Evolution Of Adaptive Traits Research Articles

Extreme genetic signatures of local adaptation in a notorious rice pest, Chilo suppressalis

ABSTRACT Climatic variation stands as a significant driving force behind genetic differentiation and the evolution of adaptive traits. Chilo (C.) suppressalis, commonly known as the rice stem borer, is a highly destructive pest that crucially harms rice production. The lack of natural population genomics data has hindered a more thorough understanding of its climate adaptation, particularly the genetic basis underlying adaptive traits. To overcome this obstacle, our study employed completely resequenced genomes of 384 individuals to explore the population structure, demographic history, and gene flow of C. suppressalis in China. This study observed that its gene flow occurred asymmetrically, moving from central populations to peripheral populations. Using genome-wide selection scans and genotype-environment association studies, we identified potential loci that may be associated with climatic adaptation. The most robust signal was found to be associated with cold tolerance, linked to a homeobox gene, goosecoid (GSC), whose expression level was significantly different in low and high latitudes. Moreover, downregulating the expression of this gene by RNAi enhances its cold tolerance phenotypes. Our findings have uncovered and delved into the genetic foundation of the ability of C. suppressalis to adapt to its environment. This is essential in ensuring the continued effectiveness and sustainability of novel control techniques.

Adaptive evolution of traits for parasitism and pathogen transmission potential in bat flies

Abstract Deciphering the mechanisms underlying the transmission and spillover of zoonoses from reservoir hosts is essential in preventing future global pandemics. Bat flies, obligate blood-feeding ectoparasites of bats, are known carriers of diverse viruses. Here, we conducted a de novo assembly of a chromosome-level genome for the bat fly species Phthiridium sp. Comparative genomic analysis unveiled genes associated with specialized traits, such as the loss of eyes and wings, as well as elongated legs, which have adapted to parasitism on the dense fur of bats. Utilizing small RNA (sRNA) sequencing, we identified a spectrum of known and previously unclassified viruses in bat flies. Notably, experimental evidence indicated that bat flies can also feed on mammalian hosts other than bats, suggesting the potential for the spillover of bat-borne viruses. Furthermore, we demonstrated the role of the bat fly's RNA interference pathway in influencing the diversity and evolution of viruses. In summary, this study not only presents a new genome catalog to unveil the evolutionary mechanisms underpinning bat fly parasitism, but also provides a novel research system that can be used to investigate the mechanisms of cross-species transmission of bat-borne viruses and the co-evolution of bats and viruses.

ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages.

The rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process. Here, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models. ToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https://github.com/pedronachtigall/ToxCodAn-Genome.

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data.

Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.

Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy.

Plant hybridization is a pathway for the evolution of adaptive traits. However, hybridization between adapted and nonadapted populations may affect the persistence of combinations of adaptive alleles evolved through natural selection. Seed dormancy is an adaptive trait for weedy rice because it regulates the timing of seed germination and the persistence of the soil seed bank. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. Here, we explored the influence of hybridization on the conservation of adaptive allele combinations by evaluating natural variation and genetic structure in seed dormancy-associated genomic regions. Based on sequence variation in the genomic regions associated with seed dormancy, hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, hybrid-derived weedy rice strains were more dormant than their parental weedy rice strains, and this trait was strongly influenced by the environment. This study suggests that hybridization between weedy rice (adaptive allelic combinations for seed dormancy) and cultivated rice (nonadaptive combinations) generates weedy rice strains expressing deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and nonadapted populations appears to be reinforcing the trajectory towards the evolution of adaptive traits.

Post-introduction evolution of a rapid life-history strategy in a newly invasive plant.

A central question in invasion biology is whether adaptive trait evolution following species introduction promotes invasiveness. A growing number of common-garden experiments document phenotypic differences between native- and introduced-range plants, suggesting that adaptive evolution in the new range may indeed contribute to the success of invasive plants. However, these studies are often subject to methodological pitfalls, resulting in weak evidence for post-introduction adaptive trait evolution and leaving its role in the invasion process uncertain. In a common-garden glasshouse study, we compared the growth, life-history, and reproductive traits of 35 native- and introduced-range Polygonum cespitosum populations. We used complementary approaches including climate-matching, standardizing parental conditions, selection analysis, and testing for trait-environment relationships to determine whether traits that increase invasiveness adaptively evolved in the species' new range. We found that the majority of introduced-range populations exhibited a novel trait syndrome consisting of a fast-paced life history and concomitant sparse, reduced growth form. Selection analysis confirmed that this trait syndrome led to markedly higher fitness (propagule production) over a limited growing season that was characteristic of regions within the introduced range. Additionally, several growth and reproductive traits showed temperature-based clines consistent with adaptive evolution in the new range. Combined, these results indicate that, subsequent to its introduction to North America over 100 generations ago, P. cespitosum has evolved key traits that maximize propagule production. These changes may in part explain the species' recent transition to invasiveness, illustrating how post-introduction evolution may contribute to the invasion process.

Mosaic Evolution of Molecular Pathways for Sex Pheromone Communication in a Butterfly.

Unraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved ancestral traits and newly evolved derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~119 million years ago. In moths, it is the females that typically emit pheromones to attract male mates, but in butterflies males emit pheromones that are used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but they have remained relatively unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics to identify genes involved in the different steps (i.e., production, regulation, and reception) of sex pheromone communication of the butterfly Bicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulating sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale investigation of the genetic pathways underlying sex pheromone communication in a butterfly.

Historical links between climate and fire on species dispersion and trait evolution

The interaction effects between climate and fire regime in controlling the type of vegetation and species composition is well established among the Earth’s biomes. Climate and the associated fire regime are never stable for long, and annual temperatures, atmospheric carbon dioxide and oxygen levels, and burn probability have varied radically over the last 350 million years. At the scale of thousands of years, floras have oscillated between spreading and retracting as climate and the dependent fire regime have fluctuated. At the scale of millions of years, distinct traits have evolved along three lines: fire resistance, fire-stimulated dormancy release, and rapid postfire growth, all limited by the type of fire (as controlled by climate) and postfire weather. Eight pairings of fire- and postfire-related traits resulting from the interplay between fire and climate are noted here. Smoke-released seed dormancy is beneficial on two counts: it increases the chance of recruitment under the present fireprone climate and increases the chances of survival should the wet season shift to another time of year where temperatures are higher or lower. Four pathways can be recognized with respect to the fire regimes induced by climate changes: (1) from non-fireprone to fireprone habitats (gains fire-adapted trait, 13 studies covering the last 115 million years (My) described here); (2) from a surface fire to a crown fire-type habitat (gains a different fire-adapted trait, 13 studies); (3) from a crown fire-type to surface fire-type habitat (loss of fire-adapted trait, 12 studies); and (4) from moderately burnt (crown fire) to non-fireprone habitat, such as desert, rainforest, or alpine habitats (loss of fire-adapted trait, 6 studies). Four case studies, at decreasing taxonomic rank, are used to illustrate the intimate relationship between climate change with its associated vegetation and fire regime change as they promote adaptive trait evolution: gain then loss of heat-released seed dormancy in Dipterocarpaceae–Cistaceae–Bixaceae over 90 My, gain then loss of serotiny in Callitroid Cupressaceae over the last 65 My, gain then loss of smoke-released seed dormancy in Proteoid Proteaceae over the last 120 My, and gain then loss of resprouting and serotiny among Hakea species (Grevilleoid Proteaceae) over the last 20 My. Examples of within-species rates of migration and trait change, including a model describing increasing degree of serotiny with intensifying drought, are given. The relevance of this historical approach to current (anthropogenic) climate change and associated fire regime alteration is discussed. Despite major threats expected to species conservation status at both the macro-(biome) and micro-(population) scales, I conclude that insufficient time or opportunities remain for effective migration to less-stressed areas or suitable adaptive responses to climate/fire regime change to evolve.

A chromosome-scale reference genome assembly of yellow mangrove (Bruguiera parviflora) reveals a whole genome duplication event associated with the Rhizophoraceae lineage.

Mangrove forest ecosystems support a diverse flora and fauna of marine and terrestrial species and have important direct and indirect economic, ecological and social values to mankind. Yellow mangrove (Bruguiera parviflora) belongs to the Rhizophoraceae family and is widely distributed in the intertidal zones along sheltered coastal areas in tropical latitudes. Here, we present a high-quality, chromosome-level assembly of the B.parviflora genome. We employed the 10x Genomics linked-read technology to obtain a preliminary assembly, which was subsequently scaffolded using the long-range chromatin contact mapping technique (HiC) to obtain a final assembly containing 213,026,782 bases in 10,045 scaffolds with an N50 length of 10,906,948 bases. Our gene prediction recovered 96.5% of the highly conserved orthologues in the Embryophyta lineage based on the Benchmarking Universal Single-Copy Orthologues (BUSCO) analysis. We analysed the transversion rate at fourfold-degenerate sites from orthologous gene pairs and discovered evidence supporting a recent whole-genome duplication event in B.parviflora and other Rhizophoreae members. Comparative studies based on single-copy orthologous genes indicated that B.parviflora and Bruguiera gymnorrhiza diverged approximately 24.1 million years ago. The population structure analysis revealed that 63 B.parviflora accessions from different geographical regions in Thailand were an admixture of two subpopulations. The examination of alternative splicing events in B.parviflora showed that the most prevalent splicing mechanism was intron retention. This high-quality genome assembly together with the genetic diversity information obtained from the germplasm provide useful genomic resources for future studies on comparative phylogenetics and evolution of adaptive traits in mangrove species.

The evolution of larger size in high-altitude Drosophila melanogaster has a variable genetic architecture.

Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus mapping approach to 4 unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of quantitative trait loci for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of quantitative trait locus regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures indicated by our quantitative trait locus mapping results for size traits mirror those from similar experiments on other recently evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.

Independent and adaptive evolution of phenotypic novelties driven by coral symbiosis in barnacle larvae.

The invasion of novel habitats is recognized as a major promotor of adaptive trait evolution in animals. We tested whether similar ecological niches entail independent and adaptive evolution of key phenotypic structures related to larval host invasion in distantly related taxa. We use disparately related clades of coral barnacles as our model system (Acrothoracica: Berndtia and Thoracicalcarea: Pyrgomatidae). We analyze the larval antennular phenotypes and functional morphologies facilitating host invasion. Extensive video recordings show that coral host invasion is carried out exclusively by cypris larvae with spear-shaped antennules. These first exercise a series of complex probing behaviors followed by repeated antennular penetration of the soft host tissues, which subsequently facilitates permanent invasion. Phylogenetic mapping of larval form and function related to niche invasion in 99 species of barnacles (Thecostraca) compellingly shows that the spear phenotype is uniquely associated with corals and penetrative behaviors. These features evolved independently in the two coral barnacle clades and from ancestors with fundamentally different antennular phenotypes. The larval host invasion system in coral barnacles likely evolved adaptively across millions of years for overcoming challenges associated with invading and entering demanding coral hosts.

Ethanol resistance in Drosophila melanogaster has increased in parallel cold-adapted populations and shows a variable genetic architecture within and between populations.

Understanding the genetic properties of adaptive trait evolution is a fundamental crux of biological inquiry that links molecular processes to biological diversity. Important uncertainties persist regarding the genetic predictability of adaptive trait change, the role of standing variation, and whether adaptation tends to result in the fixation of favored variants. Here, we use the recurrent evolution of enhanced ethanol resistance in Drosophila melanogaster during this species’ worldwide expansion as a promising system to add to our understanding of the genetics of adaptation. We find that elevated ethanol resistance has evolved at least three times in different cooler regions of the species’ modern range—not only at high latitude but also in two African high‐altitude regions. Applying a bulk segregant mapping framework, we find that the genetic architecture of ethanol resistance evolution differs substantially not only between our three resistant populations, but also between two crosses involving the same European population. We then apply population genetic scans for local adaptation within our quantitative trait locus regions, and we find potential contributions of genes with annotated roles in spindle localization, membrane composition, sterol and alcohol metabolism, and other processes. We also apply simulation‐based analyses that confirm the variable genetic basis of ethanol resistance and hint at a moderately polygenic architecture. However, these simulations indicate that larger‐scale studies will be needed to more clearly quantify the genetic architecture of adaptive evolution and to firmly connect trait evolution to specific causative loci.

Two Reference-Quality Sea Snake Genomes Reveal Their Divergent Evolution of Adaptive Traits and Venom Systems.

True sea snakes (Hydrophiini) are among the last and most successful clades of vertebrates that show secondary marine adaptation, exhibiting diverse phenotypic traits and lethal venom systems. To better understand their evolution, we generated the first chromosome-level genomes of two representative Hydrophiini snakes, Hydrophis cyanocinctus and H. curtus. Through comparative genomics we identified a great expansion of the underwater olfaction-related V2R gene family, consisting of more than 1,000 copies in both snakes. A series of chromosome rearrangements and genomic structural variations were recognized, including large inversions longer than 30 megabase (Mb) on sex chromosomes which potentially affect key functional genes associated with differentiated phenotypes between the two species. By integrating multiomics we found a significant loss of the major weapon for elapid predation, three-finger toxin genes, which displayed a dosage effect in H. curtus. These genetic changes may imply mechanisms that drove the divergent evolution of adaptive traits including prey preferences between the two closely related snakes. Our reference-quality sea snake genomes also enrich the repositories for addressing important issues on the evolution of marine tetrapods, and provide a resource for discovering marine-derived biological products.

Examining adaptive evolution of immune activity: opportunities provided by gastropods in the age of 'omics'.

Parasites threaten all free-living organisms, including molluscs. Understanding the evolution of immune defence traits in natural host populations is crucial for predicting their long-term performance under continuous infection risk. Adaptive trait evolution requires that traits are subject to selection (i.e. contribute to organismal fitness) and that they are heritable. Despite broad interest in the evolutionary ecology of immune activity in animals, the understanding of selection on and evolutionary potential of immune defence traits is far from comprehensive. For instance, empirical observations are only rarely in line with theoretical predictions of immune activity being subject to stabilizing selection. This discrepancy may be because ecoimmunological studies can typically cover only a fraction of the complexity of an animal immune system. Similarly, molecular immunology/immunogenetics studies provide a mechanistic understanding of immunity, but neglect variation that arises from natural genetic differences among individuals and from environmental conditions. Here, we review the current literature on natural selection on and evolutionary potential of immune traits in animals, signal how merging ecological immunology and genomics will strengthen evolutionary ecological research on immunity, and indicate research opportunities for molluscan gastropods for which well-established ecological understanding and/or 'immune-omics' resources are already available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Integrating evolutionary, demographic and ecophysiological processes to predict the adaptive dynamics of forest tree populations under global change

Three types of process-based models (PBMs) are traditionally used to predict the response of forest tree populations to global change (GC): (i) ecophysiological models, which simulate carbon and water fluxes in forest ecosystems by explicitly integrating the effects of climate and CO2; (ii) forest dynamics models which simulate forest successions by explicitly linking mortality, growth and regeneration processes; and (iii) evolutionary dynamics models, which simulate the variation and evolution of adaptive traits by explicitly accounting for selection, mutation, gene flow and inheritance rules. The ongoing context of rapid GC, however, questions the boundaries between these types of models. Here, we review different strategies of model integration: (i) physio-demographic PBMs, integrating physiological and demographic processes; (ii) demo-genetic PBMs, integrating demographic and evolutionary processes; and (iii) physio-demo-genetic PBMs, which attempt to integrate these three types of processes. We show that these integrative models allow a better understanding of how different functional traits influence demographic rates (the phenotype-demography map), how the variation in demographic rates influences fitness (the demography-fitness map) and how individual variations of fitness may in turn influence the genetic composition of a population. Our review highlights that accounting for inter-individual variation in ecological processes is increasingly recognized as crucial for modelling the ecosystem response to environmental change. We argue that the effort of integrating these different processes is valuable, both for a basic understanding of their interactive effects on the responses of forests to GC and for applied horizon scanning to support adaptive strategies.

Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

BackgroundEast African lake cichlids are one of the most impressive examples of an adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) in the evolution of adaptive traits across the three Great Lakes of East Africa.ResultsHere, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei. We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with “antigen processing and presentation” and other immune related categories. Our pipeline and results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events.ConclusionsAltogether, we provide the first comprehensive overview of rearrangement evolution in East African cichlids, and some important insights into their likely contribution to adaptation.

Evolutionary Pattern of High Variation Traits in Subfamily Zygophylloideae (Zygophyllaceae)

Patterns in traits and trait combinations reflect how organisms cope with their environment. Owing to different degrees of variability, the performance of traits varies during adaption to the changing environment. In this study, we focused on a taxon dominant in arid regions – the subfamily Zygophylloideae. We analyzed the evolutionary patterns of functional traits to clarify the impact of trait attributes on niche shifts. The results of phylogenetic signal analysis of traits revealed that quantitative traits, such as plant height, were not evolutionarily conserved. Phylogenetic regression pointed out that there are synergistic changes in environmental factors and in some traits within a phylogenetic context. These traits can meet the requirements of different environments more easily, possibly owing to their high variability. As a result, species in the subfamily Zygophylloideae showed clustering in some phenotypic spaces. Thus, the adaptive evolution of traits reduced niche restrictions of related environmental factors on species. The evolutionary analysis of functional traits in subfamily Zygophylloideae proved that high variability of traits allows fine-tuning according to the related environmental factors during the evolutionary process and promotes niche shifts.

Draft genomes of female and male turbot Scophthalmus maximus

Turbot (Scophthalmus maximus) is a commercially important flatfish species in aquaculture. It has a drastic sexual dimorphism, with females growing faster than males. In the present study, we sequenced and de novo assembled female and male turbot genomes. The assembled female genome was 568 Mb (scaffold N50, 6.2 Mb, BUSCO 97.4%), and the male genome was 584 Mb (scaffold N50, 5.9 Mb, BUSCO 96.6%). Using two genetic maps, we anchored female scaffolds representing 535 Mb onto 22 chromosomes. Annotation of the female anchored genome identified 87.8 Mb transposon elements and 20,134 genes. We identified 17,936 gene families, of which 369 gene families were flatfish specific. Phylogenetic analysis showed that the turbot, Japanese flounder and Chinese tongue sole form a clade that diverged from other teleosts approximately 78 Mya. This report of female and male turbot draft genomes and annotated genes provides a new resource for identifying sex determination genes, elucidating the evolution of adaptive traits in flatfish and developing genetic techniques to increase the sustainability of turbot aquaculture.

Modeling rate of adaptive trait evolution using Cox–Ingersoll–Ross process: An Approximate Bayesian Computation approach

Over the past decades, Gaussian processes have been widely used to study trait evolution. In particular, two members of Gaussian processes, Brownian motion and the Ornstein–Uhlenbeck process, have been frequently applied for describing continuous trait evolution. Several models (OUBM, OUOU, OUBMBM, OUOUBM) have been proposed to study the impact on the optimum of a trait by other traits. Applying the Cox–Ingersoll–Ross (CIR) process on rate of evolution, which prevents rates from becoming negative, is a potentially useful extension developed here as the OUBMCIR and OUOUCIR models. Since the likelihood functions of the OUBMCIR and the OUOUCIR models are intractable, a heuristic algorithm for parameter estimation and inference under Approximate Bayesian Computation (ABC) is proposed. Simulation studies show that new models perform well. Empirical analysis using several data sets from literature also provides evidence of the validity and utility of the new models. The relevant data sets and R scripts developed for this project can be accessed through the link.11https://tonyjhwueng.info/ououcir.

Building an adaptive trait simulator package to infer parametric diffusion model along phylogenetic tree

The development of an adaptive trait simulator package for inferring trait evolution along a phylogenetic tree is shown. Stochastic processes of the continuous type are broadly applied to modeling trait evolution when the evolutionary relationship among species and traits of study interest are present. By including several popular stochastic processes, evolutionary information embedded in a dataset can be revealed. The highlights of the method include:1.The implementation of the popular Cox-Ingersol-Ross process for modeling rate evolution within the package to prevent rates from becoming negative and thus is potentially a useful extension to study adaptive trait evolution in randomly evolved environment.2.The established trait simulator approach along with approximate Bayesian computation procedure provides a feasible statistical inference without model likelihood.3.The procedure proposed for trait simulator along phylogenetic tree can be applied to all established models of trait evolution in literature, thus providing users an alternative option to analyze their data.