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Zeb, Umar, Xiukang Wang, Sajid Fiaz, et al. "Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis." PLOS ONE 17, no. 1 (2022): e0262040. http://dx.doi.org/10.1371/journal.pone.0262040.
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Pinus is one of the most economical and ecological important conifers, model specie for studying sequence divergence and molecular phylogeney of gymnosperms. The less availability of information for genome resources enable researchers to conduct evolutionary studies of Pinus species. To improve understanding, we firstly reported, previously released chloroplast genome of 72 Pinus species, the sequence variations, phylogenetic relationships and genome divergence among Pinus species. The results displayed 7 divergent hotspot regions (trnD-GUC, trnY-GUA, trnH-GUG, ycf1, trnL-CAA, trnK-UUU and trnV-GAC) in studied Pinus species, which holds potential to utilized as molecular genetic markers for future phylogenetic studies in Pinnus species. In addition, 3 types of repeats (tandem, palindromic and dispersed) were also studied in Pinus species under investigation. The outcome showed P. nelsonii had the highest, 76 numbers of repeats, while P. sabiniana had the lowest, 13 13 numbers of repeats. It was also observed, constructed phylogenetic tree displayed division into two significant diverged clades: single needle (soft pine) and double-needle (hard pine). Theoutcome of present investigation, based on the whole chloroplast genomes provided novel insights into the molecular based phylogeny of the genus Pinus which holds potential for its utilization in future studies focusing genetic diversity in Pinnus species.
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LÖRZ, ANNE-NINA. "Deep-sea Rhachotropis (Crustacea: Amphipoda: Eusiridae) from New Zealand and the Ross Sea with key to the Pacific, Indian Ocean and Antarctic species." Zootaxa 2482, no. 1 (2010): 22. http://dx.doi.org/10.11646/zootaxa.2482.1.2.
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The amphipod genus Rhachotropis has a worldwide distribution. Four species new to science are described, increasing the total number of Rhachotropis species to 59. Only one species was previously known from New Zealand and none from the Ross Sea. Two species Rhachotropis chathamensis sp. nov. and R. delicata sp. nov. were collected at the same station in 420 m depth off eastern New Zealand; R. rossi sp. nov. and R. abyssalis sp. nov. were collected below 3000 m depth in the Ross Sea, Antarctica. Investigation of recently collected material as well as historic material from the NIWA Invertebrate collection revealed several specimens of Rhachotropis antarctica K.H. Barnard, 1932 sampled in the Ross Sea. Four damaged Rhachotropis specimens, recently collected from 5170 m in the Kermadec Trench, north of New Zealand, are reported. Epibionts have been discovered on the mouthparts of several specimens from New Zealand as well as the Ross Sea. Preliminary molecular investigations of the phylogeney of Rhachotropis are briefly discussed. A key to Pacific, Indian Ocean and Antarctic species of Rhachotropis is provided.
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Gawel, Nick J., Rory Mellinger, Eric Stout, and R. Sauve. "RAPD Analysis of Acer." HortScience 30, no. 4 (1995): 813F—813. http://dx.doi.org/10.21273/hortsci.30.4.813f.
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DNA from 27 Acer species was used for RAPD analysis. A relatively high number of phylogenically informative polymorphisms were detected, as would be expected in intraspecific comparisons. Principle coordinates analysis was used to discern groupings among the species and a RAPD-based phylogeny was constructed. As expected when making comparisons among species, very high levels of polymorphism were found. Cultivars that grouped together in the principle components analysis also grouped together in the phylogenic analysis. Parts of the phylogenic analysis do not agree with morphology-based phylogenies. This may be due to poor correlation between morphological and DNA markers, or perhaps RAPDs may be too discriminatory to be used for interspecies comparisons. The extremely high level of between-species variation coupled with the low level of within-species variation, indicates the potential of DNA-based identification and discrimination of Acer species is high.
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Golding, G. Brian. "Reconstructing the Prior Probabilities of Allelic Phylogenies." Genetics 161, no. 2 (2002): 889–96. http://dx.doi.org/10.1093/genetics/161.2.889.
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Abstract In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually “rare” topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4Nμ (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions.
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Stadler, Tanja, and Jana Smrckova. "Estimating shifts in diversification rates based on higher-level phylogenies." Biology Letters 12, no. 10 (2016): 20160273. http://dx.doi.org/10.1098/rsbl.2016.0273.
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Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i.e. phylogenies where one species per genus or family is included. We conduct a simulation study to validate our method in a maximum-likelihood framework. Further, this method has already been introduced into the Bayesian package M r B ayes , which led to new insights into the evolution of Hymenoptera.
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Palmer, Marike, Stephanus N. Venter, Alistair R. McTaggart, et al. "The synergistic effect of concatenation in phylogenomics: the case in Pantoea." PeerJ 7 (April 16, 2019): e6698. http://dx.doi.org/10.7717/peerj.6698.
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With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.
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Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2462–77. http://dx.doi.org/10.1098/rstb.2011.0025.
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Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of ‘regime changes’—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be ‘downshifts’. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of ‘rules’. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.
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Xie, Pingxuan, Lilei Tang, Yanzhen Luo, Changkun Liu, and Hanjing Yan. "Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae." Biology 12, no. 2 (2023): 263. http://dx.doi.org/10.3390/biology12020263.
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Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.
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Mehregan, I., K. Ghanbarpour, and M. M. Shamsabad. "EVOLUTION OF PERICARP SURFACE STRUCTURE IN NEPETA S. S. (LAMIACEAE) AS INFERRED FROM ANALYSIS OF ITS DATA." Acta Botanica Hungarica 64, no. 3-4 (2022): 369–90. http://dx.doi.org/10.1556/034.64.2022.3-4.9.
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Nutlet pericarp structure is important in the taxonomy of Lamiaceae (Labiatae) at different taxonomic levels. Within the family it has also been found that variation in pericarp structure is strongly correlated with the phylogenic results obtained from molecular DNA analyses. The genus Nepeta L., with more than 200 species mainly centred in SW Asia, is one of the taxonomically most complex genera within the family. Traditional taxonomic treatments of Nepeta are mainly based on gross morphology. As in other groups of Lamiaceae, pericarp structure provides some of the diagnostic characters in this genus. In order to investigate patterns of pericarp evolution within Nepeta, we used scanning electron microscopy to examine nutlet surfaces and pericarp cross sections and explored variation of these characters against a molecular phylogeny based on ITS sequences. Based on this phylogenetic analysis, Nepeta in its present circumscription is not monophyletic. Evolutionary trends in structure of nutlet pericarps are apparent although they require confirmation with more robust phylogenies. In particular, nutlets with tuberculate/thorny-like pericarp may have evolved once within this genus, in the common ancestor of five of the six subclades identified within Nepeta, and have been lost independently several times. We also show that evolution of tubercules in Nepeta is not related to plant life span. Our results also indicate that more genetic markers (both plastid and nuclear) are necessary to reconstruct a reliable and robust organismal phylogeny.
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Etienne, Rampal S., Bart Haegeman, Tanja Stadler, et al. "Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record." Proceedings of the Royal Society B: Biological Sciences 279, no. 1732 (2011): 1300–1309. http://dx.doi.org/10.1098/rspb.2011.1439.
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The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence ( Dendroica , Plethodon and Heliconius ). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.
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CASIRAGHI, M., T. J. C. ANDERSON, C. BANDI, C. BAZZOCCHI, and C. GENCHI. "A phylogenetic analysis of filarial nematodes: comparison with the phylogeny of Wolbachia endosymbionts." Parasitology 122, no. 1 (2001): 93–103. http://dx.doi.org/10.1017/s0031182000007149.
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Infection with the endosymbiotic bacteria Wolbachia is widespread in filarial nematodes. Previous studies have suggested concordance between the phylogeny of Wolbachia with that of their nematode hosts. However, there is only one published molecular phylogenetic study of filarial species, based on the 5S rRNA gene spacer. The phylogeny proposed by this study is partially incongruent with previous classifications of filarial nematodes, based on morphological characters. Furthermore, both traditional classifications and molecular phylogenies are, in part, inconsistent with the phylogeny of Wolbachia. Here we report mitochondrial cytochrome oxidase I (COI) gene sequences for 11 species of filaria and for another spirurid nematode which was included as an outgroup. In addition, 16S rRNA, wsp and ftsZ gene sequences were generated for the Wolbachia of several filarial species, in order to complete the available data sets and further resolve the phylogeny of Wolbachia in nematodes. We used these data to evaluate whether nematode and Wolbachia phylogenies are concordant. Some of the possible phylogenetic reconstructions based on COI gene were congruent with the phylogeny of Wolbachia and supported the grouping of the rodent filaria Litomosoides sigmodontis with the lymphatic filariae (i.e. Brugia spp. and Wuchereria spp.) and the sister group relationship of Dirofilaria spp. and Onchocerca spp. However, the placement of the Wolbachia-free filaria Acanthocheilonema viteae is ambiguous and dependent on the phylogenetic methods used.
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Hidayati, R. Misrianti, and A. Ali. "Phylogenetic tree of Kuantan cattle by DNA barcoding." Jurnal Ilmu Ternak dan Veteriner 21, no. 1 (2016): 41. http://dx.doi.org/10.14334/jitv.v21i1.1351.
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<p>Kuantan cattle is one of local beef cattle breed of Riau Province which its origin was unknown. Kuantan cattle are commonly found in Indragiri Hulu and Kuantan Singingi Regency. Based on phenotype characterizations, kuantan cattles are similar with pesisir cattle (West Sumatera beef cattle). Historically, kuantan cattle were pesisir cattle brought by “minang” immigrants (Immigrant from West Sumatera) to this region. The purpose of this study was to analyze the origin of the kuantan cattle through genetic diversity analysis using DNA barcode. DNA barcode used was Cytochrome oxidase subunit I gene which was found in the mtDNA. DNA isolation was done on 25 kuantan’s blood samples and 18 pesisir blood samples. Amplification of COI gene segment used Polymerase Chain Reaction technique. The forward primer sequence used in this study was F’5 TTCTCAACCAACCATAAAGATATTGG-3’ and the reverse primer sequence used was reverse 5’-TAGACTTCGGGGTGTCCAAAGAATCA-3. It squeezed kuantan and pesisir sequence 5711 - 6420 base (GeneBank accession number NC_005971) with length by 710 bp. Analysis result of sequence using MEGA 5.2 Program showed that there were 6 polymorphic sites establishing 7 haplotypes on kuantan cattle and 9 polymorphic sites establishing 12 haplotypes on pesisir cattle. Based on genetic distance and phylogeney tree, kuantan and pesisir cattle were in same group with <em>Bos indicus</em>. Mutation in the COI gene segment in this study was too small and was not able to distinguish the difference of those breeds. The result of neighbor joining analyze indicated that kuantan cattle origin was from <em>Bos indicus</em> just like pesisir cattle.</p><strong>Key Words: </strong>COI Gene, Polymorphic, Kuantan Cattle, Genetic Distance, Phylogenetic Tree
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Koirala, Amrit, and Volker S. Brözel. "Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea." Microorganisms 9, no. 8 (2021): 1662. http://dx.doi.org/10.3390/microorganisms9081662.
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The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.
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Temu, Stella G., Philippe Clerc, Miko R. A. Nadel, Leif Tibell, Donatha D. Tibuhwa, and Sanja Tibell. "Molecular, morphological and chemical variation of the Usnea pectinata aggregate from Tanzania, São Tomé and Príncipe." Lichenologist 54, no. 5 (2022): 291–98. http://dx.doi.org/10.1017/s0024282922000251.
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AbstractThis study investigated the molecular, chemical and morphological variation in the Usnea pectinata aggregate using 42 specimens, 22 from Tanzania and 20 from São Tomé and Príncipe. A total of 31 sequences (13 ITS, 13 nuLSU and 5 RPB1) were generated. The results are presented in two phylogenies: first a three-markers ‘backbone’ phylogeny for the U. pectinata aggregate, where six distinct, strongly supported subclades indicate considerable genetic variation in the dataset; and second, an ITS phylogeny with 47 terminals along with a mapping of morphological and chemistry data. Several well-supported monophyletic clades were recovered in both phylogenies and these may well represent separate species in the complex referred to here as the U. pectinata aggregate. Three morphotypes characterized by axis pigmentation and four by branch shape were noted. Six chemotypes were observed.
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Christensen, Henrik, Peter Kuhnert, John Elmerdahl Olsen, and Magne Bisgaard. "Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae." International Journal of Systematic and Evolutionary Microbiology 54, no. 5 (2004): 1601–9. http://dx.doi.org/10.1099/ijs.0.03018-0.
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Phylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. The monophyly of representatives of the genus Gallibacterium was recognized by analysis of all housekeeping genes, while members of Mannheimia, Actinobacillus sensu stricto and the core group of Pasteurella sensu stricto formed monophyletic groups with two out of three housekeeping genes. Representatives of Mannheimia, Actinobacillus sensu stricto, [Haemophilus] ducreyi and [Pasteurella] trehalosi formed a monophyletic unit by analysis of all three housekeeping genes, which was in contrast to the 16S rRNA gene-derived phylogeny, where these taxa occurred at separate positions in the phylogenetic tree. Representatives of the Rodent, Avian and Aphrophilus–Haemophilus 16S rRNA gene groups were weakly supported by phylogenetic analysis of housekeeping genes. Phylogenies derived by comparison of the housekeeping genes diverged significantly from the 16S rRNA gene-derived phylogeny as evaluated by the likelihood ratio test. A low degree of congruence was also observed between the individual housekeeping gene-derived phylogenies. Estimates on speciation derived from 16S rRNA and housekeeping gene sequence comparisons resulted in quite different evolutionary scenarios for members of the Pasteurellaceae. The phylogeny based on the housekeeping genes supported observed host associations between Mannheimia, Actinobacillus sensu stricto and [Pasteurella] trehalosi and animals with paired hooves.
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Schwery, Orlando, and Brian C. O’Meara. "MonoPhy: a simple R package to find and visualize monophyly issues." PeerJ Computer Science 2 (March 30, 2016): e56. http://dx.doi.org/10.7717/peerj-cs.56.
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Background.The monophyly of taxa is an important attribute of a phylogenetic tree. A lack of it may hint at shortcomings of either the tree or the current taxonomy, or can indicate cases of incomplete lineage sorting or horizontal gene transfer. Whichever is the reason, a lack of monophyly can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species.Results.The R packageMonoPhyallows assessment and exploration of monophyly of taxa in a phylogeny. It can assess the monophyly of genera using the phylogeny only, and with an additional input file any other desired higher order taxa or unranked groups can be checked as well.Conclusion.Summary tables, easily subsettable results and several visualization options allow quick and convenient exploration of monophyly issues, thus makingMonoPhya valuable tool for any researcher working with phylogenies.
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Malik, Ashar J., Anthony M. Poole, and Jane R. Allison. "Structural Phylogenetics with Confidence." Molecular Biology and Evolution 37, no. 9 (2020): 2711–26. http://dx.doi.org/10.1093/molbev/msaa100.
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Abstract For evaluating the deepest evolutionary relationships among proteins, sequence similarity is too low for application of sequence-based homology search or phylogenetic methods. In such cases, comparison of protein structures, which are often better conserved than sequences, may provide an alternative means of uncovering deep evolutionary signal. Although major protein structure databases such as SCOP and CATH hierarchically group protein structures, they do not describe the specific evolutionary relationships within a hierarchical level. Structural phylogenies have the potential to fill this gap. However, it is difficult to assess evolutionary relationships derived from structural phylogenies without some means of assessing confidence in such trees. We therefore address two shortcomings in the application of structural data to deep phylogeny. First, we examine whether phylogenies derived from pairwise structural comparisons are sensitive to differences in protein length and shape. We find that structural phylogenetics is best employed where structures have very similar lengths, and that shape fluctuations generated during molecular dynamics simulations impact pairwise comparisons, but not so drastically as to eliminate evolutionary signal. Second, we address the absence of statistical support for structural phylogeny. We present a method for assessing confidence in a structural phylogeny using shape fluctuations generated via molecular dynamics or Monte Carlo simulations of proteins. Our approach will aid the evolutionary reconstruction of relationships across structurally defined protein superfamilies. With the Protein Data Bank now containing in excess of 158,000 entries (December 2019), we predict that structural phylogenetics will become a useful tool for ordering the protein universe.
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Varón-González, Ceferino, Simon Whelan, and Christian Peter Klingenberg. "Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable." Systematic Biology 69, no. 5 (2020): 863–83. http://dx.doi.org/10.1093/sysbio/syaa003.
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Abstract In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny can be estimated reliably if dimensionality is high, even with relatively unfavorable combinations of branch lengths. By contrast, if there is phenotypic integration such that most variation is concentrated in one or a few dimensions, the reliability of phylogenetic estimates is severely reduced. Evolutionary models with stabilizing selection also produce highly unreliable estimates, which are little better than picking a phylogenetic tree at random. To examine how these results apply to phylogenies with more than four taxa, we conducted further simulations with up to eight taxa, which indicated that the effects of dimensionality and phenotypic integration extend to more than four taxa, and that convergence among internal nodes may produce additional complications specifically for greater numbers of taxa. Overall, the simulations suggest that multidimensional data, under evolutionary models that are plausible for biological data, do not produce reliable estimates of phylogeny. [Brownian motion; gene expression data; geometric morphometrics; morphological integration; squared-change parsimony; phylogeny; shape; stabilizing selection.]
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Kennedy, Martyn, and Roderic D. M. Page. "Seabird Supertrees: Combining Partial Estimates of Procellariiform Phylogeny." Auk 119, no. 1 (2002): 88–108. http://dx.doi.org/10.1093/auk/119.1.88.
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Abstract The growing use of comparative methods to address evolutionary questions has generated an increased need for robust hypotheses of evolutionary relationships for a wide range of organisms. Where a phylogeny exists for a group, often more than one phylogeny will exist for that group, and it is uncommon that the same taxa are in each of the existing trees. The types of data used to generate evolutionary trees can also vary greatly, and thus combining data sets is often difficult or impossible. To address comparative questions for groups where multiple phylogenetic hypotheses already exist, we need to combine different hypotheses in a way that provides the best estimate of the phylogeny for that group. Here, we combine seven seabird phylogenies (based on behavioral, DNA–DNA hybridization, isozyme, life history, morphological, and sequence data) to generate a comprehensive supertree for the Procellariiformes using matrix representation with parsimony. This phylogeny contains 122 taxa and represents a conservative estimate of combined relationships presented in the original seven source trees. We compared the supertree with results of a combined sequence data supermatrix for 103 seabird taxa. Results of the two approaches are broadly concordant, but matrix representation with parsimony provides a more comprehensive and more conservative estimate of the phylogeny of the group because it is less influenced by the largest of the source studies (which uses a single, relatively quickly evolving gene). Genetic data sets that can be combined in a supermatrix approach are currently less likely to be available than phylogenies that can be combined using some form of supertree approach. Although there are limitations to both of those approaches, both would be simpler if all phylogenetic studies made both their data sets and trees they generate available through databases such as TREEBASE.
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Duchen, Pablo. "Métodos de reconstrucción filogenética I: máxima verosimilitud." Tequio 4, no. 11 (2021): 69–79. http://dx.doi.org/10.53331/teq.v4i11.3953.
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Phylogenetic inference is widely used in evolutionary biology, aiming to find evolutionary relationships between different species and report the result in the form of a phylogenetic tree (phylogeny). There are several statistical methods used for phylogenetic inference. In this review, the method of maximum likelihood for phylogenetic reconstruction is presented. This technique consists of finding the likelihood of multiple candidate phylogenies, and report the one with the highest likelihood as a representative of the evolutionary relationships of a group of species. In this paper, the likelihood calculation of a phylogeny from multiple-species DNA sequences is reviewed. Also, some key DNA mutation models to calculate transition probabilities between nucleotides are presented. Such transition probabilities are used in the likelihood calculation of a given phylogeny. A simple example is shown to illustrate the necessary steps to infer a phylogeny, as well as the most common software for maximum likelihood inference for larger DNA alignments.
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Dong, Quan-Ying, Yao Wang, Zhi-Qin Wang, Yan-Fang Liu, and Hong Yu. "Phylogeny and Systematics of the Genus Tolypocladium (Ophiocordycipitaceae, Hypocreales)." Journal of Fungi 8, no. 11 (2022): 1158. http://dx.doi.org/10.3390/jof8111158.
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The taxonomy and phylogeny of the genus Tolypocladium are herein revised based on the most comprehensive dataset to date. Two species-level phylogenies of Tolypocladium were constructed: a single-gene phylogeny (ITS) of 35 accepted species and a multigene phylogeny (nrSSU, nrLSU, tef-1α, rpb1, and rpb2) of 27 accepted species. Three new species, Tolypocladium pseudoalbum sp. nov., Tolypocladium subparadoxum sp. nov., and Tolypocladium yunnanense sp. nov., are described in the present study. The genetic divergences of four markers (ITS, tef-1α, rpb1 and rpb2) among Tolypocladium species are also reported. The results indicated that species of Tolypocladium were best delimited by rpb1 sequence data, followed by the sequence data for the rpb2, tef-1α, and ITS provided regions. Finally, a key to the 48 accepted species of Tolypocladium worldwide is provided.
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Fensome, Robert A., Juan F. Saldarriaga, and “Max” F. J. R. Taylor. "Dinoflagellate phylogeny revisited: reconciling morphological and molecular based phylogenies." Grana 38, no. 2-3 (1999): 66–80. http://dx.doi.org/10.1080/00173139908559216.
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Grismer, L. Lee, Perry L. Wood, Jr., Nikolay A. Poyarkov, et al. "Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation." Vertebrate Zoology 71 (March 16, 2021): 101–54. http://dx.doi.org/10.3897/vertebrate-zoology.71.e59307.
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The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.
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Grismer, L. Lee, Perry L. Wood, Jr., Nikolay A. Poyarkov, et al. "Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation." Vertebrate Zoology 71 (March 16, 2021): 101–54. http://dx.doi.org/10.3897/vz.71.e59307.
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The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.
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Beutel, Rolf G., and Frank Friedrich. "The Phylogeny of Archostemata (Coleoptera) and new Approaches in Insect Morphology Zur Phylogenie der Archostemata (Coleoptera) und neue Ansätze zur Insektenmorphologie." Entomologia Generalis 31, no. 2 (2008): 141–54. http://dx.doi.org/10.1127/entom.gen/31/2008/141.
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O'Keefe, F. Robin, and P. Martin Sander. "Paleontological paradigms and inferences of phylogenetic pattern: a case study." Paleobiology 25, no. 4 (1999): 518–33. http://dx.doi.org/10.1017/s0094837300020364.
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In this paper we reconstruct the phylogeny of a clade of pachypleurosaurs (Reptilia: Sauropterygia) occurring in Triassic-age deposits in the Monte San Giorgio region, Switzerland. We also present the phylogeny of this clade as a case study for two paradigms of phylogeny reconstruction: cladistics and phenetic/stratigraphic methods. While this dichotomy is not held rigidly by all workers, its advancement by cladists leads us to retain it initially for rhetorical purposes. We review the philosophical bases of species, species concepts, and speciation, as well as cladograms and phylogenies, before introducing the experimental system.Data are presented from cladistic analyses, phenetic analyses, and stratigraphic information. Phylogeny of the clade is interpreted from both paradigms, and the interpretations are found to be inconsistent. Resolution of the phylogeny rests on the emphasis of one type of data over another. An interpretation of cladogenesis within the genusNeusticosaurusentails rejection of suggestive phenetic and stratigraphic data, whereas an anagenetic interpretation entails reversal of autapomorphies in ancestral taxa. Anagenesis is deemed to be the more probable interpretation, based on the strength of the stratigraphic and phenetic data relative to the character data. Implications of the test case results for phylogeny reconstruction in general are discussed, ending with a call for pluralism in approach.
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Grover, Siddhant, Alexey Markin, Tavis K. Anderson, and Oliver Eulenstein. "Phylogenetic diversity statistics for all clades in a phylogeny." Bioinformatics 39, Supplement_1 (2023): i177—i184. http://dx.doi.org/10.1093/bioinformatics/btad263.
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Abstract The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.
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Pearse, William D. "Animating and exploring phylogenies with fibre plots." F1000Research 5 (April 5, 2017): 2790. http://dx.doi.org/10.12688/f1000research.10274.3.
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Despite the progress that has been made in many other aspects of data visualisation, phylogenies are still represented in much the same way as they first were by Darwin. In this brief essay, I give a short review of what I consider to be some recent major advances, and outline a new kind of phylogenetic visualisation. This new graphic, the fibre plot, uses the metaphor of sections through a tree to describe change in a phylogeny. I suggest it is a useful tool in gaining an rapid overview of the timing and scale of diversification in large phylogenies.
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Suntsov, Victor V. "Molecular phylogenies of the plague microbe <i>Yersinia pestis</i>: an environmental assessment." AIMS Microbiology 9, no. 4 (2023): 712–23. http://dx.doi.org/10.3934/microbiol.2023036.
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<abstract> <p>Two approaches are applied to studies of the phylogeny of the plague microbe <italic>Yersinia pestis</italic>, i.e., the reconstruction of its history: Molecular genetic (MG) and ecological (ECO). The MG approach dominates. Phylogenies created with MG and ECO methods are not congruent. MG conclusions contradict the known facts and patterns of ecology, biogeography, paleontology, etc. We discuss some obvious contradictions and inconsistencies and suggest that real phylogenies of the plague microbe can be constructed only on the basis of the integration of MG and ECO approaches.</p> </abstract>
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Stettler, Jason M., Mikel R. Stevens, Lindsey M. Meservey, et al. "Improving phylogenetic resolution of the Lamiales using the complete plastome sequences of six Penstemon species." PLOS ONE 16, no. 12 (2021): e0261143. http://dx.doi.org/10.1371/journal.pone.0261143.
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The North American endemic genus Penstemon (Mitchell) has a recent geologic origin of ca. 3.6 million years ago (MYA) during the Pliocene/Pleistocene transition and has undergone a rapid adaptive evolutionary radiation with ca. 285 species of perennial forbs and sub-shrubs. Penstemon is divided into six subgenera occupying all North American habitats including the Arctic tundra, Central American tropical forests, alpine meadows, arid deserts, and temperate grasslands. Due to the rapid rate of diversification and speciation, previous phylogenetic studies using individual and concatenated chloroplast sequences have failed to resolve many polytomic clades. We investigated the efficacy of utilizing the plastid genomes (plastomes) of 29 species in the Lamiales order, including five newly sequenced Penstemon plastomes, for analyzing phylogenetic relationships and resolving problematic clades. We compared whole-plastome based phylogenies to phylogenies based on individual gene sequences (matK, ndhF, psaA, psbA, rbcL, rpoC2, and rps2) and concatenated sequences. We also We found that our whole-plastome based phylogeny had higher nodal support than all other phylogenies, which suggests that it provides greater accuracy in describing the hierarchal relationships among taxa as compared to other methods. We found that the genus Penstemon forms a monophyletic clade sister to, but separate from, the Old World taxa of the Plantaginaceae family included in our study. Our whole-plastome based phylogeny also supports the rearrangement of the Scrophulariaceae family and improves resolution of major clades and genera of the Lamiales.
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Guyeux, Christophe, Stéphane Chrétien, Nathalie M. L. Côté, and Jacques M. Bahi. "Systematic investigations of gene effects on both topologies and supports: An Echinococcus illustration." Journal of Bioinformatics and Computational Biology 15, no. 05 (2017): 1750019. http://dx.doi.org/10.1142/s0219720017500196.
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In this paper, we propose a high performance computing toolbox implementing efficient statistical methods for the study of phylogenies. This toolbox, which implements logit models and LASSO-type penalties, gives a way to better understand, measure, and compare the impact of each gene on a global phylogeny. As an application, we study the Echinococcus phylogeny, which is often considered as a particularly difficult example. Mitochondrial and nuclear genomes (19 coding sequences) of nine Echinococcus species are considered in order to investigate the molecular phylogeny of this genus. First, we check that the 19 gene trees lead to 19 totally different unsupported topologies (a topology is the sister relationship when both branch lengths and supports are ignored in a phylogenetic tree), while using the 19 genes as a whole are not sufficient for estimating the phylogeny. In order to circumvent this issue and understand the impact of the genes, we computed 43,796 trees using combinations ranging from 13 to 19 genes. By doing so, 15 topologies are obtained. Four particular topologies, appearing more robust and frequent, are then selected for more precise investigation. Refining further our statistical analysis, a particularly robust topology is extracted. We also carefully demonstrate the influence of nuclear genes on the likelihood of the phylogeny.
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Crandall, K. A., and A. R. Templeton. "Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction." Genetics 134, no. 3 (1993): 959–69. http://dx.doi.org/10.1093/genetics/134.3.959.
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Abstract Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered in order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, (2) the frequency of a haplotype is related to the number of mutational connections to other haplotypes in the cladogram and (3) geographic location can be used to infer topological positioning of haplotypes in a cladogram. These relationships can then be used to better estimate intraspecific phylogenies in two ways: (1) rooting the phylogeny and (2) resolving ambiguities in a cladogram. This information will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily on the topology of the tree.
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Guégan, Jean-François, and Jean-François Agnèse. "Parasite evolutionary events inferred from host phylogeny: the case of Labeo species (Teleostei, Cyprinidae) and their dactylogyrid parasites (Monogenea, Dactylogyridae)." Canadian Journal of Zoology 69, no. 3 (1991): 595–603. http://dx.doi.org/10.1139/z91-089.
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Independent phylogenies of West African Labeo (Teleostei, Cyprinidae) and their gill parasites of the genus Dactylogyrus (Monogenea, Dactylogyridae) are proposed. The phylogeny of Labeo is based on allele characters, whereas the phylogeny of the parasites is based on morphometric features. The comparison of host and parasite phylogenies did not correlate completely with predictions made by using Fahrenholz's rule. Parasites encountered on L. coubie and L. senegalensis seem to have evolved in parallel with their host, or by sequential colonizations between these two related hosts. Whatever the host–parasite evolutionary events between L. coubie and L. senegalensis and their specific dactylogyrids, two hypotheses of host switching on L. parvus and L. roseopunctatus are probable, reflecting a close ecological relationship between the various host taxa. Dactylogyrus brevicirrus and D. nathaliae, found on the gills of L. parvus and L. roseopunctatus, respectively, are each the sister-species of a living parasite on L. coubie. The notions of parallel evolution (or coevolution in a broader sense) and host switching with speciation are discussed. Finally, Fahrenholz's rule is analyzed as a forecasting tool that can be used in systematics.
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Duchen, Pablo. "Métodos de reconstrucción filogenética II: inferencia bayesiana." Tequio 4, no. 11 (2021): 81–89. http://dx.doi.org/10.53331/teq.v4i11.0055.
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Phylogenetic reconstruction through Bayesian inference is currently widely used. The main advantage of this method is the direct output of posterior probabilities for each clade on the final phylogeny. Thus, it does not require bootstrapping as a measure of uncertainty. Moreover, Bayesian inference is perfectly fit for dating phylogenies through molecular clocks. In this paper, the basics of Bayesian inference applied to phylogenetic reconstruction are described, starting with an explanation of Bayes’ theorem. Then, the use of the Metropolis-Hastings algorithm to sample topologies from the posterior distribution is characterized and illustrated through a simple example. At the end, there is a mention of the software used for Bayesian phylogeny reconstruction.
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Beutel, Rolf G., Hans Pohl, Evgeny V. Yan, et al. "The phylogeny of Coleopterida (Hexapoda) - morphological characters and molecular phylogenies." Systematic Entomology 44, no. 1 (2018): 75–102. http://dx.doi.org/10.1111/syen.12316.
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Endara, María-José, Phyllis D. Coley, Gabrielle Ghabash, et al. "Coevolutionary arms race versus host defense chase in a tropical herbivore–plant system." Proceedings of the National Academy of Sciences 114, no. 36 (2017): E7499—E7505. http://dx.doi.org/10.1073/pnas.1707727114.
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Coevolutionary models suggest that herbivores drive diversification and community composition in plants. For herbivores, many questions remain regarding how plant defenses shape host choice and community structure. We addressed these questions using the tree genus Inga and its lepidopteran herbivores in the Amazon. We constructed phylogenies for both plants and insects and quantified host associations and plant defenses. We found that similarity in herbivore assemblages between Inga species was correlated with similarity in defenses. There was no correlation with phylogeny, a result consistent with our observations that the expression of defenses in Inga is independent of phylogeny. Furthermore, host defensive traits explained 40% of herbivore community similarity. Analyses at finer taxonomic scales showed that different lepidopteran clades select hosts based on different defenses, suggesting taxon-specific histories of herbivore–host plant interactions. Finally, we compared the phylogeny and defenses of Inga to phylogenies for the major lepidopteran clades. We found that closely related herbivores fed on Inga with similar defenses rather than on closely related plants. Together, these results suggest that plant defenses might be more evolutionarily labile than the herbivore traits related to host association. Hence, there is an apparent asymmetry in the evolutionary interactions between Inga and its herbivores. Although plants may evolve under selection by herbivores, we hypothesize that herbivores may not show coevolutionary adaptations, but instead “chase” hosts based on the herbivore’s own traits at the time that they encounter a new host, a pattern more consistent with resource tracking than with the arms race model of coevolution.
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Zhang, Sufang, Fuli Xie, Jiangke Yang, and Youguo Li. "Phylogeny of bradyrhizobia from Chinese cowpea miscellany inferred from 16S rRNA, atpD, glnII, and 16S–23S intergenic spacer sequences." Canadian Journal of Microbiology 57, no. 4 (2011): 316–27. http://dx.doi.org/10.1139/w11-008.
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The cowpea ( Vigna unguiculata L.), peanut ( Arachis hypogaea L.), and mung bean ( Vigna radiata L.) belong to a group of plants known as the “cowpea miscellany” plants, which are widely cultivated throughout the tropic and subtropical zones of Africa and Asia. However, the phylogeny of the rhizobial strains that nodulate these plants is poorly understood. Previous studies have isolated a diversity of rhizobial strains from cowpea miscellany hosts and have suggested that, phylogenetically, they are from different species. In this work, the phylogeny of 42 slow-growing rhizobial strains, isolated from root nodules of cowpea, peanut, and mung bean from different geographical regions of China, was investigated using sequences from the 16S rRNA, atpD and glnII genes, and the 16S–23S rRNA intergenic spacer. The indigenous rhizobial strains from the cowpea miscellany could all be placed in the genus Bradyrhizobium , and Bradyrhizobium liaoningense and Bradyrhizobium yuanmingense were the main species. Phylogenies derived from housekeeping genes were consistent with phylogenies generated from the ribosomal gene. Mung bean rhizobia clustered only into B. liaoningense and B. yuanmingense and were phylogenetically less diverse than cowpea and peanut rhizobia. Geographical origin was significantly reflected in the phylogeny of mung bean rhizobia. Most cowpea rhizobia were more closely related to the 3 major groups B. liaoningense, B. yuanmingense, and Bradyrhizobium elkanii than to the minor groups Bradyrhizobium japonicum or Bradyrhizobium canariense . However, most peanut rhizobia were more closely related to the 2 major groups B. liaoningense and B. yuanmingense than to the minor group B. elkanii.
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Coetzee, Martin, Brenda Wingfield, and Michael Wingfield. "Armillaria Root-Rot Pathogens: Species Boundaries and Global Distribution." Pathogens 7, no. 4 (2018): 83. http://dx.doi.org/10.3390/pathogens7040083.
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This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.
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Chang, Jonathan, Daniel L. Rabosky, and Michael E. Alfaro. "Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions." Systematic Biology 69, no. 3 (2019): 602–11. http://dx.doi.org/10.1093/sysbio/syz081.
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Abstract Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on “sampling fractions” can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (Taxonomic Addition for Complete Trees [TACT]) that uses birth–death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling. [Birth–death process; diversification; incomplete sampling; phylogenetic uncertainty; rate heterogeneity; rate shifts; stochastic polytomy resolution.]
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Alland, David, Thomas S. Whittam, Megan B. Murray, et al. "Modeling Bacterial Evolution with Comparative-Genome-Based Marker Systems: Application to Mycobacterium tuberculosis Evolution and Pathogenesis." Journal of Bacteriology 185, no. 11 (2003): 3392–99. http://dx.doi.org/10.1128/jb.185.11.3392-3399.2003.
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ABSTRACT The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these “comparative-genome markers” (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared “reference strains.” Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI “C” strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure.
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Lee, Sean, and Toshikazu Hasegawa. "Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages." Proceedings of the Royal Society B: Biological Sciences 278, no. 1725 (2011): 3662–69. http://dx.doi.org/10.1098/rspb.2011.0518.
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Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.
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Rumpf, Robert W., Ann L. Griffen, and Eugene J. Leys. "Phylogeny of Porphyromonas gingivalis by Ribosomal Intergenic Spacer Region Analysis." Journal of Clinical Microbiology 38, no. 5 (2000): 1807–10. http://dx.doi.org/10.1128/jcm.38.5.1807-1810.2000.
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Periodontitis has been associated with the presence ofPorphyromonas gingivalis, and previous studies have shown phenotypic differences in the pathogenicities of strains of P. gingivalis. An accurate and comprehensive phylogeny of strains ofP. gingivalis would be useful in determining if there is an evolutionary basis to pathogenicity in this species. Previous phylogenies of P. gingivalis strains based on random amplified polymorphic DNA (RAPD) analysis and multilocus enzyme electrophoresis (MLEE) show little agreement. While the 16S ribosomal gene is the standard for phylogenetic reconstruction among bacterial species, it is insufficiently variable for this purpose. In the present study, the phylogeny of P. gingivalis was constructed on the basis of the sequence of the most variable region of the ribosomal operon, the intergenic spacer region (ISR). Heteroduplex analysis of the ISR has been used to study the variability of P. gingivalis strains in periodontitis. In the present study, typing by heteroduplex analysis was compared to ISR sequence-based phylogeny and close agreement was observed. The two strains of P. gingivalis whose heteroduplex types are strongly associated with periodontitis were found to be closely related and were well separated from strains whose heteroduplex types are less strongly associated with disease, suggesting a relationship between pathogenicity and phylogeny.
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SAARMA, U., I. JÕGISALU, E. MOKS, et al. "A novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence." Parasitology 136, no. 3 (2009): 317–28. http://dx.doi.org/10.1017/s0031182008005453.
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SUMMARYThe taxonomic status of Echinococcus, an important zoonotic cestode genus, has remained controversial, despite numerous attempts to revise it. Although mitochondrial DNA (mtDNA) has been the source of markers of choice for reconstructing the phylogeny of the genus, results derived from mtDNA have led to significant inconsistencies with earlier species classifications based on phenotypic analysis. Here, we used nuclear DNA markers to test the phylogenic relationships of members of the genus Echinococcus. The analysis of sequence data for 5 nuclear genes revealed a significantly different phylogeny for Echinococcus from that proposed on the basis of mitochondrial DNA sequence data, but was in agreement with earlier species classifications. The most notable results from the nuclear phylogeny were (1) E. multilocularis was placed as basal taxon, (2) all genotypes of Echinococcus granulosus grouped as a monophyletic entity, and (3) genotypes G8 and G10 clustered together. We conclude that the analysis of nuclear DNA data provides a more reliable means of inferring phylogenetic relationships within Echinococcus than mtDNA and suggest that mtDNA should not be used as the sole source of markers in future studies where the goal is to reconstruct a phylogeny that does not only reflect a maternal lineage, but aims to describe the evolutionary history at species level or higher.
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Banks, Jonathan C., and Adrian M. Paterson. "A penguin-chewing louse (Insecta : Phthiraptera) phylogeny derived from morphology." Invertebrate Systematics 18, no. 1 (2004): 89. http://dx.doi.org/10.1071/is03022.
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Penguins are parasitised by 15 species of lice in the genera Austrogoniodes and Nesiotinus and present an opportunity to analyse phylogenetic relationships of two complete genera of chewing lice parasitising a monophyletic group of hosts. Taxonomy of penguin lice has been revised several times, including the erection of the genus Cesareus to contain some of the penguin-chewing louse species. Additionally, other groups of species within Austrogoniodes have been proposed. We constructed a phylogeny for all the chewing lice parasitising penguins from 46 parsimony-informative morphological characters and found support for two groups within Austrogoniodes, but little support for the Cesareus genus. Austrogoniodes metoecus, the only Austrogoniodes species parasitising a bird other than a penguin, was basal in the phylogeny, which suggests that if A. metoecus did originate from a louse species parasitising penguins, the host-switching event was unlikely to have been recent. A�superficial comparison of louse and penguin phylogenies identified some potential instances of co-speciation. However, a full analysis of co-phylogenetic relationships between penguins and their lice awaits the publication of a better-resolved penguin phylogeny.
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COOPER, ENDYMION D. "Notes on Early Land Plants Today. 37. Towards a stable, informative classification of the Lepidoziaceae (Marchantiophyta)." Phytotaxa 97, no. 2 (2013): 44. http://dx.doi.org/10.11646/phytotaxa.97.2.4.
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Recent molecular phylogenies of the Lepidoziaceae indicate that the current classification is incongruent with the phylogeny. Although substantial uncertainties remain, an interim classification is needed. The classification proposed includes a broader definition of the Lembidioideae, reinstatement of Neolepidozia and Tricholepidozia and the recognition of the new genus Ceramanus. While the Zoopsidoideae are unlikely to represent a monophyletic group, it is not yet possible to provide a phylogenetically accurate revision of this subfamily.
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Baverstock, PR, D. King, M. King, J. Birrell, and M. Krieg. "The Evolution of Species of the Varanidae - Microcomplement Fixation Analysis of Serum Albumins." Australian Journal of Zoology 41, no. 6 (1993): 621. http://dx.doi.org/10.1071/zo9930621.
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Phylogenetic relationships among 30 of the 40 species in the Varanidae were examined in the light of molecular information on albumin evolution derived from microcomplement fixation. A phylogeny based on these results is compared with proposed phylogenies based on data obtained using other techniques. Three separate radiations of Varanus are found in Australia, The movement of varanids to Australia from south-east Asia is thought to have occurred approximately 15-20 million years ago.
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Iersel, Leo Van, Mark Jones, and Steven Kelk. "A Third Strike Against Perfect Phylogeny." Systematic Biology 68, no. 5 (2019): 814–27. http://dx.doi.org/10.1093/sysbio/syz009.
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Abstract Perfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam’s Razor such parsimonious trees are preferable as a hypothesis of evolution. A classical result states that 2-state characters permit a perfect phylogeny precisely if each subset of 2 characters permits one. More recently, it was shown that for 3-state characters the same property holds but for size-3 subsets. A long-standing open problem asked whether such a constant exists for each number of states. More precisely, it has been conjectured that for any fixed number of states $r$ there exists a constant $f(r)$ such that a set of $r$-state characters $C$ has a perfect phylogeny if and only if every subset of at most $f(r)$ characters has a perfect phylogeny. Informally, the conjecture states that checking fixed-size subsets of characters is enough to correctly determine whether input data permits a perfect phylogeny, irrespective of the number of characters in the input. In this article, we show that this conjecture is false. In particular, we show that for any constant $t$, there exists a set $C$ of $8$-state characters such that $C$ has no perfect phylogeny, but there exists a perfect phylogeny for every subset of at most $t$ characters. Moreover, there already exists a perfect phylogeny when ignoring just one of the characters, independent of which character you ignore. This negative result complements the two negative results (“strikes”) of Bodlaender et al. (1992,2000). We reflect on the consequences of this third strike, pointing out that while it does close off some routes for efficient algorithm development, many others remain open.
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Jones, Nick S., and John Moriarty. "Evolutionary inference for function-valued traits: Gaussian process regression on phylogenies." Journal of The Royal Society Interface 10, no. 78 (2013): 20120616. http://dx.doi.org/10.1098/rsif.2012.0616.
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Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated owing to phylogenetic relationships. In this paper, we give a flexible statistical model for such data, by combining assumptions from phylogenetics with Gaussian processes. We describe its use as a non-parametric Bayesian prior distribution, both for prediction (placing posterior distributions on ancestral functions) and model selection (comparing rates of evolution across a phylogeny, or identifying the most likely phylogenies consistent with the observed data). Our work is integrative, extending the popular phylogenetic Brownian motion and Ornstein–Uhlenbeck models to functional data and Bayesian inference, and extending Gaussian process regression to phylogenies. We provide a brief illustration of the application of our method.
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Parey, Elise, Alexandra Louis, Jerome Montfort, et al. "Genome structures resolve the early diversification of teleost fishes." Science 379, no. 6632 (2023): 572–75. http://dx.doi.org/10.1126/science.abq4257.
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Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.
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Ong, Christian Joseph, Richard Clemente, Oliver Alaijos, Lady Janine Pascual, Russell Neil Aguilar, and Raizza Desacula. "In-Silico Molecular Phylogeny of Philippine Myxomycetes using 18S rRNA and small subunit rRNA (SSU) Gene Sequences." Journal of Tropical Life Science 13, no. 3 (2023): 421–30. http://dx.doi.org/10.11594/jtls.13.03.01.
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Myxomycetes, commonly called plasmodial slime molds, are eukaryotic organisms usually thriving on terrestrial ecosystems, manifesting attributes of fungi and protists. The current taxonomy of myxomycetes poses serious problems and does not clearly reflect the evolutionary relationships of this group. The literature on myxomycetes in the Philippines has primarily focused on species identification, ecological and diversity studies. However, no attempts have been made yet to elucidate the evolutionary relationships of this class using molecular evidence. The use of 18S rRNA and small subunit rRNA (SSU) sequences in this study to construct phylogenies has revealed that certain taxa, traditionally considered monophyletic, exhibit inconsistencies that warrant further investigation. However, the molecular evidence that supports the division of myxomycetes into two distinct groupings (Lucisporidia and Columellidia) according to spore color remains consistent with the constructed phylogeny using 18S rRNA gene sequences. Therefore, the present study aims to assess Philippine myxomycetes' diversity and evolutionary relationships. In addition, the study aims to compare the conventional taxonomy and molecular phylogeny of myxomycetes species in the Philippines using two molecular barcode markers - the 18S rRNA and SSU sequences. The study demonstrated that it is not always possible for morphology to agree with molecular data. On the other hand, molecular data can be more beneficial in reconstructing phylogenies but only to a certain extent and should be further evaluated.