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1. What is the minimum length of gltA gene required for phylogenetic analyzes in Bartonella?

Author:
Guterres, Alexandro; Gonçalves, Jonathan; de Lemos, Elba Regina Sampaio
Source:
Research in microbiology 2019 v.170 no.1 pp. 60-64
ISSN:
0923-2508
Subject:
phylogeny,   etc   ; Bartonella; genes; sequence analysis;     Show all 4 Subjects
Abstract:
... Bartonellosis is an emerging serious diseases of zoonotic relevance caused by an expanding number of recently discovered species of Bartonella. Many studies use partial gltA gene sequencing as the method of choice for species attribution, and a plethora of studies have utilized only this gene to describe Bartonella diversity. We observe a lack of correspondence between the phylogenies constructed ...
DOI:
10.1016/j.resmic.2018.08.007

2. Climatic niche evolution in turtles is characterized by phylogenetic conservatism for both aquatic and terrestrial species

Author:
Rodrigues, João Fabrício M.; Villalobos, Fabricio; Iverson, John B.; Diniz‐Filho, José Alexandre F.
Source:
Journal of evolutionary biology 2019 v.32 no.1 pp. 66-75
ISSN:
1010-061X
Subject:
phylogeny,   etc   ; aquatic organisms; models; niches; tortoises; turtles;     Show all 6 Subjects
Abstract:
... Understanding how the climatic niche of species evolved has been a topic of high interest in current theoretical and applied macroecological studies. However, little is known regarding how species traits might influence climatic niche evolution. Here, we evaluated patterns of climatic niche evolution in turtles (tortoises and freshwater turtles) and whether species habitat (terrestrial or aquatic) ...
DOI:
10.1111/jeb.13395

3. Integrating spatial and phylogenetic information in the fourth‐corner analysis to test trait–environment relationships

Author:
Braga, João; ter Braak, Cajo J. F.; Thuiller, Wilfried; Dray, Stéphane
Source:
Ecology 2018 v.99 no.12 pp. 2667-2674
ISSN:
0012-9658
Subject:
phylogeny,   etc   ; autocorrelation; environmental factors;     Show all 3 Subjects
Abstract:
... The fourth‐corner analysis aims to quantify and test for relationships between species traits and site‐specific environmental variables, mediated by site‐specific species abundances. Since there is no common unit of observation, the significance of the relationships is tested using a double permutation procedure (site based and species based). This method implies that all species and sites are ind ...
DOI:
10.1002/ecy.2530

4. Species Concepts: What about Ticks?

Author:
Dantas-Torres, Filipe
Source:
Trends in parasitology 2018 v.34 no.12 pp. 1017-1026
ISSN:
1471-4922
Subject:
phylogeny,   etc   ; genetics; taxonomy; ticks;     Show all 4 Subjects
Abstract:
... Since ancient times, philosophers and taxonomists have tried to classify forms of life. This is what taxonomy is about: the science of identifying, naming, classifying, and describing organisms. In this article I address the issue of the species concept in tick taxonomy. While the typological species concept is still the most widely used, the biological and phylogenetic species concepts are growin ...
DOI:
10.1016/j.pt.2018.09.009

5. Going rogue

Author:
Brower, Andrew V. Z.
Source:
Cladistics 2018 v.34 no.4 pp. 467-468
ISSN:
0748-3007
Subject:
phylogeny,   etc   ; data analysis; taxonomy;     Show all 3 Subjects
Abstract:
... The problem of ‘rogue taxa’ explored by Buenaventura et al. (2017, Cladistics 33: 109–133) is due to complementary patterns of missing data in their matrix, which are evident from perusal of their supplementary table S1. ...
DOI:
10.1111/cla.12211

6. Mammals and meaningful taxonomic units: the debate about species concepts and conservation

Author:
Zachos, Frank E.
Source:
Mammal review 2018 v.48 no.3 pp. 153-159
ISSN:
0305-1838
Subject:
phylogeny,   etc   ; mammals; taxonomy;     Show all 3 Subjects
Abstract:
... Mammalian taxonomy based on the diagnosability version of the Phylogenetic Species Concept has recently been declared the only sound approach to mammalian classification. In this article, based on the underlying evolutionary ontology of species taxa, I explain the fallacy of these arguments and hold that in a ‘grey area’ after lineage sundering, completely objective species delimitation is impossi ...
DOI:
10.1111/mam.12121

7. Giant taxon‐character matrices: the future of morphological systematics

Author:
Laing, Adam M.; Doyle, Sharon; Gold, Maria Eugenia Leone; Nesbitt, Sterling J.; O'Leary, Maureen A.; Turner, Alan H.; Wilberg, Eric W.; Poole, Karen E.
Source:
Cladistics 2018 v.34 no.3 pp. 333-335
ISSN:
0748-3007
Subject:
phylogeny,   etc   ; data collection; topology;     Show all 3 Subjects
Abstract:
... Simões et al. () argued that large matrices are linked to the construction of “problematic” characters, and that those characters negatively affect tree topology. In their re‐evaluation of two squamate datasets, however, Simões et al. () simply eliminated what they termed “problematic” characters, rather than recode them. This practice ignores potential sources of phylogenetic information and, if ...
DOI:
10.1111/cla.12197

8. On the relationship between phylogenetic diversity and trait diversity

Author:
Tucker, Caroline M.; Davies, T. Jonathan; Cadotte, Marc W.; Pearse, William D.
Source:
Ecology 2018 v.99 no.6 pp. 1473-1479
ISSN:
0012-9658
Subject:
phylogeny,   etc   ; biodiversity; models;     Show all 3 Subjects
Abstract:
... Niche differences are key to understanding the distribution and structure of biodiversity. To examine niche differences, we must first characterize how species occupy niche space, and two approaches are commonly used in the ecological literature. The first uses species traits to estimate multivariate trait space (so‐called functional trait diversity, FD); the second quantifies the amount of time o ...
DOI:
10.1002/ecy.2349

9. Phylogenetic Studies on Bonomyces (Tricholomatineae, Agaricales) and Two New Combinations from Clitocybe Mycologie

Author:
Alvarado, Pablo; Moreau, Pierre-Arthur; Sesli, Ertugrul; Khodja, Lounis Youcef; Contu, Marco; Vizzini, Alfredo
Source:
Cryptogamie 2018 v.39 no.2 pp. 149-168
ISSN:
1776-100X
Subject:
phylogeny,   etc   ; Clitocybe; new combination;     Show all 3 Subjects
Abstract:
... Genus Bonomyces is here reviewed. Multigene phylogenetic analysis suggests it is related with Cleistocybe in the Tricholomatineae. Morphological and genetical studies led to a new interpretation of the type species, B. sinopicus (=C. subsinopica), and the new combinations B. afrosinopicus and B. arnoldii. ...
DOI:
10.7872/crym/v39.iss2.2018.149

10. On defining a unique phylogenetic tree with homoplastic characters

Author:
Goloboff, Pablo A.; Wilkinson, Mark
Source:
Molecular phylogenetics and evolution 2018 v.122 pp. 95-101
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; algorithms; statistical analysis;     Show all 3 Subjects
Abstract:
... This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is re ...
DOI:
10.1016/j.ympev.2018.01.020

11. Metabolomics‐based chemotaxonomy of root endophytic fungi for natural products discovery

Author:
Maciá‐Vicente, Jose G.; Shi, Yan‐Ni; Cheikh‐Ali, Zakaria; Grün, Peter; Glynou, Kyriaki; Kia, Sevda Haghi; Piepenbring, Meike; Bode, Helge B.
Source:
Environmental microbiology 2018 v.20 no.3 pp. 1253-1270
ISSN:
1462-2912
Subject:
phylogeny,   etc   ; chemotaxonomy; endophytes; fungi;     Show all 4 Subjects
Abstract:
... Fungi are prolific producers of natural products routinely screened for biotechnological applications, and those living endophytically within plants attract particular attention because of their purported chemical diversity. However, the harnessing of their biosynthetic potential is hampered by a large and often cryptic phylogenetic and ecological diversity, coupled with a lack of large‐scale natu ...
DOI:
10.1111/1462-2920.14072

12. Robustness of the approximate likelihood of the protracted speciation model

Author:
Simonet, C.; Scherrer, R.; Rego‐Costa, A.; Etienne, R. S.
Source:
Journal of evolutionary biology 2018 v.31 no.3 pp. 469-479
ISSN:
1010-061X
Subject:
phylogeny,   etc   ; extinction; models; trees;     Show all 4 Subjects
Abstract:
... The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speciation, rate of completion of speciation and extinc ...
DOI:
10.1111/jeb.13233

13. Rymovirus: a cautionary tale

Author:
Gibbs, AdrianJ.; Gibbs, MarkJ.
Source:
Archives of virology 2018 v.163 no.3 pp. 815-817
ISSN:
0304-8608
Subject:
phylogeny,   etc   ; Potyvirus; Rymovirus; viruses;     Show all 4 Subjects
Abstract:
... A recent proposal that the genus Rymovirus be assimilated into the genus Potyvirus is examined, discussed, and rejected. It illustrates the danger of using ‘sequence identity’ as a proxy for phylogenetic relatedness to distinguish closely related but distinct groups of viruses. ...
DOI:
10.1007/s00705-017-3676-7

14. Niche Estimation Above and Below the Species Level

Author:
Smith, Adam B.; Godsoe, William; Rodríguez-Sánchez, Francisco; Wang, Hsiao-Hsuan; Warren, Dan
Source:
Trends in ecology & evolution 2018
ISSN:
0169-5347
Subject:
phylogeny,   etc   ; models; niches;     Show all 3 Subjects
Abstract:
... Ecological niches reflect not only adaptation to local circumstances but also the tendency of related lineages to share environmental tolerances. As a result, information on phylogenetic relationships has underappreciated potential to inform ecological niche modeling. Here we review three strategies for incorporating evolutionary information into niche models: splitting lineages into subunits, lum ...
DOI:
10.1016/j.tree.2018.10.012

15. The Latitudinal Diversity Gradient: Novel Understanding through Mechanistic Eco-evolutionary Models

Author:
Pontarp, Mikael; Bunnefeld, Lynsey; Cabral, Juliano Sarmento; Etienne, Rampal S.; Fritz, Susanne A.; Gillespie, Rosemary; Graham, Catherine H.; Hagen, Oskar; Hartig, Florian; Huang, Shan; Jansson, Roland; Maliet, Odile; Münkemüller, Tamara; Pellissier, Loïc; Rangel, Thiago F.; Storch, David; Wiegand, Thorsten; Hurlbert, Allen H.
Source:
Trends in ecology & evolution 2018
ISSN:
0169-5347
Subject:
phylogeny,   etc   ; ecology; models;     Show all 3 Subjects
Abstract:
... The latitudinal diversity gradient (LDG) is one of the most widely studied patterns in ecology, yet no consensus has been reached about its underlying causes. We argue that the reasons for this are the verbal nature of existing hypotheses, the failure to mechanistically link interacting ecological and evolutionary processes to the LDG, and the fact that empirical patterns are often consistent with ...
DOI:
10.1016/j.tree.2018.11.009

16. Characterization of Echinostoma revolutum and Echinostoma robustum from ducks in Bangladesh based on morphology, nuclear ribosomal ITS2 and mitochondrial nad1 sequences

Author:
Mohanta, Uday Kumar; Watanabe, Takuya; Anisuzzaman,; Ohari, Yuma; Itagaki, Tadashi
Source:
Parasitology international 2019 v.69 pp. 1-7
ISSN:
1383-5769
Subject:
phylogeny,   etc   ; Echinostoma revolutum; ducks; internal transcribed spacers; mitochondria; Bangladesh;     Show all 6 Subjects
Abstract:
... Precise discrimination of Echinostoma species within the ‘revolutum’ group is quite difficult because of their morphological similarities. The objective of this study was to precisely characterize the echinostomes of ducks from Bangladesh based on both morphological and molecular characteristics. Two Echinostoma species were identified: E. revolutum and E. robustum. In the phylogenetic trees (ITS2 ...
DOI:
10.1016/j.parint.2018.11.002

17. Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species

Author:
Liu, Jiabin; Yu, Jiaojiao; Zhou, Ming; Yang, Jiandong
Source:
International journal of biological macromolecules 2019 v.125 pp. 423-431
ISSN:
0141-8130
Subject:
phylogeny,   etc   ; Agamidae; gene rearrangement; lizards; mitochondrial genes; mitochondrial genome; China;     Show all 7 Subjects
Abstract:
... Japalura flaviceps is a subarboreal species, which is endemically distributed in China. Here, we determined the complete mitogenome of J. flaviceps. This mitogenome was a typical circular molecule of 17,140 bp in size, containing 13 protein-coding genes, 22 transfer-RNA-coding genes, two ribosomal-RNA-coding genes, and one control region. Our phylogenetic result using 15 genes divided all Agamidae ...
DOI:
10.1016/j.ijbiomac.2018.12.068

18. Floral uniformity through evolutionary time in a species‐rich tree lineage

Author:
Vasconcelos, Thais N. C.; Chartier, Marion; Prenner, Gerhard; Martins, Aline C.; Schönenberger, Jürg; Wingler, Astrid; Lucas, Eve
Source:
Thenew phytologist 2019 v.221 no.3 pp. 1597-1608
ISSN:
0028-646X
Subject:
phylogeny,   etc   ; Myrcia; ecological competition; ecosystems; environmental factors; flowers; pollination; trees;     Show all 8 Subjects
Abstract:
... Changes in floral morphology are expected across evolutionary time and are often promoted as important drivers in angiosperm diversification. Such a statement, however, is in contrast to empirical observations of species‐rich lineages that show apparent conservative floral morphologies even under strong selective pressure to change from their environments. Here, we provide quantitative evidence fo ...
DOI:
10.1111/nph.15453

19. Neotropical frogs and mating songs: The evolution of advertisement calls in glassfrogs

Author:
Escalona Sulbarán, Moisés D.; Ivo Simões, Pedro; Gonzalez‐Voyer, Alejandro; Castroviejo‐Fisher, Santiago
Source:
Journal of evolutionary biology 2019 v.32 no.2 pp. 163-176
ISSN:
1010-061X
Subject:
phylogeny,   etc   ; Anura; acoustics; body size; frogs; locomotion; species richness; vocalization;     Show all 8 Subjects
Abstract:
... Anurans emit advertisement calls with the purpose of attracting mates and repelling conspecific competitors. The evolution of call traits is expected to be associated with the evolution of anatomical and behavioural traits due to the physics of call emission and transmission. The evolution of vocalizations might imply trade‐offs with other energetically costly behaviours, such as parental care. He ...
DOI:
10.1111/jeb.13406

20. Rhynie chert fossils demonstrate the independent origin and gradual evolution of lycophyte roots

Author:
Hetherington, Alexander J; Dolan, Liam
Source:
Current opinion in plant biology 2019 v.47 pp. 119-126
ISSN:
1369-5266
Subject:
phylogeny,   etc   ; extinct species; fossils; root hairs; vascular plants;     Show all 5 Subjects
Abstract:
... Mapping fossil traits onto the land plant phylogenetic framework indicates that there were at least two independent origins of roots among extant vascular plants — once in lycophytes and independently in euphyllophytes. At least two rooting structural types are found among extinct species preserved in the Rhynie chert. First, species that lacked roots and developed horizontal axes that developed r ...
DOI:
10.1016/j.pbi.2018.12.001