scholarly journals Reconciliation of evidence for the Portulacineae “backbone” phylogeny

2021 ◽  
Author(s):  
Mark Hershkovitz
Keyword(s):  
Analytical Methods ◽  
Scientific Inquiry ◽  
Evolutionary History ◽  
Fundamental Property ◽  
Evolutionary Process ◽  
Hierarchical Organization ◽  
Phylogenetic Study ◽  
Useful Knowledge ◽  
Phylogenetic Resolution ◽  
Living Organisms

Portulacineae comprise a clade of eight ostensibly monophyletic families, four of which (Anacampserotaceae, Montiaceae, Portulacaceae s. str., and Talinaceae) and part of a fifth (Didiereaceae) had been classified traditionally in Portulacaceae s. lato. The clade also includes Basellaceae, Cactaceae, and Halophytaceae. While available evidence strongly supports recognition of major clades within Portulacineae, current analyses disagree with respect to relations among them, such that the Portulacineae “backbone” phylogeny remains “unresolved.” The disagreements might owe in part to incongruent data and/or poor analysis and/or known theoretical shortcomings of the analytical methods. But I argue here that it reflects mostly the failure to appreciate the fundamental property of living organisms, viz. their inherent determinism consequent to autopoiesis. This property renders the evolutionary process as idiosyncratic. This, in turn, renders phylogeny inherently unpredictable and, strictly speaking, unrecoverable. I also emphasize that the hierarchical organization of organisms predicts that phylogeny should not be strictly tree-like. Nonetheless, evolutionary history is materially tangible, hence is within the realm of scientific inquiry. I make two proposals here. One is that (often futile) efforts to resolve phylogeny as a tree reflect a constitutive cognitive proclivity to resolve trees even when phylogeny is not tree-like and/or otherwise “resolvable.” To mitigate this tendency, I propose that the objective of phylogenetic study should be reconciliation rather than resolution. In this way, the lack of tree-like phylogenetic resolution becomes useful knowledge. In this theoretical framework, I evaluate what can be considered tentatively known about the Portulacineae backbone phylogeny.

scholarly journals The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes

2016 ◽  
Vol 283 (1835) ◽  
pp. 20160942 ◽  
Author(s):  
Jinshui Zheng ◽  
Donghai Peng ◽  
Ling Chen ◽  
Hualin Liu ◽  
Feng Chen ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Evolutionary Process ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Free Living ◽  
C Elegans ◽  
Free Living Nematode ◽  
Plant Nematode ◽  
Ditylenchus Destructor ◽  
Plant Parasitic

Plant-parasitic nematodes were found in 4 of the 12 clades of phylum Nematoda. These nematodes in different clades may have originated independently from their free-living fungivorous ancestors. However, the exact evolutionary process of these parasites is unclear. Here, we sequenced the genome sequence of a migratory plant nematode, Ditylenchus destructor . We performed comparative genomics among the free-living nematode, Caenorhabditis elegans and all the plant nematodes with genome sequences available. We found that, compared with C. elegans , the core developmental control processes underwent heavy reduction, though most signal transduction pathways were conserved. We also found D. destructor contained more homologies of the key genes in the above processes than the other plant nematodes. We suggest that Ditylenchus spp. may be an intermediate evolutionary history stage from free-living nematodes that feed on fungi to obligate plant-parasitic nematodes. Based on the facts that D. destructor can feed on fungi and has a relatively short life cycle, and that it has similar features to both C. elegans and sedentary plant-parasitic nematodes from clade 12, we propose it as a new model to study the biology, biocontrol of plant nematodes and the interaction between nematodes and plants.

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.

Establishing a New Information Paradigm

2011 ◽  
Vol 3 (4) ◽  
pp. 18-24 ◽  
Author(s):  
Dail DeWitt Doucette
Keyword(s):  
Information Science ◽  
Evolutionary Process ◽  
Scientific Discipline ◽  
Arts And Humanities ◽  
New Information ◽  
Chinese Association ◽  
Academic Information ◽  
Complex Forms ◽  
Living Organisms ◽  
Beijing China

This paper suggests a new information paradigm and recommends the establishment of a new academic and scientific discipline, or a metaphysics of information, to be built on the premise that information is also a part of all the universes, elements, systems, and conditions. Therefore, it is also an integral part of all the other individual disciplines and sciences. It is essential to look beyond the limitations of how humans use and perceive information, or even how other living organisms use information. It is proposed that information is in a continuous and dynamic evolutionary process that ranges from simple to complex forms, at every level, across all scientific and academic domains, as well as being a significant element in everything that exists. Information is a trigger mechanism, an emphasis and a nutrient, not only for information activities, but also all physical, and biological elements, systems and activities. Each existing discipline has within it a significant core informational element, which helps formulate and define that discipline. The science of information will bring together core science and academic information elements to correlate, compare and assemble a combined theoretical base. This new discipline should coexist equally with traditional scientific and academic categories such as physical, social science, arts, and humanities. It should not compete with or replace other disciplines but should stand alongside them and assist them to build comparisons and consolidations amongst multiple disciplines regarding information theories, methodologies, practices—by adding new perspectives, resources, and developments. This paper is adapted from a presentation to the Fourth International Conference on the Foundation of Information Science, held in conjunction with the Chinese Association for Artificial Intelligence at the Huazhiong University of Science and Technology in August 2010 in Beijing, China.

scholarly journals Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China

2020 ◽  
Vol 37 (7) ◽  
pp. 2099-2109 ◽  
Author(s):  
Yudong Cai ◽  
Weiwei Fu ◽  
Dawei Cai ◽  
Rasmus Heller ◽  
Zhuqing Zheng ◽  
...  
Keyword(s):  
Iron Age ◽  
Evolutionary History ◽  
De Novo ◽  
Evolutionary Process ◽  
Migration Route ◽  
Neolithic Period ◽  
Late Neolithic ◽  
Standing Variation ◽  
Modern Chinese ◽  
Chalcolithic Period

Abstract Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.

scholarly journals A transcriptome-based phylogenetic study of hard ticks (Ixodidae)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
N. Pierre Charrier ◽  
Axelle Hermouet ◽  
Caroline Hervet ◽  
Albert Agoulon ◽  
Stephen C. Barker ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Nuclear Genome ◽  
Single Copy ◽  
Phylogenetic Study ◽  
Data Sets ◽  
Hard Tick ◽  
Rna Seq ◽  
Hard Ticks ◽  
History Of ◽  
Mitochondrial Sequences

Abstract Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.

Phylogeny of the genus Tethya (Tethyidae: Hadromerida: Porifera): molecular and morphological aspects

2007 ◽  
Vol 87 (6) ◽  
pp. 1615-1627 ◽  
Author(s):  
Isabel Heim ◽  
Michael Nickel ◽  
Franz Brümmer
Keyword(s):  
Distinct Species ◽  
Morphological Characters ◽  
Phylogenetic Study ◽  
Western Atlantic ◽  
Morphological Aspects ◽  
Northern European ◽  
Phylogenetic Resolution ◽  
Phylogenetic Framework ◽  
Biogeographic Regions ◽  
Character Set

The genus Tethya represents a large cosmopolitan group of 81 recognized and a significant number of additional, still undescribed sponge species. The phylogenetic relationships within this old taxon are almost unknown. This is represented by the fact that several species are regarded as cosmopolitan. However, some of them might represent groups of closely related but distinct species. Using molecular and morphological characters, we aimed at a fundamental phylogenetic study for the genus Tethya, evaluating an existing morphological matrix and the cytochrome oxidase subunit I (COI) as a molecular marker. Intending to create a basic phylogenetic framework for the genus we selected a number of species from main biogeographic regions covered by Tethya species: from the Mediterranean Sea (T. citrina and T. aurantium), the northern European seas (T. citrina, T. norvegica and T. hibernica), the western Atlantic (T. actinia), the eastern Pacific (T. californiana), the Indo-Pacific (T. seychellensis) as well as three species of unknown biogeographical origin, originally described from aquarium habitats (T. wilhelma, T. gracilis and T. minuta). Both the morphological matrix, consisting of 29 characters and 131 character states, as well as the molecular matrices (COI nucleotide sequences of 658 bp as well as deduced amino acid sequence of 219 aa), resolved major biogeographical subgroups within the genus. However, the nucleotide based matrices revealed a higher resolution. Two major branches seem to have diverged early: an Indo-Pacific (T. seychellensis, T. wilhelma, T. minuta) and a Pan-European clade (T. citrina, T. norvegica, T. hibernica). For T. aurantium as well as a North-American group (T. californiana, T. actinia and T. minuta) our results are not conclusive. The morphological character set will have to be re-evaluated to gain a higher phylogenetic resolution. The addition of more species to our basal phylogenetic framework will allow analysing the evolution of the various biogeographical subgroups in the genus Tethya.

Towards a new role for vector systematics in parasite control

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1723-1729 ◽  
Author(s):  
MAGDALENA ZAROWIECKI ◽  
JOSE R. LOAIZA ◽  
JAN E. CONN
Keyword(s):  
Vector Control ◽  
Analytical Methods ◽  
Evolutionary History ◽  
Recent Progress ◽  
Parasite Control ◽  
Control Programmes ◽  
Mosquito Genus

SUMMARYVector systematics research is being transformed by the recent development of theoretical, experimental and analytical methods, as well as conceptual insights into speciation and reconstruction of evolutionary history. We review this progress using examples from the mosquito genusAnopheles. The conclusion is that recent progress, particularly in the development of better tools for understanding evolutionary history, makes systematics much more informative for vector control purposes, and has increasing potential to inform and improve targeted vector control programmes.

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 Demographical history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus)

2020 ◽  
Author(s):  
Huimin Hou ◽  
Hang Ye ◽  
Zhi Wang ◽  
Jiahui Wu ◽  
Yue Gao ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Evolutionary History ◽  
North China ◽  
Critical Role ◽  
Evolutionary Process ◽  
Northern China ◽  
Phylogeographic Structure ◽  
Current Pattern ◽  
Climate Oscillations ◽  
Climatic Oscillations

Abstract Background: Ulmus lamellosa, an endemic and endangered species and one ancient species of Ulmus, has undergone the climate oscillations and geographical changes. Elucidating its demographical and genetic differentiation is very important for understanding the evolutionary history and ecological adaption of forests in Northern China. Results: According to ITS and Aat sequences, eighteen and twenty-three haplotypes were detected respectively. The haplotype distribution was polymorphic in most populations. All levels-phylogeographic clades were geographically structured, namely THM, YM and YSM groups. Within U. lamellose, higher genetic diversity and significant genetic variation were present, YSM and THM had a relatively higher diversity than that of YM. The divergence of U. lamellosa intraspecies haplotypes occurred during Miocene-Pliocene that associated with Tertiary major geological and/or climatic events, which was supported by the gene exchanges among three groups. During the glaciation, YSM and THM regions might be regarded as refugia for U. lamellose. A range expansion was not expected at the evolutionary process, except the THM group based on ITS data. The series Mountains uplift (such as Yanshan Mountains and Taihang Mountains) in North China after Miocene-Pliocene and subsequently Quaternary climatic oscillations further promoted the divergence among populations. Conclusions: Geographical topology and climate change played a critical role on the phylogeographic structure of U. lamellosa, leaded to the current pattern of U. lamellosa. These results would provide important information and clues for the demographical study of the trees in Northern China.

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