Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants

Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.

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Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants

10.7287/peerj.preprints.2510v1 ◽

2016 ◽

Author(s):

Juan C Opazo ◽

Kattina Zavala ◽

Paola Krall ◽

Rodrigo A Arias

Keyword(s):

Gene Duplication ◽

Common Ancestor ◽

Gene Loss ◽

Phenotypic Diversity ◽

Phenotypic Variability ◽

Single Gene ◽

Biological Significance ◽

Gene Copy ◽

Last Common Ancestor ◽

Extant Species

Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.

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Evolution and isoforms of V-ATPase subunits.

Journal of Experimental Biology ◽

10.1242/jeb.172.1.137 ◽

1992 ◽

Vol 172 (1) ◽

pp. 137-147 ◽

Cited By ~ 1

Author(s):

J P Gogarten ◽

T Starke ◽

H Kibak ◽

J Fishman ◽

L Taiz

Keyword(s):

Gene Duplication ◽

Common Ancestor ◽

Quaternary Structure ◽

Single Gene ◽

Last Common Ancestor ◽

Atpase Subunit ◽

Ancestral Gene ◽

Catalytic Subunits ◽

Phylogenetic Implications ◽

Atpase Subunits

The structure of V- and F-ATPases/ATP synthases is remarkably conserved throughout evolution. Sequence analyses show that the V- and F-ATPases evolved from the same enzyme that was already present in the last common ancestor of all known extant life forms. The catalytic and non-catalytic subunits found in the dissociable head groups of both V-ATPases and F-ATPases are paralogous subunits, i.e. these two types of subunits evolved from a common ancestral gene. The gene duplication giving rise to these two genes (i.e. those encoding the catalytic and non-catalytic subunits) pre-dates the time of the last common ancestor. Similarities between the V- and F-ATPase subunits and an ATPase-like protein that is implicated in flagellar assembly are evaluated with regard to the early evolution of ATPases. Mapping of gene duplication events that occurred in the evolution of the proteolipid, the non-catalytic and the catalytic subunits onto the tree of life leads to a prediction of the likely quaternary structure of the encoded ATPases. The phylogenetic implications of V-ATPases found in eubacteria are discussed. Different V-ATPase isoforms have been detected in some higher eukaryotes, whereas others were shown to have only a single gene encoding the catalytic V-ATPase subunit. These data are analyzed with respect to the possible function of the different isoforms (tissue-specific, organelle-specific). The point in evolution at which the different isoforms arose is mapped by phylogenetic analysis.

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Paleohistological estimation of bone growth rate in extinct archosaurs

Paleobiology ◽

10.1666/08093.1 ◽

2012 ◽

Vol 38 (2) ◽

pp. 335-349 ◽

Cited By ~ 61

Author(s):

Jorge Cubo ◽

Nathalie Le Roy ◽

Cayetana Martinez-Maza ◽

Laetitia Montes

Keyword(s):

Growth Rate ◽

Growth Rates ◽

Bone Growth ◽

Common Ancestor ◽

Phylogenetic Signal ◽

Growth Patterns ◽

Last Common Ancestor ◽

Metabolic Rates ◽

Extant Species ◽

Validation Tests

The clade Archosauria contains two very different sister groups in terms of diversity (number of species) and disparity (phenotypic variation): Crurotarsi (taxa more closely related to crocodiles than to birds) and Ornithodira (pterosaurs and dinosaurs including birds). The extant species of Crurotarsi may constitute a biased sample of past biodiversity regarding growth patterns and metabolic rates. Bone histological characters can be conserved over hundreds of millions of years in the fossil record and potentially contain information about individual age at death, age at sexual maturity, bone growth rates, and basal metabolic rates of extinct vertebrates. Using a sample of extant amniotes, we have constructed a paleobiological model to estimate bone growth rate from bone histological traits. Cross-validation tests show that this model is reliable. We then used it to estimate bone growth rates in a sample of extinct archosaurs including Crurotarsi and Ornithodira. After testing for phylogenetic signal, optimization of femoral growth rates through squared change parsimony onto a time-calibrated tree of amniotes shows two divergent evolutionary trends: whereas bone growth rates increase from the last common ancestor of Ornithodira to extant birds, they decrease from the last common ancestor of Crurotarsi to extant crocodiles. However, we conclude, on the basis of recent evidence for unidirectional airflow in the lungs of alligators, that crocodiles may have retained the capacity of growing at high rates.

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The evolution of the cytoskeleton

The Journal of Cell Biology ◽

10.1083/jcb.201102065 ◽

2011 ◽

Vol 194 (4) ◽

pp. 513-525 ◽

Cited By ~ 161

Author(s):

Bill Wickstead ◽

Keith Gull

Keyword(s):

Gene Duplication ◽

Cell Shape ◽

Common Ancestor ◽

Last Common Ancestor ◽

Accessory Proteins ◽

The Core ◽

Domains Of Life ◽

Cytoskeletal Function ◽

And Function

The cytoskeleton is a system of intracellular filaments crucial for cell shape, division, and function in all three domains of life. The simple cytoskeletons of prokaryotes show surprising plasticity in composition, with none of the core filament-forming proteins conserved in all lineages. In contrast, eukaryotic cytoskeletal function has been hugely elaborated by the addition of accessory proteins and extensive gene duplication and specialization. Much of this complexity evolved before the last common ancestor of eukaryotes. The distribution of cytoskeletal filaments puts constraints on the likely prokaryotic line that made this leap of eukaryogenesis.

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Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

Scientific Reports ◽

10.1038/s41598-020-79160-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evy van Berlo ◽

Alejandra P. Díaz-Loyo ◽

Oscar E. Juárez-Mora ◽

Mariska E. Kret ◽

Jorg J. M. Massen

Keyword(s):

Experimental Evidence ◽

Common Ancestor ◽

Great Apes ◽

Pongo Pygmaeus ◽

Last Common Ancestor ◽

Contagious Yawning ◽

Proximate Mechanism ◽

Social Species ◽

Ultimate Causation

AbstractYawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

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Recombinant transfer in the basic genome ofEscherichia coli

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510839112 ◽

2015 ◽

Vol 112 (29) ◽

pp. 9070-9075 ◽

Cited By ~ 59

Author(s):

Purushottam D. Dixit ◽

Tin Yau Pang ◽

F. William Studier ◽

Sergei Maslov

Keyword(s):

Common Ancestor ◽

Recipient Cell ◽

Gene Clusters ◽

Selective Advantage ◽

Last Common Ancestor ◽

Genome Sequences ◽

Bacterial Genomes ◽

Basic Genome ◽

Single Base Pair ◽

Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

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Comparative Genomic and Phylogenetic Analyses of Gammaproteobacterial glg Genes Traced the Origin of the Escherichia coli Glycogen glgBXCAP Operon to the Last Common Ancestor of the Sister Orders Enterobacteriales and Pasteurellales

PLoS ONE ◽

10.1371/journal.pone.0115516 ◽

2015 ◽

Vol 10 (1) ◽

pp. e0115516 ◽

Cited By ~ 11

Author(s):

Goizeder Almagro ◽

Alejandro M. Viale ◽

Manuel Montero ◽

Mehdi Rahimpour ◽

Francisco José Muñoz ◽

...

Keyword(s):

Escherichia Coli ◽

Common Ancestor ◽

Phylogenetic Analyses ◽

Comparative Genomic ◽

Last Common Ancestor

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Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution

Molecular and Cellular Biology ◽

10.1128/mcb.10.6.2513-2520.1990 ◽

1990 ◽

Vol 10 (6) ◽

pp. 2513-2520

Author(s):

L C Samuelson ◽

K Wiebauer ◽

C M Snow ◽

M H Meisler

Keyword(s):

Gene Family ◽

Single Gene ◽

Primate Evolution ◽

Endogenous Retrovirus ◽

Gene Copy ◽

Nucleotide Sequence Analysis ◽

Ancestral Gene ◽

Molecular Events ◽

Amylase Genes ◽

History Of

We have analyzed the junction regions of inserted elements within the human amylase gene complex. This complex contains five genes which are expressed at high levels either in the pancreas or in the parotid gland. The proximal 5'-flanking regions of these genes contain two inserted elements. A gamma-actin pseudogene is located at a position 200 base pairs upstream of the first coding exon. All of the amylase genes contain this insert. The subsequent insertion of an endogenous retrovirus interrupted the gamma-actin pseudogene within its 3'-untranslated region. Nucleotide sequence analysis of the inserted elements associated with each of the five human amylase genes has revealed a series of molecular events during the recent history of this gene family. The data indicate that the entire gene family was generated during primate evolution from one ancestral gene copy and that the retroviral insertion activated a cryptic promoter.

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Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

10.1101/2021.11.19.469253 ◽

2021 ◽

Author(s):

Ksenia Juravel ◽

Luis Porras ◽

Sebastian Hoehna ◽

Davide Pisani ◽

Gert Wörheide

Keyword(s):

Common Ancestor ◽

Sister Group ◽

The Other ◽

Gene Content ◽

Statistical Hypothesis ◽

Phylogenetic Position ◽

Last Common Ancestor ◽

Statistical Hypothesis Testing ◽

Animal Phylogeny ◽

Phylogenetic Hypotheses

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

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