scholarly journals Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

2017 ◽  
Vol 4 (4) ◽  
pp. 160997 ◽  
Author(s):  
T. Cucchi ◽  
A. Mohaseb ◽  
S. Peigné ◽  
K. Debue ◽  
L. Orlando ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Temporal Dynamics ◽  
Phylogenetic Signal ◽  
Evolutionary Process ◽  
Archaeological Record ◽  
Motion Model ◽  
Geometric Morphometric ◽  
Spatial And Temporal Dynamics ◽  
History Of ◽  
Brownian Motion Model

The Plio–Pleistocene evolution of Equus and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the phylogenetic signal present in each tooth shape with an exome-wide phylogeny from 10 extant equine species. We estimated the strength of the phylogenetic signal using a Brownian motion model of evolution with multivariate K statistic, and mapped the dental shape along the molecular phylogeny using an approach based on squared-change parsimony. We found clear evidence for the relevance of dental phenotypes to accurately discriminate all modern members of the genus Equus and capture their phylogenetic relationships. These results are valuable for both palaeontologists and zooarchaeologists exploring the spatial and temporal dynamics of the evolutionary history of the horse family, up to the latest domestication trajectories of horses and donkeys.

A fossil record of land plant origins from charophyte algae

Science ◽  
2021 ◽  
Vol 373 (6556) ◽  
pp. 792-796 ◽  
Author(s):  
Paul K. Strother ◽  
Clinton Foster
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Land Plant ◽  
Fossil Plants ◽  
Fossil Plant ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Time Gap ◽  
Evolutionary Continuity

Molecular time trees indicating that embryophytes originated around 500 million years ago (Ma) during the Cambrian are at odds with the record of fossil plants, which first appear in the mid-Silurian almost 80 million years later. This time gap has been attributed to a missing fossil plant record, but that attribution belies the case for fossil spores. Here, we describe a Tremadocian (Early Ordovician, about 480 Ma) assemblage with elements of both Cambrian and younger embryophyte spores that provides a new level of evolutionary continuity between embryophytes and their algal ancestors. This finding suggests that the molecular phylogenetic signal retains a latent evolutionary history of the acquisition of the embryophytic developmental genome, a history that perhaps began during Ediacaran-Cambrian time but was not completed until the mid-Silurian (about 430 Ma).

scholarly journals Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jiguang Wang ◽  
Hossein Khiabanian ◽  
Davide Rossi ◽  
Giulia Fabbri ◽  
Valter Gattei ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Evolutionary History ◽  
Directed Graphs ◽  
Evolutionary Process ◽  
Genetic Alterations ◽  
Lymphocytic Leukemia ◽  
Cross Sectional ◽  
History Of ◽  
Evolutionary Paths ◽  
Clonal Replacement

Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

scholarly journals Belowground Carbohydrate Reserves of Mature Southern Pines Reflect Seedling Strategy to Evolutionary History of Disturbance

Forests ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 653 ◽  
Author(s):  
Joshua Mims ◽  
Joseph O’Brien ◽  
Doug Aubrey
Keyword(s):  
Evolutionary History ◽  
Temporal Dynamics ◽  
Pinus Palustris ◽  
Life History Stage ◽  
Southern Pine ◽  
Mature Trees ◽  
Carbohydrate Reserves ◽  
Selective Pressures ◽  
Southern Pines ◽  
History Of

Carbohydrate reserves provide advantages for mature trees experiencing frequent disturbances; however, it is unclear if selective pressures operate on this characteristic at the seedling or mature life history stage. We hypothesized that natural selection has favored carbohydrate reserves in species that have an evolutionary history of frequent disturbance and tested this using three southern pine species that have evolved across a continuum of fire frequencies. Longleaf pine (Pinus palustris) roots exhibited higher maximum starch concentrations than slash (P. elliottii) and loblolly (P. taeda), which were similar. Longleaf also relied on starch reserves in roots more than slash or loblolly, depleting 64, 41, and 23 mg g−1 of starch, respectively, between seasonal maximum and minimum, which represented 52%, 45%, and 26% of reserves, respectively. Starch reserves in stems did not differ among species or exhibit temporal dynamics. Our results suggest that an evolutionary history of disturbance partly explains patterns of carbohydrate reserves observed in southern pines. However, similarities between slash and loblolly indicate that carbohydrate reserves do not strictly follow the continuum of disturbance frequencies among southern pine, but rather reflect the different seedling strategies exhibited by longleaf compared to those shared by slash and loblolly. We propose that the increased carbohydrate reserves in mature longleaf may simply be a relic of selective pressures imposed at the juvenile stage that are maintained through development, thus allowing mature trees to be more resilient and to recover from chronic disturbances such as frequent fire.

Global distribution of the earliest shelly metazoans

1984 ◽  
Vol 121 (3) ◽  
pp. 185-188 ◽  
Author(s):  
Jiang Zhiwen
Keyword(s):  
Evolutionary History ◽  
Developmental Stages ◽  
Evolutionary Process ◽  
Global Distribution ◽  
Biological Factors ◽  
Animal Kingdom ◽  
Quantum Leap ◽  
History Of ◽  
Logical Extension

abstractThe appearance of the first abundant skeletal organisms in the earliest Cambrian was a quantum leap in the evolutionary history of life. It provided the foundations of the animal kingdom from Cambrian times onwards. This paper demonstrates that this evolutionary process resulted from a combination of environmental and biological factors. The author maintains that the appearance of the oldest shelly fossils is a reasonable criterion for defining the Precambrian–Cambrian boundary. This arises not only from the viewpoint of taking the Cambrian Period as the first period in the Palaeozoic Era, but is also a logical extension of regarding the history of life as being divisible into a series of developmental stages.

scholarly journals Tinjauan Literatur tentang Evolusi Supply Chain Management

2019 ◽  
Vol 2 (4) ◽  
Author(s):  
Rizkha Rida ◽  
Ratuh Ummi Kalsum
Keyword(s):  
Supply Chain ◽  
Supply Chain Management ◽  
Trade Liberalization ◽  
Evolutionary History ◽  
Evolutionary Process ◽  
Global Competition ◽  
Chain Management ◽  
History Of ◽  
Reducing Costs ◽  
And Performance

Tujuan dari makalah ini adalah untuk menciptakan pemahaman yang lebih baik dari Supply Chain Management (SCM), bagaimana ia telah berkembang dan faktor-faktor yang mempengaruhi evolusinya. Melalui meneliti literatur, tulisan ini akan menyoroti sejarah evolusi SCM dan faktor-faktor yang mempengaruhi hal itu. Menurut makalah ini, sejarah evolusi SCM dapat dibagi menjadi empat tahap: 1) SCM tahap pra, 2) tahap penciptaan, 3) tahap integrasi dan 4) tahap globalisasi. Pada bagian terakhir akan dibahas faktor- faktor yang mempengaruhi proses evolusi SCM. Beberapa faktor tersebut adalah: perusahaan fokus pada pengurangan biaya; meningkatnya persaingan global; perusahaan fokus pada efisiensi peningkatan dan kinerja; konsolidasi kebijakan liberalisasi perdagangan dan gerakan globalisasi; meningkatnya konsentrasi ritel - sentralisasi dan kekuasaan; dan perusahaan meningkat fokus pada kepuasan pelanggan.   The purpose of this paper is to create a better understanding of Supply Chain Management (SCM), how it has evolved and the factors that influence its evolution. Through examining the literature, this paper will highlight the evolutionary history of SCM and the factors that influence it. According to this paper, the evolutionary history of SCM can be divided into four stages: 1) pre-stage SCM, 2) stage of creation, 3) stage of integration and 4) stage of globalization. In the last section we will discuss the factors that influence the evolutionary process of SCM. Some of these factors are: companies focus on reducing costs; increasing global competition; the company focuses on improving efficiency and performance; consolidation of trade liberalization policies and the globalization movement; increasing retail concentration - centralization and power; and companies are increasing focus on customer satisfaction

scholarly journals Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

2018 ◽  
Author(s):  
Gang Li ◽  
Henrique V. Figueiro ◽  
Eduardo Eizirik ◽  
William J. Murphy
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Selective Sweeps ◽  
A Genome ◽  
Chromosome Recombination ◽  
History Of ◽  
Lineage Divergence ◽  
Recurrent Patterns ◽  
Ancient Gene

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

scholarly journals Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dario Karmeinski ◽  
Karen Meusemann ◽  
Jessica A. Goodheart ◽  
Michael Schroedl ◽  
Alexander Martynov ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Set Covering ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Transcriptome Data ◽  
Data Set ◽  
Sea Slugs ◽  
History Of

Abstract Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 411-416 ◽  
Author(s):  
Hikmet Budak ◽  
Robert C Shearman ◽  
Ismail Dweikat
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
Specific Marker ◽  
Buchloe Dactyloides ◽  
A Genome ◽  
Organelle Genomes ◽  
History Of

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalograss evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.Key words: buffalograss, evolution, organelle genomes, turfgrass.

scholarly journals The Evolutionary History of the Orexin/Allatotropin GPCR Family: From Placozoa and Cnidaria to Vertebrata

2018 ◽  
Author(s):  
Alzugaray María Eugenia ◽  
Bruno María Cecilia ◽  
Villalobos Sambucaro María José ◽  
Ronderos Jorge Rafael
Keyword(s):  
Evolutionary History ◽  
Transmembrane Domain ◽  
Phylogenetic Analyses ◽  
Cell Communication ◽  
Evolutionary Process ◽  
Likelihood Method ◽  
Intracellular Loop ◽  
Gpcr Family ◽  
History Of ◽  
Loop 2

ABSTRACTCell-cell communication is a basic principle in all organisms, necessary to facilitate the coordination and integration between cell populations. These systems act by mean of chemical messengers. Peptides constitute a highly diversified group of intercellular messengers widely distributed in nature, and regulate a great number of physiological processes in Metazoa. Being crucial for life, it would seem that they have appeared in the ancestral group from which Metazoa evolved, and were highly conserved along the evolutionary process. Peptides act mainly through G-protein coupled receptors (GPCRs), a great family of transmembrane molecules. GPCRs are also widely distributed in nature being present not only in metazoan, but also in Choanoflagellata (unicellular eukariotes related with metazoans), and even in Fungi. Among GPCRs, the Allatotropin/Orexin (AT/Ox) family is particularly characterized by the presence of the DRWmotif in the second intracellular loop (IC Loop 2), and seems to be present in Cnidaria, Placozoa and in Bilateria, suggesting that it also was present in the common ancestor of Metazoa. Looking for the evolutionary history of this GPCR family we searched in the GenBank for sequences corresponding to this family of receptors (i.e. seven transmembrane domain and the E/DRW motif at the second IC Loop 2). Our results show that AT/Ox receptors were highly conserved along evolutionary history of Metazoa, and that they might be defined by the presence of the E/DRWYAI motif at the level of IC Loop 2. Molecular phylogenetic analyses performed by Maximum Likelihood method suggest that AT/Ox family of receptors reflects evolutionary relationships that agree with current understanding of phylogenetic relationships in Actinopterygii and Sauropsida, including also the largely discussed position of Testudines.

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