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Molecular Phylogenetics and Evolution

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https://www.readbyqxmd.com/read/29462675/spiroides-shrubs-on-qinghai-tibetan-plateau-multilocus-phylogeography-and-palaeodistributional-reconstruction-of-spiraea-alpina-and-s-mongolica-rosaceae
#1
Gulzar Khan, Zhang Faqi, Gao Qingbo, Fu Pengcheng, Zhang Yu, Chen Shilong
A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification. Using a multilocus approach, here we assessed the influence of Qinghai-Tibetan Plateau (QTP) uplift and fluctuating regional climate on genetic diversity of two sister spiroides shrubs, Spiraea alpina and S. mongolica. Combined with palaeodistributional reconstruction modelling, we investigated the current and past-predicted distribution of these species under different climatic episodes. The study demonstrated that continuous pulses of retreat and expansion during last glacial-interglacial episodes, combined with the uplifting of QTP shaped the current distribution of these species...
February 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29454889/evolution-of-sexual-systems-and-growth-habit-in-mussaenda-rubiaceae-insights-into-the-evolutionary-pathways-of-dioecy
#2
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
https://www.readbyqxmd.com/read/29452311/phylogenetic-relationships-and-cryptic-species-diversity-in-the-brazilian-egg-brooding-tree-frog-genus-fritziana-mello-leit%C3%A3-o-1937-anura-hemiphractidae
#3
Marina Walker, Mariana L Lyra, Célio F B Haddad
The genus Fritziana (Anura: Hemiphractidae) comprises six described species (F. goeldii, F. ohausi, F. fissilis, F. ulei, F. tonimi, and F. izecksohni) that are endemic to the Brazilian Atlantic Forest. Although the genus has been the subject of studies dealing with its taxonomy, phylogeny, and systematics, there is considerable evidence for cryptic diversity hidden among the species. The present study aims to understand the genetic diversity and phylogenetic relationships among the species of Fritziana, as well as the relationships among populations within species...
February 13, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29448063/an-ant-genus-group-prenolepis-illuminates-the-biogeography-and-drivers-of-insect-diversification-in-the-indo-pacific
#4
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
https://www.readbyqxmd.com/read/29448062/geological-data-indicate-that-the-interpretation-for-the-age-calibrated-phylogeny-for-the-kurixalus-genus-frogs-of-south-south-east-and-east-asia-lv-et-al-2018-needs-to-be-rethought
#5
LETTER
Jason R Ali
Recently, Lv et al. (2018) published an age-calibrated phylogenetic tree for the Kurixalus frogs, members of which occur across parts of South, South-east and East Asia. A clade on Taiwan, represented by Kurixalus idiootocus and the Kurixalus eiffingeri species complex, is deemed to have been resident since the middle Cenozoic; its closest congeners are in southern Indochina (not in the adjacent parts of south-east China), and the split between the two is dated at 32.8 Ma. Furthermore, a sub-population of Kurixalus eiffingeri is believed to have colonized islands in the western Ryukyus c...
February 12, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29432851/filtering-of-target-sequence-capture-individuals-facilitates-species-tree-construction-in-the-plant-subtribe-iochrominae-solanaceae
#6
Daniel J Gates, Diana Pilson, Stacey D Smith
Advances in sequencing technology have made it possible to produce large multi-locus datasets required for species tree analyses. One challenge with constructing high throughput sequencing datasets, however, is that missing information is propagated at different steps in the sequence preparation process. To date, species tree studies have focused on filtering and removing errors that occur at particular loci. Given the way that high throughput sequencing datasets are constructed, however, large amounts of error or ambiguity may also manifest across individuals...
February 9, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29432850/combining-high-throughput-sequencing-and-targeted-loci-data-to-infer-the-phylogeny-of-the-adenocalymma-neojobertia-clade-bignonieae-bignoniaceae
#7
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
https://www.readbyqxmd.com/read/29428510/spiny-trapdoor-spiders-euoplos-of-eastern-australia-broadly-sympatric-clades-are-differentiated-by-burrow-architecture-and-male-morphology
#8
Jeremy D Wilson, Jane M Hughes, Robert J Raven, Michael G Rix, Daniel J Schmidt
Spiders of the infraorder Mygalomorphae are fast becoming model organisms for the study of biogeography and speciation. However, these spiders can be difficult to study in the absence of fundamental life history information. In particular, their cryptic nature hinders comprehensive sampling, and linking males with conspecific females can be challenging. Recently discovered differences in burrow entrance architecture and male morphology indicated that these challenges may have impeded our understanding of the trapdoor spider genus Euoplos in Australia's eastern mesic zone...
February 8, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29428509/evolution-of-hypolimnas-butterflies-nymphalidae-out-of-africa-origin-and-wolbachia-mediated-introgression
#9
Ranjit Kumar Sahoo, David J Lohman, Niklas Wahlberg, Chris J Müller, Oskar Brattström, Steve C Collins, Djunijanti Peggie, Kwaku Aduse-Poku, Ullasa Kodandaramaiah
Hypolimnas butterflies (Nymphalidae), commonly known as eggflies, are a popular model system for studying a wide range of ecological questions including mimicry, polymorphism, wing pattern evolution, and Wolbachia-host interactions. The lack of a time-calibrated phylogeny for this group has precluded understanding its evolutionary history. We reconstruct a species-level phylogeny using a nine gene dataset and estimate species divergence times. Based on the resulting tree, we investigate the taxon's historical biogeography, examine the evolution of host plant preferences, and test the hypothesis that the endosymbiotic bacterium Wolbachia mediates gene transfer between species...
February 8, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29427778/getting-the-ploceidae-tree-right
#10
LETTER
Thilina N de Silva, John M Bates, A Townsend Peterson
No abstract text is available yet for this article.
February 7, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29427777/unweaving-a-taxon-tangle-comments-on-de-silva-et-al-2017
#11
LETTER
Maria Prager
No abstract text is available yet for this article.
February 7, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29421312/discovista-interpretable-visualizations-of-gene-tree-discordance
#12
Erfan Sayyari, James B Whitfield, Siavash Mirarab
Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data partitions. Researchers are often left trying to make sense of such incongruences. Interpretive ways of measuring and visualizing discordance are needed, both among alternative species trees and gene trees, especially for specific focal branches of a tree. Here, we introduce DiscoVista, a publicly available tool that creates a suite of simple but interpretable visualizations...
February 5, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29408286/mitochondrial-phylogeny-divergence-history-and-high-altitude-adaptation-of-grassland-caterpillars-lepidoptera-lymantriinae-gynaephora-inhabiting-the-tibetan-plateau
#13
Ming-Long Yuan, Qi-Lin Zhang, Li Zhang, Cheng-Lin Jia, Xiao-Peng Li, Xing-Zhuo Yang, Run-Qiu Feng
Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most important pests in alpine meadows of the Tibetan Plateau (TP) and have well adapted to high-altitude environments. To further understand the evolutionary history and their adaptation to the TP, we newly determined seven complete TP Gynaephora mitogenomes. Compared to single genes, whole mitogenomes provided the best phylogenetic signals and obtained robust results, supporting the monophyly of the TP Gynaephora species and a phylogeny of Arctiinae + (Aganainae + Lymantriinae)...
February 2, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29410353/phylogeny-historical-biogeography-and-diversification-of-angiosperm-order-ericales-suggest-ancient-neotropical-and-east-asian-connections
#14
Jeffrey P Rose, Thomas J Kleist, Stefan D Löfstrand, Bryan T Drew, Jürg Schönenberger, Kenneth J Sytsma
Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points...
February 1, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29409984/molecular-phylogeny-of-neotropical-rock-frogs-reveals-a-long-history-of-vicariant-diversification-in-the-atlantic-forest
#15
Ariadne F Sabbag, Mariana L Lyra, Kelly R Zamudio, Célio F B Haddad, Renato N Feio, Felipe S F Leite, João L Gasparini, Cinthia A Brasileiro
The Brazilian Atlantic coastal forest is one of the most heterogeneous morphoclimatic domains on earth and is thus an excellent region in which to examine the role that habitat heterogeneity plays in shaping diversification of lineages and species. Here we present a molecular phylogeny of the rock frogs of the genus Thoropa Cope, 1865, native to the Atlantic forest and extending to adjacent campo rupestre of Brazil. The goal of this study is to reconstruct the evolutionary history of the genus using multilocus molecular phylogenetic analyses...
February 1, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29409906/phylogenetic-position-of-the-enigmatic-deep-sea-nematode-order-rhaptothyreida-a-molecular-analysis
#16
Daniel Leduc, Zeng Qi Zhao, Valentin Verdon, Yumei Xu
The placement of the rare deep-sea nematode order Rhaptothyreida remains unclear due to the unique morphology of this group, an unknown life cycle with morphologically distinct juvenile stages which may or may not be parasitic, and lack of molecular sequences. Here, we investigate the phylogenetic placement and status of the Rhaptothyreida based on SSU and D2-D3 of LSU rDNA sequences of Rhaptothyerus typicus specimens obtained from the continental slope of New Zealand. Molecular sequences of three adults and a late stage juvenile were identical, confirming that they belong to the same species despite pronounced morphological differences...
January 30, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29407482/a-jungle-tale-molecular-phylogeny-and-divergence-time-estimates-of-the-desmopsis-stenanona-clade-annonaceae-in-mesoamerica
#17
Andrés Ernesto Ortiz-Rodriguez, Juan Francisco Ornelas, Eduardo Ruiz-Sanchez
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade...
January 30, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29407481/on-defining-a-unique-phylogenetic-tree-with-homoplastic-characters
#18
Pablo A Goloboff, Mark Wilkinson
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 recovered (as unique most likely or most parsimonious tree) as long as the number of extra steps is within 1/4 of the number of taxa...
January 30, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29378247/convergent-herbivory-on-conifers-by-choristoneura-moths-after-boreal-forest-formation
#19
Giovanny Fagua, Fabien L Condamine, Bryan M T Brunet, Anne-Laure Clamens, Jérôme Laroche, Roger C Levesque, Michel Cusson, Felix A H Sperling
Mitogenomes are useful markers for phylogenetic studies across a range of taxonomic levels. Here, we focus on mitogenome variation across the tortricid moth genus Choristoneura and particularly the spruce budworm (Choristoneura fumiferana) species complex, a notorious pest group of North American conifer forests. Phylogenetic relationships of Tortricidae, representing two subfamilies, four tribes and nine genera, were analyzed using 21 mitogenomes. These included six newly-sequenced mitogenomes for species in the spruce budworm complex plus three additional Choristoneura species and 12 previously published mitogenomes from other tortricids and one from the Cossidae...
January 26, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29371027/atlantic-forest-to-the-all-americas-biogeographical-history-and-divergence-times-of-neotropical-ficus-moraceae
#20
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
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