phylogenetic framework
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2022 ◽  
Alex Dornburg ◽  
Katerina Zapfe ◽  
Rachel Williams ◽  
Michael Alfaro ◽  
Richard Morris ◽  

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that do not reflect the same traits as their adult forms. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which often have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. However, whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. Integrating a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence, we reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.

2022 ◽  
Vol 25 ◽  
pp. 16-21
Thomas J. Simonsen ◽  
Marcus Glahder ◽  
Thomas Pape ◽  
Kent Olsen ◽  
Marie Djernæs

We reconstruct a phylogenetic framework for the zygopteran family Lestidae based on a molecular dataset comprised of sequence data from the genes COI, 16S, 18S, 28S, and ITS1+2 from 41 ingroup taxa and 8 outgroup taxa with emphasis on the systematic position of the genus Chalcolestes Kennedy. We recover Lestidae as monophyletic with good statistical support. The family falls into two subequal clades. One, comprising the genus Sympecma Burmeister and Lestes Leach sensu lato (including the genus Archi­lestes Selys) is poorly to moderately supported. While the other, comprising the genera Austrolestes Tillyard, Indolestes Fraser, Orolestes McLachlan, and Chalcolestes is strongly supported. Chalcolestes is recovered as sister to the Oriental genus Orolestes with strong support. Our results thus support that Chalcolestes is a valid genus not closely related to Lestes. Monophyly of Lestes requires inclusion of the New World genus Archilestes, and our results support the need for a thorough revision of Lestes.

2022 ◽  
David J Williams ◽  
Patrick AD Grimont ◽  
Adrian Cazares ◽  
Francine Grimont ◽  
Elisabeth Ageron ◽  

The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We show that Serratia is a diverse genus which displays striking plasticity and ability to adapt to its environment, including a highly-varied portfolio of plasmids, and provide evidence of different patterns of gene flow across the genus. This work provides an essential platform for understanding the emergence of clinical and other lineages of Serratia.

2022 ◽  
Zongjun Li ◽  
Xiangnan Wang ◽  
Yu Zhang ◽  
Zhongtang Yu ◽  
Tingting Zhang ◽  

Understanding the biodiversity and genetics of the gut microbiome has important implications for host physiology. One underexplored and elusive group is ciliated protozoa, which play crucial roles in regulating gut microbial interactions. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies for all major abundant clades. With these genomes, we firstly resolved the taxonomic and phylogenetic framework that reclassified them into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Via extensive horizontal gene transfer and gene family expansion, rumen ciliates possess a broad array of enzymes to synergistically degrade plant and microbial carbohydrates. In particular, ~80% of the degrading enzymes in Diplodiniinae and Ophryoscolecinae act on plant cell wall, and the high activities of their cellulase, xylanase and lysozyme reflect the potential of ciliate enzymes for biomass-conversion. Additionally, the new ciliate dataset greatly facilitated the rumen metagenomic analyses by allowing ~12% of reads to be classified.

2022 ◽  
Wael Hamed Roshdy ◽  
Mohamed K Khalifa ◽  
James Emmanuel San ◽  
Houriiyah Tegally ◽  
Eduan Wilkinson ◽  

COVID-19 was first diagnosed in Egypt on 14 February 2020. By the end of November 2021, over 333,840 cases and 18,832 deaths had been reported. As part of national genomic surveillance, 1,027 SARS-CoV-2 near whole-genomes had been generated and published by the end of May 2021. Here we describe the genomic epidemiology of SARS-CoV-2 in Egypt over this period using a subset of 976 high-quality Egyptian genomes analysed together with a representative set of global sequences within a phylogenetic framework. We show that a single lineage, C.36, introduced early in the pandemic was responsible for most cases in Egypt. Furthermore, we show that to remain dominant in the face of mounting immunity from previous infection and vaccination, this lineage evolved into various sub-lineages acquiring several mutations known to confer adaptive advantage and pathogenic properties. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and enforcement of public health measures to prevent expansion of existing lineages.

2021 ◽  
Vol 11 (1) ◽  
Alejandra E. Melgar ◽  
Alicia M. Zelada

AbstractDehydrins (DHNs) are a family of plant proteins that play important roles on abiotic stress tolerance and seed development. They are classified into five structural subgroups: K-, SK-, YK-, YSK-, and KS-DHNs, according to the presence of conserved motifs named K-, Y- and S- segments. We carried out a comparative structural and phylogenetic analysis of these proteins, focusing on the less-studied KS-type DHNs. A search for conserved motifs in DHNs from 56 plant genomes revealed that KS-DHNs possess a unique and highly conserved N-terminal, 15-residue amino acid motif, not previously described. This novel motif, that we named H-segment, is present in DHNs of angiosperms, gymnosperms and lycophytes, suggesting that HKS-DHNs were present in the first vascular plants. Phylogenetic and microsynteny analyses indicate that the five structural subgroups of angiosperm DHNs can be assigned to three groups of orthologue genes, characterized by the presence of the H-, F- or Y- segments. Importantly, the hydrophilin character of DHNs correlate with the phylogenetic origin of the DHNs rather than to the traditional structural subgroups. We propose that angiosperm DHNs can be ultimately subdivided into three orthologous groups, a phylogenetic framework that should help future studies on the evolution and function of this protein family.

2021 ◽  
María Torres-Sánchez ◽  
Jennifer Villate ◽  
Sarah McGrath-Blaser ◽  
Ana V Longo

While many pathogens are limited to a single host, others can jump from host to host, which likely contributes to the emergence of infectious diseases. Despite this threat to biodiversity, traits associated with overcoming eco-evolutionary barriers to achieve host niche expansions are not well understood. Here, we examined the case of Batrachochytrium dendrobatidis (Bd), a multi-host pathogen that infects the skin of hundreds of amphibian species worldwide. To uncover functional machinery driving multi-host invasion, we analyzed Bd transcriptomic landscapes across 14 amphibian hosts and inferred the origin and evolutionary history of pathogenic genes under a phylogenetic framework comprising 12 other early-divergent zoosporic fungi. Our results not only revealed a conserved basal genetic machinery, but also highlighted the ability of Bd to display plastic infection strategies when challenged under suboptimal host environments. We found that genes related to amphibian skin exploitation have arisen mainly via gene duplications. We argue that plastic gene expression can drive variation in Bd lifecycles with different mode and tempo of development. Our findings support the idea that host skin environments exert contrasting selective pressures, such that gene expression plasticity constitutes one of the evolutionary keys leading to the success of this panzootic multi-host pathogen.

ZooKeys ◽  
2021 ◽  
Vol 1071 ◽  
pp. 175-193
Thomas Inäbnit ◽  
Adrienne Jochum ◽  
Raijko Slapnik ◽  
Eike Neubert

Recent integrative investigations of the terrestrial ellobiid genus, Zospeum, have revealed significant findings concerning its Alpine-Dinaric evolution and taxonomy. Due to the expected discrepancy between the useful, but limited, 1970s’ classification system based on shell data and the results of recent genetic analyses in the latest investigation, a revision of the entire radiation was undertaken, and a new classification system was devised by the present authors in an earlier paper. Concurrent to this work, molecular sequences from two Austrian caves were published independently of our revision by another research group. By incorporating these genetic data within our phylogenetic framework here, we show that the Austrian individuals are genetically most similar to Zospeum amoenum and consequently, classify them within that species. We additionally reveal two new genetic lineages from the largely under-sampled southern extension of Zospeum’s known distributional range. The first lineage, deriving from the region of Dubrovnik, Croatia, is a potential candidate for genetically clarifying Zospeum troglobalcanicum. The second lineage derives from the municipality of Tomislavgrad, Bosnia-Herzegovina and is herein, described a new species: Zospeum simplex Inäbnit, Jochum & Neubert, sp. nov.

2021 ◽  
Vol 288 (1963) ◽  
Nobuaki Mizumoto ◽  
Thomas Bourguignon

Termites are social cockroaches. Because non-termite cockroaches are larger than basal termite lineages, which themselves include large termite species, it has been proposed that termites experienced a unidirectional body size reduction since they evolved eusociality. However, the validity of this hypothesis remains untested in a phylogenetic framework. Here, we reconstructed termite body size evolution using head width measurements of 1638 modern and fossil termite species. We found that the unidirectional body size reduction model was only supported by analyses excluding fossil species. Analyses including fossil species suggested that body size diversified along with speciation events and estimated that the size of the common ancestor of modern termites was comparable to that of modern species. Our analyses further revealed that body size variability among species, but not body size reduction, is associated with features attributed to advanced termite societies. Our results suggest that miniaturization took place at the origin of termites, while subsequent complexification of termite societies did not lead to further body size reduction.

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