ORCID Profile
0000-0002-5479-1974
Current Organisations
IT University of Copenhagen
,
Københavns Universitet
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Phylogeny and Comparative Analysis | Molecular Evolution | Speciation and Extinction | Evolutionary Biology
ANZSRC Socio-Economic Objective (SEO)
Related Links
Publications
Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference
Publisher: Oxford University Press (OUP)
Date: 11-12-2019
Abstract: 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 received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci or subsets of loci. By analyzing a range of empirical data sets, we find consistent support for a model in which branch lengths are proportionate between subsets of loci: gene trees share the same pattern of branch lengths, but form subsets that vary in their overall tree lengths. These models had substantially better statistical support than models that assume identical branch lengths across gene trees, or those in which genes form subsets with distinct branch-length patterns. We show using simulations and empirical data that the complexity of the branch-length model with the highest support depends on the length of the sequence alignment and on the numbers of taxa and loci in the data set. Our findings suggest that models in which branch lengths are proportionate between subsets have the highest statistical support under the conditions that are most commonly seen in practice. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.
Ecological specialisation and evolutionary reticulation in extant Hyaenidae
Publisher: Cold Spring Harbor Laboratory
Date: 14-10-2020
DOI: 10.1101/2020.10.14.338871
Abstract: During the Miocene, Hyaenidae was a highly erse family of Carnivora that has since been severely reduced to four extant genera, each of which contains only a single species. These species include the bone-cracking spotted, striped, and brown hyenas, and the specialised insectivorous aardwolf. Previous genome studies have analysed the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. To tackle these questions, we generated an aardwolf genome and analysed it together with those from the other three species. We provide new insights into the evolutionary relationships between the species, the genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic ersities and demographic histories. High levels of phylogenetic discordance within the family suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection in their respective lineages, suggesting putative key adaptations to carrion or termite feeding. We also found a family-wide expansion in olfactory receptor genes suggesting that an acute sense of smell was a key early adaptation for the Hyaenidae family. Finally, we report very low levels of genetic ersity within the brown and striped hyenas despite no signs of inbreeding, which we putatively link to their similarly slow decline in N e over the last ∼2 million years. We found much higher levels of genetic ersity in both the spotted hyena and aardwolf and more stable population sizes through time. Taken together, these findings highlight how ecological specialisation can impact the evolutionary history, demographics, and adaptive genetic changes of a lineage.
Phylogenetic patterns in the geographic distributions of birds support the tropical conservatism hypothesis
Publisher: Wiley
Date: 08-09-2015
DOI: 10.1111/GEB.12370
Dietary Intake, FTO Genetic Variants, and Adiposity: A Combined Analysis of Over 16,000 Children and Adolescents
Publisher: American Diabetes Association
Date: 26-02-2015
DOI: 10.2337/DB14-1629
Abstract: The FTO gene harbors variation with the strongest effect on adiposity and obesity risk. Previous data support a role for FTO variation in influencing food intake. We conducted a combined analysis of 16,094 boys and girls aged 1–18 years from 14 studies to examine the following: 1) the association between the FTO rs9939609 variant (or a proxy) and total energy and macronutrient intake and 2) the interaction between the FTO variant and dietary intake, and the effect on BMI. We found that the BMI-increasing allele (minor allele) of the FTO variant was associated with increased total energy intake (effect per allele = 14.3 kcal/day [95% CI 5.9, 22.7 kcal/day], P = 6.5 × 10−4), but not with protein, carbohydrate, or fat intake. We also found that protein intake modified the association between the FTO variant and BMI (interactive effect per allele = 0.08 SD [0.03, 0.12 SD], P for interaction = 7.2 × 10−4): the association between FTO genotype and BMI was much stronger in in iduals with high protein intake (effect per allele = 0.10 SD [0.07, 0.13 SD], P = 8.2 × 10−10) than in those with low intake (effect per allele = 0.04 SD [0.01, 0.07 SD], P = 0.02). Our results suggest that the FTO variant that confers a predisposition to higher BMI is associated with higher total energy intake, and that lower dietary protein intake attenuates the association between FTO genotype and adiposity in children and adolescents.
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
Publisher: Wiley
Date: 12-09-2015
Abstract: Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed-clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch-specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed-clock models are more appropriate for biological data. We present an R package, NELSI, that allows the evolution of DNA sequences to be simulated according to a range of clock models. Using data generated by this package, we assessed the ability of two Bayesian phylogenetic methods to distinguish among different relaxed-clock models and to quantify rate variation among lineages. The results of our analyses show that rate autocorrelation is typically difficult to detect, even when there is complete taxon s ling. This provides a potential explanation for past failures to detect rate autocorrelation in a range of data sets.
Flight demand and environmental niche are associated with molecular evolutionary rates in a large avian radiation
Publisher: Cold Spring Harbor Laboratory
Date: 17-01-2020
DOI: 10.1101/2020.01.16.908368
Abstract: Among the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the erse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and the hand-wing index) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found evidence that species that fly less have greater wing loading and this is associated with accelerated rates of mutation. An elongated wing morphology is associated with greater flight activity and with molecular signatures of positive selection or reduced population sizes. Meanwhile, environmental temperature and UV radiation interact to explain molecular rates at sites affected by selection and population size, contrary to the expectation of their impact on mutation rates. Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size.
A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea
Publisher: Cold Spring Harbor Laboratory
Date: 24-10-2020
DOI: 10.1101/2020.10.23.352286
Abstract: The importance of post- ergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied in idual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae, Monodontidae). To investigate the role of post- ergence gene flow in the speciation process, we used a multifaceted approach, including: (i) phylogenomics, (ii) the distribution of shared derived alleles, and (iii) demographic inference. We found the ergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics, D-foil, and f -branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea we reveal the prevalence of ancient interfamilial gene flow events prior to the ersification of each family, and suggests that contemporary hybridisation events may be disadvantageous, as hybrid in iduals do not appear to contribute to the parental species’ gene pools.
Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families
Publisher: Oxford University Press (OUP)
Date: 22-09-2017
Abstract: A fundamental challenge in resolving evolutionary relationships across the tree of life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees. We find two distinct clusters of loci, each providing an estimate of the species tree that matches previously proposed resolutions of the marsupial phylogeny. We also identify a well-supported placement for the enigmatic marsupial moles (Notoryctes) that contradicts previous molecular estimates but is consistent with morphological evidence. The pattern of gene-tree variation across tree-space is characterized by changes in information content, GC content, substitution-model adequacy, and signatures of purifying selection in the data. In a simulation study, we show that incomplete lineage sorting can explain the ision of loci into the two tree-topology clusters, as found in our phylogenomic analysis of marsupials. We also demonstrate the potential benefits of minimizing uncertainty from phylogenetic conflict for molecular dating. Our analyses reveal that Australasian marsupials appeared in the early Paleocene, whereas the ersification of present-day families occurred primarily during the late Eocene and early Oligocene. Our methods provide an intuitive framework for improving the accuracy and precision of phylogenetic inference and molecular dating using genome-scale data.
Environmental niche and flight intensity are associated with molecular evolutionary rates in a large avian radiation
Publisher: Springer Science and Business Media LLC
Date: 02-08-2022
DOI: 10.1186/S12862-022-02047-0
Abstract: Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the erse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found weak evidence of a positive effect of environmental and morphological variables on mitochondrial substitution rates. Additionally, we found that temperature and UV radiation interact to explain molecular rates at nucleotide sites affected by selection and population size (non-synonymous substitutions), contrary to the expectation of their impact on sites associated with mutation rates (synonymous substitutions). We also found a negative interaction between wing shape (as described by the hand-wing index) and body mass explaining mitochondrial molecular rates, suggesting molecular signatures of positive selection or reduced population sizes in small-bodied species with greater flight activity. Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size. Data from whole genomes and detailed physiology across taxa will bring a more complete picture of the impact of metabolism, population size, and the environment on avian genome evolution.
Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus)
Publisher: Oxford University Press (OUP)
Date: 02-11-2022
Abstract: The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800–9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic ersity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene–Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.
Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts
Publisher: Springer Science and Business Media LLC
Date: 14-05-2021
DOI: 10.1038/S42003-021-02105-1
Abstract: Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 s les from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma , IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data
Publisher: Oxford University Press (OUP)
Date: 11-09-2022
Abstract: 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 demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance phylogenomics substitution model substitution saturation test statistics.]
Blue turns to grey - Palaeogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus)
Publisher: Cold Spring Harbor Laboratory
Date: 13-04-2022
DOI: 10.1101/2022.04.12.487785
Abstract: The blue antelope ( Hippotragus leucophaeus ) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan ( H. equinus ) or sable ( H. niger ) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (~200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800–9,300 cal BP, making it currently the oldest palaeogenome from Africa. Phylogenomics show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic ersity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelope’s extinction.
Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences
Publisher: Wiley
Date: 16-12-2015
Abstract: Phylogenetic estimation of evolutionary timescales has become routine in biology, forming the basis of a wide range of evolutionary and ecological studies. However, there are various sources of bias that can affect these estimates. We investigated whether tree imbalance, a property that is commonly observed in phylogenetic trees, can lead to reduced accuracy or precision of phylogenetic timescale estimates. We analysed simulated data sets with calibrations at internal nodes and at the tips, taking into consideration different calibration schemes and levels of tree imbalance. We also investigated the effect of tree imbalance on two empirical data sets: mitogenomes from primates and serial s les of the African swine fever virus. In analyses calibrated using dated, heterochronous tips, we found that tree imbalance had a detrimental impact on precision and produced a bias in which the overall timescale was underestimated. A pronounced effect was observed in analyses with shallow calibrations. The greatest decreases in accuracy usually occurred in the age estimates for medium and deep nodes of the tree. In contrast, analyses calibrated at internal nodes did not display a reduction in estimation accuracy or precision due to tree imbalance. Our results suggest that molecular-clock analyses can be improved by increasing taxon s ling, with the specific aims of including deeper calibrations, breaking up long branches and reducing tree imbalance.
PhyloMAd: Efficient assessment of phylogenomic model adequacy
Publisher: Oxford University Press (OUP)
Date: 21-02-2018
DOI: 10.1093/BIOINFORMATICS/BTY103
Abstract: Statistical phylogenetic inference plays an important role in evolutionary biology. The accuracy of phylogenetic methods relies on having suitable models of the evolutionary process. Various tools allow comparisons of candidate phylogenetic models, but assessing the absolute performance of models remains a considerable challenge. We introduce PhyloMAd, a user-friendly application for assessing the adequacy of commonly used models of nucleotide substitution and among-lineage rate variation. Our software implements a fast, likelihood-based method of model assessment that is tractable for analyses of large multi-locus datasets. PhyloMAd provides a means of informing model improvement, or selecting data to enhance the evolutionary signal in phylogenomic analyses. PhyloMAd, together with a manual, a tutorial and the source code, are freely available from the GitHub repository uchene hylomad
Urban colonization is driven by a mixture of evolutionarily conserved and labile traits
Publisher: Cold Spring Harbor Laboratory
Date: 20-01-2020
DOI: 10.1101/2020.01.20.912170
Abstract: Urbanization is a fast and dramatic transformation of habitat that generally forces native fauna into novel ecological challenges. The biological prerequisites necessary to establish in urban areas have been widely studied, but the macroevolutionary characteristics of traits that allow urban colonization remain poorly understood. Urban colonization might be facilitated by traits that are evolutionarily conserved and which lead to a ersity of closely related species. Alternatively, urban colonization might be associated with labile traits that frequently arise and are lost. In a large data set from passerine birds, we find that urban colonization has a signal of highly labile traits, despite many traits associated with colonization being highly conserved. Urban colonization is associated with traits that allow faster speciation than non-urban-colonizing counterparts, and more frequently transition to non-urban trait states than in the opposite direction. Overall, the traits that facilitate urban colonization are a mix of highly conserved and labile traits and appear to provide an evolutionarily successful strategy.
Probing the genomic limits of de-extinction in the Christmas Island rat
Publisher: Elsevier BV
Date: 04-2022
ClockstaRX: testing molecular clock hypotheses with genomic data
Publisher: Cold Spring Harbor Laboratory
Date: 03-02-2023
DOI: 10.1101/2023.02.02.526226
Abstract: 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 that use information from gene trees in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests of the dimensionality reducibility of the Euclidean space of rates, and for identifying loci and branches that have a large influence on rate variation. Using simulations to evaluate the performance of the methods implemented, we find that inferences about rates can be strongly influenced by the overall amount of rate variation in the data, the shared patterns of among-lineage rate heterogeneity across groups of loci, and missing data. In an analysis of phylogenomic data from birds, we find a higher rate of evolution in introns compared with exons across all lineages. In addition, passerine taxa are highlighted as having unique patterns of genomic evolutionary rates compared with other avian lineages. Drawing on these results, we recommend careful exploratory analyses and filtering before performing phylogenomic analyses using molecular clocks.
Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species-richness in the Proteaceae
Publisher: Springer Science and Business Media LLC
Date: 2013
Excluding loci with substitution saturation improves inferences from phylogenomic data
Publisher: Cold Spring Harbor Laboratory
Date: 28-08-2021
DOI: 10.1101/2021.08.28.457888
Abstract: 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 demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences.
New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity
Publisher: Oxford University Press (OUP)
Date: 21-02-2017
Abstract: In statistical phylogenetic analyses of DNA sequences, models of evolutionary change commonly assume that base composition is stationary through time and across lineages. This assumption is violated by many data sets, but it is unclear whether the magnitude of these violations is sufficient to mislead phylogenetic inference. We investigated the impacts of compositional heterogeneity on phylogenetic estimates using a method for assessing model adequacy. Based on a detailed simulation study, we found that common frequentist criteria are highly conservative, such that the model is often rejected when the phylogenetic estimates do not show clear signs of bias. We propose new criteria and provide guidelines for their usage. We apply these criteria to genome-scale data from 40 birds and find that loci with severely non-homogeneous base composition are uncommon. Our results show the importance of using well-informed diagnostic statistics when testing model adequacy for phylogenomic analyses.
Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
Publisher: Elsevier BV
Date: 09-2021
DOI: 10.1016/J.CELL.2021.07.032
Abstract: Only five species of the once- erse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early ergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide ersity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic ersity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference
Publisher: Cold Spring Harbor Laboratory
Date: 09-11-2018
DOI: 10.1101/467449
Abstract: 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 molecular evolution to different groups of sites, where the groups are usually defined by locus, codon position, or combinations of the two. The potential impacts of partitioning data for the assignment of substitution models are well appreciated. Meanwhile, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci. By analysing a range of empirical data sets, we find that the best-fitting model for phylogenetic inference is consistently one in which branch lengths are proportionally linked: gene trees have the same pattern of branch-length variation, but with varying absolute tree lengths. This model provided a substantially better fit than those that either assumed identical branch lengths across gene trees or that allowed each gene tree to have its own distinct set of branch lengths. Using simulations, we show that the fit of the three different models of branch lengths varies with the length of the sequence alignment and with the number of taxa in the data set. Our findings suggest that a model with proportionally linked branch lengths across loci is likely to provide the best fit under the conditions that are most commonly seen in practice. In future work, improvements in fit might be afforded by models with levels of complexity intermediate to proportional and free branch lengths. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.
Phylogenetic signal is associated with the degree of variation in root-to-tip distances
Publisher: Cold Spring Harbor Laboratory
Date: 29-01-2020
DOI: 10.1101/2020.01.28.923805
Abstract: 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 accuracy of any given gene in a data set. We examined the association between the accuracy of phylogenetic inference across genes and several characteristics of branch lengths in phylogenomic data. In a large number of published data sets, we found that the accuracy of phylogenetic inference from genes was consistently associated with their mean statistical branch support and variation in their gene tree root-to-tip distances, but not with tree length and stemminess. Therefore, a signal of constant evolutionary rates across lineages appears to be beneficial for phylogenetic inference. Identifying the causes of variation in root-to-tip lengths in gene trees also offers a potential way forward to increase congruence in the signal across genes and improve estimates of species trees from phylogenomic data sets.
Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods
Publisher: Cold Spring Harbor Laboratory
Date: 18-09-2017
DOI: 10.1101/190041
Abstract: Background: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, where the phylogenetic tree and evolutionary timescale are estimated first using maximum likelihood. Under this hybrid approach, demographic parameters are inferred from estimated trees instead of the sequence data, using maximum likelihood, Bayesian inference, or approximate Bayesian computation. This can vastly reduce the computational burden, but has the disadvantage of ignoring the uncertainty in the phylogenetic tree and evolutionary timescale. Results: We compared the performance of a fully Bayesian and a hybrid method by analysing six whole-genome SNP data sets from a range of bacteria and simulations. The estimates from the two methods were very similar, suggesting that the hybrid method is a valid alternative for very large datasets. However, we also found that congruence between these methods is contingent on the presence of strong temporal structure in the data (i.e. clocklike behaviour), which is typically verified using a date-randomisation test in a Bayesian framework. To reduce the computational burden of this Bayesian test we implemented a date-randomisation test using a rapid maximum likelihood method, which has similar performance to its Bayesian counterpart. Conclusions: Hybrid approaches can produce reliable inferences of evolutionary timescales and phylodynamic parameters in a fraction of the time required for fully Bayesian analyses. As such, they are a valuable alternative in outbreak studies involving a large number of isolates.
Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
Publisher: Oxford University Press (OUP)
Date: 10-07-2015
A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea
Publisher: Wiley
Date: 13-07-2023
DOI: 10.1111/MEC.17069
Abstract: The impact of post‐ ergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide‐ranging marine species, such as cetaceans. Here, we studied in idual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post‐ ergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the ergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding‐window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D‐statistics and f ‐branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea we reveal the prevalence of ancient interfamilial gene flow events prior to the ersification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid in iduals do not appear to contribute to the parental species' gene pools.
Differences in performance among test statistics for assessing phylogenomic model adequacy
Publisher: Oxford University Press (OUP)
Date: 18-05-2018
DOI: 10.1093/GBE/EVY094
Sexual selection, body mass and molecular evolution interact to predict diversification in birds
Publisher: The Royal Society
Date: 20-03-2019
Abstract: Sexual selection is a powerful agent of evolution, driving microevolutionary changes in the genome and macroevolutionary rates of lineage ersification. The mechanisms by which sexual selection might influence macroevolution remain poorly understood. For ex le, sexual selection might drive positive selection for key adaptations that facilitate ersification. Furthermore, sexual selection might be a general driver of molecular evolutionary rate. We lay out some of the potential mechanisms that create a link between sexual selection and ersification, based on causal effects on other life-history traits such as body mass and the rate of molecular evolution. Birds are ideally suited for testing the importance of these relationships because of their erse reproductive systems and the multiple evolutionary radiations that have produced their astounding modern ersity. We show that sexual selection (measured as the degree of polygyny) interacts with the rate of molecular evolution and with body mass to predict species richness at the genus level. A high degree of polygyny and rapid molecular evolution are positively associated with the net rate of ersification, with the two factors being especially important for explaining ersification in large-bodied taxa. Our findings further suggest that mutation rates underpin some of the macroevolutionary effects of sexual selection. We synthesize the existing theory on sexual selection as a force for ersity and propose avenues for exploring this association using genome data.
Phylogenetic evidence for recent diversification of obligate coral-dwelling gobies compared with their host corals
Publisher: Elsevier BV
Date: 10-2013
A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process
Publisher: Oxford University Press (OUP)
Date: 27-05-2019
Abstract: 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 be done, for ex le, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth–death process, which allows non-contemporaneous tips and s led ancestors while providing a model of lineage ersification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil s ling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth–death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth–death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of s led ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth–death model, which will inform further development of the method and its application to key questions in evolutionary biology.
A comparison of methods for estimating substitution rates from ancient DNA sequence data
Publisher: Springer Science and Business Media LLC
Date: 16-05-2018
Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies
Publisher: Oxford University Press (OUP)
Date: 06-05-2019
Abstract: 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 ergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our ergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present ergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.
Phylogenetic estimates of diversification rate are affected by molecular rate variation
Publisher: Wiley
Date: 20-08-2017
DOI: 10.1111/JEB.13148
Abstract: Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of ersification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of ersification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence ergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of ersification rate. In particular, a growing number of studies have revealed an association between the net ersification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of ersification time. We simulated the evolution of DNA sequences under several scenarios where rates of ersification and molecular evolution vary through time, including models where ersification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in ersification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies.
Cross-validation to select Bayesian hierarchical models in phylogenetics
Publisher: Springer Science and Business Media LLC
Date: 26-05-2016
Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations
Publisher: Oxford University Press (OUP)
Date: 06-07-2020
Abstract: Phylogenetic methods can use the s ling 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 s les. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the s ling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) s ling times, and a model in which the s les are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern s les of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.
Sex in the city: sexual selection and urban colonization in passerines
Publisher: The Royal Society
Date: 04-09-2019
Abstract: Urbanization leads to a rapid and drastic transformation of habitats, forcing native fauna to manage novel ecological challenges or to move. Sexual selection is a powerful evolutionary force, which is sometimes predicted to enhance the ability of species to adapt to novel environments because it allows females to choose high-quality males, but other times is predicted to reduce the viability of populations because it pushes males beyond naturally selected optima. However, we do not know whether or how sexual selection contributes to the likelihood that animals will establish in urban areas. We use a comparative analysis of passerine birds to test whether traits associated with pre- and post-mating sexual selection predict successful colonization of urban areas. We found that plumage dichromatism was negatively associated with urban tolerance, but found no relationship with sexual size dimorphism or testes mass relative to body mass. While we cannot determine the exact reason why species with high plumage dichromatism occur less in cities, it is likely that urban areas increase the costs of expressing bright coloration due, for instance, to dietary constraints, limited male parental care or increased predation.
Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts
Publisher: Research Square Platform LLC
Date: 03-2021
DOI: 10.21203/RS.3.RS-269923/V1
Abstract: Salmonids are important sources of protein for a large proportion of the human population. Interaction between the gut microbiota and host has been shown to affect the host phenotype in mammals, but relatively little is known about microbiota-host interaction in fish. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbial cells. Despite the frequent reported dominance of intestinal Mycoplasma species, very little is known about their phylogenetic placement, functions and potential evolutionary relationships with their salmonid hosts.In this study, we utilise 2.9 billion metagenomic reads generated from 12 s les from three different salmonid host species to I ) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II ) establish the phylogeny of these salmonid candidate Mycoplasma species using known Mycoplasma genomes, III ) perform a comprehensive pangenomic analysis of Mycoplasma , IV ) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host.Our data provide a basis for future studies examining the composition and function of the salmonid microbiota, with a potential for being further exploited in order to increase animal health and growth in aquaculture.
Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae
Publisher: Oxford University Press (OUP)
Date: 24-02-2021
Abstract: During the Miocene, Hyaenidae was a highly erse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic ersities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic ersity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic ersity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.
Genomic insights into the evolutionary relationships and demographic history of kiwi
Publisher: Public Library of Science (PLoS)
Date: 10-10-2022
DOI: 10.1371/JOURNAL.PONE.0266430
Abstract: Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic ersity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post- ergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic ersity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic ersity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.
Bird lineages colonizing urban habitats have diversified at high rates across deep time
Publisher: Wiley
Date: 19-06-2022
DOI: 10.1111/GEB.13558
Abstract: Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human‐made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long‐term patterns of ersification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood. World. Current. Passerine birds. We applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban‐tolerant species with that of urban‐avoidant species. Specifically, we examined models of state‐dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait‐dependent ersification based on relative urban abundance. We also ran simulation‐based model assessments to explore potential sources of bias. We provide evidence that historically, species with traits promoting urban colonization have undergone faster ersification than urban‐avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban‐avoidant passerines to be recent and to undergo fast ersification. All highly supported models give this result consistently. Urbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer‐term ersification. Urban avoidance is associated with high rates of recent ersification for some clades occurring in regions with relatively intact natural ecosystems and low current levels of urbanization.
Bayesian molecular dating: opening up the black box
Publisher: Wiley
Date: 15-12-2018
DOI: 10.1111/BRV.12390
Abstract: Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a 'molecular clock'. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account. But in order to do this, Bayesian dating methods rely on a range of assumptions about the evolutionary process, which vary in their degree of biological realism and empirical support. These assumptions can have substantial impacts on the estimates produced by molecular dating analyses. The aim of this review is to open the 'black box' of Bayesian molecular dating and have a look at the machinery inside. We explain the components of these dating methods, the important decisions that researchers must make in their analyses, and the factors that need to be considered when interpreting results. We illustrate the effects that the choices of different models and priors can have on the outcome of the analysis, and suggest ways to explore these impacts. We describe some major research directions that may improve the reliability of Bayesian dating. The goal of our review is to help researchers to make informed choices when using Bayesian phylogenetic methods to estimate evolutionary rates and timescales.
Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae
Publisher: Wiley
Date: 05-04-2022
DOI: 10.1111/MEC.16443
Abstract: Species of the mustelid subfamily Guloninae inhabit erse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra ( Eira barbara ), the earliest erging species in the subfamily, and compared this with the genomes available for the wolverine ( Gulo gulo ) and the sable ( Martes zibellina ). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species‐specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For ex le, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species‐specific changes in many pregnancy‐related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
Evidence for Concerted and Mosaic Brain Evolution in Dragon Lizards
Publisher: S. Karger AG
Date: 2017
DOI: 10.1159/000478738
Abstract: The brain plays a critical role in a wide variety of functions including behaviour, perception, motor control, and homeostatic maintenance. Each function can undergo different selective pressures over the course of evolution, and as selection acts on the outputs of brain function, it necessarily alters the structure of the brain. Two models have been proposed to explain the evolutionary patterns observed in brain morphology. The concerted brain evolution model posits that the brain evolves as a single unit and the evolution of different brain regions are coordinated. The mosaic brain evolution model posits that brain regions evolve independently of each other. It is now understood that both models are responsible for driving changes in brain morphology however, which factors favour concerted or mosaic brain evolution is unclear. Here, we examined the volumes of the 6 major neural sub isions across 14 species of the agamid lizard genus i Ctenophorus /i (dragons). These species have erged multiple times in behaviour, ecology, and body morphology, affording a unique opportunity to test neuroevolutionary models across species. We assigned each species to an ecomorph based on habitat use and refuge type, then used MRI to measure total and regional brain volume. We found evidence for both mosaic and concerted brain evolution in dragons: concerted brain evolution with respect to body size, and mosaic brain evolution with respect to ecomorph. Specifically, all brain sub isions increase in volume relative to body size, yet the tectum and rhombencephalon also show opposite patterns of evolution with respect to ecomorph. Therefore, we find that both models of evolution are occurring simultaneously in the same structures in dragons, but are only detectable when examining particular drivers of selection. We show that the answer to the question of whether concerted or mosaic brain evolution is detected in a system can depend more on the type of selection measured than on the clade of animals studied.
Phylogenomics
Publisher: Elsevier BV
Date: 10-2021
DOI: 10.1016/J.CUB.2021.07.039
Abstract: The reconstruction of evolutionary relationships among species is fundamental for our understanding of bio ersity. Today, evolutionary relationships are closely related with the depiction of the tree of life, and research on the topic is underpinned by methods in molecular phylogenetics that have grown in popularity since the 1960s. These methods depend on our understanding of how nucleotide or amino acid sequences evolve through time and in different lineages. Armed with this knowledge, researchers can make inferences about the relationships and amount of genomic ergence among species.
The Genome as an Evolutionary Timepiece
Publisher: Oxford University Press (OUP)
Date: 09-2016
DOI: 10.1093/GBE/EVW220
Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods
Publisher: Springer Science and Business Media LLC
Date: 19-06-2018
The performance of the date-randomization test in phylogenetic analyses of time-structured virus data
Publisher: Oxford University Press (OUP)
Date: 13-03-2015
Abstract: Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the s ling times of the viral sequences. However, the spread of these s ling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the s ling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct s ling times should not overlap with those obtained with randomized s ling times. We also investigated the behavior of the test when the s ling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus. Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results.
Bayesian molecular dating: opening up the black box
Publisher: Wiley
Date: 15-12-2018
DOI: 10.1111/BRV.12390
Abstract: Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a 'molecular clock'. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account. But in order to do this, Bayesian dating methods rely on a range of assumptions about the evolutionary process, which vary in their degree of biological realism and empirical support. These assumptions can have substantial impacts on the estimates produced by molecular dating analyses. The aim of this review is to open the 'black box' of Bayesian molecular dating and have a look at the machinery inside. We explain the components of these dating methods, the important decisions that researchers must make in their analyses, and the factors that need to be considered when interpreting results. We illustrate the effects that the choices of different models and priors can have on the outcome of the analysis, and suggest ways to explore these impacts. We describe some major research directions that may improve the reliability of Bayesian dating. The goal of our review is to help researchers to make informed choices when using Bayesian phylogenetic methods to estimate evolutionary rates and timescales.
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