Simon Y. W. Ho's research while affiliated with UNSW Sydney and other places
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Publications (438)
The progressive aridification of the Australian continent, and coincident decline of mesic forest, has been a powerful driver of allopatric and environmental speciation in native species. The relictual mesic forests of the eastern seaboard now harbor a diverse group of endemic fauna, including the wood-feeding cockroaches of the genus Panesthia, wh...
Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequ...
To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. We applied this scheme to two geographically distinct koala populations in New South Wales, Aus...
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1–3. Here we address these issues by analysing the genomes of 363 bird species⁴ (218 taxon...
Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branch...
Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient‐poor diet. To investigate if host biology has impacted Blattabact...
Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of...
Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among...
Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of...
The Ninu (Greater bilby, Macrotis lagotis ) is a desert-dwelling, culturally and ecologically important marsupial. In collaboration with Indigenous rangers and conservation managers, we generated the first Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura ) to understand th...
Lepidoziaceae are the third-largest family of liverworts, with about 860 species found on all continents. With many taxa occupying a diverse range of habitats, these plants perform a variety of ecological roles. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as the subfamily Micropterygioideae yet to be...
Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of...
The crustacean order Stomatopoda comprises approximately 500 species of mantis shrimps. These marine predators, common in tropical and subtropical waters, possess sophisticated visual systems and specialized hunting appendages. In this study, we infer the evolutionary relationships within Stomatopoda using a combined data set of 77 morphological ch...
The genetic changes that enabled the evolution of eusociality have long captivated biologists. In recent years, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic c...
Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient-poor diet. To investigate if host biology has impacted Blattabact...
Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, p...
Adaptive radiation as a result of ecological opportunity can have profound effects on the evolutionary outcome of species. On coral reefs, parrotfishes have been considered as one of the most dramatic examples of adaptive radiation unique in their extreme dietary specialisation. Using abrasion-resistant biomineralized teeth, parrotfishes are able t...
Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly...
Phylogenetic studies of genomic data can provide valuable opportunities for evaluating evolutionary timescales and drivers of rate variation. These analyses require statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. It implements methods t...
This chapter outlines the history of molecular evolutionary research in australidelphian marsupials, along with the genetic and genomic advances that have provided insights into the evolution, phylogenetic relationships, adaptation, diversification, development, and conservation of Australasian marsupials. Marsupials have long been a focus of molec...
Cockroaches are an ecologically and economically important insect group, but some fundamental aspects of their evolutionary history remain unresolved. In particular, there are outstanding questions about some of the deeper relationships among cockroach families. As a group transferred from Blaberoidea Saussure to Blattoidea Latreille, the evolution...
The Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)) was thought to have a wide range in New South Wales, Australia, spanning some 600 km north–south. A recent extensive molecular phylogenetic and population genomic analysis of E. spinifer across its geographical range revealed strong population structure corresponding to several major geo...
Lepidoziaceae are a large family of liverworts with over 700 species in about 30 genera and seven subfamilies. To date, the phylogeny of the family has not yet been resolved, with three subfamilies–Lepidozioideae, Lembidioideae, and Zoopsidoideae–previously shown not to be monophyletic by previous studies. We performed a phylogenetic analysis of a...
Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastac...
Determining the link between genomic and phenotypic evolution is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates...
Marine animals such as the southern elephant seal (Mirounga leonina) rely on a productive marine environment and are vulnerable to oceanic changes that can affect their reproduction and survival rates. Davis Base, Antarctica, acts as a moulting site for southern elephant seals that forage in Prydz Bay, but the mitochondrial haplotype diversity and...
Characterizing the detailed spatial and temporal dynamics of plant pathogens can provide valuable information for crop protection strategies. However, the epidemiological characteristics and evolutionary trajectories of pathogens can differ markedly from one country to another. The most widespread and important virus of brassica vegetables, turnip...
The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this arti...
Marine animals such as the southern elephant seal (Mirounga leonina) rely on a productive marine environment and are vulnerable to oceanic changes that can affect their reproduction and survival rates. Davis Base, Antarctica, acts as a moulting site for southern elephant seals that forage in Prydz Bay, but the genetic diversity and natal source pop...
The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this arti...
Evolutionary timescales can be estimated using a combination of genetic data and fossil evidence based on the molecular clock. Bayesian phylogenetic methods such as tip dating and total-evidence dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume...
The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demons...
The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demons...
Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified N...
Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are the most influential to species-tree estimation can help to inform the choice of data for phylogenomic...
As the global biodiversity crisis deepens, with increasing habitat fragmentation and a changing climate, innovative options for conserving species are being explored. One such conservation action is genetic rescue: introduction of new alleles to promote population fitness. However, for critically endangered species where only one viable population...
Australian freshwater fishes are a relatively species-poor assemblage, mostly comprising groups derived from older repeated freshwater invasions by marine ancestors, plus a small number of Gondwanan lineages. These taxa are both highly endemic and highly threatened, but a comprehensive phylogeny for Australian freshwater fishes is lacking. This has...
Significance
A key link to understand human history in Island Southeast Asia is the Philippine archipelago and its poorly investigated genetic diversity. We analyzed the most comprehensive set of population-genomic data for the Philippines: 1,028 individuals covering 115 indigenous communities. We demonstrate that the Philippines were populated by...
Significance
Our article presents the most comprehensive reconstruction of the evolutionary and phylogeographic history of a major plant pathogen of brassica vegetables in Eurasia. Sampling across such a large landmass poses considerable challenges, and our study attempts to describe the spatial and temporal patterns of migration for a plant pathog...
The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10% of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationship...
The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light o...
Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predati...
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes f...
Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based o...
Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the phylodynamics of the virus by analysing 253 nucleot...
Hybridization events are not uncommon in marine environments where physical barriers are attenuated. Studies of coral reef taxa have suggested that hybridization predominantly occurs between parapatric species distribu- ted along biogeographic suture zones. By contrast, little is known about the extent of sympatric hybridization on coral reefs, des...
The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (Ne) is thought to play an important role in shaping genome size [1, 2, 3]—a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the exi...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred ov...
Ancient genomes can narrow the search for the sources of zoonotic transmissions
Determining species boundaries forms an important foundation for biological research. However, the results of molecular species delimitation can vary with the data sets and methods that are used. Here we use a two-step approach to delimit species in the genus Heptathela, a group of primitively segmented trapdoor spiders that are endemic to Japanese...
Advances in sequencing technologies have revolutionized wildlife conservation genetics. Analysis of genomic data sets can provide high-resolution estimates of genetic structure, genetic diversity, gene flow, and evolutionary history. These data can be used to characterize conservation units and to effectively manage the genetic health of species in...
The phylogenetic information contained in sequence data is partly determined by the overall rate of nucleotide substitution in the genomic region in question. However, phylogenetic signal is affected by various other factors, such as heterogeneity in substitution rates across lineages. These factors might be able to predict the phylogenetic accurac...
Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigat...
Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1–3. Here we report the 409-megabase genome sequence of the blue-pe...
This book presents coverage of the principles and practice of molecular clocks, which have provided fascinating and unprecedented insights into the evolutionary timescale of life on earth. It begins by following the early development of the molecular evolutionary clock in the 1960s, and leads to the complex statistical approaches that are now used...
Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth’s climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within th...
Molecular clocks can be used to reconstruct evolutionary timescales based on analyses of genetic data, but these clocks need to be calibrated in order to give estimates in absolute time. Calibration is most often carried out using fossil evidence of the timing of evolutionary events, corresponding to internal nodes in phylogenetic trees. Early mole...
The molecular evolutionary clock was proposed in the 1960s and has undergone considerable evolution over the past six decades. After arising from early studies of the amino acid sequences of proteins, the molecular clock became a point of contention between competing theories of molecular evolution. In this chapter, I describe the origins of the mo...
Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. In phylogenetics, the potential impacts of partitioning sequence data for the assignment of substitution models are well appreciated. In contrast, the treatment of branch lengths has re...
A common goal of population genomics and molecular ecology is to reconstruct the demographic history of a species of interest. A pair of powerful tools based on the sequentially Markovian coalescent have been developed to infer past population sizes using genome sequences. These methods are most useful when sequences are available for only a limite...
Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovatio...
Bayesian phylogenetic methods derived from evolutionary biology can be used to reconstruct the history of human languages using databases of cognate words. These analyses have produced exciting results regarding the origins and dispersal of linguistic and cultural groups through prehistory. Bayesian lexical dating requires the specification of prio...
The geographic distributions of marine fishes have been shaped by ancient vicariance and ongoing dispersal events. Some species exhibit anti‐equatorial distributions, inhabiting temperate regions on both sides of the tropics while being absent from equatorial latitudes. The perciform fish Microcanthus strigatus (the stripey) exhibits such a distrib...
Cryptocercus Scudder is a genus of wingless cockroaches, which spend their lives feeding within rotting wood in old‐growth montane forests. Their dispersal capability is likely to be limited because they depend on the succession of temperate forests, but their distribution exhibits intercontinental disjunctions. Although the natural history and con...
Niche partitioning can lead to differences in the range dynamics of plant species through its impacts on habitat availability, dispersal, or selection for traits that affect colonization and persistence. We investigated whether niche partitioning into upland and riparian habitats differentiates the range dynamics of two closely related and sympatri...
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil based calibrations applied as age constraints on internal nodes of the tree. An alternative
approach is tip-dating, which explicitly includes fossil data in the analysis. This can...
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situa...
Sexual selection is a powerful agent of evolution, driving microevolutionary changes in the genome and macroevolutionary rates of lineage diversification. The mechanisms by which sexual selection might influence macroevolution remain poorly understood. For example, sexual selection might drive positive selection for key adaptations that facilitate...
TABLE S1 The control file parameter values defined for the branch models in EasyCodeML
TABLE S2 The control file parameter values defined for the branch-site models in EasyCodeML
TABLE S3 The control file parameter values defined for the site models in EasyCodeML
TABLE S4 The control file parameter values defined for the clade models in EasyCode...
The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here,...
FIGURE 1 Screenshot of the main interface of EasyCodeML under the (a) preset and (b) custom running modes. In the preset mode, all key parameters of the nested models are built-in and there is a pipeline from data input to the output of results. In the custom mode, the parameters of any codon-based model can be modified to meet the requirements of...
The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at region...
FIGURE 3 Two utilities available in EasyCodeML: (a) the LRT calculator, and Seqformat convertor in (b) a user-friendly GUI or (c) command line. Seqformat convertor can convert between diverse types of sequence data formats.
FIGURE2 Labelling branches in a tree for the branch-related models can be done in a simple and intuitive way for the (a) clade models and (b) branch and branch-site models.
Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigat...
The mantis shrimp superfamily Squilloidea, with over 185 described species, is the largest superfamily in the crustacean order Stomatopoda. To date, phylogenetic relationships within this superfamily have been comprehensively analysed using morphological data, with six major generic groupings being recovered. Here, we infer the phylogeny of Squillo...
Background:
Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estim...
Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. Appropriately modelling this heterogeneity is important for reliable phylogenetic inference. One modelling approach in statistical phylogenetics is to apply independent models of molecu...
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is Bayesian total-evidence dating, which involves the joint analysis of molecul...
Potato virus S (PVS) is a major plant pathogen that causes considerable losses in global potato production. Knowledge of the evolutionary history and spatio-temporal dynamics of PVS is vital for developing sustainable management schemes. In this study, we investigated the phylodynamics of the virus by analysing 103 nucleotide sequences of the coat...
Citations
... Wieslochia constitutes the first fossil evidence of a suboscine occurring as early as the Oligocene in Europe, followed by Crosnoornis and NT-LBR-014. The placement of a potential clade containing these three taxa within Eurylaimides is consistent with recent estimates of the crown age of Eurylaimides between 30 and 37 Ma (Claramunt & Cracraft, 2015;Prum et al., 2015;Stiller et al., 2024). ...
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... Researchers may want to know, given a model, how sensitive parameter estimates are to data set size, prior choice, model complexity, violation of model assumptions, to name a few. Studies have examined how these factors a ect estimation accuracy and precision (e.g., Zhang et al., 2023;Luo et al., 2023), as well as the mixing and convergence of MCMC chains (e.g., Nylander et al., 2004;Zhang et al., 2023). We collectively refer to these examinations as "model characterization": any analysis of model behavior beyond assessing its correctness. ...
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... The Turkestan cockroach, Periplaneta lateralis (Walker) (Blattodea: Blattidae), is a peridomestic invasive species found in many parts of the world [1][2][3][4]. Turkestan cockroaches are well adapted to the dry conditions of the southwestern United States, and they have been reported to have spread to other regions of the United States (https: //www.inaturalist.org/observations?taxon_id=1473952, accessed on 1 March 2024). This expansion of Turkestan cockroaches has been attributed partly to their biological and reproductive advantages over Blatta orientalis-a species occupying similar habitats [5,6]. ...
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... A recent extensive molecular phylogenetic and population genomic analysis of Euastacus spinifer sensu lato from across its geographical range revealed strong population structure corresponding to several major geographically correlated clades, the southernmost clade being the most genetically divergent (Van Der Wal et al. 2022). This southern clade, whose range was substantially burnt in 2019-2020, corresponds to E. clydensis and is sister to the clade comprising the remaining populations of E. spinifer and E. vesper. ...
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... Although evolutionary principles predict a relationship between rates of species diversification and morphological divergence (Omland, 1997;Adams et al., 2009), these hypotheses were focused on groups with abundant morphological change, which undoubtedly was underlaid by extensive genetic change. With the finding that many changes in DNA sequences are neutral, Pauling (1962, 1965) proposed that molecular and morphological evolution could be uncoupled, and many studies have shown that rates of speciation and morphological evolution are not always significantly correlated, such that rapid diversification can occur with little morphological change and vice-versa (Omland, 1997;Adams, 2009;Asar et al., 2022;Chase et al., 2021). Determining the link between phylogenetic and phenotypic evolution is a fundamental goal to propose classifications that reflect natural processes. ...
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... Mark-recapture and telemetry studies have shown moulting male southern elephant seals are faithful to both their natal and potential breeding sub-Antarctic islands and distant moult sites at Antarctic coastal ice-free areas. The vast majority of male southern elephant seals that were either sampled for genetic analyses, fitted with tracking devices or individually marked (flipper-tagged) at the Vestfold Hills were representative of the greater Kerguelen genetic stock, mostly from Heard Island and Îles Kerguelen (Tierney 1977, Bester 1988, Bester et al. 2020, Hindell et al. 2021, Chua et al. 2022. The terrestrial habitat requirements for seals moulting in Antarctica (ice-free, gently sloping sand beaches) can result in their co-occurrence with humans. ...
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... Most strains from the world-B group were isolated from brassicas and can infect brassica crops, while the basal-BR group was found primarily in radish hosts, but is also able to infect brassicas (Gong et al., 2019). present world population of TuMV is evolving and diverging rapidly (Gibbs et al., 2015;Kawakubo et al., 2022). The average nucleotide evolutionary rate of TuMV is around 10 -3 substitutions per site per year (Nguyen et al., 2013). ...
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... Both processes, floral specialization and hybridization, contributed to angiosperm diversification (van der Niet and Johnson 2012; Chase et al. 2010), making clear the dual role of pollinators as a primary driver of plant diversity involving microevolution and macroevolution processes. The extent of ecological interaction between plant and animal pollinators has long been investigated (van der Niet and Johnson 2012), with insects as pollinators of most angiosperms (Ollerton et al. 2011;Asar et al. 2022) and are recognized pointed out as key pollinators in angiosperm history (van der Kooi and Ollerton 2020). ...
... Subsampling a fossil record using the unresolved FBD can be accurate with an evenly sampled clade such as cetaceans ), but can be highly inaccurate if the fossils have limited phylogenetic information (O'Reilly and Donoghue 2020). An analysis of mammals (Luo et al. 2021), however, found that fossil sampling density does not have linear effects on divergence time estimates. Altogether, it is difficult to generalize about the best models, unless prior knowledge about node ages is contradicted. ...
... However, this approach requires CDS sequencing, and presents significant challenges, because complex structures, low GC content, and repetitive elements can lead to errors during sequencing [54]. In addition, excessive rapid evolution can lead to a phenomenon known as saturation, where independent mutations obscure the true evolutionary history at a particular site [55]. This effect reduces the discriminatory power of the locus, hindering the ability to distinguish between closely related lineages [56]. ...
