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Recent advances in higher‐level invertebrate phylogeny have leveraged shared features of genomic architecture to resolve contentious nodes across the tree of life. Yet, the interordinal relationships within Chelicerata have remained recalcitrant given competing topologies in recent molecular analyses. As such, relationships between topologically unstable orders remain supported primarily by morphological cladistic analyses. Solifugae, one such unstable chelicerate order, has long been thought to be the sister group of Pseudoscorpiones, forming the clade Haplocnemata, on the basis of eight putative morphological synapomorphies. The discovery, however, of a shared whole genome duplication placing Pseudoscorpiones in Arachnopulmonata provides the opportunity for a simple litmus test evaluating the validity of Haplocnemata. Here, we present the first developmental transcriptome of a solifuge (Titanopuga salinarum) and survey copy numbers of the homeobox genes for evidence of systemic duplication. We find that over 70% of the identified homeobox genes in T. salinarum are retained in a single copy, while representatives of the arachnopulmonates retain orthologs of those genes as two or more copies. Our results refute the placement of Solifugae in Haplocnemata. Subsequent reevaluation of putative interordinal morphological synapomorphies among chelicerates reveals a high incidence of homoplasy, reversals, and inaccurate coding within Haplocnemata and other small clades, as well as Arachnida more broadly, suggesting existing morphological character matrices are insufficient to resolve chelicerate phylogeny. [ABSTRACT FROM AUTHOR]

The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphological and geographical variations. To enable accurate phylogenomic inference, we assembled 801 single‐copy nuclear genes and 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, we employed a tree‐based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO), and rooted ingroups (RT). The results yielded from both nuclear and plastid analyses consistently support the monophyly of Pyrus, and two well‐supported clades, the Occidental and Oriental clades, were recovered in nine nuclear and three plastid trees. Integrating evidence from morphology and phylogenomics, we propose an updated infrageneric classification of Pyrus, which consists of two subgenera: P. subg. Pyrus and P. subg. Pashia stat. nov. This revised classification provides a more robust framework for understanding the evolutionary relationships within the pear genus. [ABSTRACT FROM AUTHOR]

The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp. obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera , including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e. the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference. [ABSTRACT FROM AUTHOR]

The cobra venom factor (CVF) is an unusual non-toxic complement system-activating protein reported in the venom of many family Elapidae snakes, and it is closely related to C3 complement. The archosaurs, including crocodilians, were traditionally considered a completely non-venomous group of animals; however, the identification of some related sequences similar to CVF proteins in the crocodilian genome may trigger important discussions and manage interesting hypotheses. The aim of this work was to identify VF-like protein in Caiman latirostris DNA samples. The results demonstrate the presence of VF-like in C. latirostris and showed a strong homology of VF-like and C3 complement, indicating a probable paralogy between both proteins in crocodilians. Also, these findings provide some potential explanations to justify presence of VF-like protein in crocodilians: one is based on the horizontal transfer of a transposable element from a virus as a vector, and another proposes the horizontal gene transfer by the predator–prey interaction between crocodilians and snakes. Our results are in accordance with investigations that propose the presence of snakes' venom components in non-venomous reptiles. However, more research will be needed to determine if VF-like in crocodilians has a similar function to CVF. [ABSTRACT FROM AUTHOR]

The evolution of genomes in all life forms involves two distinct, dynamic types of genomic changes: gene duplication (and loss) that shape families of paralogous genes and extension (and contraction) of low-complexity regions (LCR), which occurs through dynamics of short repeats in protein-coding genes. Although the roles of each of these types of events in genome evolution have been studied, their co-evolutionary dynamics is not thoroughly understood. Here, by analyzing a wide range of genomes from diverse bacteria and archaea, we show that LCR and paralogy represent two distinct routes of evolution that are inversely correlated. The emergence of LCR is a prominent evolutionary mechanism in fast evolving, young protein families, whereas paralogy dominates the comparatively slow evolution of old protein families. The analysis of multiple prokaryotic genomes shows that the formation of LCR is likely a widespread, transient evolutionary mechanism that temporally and locally affects also ancestral functions, but apparently, fades away with time, under mutational and selective pressures, yielding to gene paralogy. We propose that compensatory relationships between short-term and longer-term evolutionary mechanisms are universal in the evolution of life. [ABSTRACT FROM AUTHOR]

Aim: Cladistic biogeography is all about congruence: when individual area cladograms coincide, they result in a general area cladogram that reveals shared history. However, the complexities of the natural world hamper the reconstruction of fully solved biogeographical patterns. Herein, we present SAMBA (super area‐cladogram after resolving multiple biogeographical ambiguities), a pattern‐based method combining supertrees and area cladograms to depict the relationships among areas. We also present a prototypical implementation of SAMBA as a web‐based framework named iSAMBA. Location: Global. Taxon: Any taxon can be analysed with SAMBA. Methods: SAMBA is based on phylogenetic supertrees, a technique that combines previously calculated phylogenetic trees to produce a general area cladogram representing conciliatory and non‐ambiguous patterns of relationships. In our method, the input topologies are individual area cladograms. SAMBA is implemented through a web‐based framework named iSAMBA. We analysed a theoretical and a real scenario to compare SAMBA with primary Brooks parsimony analysis (BPA), component analysis, three area statement analysis (TAS) and the transparent method. Results: SAMBA produces area cladograms that converge with the actual history of fragmentations of both hypothetical and real scenarios used as examples of implementation of the method. Primary BPA, component analysis, TAS and the transparent method are much more affected by the "biogeographical noise" (e.g. multiple areas in a single terminal, paralogies and missing areas) than SAMBA. Main Conclusions: SAMBA results in more informative general area cladograms than other pattern‐based biogeographical methods. SAMBA reveals shared patterns of biotic distribution without generating multiple unreliable area cladograms. The main advantage of SAMBA is the simplicity of using a single technique to extract biogeographical information from individual area cladograms and combine them to depict a non‐ambiguous general pattern of relationships among areas. [ABSTRACT FROM AUTHOR]

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research. [ABSTRACT FROM AUTHOR]

Notarchirico is at a nodal point in time and space for understanding the settlement of Europe in terms of migration or in situ evolution. Former technological analyses have not shown significant differences between the different lithic assemblages at Notarchirico. Our approach here is to produce a phylogenetic analysis of the lithic assemblages taken as the terminal of the analysis and interpreted as cultural units. In the cladistic framework, characters are hypotheses of relationships between lithic assemblages, and homologies are hypotheses of relationships between lithic objects: cores, flakes, nodules. To effectively grasp informative lithic innovations in the assemblages, we formalise cladistic hypotheses as hierarchical characters in the framework of three-item analysis and propose a new algorithm to remove the high number of repeated terminals among trees inherent to a cladistic analysis of assemblages. Beyond the classic distinction of the presence or absence of bifaces, our analysis of the five Notarchirico layers, dated between 670 and 700 ka, highlights a well-supported cladogram grounded on complex hierarchical characters on lithic artefacts. This cladogram shows a paralogy event between the flake-free layer H, representing short-term occupancy, and the other layers representing long-term settlements. The resulting cladogram shows that relationships between lithic assemblages at Notarchirico do not follow the stratigraphy. Moreover, the Notarchirico lithic assemblages cannot be explained in an entirely local way, but seem to be part of a more complex European history. [ABSTRACT FROM AUTHOR]

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

The spatiality of the Internet is a complex phenomenon presupposing a wide range of ideas: that there are different environments which can be characterized, that there are subjects moving within them, that these spaces are being employed for certain ends by their users, and much more. However, various spatial descriptions of the Internet most of the time observe it as a part of a larger spatial architecture, not as a spatial architecture itself. This paper employs radical concept creation machinery conceptualized by Gilles Deleuze and Félix Guattari in What Is Philosophy? (first published in 1991), principles of paralogistic thinking proposed by Jean- François Lyotard and divergent thinking methods, finally arriving at a new conceptualization of the Internet space as the meteorological pressure system. This is an invitation to see the Internet and movements occurring within it from a new perspective: where temperatures rise and drop, winds blow and dissipate, fogs come and go; where limits of spatial characteristics are forming different climates; where each part affects the whole, and can potentially bring out various chain reactions. Such a conceptual system opens up the possibility to see the Internet as a coherent spatial structure, filled with becomings and intricate relationships. [ABSTRACT FROM AUTHOR]

The spatiality of the Internet is a complex phenomenon presupposing a wide range of ideas: that there are different environments which can be characterized, that there are subjects moving within them, that these spaces are being employed for certain ends by their users, and much more. However, various spatial descriptions of the Internet most of the time observe it as a part of a larger spatial architecture, not as a spatial architecture itself. This paper employs radical concept creation machinery conceptualized by Gilles Deleuze and Félix Guattari in What Is Philosophy? (first published in 1991), principles of paralogistic thinking proposed by Jean-François Lyotard and divergent thinking methods, finally arriving at a new conceptualization of the Internet space as the meteorological pressure system. This is an invitation to see the Internet and movements occurring within it from a new perspective: where temperatures rise and drop, winds blow and dissipate, fogs come and go; where limits of spatial characteristics are forming different climates; where each part affects the whole, and can potentially bring out various chain reactions. Such a conceptual system opens up the possibility to see the Internet as a coherent spatial structure, filled with becomings and intricate relationships.

The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogues for phylogenetic reconstruction. We developed a novel approach of detecting paralogues and utilizing them for phylogenetic tree inference, by retrieving both ortho‐ and paralogous copies and creating orthologous alignments, from which the gene trees are built. We implemented this approach in ParalogWizard and demonstrate its performance in plant groups that underwent a whole genome duplication relatively recently: the subtribe Malinae (family Rosaceae), using Angiosperms353 as well as Malinae481 probes, the genus Oritrophium (family Asteraceae), using Compositae1061 probes, and the genus Amomum (family Zingiberaceae), using Zingiberaceae1180 probes. Discriminating between orthologues and paralogues reduced gene tree discordance and increased the species tree support in the case of the Malinae, but not for Oritrophium and Amomum. This may relate to the difference in the proportion of paralogous loci between the data sets, which was highest for the Malinae. Overall, retrieving paralogues for phylogenetic reconstruction following ParalogWizard has the potential to increase the species tree support and reduce gene tree discordance in target enrichment data, particularly if the proportion of paralogous loci is high. [ABSTRACT FROM AUTHOR]

Abstract Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks ( https://github.com/biocorecrg/ExOrthist ).

Abstract Background The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

Huntington's disease (HD) is caused by the production of a mutant huntingtin (HTT) with an abnormally long poly-glutamine (polyQ) tract, forming aggregates and inclusions in neurons. Previous work by us and others has shown that an increase or decrease in polyQ-triggered aggregates can be passive simply due to the interaction of proteins with the aggregates. To search for proteins with active (functional) effects, which might be more effective in finding therapies and mechanisms of HD, we selected among the proteins that interact with HTT a total of 49 pairs of proteins that, while being paralogous to each other (and thus expected to have similar passive interaction with HTT), are located in different regions of the protein interaction network (suggesting participation in different pathways or complexes). Three of these 49 pairs contained members with opposite effects on HD, according to the literature. The negative members of the three pairs, MID1, IKBKG, and IKBKB, interact with PPP2CA and TUBB, which are known negative factors in HD, as well as with HSP90AA1 and RPS3. The positive members of the three pairs interact with HSPA9. Our results provide potential HD modifiers of functional relevance and reveal the dynamic aspect of paralog evolution within the interaction network. [ABSTRACT FROM AUTHOR]

How and to what degree gene duplication events create regulatory innovation, redundancy, or neofunctionalization remain important questions in animal evolution and comparative genetics. Ankfn1 genes are single copy in most invertebrates, partially duplicated in jawed vertebrates, and only the derived copy retained in most mammals. Null mutations in the single mouse homolog have vestibular and neurological abnormalities. Null mutation of the single Drosophila homolog is typically lethal with severe sensorimotor deficits in rare survivors. The functions and potential redundancy of paralogs in species with two copies are not known. Here, we define a vestibular role for Ankfn1 homologs in zebrafish based on the simultaneous disruption of each locus. Zebrafish with both paralogs disrupted showed vestibular defects and early lethality from swim bladder inflation failure. One intact copy at either locus was sufficient to prevent major phenotypes. Our results show that vertebrate Ankfn1 genes are required for vestibular-related functions, with at least partial redundancy between ancestral and derived paralogs. [ABSTRACT FROM AUTHOR]

Despite their suitability for studying evolution, many conifer species have large and repetitive giga‐genomes (16–31 Gbp) that create hurdles to producing high coverage SNP data sets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within Pinaceae, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost‐saving benefits of pool‐seq and exome‐capture to discover SNPs in two conifer species, Douglas‐fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco, Pinaceae) and jack pine (Pinus banksiana Lamb., Pinaceae). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong, positive correlation with those estimated by sequencing the same population as individuals (r >.948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are probably due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r >.973). Our work addresses bioinformatic challenges in non‐model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralogous artefacts, and suggests the combination of pool‐seq and exome capture to be robust for further evolutionary hypothesis testing in these systems. [ABSTRACT FROM AUTHOR]

Premise Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family‐specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family‐specific kit and those obtained with the universal kit can be merged for downstream analyses. Methods We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. Results Our results show that the Compositae1061 kit provides an average of 721 loci, with 9–46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. Discussion Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.

Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit—from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses. [ABSTRACT FROM AUTHOR]

Premise: Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family‐specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family‐specific kit and those obtained with the universal kit can be merged for downstream analyses. Methods: We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. Results: Our results show that the Compositae1061 kit provides an average of 721 loci, with 9–46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. Discussion: Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community. [ABSTRACT FROM AUTHOR]

Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the/Pavonia and/Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult. [ABSTRACT FROM AUTHOR]

Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.

The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here, we report evidence from gene duplications in LECA indicating an early origin of mitochondria. Among 163,545 duplications in 24,571 gene trees spanning 150 sequenced eukaryotic genomes, we identify 713 gene duplication events that occurred in LECA. LECA's bacterial-derived genes include numerous mitochondrial functions and were duplicated significantly more often than archaeal-derived and eukaryote-specific genes. The surplus of bacterial-derived duplications in LECA most likely reflects the serial copying of genes from the mitochondrial endosymbiont to the archaeal host's chromosomes. Clustering, phylogenies and likelihood ratio tests for 22.4 million genes from 5,655 prokaryotic and 150 eukaryotic genomes reveal no evidence for lineage-specific gene acquisitions in eukaryotes, except from the plastid in the plant lineage. That finding, and the functions of bacterial genes duplicated in LECA, suggests that the bacterial genes in eukaryotes are acquisitions from the mitochondrion, followed by vertical gene evolution and differential loss across eukaryotic lineages, flanked by concomitant lateral gene transfer among prokaryotes. Overall, the data indicate that recurrent gene transfer via the copying of genes from a resident mitochondrial endosymbiont to archaeal host chromosomes preceded the onset of eukaryotic cellular complexity, favoring mitochondria-early over mitochondria-late hypotheses for eukaryote origin. [ABSTRACT FROM AUTHOR]

Figs and fig wasps are a classic example of an obligate pollination mutualism. Decades of work untangling the ecology and evolution of these organisms has simultaneously contributed to development of the fields of mutualism, coevolution and plant–insect interactions at large. With > 800 species, figs (Ficus , Moraceae) are among some of the larger genera of angiosperms. Phylogenetic studies of Moraceae have supported the clade Castilleae as the sister lineage of Ficus. Compared to Ficus , Castilleae have many fewer species (60 species in 11 genera), suggesting changes in rates of diversification along these two branches. Relatively little is known about Castilleae compared to Ficus , and we argue that defining the clade comprising Ficus and Castilleae, hereafter Involucrata, focuses attention on opportunities for comparative studies of pollination mutualisms and diversification rates. In this study, we define Involucrata and propose a revised classification scheme that accounts for the phylogenetic reconstruction based on the most comprehensive sampling of this group to date. Moving forward, this classification will better guide and support evolutionary, ecological and comparative pollination biology studies of this group. [ABSTRACT FROM AUTHOR]

Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20–rps12 and trnL–trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL–trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL–trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes. [ABSTRACT FROM AUTHOR]

Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity. [ABSTRACT FROM AUTHOR]

Understanding the evolution of biodiversity on Earth is a central aim in biology. Currently, various disciplines of science contribute to unravel evolution at all levels of life, from individual organisms to species and higher ranks, using different approaches and specific terminologies. The search for common origin, traditionally called homology, is a connecting paradigm of all studies related to evolution. However, it is not always sufficiently taken into account that defining homology depends on the hierarchical level studied (organism, population, and species), which can cause confusion. Therefore, we propose a framework to define homologies making use of existing terms, which refer to homology in different fields, but restricting them to an unambiguous meaning and a particular hierarchical level. We propose to use the overarching term "homology" only when "morphological homology," "vertical gene transfer," and "phylogenetic homology" are confirmed. Consequently, neither phylogenetic nor morphological homology is equal to homology. This article is intended for readers with different research backgrounds. We challenge their traditional approaches, inviting them to consider the proposed framework and offering them a new perspective for their own research. [ABSTRACT FROM AUTHOR]

Increasingly, large phylogenomic data sets include transcriptomic data from nonmodel organisms. This not only has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. Although this may be expected to result in decreased phylogenetic support, it is not clear if it could also drive highly supported artifactual relationships. Many groups, including the hyperdiverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events and small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated data sets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood, and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasizes the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa. [ABSTRACT FROM AUTHOR]

Comparative genomics has proven a fruitful approach to acquire many functional and evolutionary insights into core cellular processes. Here it is argued that in order to perform accurate and interesting comparative genomics, one first and foremost has to be able to recognize, postulate, and revise different evolutionary scenarios. After all, these studies lack a simple protocol, due to different proteins having different evolutionary dynamics and demanding different approaches. The authors here discuss this challenge from a practical (what are the observations?) and conceptual (how do these indicate a specific evolutionary scenario?) viewpoint, with the aim to guide investigators who want to analyze the evolution of their protein(s) of interest. By sharing how the authors draft, test, and update such a scenario and how it directs their investigations, the authors hope to illuminate how to execute molecular evolution studies and how to interpret them. Also see the video abstract here https://youtu.be/VCt3l2pbdbQ. [ABSTRACT FROM AUTHOR]

Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous. [ABSTRACT FROM AUTHOR]

Laclau introduces three preconditions of populism: the formation of an antagonistic frontier separating the ‘people’ from the enemy; an equivalential articulation of demands; and the unification of social demands into a stable system of signification. I show that with Trump’s and Putin’s populism these preconditions change. An antagonistic frontier became perforated with double interpretation of the enemy. Dichotomy ‘we’ versus the ‘other’ is traversed by the division of the signification of the ‘other’ into the external and internal part as regards the signification of the community. An equivalential articulation of demands transforms into the paralogical chain that establishes cleavages in semantic relations among communities. There are mere ‘opening bids’ among communities without universal dimension as a result of hegemonization of a particular demand. The unification of social demands which has followed the hegemonical logic in Laclau’s account of populism turns into an allegorical unification that keeps being separated from all particular demands in order to maintain their paralogical chain. These transformations can be seen as the preconditions of metapopulism that is found in-between democracy with the particularized logic and populism with the hegemonized one. [ABSTRACT FROM AUTHOR]

Background: Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological, and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL, and HomoloGene, to identify gene families and visualize syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries among multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences, provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families. Findings: A certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we converted this pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow. Conclusions: GeneSeqToFamily represents the Ensembl GeneTrees pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy's user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualize the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project. [ABSTRACT FROM AUTHOR]

The Leavenworthia self-incompatibility locus ( S locus) consists of paralogs ( Lal2, SCRL) of the canonical Brassicaceae S locus genes ( SRK, SCR), and is situated in a genomic position that differs from the ancestral one in the Brassicaceae. Unexpectedly, in a small number of Leavenworthia alabamica plants examined, sequences closely resembling exon 1 of SRK have been found, but the function of these has remained unclear., BAC cloning and expression analyses were employed to characterize these SRK-like sequences., An SRK-positive Bacterial Artificial Chromosome clone was found to contain complete SRK and SCR sequences located close by one another in the derived genomic position of the Leavenworthia S locus, and in place of the more typical Lal2 and SCRL sequences. These sequences are expressed in stigmas and anthers, respectively, and crossing data show that the SRK/ SCR haplotype is functional in self-incompatibility. Population surveys indicate that < 5% of Leavenworthia S loci possess such alleles., An ancestral translocation or recombination event involving SRK/ SCR and Lal2/ SCRL likely occurred, together with neofunctionalization of Lal2/ SCRL, and both haplotype groups now function as Leavenworthia S locus alleles. These findings suggest that S locus alleles can have distinctly different evolutionary origins. [ABSTRACT FROM AUTHOR]

Recombination events among distinct alleles complicate phylogenetic estimation. Various in vivo and in vitro processes can bring distinct alleles into the same genome to then undergo recombination, which may subsequently mislead phylogenetic inference if not assessed properly. Among the processes bringing divergent alleles together, hybridisation is perhaps the simplest and most likely, but alternatives need to be considered before hybridisation can be accepted as the underlying cause. Such alternatives include the presence of paralogues or deeply coalescing alleles, as well as amplification artefacts. Here, we document a recombination event that apparently took place between two divergent lineages of the Silene aegyptiaca complex in the flowering plant family Caryophyllaceae. We evaluate several possible mechanisms that might be responsible for the observed pattern. An ancient introgressive hybridisation event was the simplest explanation for the observations, compatible with geographic proximity of the affected lineages, whereas paralogy and deep coalescence are difficult to reconcile with the evidence obtained from a species tree of the group based on six different, non-recombinant genes and gene trees inferred using two partitions of the recombinant locus. [ABSTRACT FROM AUTHOR]

Several well-documented evolutionary processes are known to cause conflict between species-level phylogenies and gene-level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridization and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several existing methods have dealt with these processes but none has yet been able to untangle all three at once. Here,we propose a stepwise method by which these processes can be discerned using information on genomic location coupled with coalescent simulations. In the first step, highly discordant genes within genomic blocks (putative paralogs) are identified and excluded from the data set and, in the second step, blocks of linked genes are grouped according to their hybrid history. Existing multispecies coalescent software can then be applied to recover the principal tree(s) that make up the species tree/network without violating the underlying model. The potential of the approach is evaluated on simulated data derived from a species network composed of nine species, of which one is of hybrid origin, and displaying a single-gene duplication that leads to paralogous comparisons.We apply our method to an empirical set of 12 genes from 7 species sampled in the plant genus Medicago that display phylogenetic discordance.We identify the causes of the discordance and demonstrate that the Medicago orbicularis lineage experienced an episode of ancient hybridization. Our results show promise as a new way to explore phylogenetic sequence data that can significantly improve species tree inference in presence of hybridization and undetected paralogy or other causes leading to extremely discordant gene trees. [ABSTRACT FROM AUTHOR]

The systematics of Semisulcospiridae in Korea is critically revised by means of comparative anatomy, including comprehensive review of type material and mitochondrial phylogenetics (sequences of COI and 16S). The family is represented by two genera with different reproductive modes: Semisulcospira Boettger, 1886 is viviparous and contains three species (S. coreana (Martens, 1886), S. gottschei (Martens, 1886) and S. forticosta (Martens, 1886)) while Koreoleptoxis Burch & Jung, 1988 is oviparous and also contains three species (K. globus (Martens, 1886), K. nodifila (Martens, 1886), K. tegulata (Martens, 1894)). Koreanomelania Burch & Jung, 1988 is synonymised with Koreoleptoxis. Species can be distinguished by differences in shell shape and sculpture. They form well-differentiated clusters in the mitochondrial phylogeny, consistently revealing lower intraspecific than interspecific genetic distances. Sequences of Japanese Semisulcospira species fall into three distinct major clades (A-C), rendering Semisulcospira non-monophyletic in the mitochondrial tree. Only a small number of Japanese samples were closely related to the Korean clade (Clade C). The numerically predominant Japanese mitochondrial Clade B exhibited increased lineage divergence and, when translated into amino acids, significantly more amino acid substitutions in comparison with Korean species. I conclude that these Japanese sequences may be paralogous and/or may undergo non-neutral evolution. Hence, they are not suitable for inferring phylogenetic relationships. [ABSTRACT FROM AUTHOR]

Background: Given a gene family, the relations between genes (orthology/paralogy), are represented by a relation graph, where edges connect pairs of orthologous genes and "missing" edges represent paralogs. While a gene tree directly induces a relation graph, the converse is not always true. Indeed, a relation graph is not necessarily "satisfiable", i.e. does not necessarily correspond to a gene tree. And even if that holds, it may not be "consistent", i.e. the tree may not represent a true history in agreement with a species tree. Previous studies have addressed the problem of correcting a relation graph for satisfiability and consistency. Here we consider the weighted version of the problem, where a degree of confidence is assigned to each orthology or paralogy relation. We also consider a maximization variant of the unweighted version of the problem. Results: We provide complexity and algorithmic results for the approximation of the considered problems. We show that minimizing the correction of a weighted graph does not admit a constant factor approximation algorithm assuming the unique game conjecture, and we give an n-approximation algorithm, n being the number of vertices in the graph. We also provide polynomial time approximation schemes for the maximization variant for unweighted graphs. Conclusions: We provided complexity and algorithmic results for variants of the problem of correcting a relation graph for satisfiability and consistency. For the maximization variants we were able to design polynomial time approximation schemes, while for the weighted minimization variants we were able to provide the first inapproximability results. [ABSTRACT FROM AUTHOR]

Background: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses. Results: We present a new software pipeline, Orthograph, that addresses and solves the above problems and implements useful features for a wide range of comparative genomic and transcriptomic analyses. Orthograph applies a best reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data. We demonstrate the performance of our approach on de novo-sequenced and assembled transcript libraries of 24 species of apoid wasps (Hymenoptera: Aculeata) as well as on published genomic datasets. Conclusion: With Orthograph, we implemented a best reciprocal hit approach to reference-based orthology prediction for coding nucleotide sequences such as RNAseq data. Orthograph is flexible, easy to use, open source and freely available at https://mptrsen.github.io/Orthograph. Additionally, we release 24 de novo-sequenced and assembled transcript libraries of apoid wasp species. [ABSTRACT FROM AUTHOR]

Parasite genomes typically contain unique contingency gene families encoding multi-copy effector proteins that are often expressed abundantly on the parasite cell surface and beyond. The functions of these gene families are incompletely understood but it is clear that they perform fundamental roles at the host-parasite interface. Over evolutionary timescales, the evolution of these gene families is likely to have decisive effects on the pathology and virulence of parasitic infections. In this review, I will compare the evolutionary dynamics of multiple examples from trypanosomatids and apicomplexan parasites to demonstrate how their inherent mutability makes their phylogeny very different to ‘normal’ gene families. I will argue that phylogenetic analyses could help to understand the functions of these enigmatic genes. [ABSTRACT FROM AUTHOR]