scholarly journals A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

2021 ◽  
Author(s):  
Simon Crameri ◽  
Simone Fior ◽  
Stefan Zoller ◽  
Alex Widmer
Keyword(s):  
Biological Diversity ◽  
Gene Tree ◽  
General Purpose ◽  
Ecological Genetics ◽  
Bioinformatics Pipeline ◽  
Genetic Changes ◽  
Tropical Biodiversity ◽  
Target Capture ◽  
The Family ◽  
Phylogenomic Analyses

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

scholarly journals A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

2021 ◽  
Author(s):  
Simon Crameri ◽  
Simone Fior ◽  
Stefan Zoller ◽  
Alex Widmer
Keyword(s):  
Biological Diversity ◽  
Gene Tree ◽  
General Purpose ◽  
Ecological Genetics ◽  
Bioinformatics Pipeline ◽  
Genetic Changes ◽  
Tropical Biodiversity ◽  
Target Capture ◽  
The Family ◽  
Phylogenomic Analyses

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

Another one bites the dust: taxonomic sampling of a key genus in phylogenomic datasets reveals more non-monophyletic groups in traditional scorpion classification

2020 ◽  
Vol 34 (2) ◽  
pp. 133
Author(s):  
Carlos E. Santibáñez-López ◽  
Andrés A. Ojanguren-Affilastro ◽  
Prashant P. Sharma
Keyword(s):  
Gene Tree ◽  
Sister Group ◽  
Morphological Characters ◽  
Incertae Sedis ◽  
Transcriptomic Sequencing ◽  
The Family ◽  
The Status ◽  
Significant Gene ◽  
Phylogenomic Analyses ◽  
Likelihood Mapping

Historically, morphological characters have been used to support the monophyly, composition, and phylogenetic relationships of scorpion families. Although recent phylogenomic analyses have recovered most of these traditional higher-level relationships as non-monophyletic, certain key taxa have yet to be sampled using a phylogenomic approach. Salient among these is the monotypic genus Caraboctonus Pocock,1893, the type species of the family Caraboctonidae Kraepelin, 1905. Here, we examined the putative monophyly and phylogenetic placement of this family, sampling the library of C. keyserlingi Pocock, 1893 using high throughput transcriptomic sequencing. Our phylogenomic analyses recovered Caraboctonidae as polyphyletic due to the distant placement of the genera Caraboctonus and Hadrurus Thorell, 1876. Caraboctonus was stably recovered as the sister-group of the monotypic family Superstitioniidae Stahnke, 1940, whereas Hadrurus formed an unstable relationship with Uroctonus Thorell, 1876and Belisarius Simon, 1879. Four-cluster likelihood mapping revealed that the instability inherent to the placement of Hadrurus, Uroctonus and Belisarius was attributable to significant gene tree conflict in the internodes corresponding to their divergences. To redress the polyphyly of Caraboctonidae, the following systematic actions have been taken: (1) the family Caraboctonidae has been delimited to consist of 23 species in the genera Caraboctonus and Hadruroides Pocock, 1893; (2) Caraboctonidae, previously included in the superfamily Iuroidea Thorell, 1876 or as incertae sedis, is transferred to the superfamily Caraboctonoidea (new rank); (3) the superfamily Hadruroidea (new rank) is established and the status of Hadrurinae Stahnke, 1973 is elevated to family (Hadruridae new status) including 9 species in the genera Hadrurus and Hoffmannihadrurus Fet & Soleglad, 2004 and (4) we treat Uroctonus and Belisarius as insertae sedis with respect to superfamilial placement. Our systematic actions engender the monophyly of both Iuroidea and Caraboctonidae. Future phylogenomic investigations should target similar taxon-poor and understudied lineages of potential phylogenetic significance, which are anticipated to reveal additional non-monophyletic groups.

scholarly journals Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

2020 ◽  
Author(s):  
Fernando Lopes ◽  
Larissa R Oliveira ◽  
Amanda Kessler ◽  
Yago Beux ◽  
Enrique Crespo ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Molecular Data ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Data Types ◽  
High Coverage ◽  
Sea Lions ◽  
The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

The place of sexual health education in the life of children and adolescents

2021 ◽  
Vol 15 (2) ◽  
pp. 92-95
Author(s):  
Melek Anday Rifat qızı Tolunay ◽  
Keyword(s):  
Health Education ◽  
Young People ◽  
Sexual Health ◽  
General Purpose ◽  
After School ◽  
Sufficient Information ◽  
Sexual Health Education ◽  
The Family ◽  
Questions And Answers ◽  
Age Range

The general purpose of planned sexual health education for children and young people is to provide them with sufficient information about sexual health according to their age range, to inform them about attitude-value and understanding, to gain relationship and interpersonal skills, to develop their necessary responsibilities. The protection, development and maintenance of sexual health depends on the awareness of individuals about sexuality and sexual health. Awareness begins in the family and is provided with comprehensive sexual health education in accordance with the needs in all periods of life such as preschool, school and after school. Sexual health education is not welcomed in developing countries. At the heart of this is the belief that sexual health education will encourage young people to have sexual intercourse. The development of sexual education is achieved in all age ranges with questions and answers that arise according to different age characteristics. Sexual health education is a very important factor for the psychological and physiological health of individuals in a society. Key words: sexual health education, sexual health education, reproductive health, abuse , parents, child abuse, Source of sexual information

scholarly journals Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field

2020 ◽  
Vol 70 (3) ◽  
pp. 1785-1792 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Diamino Acid ◽  
Phylogenomic Analyses ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae , for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

scholarly journals Integrative taxonomy reveals a rare and new cusk-eel species of Luciobrotula (Teleostei, Ophidiidae) from the Solomon Sea, West Pacific

2021 ◽  
Vol 750 ◽  
pp. 52-69
Author(s):  
Man-Kwan Wong ◽  
Mao-Ying Lee ◽  
Wei-Jen Chen
Keyword(s):  
Lateral Line ◽  
Gene Tree ◽  
Distinct Species ◽  
Integrative Taxonomy ◽  
Coi Gene ◽  
Valid Species ◽  
The West ◽  
West Pacific ◽  
Fin Ray ◽  
The Family

With six valid species, Luciobrotula is a small genus of the family Ophidiidae, commonly known as cusk-eels. They are benthopelagic fishes occurring at depths ranging from 115–2300 m in the Atlantic, Indian, and Pacific Oceans. Among them, Luciobrotula bartschi is the only known species in the West Pacific. Three specimens of Luciobrotula were collected from the Philippine Sea, Bismarck Sea, and Solomon Sea in the West Pacific during the AURORA, PAPUA NIUGINI, and MADEEP expeditions under the Tropical Deep-Sea Benthos program, and all of them were initially identified as L. bartschi. Subsequent examination with integrative taxonomy indicates that they belong to two distinct species, with the specimen collected from the Solomon Sea representing a new species, which is described here. In terms of morphology, Luciobrotula polylepis sp. nov. differs from its congeners by having a relatively longer lateral line (end of the lateral line below the 33rd dorsal-fin ray) and fewer vertebrae (abdominal vertebrae 13, total vertebrae 50). In the inferred COI gene tree, the two western Pacific species of Luciobrotula do not form a monophyletic group. The genetic K2P distance between the two species is 13.8% on average at the COI locus.

Acute Leukemia in Children: Time Spent in Hospitalization

PEDIATRICS ◽  
1972 ◽  
Vol 49 (5) ◽  
pp. 765-766
Author(s):  
Donald J. Fernbach ◽  
William L. Henrich ◽  
Kenneth A. Starling
Keyword(s):  
Acute Leukemia ◽  
Family Physician ◽  
General Purpose ◽  
Study Group ◽  
Baylor College ◽  
Research Protocols ◽  
The Family ◽  
Local Physician ◽  
Chemotherapy Study ◽  
Leukemia In Children

Since 1958 the Hematology and Oncology Section of the Department of Pediatrics, Baylor College of Medicine, has participated in the studies of the Southwest Cancer Chemotherapy Study Group. From the beginning it was intended that this section would maintain an emphasis on ambulatory care for children with neoplastic diseases and would develop a close liaison with the practicing physician. The general purpose was to supplement the care given by the local physician rather than to assume total management of the patient. The key to the success of any such program, where virtually all patients are referred and are registered on research protocols, is to maintain close communication with the family physician at all times.

scholarly journals Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

2015 ◽  
Vol 82 (4) ◽  
pp. 1215-1226 ◽  
Author(s):  
Francy Jimenez-Infante ◽  
David Kamanda Ngugi ◽  
Manikandan Vinu ◽  
Intikhab Alam ◽  
Allan Anthony Kamau ◽  
...  
Keyword(s):  
Red Sea ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Niche Differentiation ◽  
Content Type ◽  
Nadh:Quinone Oxidoreductase ◽  
Distinct Cluster ◽  
The Family ◽  
Phylogenomic Analyses ◽  
Cultivation Techniques

ABSTRACTThe OM43 clade within the familyMethylophilaceaeofBetaproteobacteriarepresents a group of methylotrophs that play important roles in the metabolism of C1compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.

scholarly journals Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

2016 ◽  
Author(s):  
Michael S. Barker ◽  
Zheng Li ◽  
Thomas I. Kidder ◽  
Chris R. Reardon ◽  
Zhao Lai ◽  
...  
Keyword(s):  
Gene Family ◽  
Linkage Map ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Nuclear Gene ◽  
Flowering Plants ◽  
The Family ◽  
History Of ◽  
Phylogenomic Analyses

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

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