scholarly journals Biased Gene Retention in the Face of Introgression Obscures Species Relationships

2020 ◽  
Vol 12 (9) ◽  
pp. 1646-1663 ◽  
Author(s):  
Evan S Forsythe ◽  
Andrew D L Nelson ◽  
Mark A Beilstein
Keyword(s):  
Statistical Tests ◽  
Nuclear Genome ◽  
Introgressive Hybridization ◽  
Species Relationships ◽  
Genome Composition ◽  
Haplotype Blocks ◽  
Gene Retention ◽  
The Face ◽  
Phylogenomic Analyses ◽  
Close Relatives

Abstract Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We applied phylogenomic techniques and several complementary statistical tests to show that introgressive hybridization appears to have occurred between close relatives of Arabidopsis, resulting in cytonuclear discordance and impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear–nuclear interactions likely acted during introgression, whereas linkage also contributed to genome composition through the retention of ancient haplotype blocks. We also applied divergence-based tests to determine the species branching order and distinguish donor from recipient lineages. Surprisingly, these analyses suggest that cytonuclear discordance arose via extensive nuclear, rather than cytoplasmic, introgression. If true, this would mean that most of the nuclear genome was displaced during introgression whereas only a small proportion of native alleles were retained.

scholarly journals Biased gene retention in the face of massive nuclear introgression obscures species relationships

2017 ◽  
Author(s):  
Evan S. Forsythe ◽  
Andrew D. L. Nelson ◽  
Mark A. Beilstein
Keyword(s):  
Introgressive Hybridization ◽  
Taxon Sampling ◽  
Species Relationships ◽  
Genome Composition ◽  
Haplotype Blocks ◽  
Gene Retention ◽  
The Face ◽  
Phylogenomic Analyses ◽  
Close Relatives ◽  
Cytoplasmic Introgression

AbstractPhylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We exploit a suite of genomic resources to show that introgressive hybridization occurred between close relatives of Arabidopsis, impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear-nuclear interactions likely acted during introgression, while neutral processes also contributed to genome composition through the retention of ancient haplotype blocks. We also developed a divergence-based test to distinguish donor from recipient lineages without the requirement of additional taxon-sampling. Finally, to our great surprise, we find that cytonuclear discordance appears to have arisen via extensive nuclear, rather than cytoplasmic, introgression, meaning that most of the genome was displaced during introgression, while only a small proportion of native alleles were retained.

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Phylogenomic Analyses ◽  
Close Relatives

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).

scholarly journals The Preparedness Level of Families with Disabilities Children in Facing the Earthquake and Tsunami Disaster in Padang, West Sumatra

2021 ◽  
Vol 4 (1) ◽  
pp. 61
Author(s):  
Muchsin Riviwanto ◽  
Darwel Darwel ◽  
Defriani Dwiyanti ◽  
Juanda Juanda
Keyword(s):  
Disaster Preparedness ◽  
Local Governments ◽  
Statistical Tests ◽  
Disaster Mitigation ◽  
Special Treatment ◽  
Preparedness Plan ◽  
Tsunami Disaster ◽  
West Sumatra ◽  
The Face ◽  
Index Value

Disability groups are groups vulnerable to disaster risk. Most families with disabilities feel worried about defending themselves in the event of a disaster. They are less socialized with disaster mitigation efforts. This research has provided an overview of the preparedness of families with disabilities children in increasing disaster resilience. Analytical research was conducted on families with disabilities children in the city of Padang. Data collection tools in this study used a standard questionnaire from LIPI-UNESCO / ISDR. The data were processed by a computer and analyzed using multiple regression statistical tests. The results showed the preparedness of Families With Disabilities Children in the face of disasters; it was seen that the knowledge category was ready (42.2%), the preparedness plan category was not ready (37.8%), the disaster warning category was not ready (46.7%), the resource mobilization category was not ready, ready (82.2%), the tsunami disaster preparedness index value is 57% (ready category). This research recommended local governments must provide special treatment for people with disabilities by increasing training, seminars, and disaster simulations.

scholarly journals Genomic divergence and lack of introgressive hybridization between two 13-year periodical cicadas support life cycle switching in the face of climate change

2016 ◽  
Vol 25 (21) ◽  
pp. 5543-5556 ◽  
Author(s):  
Takuya Koyama ◽  
Hiromu Ito ◽  
Tomochika Fujisawa ◽  
Hiroshi Ikeda ◽  
Satoshi Kakishima ◽  
...  
Keyword(s):  
Climate Change ◽  
Life Cycle ◽  
Introgressive Hybridization ◽  
Periodical Cicadas ◽  
Genomic Divergence ◽  
The Face

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals PENGARUH YOGA ANTENATAL TERHADAP TINGKAT KECEMASAN PADA IBU HAMIL TW III DALAM MENGHADAPI PROSES PERSALINAN DI KLINIK YAYASAN BUMI SEHAT

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Ni Gusti Ayu Pramita Aswitami
Keyword(s):  
Pregnant Women ◽  
Statistical Tests ◽  
Labor Process ◽  
P Value ◽  
Birth Process ◽  
Match Pair ◽  
Optimal Health ◽  
The Face ◽  
The One ◽  
Wilcoxon Match Pair

<p>ABSTRAK<br />Kecemasan dalam menghadapi proses persalinan dapat terjadi pada masa kehamilan yang dapat menyebabkan syok, perdarahan dan berujung pada kematian. Adanya pelayanan kesehatan yang optimal, diharapkan dapat mengurangi tingkat kecemasan ibu hamil dalam menghadapi proses persalinan. Berdasarkan studi pendahuluan di Klinik Yayasan Bumi Sehat, terlihat dari 10 orang ibu hamil, terdapat 7 orang mengalami kecemasan dalam menghadapi proses persalinan dan 3 orang tidak mengalami kecemasan dalam menghadapi proses persalinan. Kecemasan pada ibu hamil terjadi karena ibu banyak mendengar cerita yang mengatakan melahirkan itu menyakitkan dan juga karena trauma ibu dengan persalinan yang lalu. Yoga antenatal merupakan salah satu cara yang dapat dilakukan oleh ibu hamil untuk mengurangi kecemasan dalam menghadapi proses persalinan. Tujuan penelitian ini adalah untuk mengetahui pengaruh yoga antenatal terhadap tingkat kecemasan dalam menghadapi proses persalinan.Pada penelitian ini menggunakan desain pre eksperimental dengan rancangan One-Group Pretest-Posttest design. Penelitian ini dilaksanakan di Klinik Yayasan Bumi Sehat, pada bulan Agustus-September 2016. Analisis data menggunakan uji statistik Wilcoxon Match Pairs Test.Hasil penelitian menggunakan uji statistik Wilcoxon Match Pair diperoleh p value sebesar 0,000 lebih kecil dari α 0,05 maka H0 ditolak atau hipotesis dalam penelitian ini diterima yaitu ada pengaruh pemberian yoga antenatal terhadap tingkat kecemasan pada ibu hamil TW III dalam menghadapi proses persalinan. Yoga antenatal yang diberikan pada ibu hamil memiliki pengaruh yang cukup signifikan untuk mengurangi kecemasan dalam menghadapi proses persalinan.<br />Kata Kunci : yoga antenatal, tingkat kecemasan, ibu hamil<br />ABSTRACT Anxiety in the labor process can occur during pregnancy which can cause shock, bleeding and lead to death. The existence of optimal health services, is expected to reduce the level of anxiety pregnant women in the process of childbirth. Based on preliminary studies in Clinical Yayasan Bumi Sehat, that of 10 pregnant women 7 women experience anxiety in labor and three people who did not experience anxiety in the face of labor, because the mother heard many stories - stories of the others say giving birth is painful and there mothers also traumatized by childbirth lalu.salah a way that can be done by pregnant women to reduce anxiety in the face of the delivery process is to conduct antenatal yoga. The purpose of this study was to determine the effect of antenatal yoga with the level of anxiety in the face of the delivery process. This study design is a pre-experimental research design with the design of the One-group pretest-posttest design. This research was conducted at the Yayasan Bumi Sehat Clinic, in August-September 2016. Data were analyzed using statistical tests Wilcoxon Match Pairs Test. The results using statistical test of Wilcoxon Match Pair obtained p value of 0.000 is smaller than α 0.05 then Ho is rejected or accepted the hypothesis in this study that there is the effect of antenatal yoga with anxiety levels in pregnant women TW III facing the birth process. Yoga antenatal given to pregnant women to have a significant effect on reducing anxiety in the face of the delivery process. The results of this research is also expected to be further developed by other research<br />Keyword : Antenatal Yoga, Level Anxiety, Pregnancy</p>

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2463 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V. Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen-Influenced Gene Space Adaptation

2019 ◽  
Author(s):  
Martha Rendón-Anaya ◽  
Enrique Ibarra-Laclette ◽  
Alfonso Méndez Bravo ◽  
Tianying Lan ◽  
Chunfang Zheng ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Tree ◽  
Nuclear Genome ◽  
Introgressive Hybridization ◽  
Persea Americana ◽  
Phylogenetic Position ◽  
General View ◽  
Adaptive Landscapes ◽  
Fruit Species ◽  
Phenylpropanoid Biosynthesis

ABSTRACTThe avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently-diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced two lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species.SIGNIFICANCE STATEMENTAvocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings, the admixed nature of Hass, and provide a look at how pathogen interactions have shaped avocado’s more recent genomic evolutionary history.

scholarly journals Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

2015 ◽  
Vol 117 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Karolina Heyduk ◽  
Dorset W. Trapnell ◽  
Craig F. Barrett ◽  
Jim Leebens-Mack
Keyword(s):  
Species Relationships ◽  
Sequence Capture ◽  
Phylogenomic Analyses ◽  
Targeted Sequence Capture

scholarly journals Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms

2021 ◽  
Author(s):  
Evan S Forsythe ◽  
Alissa M Williams ◽  
Daniel B Sloan
Keyword(s):  
Nuclear Genome ◽  
Protein Translation ◽  
Nuclear Genes ◽  
Sequence Evolution ◽  
Cellular Functions ◽  
Transmission Modes ◽  
Chloroplast Genomes ◽  
Genome Wide ◽  
Genes Encoding ◽  
Phylogenomic Analyses

Abstract Nuclear and plastid (chloroplast) genomes experience different mutation rates, levels of selection, and transmission modes, yet key cellular functions depend on their coordinated interactions. Functionally related proteins often show correlated changes in rates of sequence evolution across a phylogeny (evolutionary rate covariation or ERC), offering a means to detect previously unidentified suites of coevolving and cofunctional genes. We performed phylogenomic analyses across angiosperm diversity, scanning the nuclear genome for genes that exhibit ERC with plastid genes. As expected, the strongest hits were highly enriched for genes encoding plastid-targeted proteins, providing evidence that cytonuclear interactions affect rates of molecular evolution at genome-wide scales. Many identified nuclear genes functioned in post-transcriptional regulation and the maintenance of protein homeostasis (proteostasis), including protein translation (in both the plastid and cytosol), import, quality control and turnover. We also identified nuclear genes that exhibit strong signatures of coevolution with the plastid genome, but their encoded proteins lack organellar-targeting annotations, making them candidates for having previously undescribed roles in plastids. In sum, our genome-wide analyses reveal that plastid-nuclear coevolution extends beyond the intimate molecular interactions within chloroplast enzyme complexes and may be driven by frequent rewiring of the machinery responsible for maintenance of plastid proteostasis in angiosperms.

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