Evolution of disintegrin cysteine-rich and mammalian matrix-degrading metalloproteinases: Gene duplication and divergence of a common ancestor rather than convergent evolution

1996 ◽  
Vol 43 (3) ◽  
pp. 263-269 ◽  
Author(s):  
Ana M. Moura-da-Silva ◽  
R. David G. Theakston ◽  
Julian M. Cramptonl
Keyword(s):  
Gene Duplication ◽  
Convergent Evolution ◽  
Common Ancestor

Biomineralization Processes

1989 ◽  
Author(s):  
Heinz A. Lowenstam ◽  
Stephen Weiner
Keyword(s):  
Continuous Spectrum ◽  
Convergent Evolution ◽  
Common Ancestor ◽  
External Medium ◽  
The Other ◽  
Mineral Formation ◽  
Mineralization Processes ◽  
Established Fact ◽  
Different Sources ◽  
Almost Continuous

The large number of different minerals formed by organisms from almost 50 different phyla described in Chapter 2 should in itself discourage anyone from searching for the mechanism of biomineralization. On the other hand, the survey of macromolecules used by many organisms to control mineralization (Chapter 2), even though limited primarily to carbonate- and phosphate-bearing mineralized hard parts, shows that similar and rather unusual acidic glycoproteins and proteoglycans are widely utilized in biomineralization. This raises the possibility that many organisms may have adopted common approaches or strategies for regulating mineral formation. We do not know whether this arose as a result of divergence from a common ancestor or is a product of convergent evolution in which many different phyla independently began utilizing similar macromolecules for controlling mineralization (see Chapter 12). Either way we view the diversity in biomineralization as the product of a very broad and almost continuous spectrum of processes that organisms use to control mineralization. This ranges from no apparent control at one end to, it seems, control over every detail at the other. However, this is achieved by a fairly limited number of different basic processes used in various combinations and ways to produce a unique final product. This last statement is, we readily admit at this point in time, more an act of faith than an established fact. In this chapter we will try to identify and/or speculate about some of these basic processes. We will draw upon material from many different sources, and, in particular, we will refer whenever possible to the more detailed descriptions of mineralization processes given in the chapters that follow. As a consequence, this chapter may also be used by the reader as a guide toward more discriminating reading on selected topics in the remainder of the book. The spectrum of biomineralization processes can in principle be easily divided into cases in which control is exercised in some way over mineralization and those in which it is not. In practice the differentiation is not that simple as all organisms do exercise some control at one level or another, even if it simply involves, for example, removing from the cell some undesirable metabolic end-product or ion that combines with another ion in the external medium and precipitates.

Evolution of Placental Function in Mammals: The Molecular Basis of Gas and Nutrient Transfer, Hormone Secretion, and Immune Responses

2012 ◽  
Vol 92 (4) ◽  
pp. 1543-1576 ◽  
Author(s):  
Anthony M. Carter
Keyword(s):  
Gene Duplication ◽  
Convergent Evolution ◽  
Globin Gene ◽  
Hormone Secretion ◽  
Human Leukocyte ◽  
Amino Acid Transporters ◽  
Placental Lactogens ◽  
Wide Range ◽  
Duplication Events ◽  
Range Of Functions

Placenta has a wide range of functions. Some are supported by novel genes that have evolved following gene duplication events while others require acquisition of gene expression by the trophoblast. Although not expressed in the placenta, high-affinity fetal hemoglobins play a key role in placental gas exchange. They evolved following duplications within the beta-globin gene family with convergent evolution occurring in ruminants and primates. In primates there was also an interesting rearrangement of a cassette of genes in relation to an upstream locus control region. Substrate transfer from mother to fetus is maintained by expression of classic sugar and amino acid transporters at the trophoblast microvillous and basal membranes. In contrast, placental peptide hormones have arisen largely by gene duplication, yielding for example chorionic gonadotropins from the luteinizing hormone gene and placental lactogens from the growth hormone and prolactin genes. There has been a remarkable degree of convergent evolution with placental lactogens emerging separately in the ruminant, rodent, and primate lineages and chorionic gonadotropins evolving separately in equids and higher primates. Finally, coevolution in the primate lineage of killer immunoglobulin-like receptors and human leukocyte antigens can be linked to the deep invasion of the uterus by trophoblast that is a characteristic feature of human placentation.

scholarly journals New Caledonian crows plan for specific future tool use

2020 ◽  
Vol 287 (1938) ◽  
pp. 20201490
Author(s):  
M. Boeckle ◽  
M. Schiestl ◽  
A. Frohnwieser ◽  
R. Gruber ◽  
R. Miller ◽  
...  
Keyword(s):  
Tool Use ◽  
Convergent Evolution ◽  
Food Item ◽  
Common Ancestor ◽  
Research Effort ◽  
Human Intelligence ◽  
Future Events ◽  
New Caledonian Crows ◽  
Future Task ◽  
The Right

The ability to plan for future events is one of the defining features of human intelligence. Whether non-human animals can plan for specific future situations remains contentious: despite a sustained research effort over the last two decades, there is still no consensus on this question. Here, we show that New Caledonian crows can use tools to plan for specific future events. Crows learned a temporal sequence where they were (a) shown a baited apparatus, (b) 5 min later given a choice of five objects and (c) 10 min later given access to the apparatus. At test, these crows were presented with one of two tool–apparatus combinations. For each combination, the crows chose the right tool for the right future task, while ignoring previously useful tools and a low-value food item. This study establishes that planning for specific future tool use can evolve via convergent evolution, given that corvids and humans shared a common ancestor over 300 million years ago, and offers a route to mapping the planning capacities of animals.

scholarly journals Prediction and Characterization of RXLR Effectors in Pythium Species

2019 ◽  
Author(s):  
Gan Ai ◽  
Kun Yang ◽  
Yuee Tian ◽  
Wenwu Ye ◽  
Hai Zhu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Plant Pathogens ◽  
Genome Rearrangement ◽  
Common Ancestor ◽  
De Novo ◽  
Protein Structures ◽  
Plant Diseases ◽  
Biocontrol Agents ◽  
Ecological Niches ◽  
Rxlr Effectors

AbstractBeing widely existed in oomycetes, the RXLR effector features conserved RXLR-dEER motifs in its N terminal. Every known Phytophthora or Hyaloperonospora pathogen harbors hundreds of RXLRs. In Pythium species, however, none of the RXLR effectors has been characterized yet. Here, we developed a stringent method for de novo identification of RXLRs and characterized 359 putative RXLR effectors from nine tested Pythium species. Phylogenetic analysis revealed a single superfamily formed by all oomycetous RXLRs, suggesting they descent from a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures and genome locations. In particular, the mosquito biological agent P. guiyangense contains a significantly larger RXLR repertoire than the other eight Pythium species examined, which may result from gene duplication and genome rearrangement events as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts from the vast majority of predicted RXLRs with some of them being induced at infection stages. One such RXLRs showed necrosis-inducing activity. Furthermore, all predicted RXLRs were cloned from two biocontrol agents P. oligandrum and P. periplocum. Three of them were found to encode effectors inducing defense response in Nicotiana benthamiana. Taken together, our findings represent the first complete synopsis of Pythium RXLR effectors, which provides critical clues on their evolutionary patterns as well as the mechanisms of their interactions with diverse hosts.Author summaryPathogens from the Pythium genus are widespread across multiple ecological niches. Most of them are soilborne plant pathogens whereas others cause infectious diseases in mammals. Some Pythium species can be used as biocontrol agents for plant diseases or mosquito management. Despite that phylogenetically close oomycete pathogens secrete RXLR effectors to enable infection, no RXLR protein was previously characterized in any Pythium species. Here we developed a stringent method to predict Pythium RXLR effectors and compared them with known RXLRs from other species. All oomycetous RXLRs form a huge superfamily, which indicates they may share a common ancestor. Our sequence analysis results suggest that the expansion of RXLR repertoire results from gene duplication and genome recombination events. We further demonstrated that most predicted Pythium RXLRs can be transcribed and some of them encode effectors exhibiting pathogenic or defense-inducing activities. This work expands our understanding of RXLR evolution in oomycetes in general, and provides novel insights into the molecular interactions between Pythium pathogens and their diverse hosts.

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

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.

scholarly journals An Alternative Molecular View of Evolution: How DNA was Altered over Geological Time

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 5081
Author(s):  
Fredric M. Menger
Keyword(s):  
Natural Selection ◽  
Complex Traits ◽  
Convergent Evolution ◽  
Common Ancestor ◽  
Cambrian Explosion ◽  
Natural Phenomena ◽  
Geological Time ◽  
Multiple Mutation ◽  
Total Lack ◽  
Physical Changes

Four natural phenomena are cited for their defiance of conventional neo-Darwinian analysis: human intelligence; cat domesticity; the Cambrian explosion; and convergent evolution. 1. Humans are now far more intelligent than needed in their hunting–gathering days >10,000 years ago. 2. Domestic cats evolved from wildcats via major genetic and physical changes, all occurring in less than 12,000 years. 3. The Cambrian explosion refers to the remarkable expansion of species that mystifies evolutionists, as there is a total lack of fossil evidence for precursors of this abundant new life. 4. Convergent evolution often involves formation of complex, multigene traits in two or more species that have no common ancestor. These four evolutionary riddles are discussed in terms of a proposed “preassembly” mechanism in which genes and gene precursors are collected silently and randomly over extensive time periods within huge non-coding sections of DNA. This is followed by epigenetic release of the genes, when the environment so allows, and by natural selection. In neo-Darwinism, macroevolution of complex traits involves multiple mutation/selections, with each of the resulting intermediates being more favorable to the species than the previous one. Preassembly, in contrast, invokes natural selection only after a partially or fully formed trait is already in place. Preassembly does not supplant neo-Darwinism but, instead, supplements neo-Darwinism in those important instances where the classical theory is wanting.

scholarly journals Evolution of the Heme Peroxidases of Culicidae (Diptera)

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Austin L. Hughes
Keyword(s):  
Amino Acid ◽  
Gene Duplication ◽  
Common Ancestor ◽  
Expression Patterns ◽  
Amino Acid Level ◽  
Recent Common Ancestor ◽  
Amino Acid Sequence Level ◽  
Most Recent Common Ancestor ◽  
High Level ◽  
Heme Peroxidases

Phylogenetic analysis of heme peroxidases (HPXs) of Culicidae and other insects revealed six highly conserved ancient HPX lineages, each of which originated by gene duplication prior to the most recent common ancestor (MRCA) of Hemimetabola and Holmetabola. In addition, culicid HPX7 and HPX12 arose by gene duplication after the MRCA of Culicidae and Drosophilidae, while HPX2 orthologs were not found in any other order analyzed except Diptera. Within Diptera, HPX2, HPX7, and HPX12 were relatively poorly conserved at the amino acid level in comparison to the six ancient lineages. The genome ofAnopheles gambiaeincluded genes ecoding five proteins (HPX10, HPX11, HPX13, HXP14, and HPX15) without ortholgs in other genomes analyzed. Overall, gene expression patterns did not seem to reflect phylogenetic relationships, but genes that evolved rapidly at the amino acid sequence level tended to have divergent expression patterns as well. The uniquely high level of duplication of HPXs inA. gambiaemay have played a role in coevolution with malaria parasites.

scholarly journals An insect-like mushroom body in a crustacean brain

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Gabriella Hannah Wolff ◽  
Hanne Halkinrud Thoen ◽  
Justin Marshall ◽  
Marcel E Sayre ◽  
Nicholas James Strausfeld
Keyword(s):  
Spatial Memory ◽  
Learning And Memory ◽  
Sensory Integration ◽  
Mushroom Body ◽  
Convergent Evolution ◽  
Visual Recognition ◽  
Common Ancestor ◽  
Mushroom Bodies ◽  
Morphological Criteria

Mushroom bodies are the iconic learning and memory centers of insects. No previously described crustacean possesses a mushroom body as defined by strict morphological criteria although crustacean centers called hemiellipsoid bodies, which serve functions in sensory integration, have been viewed as evolutionarily convergent with mushroom bodies. Here, using key identifiers to characterize neural arrangements, we demonstrate insect-like mushroom bodies in stomatopod crustaceans (mantis shrimps). More than any other crustacean taxon, mantis shrimps display sophisticated behaviors relating to predation, spatial memory, and visual recognition comparable to those of insects. However, neuroanatomy-based cladistics suggesting close phylogenetic proximity of insects and stomatopod crustaceans conflicts with genomic evidence showing hexapods closely related to simple crustaceans called remipedes. We discuss whether corresponding anatomical phenotypes described here reflect the cerebral morphology of a common ancestor of Pancrustacea or an extraordinary example of convergent evolution.

scholarly journals Reconstructing the evolutionary origins of extreme halophilic Archaeal lineages

2019 ◽  
Author(s):  
Yutian Feng ◽  
Uri Neri ◽  
Sean Gosselin ◽  
Artemis S. Louyakis ◽  
R. Thane Papke ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Common Ancestor ◽  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
Halophilic Archaea ◽  
Gene Families ◽  
Catalytic Subunits ◽  
Evolutionary Origins ◽  
Extremely Halophilic Archaea

AbstractInterest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; while the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the halobacteriales, and archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (unrelated groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the crenarchaeota, euryarchaeota, and the DPANN superphylum. In addition, we sampled and assembled 7 new representatives of the Nanohaloarchaea, from distinct geographic locations. Phylogenies derived from these data imply the highly conserved ATP synthase catalytic/non-catalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. This relationship, with strong support, was also observed for several other gene families. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum. We employed phylogenetic reconstruction, constrained topology tests, and gene concordance factors to explore the support for and against the monophyly of the Haloarchaea, Nanohaloarchaea, and Methanonatronarchaeia.

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