Genomics of a complete butterfly continent

Never before have we had the luxury of choosing a continent, picking a large phylogenetic group of animals, and obtaining genomic data for its every species. Here, we sequence all 845 species of butterflies recorded from North America north of Mexico. Our comprehensive approach reveals the pattern of diversification and adaptation occurring in this phylogenetic lineage as it has spread over the continent, which cannot be seen on a sample of selected species. We observe bursts of diversification that generated taxonomic ranks: subfamily, tribe, subtribe, genus, and species. The older burst around 70 Mya resulted in the butterfly subfamilies, with the major evolutionary inventions being unique phenotypic traits shaped by high positive selection and gene duplications. The recent burst around 5 Mya is caused by explosive radiation in diverse butterfly groups associated with diversification in transcription and mRNA regulation, morphogenesis, and mate selection. Rapid radiation correlates with more frequent introgression of speciation-promoting and beneficial genes among radiating species. Radiation and extinction patterns over the last 100 million years suggest the following general model of animal evolution. A population spreads over the land, adapts to various conditions through mutations, and diversifies into several species. Occasional hybridization between these species results in accumulation of beneficial alleles in one, which eventually survives, while others become extinct. Not only butterflies, but also the hominids may have followed this path.

Download Full-text

Genotypic and Phenotypic Traits That Distinguish Neonatal Meningitis-Associated Escherichia coli from Fecal E. coli Isolates of Healthy Human Hosts

Applied and Environmental Microbiology ◽

10.1128/aem.07869-11 ◽

2012 ◽

Vol 78 (16) ◽

pp. 5824-5830 ◽

Cited By ~ 35

Author(s):

Catherine M. Logue ◽

Curt Doetkott ◽

Paul Mangiamele ◽

Yvonne M. Wannemuehler ◽

Timothy J. Johnson ◽

...

Keyword(s):

Escherichia Coli ◽

Phylogenetic Group ◽

Neonatal Meningitis ◽

Phenotypic Traits ◽

Healthy Human ◽

Content Type ◽

Plasmid Content ◽

E Coli ◽

Healthy Humans ◽

Definition Of

ABSTRACTNeonatal meningitisEscherichia coli(NMEC) is one of the top causes of neonatal meningitis worldwide. Here, 85 NMEC and 204 fecalE. coliisolates from healthy humans (HFEC) were compared for possession of traits related to virulence, antimicrobial resistance, and plasmid content. This comparison was done to identify traits that typify NMEC and distinguish it from commensal strains to refine the definition of the NMEC subpathotype, identify traits that might contribute to NMEC pathogenesis, and facilitate choices of NMEC strains for future study. A large number ofE. colistrains from both groups were untypeable, with the most common serogroups occurring among NMEC being O18, followed by O83, O7, O12, and O1. NMEC strains were more likely than HFEC strains to be assigned to the B2 phylogenetic group. Few NMEC or HFEC strains were resistant to antimicrobials. Genes that best discriminated between NMEC and HFEC strains and that were present in more than 50% of NMEC isolates were mainly from extraintestinal pathogenicE. coligenomic and plasmid pathogenicity islands. Several of these defining traits had not previously been associated with NMEC pathogenesis, are of unknown function, and are plasmid located. Several genes that had been previously associated with NMEC virulence did not dominate among the NMEC isolates. These data suggest that there is much about NMEC virulence that is unknown and that there are pitfalls to studying single NMEC isolates to represent the entire subpathotype.

Download Full-text

Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa192 ◽

2020 ◽

Vol 37 (12) ◽

pp. 3563-3575 ◽

Cited By ~ 1

Author(s):

Juan David Bayona-Serrano ◽

Vincent Louis Viala ◽

Rhett M Rautsaw ◽

Tristan D Schramer ◽

Gesiele A Barros-Carvalho ◽

...

Keyword(s):

Snake Venom ◽

Evolutionary History ◽

Phenotypic Traits ◽

Gene Duplications ◽

Snake Venoms ◽

Venom Component ◽

History Of ◽

Biochemical Components ◽

Functional Analyses ◽

Specific Sequences

Abstract Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an “SVMP-like” function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.

Download Full-text

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

10.1101/816967 ◽

2019 ◽

Author(s):

Drew A. Larson ◽

Joseph F. Walker ◽

Oscar M. Vargas ◽

Stephen A. Smith

Keyword(s):

Gene Tree ◽

Gene Duplications ◽

Species Relationships ◽

Rapid Radiation ◽

Genome Duplications ◽

Tree Inference ◽

History Of ◽

Rapid Diversification ◽

Clustering Approach ◽

Edge Based

ABSTRACTPremise of studyLarge genomic datasets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.MethodsWe used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods and is summarized in a consensus framework.Key ResultsOur consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships due to lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole genome duplication before the radiation of all or most ericalean families and demonstrate that tree topology and heterogeneous evolutionary rates impact the inferred placement of genome duplications.ConclusionsOur approach provides a novel hypothesis regarding the history of Ericales and confidently resolves most nodes. We demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

Download Full-text

Beware the Jaccard: the choice of metric is important and non-trivial in genomic colocalisation analysis

10.1101/479253 ◽

2018 ◽

Author(s):

Stefania Salvatore ◽

Knut Dagestad Rand ◽

Ivar Grytten ◽

Egil Ferkingstad ◽

Diana Domanska ◽

...

Keyword(s):

Genomic Data ◽

Real Data ◽

Jaccard Index ◽

Phenotypic Traits ◽

Wide Binary ◽

Genome Wide ◽

Dataset Size ◽

Genome Wide Data ◽

Modelling Assumptions ◽

Systematic Collection

AbstractBackgroundThe generation and systematic collection of genome-wide data is ever-increasing. This vast amount of data has enabled researchers to study relations between a variety of genomic and epigenomic features, including genetic variation, gene regulation, and phenotypic traits. Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors. A variety of metrics have been proposed for this problem in other fields like ecology. However, while several of these metrics have been employed for assessing genomic co-occurrence, their appropriateness for the genomic setting has never been investigated.ResultsWe show that the choice of metric may strongly influence results and propose two alternative modelling assumptions that can be used to guide this choice. On both simulated and real genomic data, the Jaccard index is strongly affected by dataset size and should be used with caution. The Forbes coefficient (fold change) and tetrachoric correlation are less affected by dataset size, but one should be aware of increased variance for small datasets.AvailabilityAll results on simulated and real data can be inspected and reproduced athttps://hyperbrowser.uio.no/sim-measure

Download Full-text

Genomics Reveals the Origins of Historical Specimens

Molecular Biology and Evolution ◽

10.1093/molbev/msab013 ◽

2021 ◽

Author(s):

Qian Cong ◽

Jinhui Shen ◽

Jing Zhang ◽

Wenlin Li ◽

Lisa N Kinch ◽

...

Keyword(s):

Genomic Data ◽

Species Concepts ◽

Morphological Features ◽

Phenotypic Traits ◽

Museum Specimens ◽

Biodiversity Research ◽

Extant Species

Abstract Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computational protocols to overcome these challenges and applied our methods to resolve a series of long-standing controversies involving a group of butterflies. We deduced the geographical origins of several historical specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old specimens that serve as irreplaceable embodiments of species concepts cannot be confidently assigned to extant species or population due to the lack of diagnostic morphological features and clear documentation of the collection locality. The ability to determine where they were collected will resolve many on-going disputes. More broadly, we show the utility of applying genomics to historical museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

Download Full-text

Spider Diversification Through Space and Time

Annual Review of Entomology ◽

10.1146/annurev-ento-061520-083414 ◽

2021 ◽

Vol 66 (1) ◽

pp. 225-241 ◽

Cited By ~ 1

Author(s):

Dimitar Dimitrov ◽

Gustavo Hormiga

Keyword(s):

Species Richness ◽

Species Diversity ◽

Genomic Data ◽

Terrestrial Ecosystems ◽

Phenotypic Traits ◽

Comparative Analyses ◽

Space And Time ◽

Web Architecture ◽

Recent Advances ◽

Key Innovations

Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing of some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.

Download Full-text