How to build phylogenetic species trees with OMA

Dylus, David; Nevers, Yannis; Altenhoff, Adrian M.; Gürtler, Antoine; Dessimoz, Christophe; Glover, Natasha

doi:10.12688/f1000research.23790.2

Cited by 4 publications

(1 citation statement)

References 29 publications

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“…Whole genome alignments of single-copy orthologs trimmed with trimAl v1.4.rev15 (Capella-Gutiérrez et al, 2009) from 22 SIMR bat models and two outgroups (Supp Table 1) were used to generate a phylogenomic tree (Dylus et al, 2022) using RaxML version 8.1.15 (PROTFAMMAUTO model). Our molecular phylogeny, which matches published species topologies (Rojas et al, 2016; Potter et al, 2021), includes a broad taxonomic sampling, incorporating Miniopteridae, Vespertilionidae, and Molossidae (Figure 2, Branch A; Miller-Butterworth et al, 2007; Lim, 2009).…”

Section: Methodsmentioning

confidence: 99%

Sugar assimilation underlying dietary evolution of Neotropical bats

Camacho¹,

Bernal-Rivera²,

Robb³

et al. 2023

Preprint

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Specializations in animal diets drive selective demands on morphology, anatomy, and physiology. Studying adaptations linked to diet evolution benefits from examining Neotropical bats, a remarkable group with high taxonomic and trophic diversity. In this study we performed glucose tolerance tests on wild-caught bats, which revealed distinct responses to three sugars present in different foods: trehalose (insects), sucrose and glucose (fruits and nectar). Insect eating bats responded most strongly to trehalose, while bats with nectar and fruit-based diets exhibited heightened response to glucose and sucrose, reaching blood sugar levels over 600 mg/dL. To reveal positive selection in sugar assimilation genes we performed genome analysis of 22 focal bat species and 2 outgroup species. We identified selection in the ancestral vespertilionid branch (insect-eaters) for the digestive enzyme Trehalase, while sucrase-isomaltase exhibited selection in branches leading to omnivorous and nectar diets. Unexpectedly, the insect-eating lineageMyotisexhibited sucrase-isomaltase selection, potentially explaining their heightened sucrose assimilation. Furthermore, the glucose transporters SLC2A3 and SLC2A2 showed selection in lineages associated with nectar and blood diets. By examining cellular features of the small intestine, we discovered that sugar consumption strongly impacted numerous digestive traits, providing valuable insight into the physiological implications of the identified molecular adaptations. To elucidate this further, we used HCR RNA-FISH to perform single molecule ex vivo gene expression analysis of enterocyte response to a glucose meal in three focal species. We observed unusually high activity in the glucose transporter geneSlc2a2during the fasted state of nectar bats that did not change upon feeding. Comparatively, nectar bats exhibited an enhanced capacity for intestinal absorption of dietary sugar primarily throughSlc2a2, while fruit bats relied on increasing levels ofSlc5a1. Overall, this study highlights the intricate interplay between molecular, morphological, and physiological aspects of diet evolution and provides new insights to our understanding of sugar assimilation mechanisms in mammals.

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Section: Methodsmentioning

confidence: 99%

Sugar assimilation underlying dietary evolution of Neotropical bats

Camacho¹,

Bernal-Rivera²,

Robb³

et al. 2023

Preprint

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Adaptive evolution and functional significance of the PPARGC1A gene across diverse animal species

Hosseini,

Ullah,

Ahmad

et al. 2024

Ecology and Evolution

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Codon‐based analyses of the PPARGC1A gene across 38 vertebrate species were deployed to elucidate patterns of evolutionary change. Employing maximum likelihood assessments through MEGA, we scrutinized 447 codon positions addressing the entire coding region, excluding positions mired by gaps or missing data. Distinct codons manifested variance in selection pressures, particularly codons 4, 11, 66, and 123, which exhibited positive dN‐dS values suggestive of positive selection. Codon 137 displayed the most pronounced dN‐dS value, signifying intensified selective advantage. Meanwhile, codons 30 and 90 portrayed near‐neutral scores, indicative of purifying selection. Complementary computational methods (IFEL, REL, FUBAR, and SLAC) confirmed positive selection at specific codon sites, with varying degrees of corroboration. The integration of mixed‐effect modeling (MEME) identified episodic diversifying selection, pinpointing codons that underwent selection episodes in certain lineages. Refined codon model selection lent insight into substitution rates, revealing nuanced degrees of evolutionary conservation among different codons. Supporting these genetic insights, the phylogenetic analysis highlighted relationships among the PPARGC1A sequences and domain analysis confirmed conserved features across species, while protein–protein interaction networks suggested a complex web of functional interdependencies. These findings advance our understanding of the PPARGC1A gene's evolutionary trajectory and underscore the gene's potential adaptive significance within diverse vertebrate lineages.

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From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)

Nesterenko

Miroliubov

2022

F1000Res

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Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, the system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into “zombies”. Despite all these amazing traits, there is no genomic and transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: externa and main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for both P. reticulata and Rhizocephala. Based on the results obtained, the spatial heterogeneity of protein-coding genes expression in different regions of P. reticulata adult female body was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans “got stuck in the metamorphosis”, even in their reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of this amazing parasites.

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How to build phylogenetic species trees with OMA

Cited by 4 publications

References 29 publications

Sugar assimilation underlying dietary evolution of Neotropical bats

Sugar assimilation underlying dietary evolution of Neotropical bats

Adaptive evolution and functional significance of the PPARGC1A gene across diverse animal species

From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)

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