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1. 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 2019 v.34 no.3 pp. 260-273
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

2. 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 2019 v.34 no.3 pp. 211-223
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

3. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses

Author:
Simmons, Mark P.; Sloan, Daniel B.; Springer, Mark S.; Gatesy, John
Source:
Molecular phylogenetics and evolution 2019 v.131 pp. 80-92
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; empirical research; genes;     Show all 3 Subjects
Abstract:
... In summary (“two-step”) coalescent analyses of empirical data, researchers typically apply the bootstrap to quantify branch support for clades inferred on the optimal species tree. We tested whether site-wise bootstrap analyses provide consistently more conservative support than gene-wise bootstrap analyses. We did so using data from three empirical phylogenomic studies and employed four coalescen ...
DOI:
10.1016/j.ympev.2018.10.001

4. Phylogenetic reconstruction of the genus Pseudaeginella (Amphipoda: Caprellidae), with the description of a new species from Brazil

Author:
Iwasa-Arai, Tammy; Siqueira, Silvana Gomes Leite; Machado, Glauco Barreto De Oliveira; Leite, Fosca Pedini Pereira
Source:
Systematics and biodiversity 2019 v.17 no.2 pp. 179-189
ISSN:
1478-0933
Subject:
phylogeny,   etc   ; Caprellidae; new species; Brazil;     Show all 4 Subjects
Abstract:
... The genus Pseudaeginella is analysed herein by cladistic methods based on a morphological data matrix of 49 characters × 18 terminal taxa. Based on the results, we comment on the phylogenetic position of Paradeutella within Pseudaeginella, and we propose Pseudaeginella multispinosa comb. nov. and Pseudaeginella tanzaniensis comb. nov. Pseudaeginella freirei sp. nov. is described from the Abrolhos ...
DOI:
10.1080/14772000.2019.1572668

5. 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

6. Plant chemophenetics − a new term for plant chemosystematics/plant chemotaxonomy in the macro-molecular era

Author:
Zidorn, Christian
Source:
Phytochemistry 2019
ISSN:
0031-9422
Subject:
phylogeny,   etc   ; chemotaxonomy; methodology; secondary metabolites;     Show all 4 Subjects
Abstract:
... Plant chemosystematic or chemotaxonomic studies based purely on the profiles of small molecules have become obsolete as tools to study phylogenetic relationships of higher plants due to the advent of the much more powerful (macro-)molecular techniques and new methods of data analysis established in parallel to these techniques. A new term is herein proposed for the field of studies aimed at the ex ...
DOI:
10.1016/j.phytochem.2019.02.013

7. Protein engineers turned evolutionists—the quest for the optimal starting point

Author:
Trudeau, Devin L; Tawfik, Dan S
Source:
Current opinion in biotechnology 2019 v.60 pp. 46-52
ISSN:
0958-1669
Subject:
phylogeny,   etc   ; bioengineering; bioinformatics; directed evolution; enzymes; plasticity;     Show all 6 Subjects
Abstract:
... The advent of laboratory directed evolution yielded a fruitful crosstalk between the disciplines of molecular evolution and bio-engineering. Here, we outline recent developments in both disciplines with respect to how one can identify the best starting points for directed evolution, such that highly efficient and robust tailor-made enzymes can be obtained with minimal optimization. Directed evolut ...
DOI:
10.1016/j.copbio.2018.12.002

8. Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures

Author:
Tavares, Rafael C.A.; Pyle, Anna Marie; Somarowthu, Srinivas
Source:
Journal of molecular biology 2019 v.431 no.8 pp. 1592-1603
ISSN:
0022-2836
Subject:
phylogeny,   etc   ; RNA; mammals; prediction; sequence alignment;     Show all 5 Subjects
Abstract:
... The existence of evolutionary conservation in base pairing is strong evidence for functional elements of RNA structure, although available tools for rigorous identification of structural conservation are limited. R-scape is a recently developed program for statistical prediction of pairwise covariation from sequence alignments, but it initially showed limited utility on long RNAs, especially those ...
DOI:
10.1016/j.jmb.2019.03.012

9. Diversification and functional evolution of reef fish feeding guilds

Author:
Gajdzik, Laura; Aguilar‐Medrano, Rosalia; Frédérich, Bruno
Source:
Ecology letters 2019 v.22 no.4 pp. 572-582
ISSN:
1461-023X
Subject:
phylogeny,   etc   ; Labridae; Pomacentridae; ecosystems; feeding methods; fish;     Show all 6 Subjects
Abstract:
... A core eco‐evolutionary aim is to better understand the factors driving the diversification of functions in ecosystems. Using phylogenetic, trophic, and functional information, we tested whether trophic habits (i.e. feeding guilds) affect lineage and functional diversification in two major radiations of reef fishes. Our results from wrasses (Labridae) and damselfishes (Pomacentridae) do not fully ...
DOI:
10.1111/ele.13219

10. Geometric morphometrics, homology and cladistics: review and recommendations

Author:
Palci, Alessandro; Lee, Michael S. Y.
Source:
Cladistics 2019 v.35 no.2 pp. 230-242
ISSN:
0748-3007
Subject:
phylogeny,   etc   ; ancestry; geometry; guidelines; morphometry; trees;     Show all 6 Subjects
Abstract:
... Geometric morphometric (GM) data has a long and contentious history in phylogenetic analyses. Often associated with phenetics, GM has been considered by many to be unable to provide meaningful information on phylogenetic relationships. However, the concepts of primary and secondary homology as developed for discrete characters can be readily extended to GM data: raw similarity in aligned landmark ...
DOI:
10.1111/cla.12340

11. The last phase of conodont evolution during the Late Triassic: Integrating biostratigraphic and phylogenetic approaches

Author:
Karádi, Viktor; Cau, Andrea; Mazza, Michele; Rigo, Manuel
Source:
Palaeogeography, palaeoclimatology, palaeoecology 2019
ISSN:
0031-0182
Subject:
phylogeny,   etc   ; Triassic period; basins; taxonomy; Hungary; Italy;     Show all 6 Subjects
Abstract:
... For the Upper Triassic, conodonts are the primary tools utilized in biostratigraphic investigations. For an effective biostratigraphic zonation, the species should be constrained by clear phylogenetic relationships, in which the stratigraphic ranges and taxonomy are reliable. Unfortunately, a phylogenetic framework for the Late Triassic pectiniform conodonts is almost missing, except for particula ...
DOI:
10.1016/j.palaeo.2019.03.045

12. Two new records of ascomycetes from Japan, Pyrenopeziza protrusa and P. nervicola (Helotiales, Dermateaceae sensu lato)

Author:
Itagaki, Hiyori; Nakamura, Yasuhide; Hosoya, Tsuyoshi
Source:
Mycoscience 2019
ISSN:
1340-3540
Subject:
phylogeny,   etc   ; Pyrenopeziza; asci; ascospores; ribosomal DNA; Japan;     Show all 6 Subjects
Abstract:
... Two Pyrenopeziza species, P. protrusa and P. nervicola known to have similar morphology, were newly reported from Japan. This study clarified that P. protrusa morphologically differs from P. nervicola in (1) more protruded outermost cells in ectal excipulum, (2) smaller ascospores, and (3) longer and thinner asci. Pyrenopeziza protrusa produces chlamydospore-like brown cells under culture while P. ...
DOI:
10.1016/j.myc.2019.02.008

13. Brain evolution in social insects: advocating for the comparative approach

Author:
Godfrey, R. Keating; Gronenberg, Wulfila
Source:
Journal of comparative physiology 2019 v.205 no.1 pp. 13-32
ISSN:
0340-7594
Subject:
phylogeny,   etc   ; Hymenoptera; brain; social behavior; social insects;     Show all 5 Subjects
Abstract:
... Sociality is classified as one of the major transitions in the evolution of complexity and much effort has been dedicated to understanding what traits predispose lineages to sociality. Conversely, studies addressing the role of sociality in brain evolution (e.g., the social brain hypothesis) have not focused on particular traits and instead relied largely on measurements of relative brain composit ...
DOI:
10.1007/s00359-019-01315-7

14. GeX: an automated tool for generating XYD files for analysis of endemicity using VNDM

Author:
Santos, Charles Morphy D.; Fuhlendorf, Max
Source:
Cladistics 2019 v.35 no.1 pp. 125-129
ISSN:
0748-3007
Subject:
phylogeny,   etc   ; algorithms; automation; georeferencing; indigenous species;     Show all 5 Subjects
Abstract:
... In the last decade, a method widely used to delimit areas of endemism is the analysis of endemicity (AE), a non‐hierarchical and grid‐dependent algorithm implemented through the package NDM/VNDM. Its input files are based on lists of georeferenced taxa, and any mistakes in their preparation will influence the results of the analyses. We describe here a free online automated tool for generating the ...
DOI:
10.1111/cla.12236

15. Revision of some central European species of Inocybe (Fr.: Fr.) Fr. subgenus Inocybe, with the description of five new species

Author:
Bandini, Ditte; Oertel, Bernd; Ploch, Sebastian; Ali, Tahir; Vauras, Jukka; Schneider, Anja; Scholler, Markus; Eberhardt, Ursula; Thines, Marco
Source:
Mycological progress 2019 v.18 no.1-2 pp. 247-294
ISSN:
1617-416X
Subject:
phylogeny,   etc   ; Inocybe; new species; photographs; type collections;     Show all 5 Subjects
Abstract:
... The subgenus Inocybe is widespread in the Holarctic but, due to a superficially similar appearance of the species, much of its diversity has been overlooked. In this study, a revision of some Central European species of the subgenus is carried out. On the basis of detailed morphological and phylogenetic investigation, five new species of Inocybe, subgenus Inocybe are described. Three of these are ...
DOI:
10.1007/s11557-018-1439-9

16. Assessing Phylogenetic Information to Reveal Uncertainty in Historical Data: An Example Using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae)

Author:
Parker, Elyse; Dornburg, Alex; Domínguez-Domínguez, Omar; Piller, Kyle R.
Source:
Molecular phylogenetics and evolution 2019
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; Goodeidae; freshwater fish; uncertainty; Mexico;     Show all 5 Subjects
Abstract:
... A major emerging challenge to resolution of a stable phylogenetic Tree of Life has been incongruent inference among studies. Given the increasing ubiquity of incongruent studies, analyzing the predicted phylogenetic utility and quantitative evidence regarding contributions toward resolution of commonly-used markers in historical studies over the last decade represents an important, yet neglected, ...
DOI:
10.1016/j.ympev.2019.01.025

17. DNA barcode, taxonomic and ecological notes for the identification of the invasive amphipod Monocorophium acherusicum (Costa, 1851)

Author:
Albano, Mariano J.; Rumbold, Carlos; Chiesa, Ignacio L.; Vazquez, Guadalupe; Spivak, Eduardo D.; Obenat, Sandra M.
Source:
New Zealand journal of marine and freshwater research 2019 v.53 no.1 pp. 15-32
ISSN:
1175-8805
Subject:
phylogeny,   etc   ; Amphipoda; DNA barcoding; biofouling; summer; Argentina;     Show all 6 Subjects
Abstract:
... We report the occurrence of the invasive amphipod Monocorophium acherusicum in Mar del Plata port, Argentina, using morphological and molecular analysis and estimated mean abundance to detect monthly variations of this population. We compared M. acherusicum morphology with that of M. insidiosum and Crassicorophium bonelli, the two most similar locally occurring species, to establish the diagnostic ...
DOI:
10.1080/00288330.2018.1469514

18. Polychaete meets octopus: symbiotic relationship between Spathochaeta octopodis gen. et sp. nov. (Annelida: Chrysopetalidae) and Octopus sp. (Mollusca: Octopodidae)

Author:
Jimi, Naoto; Moritaki, Takeya; Kajihara, Hiroshi
Source:
Systematics and biodiversity 2019 v.17 no.1 pp. 80-85
ISSN:
1478-0933
Subject:
phylogeny,   etc   ; Bivalvia; Octopodidae; Polychaeta; cold; symbiosis; Japan;     Show all 7 Subjects
Abstract:
... Marine annelids in the subfamily Calamyzinae (family Chrysopetalidae) are either symbiotic or free-living forms that have been mainly reported from deep-sea chemosynthetic systems. Symbiotic calamyzines mainly live in the mantle cavity of bivalves in hydrothermal vents or cold seeps, but one species is also found to be inserted into the epidermis of polychaetes. We found a single specimen of calam ...
DOI:
10.1080/14772000.2018.1520753

19. 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

20. Multi-allele species reconstruction using ASTRAL

Author:
Rabiee, Maryam; Sayyari, Erfan; Mirarab, Siavash
Source:
Molecular phylogenetics and evolution 2019 v.130 pp. 286-296
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; algorithms; alleles; data collection; system optimization;     Show all 5 Subjects
Abstract:
... Genome-wide phylogeny reconstruction is becoming increasingly common, and one driving factor behind these phylogenomic studies is the promise that the potential discordance between gene trees and the species tree can be modeled. Incomplete lineage sorting is one cause of discordance that bridges population genetic and phylogenetic processes. ASTRAL is a species tree reconstruction method that seek ...
DOI:
10.1016/j.ympev.2018.10.033