Mosaic evolution in the middle Miocene planktonic foraminifera Fohsella lineage

Paleobiology ◽  
2018 ◽  
Vol 44 (2) ◽  
pp. 263-272
Author(s):  
Weimin Si ◽  
William A. Berggren ◽  
Marie-Pierre Aubry
Keyword(s):  
Evolutionary History ◽  
Middle Miocene ◽  
Planktonic Foraminifera ◽  
Phenotypic Traits ◽  
Geographic Ranges ◽  
History Of ◽  
Morphologic Evolution ◽  
Coiling Direction ◽  
Directional Trend ◽  
Selection Of

AbstractRecent studies have shown that modes of evolution, namely directional trend, random walk, and stasis, vary across morphologic traits and over the geographic range of a taxon. If so, is it possible that our interpretation of evolutionary modes is actually driven by our selection of traits in a study? In an attempt to answer this question, we have restudied the middle Miocene planktonic foraminifera Fohsella lineage, an iconic example of gradual morphologic evolution. In contrast to previous studies that have focused on the gross morphology as embodied by the edge view of tests, we analyze here multiple phenotypic traits chosen because their biologic and ecologic significance is well understood in living populations. We find that traits in the lineage did not evolve in concert. The timing and geographic pattern of changes in shape, coiling direction, size, and ecology were different. The evolution of this lineage is a mosaic combination of different evolutionary modes for different traits. We suggest that overemphasis on the evolution of some single trait, such as the edge-view outline, from narrow geographic ranges has significantly underestimated the dynamic evolutionary history of this group.

Evolution Caught in the Act: Evidence from Microfossil Morphology

2002 ◽  
Vol 11 ◽  
pp. 127-138
Author(s):  
Stephen J. Culver
Keyword(s):  
Deep Sea ◽  
Fossil Record ◽  
Evolutionary History ◽  
Planktonic Foraminifera ◽  
Extensive Study ◽  
Calcareous Nannoplankton ◽  
Great Abundance ◽  
Morphologic Evolution ◽  
The Subject ◽  
Hand Sample

Microfossils are of prime importance in documenting patterns of evolution due to their great abundance (often tens of thousands to millions of specimens in a hand sample) and widespread distribution (in both time and space) in the fossil record. The term “microfossil” is often used for paleontological material that requires a microscope for its study, no matter what its biological affinities. For the purposes of this article we will be looking at the remains of protists (single-celled organisms). The several examples I discuss in this chapter are of three groups of planktonic (floating) protists: the calcareous nannoplankton (tiny plant-like protists whose single cell is covered in minute calcitic scales), the radiolaria (animal-like protists with siliceous shells), and the planktonic foraminifera (animal-like protists with calcitic shells). These organisms have been the subject of extensive study because the material from which they are often extracted, cores of deep-sea sediments, are usually comprised of a more complete sedimentological record (i.e., have fewer breaks) than shallow shelf deposits. Hypotheses of evolutionary history have been constructed for many groups (lineages) of microfossils using specimens from deep-sea cores. Ancestor-descendent relationships have been recognized by tracking shape and form (morphologic) changes through time. This approach to reconstruction of evolutionary history provides an empirical record of morphologic evolution; that is, a record based on observations.

scholarly journals Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes

2020 ◽  
Vol 37 (12) ◽  
pp. 3563-3575 ◽  
Author(s):  
Juan David Bayona-Serrano ◽  
Vincent Louis Viala ◽  
Rhett M Rautsaw ◽  
Tristan D Schramer ◽  
Gesiele A Barros-Carvalho ◽  
...  
Keyword(s):  
Snake Venom ◽  
Evolutionary History ◽  
Phenotypic Traits ◽  
Gene Duplications ◽  
Snake Venoms ◽  
Venom Component ◽  
History Of ◽  
Biochemical Components ◽  
Functional Analyses ◽  
Specific Sequences

Abstract Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an “SVMP-like” function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.

The Early Evolutionary History of Planktonic Foraminifera

1997 ◽  
Author(s):  
M. K. BouDagher-Fadel ◽  
F. T. Banner ◽  
J. E. Whittaker
Keyword(s):  
Evolutionary History ◽  
Planktonic Foraminifera ◽  
History Of

scholarly journals Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas

2020 ◽  
Vol 37 (6) ◽  
pp. 1577-1592 ◽  
Author(s):  
XiaoYun Wang ◽  
Dan Liang ◽  
Wei Jin ◽  
MingKun Tang ◽  
Shalayiwu ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Evolutionary History ◽  
Middle Miocene ◽  
Divergence Time ◽  
Sister Group ◽  
Last Common Ancestor ◽  
Center Of Origin ◽  
History Of ◽  
Phylogenomic Analyses ◽  
Alpine Environments

Abstract Pikas are widely distributed in the Northern Hemisphere and are highly adapted to cold and alpine environments. They are one of the most complex and problematic groups in mammalian systematics, and the origin and evolutionary history of extant pikas remain controversial. In this study, we sequenced the whole coding sequences of 105 pika samples (29 named species and 1 putative new species) and obtained DNA data for more than 10,000 genes. Our phylogenomic analyses recognized four subgenera of extant pikas: Alienauroa, Conothoa, Ochotona, and Pika. The interrelationships between the four subgenera were strongly resolved as (Conothoa, (Alienauroa, (Ochotona, Pika))), with the mountain group Conothoa being the sister group of all other pikas. Our divergence time and phylogeographic analyses indicated that the last common ancestor of extant pikas first occurred on in the middle Miocene, ∼14 Ma. The emergence of opportunities related to the climate, food supply, and spreading paths in concert promoted the dispersal of pikas from the Qinghai-Tibetan Plateau (QTP) to other parts of Eurasia and North America. We found that the genes that were positively selected in the early evolution of pikas were most concentrated in functional categories related to cold tolerance. These results suggest that the QTP may have served as a training ground for cold tolerance in early pikas, which gives pikas a great advantage when the climate continued to cool after the middle Miocene. Our study highlights the importance of the QTP as a center of origin for many cold-adapted animals.

scholarly journals Automated selection of homologs to track the evolutionary history of proteins

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Pablo Mier ◽  
Antonio J. Pérez-Pulido ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Evolutionary History ◽  
History Of ◽  
Selection Of

Evolution Caught in the Act: Evidence from Microfossil Morphology

1999 ◽  
Vol 9 ◽  
pp. 155-170
Author(s):  
Stephen J. Culver
Keyword(s):  
Deep Sea ◽  
Fossil Record ◽  
Evolutionary History ◽  
Planktonic Foraminifera ◽  
Extensive Study ◽  
Calcareous Nannoplankton ◽  
Great Abundance ◽  
Morphologic Evolution ◽  
The Subject ◽  
Hand Sample

Microfossils are of prime importance in documenting patterns of evolution due to their great abundance (often tens of thousands to millions of specimens in a hand sample) and widespread distribution (in both time and space) in the fossil record. The term “microfossil” is often used for paleontological material that requires a microscope for its study, no matter what its biological affinities. For the purposes of this article we will be looking at the remains of protists (single-celled organisms). The several examples I discuss in this chapter are of three groups of planktonic (floating) protists, the calcareous nannoplankton (tiny plant-like protists whose single cell is covered in minute calcitic scales), the radiolaria (animal-like protists with siliceous shells) and the planktonic foraminifera (animal-like protists with calcitic shells). These organisms have been the subject of extensive study because the material from which they are often extracted, cores of deep-sea sediments, are usually comprised of a more complete sedimentological record (i.e., fewer breaks) than shallow shelf deposits. Hypotheses of evolutionary history have been constructed for many groups (lineages) of microfossils using specimens from deep-sea cores. Ancestor-descendent relationships have been recognized by tracking shape and form (morphologic) changes through time. This approach to reconstruction of evolutionary history provides an empirical record of morphologic evolution; that is, a record based on observations.

scholarly journals The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1032 ◽  
Author(s):  
Yulia Vakulenko ◽  
Andrei Deviatkin ◽  
Alexander Lukashev
Keyword(s):  
Evolutionary History ◽  
Large Datasets ◽  
Sequencing Errors ◽  
Sample Bias ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
History Of ◽  
Sequence Position ◽  
Annotation Errors ◽  
Selection Of

Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.

The Early Evolutionary History of Planktonic Foraminifera

1998 ◽  
Vol 44 (2) ◽  
pp. 207 ◽  
Author(s):  
Felix Gradstein ◽  
M. K. Boudagher-Fadel ◽  
E. T. Banner ◽  
J. E. Whittaker
Keyword(s):  
Evolutionary History ◽  
Planktonic Foraminifera ◽  
History Of
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