scholarly journals Reticulate evolution in a neutral model: speciation, extinctions, and hybridizations

2021 ◽  
Author(s):  
Larissa Lubiana Botelho ◽  
Flavia Maria Darcie Marquitti ◽  
Marcus A. M. de Aguiar
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Process ◽  
Abundant Species ◽  
Reticulate Evolution ◽  
Small Population ◽  
Spatial Proximity ◽  
Extinction Rate ◽  
Neutral Model ◽  
Hybridization Rate ◽  
Speciation Event

Evolution is usually pictured as a tree where ancient species branch into new ones and eventually disappear. In this simplified view, the balance between speciation and extinction fully determines the diversity of life. Hybridization, however, introduces another level of complexity, allowing neighboring branches of the tree to interact, mixing their genetic content. This generates further diversity leading to reticulated phylogenetic trees. In this paper we study processes of speciation, extinction and hybridization using a genetically and spatially explicit neutral model of diversification. Speciation, extinction and hybridization events are tracked throughout the evolutionary process leading to complete and exact phylogenetic trees. We found that genome size played a key role in these processes, increasing the extinction rate and decreasing the hybridization rate. In our simulations, hybridization after one speciation event occurred throughout the evolutionary process but hybridization after two speciation events was only observed during the initial radiation. Most hybridization occurred between relatively abundant species, discarding lack of sexual partners or small population sizes as potential causes. We found that hybridization occurred mostly because of opportunity (genetic similarity and spatial proximity) between recently branched species, when the number of accumulated mutations is not yet too large.

scholarly journals Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

2000 ◽  
Vol 64 (1) ◽  
pp. 202-236 ◽  
Author(s):  
Carl R. Woese ◽  
Gary J. Olsen ◽  
Michael Ibba ◽  
Dieter Söll
Keyword(s):  
Genetic Code ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Evolutionary Process ◽  
Group Iv ◽  
Evolutionary Relationships ◽  
Evolutionary Stage ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
The Individual

SUMMARY The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.

scholarly journals Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus

2014 ◽  
Vol 95 (12) ◽  
pp. 2734-2747 ◽  
Author(s):  
Jana Sachsenröder ◽  
Anne Braun ◽  
Patrycja Machnowska ◽  
Terry Fei Fan Ng ◽  
Xutao Deng ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Enteric Viruses ◽  
Abundant Species ◽  
Human Virus ◽  
Rotavirus A ◽  
Zoonotic Risk ◽  
Group A ◽  
Circular Ssdna ◽  
Wild Rats ◽  
Ssdna Viruses

Rats are known as reservoirs and vectors for several zoonotic pathogens. However, information on the viruses shed by urban wild rats that could pose a zoonotic risk to human health is scare. Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids. The determined faecal viromes of rats consisted of a variety of known and unknown viruses, and were highly variable among the individuals. Members of the families Parvoviridae and Picobirnaviridae represented the most abundant species. Novel picornaviruses, bocaviruses, sapoviruses and stool-associated circular ssDNA viruses were identified, which showed only low sequence identity to known representatives of the corresponding taxa. In addition, noroviruses and rotaviruses were detected as potential zoonotic gastroenteritis viruses. However, partial-genome sequence analyses indicated that the norovirus was closely related to the recently identified rat norovirus and the rotavirus B was closely related to the rat rotavirus strain IDIR; both viruses clustered separately from respective human virus strains in phylogenetic trees. In contrast, the rotavirus A sequences showed high identity to human and animal strains. Analysis of the nearly complete genome of this virus revealed the known genotypes G3, P[3] and N2 for three of the genome segments, whereas the remaining eight genome segments represented the novel genotypes I20–R11–C11–M10–A22–T14–E18–H13. Our results indicated a high heterogeneity of enteric viruses present in urban wild rats; their ability to be transmitted to humans remains to be assessed in the future.

scholarly journals Simultaneous Bayesian inference of phylogeny and molecular coevolution

2019 ◽  
Vol 116 (11) ◽  
pp. 5027-5036 ◽  
Author(s):  
Xavier Meyer ◽  
Linda Dib ◽  
Daniele Silvestro ◽  
Nicolas Salamin
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Organic Molecules ◽  
Evolutionary Process ◽  
Protein Coding ◽  
Rrna Molecule ◽  
Shared Ancestry ◽  
History Of ◽  
Dependent Site ◽  
Synthetic Datasets

Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Conversely, disregarding the dependent evolution of sites when studying the history of genes negatively impacts the accuracy of the inferred phylogenetic trees. Although molecular coevolution and phylogenetic history are interdependent, analyses of the two processes are conducted separately, a choice dictated by computational convenience, but at the expense of accuracy. We present a Bayesian method and associated software to infer how many and which sites of an alignment evolve according to an independent or a pairwise dependent evolutionary process, and to simultaneously estimate the phylogenetic relationships among sequences. We validate our method on synthetic datasets and challenge our predictions of coevolution on the 16S rRNA molecule by comparing them with its known molecular structure. Finally, we assess the accuracy of phylogenetic trees inferred under the assumption of independence among sites using synthetic datasets, the 16S rRNA molecule and 10 additional alignments of protein-coding genes of eukaryotes. Our results demonstrate that inferring phylogenetic trees while accounting for dependent site evolution significantly impacts the estimates of the phylogeny and the evolutionary process.

The Gene and Gene Expression (GAGE) Species Concept: An Universal Approach for All Eukaryotic Organisms

2020 ◽  
Vol 69 (5) ◽  
pp. 1033-1038
Author(s):  
Bernhard Seifert
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Dna ◽  
Species Concept ◽  
Cluster Formation ◽  
Reticulate Evolution ◽  
Evolutionary Divergence ◽  
Character System ◽  
Cytoplasmic Dna

Abstract The Gene and Gene Expression (GAGE) species concept, a new version of the Pragmatic Species Concept of Seifert (2014), is proposed as a concept applicable to any described recent or fossil eukaryotic organism independent from its mode of reproduction or evolutionary history. In addition to presenting the concept as such, the article also provides practical recommendations for taxonomists when delimiting species and describing taxa. The wording of the new concept contains a heading core sentence plus five attached sentences addressing essential conditions for its translation into a sound taxonomic practice: “Species are separable clusters that have passed a threshold of evolutionary divergence and are exclusively defined by nuclear DNA sequences and/or their expression products. Nuclear DNA sequences and their expression products are different character systems but have a highly correlated indicative function. Character systems with the least risk of epigenetic or ontogenetic modification have superior indicative value when conflicts between character systems of integrative studies arise. All character systems have to be described by an adequate numerics allowing cluster formation and determination of thresholds. Thresholds for each character system should be fixed by consensus among the experts under the principle of avoiding oversplitting or lumping. Clusters must not be the expression of intraspecific polymorphism.” Recognizing the distortions and conflicts caused to taxonomy through barcoding or through assessment on the basis of association with other organisms, the GAGE species concept strongly downgrades the use of cytoplasmic DNA of endosymbiotic origin (mtDNA, cpDNA) or DNA of closely associated microbes (e.g., Wolbachia bacteria) for final taxonomic decision-making. Recognizing the distortion of phylogenies by the high frequency of reticulate evolution, it is argued that delimiting and naming species has to be separated from constructing bifurcating phylogenetic trees. [Cytoplasmic DNA; lumping; nuclear DNA; numeric taxonomy; oversplitting; reticulate evolution.]

scholarly journals The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4916 ◽  
Author(s):  
Narjara Lopes de Abreu ◽  
Ruy José Válka Alves ◽  
Sérgio Ricardo Sodré Cardoso ◽  
Yann J.K. Bertrand ◽  
Filipe Sousa ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Diploid Species ◽  
Distinct Species ◽  
Reticulate Evolution ◽  
Model Organisms ◽  
Current Evidence ◽  
Genomic Libraries ◽  
Coding Regions ◽  
Phylogenetic Implications

BackgroundCurrent evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found inPolystachyaHook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic.MethodsWe generated the complete plastid genome of 40 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the plastid genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analyzing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops).ResultsWe retrieved 131,214 bp, including coding and non-coding regions of the plastid genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species.DiscussionOur results indicate that using the entire plastid genome is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions ofPolystachya concreta(Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy.Polystachya estrellensisRchb.f. can be considered a genetically distinct species fromP. concretaandP. foliosa(Lindl.) Rchb.f., but the delimitation ofP. concretaremains uncertain. Our study shows that NGS provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.

Genetics and the conservation of Australian birds

1997 ◽  
Vol 3 (3) ◽  
pp. 306 ◽  
Author(s):  
Janette Norman ◽  
Les Christidis
Keyword(s):  
Wildlife Management ◽  
Molecular Genetic ◽  
Taxonomic Diversity ◽  
Abundant Species ◽  
Small Population ◽  
Careful Consideration ◽  
Population Variation ◽  
Bird Populations ◽  
Molecular Studies ◽  
Breeding Programmes

Molecular genetic techniques can be used to address a wide array of contemporary conservation problems encountered in the management of captive and wild bird populations. Most applications pertain to issues relevant to the management of populations or species. These range from sex identification in breeding programmes involving species in which the sexes are phenotypically monomorphic, to the identification of taxonomic diversity at the level of species, subspecies and populations. Additionally, comparative analyses of intra-population variation provide a means of identifying populations more at risk from inbreeding and a loss of diversity. This provides a more tractable approach for the conservation and management of genetic diversity than derived from theoretical considerations about the genetic consequences of small population size. A recent development away from these traditional species-based approaches is the use of information revealed by studies of comparative phylogeography to address issues relevant to the management of entire communities and ecosystems. Molecular studies of non-threatened taxa are also an important tool for wildlife management. Nonthreatened species can be used as indicators of regional biodiversity or to provide information which will assist in the conservation of a closely related species. Molecular studies of apparently widespread and abundant species may also reveal previously unrecognized taxonomic diversity of significance for conservation. With the impressive array of molecular tools now available for addressing issues in conservation biology it is important that they not be applied indiscriminately. Careful consideration needs to be given to the specific needs of wildlife management and the appropriateness of genetic studies should be evaluated on a case by case basis. In some instances molecular studies may not be warranted, providing little information beyond that which has been obtained from ecological and demographic studies or contained in traditional taxonomies.

scholarly journals Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

2016 ◽  
Vol 2 (4) ◽  
pp. e1501385 ◽  
Author(s):  
Bastien Llamas ◽  
Lars Fehren-Schmitz ◽  
Guido Valverde ◽  
Julien Soubrier ◽  
Swapan Mallick ◽  
...  
Keyword(s):  
Native Americans ◽  
Small Population ◽  
Phylogeographic Structure ◽  
Data Sets ◽  
Extinction Rate ◽  
Low Genetic Diversity ◽  
Coalescent Simulations ◽  
Peopling Of The Americas ◽  
European Colonization ◽  
Limited Gene Flow

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

Molecular evolution of serine protease and its inhibitor with special reference to domain evolution

1994 ◽  
Vol 344 (1310) ◽  
pp. 411-415 ◽  
Keyword(s):  
Special Reference ◽  
Serine Protease ◽  
Serine Proteases ◽  
Phylogenetic Trees ◽  
Evolutionary Process ◽  
Life Forms ◽  
Functional Domains ◽  
Functional Domain ◽  
Evolutionary Analysis ◽  
Domain Evolution

The evolution of serine protease and its inhibitor are discussed with special reference to domain evolution. It is now known that most proteins are composed of more than one functional domain. Because serine proteases such as urokinase and plasminogen are made of various functional domains, these proteins are typical examples of the so-called mosaic proteins. When Kringle domains in serine proteases and a Kunitz-type protease inhibitor domain in the amyloid B precursor protein in Alzheimer’s disease patients were examined by the molecular evolutionary analysis, the phylogenetic trees constructed showed that these functional domains had undergone dynamic changes in the evolutionary process. In particular, these domains are evolutionarily movable. Thus, it is concluded that various functional domains evolved independently of each other and that they have been shuffled to create the existent mosaic proteins. This conclusion leads us to the reasonable speculation that those functional domains must have been minigenes possibly at the time of primordial life or the origin of life. We call these minigenes ‘ancestral minigenes’. Every effort should be made to answer the question about the minimum set of ancestral minigenes that must have existed and must have been needed for maintaining life forms. The DNA sequence database is useful for making attempts to answer such difficult but significant questions.

scholarly journals Anatomical Variation, Hominins, Species, and Self-Domestication

OBM Genetics ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 1-1
Author(s):  
Niccolo Caldararo ◽  
Keyword(s):  
Phylogenetic Trees ◽  
Brain Size ◽  
Anatomical Variation ◽  
Cognitive Activity ◽  
Evolutionary Process ◽  
Gene Clusters ◽  
Upper Paleolithic ◽  
Ice Age ◽  
Middle Pleistocene ◽  
Mathematical Methods

The evolution of hominins, members of the zoological tribe Hominini, has been a much-studied topic, and the construction of phylogenetic trees has been the key method in molecular evolutionary studies. How scientists determine the phylogenetic trees are governed by the assumptions they place on the construction of similarities and differences in morphological traits, the differences in the number of base pairs in the genomes, and the number of similar gene clusters that code for traits (haplotypes) or are error sequences (SNPs). Among the several methods employed for the construction of a phylogenetic tree, mathematical methods (utilized for sorting data, including fabrication of algorithms) are the most significant ones; also, the nature of population structuring plays an important role in the evolutionary process. In this paper, I will not only describe the drawbacks of current assumptions in hominin evolution during the Middle Pleistocene era (based on fossil evidence) but also the aspects of brain evolution and the self-domestication of our species. The evolution of the brain is usually associated with an increase in neurons and other types of cells associated with signal processing (connectivity) and memory. Assessing actual neuron counts in fossils is challenging; moreover, new research has shown decreased neuron numbers in the neocortex and demonstrated large counts in the cerebellum, leading to a decreased focus on brain size. The idea of increased brain size in the Pleistocene era without a substantial increase in the evidence of cognitive activity in complex behavior residues might be explained by increased myelination to provide additional insulation in Ice Age conditions and faster transition of signals due to increased competition for reduced food supplies. Other cold-adaptation features can also be noted. Such a model can provide a new approach to assess the apparent brain size reduction in the Upper Paleolithic period.

Evidence of inter-sectional chloroplast capture in Corymbia among sections Torellianae and Maculatae

2018 ◽  
Vol 66 (5) ◽  
pp. 369 ◽  
Author(s):  
Adam Healey ◽  
David J. Lee ◽  
Agnelo Furtado ◽  
Robert J. Henry
Keyword(s):  
Phylogenetic Trees ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Wide Crosses ◽  
Chloroplast Capture ◽  
Chloroplast Genomes ◽  
External Transcribed Spacer ◽  
Corymbia Citriodora ◽  
Generation Sequencing

Chloroplast capture through hybridisation and introgression is well described within Eucalyptus. Despite the propensity of the Corymbia genus (eucalypts) to form hybrids from wide crosses, description of chloroplast capture in Corymbia has, until recently, been limited. In this study our aim was to investigate evidence of intersectional chloroplast capture between sections Torellianae and Maculatae. Using whole-genome next-generation sequencing data, the complete chloroplast genomes were assembled from four Corymbia taxa: Corymbia citriodora subspecies citriodora (Hook.) K.D.Hill & L.A.S.Johnson, Corymbia citriodora subspecies variegata (F.Muell.) A.R.Bean & M.W.McDonald, Corymbia henryi (S.T.Blake) K.D.Hill & L.A.S.Johnson, and Corymbia torelliana (F.Muell.) K.D.Hill & L.A.S.Johnson, represented by eight genotypes. Phylogenetic analysis and comparison among Corymbia chloroplast genomes and nuclear external transcribed spacer (ETS) sequences revealed chloroplast capture among Corymbia species across distinct sections Torellianae and Maculatae within subgenus Blakella. Reticulate evolution, along with Eucalyptus, likely extends into Corymbia as evidenced by incongruent plastid and nuclear phylogenetic trees, suggestive of its importance of hybridisation and introgression during the evolution of eucalypts.

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