FishPhyloMaker: An R package to generate phylogenies for ray-finned fishes

Nakamura, Gabriel; Richter, Aline; Soares, Bruno Eleres

doi:10.1101/2021.05.07.442752

Cited by 8 publications

(3 citation statements)

References 55 publications

(53 reference statements)

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“…PGLS can incorporate potential bias in phylogenetic relatedness among target species, assuming that the similarity of model residuals between species depends on their phylogenetic relatedness. To feed on the PGLS, we constructed a single phylogeny of the species analysed in this study only, using the R package 'FishPhyloMaker' (Nakamura et al, 2021; Figure S2). Because data points in the analyses included both populations of a single species and pairs of sister species, we considered the species pair (instead of a single species) as the tip of the phylogenetic tree when necessary (Figure S2).…”

Section: Effect Of Body Size On Barrier Transposal Across Timementioning

confidence: 99%

The Amazon‐Orinoco Barrier as a driver of reef‐fish speciation in the Western Atlantic through time

Araujo

Rocha

Lastrucci

et al. 2022

Journal of Biogeography

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Aim The Amazon‐Orinoco plume is the major biogeographical barrier between the Great Caribbean and the Brazilian Province. No study has so far addressed the influence of this barrier in a broad chrono‐phylogenetic context. Here, we evaluate the effects of the Amazon‐Orinoco plume barrier on the patterns of diversification of Western Atlantic reef fishes through time. Location Tropical Western Atlantic. Taxon Reef Fishes (Percomorpha). Methods We compiled DNA sequence data of 21 molecular markers from sister species/population pairs across 33 reef‐fish families in the Greater Caribbean biogeographical region and the Brazilian Province. The data included estimated divergence times between sister‐pairs based on previously published phylogenies and 94 newly proposed time‐trees. Divergence dates were compared with variations in the sedimentation discharge rate of the Amazon River and sea‐level fluctuations. To address the hypothesis that fishes with different adult sizes are affected differently by the Amazon‐Orinoco plume, we used a phylogenetic least squares regression to test the relationship between maximum total body length and divergence times between the Caribbean and Brazilian sister‐pairs. Results We identified an increase in the rates of lineage diversification between sister‐pairs of the Greater Caribbean and Brazilian Province reef fishes in the past 2.4 million years, in accordance with the period of higher sedimentation rates of the Amazon River and the more frequent sea‐level fluctuations in the Pleistocene. A strong relationship between total body length and effectiveness of the barrier through time was confirmed, with smaller species typically diverging earlier in periods when sedimentation rates of the Amazon River were significantly lower. Conclusions The strong biogeographical signal detected in this study across different lineages of reef fishes clearly indicates that the Amazon‐Orinoco plume played a significant role in the diversification of the Atlantic reef‐fish fauna. The temporal pattern of diversifications indicates a correlation between the permeability of the plume, sea‐level fluctuations, variability in the volume of the discharge and fish body size, with the barrier's influence being weaker on larger fishes.

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Section: Effect Of Body Size On Barrier Transposal Across Timementioning

confidence: 99%

The Amazon‐Orinoco Barrier as a driver of reef‐fish speciation in the Western Atlantic through time

Araujo

Rocha

Lastrucci

et al. 2022

Journal of Biogeography

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“…We created a fish phylogenetic tree using FishPhyloMaker to define the evolutionary distance relationships between a broad selection of teleost and condrostrean fish species ( Figure 8 ; Nakamura et al, 2021 ). As expected, the sturgeon family of condrostrean fishes is clearly separated from the teleost fishes.…”

Section: Discussionmentioning

confidence: 99%

Serum N-Glycome Diversity in Teleost and Chondrostrean Fishes

Aoki

Kumagai

Ranzinger

et al. 2021

Front. Mol. Biosci.

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Recent advances in carbohydrate chemistry, chemical biology, and mass spectrometric techniques have opened the door to rapid progress in uncovering the function and diversity of glycan structures associated with human health and disease. These strategies can be equally well applied to advance non-human health care research. To date, the glycomes of only a handful of non-human, non-domesticated vertebrates have been analyzed in depth due to the logistic complications associated with obtaining or handling wild-caught or farm-raised specimens. In contrast, the last 2 decades have seen advances in proteomics, glycoproteomics, and glycomics that have significantly advanced efforts to identify human serum/plasma biomarkers for various diseases. In this study, we investigated N-glycan structural diversity in serum harvested from five cultured fish species. This biofluid is a useful starting point for glycomic analysis because it is rich in glycoproteins, can be acquired in a sustainable fashion, and its contents reflect dynamic physiologic changes in the organism. Sera acquired from two chondrostrean fish species, the Atlantic sturgeon and shortnose sturgeon, and three teleost fish species, the Atlantic salmon, Arctic char, and channel catfish, were delipidated by organic extraction and the resulting protein-rich preparations sequentially treated with trypsin and PNGaseF to generate released N-glycans for structural analysis. Released N-glycans were analyzed as their native or permethylated forms by nanospray ionization mass spectrometry in negative or positive mode. While the basic biosynthetic pathway that initiates the production of glycoprotein glycan core structures is well-conserved across the teleost fish species examined in this study, species-specific structural differences were detected across the five organisms in terms of their monosaccharide composition, sialylation pattern, fucosylation, and degree of O-acetylation. Our methods and results provide new contributions to a growing library of datasets describing fish N-glycomes that can eventually establish species-normative baselines for assessing N-glycosylation dynamics associated with pathogen invasion, environmental stress, and fish immunologic responses.

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“…These characteristic glycosylation profiles may contribute to speciesspecific differences in the regulation of inflammatory and immune responses in fish biology. We created a fish phylogenetic tree using FishPhyloMaker to define the evolutionary distance relationships between a broad selection of teleost and condrostrean fish species (Figure 8; Nakamura et al, 2021). As expected, the sturgeon family of condrostrean fishes is clearly separated from the teleost fishes.…”

Section: Discussionmentioning

confidence: 71%

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FishPhyloMaker: An R package to generate phylogenies for ray-finned fishes

Cited by 8 publications

References 55 publications

The Amazon‐Orinoco Barrier as a driver of reef‐fish speciation in the Western Atlantic through time

The Amazon‐Orinoco Barrier as a driver of reef‐fish speciation in the Western Atlantic through time

Serum N-Glycome Diversity in Teleost and Chondrostrean Fishes

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