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Ancestral character reconstruction

William G R Crampton, Carlos David de Santana, Joseph C Waddell, Nathan R Lovejoy
A species-level phylogenetic reconstruction of the Neotropical bluntnose knifefish genus Brachyhypopomus (Gymnotiformes, Hypopomidae) is presented, based on 60 morphological characters, approximately 1100 base pairs of the mitochondrial cytb gene, and approximately 1000 base pairs of the nuclear rag2 gene. The phylogeny includes 28 species of Brachyhypopomus and nine outgroup species from nine other gymnotiform genera, including seven in the superfamily Rhamphichthyoidea (Hypopomidae and Rhamphichthyidae). Parsimony and Bayesian total evidence phylogenetic analyses confirm the monophyly of the genus, and identify nine robust species groups...
2016: PloS One
Martín O Pereyra, Molly C Womack, J Sebastián Barrionuevo, Boris L Blotto, Diego Baldo, Mariane Targino, Jhon Jairo Ospina-Sarria, Juan M Guayasamin, Luis A Coloma, Kim L Hoke, Taran Grant, Julián Faivovich
Most anurans possess a tympanic middle ear (TME) that transmits sound waves to the inner ear; however, numerous species lack some or all TME components. To understand the evolution of these structures, we undertook a comprehensive assessment of their occurrence across anurans and performed ancestral character state reconstructions. Our analysis indicates that the TME was completely lost at least 38 independent times in Anura. The inferred evolutionary history of the TME is exceptionally complex in true toads (Bufonidae), where it was lost in the most recent common ancestor, preceding a radiation of >150 earless species...
September 28, 2016: Scientific Reports
Josef C Uyeda, Luke J Harmon, Carrine E Blank
Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record-phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth's history have shaped-and been shaped by-evolution in Cyanobacteria...
2016: PloS One
Maria Fernanda Calió, Katherine B Lepis, José Rubens Pirani, Lena Struwe
The monophyletic and Neotropical tribe Helieae of the worldwide family Gentianaceae (Gentianales, Asterids, Angiospermae) is well known for its problematic generic classifications. An initial phylogenetic analysis of Helieae shed light onto the relationships between genera, and indicated that traditional generic limits did not correspond to monophyletic groups. In order to obtain a more thorough understanding of generic relationships within the group, we enhanced sampling within the so-called Symbolanthus clade and performed phylogenetic analyses from DNA sequences from one plastid region (matK) and two nuclear regions (ITS and 5S-NTS), plus 112 morphological characters, which were analyzed separately and in combination, using parsimony and Bayesian approaches...
September 15, 2016: Molecular Phylogenetics and Evolution
Li-Yaung Kuo, Atsushi Ebihara, Wataru Shinohara, Germinal Rouhan, Kenneth R Wood, Chun-Neng Wang, Wen-Liang Chiou
The wide geographical distribution of many fern species is related to their high dispersal ability. However, very limited studies surveyed biological traits that could contribute to colonization success after dispersal. In this study, we applied phylogenetic approaches to infer historical biogeography of the fern genus Deparia (Athyriaceae, Eupolypods II). Because polyploids are suggested to have better colonization abilities and are abundant in Deparia, we also examined whether polyploidy could be correlated to long-distance dispersal events and whether polyploidy could play a role in these dispersals/establishment and range expansion...
November 2016: Molecular Phylogenetics and Evolution
Mark N Puttick
Ancestral state reconstruction of discrete character traits is often vital when attempting to understand the origins and homology of traits in living species. The addition of fossils has been shown to alter our understanding of trait evolution in extant taxa, but researchers may avoid using fossils alongside extant species if only few are known, or if the designation of the trait of interest is uncertain. Here, I investigate the impacts of fossils and incorrectly coded fossils in the ancestral state reconstruction of discrete morphological characters under a likelihood model...
August 2016: Biology Letters
Maxi Polihronakis Richmond, Jane Park, Charles S Henry
Genitalia diversity in insects continues to fuel investigation of the function and evolution of these dynamic structures. While most studies have focused on variation in male genitalia, an increasing number of studies on female genitalia have uncovered comparable diversity among females, but often at a much finer morphological scale. In this study, we analyze the function and evolution of male and female genitalia in Phyllophaga scarab beetles, a group in which both sexes exhibit genitalic diversity. To document the interaction of male and female structures during mating, we dissected flash-frozen mating pairs from three Phyllophaga species and investigated fine scale morphology using SEM...
July 30, 2016: Journal of Evolutionary Biology
Katarína Olšavská, Marek Slovák, Karol Marhold, Eliška Štubňová, Jaromír Kučera
BACKGROUND AND AIMS: The Balkan Peninsula is one of the most important centres of plant diversity in Europe. Here we aim to fill the gap in the current knowledge of the evolutionary processes and factors modelling this astonishing biological richness by applying multiple approaches to the Cyanus napulifer group. METHODS: To reconstruct the mode of diversification within the C. napulifer group and to uncover its relationships with potential relatives with x = 10 from Europe and Northern Africa, we examined variation in genetic markers (amplified fragment length polymorphisms [AFLPs]; 460 individuals), relative DNA content (4',6-diamidino-2-phenylindole [DAPI] flow cytometry, 330 individuals) and morphology (multivariate morphometrics, 40 morphological characters, 710 individuals)...
July 21, 2016: Annals of Botany
Courtney C Stepien, Catherine A Pfister, J Timothy Wootton
Understanding functional trait distributions among organisms can inform impacts on and responses to environmental change. In marine systems, only 1% of dissolved inorganic carbon in seawater exists as CO2. Thus the majority of marine macrophytes not only passively access CO2 for photosynthesis, but also actively transport CO2 and the more common bicarbonate (HCO3-, 92% of seawater dissolved inorganic carbon) into their cells. Because species with these carbon concentrating mechanisms (CCMs) are non-randomly distributed in ecosystems, we ask whether there is a phylogenetic pattern to the distribution of CCMs among algal species...
2016: PloS One
Ezgi Ogutcen, Jana C Vamosi
PREMISE OF THE STUDY: Antirrhineae is a large tribe within Plantaginaceae. Mostly concentrated in the Mediterranean Basin, the tribe members are present both in the Old World and the New World. Current Antirrhineae phylogenies have different views on taxonomic relationships, and they lack homogeneity in terms of geographic distribution and ploidy levels. This study aims to investigate the changes in the chromosome numbers along with dispersal routes as definitive characters identifying clades...
June 2016: American Journal of Botany
Mileidy Betancourth-Cundar, Albertina P Lima, Walter Hӧdl, Adolfo Amézquita
During acoustic communication, an audible message is transmitted from a sender to a receiver, often producing changes in behavior. In a system where evolutionary changes of the sender do not result in a concomitant adjustment in the receiver, communication and species recognition could fail. However, the possibility of an evolutionary decoupling between sender and receiver has rarely been studied. Frog populations in the Allobates femoralis cryptic species complex are known for their extensive morphological, genetic and acoustic variation...
2016: PloS One
Carolina Carrizo García, Michael H J Barfuss, Eva M Sehr, Gloria E Barboza, Rosabelle Samuel, Eduardo A Moscone, Friedrich Ehrendorfer
BACKGROUND AND AIMS: Capsicum (Solanaceae), native to the tropical and temperate Americas, comprises the well-known sweet and hot chili peppers and several wild species. So far, only partial taxonomic and phylogenetic analyses have been done for the genus. Here, the phylogenetic relationships between nearly all taxa of Capsicum were explored to test the monophyly of the genus and to obtain a better knowledge of species relationships, diversification and expansion. METHODS: Thirty-four of approximately 35 Capsicum species were sampled...
July 2016: Annals of Botany
Manuela Royer-Carenzi, Gilles Didier
Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide...
September 7, 2016: Journal of Theoretical Biology
Maximilian O Press, Christine Queitsch, Elhanan Borenstein
Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized...
June 2016: Genome Research
Sora Kim, Lauri Kaila, Seunghwan Lee
Phylogenetic relationships within family Oecophoridae have been poorly understood. Consequently the subfamily and genus level classifications with this family problematic. A comprehensive phylogenetic analysis of Oecophoridae, the concealer moths, was performed based on analysis of 4444 base pairs of mitochondrial COI, nuclear ribosomal RNA genes (18S and 28S) and nuclear protein coding genes (IDH, MDH, Rps5, EF1a and wingless) for 82 taxa. Data were analyzed using maximum likelihood (ML), parsimony (MP) and Bayesian (BP) phylogenetic frameworks...
August 2016: Molecular Phylogenetics and Evolution
Jefferson G Carvalho-Sobrinho, William S Alverson, Suzana Alcantara, Luciano P Queiroz, Aline C Mota, David A Baum
Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species)...
August 2016: Molecular Phylogenetics and Evolution
Hervey C Peoples, Pavel Duda, Frank W Marlowe
Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs...
September 2016: Human Nature: An Interdisciplinary Biosocial Perspective
Katy Frederick, Johannes Schul
The katydid genus Neoconocephalus is characterized by high diversity of the acoustic communication system. Both male signals and female preferences have been thoroughly studied in the past. This study used Bayesian character state reconstruction to elucidate the evolutionary history of diverse call traits, based on an existing, well supported phylogenetic hypothesis. The most common male call pattern consisted of continuous calls comprising one fast pulse rate; this pattern is the likely ancestral state in this genus...
2016: PLoS Currents
Barbara Turner, Ovidiu Paun, Jérôme Munzinger, Mark W Chase, Rosabelle Samuel
BACKGROUND AND AIMS: Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low...
June 2016: Annals of Botany
Igor R Pozdnyakov, Sergey A Karpov
Every large clade of Eukarya has its own pattern of kinetid (flagellar apparatus) structure, which is stable and specific within the group, thereby being a good phylogenetic marker. The kinetid structure of sponge choanocytes might be a candidate for such marker for the phylogeny of Porifera. Kinetids of two heteroscleromorphs, Halichondria sp. (Suberitida) and Crellomima imparidens (Poecilosclerida), have been investigated here for the first time, and a reconstruction of the kinetid for each species is provided...
July 2016: Journal of Morphology
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