scholarly journals Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Guillaume Morel ◽  
Lieven Sterck ◽  
Dominique Swennen ◽  
Marina Marcet-Houben ◽  
Djamila Onesime ◽  
...  
Keyword(s):  
Plant Material ◽  
Evolutionary History ◽  
Geotrichum Candidum ◽  
Evolutionary Relationships ◽  
Specific Gene ◽  
Gene Retention ◽  
History Of ◽  
Differential Gene ◽  
Phenotypic Specificity ◽  
Similar Gene

Abstract The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.

scholarly journals Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

2019 ◽  
Vol 11 (9) ◽  
pp. 2531-2541 ◽  
Author(s):  
Valeria Mateo-Estrada ◽  
Lucía Graña-Miraglia ◽  
Gamaliel López-Leal ◽  
Santiago Castillo-Ramírez
Keyword(s):  
Evolutionary History ◽  
Ad Hoc ◽  
Acinetobacter Calcoaceticus ◽  
Recent Attempt ◽  
Evolutionary Relationships ◽  
Closely Related Species ◽  
Acinetobacter Baumannii Complex ◽  
History Of ◽  
To Come ◽  
Clear Cases

Abstract The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

VERIFICATION OF PHYLOGENETIC INFERENCE PROGRAMS USING METAMORPHIC TESTING

2011 ◽  
Vol 09 (06) ◽  
pp. 729-747 ◽  
Author(s):  
MD. SHAIK SADI ◽  
FEI-CHING KUO ◽  
JOSHUA W. K. HO ◽  
MICHAEL A. CHARLESTON ◽  
T. Y. CHEN
Keyword(s):  
Amino Acids ◽  
Software Testing ◽  
Evolutionary History ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Testing Technique ◽  
Metamorphic Testing ◽  
History Of ◽  
Scoring Algorithms

Many phylogenetic inference programs are available to infer evolutionary relationships among taxa using aligned sequences of characters, typically DNA or amino acids. These programs are often used to infer the evolutionary history of species. However, in most cases it is impossible to systematically verify the correctness of the tree returned by these programs, as the correct evolutionary history is generally unknown and unknowable. In addition, it is nearly impossible to verify whether any non-trivial tree is correct in accordance to the specification of the often complicated search and scoring algorithms. This difficulty is known as the oracle problem of software testing: there is no oracle that we can use to verify the correctness of the returned tree. This makes it very challenging to test the correctness of any phylogenetic inference programs. Here, we demonstrate how to apply a simple software testing technique, called Metamorphic Testing, to alleviate the oracle problem in testing phylogenetic inference programs. We have used both real and randomly generated test inputs to evaluate the effectiveness of metamorphic testing, and found that metamorphic testing can detect failures effectively in faulty phylogenetic inference programs with both types of test inputs.

scholarly journals Deep Ancestry of Orthologs and a Theoretical, Gradualist Perspective for the Formation of the LUCA’s (Last Universal Common Ancestor) Genome

2018 ◽  
Author(s):  
Francisco Prosdocimi ◽  
Sávio Torres de Farias
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Deep Understanding ◽  
Sister Group ◽  
Recent Common Ancestor ◽  
Evolutionary Relationships ◽  
Universal Common Ancestor ◽  
History Of ◽  
Group Relationships ◽  
Level Of Understanding

Genes and gene trees have been extensively used to study the evolutionary relationships among populations, species, families and higher systematic clades of organisms. This brought modern Biology into a sophisticated level of understanding about the evolutionary relationships and diversification patterns that happened along the entire history of organismal evolution in Earth. Genes however have not been placed in the center of questions when one aims to unravel the evolutionary history of genes themselves. Thus, we still ignore whether Insulin share a more recent common ancestor to Hexokinase or DNA polymerase. This brought modern Genetics into a very poor level of understanding about sister group relationships that happened along the entire evolutionary history of genes. Many conceptual challenges must be overcome to allow this broader comprehension about gene evolution. Here we aim to clear the intellectual path in order to provide a fertile research program that will help geneticists to understand the deep ancestry and sister group relationships among different gene families (or orthologs). We aim to propose methods to study gene formation starting from the establishment of the genetic code in pre-cellular organisms like the FUCA (First Universal Common Ancestor) until the formation of the highly complex genome of LUCA (Last UCA), that harbors hundreds of genes families working coordinated into a cellular organism. The deep understanding of ancestral relationships among orthologs will certainly inspire biotechnological and biomedical approaches and allow a deep understanding about how Darwinian molecular evolution operates inside cells and before the appearance of cellular organisms.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Alex Dornburg ◽  
Thomas J. Near
Keyword(s):  
Paradigm Shift ◽  
Evolutionary History ◽  
First Century ◽  
Evolutionary Relationships ◽  
Annual Review ◽  
Publication Date ◽  
Living Fossils ◽  
Actinopterygian Fishes ◽  
History Of ◽  
Phylogenetic Perspective

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Reconstructing the past

2019 ◽  
pp. 214-249
Author(s):  
Glenn-Peter Sætre ◽  
Mark Ravinet
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Sequence Data ◽  
Modern Human ◽  
Evolutionary Relationships ◽  
Human Populations ◽  
Gene Trees ◽  
Exciting Field ◽  
History Of ◽  
Life On Earth

How can genetics and genomics be used to understand the evolutionary history of organisms? This chapter focuses on such methods. First, the field of phylogenetics is introduced, as a way to visualize and quantify the evolutionary relationships among species. The chapter outlines how we go from aligning DNA sequence data to building gene trees and we argue that “tree-thinking” is fundamentally important for understanding evolution. The chapter also goes beyond phylogenetic trees to focus on phylogeography, i.e. the understanding of evolutionary relationships in a spatial context. More recently, the explosion of genomic data from ancient and modern human populations has made this an extremely exciting field which is transforming our understanding of our own evolutionary history. Before that, though, the chapter reviews how modern phylogenetics has arisen from historical efforts to classify life on Earth.

scholarly journals Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation

2015 ◽  
Vol 2 (9) ◽  
pp. 150196 ◽  
Author(s):  
Jessica A. Goodheart ◽  
Adam L. Bazinet ◽  
Allen G. Collins ◽  
Michael P. Cummings
Keyword(s):  
Evolutionary History ◽  
Evolutionary Relationships ◽  
Phylogenetic Hypothesis ◽  
Rna Seq ◽  
Initial Investigation ◽  
Sequence Read Archive ◽  
History Of ◽  
Phylogenetic Hypotheses ◽  
Transcript Assembly ◽  
Ncbi Sequence Read Archive

Cladobranchia (Gastropoda: Nudibranchia) is a diverse (approx. 1000 species) but understudied group of sea slug molluscs. In order to fully comprehend the diversity of nudibranchs and the evolution of character traits within Cladobranchia, a solid understanding of evolutionary relationships is necessary. To date, only two direct attempts have been made to understand the evolutionary relationships within Cladobranchia, neither of which resulted in well-supported phylogenetic hypotheses. In addition to these studies, several others have addressed some of the relationships within this clade while investigating the evolutionary history of more inclusive groups (Nudibranchia and Euthyneura). However, all of the resulting phylogenetic hypotheses contain conflicting topologies within Cladobranchia. In this study, we address some of these long-standing issues regarding the evolutionary history of Cladobranchia using RNA-Seq data (transcriptomes). We sequenced 16 transcriptomes and combined these with four transcriptomes from the NCBI Sequence Read Archive. Transcript assembly using Trinity and orthology determination using H a MS t R yielded 839 orthologous groups for analysis. These data provide a well-supported and almost fully resolved phylogenetic hypothesis for Cladobranchia. Our results support the monophyly of Cladobranchia and the sub-clade Aeolidida, but reject the monophyly of Dendronotida.

scholarly journals Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales

2018 ◽  
Author(s):  
Jacob M. Musser ◽  
Günter P. Wagner ◽  
Cong Liang ◽  
Frank A. Stabile ◽  
Alison Cloutier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary History ◽  
Theropod Dinosaurs ◽  
Skin Appendages ◽  
Key Factor ◽  
History Of ◽  
Tetrapod Evolution ◽  
Similar Gene ◽  
Complex Evolutionary History

AbstractBirds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.

scholarly journals Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

2020 ◽  
Vol 6 (11) ◽  
pp. eaay0456
Author(s):  
Michael V. Westbury ◽  
Stefanie Hartmann ◽  
Axel Barlow ◽  
Michaela Preick ◽  
Bogdan Ridush ◽  
...  
Keyword(s):  
Gene Flow ◽  
Late Pleistocene ◽  
Evolutionary History ◽  
Population Level ◽  
Evolutionary Relationships ◽  
Spotted Hyena ◽  
High Frequencies ◽  
History Of ◽  
The Cross ◽  
Complex Evolutionary History

The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.

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