Molecular Evolutionary Analyses of Tooth Genes Support Sequential Loss of Enamel and Teeth in Baleen Whales (Mysticeti)

The loss of teeth and evolution of baleen racks in Mysticeti was a profound transformation that permitted baleen whales to radiate and diversify into a previously underutilized ecological niche of bulk filter-feeding on zooplankton and other small prey. Ancestral state reconstructions suggest that teeth were lost in the common ancestor of crown Mysticeti. Genomic studies provide some support for this hypothesis and suggest that the genetic toolkit for enamel production was inactivated in the common ancestor of living baleen whales. However, molecular studies to date have not provided direct evidence for the complete loss of teeth, including their dentin component, on the stem mysticete branch. Given these results, several questions remain unanswered: (1) Were teeth lost in a single step or did enamel loss precede dentin loss? (2) Was enamel lost early or late on the stem mysticete branch? (3) If enamel and dentin/tooth loss were decoupled in the ancestry of baleen whales, did dentin loss occur on the stem mysticete branch or independently in different crown mysticete lineages? To address these outstanding questions, we compiled and analyzed complete protein-coding sequences for nine tooth-related genes from cetaceans with available genome data. Seven of these genes are associated with enamel formation (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) whereas two other genes are either dentin-specific (DSPP) or tooth-specific (ODAPH) but not enamel-specific. Molecular evolutionary analyses indicate that all seven enamel-specific genes have inactivating mutations that are scattered across branches of the mysticete tree. Three of the enamel genes (ACP4, KLK4, MMP20) have inactivating mutations that are shared by all mysticetes. The two genes that are dentin-specific (DSPP) or tooth-specific (ODAPH) do not have any inactivating mutations that are shared by all mysticetes, but there are shared mutations in Balaenidae as well as in Plicogulae (Neobalaenidae + Balaenopteroidea). These shared mutations suggest that teeth were lost at most two times. Shared inactivating mutations and dN/dS analyses, in combination with cetacean divergence times, were used to estimate inactivation times of genes and by proxy enamel and tooth phenotypes. The results of these analyses are most compatible with a two-step model for the loss of teeth in the ancestry of living baleen whales: enamel was lost very early on the stem Mysticeti branch followed by the independent loss of dentin (and teeth) in the common ancestors of Balaenidae and Plicogulae, respectively. These results imply that some stem mysticetes, and even early crown mysticetes, may have had vestigial teeth comprised of dentin with no enamel. Our results also demonstrate that all odontocete species (in our study) with absent or degenerative enamel have inactivating mutations in one or more of their enamel genes.

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Loss of plastid developmental genes coincides with a reversion to monoplastidy in hornworts

10.1101/2022.01.11.475830 ◽

2022 ◽

Author(s):

Alexander Istvan MacLeod ◽

Parth K Raval ◽

Simon Stockhorst ◽

Michael Knopp ◽

Eftychios Frangedakis ◽

...

Keyword(s):

Common Ancestor ◽

Nuclear Division ◽

Developmental Pathways ◽

Ancestral State ◽

Plastid Division ◽

Plastid Development ◽

State Reconstruction ◽

Transcriptomic Data ◽

The Common ◽

Almost All

The first plastid evolved from an endosymbiotic cyanobacterium in the common ancestor of the Archaeplastida. The transformative steps from cyanobacterium to organelle included the transfer of control over developmental processes; a necessity for the host to orchestrate, for example, the fission of the organelle. The plastids of almost all embryophytes divide independent from nuclear division, leading to cells housing multiple plastids. Hornworts, however, are monoplastidic (or near-monoplastidic) and their photosynthetic organelles are a curious exception among embryophytes for reasons such as the occasional presence of pyrenoids. Here we screened genomic and transcriptomic data of eleven hornworts for components of plastid developmental pathways. We find intriguing differences among hornworts and specifically highlight that pathway components involved in regulating plastid development and biogenesis were differentially lost in this group of bryophytes. In combination with ancestral state reconstruction, our data suggest that hornworts have reverted back to a monoplastidic phenotype due to the combined loss of two plastid division-associated genes: ARC3 and FtsZ2.

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ACPT gene is inactivated in mammalian lineages that lack enamel or teeth

PeerJ ◽

10.7717/peerj.10219 ◽

2021 ◽

Vol 9 ◽

pp. e10219

Author(s):

Yuan Mu ◽

Xin Huang ◽

Rui Liu ◽

Yulin Gai ◽

Na Liang ◽

...

Keyword(s):

Fossil Record ◽

Common Ancestor ◽

Selective Pressure ◽

Tooth Enamel ◽

Sperm Whale ◽

Coding Region ◽

Evolutionary Mechanisms ◽

Baleen Whales ◽

The Common ◽

Exon 4

Loss of tooth or enamel is widespread in multiple mammal lineages. Although several studies have been reported, the evolutionary mechanisms of tooth/enamel loss are still unclear. Most previous studies have found that some tooth-related genes have been inactivated in toothless and/or enamel-less mammals, such as ENAM, ODAM, C4orf26, AMBN, AMTN, DSPP, etc. Here, we conducted evolutionary analyses on ACPT playing a key role in amelogenesis, to interrogate the mechanisms. We obtained the ACPT sequences from 116 species, including edentulous and enamel-less mammals. The results shows that variant ORF-disrupting mutations were detected in ACPT coding region among nine edentulous baleen whales and three enamel-less taxa (pygmy sperm whale, aardvark, nine-banded armadillo). Furtherly, selective pressure uncovered that the selective constraints have been relaxed among all toothless and enamel-less lineages. Moreover, our results support the hypothesis that mineralized teeth were lost or degenerated in the common ancestor of crown Mysticeti through two shared single-base sites deletion in exon 4 and 5 of ACPT among all living baleen whales. DN/dS values on transitional branches were used to estimate ACPT inactivation records. In the case of aardvark, inactivation of ACPT was estimated at ~23.60–28.32 Ma, which is earlier than oldest aardvark fossil record (Orycteropus minutus, ~19 Ma), suggesting that ACPT inactivation may result in degeneration or loss of enamel. Conversely, the inactivation time of ACPT estimated in armadillo (~10.18–11.30 Ma) is later than oldest fossil record, suggesting that inactivation of ACPT may result from degeneration or loss of enamel in these mammals. Our findings suggested that different mechanisms of degeneration of tooth/enamel might exist among toothless and enamel-less lineages during evolution. Our study further considered that ACPT is a novel gene for studying tooth evolution.

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Comparative Transcriptomics Provides Insights into Reticulate and Adaptive Evolution of a Butterfly Radiation

Genome Biology and Evolution ◽

10.1093/gbe/evz202 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2963-2975 ◽

Cited By ~ 3

Author(s):

Wei Zhang ◽

Brian X Leon-Ricardo ◽

Bas van Schooten ◽

Steven M Van Belleghem ◽

Brian A Counterman ◽

...

Keyword(s):

Common Ancestor ◽

Data Sets ◽

Orthologous Genes ◽

Holistic View ◽

Visual Signaling ◽

Genome Data ◽

Evolutionary Changes ◽

Outgroup Species ◽

The Common ◽

Ancient Hybridization

Abstract Butterfly eyes are complex organs that are composed of a diversity of proteins and they play a central role in visual signaling and ultimately, speciation, and adaptation. Here, we utilized the whole eye transcriptome to obtain a more holistic view of the evolution of the butterfly eye while accounting for speciation events that co-occur with ancient hybridization. We sequenced and assembled transcriptomes from adult female eyes of eight species representing all major clades of the Heliconius genus and an additional outgroup species, Dryas iulia. We identified 4,042 orthologous genes shared across all transcriptome data sets and constructed a transcriptome-wide phylogeny, which revealed topological discordance with the mitochondrial phylogenetic tree in the Heliconius pupal mating clade. We then estimated introgression among lineages using additional genome data and found evidence for ancient hybridization leading to the common ancestor of Heliconius hortense and Heliconius clysonymus. We estimated the Ka/Ks ratio for each orthologous cluster and performed further tests to demonstrate genes showing evidence of adaptive protein evolution. Furthermore, we characterized patterns of expression for a subset of these positively selected orthologs using qRT-PCR. Taken together, we identified candidate eye genes that show signatures of adaptive molecular evolution and provide evidence of their expression divergence between species, tissues, and sexes. Our results demonstrate: 1) greater evolutionary changes in younger Heliconius lineages, that is, more positively selected genes in the cydno–melpomene–hecale group as opposed to the sara–hortense–erato group, and 2) suggest an ancient hybridization leading to speciation among Heliconius pupal-mating species.

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ACPT gene is inactivated in mammalian lineages that lack enamel and teeth

10.1101/861633 ◽

2019 ◽

Author(s):

Yuan Mu ◽

Xin Huang ◽

Rui Liu ◽

Yulin Gai ◽

Na Liang ◽

...

Keyword(s):

Common Ancestor ◽

Selective Pressure ◽

Tooth Enamel ◽

Sperm Whale ◽

Coding Region ◽

Evolutionary Mechanisms ◽

Baleen Whales ◽

Single Base ◽

The Common ◽

Exon 4

AbstractLoss of tooth or enamel is widespread in multiple mammal lineages. Although several studies have been reported, the evolutionary mechanisms of tooth / enamel loss are still unclear. Most previous studies have found that some tooth-related genes have been inactivated in toothless and / or enamel-less mammals, such as ENAM, ODAM, C4orf26, AMBN, AMTN, DSPP, etc. Here, we conducted evolutionary analyses on ACPT plays a key role in amelogenesis, to interrogate the mechanisms. We obtained the ACPT sequences from 116 species, including edentulous and enamel-less mammals, then evolutionary analyses were implemented. The results showed that variant ORF-disrupting mutations have been detected in ACPT coding region among nine edentulous baleen whales and three enamel-less taxa (pygmy sperm whale, aardvark, nine-banded armadillo). Furtherly, selective pressure uncovered that the selective constraints have been relaxed among all toothless and enamel-less lineages. Moreover, our results support the hypothesis that mineralized teeth were lost or degenerated in the common ancestor of crown Mysticeti through two shared single-base sites deletion in exon 4 and 5 of ACPT among all living baleen whales. DN / dS values on transitional branches were used to estimate ACPT inactivation times. In the case of aardvark, inactivation of ACPT was estimated at ~23.60-28.32 Ma, which is earlier than the oldest pangolin fossil time (Orycteropus minutus, ~19Ma), suggesting that ACPT inactivation may result in degeneration or loss of enamel. Conversely, the inactivation time of ACPT estimated in armadillo (~10.18-11.30 Ma) is later than the oldest fossil time, suggesting that inactivation of ACPT may result from degeneration or loss of enamel in these mammals. Our findings suggested that different mechanisms of degeneration of tooth / enamel might exist among toothless and enamel-less lineages during evolution. Our study further considered that ACPT is a novel gene for studying tooth evolution.

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Ancestral State Reconstruction of the Apoptosis Machinery in the Common Ancestor of Eukaryotes

G3 Genes|Genome|Genetics ◽

10.1534/g3.118.200295 ◽

2018 ◽

Vol 8 (6) ◽

pp. 2121-2134 ◽

Cited By ~ 9

Author(s):

Joanna Klim ◽

Arkadiusz Gładki ◽

Roza Kucharczyk ◽

Urszula Zielenkiewicz ◽

Szymon Kaczanowski

Keyword(s):

Common Ancestor ◽

Ancestral State Reconstruction ◽

Ancestral State ◽

State Reconstruction ◽

The Common

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Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.1280 ◽

2010 ◽

Vol 278 (1708) ◽

pp. 993-1002 ◽

Cited By ~ 60

Author(s):

Robert W. Meredith ◽

John Gatesy ◽

Joyce Cheng ◽

Mark S. Springer

Keyword(s):

Common Ancestor ◽

Baleen Whales ◽

The Common

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Open cup nests evolved from roofed nests in the early passerines

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.2708 ◽

2017 ◽

Vol 284 (1848) ◽

pp. 20162708 ◽

Cited By ~ 16

Author(s):

J. Jordan Price ◽

Simon C. Griffith

Keyword(s):

Adaptive Radiation ◽

Common Ancestor ◽

Terrestrial Ecosystems ◽

Ancestral State ◽

Passerine Birds ◽

Australian Continent ◽

Nest Design ◽

Relative Rarity ◽

The Common ◽

Order Passeriformes

The architectural diversity of nests in the passerine birds (order Passeriformes) is thought to have played an important role in the adaptive radiation of this group, which now comprises more than half of avian species and occupies nearly all terrestrial ecosystems. Here, we present an extensive survey and ancestral state reconstruction of nest design across the passerines, focusing on early Australian lineages and including members of nearly all passerine families worldwide. Most passerines build open cup-shaped nests, whereas a minority build more elaborate domed structures with roofs. We provide strong evidence that, despite their relative rarity today, domed nests were constructed by the common ancestor of all modern passerines. Open cup nests evolved from enclosed domes at least four times independently during early passerine evolution, at least three of which occurred on the Australian continent, yielding several primarily cup-nesting clades that are now widespread and numerically dominant among passerines. Our results show that the ubiquitous and relatively simple cup-shaped nests of many birds today evolved multiple times convergently, suggesting adaptive benefits over earlier roofed designs.

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Migraine: Genetic Variants and Clinical Phenotypes

Current Medicinal Chemistry ◽

10.2174/0929867325666180719120215 ◽

2019 ◽

Vol 26 (34) ◽

pp. 6207-6221 ◽

Cited By ~ 1

Author(s):

Innocenzo Rainero ◽

Alessandro Vacca ◽

Flora Govone ◽

Annalisa Gai ◽

Lorenzo Pinessi ◽

...

Keyword(s):

Genetic Variants ◽

Association Studies ◽

Mthfr Gene ◽

Genome Wide Association Studies ◽

Clinical Phenotypes ◽

Network Analyses ◽

Genome Wide ◽

Genomic Studies ◽

The Common ◽

The Relationship

Migraine is a common, chronic neurovascular disorder caused by a complex interaction between genetic and environmental risk factors. In the last two decades, molecular genetics of migraine have been intensively investigated. In a few cases, migraine is transmitted as a monogenic disorder, and the disease phenotype cosegregates with mutations in different genes like CACNA1A, ATP1A2, SCN1A, KCNK18, and NOTCH3. In the common forms of migraine, candidate genes as well as genome-wide association studies have shown that a large number of genetic variants may increase the risk of developing migraine. At present, few studies investigated the genotype-phenotype correlation in patients with migraine. The purpose of this review was to discuss recent studies investigating the relationship between different genetic variants and the clinical characteristics of migraine. Analysis of genotype-phenotype correlations in migraineurs is complicated by several confounding factors and, to date, only polymorphisms of the MTHFR gene have been shown to have an effect on migraine phenotype. Additional genomic studies and network analyses are needed to clarify the complex pathways underlying migraine and its clinical phenotypes.

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A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution

Mycological Progress ◽

10.1007/s11557-021-01710-y ◽

2021 ◽

Vol 20 (7) ◽

pp. 889-904

Author(s):

M. Prieto ◽

Javier Etayo ◽

I. Olariaga

Keyword(s):

New Species ◽

Common Ancestor ◽

External Surface ◽

Evolutionary Relationships ◽

New Order ◽

Ancestral State ◽

Multigene Phylogeny ◽

State Reconstruction ◽

Distinct Structure ◽

Dark Violet

AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

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The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽

10.3390/genes12040483 ◽

2021 ◽

Vol 12 (4) ◽

pp. 483

Author(s):

Wen-Juan Ma ◽

Paris Veltsos

Keyword(s):

Sex Determination ◽

Sex Chromosomes ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Comparative Genomic ◽

Ancestral State ◽

Heteromorphic Sex Chromosomes ◽

Genomic Studies ◽

Evolutionary Trajectories ◽

Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

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