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1
Lewis, R. Barry. "Who's on First?: Genealogies with Family Tree Maker®." CAM Journal 10, no. 2 (May 1998): 37–40. http://dx.doi.org/10.1177/1525822x980100020401.
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Kasful, Kasful. "The Leadership of Kyai in Islamic Boarding School (A Study of Islamic Boarding School in Jambi)." Al-Ta lim Journal 22, no. 1 (February 28, 2015): 88–95. http://dx.doi.org/10.15548/jt.v22i1.113.
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This study was conducted based on the problem of kyai leadership pattern in Islamic boarding school in Jambi which is considered as paternalistic and centralistic. The study was aimed at exploring the effectiveness of kyai leadership at Islamic boarding schools in Jambi dealing with the following questions: 1) What kind of system is applied in the election of Islamic boarding school leader? 2) What kind of leadership model used in Islamic boarding school Jambi? 3) What is the effectiveness of the kyai leadership in relation with the vision, mission, management, and policy maker of that school? 4) What were the roles of kyai as the leader of Islamic boarding school among the society? Qualitative design was used in this study and purposive sampling was employed to determine the respondents. Observation, interview and documentation were used to collect the data. It was found that: 1) The Islamic Boarding School of Nurul Iman applied deliberation and consensus system leader in which teachers, board of trustees and coordinator of Pecinan are participating in when electing the leader and the model of leadership in this school is charismatic. The As’ad School leader’s election was based on family-tree system and the model of leadership in this school was paternalistic. In PKP Al-Hidayah, the leader is elected directly by the government of Jambi province as the owner of the school. 2) In general, the model of leadership applied in Islamic boarding school in Jambi was collective-passive model because generally Islamic boarding school at Jambi are under the management of particular foundation.3) The leadership of kyai is not effective because the management system applied was not effective. 4) The role of kyai among the society ran harmoniously. Based on the research findings, democratic and open election system are recommended in Islamic boarding school leader election to respect individual right to consider leader’s credibility, quality and acceptability. Copyright © 2015 by Al-Ta'lim All right reserved
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Johnson, G. R., N. C. Wheeler, and S. H. Strauss. "Financial feasibility of marker-aided selection in Douglas-fir." Canadian Journal of Forest Research 30, no. 12 (December 1, 2000): 1942–52. http://dx.doi.org/10.1139/x00-122.
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The land area required for a marker-aided selection (MAS) program to break-even (i.e., have equal costs and benefits) was estimated using computer simulation for coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in the Pacific Northwestern United States. We compared the selection efficiency obtained when using an index that included the phenotype and marker score with that obtained using only the phenotype. It was assumed that MAS was restricted to within-family selection, that the rotation age was 50 years, and that growth rate (h2 = 0.25), tree form (h2 = 0.25), and (or) wood density (h2 = 0.45) were the objects of improvement. Several population quantitative trait loci (QTL) models, selection population sizes, and interest rates were considered. When large selection population sizes were employed (500 trees per family) MAS gave considerable increases in efficiency of within-family selection; however, results showed that the combination of small selection population sizes (100 trees per family) and many QTL of moderate effect could lead to losses in gain from MAS compared with phenotypic selection. For many reasonable selection scenarios and the simplified assumptions in our model, the land base required for breeding programs to break-even is smaller or near to the limit of those in place under operational breeding programs in the region. Considerably more research is needed to reasonably predict whether MAS would be cost-effective in practice. However, before some of the basic research needed to implement MAS can be done, organizations need to establish large blocks of full-sib families to allow for QTL identification.
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Moriguchi, Yoshinari, Saneyoshi Ueno, Yoichi Hasegawa, Takumi Tadama, Masahiro Watanabe, Ryunosuke Saito, Satoko Hirayama, Junji Iwai, and Yukinori Konno. "Marker-Assisted Selection of Trees with MALE STERILITY 1 in Cryptomeria japonica D. Don." Forests 11, no. 7 (July 6, 2020): 734. http://dx.doi.org/10.3390/f11070734.
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The practical use of marker-assisted selection (MAS) is limited in conifers because of the difficulty with developing markers due to a rapid decrease in linkage disequilibrium, the limited genomic information available, and the diverse genetic backgrounds among the breeding material collections. First, in this study, two families were produced by artificial crossing between two male-sterile trees, ‘Shindai11’ and ‘Shindai12’, and a plus tree, ‘Suzu-2’ (Ms1/ms1) (S11-S and S12-S families, respectively). The segregation ratio between the male-sterile and male-fertile trees did not deviate significantly from the expected 1:1 ratio in either family. These results clearly suggested that the male-sterile gene of ‘Shindai11’ and ‘Shindai12’ is MALE STERILITY 1 (MS1). Since it is difficult to understand the relative positions of each marker, due to the lack of a linkage map which all the closely linked markers previously reported are mapped on, we constructed a partial linkage map of the region encompassing MS1 using the S11-S and S12-S families. For the S11-S and S12-S families, 19 and 18 markers were mapped onto the partial linkage maps of the MS1 region, respectively. There was collinearity (conserved gene order) between the two partial linkage maps. Two markers (CJt020762_ms1-1 and reCj19250_2335) were mapped to the same position as the MS1 locus on both maps. Of these markers, we used CJt020762 for the MAS in this study. According to the MAS results for 650 trees from six prefectures of Japan (603 trees from breeding materials and 47 trees from the Ishinomaki natural population), five trees in Niigata Prefecture and one tree in Yamagata Prefecture had heterozygous ms1-1, and three trees in Miyagi Prefecture had heterozygous ms1-2. The results obtained in this study suggested that ms1-1 and ms1-2 have different geographical distributions. Since MAS can be used effectively to reduce the labor and time required for selection of trees with a male-sterile gene, the research should help ensure that the quantity of breeding materials will increase to assist future tree-breeding efforts.
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Enache, Madalin, Takashi Itoh, Tadamasa Fukushima, Ron Usami, Lucia Dumitru, and Masahiro Kamekura. "Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences." International Journal of Systematic and Evolutionary Microbiology 57, no. 10 (October 1, 2007): 2289–95. http://dx.doi.org/10.1099/ijs.0.65190-0.
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In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.
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Nishio, Sogo, Masahiko Yamada, Yutaka Sawamura, Norio Takada, and Toshihiro Saito. "Environmental Variance Components of Fruit Ripening Date as Used in Both Phenotypic and Marker-assisted Selection in Japanese Pear Breeding." HortScience 46, no. 11 (November 2011): 1540–44. http://dx.doi.org/10.21273/hortsci.46.11.1540.
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The effectiveness of detected quantitative trait loci (QTLs) and molecular markers associated with them in tree fruit breeding is measured by the percentages of the variance associated with detected QTL effects accounting for not phenotypic variance, but genetic variance of the trait. The genetic variance can be obtained by subtracting environmental variance from the phenotypic variance. Once accurate environmental variance components are obtained for a given selection field, environmental variances under any number of replications and measurement repetitions can be estimated. We estimated environmental variance components of fruit ripening date measured by days in a Japanese pear (Pyrus pyrifolia Nakai) breeding field in the National Institute of Fruit Tree Science, Tsukuba, Ibaraki, Japan. We estimated variance among fruits within a tree (σf2) as 25.6, among trees within a genotype (σt2) as 0.2, among years (σy2) as 9.4, associated with genotype × year interaction (σgy2) as 7.9, and associated with tree × year interaction (σty2) as 1.2. Because σf2 was the largest environmental variance component, increasing the number of fruit evaluated would most effectively reduce the environmental variance, and tree replication would not because of very small σt2 and σty2. The 95% confidence limit of a genotypic value was ± 10 days in the evaluation of five fruits on a single tree in a year and ± 7 days over 2 years. Broad-sense heritability in a family, each offspring in which was evaluated using five fruits on a single tree in a single year, was estimated at 0.83 for three full-sib families analyzed.
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Lin, Z., B. J. Hayes, and H. D. Daetwyler. "Genomic selection in crops, trees and forages: a review." Crop and Pasture Science 65, no. 11 (2014): 1177. http://dx.doi.org/10.1071/cp13363.
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Genomic selection is now being used at an accelerating pace in many plant species. This review first discusses the factors affecting the accuracy of genomic selection, and then interprets results of existing plant genomic selection studies in light of these factors. Differences between genomic breeding strategies for self-pollinated and open-pollinated species, and between-population level v. within-family design, are highlighted. As expected, more training individuals, higher trait heritability and higher marker density generally lead to better accuracy of genomic breeding values in both self-pollinated and open-pollinated plants. Most published studies to date have artificially limited effective population size by using designs of bi-parental or within-family structure to increase accuracies. The capacity of genomic selection to reduce generation intervals by accurately evaluating traits at an early age makes it an effective tool to deliver more genetic gain from plant breeding in many cases.
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Patton-Imani, Sandra. "Legitimacy and the Transfer of Children: Adoption, Belonging, and Online Genealogy." Genealogy 2, no. 4 (September 20, 2018): 37. http://dx.doi.org/10.3390/genealogy2040037.
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A great deal of both scholarly and public attention has been paid to questions of nature versus nurture in understanding identity and family construction in adoptees, yet much less attention has been given to the ways that power shapes the social reproduction of families through adoption. In this feminist interdisciplinary self-reflexive ethnographic research, I enter the world of online genealogy sites to critically explore the social practice of constructing a family tree as an adoptee. I explore genealogy as a culturally and historically specific representation of patriarchal heteronormative whiteness. I argue that adoptees’ liminal locations between socially understood categories of nature and nurture embedded in online family heritage websites make evident the ways that genealogical templates and stories reproduce mainstream family ideology through the erasure of “illegitimacy”. I consider what I found in my adoptive family history, critically exploring my “legitimate” relationship to my family in relation to the “illegitimate” (and unrecognized) relationship between my family and an enslaved child transferred as property between family members in 1813. This research makes visible power inequalities governing family reproduction at macro levels by exploring the contradictions and slippages regarding family “legitimacy” in micro level online genealogical constructions of adoptees’ family trees.
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Zhou, Ying, Jing Li, Schuyler S. Korban, and Yuepeng Han. "Apple SSRs present in coding and noncoding regions of expressed sequence tags show differences in transferability to other fruit species in Rosaceae." Canadian Journal of Plant Science 93, no. 2 (March 2013): 183–90. http://dx.doi.org/10.4141/cjps2012-259.
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Zhou, Y., Li, J., Korban, S. S. and Han, Y. 2013. Apple SSRs present in coding and noncoding regions of expressed sequence tags show differences in transferability to other fruit species in Rosaceae. Can. J. Plant Sci. 93: 183–190. Simple sequence repeat markers derived from expressed sequence tags (ESTs) are referred to as eSSRs. To develop molecular markers for non-model plants in Rosaceae, we investigated the transferability of apple eSSRs across seven fruit trees, belonging to four genera and 11 species of the Rosaceae family, including peach, quince, pear, loquat, apricot, cherry, and plum. Of the 98 apple eSSRs tested, 86 successfully amplified PCR products in at least one of the fruit tree species. Five apple eSSRs produced amplicons in more than five fruit tree species, and were deemed as a widely transferable Rosaceae marker set. Frequency of transferability of apple eSSRs across all seven fruit trees of Rosaceae varied widely among genera and species, with an average transferability of 29.0%. Overall, apple eSSRs transferred more easily to peach and pear than to plum and loquat. Interestingly, apple eSSRs present in coding sequences (CDS) showed higher levels of transferability to other fruit trees than those present in noncoding or untranslated regions (UTRs). Interestingly, apple eSSRs present in 5'UTRs showed lower frequencies of transfer than those present in 3'UTRs. The latter finding suggested that 5'UTRs might have diverged more rapidly than 3'UTRs in Rosaceae.
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Sanders Allen, Eva, and Kevin E. Omland. "Novel Intron Phylogeny Supports Plumage Convergence in Orioles (Icterus)." Auk 120, no. 4 (October 1, 2003): 961–69. http://dx.doi.org/10.1093/auk/120.4.961.
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Abstract A recent study of New World orioles (Icterus spp.), which traced a large number of plumage characters onto a mitochondrial DNA phylogeny, reported high frequencies of evolutionary convergence and reversal of plumage characters (Omland and Lanyon 2000). Although those results are consistent with other smaller scale studies that have documented plumage homoplasy, the mitochondrial genome is inherited as a single linkage group, so mitochondrial data represent only one gene tree. The mitochondrial (mt) DNA tree may not reflect the true evolutionary history of a lineage; therefore, it remains possible that the plumage characters could reflect the true species phylogeny. Other rapidly evolving regions of DNA can provide independent phylogenetic hypotheses useful for evaluating mitochondrial gene trees. A novel phylogenetic marker, a region of the nuclear gene ornithine decarboxylase (ODC) spanning from exon 6 to exon 8, was sequenced in 10 oriole species. The resultant nuclear gene tree reconstructs the same three major oriole clades as the mtDNA tree (Omland et al. 1999), supporting the conclusion that plumage evolution in the New World orioles has been highly homoplastic. Although most phylogenetic studies that have employed introns report greatest resolution at the genus or family level, ODC appears to offer some degree of phylogenetic resolution for infrageneric analyses. However, that intron has clearly not sorted to monophyly within or between closely related species.
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Hutchins, Carleen M. "Measurable Characteristics of Violin-Family Instruments in Relation to the Sound of a High-Quality Violin." MRS Bulletin 20, no. 3 (March 1995): 29–31. http://dx.doi.org/10.1557/s0883769400044365.
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The extreme variations in the mechanical as well as acoustical properties of wood, not only within a given species, but even within the same tree, have plagued violin researchers for nearly 100 years and violin makers for more than 300 years. The lore of violin making tells us that a spruce tree growing on the north side of a mountain should be cut in the spring when the water is moving up in the wood cells, and that the first six or eight feet of the trunk should be discarded because the twisting and the weight of the big trunk cause increased density in the wood with a less even grain structure. The wood should then be cut into lengths, free of knots and sap cracks, and split into so-called flitches that can be used for various violin-family instruments, depending on size. When a flitch is properly cut and joined for a violin top, the annual-ring spacing, or grain, ideally should be narrow in the center of the violin top, gradually becoming wider toward the edges. Also, the grain should be vertical to the bottom surface of the top plate. The more researchers study the desirable parameters of spruce for the proper tuning of violin top and back free plates and the effects they have on the finished instrument, the more the seemingly unsupported lore of violin making makes very good sense.
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Thompson, C. C., F. L. Thompson, K. Vandemeulebroecke, B. Hoste, P. Dawyndt, and J. Swings. "Use of recA as an alternative phylogenetic marker in the family Vibrionaceae." International Journal of Systematic and Evolutionary Microbiology 54, no. 3 (May 1, 2004): 919–24. http://dx.doi.org/10.1099/ijs.0.02963-0.
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This study analysed the usefulness of recA gene sequences as an alternative phylogenetic and/or identification marker for vibrios. The recA sequences suggest that the genus Vibrio is polyphyletic. The high heterogeneity observed within vibrios was congruent with former polyphasic taxonomic studies on this group. Photobacterium species clustered together and apparently nested within vibrios, while Grimontia hollisae was apart from other vibrios. Within the vibrios, Vibrio cholerae and Vibrio mimicus clustered apart from the other genus members. Vibrio harveyi- and Vibrio splendidus-related species formed compact separated groups. On the other hand, species related to Vibrio tubiashii appeared scattered in the phylogenetic tree. The pairs Vibrio coralliilyticus and Vibrio neptunius, Vibrio nereis and Vibrio xuii and V. tubiashii and Vibrio brasiliensis clustered completely apart from each other. There was a correlation of 0·58 between recA and 16S rDNA pairwise similarities. Strains of the same species have at least 94 % recA sequence similarity. recA gene sequences are much more discriminatory than 16S rDNA. For 16S rDNA similarity values above 98 % there was a wide range of recA similarities, from 83 to 99 %.
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Darge, Wendu A., and Samuel S. Woldemariam. "Botryosphaeria Tree Fungal Pathogens and Their Diversity." International Journal of Phytopathology 10, no. 1 (April 30, 2021): 49–56. http://dx.doi.org/10.33687/phytopath.010.01.3447.
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The genus Botryosphaeria identified in 1863 as saprophytes of dead tissue of woody plants have been described as pathogens of economically important plantation trees in agriculture and native forests. The genus is a species-rich, worldwide distributed occurring on diverse host ranges. Species of the Botryosphaeria are reported as the pathogens of many plantation trees, including species of Acacia, Eucalyptus, and Pinus causing canker and rapid dieback diseases which often end up in death. Botryosphaeria fungal pathogens have cross pathogenicity on different host tree species which enables them important and focus area of research. The taxonomy of Botryosphaeria spp. have been under research, identification of these fungi has generally been based on morphological features of the anamorph that usually seen under the microscope. Characters that are used to classify genera in the Botryosphaeria have mostly relied on the macroscopic features of the ascospores and the conidial features. Currently, molecular techniques such as DNA sequencing involving amplification of ITS region are important for exact identification of the genera to species level. Recent molecular, phylogenetic and morphological findings showed that order Botryosphaeriales is diverse consisting nine families and 33 genera with 23 genera only in the family Botryosphaeriaceae. Botryosphaeria spp. are naturally endophytes associated with tree plants known to cause monocyclic or polycyclic diseases resulting in polyetic epidemics. The factor that makes plants more prone to Botryosphaeria fungal species is assumed to be stress or wounding associated with the host plants. Global climate change driven drought is an important factor that initiate stress resulting in nutrient deficiencies. Botryosphaeria fungal tree diseases can be best managed by ensuring plants are in optimal health through appropriate integration of cultural, silvicultural and fungicidal applications to effectively prevent and control the diseases.
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Lestari, Dewi Ayu, Rodiyati Azrianingsih, and H. Hendrian. "Filogenetik Jenis-jenis Annonaceae dari Jawa Timur Koleksi Kebun Raya Purwodadi Berdasarkan Coding dan Non-coding sekuen DNA." Journal of Tropical Biodiversity and Biotechnology 3, no. 1 (April 3, 2018): 1. http://dx.doi.org/10.22146/jtbb.28308.
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Annonaceae species of Purwodadi Botanic Garden collections from East Java encountered problems in species identification based on morphological characters. In addition, the unavailability of molecular data to support identification based on morphological characters hinders accurate identification of species. The aim of this research is to discern phylogenetic of Annonaceae species from East Java collections of Purwodadi Botanic Garden based on coding and non-coding sequence DNA. Annonaceae species used in this study are 30 species, includes outgroup from family of Magnoliaceae. Materials for DNA analysis were young leaves which were processed through DNA extraction, DNA amplification through PCR technique, DNA sequencing and data analysis with Maximum Likelihood (ML), Maximum Parsimony (MP) and Neighbour-Joining (NJ) method analysis. The results show that phylogenetic tree is divided into two subfamilies, i.e. Annonoideae and Malmeoideae. The topology of phylogenetic tree from three DNA molecular marker shows that non-coding sequence DNA (trnL-F molecular marker) has the best grouping of relationship and be able to explain the relationship between species of Annonaceae than rbcL and matK molecular marker as coding sequence DNA. Bootstrap value of trnL-F tree is very weak to high (36-100%) while rbcL is very weak to weak (17-63%) and matK tree is high (98-99%).
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RAVITCHANDIRANE, Vaithilingam, Vaithianathan GEETHA, Vijayan RAMYA, Bilavendiran JANIFER, Muthusamy THANGARAJ, Jayachandran SUBBURAJ, Vellaichamy RAMANADEVI, and Takshnamurthy GANESAN. "Molecular Identification and Phylogenetic Relationships of Threadfin Breams (Family: Nemipteridae) Using mtDNA Marker." Notulae Scientia Biologicae 4, no. 2 (May 10, 2012): 13–18. http://dx.doi.org/10.15835/nsb427602.
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Cytochrome c oxidase-1 gene sequences of mitochondrial genome were analyzed for species identification and phylogenetic relationship among the commercially important Nemipterus species. Sequence analysis of COI gene clearly indicated that all the nine fish species fell into distinct clads, which are genetically distant from each other and exhibited identical phylogenetic reservation. All the COI gene sequences provide sufficient phylogenetic information and evolutionary relationship to distinguish the nine Nemipterus species unambiguously. As per the neighbour-joining (NJ) and maximum likelihood (ML) trees, all the nine species are genetically distant from each other and exhibited identical phylogenetic reservation. Based on the NJ and ML phylogenetic trees N. mesoprion, N. zysron, N. hexodon, N. nematophorus, N. virgatus and N. bipunctatus were closely related with high bootstrap value (97). The overall mean Kimura two parameter (K2P) distances between the nine species was 0.109. The intra species K2P distance was high in N. japonicus (0.069) followed by N. peronii (0.050) and N. mesoprion (0.002). This study proves the use of mtDNA COI gene sequence based approach is an alternative tool for identifying fish species at a faster pace.
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Chung, Jeng-Der, Gordon Nigh, Ching-Te Chien, and Cheng C. Ying. "Genetic Variation and Tree Improvement of Konishii fir (Cunninghamia lanceolata (Lamb.) Hook. var. konishii) in Taiwan." Silvae Genetica 60, no. 1-6 (December 1, 2011): 196–205. http://dx.doi.org/10.1515/sg-2011-0026.
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AbstractWe analyzed a 21-year old progeny test of Konishii fir (Cunninghamia lanceolata(Lamb.) Hook. var.konishii) involving 75 families. Tree height and diameter at breast height (DBH) were periodically recorded. At age 21, average height, DBH, and volume were 15.2 m, 20.2 cm, and 278 dm3, respectively. At this age, family accounted for 9, 12, and 11% of the total variance in height, DBH and volume, respectively. Also at age 21, individual tree heritability was 0.35, 0.49, and 0.45 for height, DBH and volume, respectively, and family heritability was 0.53, 0.69, and 0.66 for the three respective characteristics. The age trend for all genetic parameters was more stable for DBH than for height and volume. Family (backward) selection for DBH at age 21 resulted in a 9.6% gain and indirectly 5.1 and 21.0% gains for height and volume, respectively, compared to 5.2 and 20.1% gains for height and volume, respectively, when selection for these characteristics is done directly. DBH is an effective proxy trait for selection in growth. DBH is also less susceptible than height to typhoon damage, which frequently afflicts tree plantations in Taiwan. Therefore, DBH should be considered as the primary trait for selection for Konishii fir in Taiwan. Konishii fir is a genetically variable species despite its limited geographic range, and is fast growing which makes it a viable candidate species for tree improvement.
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Kamran, Muhammad, Atif Yaqub, Naila Malkani, Khalid Mahmood Anjum, Muhammad Nabeel Awan, and Hamid Paknejad. "Identification and Phylogenetic Analysis of Channa Species from Riverine System of Pakistan Using COI Gene as a DNA Barcoding Marker." Journal of Bioresource Management 7, no. 2 (July 18, 2020): 88–98. http://dx.doi.org/10.35691/jbm.0202.0135.
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Channa are the freshwater and important food fish species in Pakistan belonging to family Channidae. However, identification and phylogenetic analysis based on molecular tools of these species in Pakistan was not well known. Herein, the current investigation was conceptualized, which dealt with mitochondrial DNA sequences from three geographically distinct populations of this species from Pakistan’s water system. DNA from fin tissues was extracted. COI region of mtDNA was amplified using universal primers for fish. PCR products were sequenced. Phylogenetic analysis conducted in the present study, i.e. neighbor-joining (NJ) cladogram, maximum likelihood, K2P genetic divergence and histogram suggests that the studied species of family Channidae are genetically different. The K2P intraspecific divergences were lower than interspecific divergences. The clades in the evolutionary tree for three species were clearly separated.Channa are the freshwater and important food fish species in Pakistan belonging to family Channidae. However, identification and phylogenetic analysis based on molecular tools of these species in Pakistan was not well known. Herein, the current investigation was conceptualized, which dealt with mitochondrial DNA sequences from three geographically distinct populations of this species from Pakistan’s water system. DNA from fin tissues was extracted. COI region of mtDNA was amplified using universal primers for fish. PCR products were sequenced. Phylogenetic analysis conducted in the present study, i.e. neighbor-joining (NJ) cladogram, maximum likelihood, K2P genetic divergence and histogram suggests that the studied species of family Channidae are genetically different. The K2P intraspecific divergences were lower than interspecific divergences. The clades in the evolutionary tree for three species were clearly separated.
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Girard, Geneviève, Bjørn A. Traag, Vartul Sangal, Nadine Mascini, Paul A. Hoskisson, Michael Goodfellow, and Gilles P. van Wezel. "A novel taxonomic marker that discriminates between morphologically complex actinomycetes." Open Biology 3, no. 10 (October 2013): 130073. http://dx.doi.org/10.1098/rsob.130073.
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In the era when large whole genome bacterial datasets are generated routinely, rapid and accurate molecular systematics is becoming increasingly important. However, 16S ribosomal RNA sequencing does not always offer sufficient resolution to discriminate between closely related genera. The SsgA-like proteins are developmental regulatory proteins in sporulating actinomycetes, whereby SsgB actively recruits FtsZ during sporulation-specific cell division. Here, we present a novel method to classify actinomycetes, based on the extraordinary way the SsgA and SsgB proteins are conserved. The almost complete conservation of the SsgB amino acid (aa) sequence between members of the same genus and its high divergence between even closely related genera provides high-quality data for the classification of morphologically complex actinomycetes. Our analysis validates Kitasatospora as a sister genus to Streptomyces in the family Streptomycetaceae and suggests that Micromonospora , Salinispora and Verrucosispora may represent different clades of the same genus. It is also apparent that the aa sequence of SsgA is an accurate determinant for the ability of streptomycetes to produce submerged spores, dividing the phylogenetic tree of streptomycetes into liquid-culture sporulation and no liquid-culture sporulation branches. A new phylogenetic tree of industrially relevant actinomycetes is presented and compared with that based on 16S rRNA sequences.
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Grattapaglia, Dario, Fernando L. G. Bertolucci, Ricardo Penchel, and Ronald R. Sederoff. "Genetic Mapping of Quantitative Trait Loci Controlling Growth and Wood Quality Traits in Eucalyptus grandis Using a Maternal Half-sib Family and RAPD Markers." Genetics 144, no. 3 (November 1, 1996): 1205–14. http://dx.doi.org/10.1093/genetics/144.3.1205.
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Abstract Quantitative trait loci (QTL) mapping of forest productivity traits was performed using an open pollinated half-sib family of Eucalyptus grandis. For volume growth, a sequential QTL mapping approach was applied using bulk segregant analysis (BSA), selective genotyping (SG) and cosegregation analysis (CSA). Despite the low heritability of this trait and the heterogeneous genetic background employed for mapping, BSA detected one putative QTL and SG two out of the three later found by CSA. The three putative QTL for volume growth were found to control 13.7% of the phenotypic variation, corresponding to an estimated 43.7% of the genetic variation. For wood specific gravity five QTL were identified controlling 24.7% of the phenotypic variation corresponding to 49% of the genetic variation. Overlapping QTL for CBH, WSG and percentage dry weight of bark were observed. A significant case of digenic epistasis was found, involving unlinked QTL for volume. Our results demonstrate the applicability of the within half-sib design for QTL mapping in forest trees and indicate the existence of major genes involved in the expression of economically important traits related to forest productivity in Eucalyptus grandis. These findings have important implications for marker-assisted tree breeding.
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Thavamanikumar, Saravanan, Roger J. Arnold, Jianzhong Luo, and Bala R. Thumma. "Genomic Studies Reveal Substantial Dominant Effects and Improved Genomic Predictions in an Open-Pollinated Breeding Population of Eucalyptus pellita." G3: Genes|Genomes|Genetics 10, no. 10 (August 11, 2020): 3751–63. http://dx.doi.org/10.1534/g3.120.401601.
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Most of the genomic studies in plants and animals have used additive models for studying genetic parameters and prediction accuracies. In this study, we used genomic models with additive and nonadditive effects to analyze the genetic architecture of growth and wood traits in an open-pollinated (OP) population of Eucalyptus pellita. We used two progeny trials consisting of 5742 trees from 244 OP families to estimate genetic parameters and to test genomic prediction accuracies of three growth traits (diameter at breast height - DBH, total height - Ht and tree volume - Vol) and kraft pulp yield (KPY). From 5742 trees, 468 trees from 28 families were genotyped with 2023 pre-selected markers from candidate genes. We used the pedigree-based additive best linear unbiased prediction (ABLUP) model and two marker-based models (single-step genomic BLUP – ssGBLUP and genomic BLUP – GBLUP) to estimate the genetic parameters and compare the prediction accuracies. Analyses with the two genomic models revealed large dominant effects influencing the growth traits but not KPY. Theoretical breeding value accuracies were higher with the dominance effect in ssGBLUP model for the three growth traits. Accuracies of cross-validation with random folding in the genotyped trees have ranged from 0.60 to 0.82 in different models. Accuracies of ABLUP were lower than the genomic models. Accuracies ranging from 0.50 to 0.76 were observed for within family cross-validation predictions with low relationships between training and validation populations indicating part of the functional variation is captured by the markers through short-range linkage disequilibrium (LD). Within-family phenotype predictive abilities and prediction accuracies of genetic values with dominance effects are higher than the additive models for growth traits indicating the importance of dominance effects in predicting phenotypes and genetic values. This study demonstrates the importance of genomic approaches in OP families to study nonadditive effects. To capture the LD between markers and the quantitative trait loci (QTL) it may be important to use informative markers from candidate genes.
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Gogorcena, Y., and D. E. Parfitt. "RAPD MARKER DIVERSITY AMONG PAKISTANI APRICOTS." HortScience 27, no. 6 (June 1992): 573e—573. http://dx.doi.org/10.21273/hortsci.27.6.573e.
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A number of 10 base primers were screened to identify RAPD polymorphisms among a population of semi wild apricot genotypes that had been collected by Maxine Thompson in 1988. 30 families collected from trees at 6 locations were analyzed. DNA from leaf tissue of 180 plants, ca. 6 genotypes per family, were isolated and tested against 20 primers. Seven primers were identified that produced consistent results with relatively few (thus, scoreable) and consistent bands. DNA was isolated using the cTAB method and the effects of additional CsCl centrifugation isolation were tested. No differences were found. Reaction conditions were tested to ensure consistent results. Considerable RAPD polymorphism was observed in this population. Parsimony analysis is being conducted to assess the relative variation among and within populations and to determine whether collection location had a more significant effect on DNA variation than other factors such as outcrossing or level of heterogeneity within populations.
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Adeoba, Mariam, Solomon G. Tesfamichael, and Kowiyou Yessoufou. "Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis." Genome 62, no. 3 (March 2019): 170–82. http://dx.doi.org/10.1139/gen-2018-0023.
Full textAbstract:
Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.
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Li, Guang, Xiaopeng An, Jinxing Hou, Ling Li, Dan Han, Mingming Yang, Yana Wang, et al. "Study on polymerization effect of polyembryony genes by SSCP marker and family trees in Chinese goats." Molecular Biology Reports 38, no. 2 (April 7, 2010): 739–44. http://dx.doi.org/10.1007/s11033-010-0161-8.
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Romanowski ,, Carol J., and Rakesh Nagi. "A Data Mining Approach to Forming Generic Bills of Materials in Support of Variant Design Activities." Journal of Computing and Information Science in Engineering 4, no. 4 (December 1, 2004): 316–28. http://dx.doi.org/10.1115/1.1812556.
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In variant design, the proliferation of bills of materials makes it difficult for designers to find previous designs that would aid in completing a new design task. This research presents a novel, data mining approach to forming generic bills of materials (GBOMs), entities that represent the different variants in a product family and facilitate the search for similar designs and configuration of new variants. The technical difficulties include: (i) developing families or categories for products, assemblies, and component parts; (ii) generalizing purchased parts and quantifying their similarity; (iii) performing tree union; and (iv) establishing design constraints. These challenges are met through data mining methods such as text and tree mining, a new tree union procedure, and embodying the GBOM and design constraints in constrained XML. The paper concludes with a case study, using data from a manufacturer of nurse call devices, and identifies a new research direction for data mining motivated by the domains of engineering design and information.
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Kumar, Satish, and D. J. Garrick. "Genetic response to within-family selection using molecular markers in some radiata pine breeding schemes." Canadian Journal of Forest Research 31, no. 5 (May 1, 2001): 779–85. http://dx.doi.org/10.1139/x01-009.
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Marker-assisted selection (MAS) provides an opportunity to increase the efficiency of within-family selection in forest tree breeding. Within-family MAS involves selection decisions first made on conventional breeding values and quantitative trait loci (QTL) information used for within-family selection. In this study genetic response obtained by using MAS was compared with conventional methods for three options: "full-sib family forestry," "clonal forestry," and "forward selection for deployment." This comparison was undertaken using stochastic simulation for a locus that explained 10 or 20% of the genetic variance. In the full-sib family forestry scenario, markers were used to select genotypes (among juvenile individuals in a family) for vegetative propagation. Markers were used to preselect genotypes for clonal testing in clonal forestry option. In case of forward selection for deployment option, offspring that have favourable marker haplotype and a superior phenotype were selected from each family. The comparison between the MAS and the conventional strategy was evaluated in genetic terms based on comparison of the average genetic merit of the genotypes used for deployment in production plantations. The relative genetic gain (%) using MAS were found to be 48% and 23% higher compared with conventional strategy for full-sib family forestry and clonal forestry options, respectively. In case of forward selection for deployment option, MAS was generally found to be providing higher genetic gain only when the heritability is low.
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Kubach, Jan, Petra Lutter, Tobias Bopp, Sabine Stoll, Christian Becker, Eva Huter, Christoph Richter, et al. "Human CD4+CD25+ regulatory T cells: proteome analysis identifies galectin-10 as a novel marker essential for their anergy and suppressive function." Blood 110, no. 5 (September 1, 2007): 1550–58. http://dx.doi.org/10.1182/blood-2007-01-069229.
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Abstract CD4+CD25+Foxp3+ regulatory T cells (CD25+ Treg cells) direct the maintenance of immunological self-tolerance by active suppression of autoaggressive T-cell populations. However, the molecules mediating the anergic state and regulatory function of CD25+ Treg cells are still elusive. Using differential proteomics, we identified galectin-10, a member of the lectin family, as constitutively expressed in human CD25+ Treg cells, while they are nearly absent in resting and activated CD4+ T cells. These data were confirmed on the mRNA and protein levels. Single-cell staining and flow cytometry showed a strictly intracellular expression of galectin-10 in CD25+ Treg cells. Specific inhibition of galectin-10 restored the proliferative capacity of CD25+ Treg cells and abrogated their suppressive function. Notably, first identified here as expressed in human T lymphocytes, galectin-10 is essential for the functional properties of CD25+ Treg cells.
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Nagpal, R., V. G. Jhanwar, A. K. Mital, and E. M. D. Warrier. "IECs, Drug Trials and Regulators–the Hounds Barking up the Wrong Tree." European Psychiatry 41, S1 (April 2017): S612. http://dx.doi.org/10.1016/j.eurpsy.2017.01.971.
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As India hurtles on into the 21st century with dizzying speed, the constantly evolving ethics, law and its interpretations fall behind. The cut and paste policy makers constantly impose regulations out of sync with the geopolitical realities. The Mental Health Care Bill now awaiting approval arose because we signed first on a global body convention and now are forced to comply. The family, a ubiquitous feature of our patient support system is slowly being derecognized. Instead, NGOs are the new approved caregivers. Our patriarchal society, earlier a repository of warmth and security is now jeered at. The mental health professional, the last mile delivery of mental health is in a quixotic position and some of the tantalizing issues of surreptitious drug administration, informed consent, the newer laws enacted or being enacted, narcoanalysis and drug trials will be discussed with pragmatic solutions offered to a disinterested regulator.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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Hiesl, Patrick, and Shari L. Rodriguez. "Quantifying the Impact of a Flood and Hurricane Event on Tree Farms in South Carolina: A Survey." Forests 10, no. 7 (June 29, 2019): 546. http://dx.doi.org/10.3390/f10070546.
Full textAbstract:
Natural disturbances in forested landscapes are increasing in frequency. Hurricanes and flooding events can cause extreme damages to forested ecosystems and the forest products industry. The state of South Carolina experienced four major hurricanes and flooding events between 2015 and 2018. A survey was sent out to the members of the American Tree Farm System (ATFS) in South Carolina in 2017 to better understand the impact of two of these events—the historical flood of October 2015 and hurricane Matthew in October 2016—on family forest operations. Forty-eight percent of surveys were returned. Surveys were received from all counties except one. Average losses of $6.21/acre and $6.48/acre for flood and hurricane damage, respectively, were reported across all of the respondents. Major damage from the flood was reported to be on forest roads, while uprooted and broken trees were the most reported damage from the hurricane. Extrapolating damages to the state level indicated total estimated damages that were in excess of $80 million for each event. The responses also showed that only one-third of respondents were aware of disaster relief programs and less than 2% actually received financial aid. The results from this survey provide forest managers, policy makers, and extension personnel with information regarding the damages that were associated with the 2015 flood and the 2016 hurricane. Events such as these are bound to happen again in the future and information from this survey may allow foresters, policy makers, and forestry associations to refine the ways that financial aid information is distributed to increase the awareness of these programs.
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Adeoba, Mariam I., Ronny Kabongo, Herman Van der Bank, and Kowiyou Yessoufou. "Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)." ZooKeys 746 (March 26, 2018): 105–21. http://dx.doi.org/10.3897/zookeys.746.13502.
Full textAbstract:
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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Adeoba, Mariam I., Ronny Kabongo, Herman Van der Bank, and Kowiyou Yessoufou. "Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)." ZooKeys 744 (March 19, 2018): 67–84. http://dx.doi.org/10.3897/zookeys.744.13502.
Full textAbstract:
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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Adeoba, Mariam I., Ronny Kabongo, Herman Van der Bank, and Kowiyou Yessoufou. "Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)." ZooKeys 740 (March 1, 2018): 97–113. http://dx.doi.org/10.3897/zookeys.740.13502.
Full textAbstract:
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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García-Díaz, Vicente, Edward Rolando Núñez-Valdez, Cristian González García, Alberto Gómez-Gómez, and Rubén González Crespo. "JGraphs: A Toolset to Work with Monte-Carlo Tree Search-Based Algorithms." International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems 28, Supp02 (December 2020): 1–22. http://dx.doi.org/10.1142/s0218488520400115.
Full textAbstract:
Monte-Carlo methods are the basis for solving many computational problems using repeated random sampling in scenarios that may have a deterministic but very complex solution from a computational point of view. In recent years, researchers are using the same idea to solve many problems through the so-called Monte-Carlo Tree Search family of algorithms, which provide the possibility of storing and reusing previously calculated results to improve precision in the calculation of future outcomes. However, developers and researchers working in this area tend to have to carry out software developments from scratch to use their designs or improve designs previously created by other researchers. This makes it difficult to see improvements in current algorithms as it takes a lot of hard work. This work presents JGraphs, a toolset implemented in the Java programming language that will allow researchers to avoid having to reinvent the wheel when working with Monte-Carlo Tree Search. In addition, it will allow testing experiments carried out by others in a simple way, reusing previous knowledge.
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Suriani, Cicik, Eko Prasetya, Tri Harsono, Johannes Manurung, Hary Prakasa, Dina Handayani, Miftahul Jannah, and Yuanita Rachmawati. "DNA Barcoding of Andaliman (Zanthoxylum acanthopodium DC) from North Sumatra Province of Indonesia using maturase K Gene." Tropical Life Sciences Research 32, no. 2 (June 29, 2021): 15–28. http://dx.doi.org/10.21315/tlsr2021.32.2.2.
Full textAbstract:
Andaliman (Zanthoxylum acanthopodium DC) is a native plant of North Sumatra province. Zanthoxylum acanthopodium is a member of Rutaceae family widely found in northern Sumatra, Indonesia. The aim of this study was to barcode Z. acanthopodium in North Sumatra province, Indonesia based on cpDNA maturase K (matK). Samples were collected in seven localities across six regions of North Sumatra province. Phylogenetic analysis was conducted using Maximum Likelihood method. The results of phylogenetic analysis indicate that Z. acanthopodium is a monophyletic group that is derived from a common ancestor. The results of the phylogenetic tree construction show that there is a grouping of accession between Z. acanthopodium species separate from other species in the Zanthoxylum genus as well as those of the Rutaceae family. The results showed that cpDNA matK marker can effectively be used as DNA barcoding to identify Z. acanthopodium.
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Izod, John, and Joanna Dovalis. "Ogni pensiero vola: the embodied psyche in Terrence Malick's The Tree of Life." International Journal of Jungian Studies 6, no. 2 (May 4, 2014): 151–58. http://dx.doi.org/10.1080/19409052.2014.906484.
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The Tree of Life touches on embodiment of the soul in an early sequence covering courtship, marriage and the first pregnancy of a young couple. In a delicate formal scene, Mrs O'Brien, nearing full term, treads gently along a river's edge summoning infant souls luminous in white linen. She opens a minute book of life to one of them, preparing his entry through the iron gates that open on embodied life. Presently, the infant soul rises up from his underwater home beyond the reach of conscious awareness: Mrs O'Brien gives birth to her first son, Jack. This is the boy who will eventually become a middle-aged man in crisis. Ravaged then by grief for his long-dead younger brother and his own inability to live at peace with his family or himself, his memories, visions and reflections accumulate in a way that makes him a suffering Hermes for the early twenty-first century. The initiating episode of the infant's birth complements the embodied and affective experiences of those in the audience who accept the film's sensual invitation to steep themselves in the immense scale of its gorgeous sounds and images. They then discover on the pulse that, more than the history of one Texan family, it attempts nothing less than the necessary re-creation of the godhead for the early twenty-first century. Contrary to the rigid medieval dogmas of so many orthodox religions, The Tree of Life assures us not of a changeless eternity but rather the sacred and ceaseless metamorphosis of numinous energy.
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Baird, Vance. "Progress in Prunus Mapping and Application of Molecular Markers to Germplasm Improvement." HortScience 30, no. 4 (July 1995): 748–49. http://dx.doi.org/10.21273/hortsci.30.4.748.
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Prunus, which includes peach/nectarine, almond, apricot, cherry, and plum, is a large and economically important genus in the family Rosaceae. The size and long generation time of these tree crops have hampered improvement through classical breeding and long-term selection programs. With the advent of DNA-based molecular diagnostics, an exciting era in germplasm improvement has dawned. Efforts are underway, notably in the United States (e.g., California, Michigan, North Carolina, and South Carolina) and the European Community (e.g., England, France, Italy, and Spain), to apply the tools of molecular mapping and marker-assisted selection to this important genus. The objective of these projects is to develop molecular linkage maps of sufficient marker density to tag phenotypic trait loci of agronomic importance. These include traits controlled by single genes (e.g., flower color, compatibility, flesh color, pest resistance), as well as more-complex, quantitative traits (e.g., cold hardiness, tree architecture, sugar content). An immediate outcome of these mapping efforts has been the development of DNA “fingerprints,” allowing for the discrimination of cultivars—both scion and rootstock. The maps will be used by breeders and molecular biologists to monitor gene introgression from wild species into elite lines, for marker-assisted selection of desired trait combinations, and for map-based cloning of specific genes. The molecular markers used in these mapping projects include RFLPs, RAPDs, and microsatellites. Each has their appropriate applications and advantages depending upon the resources at hand and the project's specific goals.
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Yan, Si Qi, Xiao Hong Liu, Ling Zhi Wei, Xiao Hui Zhou, Liu Yang, and Xiao Ping Lu. "Preliminary Study of Compositae Family Plants Classification Based on Petal Pigments." Advanced Materials Research 955-959 (June 2014): 751–57. http://dx.doi.org/10.4028/www.scientific.net/amr.955-959.751.
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Abatract: Choose 32Compositaefamily plants which come from 14 different species (mainly based on yellow petals) were chosed, extract their pigments with anhydrous ethanol and N-butyl alcohol: Formic acid: water=4:1:2(in volume) as solution for chromatographywere extracted, and observe each petal band under 254nm ultraviolet light and write down Rf value of each band was observed. In the end, using NTSYS-pc 2.10e software to construct petal pigments phylogenetic tree with UPGMA method. The cluster analysis suggested that petal pigments of 32Compositaefamily plants had certain polymorphism, and they could be classified into 4 groups at 0.70. In the 4 groups, most of the material (81.25%) belonged to group I, and the rest were classified into group II、III、IV respectively. Most of them which had a close relationship could be in one group, and those had remote relationship could be distinguished from each other.Classification ofCompositaespecies based on petal pigments is feasible, which has an advantage of rapid, stable, low-carbon, environmental friendly when compared with mmolecular marker technology.
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Li, Huiguang, Yanli Yang, Houling Wang, Sha Liu, Fuli Jia, Yanyan Su, Shuang Li, et al. "The Receptor-Like Kinase ERECTA Confers Improved Water Use Efficiency and Drought Tolerance to Poplar via Modulating Stomatal Density." International Journal of Molecular Sciences 22, no. 14 (July 6, 2021): 7245. http://dx.doi.org/10.3390/ijms22147245.
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Poplar is one of the most important tree species in the north temperate zone, but poplar plantations are quite water intensive. We report here that CaMV 35S promoter-driven overexpression of the PdERECTA gene, which is a member of the LRR-RLKs family from Populus nigra × (Populus deltoides × Populus nigra), improves water use efficiency and enhances drought tolerance in triploid white poplar. PdERECTA localizes to the plasma membrane. Overexpression plants showed lower stomatal density and larger stomatal size. The abaxial stomatal density was 24–34% lower and the stomatal size was 12–14% larger in overexpression lines. Reduced stomatal density led to a sharp restriction of transpiration, which was about 18–35% lower than the control line, and instantaneous water use efficiency was around 14–63% higher in overexpression lines under different conditions. These phenotypic changes led to increased drought tolerance. PdERECTA overexpression plants not only survived longer after stopping watering but also performed better when supplied with limited water, as they had better physical and photosynthesis conditions, faster growth rate, and higher biomass accumulation. Taken together, our data suggest that PdERECTA can alter the development pattern of stomata to reduce stomatal density, which then restricts water consumption, conferring enhanced drought tolerance to poplar. This makes PdERECTA trees promising candidates for establishing more water use efficient plantations.
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Liesebach, H., and V. Schneck. "Chloroplast DNA variation in planted and natural regenerated stands of black locust (Robinia pseudoacacia L.)." Silvae Genetica 61, no. 1-6 (December 1, 2012): 27–35. http://dx.doi.org/10.1515/sg-2012-0004.
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AbstractBlack locust (Robinia pseudoacacia L.), native in mountainous regions in USA, is increasing in importance for forestry in many countries as a „multi-purpose tree“ associated with breeding efforts at the family and clonal levels. A few population genetic studies exist with nuclear, codominantly inherited markers. Here we present an additional marker type, the maternally inherited chloroplast haplotypes. The studied material included samples from the natural range and from artificial stands from three European countries as well as samples from a clone collection. Eleven haplotypes belonging to two clearly separated groups of related haplotypes were found using the PCR-RFLP method. The variation pattern of chloroplast haplotypes in artificial stands is strongly influenced by the local silvicultural management.
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Steele-Petrovich, H. Miriam. "Replacement name for Tetradium Dana, 1846." Journal of Paleontology 85, no. 4 (July 2011): 802–3. http://dx.doi.org/10.1666/10-137.1.
Full textAbstract:
It was shown recently that Tetradium Dana, 1846 (type species: Tetradium fibratum Safford, 1856), a common Middle and Upper Ordovician fossil, is a calcareous filamentous florideophyte alga (Phylum Rhodophyta) (Steele-Petrovich, 2009a, 2009b), and not a tabulate coral or a chaetetid sponge, as traditionally classified. Reassigning Tetradium Dana from an animal to an alga subjects it to the International Code of Botanical Nomenclature (ICBN) (McNeill et al., 2006), which makes it a later homonym of Tetradium Loureiro, 1790 (see Farr et al., 1979), a Recent tree of the citrus family (Rutaceae). According to the ICBN (Articles 14, 53.1, 54.1), the name Tetradium Dana cannot be conserved and must be replaced, since Tetradium Loureiro is currently in use.
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Sequeira, Fernando, Nuno Ferrand, and D. James Harris. "Assessing the phylogenetic signal of the nuclear β-Fibrinogen intron 7 in salamandrids (Amphibia: Salamandridae)." Amphibia-Reptilia 27, no. 3 (2006): 409–18. http://dx.doi.org/10.1163/156853806778190114.
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AbstractThe potential of the seventh intron of the β-subunit of the fibrinogen gene (β-fibint 7) for phylogenetic analysis within the Salamandridae family was explored, comparing the topologies of trees based on this marker to those based on mitochondrial 12S rRNA gene previously published. Using primers designed specifically for amphibians, we amplified 25 sequences of β-fibint 7 corresponding to 15 species of salamandrids and one plethodontid species. There was considerable length variation among the β-fibint 7 sequences examined, ranging from 1123 bp in S. atra to 400 bp in P. waltl. Many aspects of the phylogenetic relationships estimated by the two independent loci were congruent and corroborate current taxonomic hypothesis. Although the number of taxa analysed is small, the data obtained in this work suggested that β-fibint 7 is a useful marker for assessing phylogenetic relationships within the Salamandridae family, and is probably appropriate for phylogenetic studies among closely related salamanders that have diverged over the last 20 Myr.
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Sanchez, Gustavo, Davin H. E. Setiamarga, Surangkana Tuanapaya, Kittichai Tongtherm, Inger E. Winkelmann, Hannah Schmidbaur, Tetsuya Umino, et al. "Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas." PeerJ 6 (February 12, 2018): e4331. http://dx.doi.org/10.7717/peerj.4331.
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Comprising more than 800 extant species, the class Cephalopoda (octopuses, squid, cuttlefish, and nautiluses) is a fascinating group of marine conchiferan mollusks. Recently, the first cephalopod genome (of Octopus bimaculoides) was published, providing a genomic framework, which will enable more detailed investigations of cephalopod characteristics, including developmental, morphological, and behavioural traits. Meanwhile, a robust phylogeny of the members of the subclass Coleoidea (octopuses, squid, cuttlefishes) is crucial for comparative and evolutionary studies aiming to investigate the group’s traits and innovations, but such a phylogeny has proven very challenging to obtain. Here, we present the results of phylogenetic inference at the genus level using mitochondrial and nuclear marker sequences available from public databases. Topologies are presented which show support for (1) the monophyly of the two main superorders, Octobrachia and Decabrachia, and (2) some of the interrelationships at the family level. We have mapped morphological characters onto the tree and conducted molecular dating analyses, obtaining congruent results with previous estimates of divergence in major lineages. Our study also identifies unresolved phylogenetic relationships within the cephalopod phylogeny and insufficient taxonomic sampling among squids excluding the Loliginidae in the Decabrachia and within the Order Cirromorphida in the Octobrachia. Genomic and transcriptomic resources should enable resolution of these issues in the relatively near future. We provide our alignment as an open access resource, to allow other researchers to reconstruct phylogenetic trees upon this work in the future.
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REIS, ROBERTO E., HERALDO A. BRITSKI, MARCELO R. BRITTO, PAULO A. BUCKUP, BÁRBARA B. CALEGARI, PRISCILA CAMELIER, MARIA LAURA S. DELAPIEVE, et al. "Poor taxonomic sampling undermines nomenclatural stability: A reply to Roxo et al. (2019)." Zootaxa 4701, no. 5 (December 2, 2019): 497–500. http://dx.doi.org/10.11646/zootaxa.4701.5.10.
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A recent study based on genomic data by Roxo et al. (2019) provided a phylogeny of the Loricariidae, the largest catfish family and second largest Neotropical fish family with approximately 1,000 species. The study represents a valuable and innovative contribution for understanding higher-level relationships within the family. The phylogenetic tree inferred by Roxo et al. (2019) thoroughly corroborates the monophyly and relationships of most currently accepted subfamilies of Loricariidae, based on a fair taxon sampling (nearly 14% of the species in the family) representing most genera of each but one of the subfamilies, the Lithogeninae, the sister-group of the remaining members of the family (Pereira & Reis, 2017; Reis et al., 2017). In addition to a hypothesis of relationships, Roxo et al. (2019) also proposed a series of lower-level taxonomic changes, which are deemed premature considering that the taxonomic sampling of the study targeted higher-level clades, and go against one of the pillars of biological classification: nomenclatural stability (e.g., Heterick & Majer, 2018; Beninger & Backeljau, 2019). Here we (1) discuss implications of inadequate taxonomic sampling as a basis for changes in classification of species; (2) explain why the taxonomic sampling design of Roxo et al. (2019) is inadequate for the proposed nomenclatural changes; and (3) advocate that changes to classifications must be grounded on phylogenies with dense sampling of taxa at the relevant level.
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Baeza, J. Antonio. "Molecular phylogeny of porcelain crabs (Porcellanidae:Petrolisthesand allies) from the south eastern Pacific: the generaAllopetrolisthesandLiopetrolisthesare not natural entities." PeerJ 4 (March 10, 2016): e1805. http://dx.doi.org/10.7717/peerj.1805.
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Porcelain crabs from the closely related generaPetrolisthes,Liopetrolisthes, andAllopetrolisthesare known for their diversity of lifestyles, habitats, and coloration. The evolutionary relationships among the species belonging to these three genera is not fully resolved. A molecular phylogeny of the group may help to resolve the long-standing taxonomic question about the validity of the generaAllopetrolisthesandLiopetrolisthes. Using both ‘total evidence’ and single-marker analyses based on a 362-bp alignment of the 16S rRNA mitochondrial DNA and a 328-bp alignment of the Histone 3 nuclear DNA, the phylogenetic relationships among 11 species fromPetrolisthes(6 species),Liopetrolisthes(2 species), andAllopetrolisthes(3 species), all native to the south eastern Pacific, were examined. The analyses supported three pairs of sister species:L. mitra+L. patagonicus,P. tuberculatus+P. tuberculosus, andA. angulosus+A. punctatus. No complete segregation of species, according to genera, was evident from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of an alternative tree in which monophyly of the three genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the generaPetrolisthes,Liopetrolisthes, andAllopetrolisthes. Taking into account the above and other recent molecular phylogenetic analyses focused on other representatives from the family Porcellanidae, it is tentatively proposed to eliminate the generaLiopetrolisthesandAllopetrolisthes, and to transfer their members to the genusPetrolisthes.
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Witmer, P. D. "The Development of a Highly Informative Mouse Simple Sequence Length Polymorphism (SSLP) Marker Set and Construction of a Mouse Family Tree Using Parsimony Analysis." Genome Research 13, no. 3 (March 1, 2003): 485–91. http://dx.doi.org/10.1101/gr.717903.
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Li, Xiang, Xiao-Ting Liu, Jia-Tong Wei, Yan Li, Mulualem Tigabu, and Xi-Yang Zhao. "Genetic Improvement of Pinus koraiensis in China: Current Situation and Future Prospects." Forests 11, no. 2 (January 28, 2020): 148. http://dx.doi.org/10.3390/f11020148.
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Pinus koraiensis (Sieb.et Zucc) is an economically and ecologically important tree species, naturally distributed in northeastern China. Conservation efforts and genetic improvement for this species began in the 1960s and 1980s, with the establishment of several primary seed orchards based on range-wide provenance evaluations. The original breeding objective was to improve growth and wood yield, but during the recent decade, it was redefined to include other traits, such as an enhancement of wood properties, seed oil content, cone yield, and the development of elite provenance with families, clones, and varieties with good tolerance to biotic and abiotic stresses. However, improvement processes are slow due to a long breeding cycle, and the number of improved varieties is still low. In this review, we summarize the recent progress in the selective improvement of P. koraiensis varieties, such as elite provenance, family, and clones, using various breeding procedures. We collate information on advances in the improvement of P. koraiensis, based on conventional breeding and molecular marker-assisted breeding methods; identify gaps in our understanding of the tree improvement processes; and propose future research directions, which will provide new insight for subsequent genetic breeding research on P. koraiensis.
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Maajida Aafreen M, Geetha RV, and Lakshmi Thangavelu. "Evaluation oEvaluation of anti-inflammatory action of Laurus nobilis-an in vitro studyf anti-inflammatory action of Laurus nobilis-an in vitro study." International Journal of Research in Pharmaceutical Sciences 10, no. 2 (April 14, 2019): 1209–13. http://dx.doi.org/10.26452/ijrps.v10i2.408.
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Bay leaf is also called as Laurus nobilis an aromatic evergreen tree or large shrub with green, glabrous leaves, in the flowering plant family Lauraceae. It is native to the Mediterranean region and is used as a bay leaf for seasoning in cooking. Its common names include bay laurel, sweet bay, bay (esp. United Kingdom) true laurel, Grecian laurel, laurel tree or simply laurel. Bay leaf refers to the aromatic leaves of several plants which are used in cooking for their distinctive flavour and fragrance. It has many medicinal properties which can also be used to treat cancer as well as gastric problems. Bay leaf is also commonly used to treat muscles and joint pain. Aqueous extracts of bay laurel can also be used as astringents and even as a reasonable salve for open wounds. The anti-inflammatory activity of bay leaf was determined but its ability to inhibit protein denaturation where denaturation of proteins is a well-documented cause of inflammation. The anti-inflammatory effect of the herb was comparable to reference analgesics and non-steroid anti-inflammatory drugs. The present study makes the herb worthy of further investigation.
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Dong, He, Zhao, Zhang, Yuan, and Zhang. "Genetic Mapping of Prince Rupprecht’s Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing." Genes 10, no. 8 (July 31, 2019): 583. http://dx.doi.org/10.3390/genes10080583.
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A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.
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ENACHE, Iuliana-Maria, Gigi COMAN, Sanda ROȘCA, Camelia VIZIREANU, and Liliana MIHALCEA. "The optimization of a conventional extraction of bioactive compounds from Cornus mas by RSM and the determination of favourability factors by GIS technique." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 49, no. 2 (June 14, 2021): 12307. http://dx.doi.org/10.15835/nbha49212307.
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Rich in vitamins, polyphenols, carotenoids, carbohydrates, with a high antioxidant activity, cornelian cherry (Cornus mas) is one of the 65 species of Cornaceae family, fruits that are used in food industry, cosmetic industry or homeopathic medicine. The valuable bioactive compounds and the high economical potential of this tree makes suitable to be considered as a raw material to study the optimum extraction conditions in order to maximize the bioactive compounds’ concentration. In this study, the main purpose was to investigate both the favourable and restrictive conditions for Cornus mas using the GIS technique. The Remote Sensing and Geographic Information Systems (GIS) technique indicated the favourability factors for Cornus mas trees in Romania country. The response surface methodology was employed to study the effect of temperature, time and solvent concentration on the flavonoids’ (TFC) and polyphenols (TPC) concentrations and the antioxidant activity values. The maximum concentration of TPC (24.70 mg GAE/g raw material) and TFC (1.36 mg QE/g raw material) were obtained with 60% ethanol concentration at different temperature and time values. The cube model with centred faces for the Box-Behnken central composition revealed the highest value of the concentration of TAA (101.31 mg TE/g raw material) at 100% ethanol concentration, 50 °C extraction temperature and the maximum extraction time of 30 min. The most relevant variable was the solvent concentration and the obtained results suggested that the central-face cube model (86% for TPC, 97% for TFC and 95% antioxidant activity) approximated the experimental data.
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Orozco Ávila, Javier, Argemiro Valencia Marín, and Jhon Fredy Betancur Pérez. "Estimation of the transfer of vascular epiphytes, as a conservation strategy in the municipality of Aguazul, Casanare, Colombia." Revista de Investigación Agraria y Ambiental 8, no. 1 (June 5, 2017): 27–37. http://dx.doi.org/10.22490/21456453.1830.
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Epiphytes are plants that grow mainly attached to trunks, branches of trees and shrubs. This research was conducted in the municipality of Aguazul, Casanare, Colombia, in order to evaluate conservation strategies through the transfer and recovery of vascular epiphytes. The selected population was 119 individuals. The variables were number of leaves, number of flowers, number of fruits, mortality rate, herbivory and associated entomofauna. The information collected was analyzed using descriptive statistics. As a result, it was found that the Bromeliaceae Family had the highest leaf development in the three monitorings. Bromeliaceae and Cactaceae Families did not present flowering and Orchidaceae presented low flowering. Fruiting had a similar behavior for these three families. Cactaceae Family did not present mortality, Orchidaceae recorded 2.02% and Bromeliaceae Family recorded 5.56% of mortality. As for herbivory, the orchid family filed a percentage of 0.06%; the Bromeliaceae Family reported 0.11%, while the cactus family did not record any kind. The entomofauna was found mainly in the Formicidae group for the three families, being the Cactaceae Family the one with a greater association, with 100%. According to the results, it is possible to move the vascular epiphytic species to new habitats, which makes it a viable alternative for revegetation of the affected area with conservation purposes.
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Koido, Tatsuki, Yukimitsu Imahara, and Hironobu Fukami. "High species diversity of the soft coral family Xeniidae (Octocorallia, Alcyonacea) in the temperate region of Japan revealed by morphological and molecular analyses." ZooKeys 862 (July 9, 2019): 1–22. http://dx.doi.org/10.3897/zookeys.862.31979.
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The soft coral family Xeniidae, commonly found in tropical and subtropical regions, consists of 20 genera and 162 species. To date, few studies on this family have been conducted in Japan, especially at higher latitudes. Although molecular phylogenetic analyses have recently been used to distinguish soft coral species, it is difficult to identify species and genera in this family due to the limited taxonomic indices and high morphological variation. In this study, we found a large Xeniidae community off the coast of Oshima Island (31°31.35'N, 131°24.27'E) at Miyazaki, Kyushu Island, located in the temperate region of Japan. The species composition and molecular phylogenetic relationships were investigated to uncover the species diversity of Xeniidae in this community. A total of 182 xeniid specimens were collected and identified to the species level, after which the samples were molecularly analyzed using a mitochondrial marker (ND2) and a nuclear marker (ITS) to infer the phylogenetic relationships. A total of 14 xeniid species were identified, including five undescribed species from five genera (Anthelia, Heteroxenia, Sympodium, Xenia, and Yamazatum). Miyazaki was identified as having the highest xeniid species diversity in Japan. The molecular phylogenetic trees inferred from each marker recovered very similar topologies: four genera (Anthelia, Heteroxenia, Sympodium, and Yamazatum) were monophyletic, whereas one (Xenia) was polyphyletic. Thus, except for Xenia, the morphological characteristics used for traditional taxonomy well reflected the phylogeny of the Xeniidae at the genus level. On the other hand, our results show that further taxonomic revisions of Xenia are needed.