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

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.]

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Phylogeny and higher classification of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea)*

Zootaxa ◽

10.11646/zootaxa.1668.1.22 ◽

2007 ◽

Vol 1668 (1) ◽

pp. 413-425 ◽

Cited By ~ 66

Author(s):

P. J. GULLAN ◽

L. G. COOK

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Nuclear Dna ◽

Sister Group ◽

Scale Insect ◽

Scale Insects ◽

Morphological Data ◽

Adult Males ◽

Plant Feeding ◽

Phylogenetic Studies

The superfamily Coccoidea contains nearly 8000 species of plant-feeding hemipterans comprising up to 32 families divided traditionally into two informal groups, the archaeococcoids and the neococcoids. The neococcoids form a monophyletic group supported by both morphological and genetic data. In contrast, the monophyly of the archaeococcoids is uncertain and the higher level ranks within it have been controversial, particularly since the late Professor Jan Koteja introduced his multi-family classification for scale insects in 1974. Recent phylogenetic studies using molecular and morphological data support the recognition of up to 15 extant families of archaeococcoids, including 11 families for the former Margarodidae sensu lato, vindicating Koteja’s views. Archaeococcoids are represented better in the fossil record than neococcoids, and have an adequate record through the Tertiary and Cretaceous but almost no putative coccoid fossils are known from earlier. In contrast, the sister group of the scale insects (Aphidoidea) has a more informative Jurassic and Triassic record. Relationships among most scale insect families are unresolved in phylogenetic trees based on nuclear DNA sequences, and most nodes in trees based on morphological data, including those from adult males, are poorly supported. Within the neococcoids, the Eriococcidae is not monophyletic and the monophyly of the Coccidae and Diaspididae may be compromised by the current family-level recognition of a few species-poor autapomorphic groups.

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A combined analysis of morphological traits, chloroplast and nuclear DNA sequences within Santiria trimera (Burseraceae) suggests several species following the Biological Species Concept

Plant Ecology and Evolution ◽

10.5091/plecevo.2010.433 ◽

2010 ◽

Vol 143 (2) ◽

pp. 160-169 ◽

Cited By ~ 16

Author(s):

K. Guillaume Koffi ◽

Myriam Heuertz ◽

Charles Doumenge ◽

Jean Michel Onana ◽

Frederick Gavory ◽

...

Keyword(s):

Dna Sequences ◽

Morphological Traits ◽

Nuclear Dna ◽

Species Concept ◽

Biological Species ◽

Biological Species Concept ◽

Combined Analysis

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Sequence-Based Deep Learning Frameworks on Enhancer-Promoter Interactions Prediction

Current Pharmaceutical Design ◽

10.2174/1381612826666201124112710 ◽

2020 ◽

Vol 26 ◽

Author(s):

Xiaoping Min ◽

Fengqing Lu ◽

Chunyan Li

Keyword(s):

Gene Expression ◽

Deep Learning ◽

Dna Sequences ◽

Experimental Methods ◽

Learning Methods ◽

Comprehensive Review ◽

Genomic Features ◽

Disease Mechanisms ◽

Evaluation Strategies ◽

Learning Frameworks

: Enhancer-promoter interactions (EPIs) in the human genome are of great significance to transcriptional regulation which tightly controls gene expression. Identification of EPIs can help us better deciphering gene regulation and understanding disease mechanisms. However, experimental methods to identify EPIs are constrained by the fund, time and manpower while computational methods using DNA sequences and genomic features are viable alternatives. Deep learning methods have shown promising prospects in classification and efforts that have been utilized to identify EPIs. In this survey, we specifically focus on sequence-based deep learning methods and conduct a comprehensive review of the literatures of them. We first briefly introduce existing sequence-based frameworks on EPIs prediction and their technique details. After that, we elaborate on the dataset, pre-processing means and evaluation strategies. Finally, we discuss the challenges these methods are confronted with and suggest several future opportunities.

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Systematics and evolution of Nepenthes

10.1093/oso/9780198779841.003.0005 ◽

2018 ◽

Cited By ~ 4

Author(s):

Charles Clarke ◽

Jan Schlauer ◽

Jonathan Moran ◽

Alastair Robinson

Keyword(s):

Southeast Asia ◽

Analytical Methods ◽

Best Practice ◽

Species Concept ◽

Reticulate Evolution ◽

Ecological Information ◽

Plastid Genomes ◽

The Status ◽

Species Descriptions ◽

Adequate Research

Nepenthes is a genus of 130-160 species, almost half of which were described after 2001. The recent, rapid increase in species descriptions has been driven by application of a less rigorous species concept by botanists, taxonomic inflation, and discoveries of new taxa during explorations of remote parts of Southeast Asia. Many recently published species descriptions of Nepenthes are based entirely upon qualitative morphological information and are not supported by adequate research. Accordingly, the status of many Nepenthes taxa is contested. Evolution within the genus is not well understood, because nuclear and maternally inherited plastid genomes cannot resolve relationships between many species, particularly those that evolved recently through introgression or reticulate evolution. Improvement in our understanding of the systematics and evolution of Nepenthes requires the adoption of ‘best practice’ collection and preservation methods, and the application of quantitative analytical methods for morphological, genetic, and ecological information.

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Global phylogeography of a pantropical mangrove genus Rhizophora

Scientific Reports ◽

10.1038/s41598-021-85844-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Koji Takayama ◽

Yoichi Tateishi ◽

Tadashi Kajita

Keyword(s):

Phylogenetic Trees ◽

Nuclear Dna ◽

Divergence Time ◽

Long Distance ◽

F1 Hybrid ◽

The Pacific ◽

Comprehensive Picture ◽

Dated Phylogeny ◽

Stochastic Mapping ◽

Historical Scenario

AbstractRhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.

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Polycombs and microRNA-223 regulate human granulopoiesis by transcriptional control of target gene expression

Blood ◽

10.1182/blood-2011-08-371344 ◽

2012 ◽

Vol 119 (17) ◽

pp. 4034-4046 ◽

Cited By ~ 101

Author(s):

Giuseppe Zardo ◽

Alberto Ciolfi ◽

Laura Vian ◽

Linda M. Starnes ◽

Monia Billi ◽

...

Keyword(s):

Gene Expression ◽

Dna Sequences ◽

Transcriptional Control ◽

Transcriptional Level ◽

Seed Region ◽

Mrna Targets ◽

Epigenetic Events ◽

Evolutionarily Conserved ◽

Lineage Decision ◽

Chromatin Remodeling Complexes

Abstract Epigenetic modifications regulate developmental genes involved in stem cell identity and lineage choice. NFI-A is a posttranscriptional microRNA-223 (miR-223) target directing human hematopoietic progenitor lineage decision: NFI-A induction or silencing boosts erythropoiesis or granulopoiesis, respectively. Here we show that NFI-A promoter silencing, which allows granulopoiesis, is guaranteed by epigenetic events, including the resolution of opposing chromatin “bivalent domains,” hypermethylation, recruitment of polycomb (PcG)–RNAi complexes, and miR-223 promoter targeting activity. During granulopoiesis, miR-223 localizes inside the nucleus and targets the NFI-A promoter region containing PcGs binding sites and miR-223 complementary DNA sequences, evolutionarily conserved in mammalians. Remarkably, both the integrity of the PcGs-RNAi complex and DNA sequences matching the seed region of miR-223 are required to induce NFI-A transcriptional silencing. Moreover, ectopic miR-223 expression in human myeloid progenitors causes heterochromatic repression of NFI-A gene and channels granulopoiesis, whereas its stable knockdown produces the opposite effects. Our findings indicate that, besides the regulation of translation of mRNA targets, endogenous miRs can affect gene expression at the transcriptional level, functioning in a critical interface between chromatin remodeling complexes and the genome to direct fate lineage determination of hematopoietic progenitors.

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Phylogenetic relationships among the ciliate arthrodontous mosses: Evidence from chloroplast and nuclear DNA sequences

Plant Systematics and Evolution ◽

10.1007/bf00984651 ◽

1999 ◽

Vol 215 (1-4) ◽

pp. 119-139 ◽

Cited By ~ 51

Author(s):

Cymon J. Cox ◽

Terry A. J. Hedderson

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Nuclear Dna

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Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus

Insects ◽

10.3390/insects12050453 ◽

2021 ◽

Vol 12 (5) ◽

pp. 453

Author(s):

Zi-Yi Zhang ◽

Jia-Yin Guan ◽

Yu-Rou Cao ◽

Xin-Yi Dai ◽

Kenneth B. Storey ◽

...

Keyword(s):

Gene Expression ◽

Phylogenetic Trees ◽

Mitochondrial Gene ◽

Mitochondrial Protein ◽

Pine Wilt Disease ◽

Bursaphelenchus Xylophilus ◽

Monochamus Alternatus ◽

Genome Database ◽

Protein Coding ◽

Nd5 Gene

We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4–5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.

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