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Ancestral character reconstruction

Weston Testo, Benjamin Øllgaard, Ashley Field, Thaís Almeida, Michael Kessler, David Barrington
The Neotropical clade of the lycophyte genus Phlegmariurus is comprised of an estimated 150 described species and exhibits exceptional morphological and ecological diversity. Because of their simple morphology, frequent convergent evolution, and the recentness of the group's diversification, the delimitation of species and species groups has remained challenging. Here, we present a robustly support phylogeny of Neotropical Phlegmariurus based on six chloroplast markers and ca. 70% of known species, and use ancestral character state reconstruction to investigate morphological evolution in the clade, and define natural species groups...
March 17, 2018: Molecular Phylogenetics and Evolution
M Mardones, T Trampe-Jaschik, S Oster, M Elliott, H Urbina, I Schmitt, M Piepenbring
The order Phyllachorales ( Pezizomycotina , Ascomycota ) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae , based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling...
December 2017: Persoonia
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
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
Rui Borges, Warren E Johnson, Stephen J O'Brien, Cidália Gomes, Christopher P Heesy, Agostinho Antunes
BACKGROUND: Based on evolutionary patterns of the vertebrate eye, Walls (1942) hypothesized that early placental mammals evolved primarily in nocturnal habitats. However, not only Eutheria, but all mammals show photic characteristics (i.e. dichromatic vision, rod-dominated retina) suggestive of a scotopic eye design. RESULTS: Here, we used integrative comparative genomic and phylogenetic methodologies employing the photoreceptive opsin gene family in 154 mammals to test the likelihood of a nocturnal period in the emergence of all mammals...
February 5, 2018: BMC Genomics
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
Marcelo Fernando Devecchi, William Wayt Thomas, Gregory M Plunkett, José Rubens Pirani
Generic circumscriptions in the mostly pantropical family Simaroubaceae are somewhat controversial. Simaba is the largest genus, currently defined as exclusively neotropical, with around 25 species of trees and shrubs, but both its limits and infrageneric classification have been a matter of discussion and divergence. Traditionally, species of the genus have been treated in three sections: Simaba sect. Tenuiflorae, S. sect. Floribundae and S. sect. Grandiflorae, but a phylogenetic analysis suggested that the latter two may not be monophyletic...
March 2018: Molecular Phylogenetics and Evolution
Félicien Tosso, Olivier J Hardy, Jean-Louis Doucet, Kasso Daïnou, Esra Kaymak, Jérémy Migliore
Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction...
March 2018: Molecular Phylogenetics and Evolution
J Ruiz-Martín, R Santos-Gally, M Escudero, J J Midgley, R Pérez-Barrales, J Arroyo
Heterostyly is a sex polymorphism which has challenged evolutionary biologists ever since Darwin. One of the lineages where heterostyly, and related stylar conditions, appears more frequently is the family Linaceae and its most diverse and widespread genus, Linum. Thus, this group is particularly suitable for testing competing hypotheses about ancestral and transitional stages on the evolutionary building up of heterostyly. We generated a well-resolved phylogeny of Linum based on extensive sampling and plastid and nuclear DNA sequences, and used it to trace the evolution of character states of style polymorphism and its association with traits related to pollination and breeding systems, obtained from our samples and the literature...
November 22, 2017: Plant Biology
Marek Slovák, Jaromír Kučera, Hans Walter Lack, Jotham Ziffer-Berger, Andrea Melicharková, Eliška Záveská, Peter Vďačný
Understanding transcontinental biogeographic patterns has been one of the main foci of the field of biogeography. While multiple explanations for transcontinental disjunctions have been proposed, little is still known about the relative importance of intrinsic and extrinsic traits for the diversification dynamics of disjunct taxa. Here, we study the evolutionary history of the genus Picris L. (Compositae), a great model for investigating the diversification dynamics of transoceanic bipolar disjunct organisms...
February 2018: Molecular Phylogenetics and Evolution
Julia L Molnar, Rui Diogo, John R Hutchinson, Stephanie E Pierce
The question of how tetrapod limbs evolved from fins is one of the great puzzles of evolutionary biology. While palaeontologists, developmental biologists, and geneticists have made great strides in explaining the origin and early evolution of limb skeletal structures, that of the muscles remains largely unknown. The main reason is the lack of consensus about appendicular muscle homology between the closest living relatives of early tetrapods: lobe-finned fish and crown tetrapods. In the light of a recent study of these homologies, we re-examined osteological correlates of muscle attachment in the pectoral girdle, humerus, radius, and ulna of early tetrapods and their close relatives...
November 10, 2017: Biological Reviews of the Cambridge Philosophical Society
Bing Feng, Yu Lin, Lingxi Zhou, Yan Guo, Robert Friedman, Ruofan Xia, Fei Hu, Chao Liu, Jijun Tang
Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution...
November 9, 2017: Scientific Reports
Étienne Léveillé-Bourret, Julian R Starr, Bruce A Ford
For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers...
February 2018: Molecular Phylogenetics and Evolution
J C Lopes, L W Chatrou, R Mello-Silva, P J Rudall, M G Sajo
Androdioecy is the rarest sexual system among plants. The majority of androdioecious species are herbaceous plants that have evolved from dioecious ancestors. Nevertheless, some woody and androdioecious plants have hermaphrodite ancestors, as in the Annonaceae, where androdioecious genera have arisen several times in different lineages. The majority of androdioecious species of Annonaceae belong to the Neotropical tribe Malmeeae. In addition to these species, Pseudoxandra spiritus-sancti was recently confirmed to be androdioecious...
October 27, 2017: Molecular Phylogenetics and Evolution
Daniel F Mokodongan, Javier Montenegro, Koji Mochida, Shingo Fujimoto, Asano Ishikawa, Ryo Kakioka, Lengxob Yong, Mulis, Renny K Hadiaty, Ixchel F Mandagi, Kawilarang W A Masengi, Nakatada Wachi, Yasuyuki Hashiguchi, Jun Kitano, Kazunori Yamahira
The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations...
October 9, 2017: Molecular Phylogenetics and Evolution
Dimitrios Paraskevis, Evangelia Kostaki, Georgios K Nikolopoulos, Vana Sypsa, Mina Psichogiou, Julia Del Amo, Ioannis Hodges-Mameletzis, Dimitra Paraskeva, Athanasios Skoutelis, Meni Malliori, Leslie Williams, Samuel R Friedman, Georgios L Daikos, Angelos Hatzakis
Background: High numbers of human immunodeficiency virus type 1 (HIV-1) infections among people who inject drugs (PWID) have been diagnosed in Athens, Greece, since 2011. We aimed to trace the geographic origin of HIV-1 infection for migrants who inject drugs and to investigate whether transmissions occur more frequently among migrants than among Greek nationals. Methods: Multiple cross-sectional studies were pooled to assemble all persons diagnosed with HIV-1 in Greece between 1 January 2011 and 31 October 2014...
November 29, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Lina Herbst, Mareike Fischer
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees...
December 2017: Bulletin of Mathematical Biology
Robert M Zink, Aubrey S Gardner
Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents...
September 2017: Science Advances
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