardsii across the Tasman sea and described high levels of self-recruitment in a Stewart Island subpopulation. A disregard for the underlying genetic structure in the management of a fishery can lead to excessive removal of individuals from populations contributing to the overall genetic diversity of the stock and thus reduce the species adaptability. The ability to adapt to new environments is particularly important in the context of global climate change and can significantly affect the long-term sustainability of the stock. Thus, the goal of this study was to identify specific patterns of genetic diversity of Jasus edwardsii population and provide an interpretation and assessment of the impact on the NZ fishery. The first objective was to optimize and validate molecular and bioinformatic protocols of Single Nucleotide Polymorphism (SNP) discovery for the red rock lobster Jasus edwardsii. The double digest restriction-site associated DNA (ddRADseq) protocol was optimized for the relatively large red rock lobster genome, which also has a high paralog content. The impact of bioinformatic processing on the population genetic inferences was then assessed by testing three different SNP discovery pipelines with the Rad-loci pipeline producing the most optimal marker discovery rate with a low level of missing data and a low SNP error rate. An analysis of technical replicates confirmed the reproducibility of both the molecular and bioinformatic protocols and also the validated the data generation process suitable for population genetic analyses. The second objective of my thesis was to investigate the genetic structure and population connectivity of adult red rock lobsters. The SNPs discovered were characterised as selectively neutral or under divergent selection (outlier) and both types of markers were analysed using Bayesian model-based clustering (STRUCTURE), non model-based multivariate analysis (Discriminant Analysis of Principal Components (DAPC)) and F-statistics. A lack of population differentiation using neutral genetic markers indicated a high level of gene flow and connectivity between populations. In contrast, there was evidence for selective pressure as a result of the analysis of outlier markers. Three main regions were identified: North-East NZ, North-West NZ and South NZ sub-populations, as part of a larger NZ metapopulation (FST ranged from 0.025 to 0.049, P < 0.001). The results of this study suggested that high levels of gene flow and connectivity are counteracted to some extent by the local selection that promotes the survival and reproduction of locally adapted genotypes. However, the strength of this selective pressure still permits low levels of survival and reproduction of non-optimal genotypes causing allele frequency homogenisation of the new generation of lobsters. The third objective was to investigate the levels of connectivity and adaptive divergence of the red rock lobster pueruli/juvenile lobsters for comparison with pattern of divergence of adult lobster in order to investigate the mechanisms of population structure formation. A suite of Bayesian clustering, non-model multivariate analysis and F-statistics were employed in the assessment of neutral and outlier markers developed for pueruli/juveniles. Similar to adult lobsters, pueruli/juveniles were characterised by a low level of divergence of the neutral markers indicating effective larvae dispersal. Outlier markers detected population differentiation patterns likely to originate from a phenotype – environment mismatch resulting in post-settlement mortality of non-adapted genotypes. The similarity between patterns of genetic divergence of adult lobsters and late juvenile/early juveniles indicates that post-settlement mortality, driven by local environmental conditions, has most likely occurred on earlier developmental stages of Jasus edwardsii, which were not possible to sample in my study. The final objective was to explore environment–genotype associations of Jasus edwardsii. Biological Environment Stepwise (BEST) analyses, redundancy analyses (RDA) and generalized linear modelling (GLM) consistently indicated a correlation between the annual amplitude of sea surface temperature (SST) and adaptive population divergence. In addition, an influence of spatial distribution on the patterns of adaptive population differentiation was also detected via RDA. From these results I propose a mechanism underlying the patterns of population differentiation discovered in Chapters 3 and 4: a latitudinal gradient of SST appears to be the selective force promoting the adaptive divergence of the lobster populations with local patterns of connectivity distorting the gradient and thus forming three distinct temperature adapted genotypes (North-West, North-East, and South). An environmental association analysis offered 43 candidate loci, which after alignment of transcriptome-mapped reference catalog sequences to annotated protein databases identified a candidate gene for thermal adaptation - UDP-glycosyltransferase (UGT). UGT is a detoxification enzyme involved in the metabolization of a variety of endogenous and environmental compounds and its activity and gene expression patterns have been linked to temperature. This study provides evidence for the local adaptations of the NZ population of Jasus edwardsii to SST, which together with the efficient mechanism of larval dispersal creates a system likely resilient to changes in temperature. This feature is important in the light of climate change-induced range shifts and supports the long-term sustainability of the red rock lobster fishery. The three genetically distinct regions identified coincide with existing boundaries of the management units and therefore do not require an adjustment of the current management regime.</p>

Genome-wide SNP analysis reveals patterns of population differentiation and adaptation of red rock lobster Jasus edwardsii

<p>Declines in global marine finfish catches, which accounts for ~15% of the animal protein consumed by humans, has caused a 6-fold increase in total reported catch of invertebrates since 1950. This has led to the over-exploitation and decline of many marine invertebrate fisheries. The red rock lobster (Jasus edwardsii) fishery is New Zealand’s most economically valuable inshore fishery. The current management strategy relies on the assumption that the stock is comprised of a single panmictic population. However, more recent studies have challenged the genetic homogeneity of Jasus edwardsii across the Tasman sea and described high levels of self-recruitment in a Stewart Island subpopulation. A disregard for the underlying genetic structure in the management of a fishery can lead to excessive removal of individuals from populations contributing to the overall genetic diversity of the stock and thus reduce the species adaptability. The ability to adapt to new environments is particularly important in the context of global climate change and can significantly affect the long-term sustainability of the stock. Thus, the goal of this study was to identify specific patterns of genetic diversity of Jasus edwardsii population and provide an interpretation and assessment of the impact on the NZ fishery. The first objective was to optimize and validate molecular and bioinformatic protocols of Single Nucleotide Polymorphism (SNP) discovery for the red rock lobster Jasus edwardsii. The double digest restriction-site associated DNA (ddRADseq) protocol was optimized for the relatively large red rock lobster genome, which also has a high paralog content. The impact of bioinformatic processing on the population genetic inferences was then assessed by testing three different SNP discovery pipelines with the Rad-loci pipeline producing the most optimal marker discovery rate with a low level of missing data and a low SNP error rate. An analysis of technical replicates confirmed the reproducibility of both the molecular and bioinformatic protocols and also the validated the data generation process suitable for population genetic analyses. The second objective of my thesis was to investigate the genetic structure and population connectivity of adult red rock lobsters. The SNPs discovered were characterised as selectively neutral or under divergent selection (outlier) and both types of markers were analysed using Bayesian model-based clustering (STRUCTURE), non model-based multivariate analysis (Discriminant Analysis of Principal Components (DAPC)) and F-statistics. A lack of population differentiation using neutral genetic markers indicated a high level of gene flow and connectivity between populations. In contrast, there was evidence for selective pressure as a result of the analysis of outlier markers. Three main regions were identified: North-East NZ, North-West NZ and South NZ sub-populations, as part of a larger NZ metapopulation (FST ranged from 0.025 to 0.049, P < 0.001). The results of this study suggested that high levels of gene flow and connectivity are counteracted to some extent by the local selection that promotes the survival and reproduction of locally adapted genotypes. However, the strength of this selective pressure still permits low levels of survival and reproduction of non-optimal genotypes causing allele frequency homogenisation of the new generation of lobsters. The third objective was to investigate the levels of connectivity and adaptive divergence of the red rock lobster pueruli/juvenile lobsters for comparison with pattern of divergence of adult lobster in order to investigate the mechanisms of population structure formation. A suite of Bayesian clustering, non-model multivariate analysis and F-statistics were employed in the assessment of neutral and outlier markers developed for pueruli/juveniles. Similar to adult lobsters, pueruli/juveniles were characterised by a low level of divergence of the neutral markers indicating effective larvae dispersal. Outlier markers detected population differentiation patterns likely to originate from a phenotype – environment mismatch resulting in post-settlement mortality of non-adapted genotypes. The similarity between patterns of genetic divergence of adult lobsters and late juvenile/early juveniles indicates that post-settlement mortality, driven by local environmental conditions, has most likely occurred on earlier developmental stages of Jasus edwardsii, which were not possible to sample in my study. The final objective was to explore environment–genotype associations of Jasus edwardsii. Biological Environment Stepwise (BEST) analyses, redundancy analyses (RDA) and generalized linear modelling (GLM) consistently indicated a correlation between the annual amplitude of sea surface temperature (SST) and adaptive population divergence. In addition, an influence of spatial distribution on the patterns of adaptive population differentiation was also detected via RDA. From these results I propose a mechanism underlying the patterns of population differentiation discovered in Chapters 3 and 4: a latitudinal gradient of SST appears to be the selective force promoting the adaptive divergence of the lobster populations with local patterns of connectivity distorting the gradient and thus forming three distinct temperature adapted genotypes (North-West, North-East, and South). An environmental association analysis offered 43 candidate loci, which after alignment of transcriptome-mapped reference catalog sequences to annotated protein databases identified a candidate gene for thermal adaptation - UDP-glycosyltransferase (UGT). UGT is a detoxification enzyme involved in the metabolization of a variety of endogenous and environmental compounds and its activity and gene expression patterns have been linked to temperature. This study provides evidence for the local adaptations of the NZ population of Jasus edwardsii to SST, which together with the efficient mechanism of larval dispersal creates a system likely resilient to changes in temperature. This feature is important in the light of climate change-induced range shifts and supports the long-term sustainability of the red rock lobster fishery. The three genetically distinct regions identified coincide with existing boundaries of the management units and therefore do not require an adjustment of the current management regime.</p>

Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower

Natural selection is responsible for much of the diversity we see in nature. Just as it drives the evolution of new traits, it can also lead to new species. However, it is unclear whether natural selection conferring adaptation to local environments can drive speciation through the evolution of hybrid sterility between populations. Here, we show that adaptive divergence in shoot gravitropism, the ability of a plant’s shoot to bend upwards in response to the downward pull of gravity, contributes to the evolution of hybrid sterility in an Australian wildflower, Senecio lautus. We find that shoot gravitropism has evolved multiple times in association with plant height between adjacent populations inhabiting contrasting environments, suggesting that these traits have evolved by natural selection. We directly tested this prediction using a hybrid population subjected to eight rounds of recombination and three rounds of selection in the field. Our experiments revealed that shoot gravitropism responds to natural selection in the expected direction of the locally adapted population. Using the advanced hybrid population, we discovered that individuals with extreme differences in gravitropism had more sterile crosses than individuals with similar gravitropic responses, which were largely fertile, indicating that this adaptive trait is genetically correlated with hybrid sterility. Our results suggest that natural selection can drive the evolution of locally adaptive traits that also create hybrid sterility, thus revealing an evolutionary connection between local adaptation and the origin of new species.