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Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Although some authors have suggested that the clade experienced a decline in diversity, potentially starting millions of years before the end-Cretaceous mass extinction, others have suggested that the group remained highly diverse right up until the Cretaceous-Paleogene (K-Pg) boundary. Our results show that model assumptions, likely with respect to incomplete sampling, have a large impact on whether dinosaurs appear to have experienced a long-term decline or not. The results are also highly sensitive to the topology and branch lengths of the phylogeny used. Developing comprehensive models of sampling bias, and building larger and more accurate phylogenies, are likely to be necessary steps for us to determine whether dinosaur diversity was or was not in decline before the end-Cretaceous mass extinction.

Abstract Stochastic population dynamics simulations are essential for many ecological and epidemiological studies to generate time series and genealogies that capture the relatedness between individuals. Many software packages allow one to simulate phylogenetic trees but these tend to suffer from one or two major limitations. First, the underlying population dynamics model is often simplistic (e.g. constant population size or exponential growth). Second, the software packages are not appropriate to simulate a large number of trees. We introduce TiPS, an R package to generate trajectories and phylogenetic trees associated with a compartmental model. Trajectories are simulated using Gillespie's exact or approximate stochastic simulation algorithm, or a newly proposed mixed version of the two. Phylogenetic trees are simulated from a trajectory under a backwards‐in‐time approach (i.e. coalescent). TiPS is based on the Rcpp package, allowing to combine the flexibility of R for model definition and the speed of C++ for simulations execution. The model is defined in R with a set of reactions, which allow capturing heterogeneity in life cycles or any sort of population structure. TiPS converts the model into C++ code and compiles it into a simulator that is interfaced in R via a function. TiPS is flexible, easy‐to‐use and available on the CRAN at https://cran.r‐project.org/package=TiPS. Plus, benchmarking analyses show that TiPS is faster than existing packages. This package is particularly well suited for population genetics and phylodynamics studies that need to generate a large number of phylogenies used for population dynamics studies.

The recently proposed concept of ´endangered living fossils’ (ELFs) integrates high-endangered status and evolutionary singularity for any species. In this review, I gathered monotypic genera (single-species genera) that satisfy the three ELF criteria: (i) scarcity and narrow distribution of populations, i.e., considering every species categorized ‘critically endangered’ or contemporary ´extinct´ by IUCN criteria; (ii) evolutionary singularity, i.e., both morphological and phylogenetic singularities of a single-species lineage as a result of a null net diversification rate; and (iii) ancient divergence, i.e., split from the closest extant relatives predating a particular geological epoch. A total of 3,706 monotypic genera of vertebrates and angiosperms were analyzed. I found 109 critically endangered and contemporary extinct genera of which 57 were ELFs. The emergent patterns are: (1) taxonomy (generic level) is a reliable first approach to identifying ELFs; (2) ´morphological singularity´ displayed by monotypic genera does not always help identify ELFs on islands; (3) species of monotypic genera tend to be more threatened than average species; (4) extinction appears to be biased against some animal and plant groups; (5) contemporary extinct genera are strongly associated with distribution on islands, particularly for flightless birds vulnerable to human prosecution; and (6) the ELF approach is a relatively quick method to identify the species of floras and faunas most urgently in need of protection in the world. This approach is complementary to any method searching for phylogenetic diversity (e. g. EDGE), which is also discussed. I argue that ELFs should be prioritized in conservation because they are the most threatened lineages representing an exceptional evolutionary heritage in the world.

Phylogenetic diversity (PD) is an important measure for identifying areas of conservation. Phylogenetic diversity is a robust biodiversity metric because it accounts for the relationships among species, and not just the number of species. For this reason, it is an essential element for conservation planning. Unfortunately, PD metrics are not used by many for conservation planning. In the case of Colombia, which is rich in crop and wild plant biodiversity, lacks information on genetic resources of Crop Wild Relatives (CWR). Due to deforestation and agriculture expansion, the habitat, where these crop wild relatives grow, is being reduced at an alarming rate and could be destroyed altogether. This study focuses on crop wild relatives in Colombia, comparing species diversity versus PD‐based metrics to show the advantages of using evolutionary information for conservation planning. We identified new areas with high PD and endemism among CWR diversity which are important to establishing comprehensive conservation strategies. [ABSTRACT FROM AUTHOR]

Stochastic population dynamics simulations are essential for many ecological and epidemiological studies to generate time series and genealogies that capture the relatedness between individuals. Many software packages allow one to simulate phylogenetic trees but these tend to suffer from one or two major limitations. First, the underlying population dynamics model is often simplistic (e.g. constant population size or exponential growth). Second, the software packages are not appropriate to simulate a large number of trees.We introduce TiPS, an R package to generate trajectories and phylogenetic trees associated with a compartmental model. Trajectories are simulated using Gillespie's exact or approximate stochastic simulation algorithm, or a newly proposed mixed version of the two. Phylogenetic trees are simulated from a trajectory under a backwards‐in‐time approach (i.e. coalescent). TiPS is based on the Rcpp package, allowing to combine the flexibility of R for model definition and the speed of C++ for simulations execution. The model is defined in R with a set of reactions, which allow capturing heterogeneity in life cycles or any sort of population structure. TiPS converts the model into C++ code and compiles it into a simulator that is interfaced in R via a function.TiPS is flexible, easy‐to‐use and available on the CRAN at https://cran.r‐project.org/package=TiPS. Plus, benchmarking analyses show that TiPS is faster than existing packages.This package is particularly well suited for population genetics and phylodynamics studies that need to generate a large number of phylogenies used for population dynamics studies. [ABSTRACT FROM AUTHOR]

A new genus of Neotropical Satyrinae butterflies, Viloriodes Pyrcz & Espeland gen. n. is described in the Pedaliodes Butler complex comprising 11–13 genera and more than 400 species. Support for the new genus is provided by a phylogenetic analysis based on target enrichment (TE) data including 618 nuclear loci with a total of 248,940 nucleotides, and the mitochondrial gene cytochrome oxidase subunit 1 (COI). Five species, whose DNA sequences were obtained by TE during this study, form a strongly supported clade sister to the large clade comprising Pedaliodes and four other genera. Complementary COI analysis confirms the monophyly of Viloriodes gen. n., with the above five plus eight other species clustering in highly supported clades in both Bayesian Inference and Maximum Likelihood analyses, and a TE + COI concatenated tree. Based on molecular and morphological data, 30 species are assigned to Viloriodes gen. n. The new genus can be recognized by a set of subtle morphological characteristics of colour patterns and male and female genitalia. An analysis of divergence times indicates that Viloriodes gen. n. and Steromapedaliodes Forster separated around 5.9 Mya. Viloriodes gen. n. has a wider geographic distribution than any other genus of the Pedaliodes complex, being found from central Mexico to northern Argentina and to the Guyana Shield, typically occurring at lower elevations than Pedaliodes. [ABSTRACT FROM AUTHOR]

A lot of what we know about past speciation and extinction dynamics is based on statistically fitting birth–death processes to phylogenies of extant species. Despite their wide use, the reliability of these tools is regularly questioned. It was recently demonstrated that vast 'congruent' sets of alternative diversification histories cannot be distinguished (i.e., are not identifiable) using extant phylogenies alone, reanimating the debate about the limits of phylogenetic diversification analysis. Here, we summarize what we know about the identifiability of the birth–death process and how identifiability issues can be addressed. We conclude that extant phylogenies, when combined with appropriate prior hypotheses and regularization techniques, can still tell us a lot about past diversification dynamics. Reconstructing past speciation and extinction dynamics from extant phylogenies is one of the main approaches to study the build-up of biodiversity on geological time scales. These reconstructions typically involve a prior hypothesis on the functional form of temporal variations in speciation and extinction rates. Avoiding to formulate a priori hypotheses while still being able to separate speciation and extinction dynamics will require other information such as fossils, constraints on complexity, or statistical regularization techniques. [ABSTRACT FROM AUTHOR]

Despite its current low diversity, the penguin clade (Sphenisciformes) is one of the groups of birds with the most complete fossil record. Likewise, from the evolutionary point of view, it is an interesting group given the adaptations developed for marine life and the extreme climatic occupation capacity that some species have shown. In the present contribution, we reviewed and integrated all of the geographical and phylogenetic information available, together with an exhaustive and updated review of the fossil record, to establish and propose a biogeographic scenario that allows the spatial-temporal reconstruction of the evolutionary history of the Sphenisciformes, discussing our results and those obtained by other authors. This allowed us to understand how some abiotic processes are responsible for the patterns of diversity evidenced both in modern and past lineages. Thus, using the BioGeoBEARS methodology for biogeographic estimation, we were able to reconstruct the biogeographical patterns for the entire group based on the most complete Bayesian phylogeny of the total evidence. As a result, a New Zealand origin for the Sphenisciformes during the late Cretaceous and early Paleocene is indicated, with subsequent dispersal and expansion across Antarctica and southern South America. During the Eocene, there was a remarkable diversification of species and ecological niches in Antarctica, probably associated with the more temperate climatic conditions in the Southern Hemisphere. A wide morphological variability might have developed at the beginning of the Paleogene diversification. During the Oligocene, with the trends towards the freezing of Antarctica and the generalized cooling of the Neogene, there was a turnover that led to the survival (in New Zealand) of the ancestors of the crown Sphenisciform lineages. Later these expanded and diversified across the Southern Hemisphere, strongly linked to the climatic and oceanographic processes of the Miocene. Finally, it should be noted that the Antarctic recolonization and its hostile climatic conditions occurred in some modern lineages during the Pleistocene, possibly due to exaptations that made possible the repeated dispersion through cold waters during the Cenozoic, also allowing the necessary adaptations to live in the tundra during the glaciations. [ABSTRACT FROM AUTHOR]

Vocal production learning (VPL) is the experience-driven ability to produce novel vocal signals through imitation or modification of existing vocalizations. A parallel strand of research investigates acoustic allometry, namely how information about body size is conveyed by acoustic signals. Recently, we proposed that deviation from acoustic allometry principles as a result of sexual selection may have been an intermediate step towards the evolution of vocal learning abilities in mammals. Adopting a more hypothesis-neutral stance, here we perform phylogenetic regressions and other analyses further testing a potential link between VPL and being an allometric outlier. We find that multiple species belonging to VPL clades deviate from allometric scaling but in the opposite direction to that expected from size exaggeration mechanisms. In other words, our correlational approach finds an association between VPL and being an allometric outlier. However, the direction of this association, contra our original hypothesis, may indicate that VPL did not necessarily emerge via sexual selection for size exaggeration: VPL clades show higher vocalization frequencies than expected. In addition, our approach allows us to identify species with potential for VPL abilities: we hypothesize that those outliers from acoustic allometry lying above the regression line may be VPL species. Our results may help better understand the cross-species diversity, variability and aetiology of VPL, which among other things is a key underpinning of speech in our species. [ABSTRACT FROM AUTHOR]

Harvesting models are based upon the ideology that removing large, old individuals provides space for young, fast‐growing counterparts that can maximize (fisheries) yields while maintaining population stability and ecosystem function. Yet, this compensatory density dependent response has rarely been examined in multispecies systems. We combined extensive data sets from coral‐reef fisheries across a suite of Pacific islands and provided unique context to the universal assumptions of compensatory density dependence. We reported that size‐and‐age truncation only existed for 49% of target coral‐reef fishes exposed to growing fishing pressure across a suite of Pacific islands. In contrast, most of the remaining species slowly disappeared from landings and reefs with limited change to their size structure (i.e., little to no compensation), often becoming replaced by smaller‐bodied sister species. To understand these remarkable and disparate differences, we constructed phylogenies for dominant fish families and discovered that large patristic distances between sister species, or greater phylogenetic isolation, predicted size‐and‐age truncation. Isolated species appeared to have greater niche dominance or breadth, supported by their faster growth rates compared to species with similar sizes and within similar guilds, and many also have group foraging behavior. In contrast, closely related species may have more restricted, realized niches that led to their disappearance and replacement. We conclude that phylogenetic attributes offered novel guidance to proactively manage multispecies fisheries and improve our understanding of ecological niches and ecosystem stability. [ABSTRACT FROM AUTHOR]

Abstract Background Knowledge of HIV-1 molecular transmission clusters (MTCs) is important, especially in large-scale datasets, for designing prevention programmes and public health intervention strategies. We used a large-scale HIV-1 sequence dataset from nine European HIV cohorts and one Canadian, to identify MTCs and investigate factors associated with the probability of belonging to MTCs. Methods To identify MTCs, we applied maximum likelihood inferences on partial pol sequences from 8955 HIV-positive individuals linked to demographic and clinical data. MTCs were defined using two different criteria: clusters with bootstrap support >75% (phylogenetic confidence criterion) and clusters consisting of sequences from a specific region at a proportion of >75% (geographic criterion) compared to the total number of sequences within the network. Multivariable logistic regression analysis was used to assess factors associated with MTC clustering. Results Although 3700 (41%) sequences belonged to MTCs, proportions differed substantially by country and subtype, ranging from 7% among UK subtype C sequences to 63% among German subtype B sequences. The probability of belonging to an MTC was independently less likely for women than men (OR = 0.66; P < 0.001), older individuals (OR = 0.79 per 10-year increase in age; P < 0.001) and people of non-white ethnicity (OR = 0.44; P < 0.001 and OR = 0.70; P = 0.002 for black and ‘other’ versus white, respectively). It was also more likely among men who have sex with men (MSM) than other risk groups (OR = 0.62; P < 0.001 and OR = 0.69; P = 0.002 for people who inject drugs, and sex between men and women, respectively), subtype B (ORs 0.36–0.70 for A, C, CRF01 and CRF02 versus B; all P < 0.05), having a well-estimated date of seroconversion (OR = 1.44; P < 0.001), a later calendar year of sampling (ORs 2.01–2.61 for all post-2002 periods versus pre-2002; all P < 0.01), and being naïve to antiretroviral therapy at sampling (OR = 1.19; P = 0.010). Conclusions A high proportion (>40%) of individuals belonged to MTCs. Notably, the HIV epidemic dispersal appears to be driven by subtype B viruses spread within MSM networks. Expansion of regional epidemics seems mainly associated with recent MTCs, rather than the growth of older, established ones. This information is important for designing prevention and public health intervention strategies.

Despite its current low diversity, the penguin clade (Sphenisciformes) is one of the groups of birds with the most complete fossil record. Likewise, from the evolutionary point of view, it is an interesting group given the adaptations developed for marine life and the extreme climatic occupation capacity that some species have shown. In the present contribution, we reviewed and integrated all of the geographical and phylogenetic information available, together with an exhaustive and updated review of the fossil record, to establish and propose a biogeographic scenario that allows the spatial-temporal reconstruction of the evolutionary history of the Sphenisciformes, discussing our results and those obtained by other authors. This allowed us to understand how some abiotic processes are responsible for the patterns of diversity evidenced both in modern and past lineages. Thus, using the BioGeoBEARS methodology for biogeographic estimation, we were able to reconstruct the biogeographical patterns for the entire group based on the most complete Bayesian phylogeny of the total evidence. As a result, a New Zealand origin for the Sphenisciformes during the late Cretaceous and early Paleocene is indicated, with subsequent dispersal and expansion across Antarctica and southern South America. During the Eocene, there was a remarkable diversification of species and ecological niches in Antarctica, probably associated with the more temperate climatic conditions in the Southern Hemisphere. A wide morphological variability might have developed at the beginning of the Paleogene diversification. During the Oligocene, with the trends towards the freezing of Antarctica and the generalized cooling of the Neogene, there was a turnover that led to the survival (in New Zealand) of the ancestors of the crown Sphenisciform lineages. Later these expanded and diversified across the Southern Hemisphere, strongly linked to the climatic and oceanographic processes of the Miocene. Finally, it should be noted that the Antarctic recolonization and its hostile climatic conditions occurred in some modern lineages during the Pleistocene, possibly due to exaptations that made possible the repeated dispersion through cold waters during the Cenozoic, also allowing the necessary adaptations to live in the tundra during the glaciations.

During 2017-2018, Barmah Forest virus was recovered from mosquitoes trapped in military training areas in Australia and from a soldier infected at 1 of these areas. Phylogenies of the nucleotide sequences of the envelope glycoprotein gene E2 and the 3' untranslated region suggest that 2 lineages are circulating in eastern Australia. [ABSTRACT FROM AUTHOR]

Over the last 10 years, several fungi were isolated from grapevines with grapevine trunk disease (GTD) symptoms, in the Apulia and Molise regions of Italy. Morphological and molecular analyses allowed the identification of species belonging to Botryosphaeriaceae, Phaeoacremonium species, Phaeomoniella chlamydospora, Pleurostoma richardsiae and less-common fungi associated with grapevine trunk diseases, such as Cadophora, Colletotrichum, Seimatosporium and Truncatella. These last genera were isolated at significant frequencies, so they were investigated for possible involvement in GTDs. To screen the large numbers of isolates collected, microsatellite-PCR analysis was carried out with the M13 primer, and 29 strains were further studied by amplification of different genes, for multi-locus analyses. Phylogenies and morphological analyses allowed identification, for first time in Italy, of fungi associated with GTDs, including Cadophora luteo-olivacaea, Colletotrichum fioriniae, Seimatosporium vitis-vinifera and Truncatella angustata. Pathogenicity assays with these fungi and other fungi known to be pathogens for grapevines (Lasiodiplodia citricola, Phaeoacremonium italicum, Pleurostoma richardsiae) showed that they caused disease symptoms on two Italian grapevine cultivars (‘Bombino bianco’, ‘Nero di Troia’), although with different degrees of severity. Among the fungi isolated for the first time in Italy, Sei. vitis-vinifera was the most aggressive, while C. fioriniae the least pathogenic. All of these fungi were re-isolated from grapevine, and thus fulfilled Koch’s postulates, confirming their pathogenicity on grapevine.

Flowering plants exhibit two principal life-history strategies: annuality (living and reproducing in one year) and perenniality (living more than one year). The advantages of either strategy depend on the relative benefits of immediate reproduction balanced against survivorship and future reproduction. This trade-off means that life-history strategies are associated with particular environments, with annuals being found more often in unpredictable habitats. Annuality and perenniality are the outcome of developmental genetic programs responding to their environment, with perennials being distinguished by their delayed competence to flower and reversion to growth after flowering. Evolutionary transitions between these strategies are frequent and have consequences for mating systems and genome evolution, with perennials being more likely to outcross with higher inbreeding depression and lower rates of molecular evolution. Integrating expectations from life-history theory with knowledge of the developmental genetics of flowering and seasonality is required to understand the mechanisms involved in the evolution of annual and perennial life histories. [ABSTRACT FROM AUTHOR]

Dans la lignée des épidémies récentes des virus Ebola et Zika, la pandémie de Covid-19 a donné lieu à une avalanche de données génomiques. Celles-ci ont permis de mieux comprendre l'origine de ce virus, de dater son apparition en Chine mais aussi en France et d'analyser la propagation de l'épidémie grâce aux techniques issues du champ émergent qu'est la phylodynamique. In line with the recent Ebola and Zika virus epidemics, the Covid-19 pandemic has led to an avalanche of genomic data. These data made it possible to better understand the origin of this virus, to date its emergence in China, but also in France, and to analyse the spread of the epidemic using techniques from the emerging field of phylodynamics. [ABSTRACT FROM AUTHOR]

Access and reuse of authoritative phylogenetic knowledge have been a longstanding challenges in the evolutionary biology community — leading to a number of research efforts (e.g. focused on interoperation, standardization of formats, and development of minimum reporting requirements). The Phylotastic project was launched to provide an answer to such challenges — as an architectural concept collaboratively designed by evolutionary biologists and computer scientists. This paper describes the first comprehensive implementation of the Phylotastic architecture, based on an open platform for Web services composition. The implementation provides a portal, which composes Web services along a fixed collection of workflows, as well as an interface to allow users to develop novel workflows. The Web services composition is guided by automated planning algorithms and built on a Web services registry and an execution monitoring engine. The platform provides resilience through seamless automated recovery from failed services. [ABSTRACT FROM AUTHOR]

The aim of the present paper is to introduce students to tree-thinking through a ludic activity. Phylogenetic trees are the appropriate way to explain biodiversity under the theoretical framework of current evolutionary hypothesis and they should take a central place in public understanding of evolution. Misinterpretation of phylogenies plus the unavailability of didactic material in Spanish for teachers ends up in the reproduction of misunderstandings on the evolutionary theory. The combination of these errors with epistemological problems of evolutionary theories learning generates even more confusion in these subjects. The ludic activity as a learning process provides powerful tools when it comes to acquiring concepts that require abstraction in contents. Educational natural science games, both classical and modern approaches as Game-based learning theory, provide a sense of achievement to players/apprentices and they improve knowledge acquisition. In this context, the activity proposed here invites students to think under the scientific method and it allows them to assimilate abstract concepts by the resolution of evolutionary riddles. This activity gives the concepts to introduce scholars to the study of evolutionary processes, and the diversity of life on Earth under the current educational paradigms. [ABSTRACT FROM AUTHOR]

Abstract Background Bovine babesiosis is one of the most economically important tick-borne diseases threatening the livestock industry globally including South Africa. This disease is induced by members of Babesia bovis species. Antigenic variations among geographical strains of B. bovis, and these heterogeneities are cited as the mechanism by which parasites evade from host immune system and they hamper the successful development of a single vaccine that could confer absolute protection. Given the economic importance of livestock industry in South Africa, the extent of genetic diversity among field isolates of B. bovis merits extensive investigation. In this study, we genetically characterized partial genes of B. bovis and studied the phylogenetic relationship among B. bovis isolates of South African origin. The genes, which were PCR-amplified from bovine samples collected from different locations across South Africa, coded for rhoptry-associated protein 1 (BbRAP-1), cysteine peptidase 2 (BbCP2), spherical body protein 4 (BbSBP-4) and β-tubulin (BbβTUB). Phylogenies were inferred from newly determined sequences using the neighbour-joining approach. Results Nested PCR assays with gene-specific primers indicated that, of the 54 bovine samples tested, 59.3% (32/54; 95% CI = 46.0–71.3%), 27.8% (15/54; 95% CI = 17.6–40.9%), 37.0% (20/54; 95% CI = 25.4–50.4%) and 29.6% (16/54; 95% CI = 19.1–42.8%) possessed BbRAP-1, BbCP2, BbSBP-4 and BbβTUB fragments, respectively. Sequencing of PCR-generated fragments revealed that nucleotide sequences of each of the four genes were highly conserved among the B. bovis isolates examined. Phylogenetic analyses of BbCP2, BbSBP-4 and BbβTUB sequences indicated a close phylogenetic relatedness among South African-derived sequences and those of global B. bovis strains. Conclusion The data reported in this study indicated that there is a high conservation among the genes of B. bovis isolates from cattle in South Africa. These findings give an indication that immunologically important proteins encoded by these genes could potentially be considered for exploitation as viable candidates for inclusion in recombinant subunit vaccines.

Over the last 10 years, several fungi were isolated from grapevines with grapevine trunk disease (GTD) symptoms, in the Apulia and Molise regions of Italy. Morphological and molecular analyses allowed the identification of species belonging to Botryosphaeriaceae, Phaeoacremonium species, Phaeomoniella chlamydospora, Pleurostoma richardsiae and less-common fungi associated with grapevine trunk diseases, such as Cadophora, Colletotrichum, Seimatosporium and Truncatella. These last genera were isolated at significant frequencies, so they were investigated for possible involvement in GTDs. To screen the large numbers of isolates collected, microsatellite-PCR analysis was carried out with the M13 primer, and 29 strains were further studied by amplification of different genes, for multi-locus analyses. Phylogenies and morphological analyses allowed identification, for first time in Italy, of fungi associated with GTDs, including Cadophora luteo-olivacaea, Colletotrichum fioriniae, Seimatosporium vitis-vinifera and Truncatella angustata. Pathogenicity assays with these fungi and other fungi known to be pathogens for grapevines (Lasiodiplodia citricola, Phaeoacremonium italicum, Pleurostoma richardsiae) showed that they caused disease symptoms on two Italian grapevine cultivars ('Bombino bianco', 'Nero di Troia'), although with different degrees of severity. Among the fungi isolated for the first time in Italy, Sei. vitis-vinifera was the most aggressive, while C. fioriniae the least pathogenic. All of these fungi were re-isolated from grapevine, and thus fulfilled Koch's postulates, confirming their pathogenicity on grapevine. [ABSTRACT FROM AUTHOR]

The field of viral genomic studies has experienced an unprecedented increase in data volume. New strains of known viruses are constantly being added to the GenBank database and so are completely new species with little or no resemblance to our databases of sequences. In addition to this, metagenomic techniques have the potential to further increase the number and rate of sequenced genomes. Besides, it is important to consider that viruses have a set of unique features that often break down molecular biology dogmas, e.g., the flux of information from RNA to DNA in retroviruses and the use of RNA molecules as genomes. As a result, extracting meaningful information from viral genomes remains a challenge and standard methods for comparing the unknown and our databases of characterized sequences may need adaptations. Thus, several bioinformatic approaches and tools have been created to address the challenge of analyzing viral data. This chapter offers descriptions and protocols of some of the most important bioinformatic techniques for comparative analysis of viruses. The authors also provide comments and discussion on how viruses' unique features can affect standard analyses and how to overcome some of the major sources of problems. Protocols and topics emphasize online tools (which are more accessible to users) and give the real experience of what most bioinformaticians do in day-by-day work with command-line pipelines. The topics discussed include (1) clustering related genomes, (2) whole genome multiple sequence alignments for small RNA viruses, (3) protein alignment for marker genes and species affiliation, (4) variant calling and annotation, and (5) virome analyses and pathogen identification., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology, and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates their analysis. While our mathematical, algorithmic, and probabilistic understanding of phylogenies in their metric space is mature, rigorous inferential infrastructure is as yet undeveloped. In this manuscript, we unify recent computational and probabilistic advances to construct tree–valued confidence sets. The procedure accounts for both center and multiple directions of tree–valued variability. We draw on block replicates to improve testing, identifying the best supported most recent ancestor of the Zika virus, and formally testing the hypothesis that a Floridian dentist with AIDS infected two of his patients with HIV. The method illustrates connections between variability in Euclidean and tree space, opening phylogenetic tree analysis to techniques available in the multivariate Euclidean setting. Supplementary materials for this article are available online. [ABSTRACT FROM AUTHOR]

Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos. [ABSTRACT FROM AUTHOR]

Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 233 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain. [ABSTRACT FROM AUTHOR]

Age-mixing patterns are of key importance for understanding the dynamics of human immunodeficiency virus (HIV)-epidemics and target public health interventions.We use the densely sampled Swiss HIV Cohort Study (SHCS) resistance database to study the age difference at infection in HIV transmission pairs using phylogeneticmethods. In addition, we investigate whether themean age difference of pairs in the phylogenetic tree is influenced by sampling as well as by additional distance thresholds for including pairs. HIV-1 pol-sequences of 11,922 SHCS patients and approximately 240,000 Los Alamos background sequences were used to build a phylogenetic tree. Using this tree, 100 per cent down to 1 per cent of the tips were sampled repeatedly to generate pruned trees (N=500 for each sample proportion), of which pairs of SHCS patients were extracted.The mean of the absolute age differences of the pairs,measured as the absolute difference of the birth years, was analyzed with respect to this sample proportion and a distance criterion for inclusion of the pairs. In addition, the transmission groups men having sex with men (MSM), intravenous drug users (IDU), and heterosexuals (HET) were analyzed separately. Considering the tree with all 11,922 SHCS patients, 2,991 pairs could be extracted, with 954 (31.9 per cent) MSM-pairs, 635 (21.2 per cent) HET-pairs, 414 (13.8 per cent) IDU-pairs, and 352 (11.8 per cent) HET/IDU-pairs. For all transmission groups, the age difference at infection was significantly (P<0.001) smaller for pairs in the tree compared with randomly assigned pairs,meaning that patients of similar age aremore likely to be pairs. Themean age difference in the phylogenetic analysis, using a fixed distance of 0.05, was 9.2, 9.0, 7.3 and 5.6 years for MSM-, HET-, HET/IDU-, and IDU-pairs, respectively. Decreasing the cophenetic distance threshold from 0.05 to 0.01 significantly decreased themean age difference. Similarly, repeated sampling of 100 per cent down to 1 per cent of the tips revealed an increased age difference at lower sample proportions. HIV-transmission is age-assortative, but the age difference of transmission pairs detected by phylogenetic analyses depends on both sampling proportion and distance criterion. Themean age difference decreases when usingmore conservative distance thresholds, implying an underestimation of age-assortativity when using liberal distance criteria. Similarly, overestimation of themean age difference occurs for pairs fromsparsely sampled trees, as it is often the case in sub-Saharan Africa. [ABSTRACT FROM AUTHOR]

In recent years, to infer phylogenies, which are NP-hard problems, more and more research has focused on using metaheuristics. Maximum Parsimony and Maximum Likelihood are two effective ways to conduct inference. Based on these methods, which can also be considered as the optimal criteria for phylogenies, various kinds of multi-objective metaheuristics have been used to reconstruct phylogenies. However, combining these two time-consuming methods results in those multi-objective metaheuristics being slower than a single objective. Therefore, we propose a novel, multi-objective optimization algorithm, MOEA-RC, to accelerate the processes of rebuilding phylogenies using structural information of elites in current populations. We compare MOEA-RC with two representative multi-objective algorithms, MOEA/D and NAGA-II, and a non-consensus version of MOEA-RC on three real-world datasets. The result is, within a given number of iterations, MOEA-RC achieves better solutions than the other algorithms. [ABSTRACT FROM AUTHOR]

Background: Bovine babesiosis is one of the most economically important tick-borne diseases threatening the livestock industry globally including South Africa. This disease is induced by members of Babesia bovis species. Antigenic variations among geographical strains of B. bovis, and these heterogeneities are cited as the mechanism by which parasites evade from host immune system and they hamper the successful development of a single vaccine that could confer absolute protection. Given the economic importance of livestock industry in South Africa, the extent of genetic diversity among field isolates of B. bovis merits extensive investigation. In this study, we genetically characterized partial genes of B. bovis and studied the phylogenetic relationship among B. bovis isolates of South African origin. The genes, which were PCR-amplified from bovine samples collected from different locations across South Africa, coded for rhoptry-associated protein 1 (BbRAP-1), cysteine peptidase 2 (BbCP2), spherical body protein 4 (BbSBP-4) and β-tubulin (BbβTUB). Phylogenies were inferred from newly determined sequences using the neighbour-joining approach. Results: Nested PCR assays with gene-specific primers indicated that, of the 54 bovine samples tested, 59.3% (32/ 54; 95% CI = 46.0-71.3%), 27.8% (15/54; 95% CI = 17.6-40.9%), 37.0% (20/54; 95% CI = 25.4-50.4%) and 29.6% (16/54; 95% CI = 19.1-42.8%) possessed BbRAP-1, BbCP2, BbSBP-4 and BbβTUB fragments, respectively. Sequencing of PCRgenerated fragments revealed that nucleotide sequences of each of the four genes were highly conserved among the B. bovis isolates examined. Phylogenetic analyses of BbCP2, BbSBP-4 and BbβTUB sequences indicated a close phylogenetic relatedness among South African-derived sequences and those of global B. bovis strains. Conclusion: The data reported in this study indicated that there is a high conservation among the genes of B. bovis isolates from cattle in South Africa. These findings give an indication that immunologically important proteins encoded by these genes could potentially be considered for exploitation as viable candidates for inclusion in recombinant subunit vaccines. [ABSTRACT FROM AUTHOR]

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k-mers (subsequences at fixed length k). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel’s idea of ontogeny, we argue that genome phylogenies can be inferred using k-mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Heavy metal pollution is an increasing global concern. Among heavy metals, mercury (Hg) is especially dangerous because of its massive release into the environment and high toxicity, especially for aquatic organisms. The molecular response mechanisms of algae to Hg exposure are mostly unknown. Here, we combine physiological, biochemical, and transcriptomic analysis to provide, for the first time, a comprehensive view on the pathways activated in Chromera velia in response to toxic levels of Hg. Production of hydrogen peroxide and superoxide anion, two reactive oxygen species (ROS), showed opposite patterns in response to Hg2+ while reactive nitrogen species (RNS) levels did not change. A deep RNA sequencing analysis generated a total of 307,738,790 high-quality reads assembled in 122,874 transcripts, representing 89,853 unigenes successfully annotated in databases. Detailed analysis of the differently expressed genes corroborates the biochemical results observed in ROS production and suggests novel putative molecular mechanisms in the algal response to Hg2+. Moreover, we indicated that important transcription factor (TF) families associated with stress responses differentially expressed in C. velia cultures under Hg stress. Our study presents the first in-depth transcriptomic analysis of C. velia, focusing on the expression of genes involved in different detoxification defense systems in response to heavy metal stress.

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on molecular sequences. A typical phylogenetic inference aims to capture and represent, in the form of a tree, the evolutionary history of a family of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. However, this approach ignores important evolutionary processes that are known to shape the genomes of microbes (bacteria, archaea and some morphologically simple eukaryotes). Recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k-mers (subsequences at fixed length k). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel’s idea of ontogeny, we argue that genome phylogenies can be inferred using k-mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Aim Current geographical distributions in conjunction with species-level phylogenies have been viewed as offering an enormous potential for investigating the causes of speciation. However, many authors have concluded that species ranges are too dynamic to retain the historical signal of the speciation processes. We develop an approach to explore the extent to which range changes have erased the geographical signal of speciation in the current distribution of species lineages, and whether phylogenetic relationships among species and their current distributions can provide information regarding the geography of diversification. As case studies we used different lineages of aquatic Coleoptera. Location Western Palaearctic. Methods We first assessed the persistence of a geographical signal in the current distribution of a clade from the association between evolutionary relationships and geography using Mantel tests. We then tested two potential scenarios of diversification using bivariate plots of the geographical distance between the centroids of the species ranges and phylogenetic distances, and an assessment of the match between the observed geographical distribution and the phylogenetic topology. We used as a study system a set of 10 monophyletic lineages of water beetles with different ecological characteristics (either standing water, running water or a mixture of both habitat types). Results Our results point to a common pattern of geographically conserved ranges where current species seem to have originated through range fragmentation of formerly more widespread species. Exclusive standing water clades showed a much weaker signal, as expected from their higher mobility, which erases the geographical signal at much shorter temporal scales. Main conclusions Overall, our findings show that for at least some lineages it is possible to obtain strong evidence of stasis of the geographical ranges of species, as well as information regarding the diversification process, through the study of their current distributions and phylogenetic relationships. [ABSTRACT FROM AUTHOR]

Issues on the correlation of viral genetic diversity and treatment response to the hepatitis C infection remain uncertain. The bottleneck effect dictates the characteristics of the viral population that will establish the infection in a new host and is related to how the immune system and treatment will be effective against the virus. Here we evaluated the phylogenetic characteristics of quasispecies population and the treatment response pattern of a HCV infected couple. We also analyzed whether the viral population of these patients indicated that they were exposed to the same source for primer infection. This study included two patients (P10 and P11) HCV genotype 1b infected. The couple presented horizontal transmission. Viral RNA was isolated from serum samples collected before, during and after treatment, at specific time points. The HCV NS5A gene sequence was amplified, cloned and sequenced. Genetic and evolutionary analyses were performed to compare the quasispecies population of these two patients and local control patients. Genetic distance and diversity were calculated. Phylogenetic analyses were performed by using maximum likelihood and Bayesian methodologies. The analysis of the baseline samples showed that the genetic distance of the viral populations of patients P10 and P11 was significantly lower than when these patients and the control group based on sequences from local patients were analyzed, supporting the horizontal transmission hypothesis. Phylogenetic analysis with sequences from all the time point samples also demonstrated two patterns of evolution depending on the treatment response. The Bayesian analysis showed that one isolate corresponding to the baseline sample of P10 was grouped into the P11 clade, suggesting a way of infection and a bottleneck effect. Our data suggests that the patient P11 viral population may be originated from variants from P10 patient and consequently showing that clinical differences between treatment responses can emerge from the bottleneck effect on viral populations. [ABSTRACT FROM AUTHOR]

Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The r software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new r package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set. [ABSTRACT FROM AUTHOR]

Polyketide synthase (PKSs) and nonribosomal peptide synthetase (NRPSs) are large multimodular enzymes involved in biosynthesis of polyketide and peptide toxins produced by fungi. Furthermore, hybrid enzymes, in which a reducing PKS region is fused to a single NRPS module, are also responsible of the synthesis of peptide-polyketide metabolites in fungi. The genes encoding for PKSs and NRPSs have been exposed to complex evolutionary mechanisms, which have determined the great number and diversity of metabolites. In this study, we considered the most important polyketide and peptide mycotoxins and, for the first time, a phylogenetic analysis of both PKSs and NRPSs involved in their biosynthesis was assessed using two domains for each enzyme: β-ketosynthase (KS) and acyl-transferase (AT) for PKSs; adenylation (A) and condensation (C) for NRPSs. The analysis of both KS and AT domains confirmed the differentiation of the three classes of highly, partially and non-reducing PKSs. Hybrid PKS-NRPSs involved in mycotoxins biosynthesis grouped together in the phylogenetic trees of all the domains analyzed. For most mycotoxins, the corresponding biosynthetic enzymes from distinct fungal species grouped together, except for PKS and NRPS involved in ochratoxin A biosynthesis, for which an unlike process of evolution could be hypothesized in different species.

In this note, I discuss the advantages of the usage of subgenera as a practical taxonomic rank in mammalian taxonomy. Use of this category preserves traditional usage, reduces nomenclatural instability and avoids unnecessary change of names. Subgenera are useful to label diagnosable clades of closely related species, especially in morphologically and ecologically diverse monophyletic genera, without alteration of traditional binomial usage. Contrary to informal names such as "divisions" or "groups", subgenera are governed by the rules of the International Commission on Zoological Nomenclature (ICZN), having usage constrained (and stability promoted) by typification and priority. [ABSTRACT FROM AUTHOR]