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Ancestral state reconstruction

Peter J Hundt, Andrew M Simons
The dentition of fishes can be quite striking and is often correlated with a specific diet. Combtooth blennies have long incisiform oral teeth, unlike most actinopterygians. It has been suggested that the long tooth morphology is an adaptation for detritivory, but given the diversity of diets (detritus, coral polyps, polychaetes, and pieces of other fishes), are blenny teeth indeed monomorphic? Or does tooth variation associated with diet still exist at this extreme? To explore tooth and diet diversification, we used a new phylogenetic hypothesis of Blenniidae, measured tooth shape, number, and mode of attachment, and quantified blenniid diet...
February 18, 2018: Evolution; International Journal of Organic Evolution
Renato Caparroz, Amanda V Rocha, Gustavo S Cabanne, Pablo Tubaro, Alexandre Aleixo, Emily M Lemmon, Alan R Lemmon
At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined...
February 17, 2018: Molecular Biology Reports
Tingting Duan, Xiaofang Deng, Shi Chen, Zhonglai Luo, Zhongtao Zhao, TieYao Tu, Nguyen Sinh Khang, Sylvain G Razafimandimbison, Dianxiang Zhang
Dioecy is a rare sexual system that is thought to represent an "evolutionary dead end". While many studies have addressed the evolution of dioecy and/or its relationship with the evolution of the woody habit, few have explored the relationship between dioecy and climbing habit, and their effects on diversification rates. Here, we study the evolution of sexual systems and growth habit in Mussaenda (Rubiaceae) using a robust phylogeny of the genus based on eight plastid regions and a broad sampling of taxa (92 of the 132 species were sampled)...
February 15, 2018: Molecular Phylogenetics and Evolution
Pável Matos-Maraví, Ronald M Clouse, Eli M Sarnat, Evan P Economo, John S LaPolla, Michaela Borovanska, Christian Rabeling, Jesse Czekanski-Moir, Fransina Latumahina, Edward O Wilson, Milan Janda
The Malay Archipelago and the tropical South Pacific (hereafter the Indo-Pacific region) are considered biodiversity hotspots, yet a general understanding of the origins and diversification of species-rich groups in the region remains elusive. We aimed to test hypotheses for the evolutionary processes driving insect species diversity in the Indo-Pacific using a higher-level and comprehensive phylogenetic hypothesis for an ant clade consisting of seven genera. We estimated divergence times and reconstructed the biogeographical history of ant species in the Prenolepis genus-group (Formicidae: Formicinae: Lasiini)...
February 12, 2018: Molecular Phylogenetics and Evolution
Luiz Henrique M Fonseca, Lúcia G Lohmann
Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups...
February 9, 2018: Molecular Phylogenetics and Evolution
Breno Frederico de Carvalho Dominguez Souza, Alexander König, Andrea Rasche, Ianei de Oliveira Carneiro, Nora Stephan, Victor Max Corman, Pia Luise Roppert, Nora Goldmann, Ramona Kepper, Simon Franz Müller, Christof Völker, Alex Junior Souza de Souza, Michele Soares Gomes-Gouvêa, Andrés Moreira-Soto, Andreas Stöcker, Michael Nassal, Carlos Roberto Franke, João Renato Rebello Pinho, Manoel do Carmo Pereira Soares, Joachim Geyer, Philippe Lemey, Christian Drosten, Eduardo Martins Netto, Dieter Glebe, Jan Felix Drexler
BACKGROUND & AIMS: All known hepatitis B virus (HBV) genotypes occur in humans and hominoid Old World nonhuman primates (NHP). The divergent Woolly Monkey HBV (WMHBV) forms another orthohepadnavirus species. The evolutionary origins of HBV are unclear. METHODS: We analyzed sera from 124 Brazilian monkeys collected during 2012-2016 for hepadnaviruses using molecular and serological tools and conducted evolutionary analyses. RESULTS: We identified a novel orthohepadnavirus species in capuchin monkeys (CMHBV)...
February 8, 2018: Journal of Hepatology
M Desroches, G Royer, D Roche, M Mercier-Darty, D Vallenet, C Médigue, K Bastard, C Rodriguez, O Clermont, E Denamur, J-W Decousser
More than a century ago, Theodor Escherich isolated the bacterium that was to become Escherichia coli, one of the most studied organisms. Not long after, the strain began an odyssey and landed in many laboratories across the world. As laboratory culture conditions could be responsible for major changes in bacterial strains, we conducted a genome analysis of isolates of this emblematic strain from different culture collections (England, France, the United States, Germany). Strikingly, many discrepancies between the isolates were observed, as revealed by multilocus sequence typing (MLST), the presence of virulence-associated genes, core genome MLST, and single nucleotide polymorphism/indel analyses...
January 2018: MSphere
Sophie Cardinal, Stephen L Buchmann, Avery L Russell
Over 22,000 species of biotically pollinated flowering plants, including some major agricultural crops, depend primarily on bees capable of floral sonication for pollination services. The ability to sonicate ("buzz") flowers is widespread in bees but not ubiquitous. Despite the prevalence of this pollinator behavior and its importance to natural and agricultural systems, the evolutionary history of floral sonication in bees has not been previously studied. Here, we reconstruct the evolutionary history of floral sonication in bees by generating a time-calibrated phylogeny and reconstructing ancestral states for this pollen extraction behavior...
February 1, 2018: Evolution; International Journal of Organic Evolution
Anderson Ferreira Pinto Machado, Nina Rønsted, Sam Bruun-Lund, Rodrigo Augusto Santinelo Pereira, Luciano Paganucci de Queiroz
Ficus (Moraceae) is well diversified in the Neotropics with two lineages inhabiting the wet forests of this region. The hemiepiphytes of section Americanae are the most diversified with c. 120 species, whereas section Pharmacosycea includes about 20 species mostly with a terrestrial habit. To reconstruct the biogeographical history and diversification of Ficus in the Americas, we produced a dated Bayesian phylogenetic hypothesis of Neotropical Ficus including two thirds of the species sequenced for five nuclear regions (At103, ETS, G3pdh, ITS/5...
January 22, 2018: Molecular Phylogenetics and Evolution
Jeramiah J Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C Keinath, Hugo J Parker, Malcolm E Cook, Jon E Hess, Shawn R Narum, Francesco Lamanna, Henrik Kaessmann, Vladimir A Timoshevskiy, Courtney K M Waterbury, Cody Saraceno, Leanne M Wiedemann, Sofia M C Robb, Carl Baker, Evan E Eichler, Dorit Hockman, Tatjana Sauka-Spengler, Mark Yandell, Robb Krumlauf, Greg Elgar, Chris T Amemiya
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters...
January 22, 2018: Nature Genetics
Sarah Kieren, Max Sparreboom, Axel Hochkirch, Michael Veith
Amphibians have a complex reproductive behaviour, which shows the highest diversity among tetrapodes. The family Salamandridae, distributed across the entire Holarctic, is one of the most diverse groups of extant salamanders comprising 114 species in 21 genera. The family has a remarkable diversity of courtship modes, amplexus and sperm transfer. It is often hypothesised that this diversity has evolved in adaptation to a specific mating and/or breeding habitat. We test this hypothesis based upon a phylogenetic reconstruction using the complete mitochondrial genome sequences of 45 Salamandridae species, representing all existing genera...
January 9, 2018: Molecular Phylogenetics and Evolution
Hongjie Li, You He, Jiamei Jiang, Zhizhi Liu, Chenhong Li
The Odontobutidae is a group of freshwater sleepers endemic to East and Southeast Asia. The composition of the Odontobutidae is controversial and the systematics position of some species (e.g. Philypnus chalmersi) remains unknown. Phylogenetic relationship among the odontobutids has never been really tested due to the lack of informative morphological characters, and that molecular data have not been collected in many species. Here, we sampled 41 specimens, representing all known genera of the Odontobutidae except the Laotian genus Terateleotris, in addition to a disputable odontobutid species, Philypnus chalmersi and 14 outgroups (six families)...
December 27, 2017: Molecular Phylogenetics and Evolution
Dustin S Siegel, Michael S Taylor, David M Sever, Stanley E Trauth
Nasolacrimal ducts are a terrestrial vertebrate adaptation and appear to have co-evolved with orbital glands. Although plethodontid salamanders possess orbital glands, a recent study concluded that plethodontid salamanders lack nasolacrimal ducts. Functionally, the absence of nasolacrimal ducts closes the route for orbital gland secretion passage into the nasal and vomeronasal organ cavities. Orbital glands have been implicated in enhancement of vomeronasal function so loss could have important implications for communication...
December 28, 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
Pedro Jiménez-Mejías, Carmen Benítez-Benítez, Mario Fernández-Mazuecos, Santiago Martín-Bravo
Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts...
2017: PloS One
Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Eric Tannier, Cedric Chauve
Comparative genomics considers the detection of similarities and differences between extant genomes, and, based on more or less formalized hypotheses regarding the involved evolutionary processes, inferring ancestral states explaining the similarities and an evolutionary history explaining the differences. In this chapter, we focus on the reconstruction of the organization of ancient genomes into chromosomes. We review different methodological approaches and software, applied to a wide range of datasets from different kingdoms of life and at different evolutionary depths...
2018: Methods in Molecular Biology
Clare H Scott Chialvo, Pablo Chialvo, Jeffrey D Holland, Timothy J Anderson, Jesse W Breinholt, Akito Y Kawahara, Xin Zhou, Shanlin Liu, Jennifer M Zaspel
Host species utilize a variety of defenses to deter feeding, including secondary chemicals. Some phytophagous insects have evolved tolerance to these chemical defenses, and can sequester secondary defense compounds for use against their own predators and parasitoids. While numerous studies have examined plant-insect interactions, little is known about lichen-insect interactions. Our study focused on reconstructing the evolution of lichen phenolic sequestration in the tiger moth tribe Lithosiini (Lepidoptera: Erebidae: Arctiinae), the most diverse lineage of lichen-feeding moths, with 3,000 described species...
December 20, 2017: Molecular Phylogenetics and Evolution
Andressa Paladini, Daniela M Takiya, Julie M Urban, Jason R Cryan
The spittlebug family Cercopidae (Hemiptera: Auchenorrhyncha: Cicadomorpha: Cercopoidea) is distributed worldwide, with highest species diversity in the tropics. Several included species are economically important pests of major agricultural crops and cultivated pasture grasses. Taxonomically, Cercopidae is divided into two subfamilies: the paraphyletic Old World Cercopinae and the monophyletic New World Ischnorhininae. Results are here presented from an investigation of phylogenetic relationships within Ischnorhininae based on DNA sequences from seven loci (18S rDNA, 28S rDNA, Histone 2A, Histone 3, Wingless, Cytochrome Oxidase I, and Cytochrome Oxidase II) generated from exemplars of 119 spittlebug species...
December 20, 2017: Molecular Phylogenetics and Evolution
Davide Guerra, Karim Bouvet, Sophie Breton
The mitochondrial genome architecture of polyplacophorans has been usually regarded as being very ancient in comparison to all mollusks. However, even if some complete chiton mtDNAs have been recently sequenced, thorough studies of their evolution are lacking. To further expand the set of complete chiton mtDNAs and perform such analysis, we sequenced the mitochondrial genome of the Eastern beaded chiton Chaetopleura apiculata (Chaetopleuridae) using next-generation sequencing. With mitochondrial sequences from all available chiton mtDNAs, we also built a phylogeny on which we reconstructed the evolution of gene arrangement in this class...
December 16, 2017: Molecular Phylogenetics and Evolution
Ghadeer Bukhari, Jingbo Zhang, Peter F Stevens, Wenheng Zhang
PREMISE OF THE STUDY: Observations of floral ontogeny indicated that floral organ initiation in pentapetalous flowers most commonly results in a median-abaxial (MAB) petal during early development, a median-adaxial (MAD) petal being less common. Such different patterns of floral organ initiation might be linked with different morphologies of floral zygomorphy that have evolved in Asteridae. Here, we provide the first study of zygomorphy in pentapetalous angiosperms placed in a phylogenetic framework, the goal being to find if the different patterns of floral organ initiation are connected with particular patterns of zygomorphy...
December 15, 2017: American Journal of Botany
Xiao Yang, Brett M Tyler, Chuanxue Hong
A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P...
December 2017: IMA Fungus
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