RERconverge: an R package for associating evolutionary rates with convergent traits

Kowalczyk, Amanda; Meyer, Wynn K.; Partha, Raghavendran; Mao, Weiguang; Clark, Nathan L.; Chikina, Maria

doi:10.1093/bioinformatics/btz468

Cited by 92 publications

(118 citation statements)

References 14 publications

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“…For each amino acid alignment, we estimated branch lengths using aaml in the phylogenetic analysis using maximum likelihood (PAML) package ( Yang, 2007 ). ERC values (correlation coefficients) for all genes with NGLY1 were calculated using the RERconverge package ( Kowalczyk et al, 2019 ). We report the ERC results for the mammalian group as the negative log of their p-values for each gene pair ( Supplementary file 5 ‘nlogpvbest1’).…”

Section: Methodsmentioning

confidence: 99%

A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency

Talsness

Owings

Coelho

et al. 2020

eLife

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N-Glycanase 1 (NGLY1) is a cytoplasmic deglycosylating enzyme. Loss-of-function mutations in the NGLY1 gene cause NGLY1 deficiency, which is characterized by developmental delay, seizures, and a lack of sweat and tears. To model the phenotypic variability observed among patients, we crossed a Drosophila model of NGLY1 deficiency onto a panel of genetically diverse strains. The resulting progeny showed a phenotypic spectrum from 0 to 100% lethality. Association analysis on the lethality phenotype, as well as an evolutionary rate covariation analysis, generated lists of modifying genes, providing insight into NGLY1 function and disease. The top association hit was Ncc69 (human NKCC1/2), a conserved ion transporter. Analyses in NGLY1-/- mouse cells demonstrated that NKCC1 has an altered average molecular weight and reduced function. The misregulation of this ion transporter may explain the observed defects in secretory epithelium function in NGLY1 deficiency patients.

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Section: Methodsmentioning

confidence: 99%

A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency

Talsness

Owings

Coelho

et al. 2020

eLife

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“…Relative evolutionary rates were estimated using the program RERConverge (parameters ‘ transform = "sqrt" , weighted = T , scale = T , cutoff = 0’)[ 67 ]. As long branches exhibit higher degrees of variance compared to short branches, RERconverge includes a heteroskedasticity correction that increases comparative statistical power across the phylogeny [ 68 ].…”

Section: Methodsmentioning

confidence: 99%

Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change

et al. 2020

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In the frigid, oxygen-rich Southern Ocean (SO), Antarctic icefishes (Channichthyidae; Notothenioidei) evolved the ability to survive without producing erythrocytes and hemoglobin, the oxygen-transport system of virtually all vertebrates. Here, we integrate paleoclimate records with an extensive phylogenomic dataset of notothenioid fishes to understand the evolution of trait loss associated with climate change. In contrast to buoyancy adaptations in this clade, we find relaxed selection on the genetic regions controlling erythropoiesis evolved only after sustained cooling in the SO. This pattern is seen not only within icefishes but also occurred independently in other high-latitude notothenioids. We show that one species of the red-blooded dragonfish clade evolved a spherocytic anemia that phenocopies human patients with this disease via orthologous mutations. The genomic imprint of SO climate change is biased toward erythrocyte-associated conserved noncoding elements (CNEs) rather than to coding regions, which are largely preserved through pleiotropy. The drift in CNEs is specifically enriched near genes that are preferentially expressed late in erythropoiesis. Furthermore, we find that the hematopoietic marrow of icefish species retained proerythroblasts, which indicates that early erythroid development remains intact. Our results provide a framework for understanding the interactions between development and the genome in shaping the response of species to climate change.

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“…Another approach for investigating convergent protein evolution is examining rates of protein evolution across branches of a species tree and isolating instances where accelerated rates of evolution occur independently on branches leading to organisms with convergent phenotypes [21,22,81]. Such methods use amino acid distance trees that are normalized by average divergence rates across the genome for each tree branch and estimate the correlation royalsocietypublishing.org/journal/rstb Phil.…”

Section: (C) Molecular Convergence In Protein Evolutionmentioning

confidence: 99%

Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

Card

Grayson

Tonini

et al. 2019

Phil. Trans. R. Soc. B

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Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

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RERconverge: an R package for associating evolutionary rates with convergent traits

Cited by 92 publications

References 14 publications

A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency

A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency

Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change

Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

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