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Phylogenetic trees are types of networks that describe the temporal relationship between individuals, species, or other units that are subject to evolutionary diversification. Many phylogenetic trees are constructed from molecular data that is often only available for extant species, and hence they lack all or some of the branches that did not make it into the present. This feature makes inference on the diversification process challenging. For relatively simple diversification models, analytical or numerical methods to compute the likelihood exist, but these do not work for more realistic models in which the likelihood depends on properties of the missing lineages. In this article, we study a general class of species diversification models, and we provide an expectation‐maximization framework in combination with a uniform sampling scheme to perform maximum likelihood estimation of the parameters of the diversification process.

[EN] A wide range of applications and research has been done with genome-scale metabolic models. In this work, we describe an innovative methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this comparison in order to infer evolutionary distances between different organisms. Our methodology allows a quantification of the metabolic differences between different species from a broad range of families and even kingdoms. This quantification is then applied in order to reconstruct phylogenetic trees for sets of various organisms. ; The research leading to these results has received funding from the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement number 308518 (CyanoFactory). ; Gamermann, D.; Montagud Aquino, A.; Conejero Casares, JA.; Urchueguía Schölzel, JF.; Fernández De Córdoba Castellá, PJ. (2014). New approach for phylogenetic tree recovery based on genome-scale metabolic networks. Journal of Computational Biology. 21(7):508-519. https://doi.org/10.1089/cmb.2013.0150 ; S ; 508 ; 519 ; 21 ; 7

16S ribosomal RNA (16S rRNA) gene sequences used to study bacterial phylogeny and taxonomy have been by far the most common housekeeping genetic marker utilized for identification and ancestor determination. This study aimed to investigate, for the first time, the relationship between Klebsiella spp. isolated from clinical and environmental samples in Iraq.
Fifty Klebsiella spp. isolates were isolated from clinical and environmental sources. Twenty-five isolates were collected from a fresh vegetable (Apium graveolens) and 25 from clinical samples (sputum, wound swab, urine). Enteric bacteria were isolated on selective and differential media and identified by an automatic identification system, vitek-2. The total DNA was extracted and PCR amplified for selected isolates. The 16S rRNA gene was amplified by using the universal primer 27F (5'- AGAGTTTGATCCTGGCTCAG- 3') and 1492R (5'- GGTTACCTTGTTACGACTT- 3'). The 16SrRNA gene sequence was analysed among some local isolates, and the results were compared with the standard data of similar registered strains in NCBI. The most common species of Klebsiella was Klebsiella pneumoniae pneumoniae (Kpp), followed by Klebsiella pneumoniae ozaenae (Kpo) and Klebsiella oxytoca (Ko). The results of the identification of species and sub species by using the biochemical test (vitek-2) were more precise than those obtained by the use of the universal primer.Phylogenetic tree strategies have clearly indicated a relatively close similarity amongst all analysed Klebsiella isolates and revealed the intra-species genetic distance between the individual isolates of the Klebsiella spp. In conclusion, our results revealed the main advantage of using universal primers for the identification of Klebsiella spp. and their root from nature.

16S ribosomal RNA (16S rRNA) gene sequences used to study bacterial phylogeny and taxonomy have been by far the most common housekeeping genetic marker utilized for identification and ancestor determination. This study aimed to investigate, for the first time, the relationship between Klebsiella spp. isolated from clinical and environmental samples in Iraq.
Fifty Klebsiella spp. isolates were isolated from clinical and environmental sources. Twenty-five isolates were collected from a fresh vegetable (Apium graveolens) and 25 from clinical samples (sputum, wound swab, urine). Enteric bacteria were isolated on selective and differential media and identified by an automatic identification system, vitek-2. The total DNA was extracted and PCR amplified for selected isolates. The 16S rRNA gene was amplified by using the universal primer 27F (5'- AGAGTTTGATCCTGGCTCAG- 3') and 1492R (5'- GGTTACCTTGTTACGACTT- 3'). The 16SrRNA gene sequence was analysed among some local isolates, and the results were compared with the standard data of similar registered strains in NCBI. The most common species of Klebsiella was Klebsiella pneumoniae pneumoniae (Kpp), followed by Klebsiella pneumoniae ozaenae (Kpo) and Klebsiella oxytoca (Ko). The results of the identification of species and sub species by using the biochemical test (vitek-2) were more precise than those obtained by the use of the universal primer.Phylogenetic tree strategies have clearly indicated a relatively close similarity amongst all analysed Klebsiella isolates and revealed the intra-species genetic distance between the individual isolates of the Klebsiella spp. In conclusion, our results revealed the main advantage of using universal primers for the identification of Klebsiella spp. and their root from nature.

A total of 77 (35 female and 42 male) hard ticks samples were isolated from 22 long-eared hedgehog during January 2021 to May 2022. All animals were infested with one or two species of hard ticks with 100% infestation rate With the density of infestation mean of 3.5. The areas of collection were Baghdad, Wasit, Karbala and Al-Anbar provinces. Morphological study revealed that both species belonged to one genus of hard ticks: Rhipicephalus sanguineus (Neumann, 1904) 50.64% and Rhipicephalus turanicus (Morel, 1969) 49.35%. The molecular investigation of current study revealed that the sensitive and specific PCR assay allowing rapid and reliable identification of Rhipicephalus sp. by the fragment size amplified, was 390- 400 bp 12S ribosomal RNA gene in Rhipicephalus turanicus and Rhipicephalus sanguineus isolate samples from the under-study animals. The accession numbers in NCBI-Genbank are ON211060 and ON211307 respectively.
Phylogenetic tree analysis was based on small subunit ribosomal RNA gene partial sequence in local Rhipicephalus turanicus Iraqi isolate that was used for genetic relationship analysis. The local Rhipicephalus turanicus Iraqi isolate showed close relationship to NCBI-BLAST Rhipicephalus turanicus from Iran, Turkmenistan, Italy, Greece, Saudi Arabia and the Chinese isolates with total genetic changes at 0.01%. Whereas Phylogenetic tree analysis based on small subunit ribosomal RNA gene partial sequence in local Rhipicephalus sanguineus Iraqi isolate showed clear genetic difference to NCBI-BLAST Rhipicephalus sanguineus isolates from Argentina, Italy, Brazil, France, Portugal, USA and Spain at total genetic changes of 0.005-0.0020%.

Aeromonas hydrophila is widely distributed throughout the world and causes diseases to animals and human exposed to contaminated environments such as water and soil. This study aimed to compare between isolates of A. hydrophila collected from clinical and environmental samples, through investigating the phenotype of some virulence factors in vitro, including hemolysin, protease, lipase, nuclease and biofilm formation ability. Also, the antimicrobial susceptibility for different antibiotics was determined using disc diffusion method. For genotypic identification of isolates and phylogenetic tree construction, 16S rDNA target gene was amplified and sequenced. The phenotypic results showed some differences between the isolates (clinical and environmental). All isolates were resistance to clindamycin, amoxicillin and erythromycin while susceptible to gentamicin, amikacin and vancomycin. Sequences of 16S rDNA confirmed the identification of the studied bacteria as A. hydrophila with 99-100% , and identity and phylogenetic tree by neighbor-joining clearly separated the isolates in a branching pattern which displayed similarity to the GenBank isolates obtained from Asian regions. The clinical isolates showed less polymorphism than the environmental isolates.

Abstract: Plant diversity begets diversity at other trophic levels. While species richness is the most commonly used measure for plant diversity, the number of evolutionary lineages (i.e. phylogenetic diversity) could theoretically have a stronger influence on the community structure of co‐occurring organisms. However, this prediction has only rarely been tested in complex real‐world ecosystems.Using a comprehensive multitrophic dataset of arthropods and fungi from a species‐rich subtropical forest, we tested whether tree species richness or tree phylogenetic diversity relates to the diversity and composition of organisms.We show that tree phylogenetic diversity but not tree species richness determines arthropod and fungi community composition across trophic levels and increases the diversity of predatory arthropods but decreases herbivorous arthropod diversity. The effect of tree phylogenetic diversity was not mediated by changed abundances of associated organisms, indicating that evolutionarily more diverse plant communities increase niche opportunities (resource diversity) but not necessarily niche amplitudes (resource amount).Our findings suggest that plant evolutionary relatedness structures multitrophic communities in the studied species‐rich forests and possibly other ecosystems at large. As global change non‐randomly threatens phylogenetically distinct plant species, far‐reaching consequences on associated communities are expected

This is the peer reviewed version of the following article: Honorio Coronado, E. N., Dexter, K. G., Pennington, R. T., Chave, J., Lewis, S. L., Alexiades, M. N., Alvarez, E., Alves de Oliveira, A., Amaral, I. L., Araujo-Murakami, A., Arets, E. J. M. M., Aymard, G. A., Baraloto, C., Bonal, D., Brienen, R., Cerón, C., Cornejo Valverde, F., Di Fiore, A., Farfan-Rios, W., Feldpausch, T. R., Higuchi, N., Huamantupa-Chuquimaco, I., Laurance, S. G., Laurance, W. F., López-Gonzalez, G., Marimon, B. S., Marimon-Junior, B. H., Monteagudo Mendoza, A., Neill, D., Palacios Cuenca, W., Peñuela Mora, M. C., Pitman, N. C. A., Prieto, A., Quesada, C. A., Ramirez Angulo, H., Rudas, A., Ruschel, A. R., Salinas Revilla, N., Salomão, R. P., Segalin de Andrade, A., Silman, M. R., Spironello, W., ter Steege, H., Terborgh, J., Toledo, M., Valenzuela Gamarra, L., Vieira, I. C. G., Vilanova Torre, E., Vos, V., Phillips, O. L. (2015), Phylogenetic diversity of Amazonian tree communities. Diversity and Distributions, 21: 1295–1307. doi:10.1111/ddi.12357, which has been published in final form at 10.1111/ddi.12357 ; Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival. Results: PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Main conclusions: High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities. ; FINCyT - PhD studentship ; School of Geography of the University of Leeds ; Royal Botanic Garden Edinburgh ; Natural Environment Research Council (NERC) ; Gordon and Betty Moore Foundation ; European Union's Seventh Framework Programme ; ERC ; CNPq/PELD ; NSF - Fellowship

"This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography -- the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis -- Parametric phylogenetics including maximum likelihood and Bayesian approaches -- Phylogenetic classification -- Critiques of evolutionary taxonomy, phenetics, and transformed cladistics -- Specimen selection, field collecting, and curating -- Systematic publication and the rules of nomenclature. Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology."--Provided by publisher

The transfer distance (TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching. Recently, Lemoine et al. (2018) showed that TD can be a powerful tool to assess the branch support of phylogenies with large data sets, thus providing a relevant alternative to Felsenstein's bootstrap. This distance allows a reference branch β in a reference tree T to be compared to a branch b from another tree T, both on the same set of n taxa. The TD between these branches is the number of taxa that must be transferred from one side of b to the other in order to obtain β. By taking the minimum TD from β to all branches in T we define the transfer index, denoted by ϕ(β,T), measuring the degree of agreement of T with β. Let us consider a reference branch β having p tips on its light side and define the transfer support (TS) as 1 - ϕ(β,T)/(p-1). The aim of this article is to provide evidence that p-1 is a meaningful normalization constant in the definition of TS, and measure the statistical significance of TS, assuming that β is compared to a tree T drawn according to a null model. We obtain several results that shed light on these questions in a number of settings. In particular, we study the asymptotic behavior of TS when n tends to ∞, and fully characterize the distribution of ϕ when T is a caterpillar tree. ; European Union

International audience ; This review expands on a talk I gave during the "Biology of Anthrax" meeting held in Bari, Italy (September 3 rd-6 th , 2019). The talk was a synthesis of recent investigations taking advantage of the topology of the Bacillus anthracis phylogenetic tree to propose tentative dating points and scenarios. Currently available whole-genome sequence (WGS) data allowed identifying single nucleotide polymorphisms (SNPs) among B. anthracis strains and drawing phylogenetic trees. The geographic origin of the strains and the topology of the tree were used to infer spreading events. Five star-like patterns in the tree (polytomies), each containing at least six branches, were detected. The analysis of the geographic distribution of the strains constituting one such polytomy suggests that it emerged not more than a few centuries ago. The key observation allowing this dating is the finding that the polytomy is anchored into Western Europe and that the main North-American lineage emerged from one of its branches, indicative of a post-Columbian export. From this point, I propose additional working hypotheses which may allow dating key nodes along the phylogeny of B. anthracis corresponding to four "Out-of-Africa" events. While trade of contaminated animal products seems to be the predominant driving force underlying modern long-distance spreading of B. anthracis , invasive military operations and more generally borders instabilities may have played an important role in earlier times. The testing of these hypotheses will require the sequencing of a significant number of additional strains from many countries. ; Cette revue découle d'une présentation faite lors du congrès "Biologie de la maladie du charbon" qui s'est tenu à Bari, Italie, du 3 au 6 septembre 2019. La présentation était une synthèse de travaux récents tirant parti de la topologie de l'arbre phylogénétique de Bacillus anthracis pour proposer une datation et un scenario d'évolution. Les analyses faites s'appuient sur les données de séquençage ...

International audience ; This review expands on a talk I gave during the "Biology of Anthrax" meeting held in Bari, Italy (September 3 rd-6 th , 2019). The talk was a synthesis of recent investigations taking advantage of the topology of the Bacillus anthracis phylogenetic tree to propose tentative dating points and scenarios. Currently available whole-genome sequence (WGS) data allowed identifying single nucleotide polymorphisms (SNPs) among B. anthracis strains and drawing phylogenetic trees. The geographic origin of the strains and the topology of the tree were used to infer spreading events. Five star-like patterns in the tree (polytomies), each containing at least six branches, were detected. The analysis of the geographic distribution of the strains constituting one such polytomy suggests that it emerged not more than a few centuries ago. The key observation allowing this dating is the finding that the polytomy is anchored into Western Europe and that the main North-American lineage emerged from one of its branches, indicative of a post-Columbian export. From this point, I propose additional working hypotheses which may allow dating key nodes along the phylogeny of B. anthracis corresponding to four "Out-of-Africa" events. While trade of contaminated animal products seems to be the predominant driving force underlying modern long-distance spreading of B. anthracis , invasive military operations and more generally borders instabilities may have played an important role in earlier times. The testing of these hypotheses will require the sequencing of a significant number of additional strains from many countries. ; Cette revue découle d'une présentation faite lors du congrès "Biologie de la maladie du charbon" qui s'est tenu à Bari, Italie, du 3 au 6 septembre 2019. La présentation était une synthèse de travaux récents tirant parti de la topologie de l'arbre phylogénétique de Bacillus anthracis pour proposer une datation et un scenario d'évolution. Les analyses faites s'appuient sur les données de séquençage ...