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Molecular Phylogenetics and Evolution

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https://www.readbyqxmd.com/read/28428147/title-high-genetic-diversities-between-isolates-of-the-fish-parasite-cryptocaryon-irritans-ciliophora-suggest-multiple-cryptic-species
#1
Hongshu Chi, Patricia Taik, Emily J Foley, Alycia C Racicot, Hilary M Gray, Katherine E Guzzetta, Hsin-Yun Lin, Yen-Ling Song, Che-Huang Tung, Kosuke Zenke, Tomoyoshi Yoshinaga, Chao-Yin Cheng, Wei-Jen Chang, Hui Gong
The ciliate protozoan Cryptocaryon irritans parasitizes marine fish and causes lethal white spot disease. Sporadic infections as well as large-scale outbreaks have been reported globally and the parasite's broad host range poses particular threat to the aquaculture and ornamental fish markets. In order to better understand C. irritans' population structure, we sequenced and compared mitochondrial cox-1, SSU rRNA, and ITS-1 sequences from 8 new isolates of C. irritans collected in China, Japan, and Taiwan. We detected two SSU rRNA haplotypes, which differ at three positions, separating the isolates into two main groups (I and II)...
April 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28414099/molecular-evolution-of-the-plastid-genome-during-diversification-of-the-cotton-genus
#2
Zhiwen Chen, Corrinne E Grover, Pengbo Li, Yumei Wang, Hushuai Nie, Yanpeng Zhao, Meiyan Wang, Fang Liu, Zhongli Zhou, Xingxing Wang, Xiaoyan Cai, Kunbo Wang, Jonathan F Wendel, Jinping Hua
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and one tetraploid genomic group, namely AD. To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome duringdiversification, chloroplast genomes (cpDNA) from 6 D-genome and 2 G-genome species of Gossypium (G. armourianum D2-1, G. harknessii D2-2, G. davidsonii D3-d, G. klotzschianum D3-k, G. aridum D4, G. trilobum D8, and G. australe G2, G. nelsonii G3) were newly reported here...
April 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28412536/title-molecular-phylogenetics-and-dating-of-the-problematic-new-guinea-microhylid-frogs-amphibia-anura-reveals-elevated-speciation-rates-and-need-for-taxonomic-reclassification
#3
Julio A Rivera, Fred Kraus, Allen Allison, Marguerite A Butler
Asterophryinae is a large monophyletic subfamily of Anurans containing over 300 species distributed across one of the world's most geologically active areas -- New Guinea and its satellite islands, Australia and the Philippines. The tremendous ecological and morphological diversity of this clade, with apparent specializations for burrowing, terrestrial, semi-aquatic, and arboreal lifestyle, suggests an evolutionary process of adaptive radiation. Despite this spectacular diversity, this and many other questions of evolutionary processes have received little formal study because until now the phylogeny of this spececies-rich clade has remained uncertain...
April 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28412535/complex-biogeographic-scenarios-revealed-in-the-diversification-of-the-largest-woodpecker-radiation-in-the-new-world
#4
Adolfo G Navarro-Sigüenza, Hernán Vázquez-Miranda, Germán Hernández-Alonso, Erick A García-Trejo, Luis A Sánchez-González
Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions...
April 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28411162/insights-into-evolution-in-andean-polystichum-dryopteridaceae-from-expanded-understanding-of-the-cytosolic-phosphoglucose-isomerase-gene
#5
Brendan M Lyons, Monique A McHenry, David S Barrington
Cytosolic phosphoglucose isomerase (pgiC) is an enzyme essential to glycolysis found universally in eukaryotes, but broad understanding of variation in the gene coding for pgiC is lacking for ferns. We used a substantially expanded representation of the gene for Andean species of the fern genus Polystichum to characterize pgiC in ferns relative to angiosperms, insects, and an amoebozoan; assess the impact of selection versus neutral evolutionary processes on pgiC; and explore evolutionary relationships of selected Andean species...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28411161/a-reassessment-of-the-phylogeny-and-circumscription-of-zaluzianskya-scrophulariaceae
#6
Jenny K Archibald, Jacqueline Cook, Bruce Anderson, Steven D Johnson, Mark E Mort
The genus Zaluzianskya (Scrophulariaceae s.s.) encompasses a diversity of traits, such as flowers ranging from 4 to 60 mm in length with various patterns of color and indumentum. However, this diversity, as described by the current taxonomic circumscription of Zaluzianskya, is an underestimate. The boundaries of this genus require expansion via incorporation of species from other genera and recognition of unnamed species. This study advances prior molecular phylogenies for the southern African genus through the addition of DNA regions and an up to 70% increase in population sampling, targeting specific taxa...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28411160/life-on-the-rocks-multilocus-phylogeography-of-rock-hyrax-procavia-capensis-from-southern-africa
#7
K Amanda Maswanganye, Michael J Cunningham, Nigel C Bennett, Christian T Chimimba, Paulette Bloomer
Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis. Using a multilocus coalescent approach, we assessed the influence of strong habitat dependence and fluctuating regional climates on genetic diversity. We sequenced a mitochondrial gene (cytochrome b) and two nuclear introns (AP5, PRKC1) supplemented with microsatellite genotyping, in order to assess evolutionary processes over multiple temporal scales...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28408324/recurrent-breakdowns-of-mutualisms-with-ants-in-the-neotropical-ant-plant-genus-cecropia-urticaceae
#8
Juanita Gutiérrez-Valencia, Guillaume Chomicki, Susanne S Renner
Mutualisms could be evolutionarily unstable, with changes in partner abundances or in the spatial context of interactions potentially promoting their dissolution. We test this prediction using the defense mutualisms between species of the Neotropical genus Cecropia and Azteca ants. A new, multigene phylogeny with representatives of all five genera of Cecropieae (most of them from the Neotropics) and half of the 61 species of Cecropia shows the West African endemic Musanga (2spp.) as sister to Cecropia, implying dispersal from the Neotropics to Africa, with a molecular clock suggesting that this occurred about 23Mya...
April 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28404508/model-based-analyses-reveal-insular-population-diversification-and-cryptic-frog-species-in-the-ischnocnema-parva-complex-in-the-atlantic-forest-of-brazil
#9
Marcelo Gehara, Adriane Barth, Eliana Faria de Oliveira, Marco Antonio Costa, Célio Fernando Baptista Haddad, Miguel Vences
The Atlantic Forest (AF) of Brazil has long been recognized as a biodiversity conservation hotspot. Despite decades of studies the species inventory of this biome continues to increase with the discovery of cryptic diversity and the description of new species. Different diversification mechanisms have been proposed to explain the diversity in the region, including models of forest dynamics, barriers to gene flow and dispersal. Also, sea level change is thought to have influenced coastal diversification and isolated populations on continental islands...
April 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28400275/mutational-analysis-employing-a-phylogenetic-mass-tree-approach-in-a-study-of-the-evolution-of-the-influenza-virus
#10
Elma H Akand, Kevin M Downard
A mass based approach has been advanced to enable mutations associated with the evolution of proteins to be both charted and interrogated using phylogenetic trees built solely from the masses of peptides generated upon protein proteolysis. The modified MassTree algorithm identifies and displays all such mutations and calculates the frequency of a particular mutation across a tree. Its significance in terms of its position(s) on the tree is scored, where mutations that occur toward the basis of the tree are weighted more favourably...
April 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28392486/species-delimitation-of-the-blue-spotted-spiny-lizard-within-a-multilocus-multispecies-coalescent-framework-results-in-the-recognition-of-a-new-sceloporus-species
#11
Brenda Díaz-Cárdenas, Eduardo Ruiz-Sanchez, Patricia Castro-Felix, Gamaliel Castañeda-Gaytán, Sergio Ruiz-Santana, Héctor Gadsden
Species delimitation is a major topic in systematics. Species delimitation methods based on molecular data have become more common since this approach provides insights about species identification via levels of gene flow, the degree of hybridization and phylogenetic relationships. Also, combining multilocus mitochondrial and nuclear DNA leads to more reliable conclusions about species limits. Coalescent-based species delimitation methods explicitly reveal separately evolving lineages using probabilistic approaches and testing the delimitation hypotheses for several species...
April 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28390909/deep-reticulation-and-incomplete-lineage-sorting-obscure-the-diploid-phylogeny-of-rain-lilies-and-allies-amaryllidaceae-tribe-hippeastreae
#12
Nicolás García, Ryan A Folk, Alan W Meerow, Srikar Chamala, Matthew A Gitzendanner, Renata Souza de Oliveira, Douglas E Soltis, Pamela S Soltis
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups...
April 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28390910/genome-wide-snps-resolve-phylogenetic-relationships-in-the-north-american-spruce-budworm-choristoneura-fumiferana-species-complex
#13
J R Dupuis, B M T Brunet, H M Bird, L M Lumley, G Fagua, B Boyle, R Levesque, M Cusson, J A Powell, F A H Sperling
High throughput sequencing technologies have revolutionized the potential to reconcile incongruence between gene and species trees, and numerous approaches have been developed to take advantage of these advances. Genotyping-by-sequencing is becoming a regular tool for gathering phylogenetic data, yet comprehensive evaluations of phylogenetic methods using these data are sparse. Here we use multiple phylogenetic and population genetic methods for genotyping-by-sequencing data to assess species relationships in a group of forest insect pests, the spruce budworm (Choristoneura fumiferana) species complex...
April 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28390908/molecular-phylogeny-and-biogeography-of-the-land-snail-family-hygromiidae-gastropoda-helicoidea
#14
Marco T Neiber, Oihana Razkin, Bernhard Hausdorf
The Hygromiidae is a highly diverse group of land snails with a distribution range stretching throughout the Palearctic region from the Macaronesian Islands to the Russian Far East and reaching southwards to the north-eastern Ethiopian region. So far, the classification of the family largely rested on the structure of the dart apparatus, an accessory genital organ. We used nuclear and mitochondrial DNA sequences of almost all genera to reconstruct the phylogeny of the Hygromiidae. Several of the clades found in the molecular phylogenetic analyses represent regional radiations that partly show a high variation in the structure of the dart apparatus...
April 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28390323/the-impact-of-gc-bias-on-phylogenetic-accuracy-using-targeted-enrichment-phylogenomic-data
#15
Silas Bossert, Elizabeth A Murray, Bonnie B Blaimer, Bryan N Danforth
The field of sequence based phylogenetic analyses is currently being transformed by novel hybrid-based targeted enrichment methods, such as the use of ultraconserved elements (UCEs). Rather than analyzing relationships among organisms using a small number of genes, these methods now allow us to evaluate relationships with many hundreds to thousands of individual gene loci. However, the inclusion of thousands of loci does not necessarily overcome the long-standing challenge of incongruence among phylogenetic trees derived from different genes or gene regions...
April 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28385604/the-niche-and-phylogeography-of-a-passerine-reveal-the-history-of-biological-diversification-between-the-andean-and-the-atlantic-forests
#16
Natalia Trujillo-Arias, Gisele Dantas, Enrique Arbeláez-Cortés, Kazuya Naoki, Maria I Gómez, Fabricio R Santos, Cristina Y Miyaki, Alexandre Aleixo, Pablo L Tubaro, Gustavo S Cabanne
The Atlantic Forest is separated from the Andean tropical forest by dry and open vegetation biomes (Chaco and Cerrado). Despite this isolation, both rainforests share closely related lineages, which suggest a past connection. This connection could have been important for forest taxa evolution. In this study, we used the Saffron-billed Sparrow (Arremon flavirostris) as a model to evaluate whether the Andean and the Atlantic forests act as a refugia system, as well as to test for a history of biogeographic connection between them...
April 3, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28366817/coral-hybridization-or-phenotypic-variation-genomic-data-reveal-gene-flow-between-porites-lobata-and-p-compressa
#17
Z H Forsman, I S S Knapp, K Tisthammer, D A R Eaton, M Belcaid, R J Toonen
Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals...
March 31, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28363818/ancient-dna-analysis-of-the-extinct-north-american-flat-headed-peccary-platygonus-compressus
#18
Tahlia Perry, Ayla L van Loenen, Holly Heiniger, Carol Lee, Jaime Gongora, Alan Cooper, Kieren J Mitchell
The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved...
March 28, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28347889/genome-wide-data-delimits-multiple-climate-determined-species-ranges-in-a-widespread-australian-fish-the-golden-perch-macquaria-ambigua
#19
Luciano B Beheregaray, Lauren V Pfeiffer, Catherine R M Attard, Jonathan Sandoval-Castillo, Fabricius M C B Domingos, Leanne K Faulks, Dean M Gilligan, Peter J Unmack
Species range limits often fluctuate in space and time in response to variation in environmental factors and to gradual niche evolution due to changes in adaptive traits. We used genome-wide data to investigate evolutionary divergence and species range limits in a generalist and highly dispersive fish species that shows an unusually wide distribution across arid and semi-arid regions of Australia. We generated ddRAD data (18,979 filtered SNPs and 1.725million bp of sequences) for samples from 27 localities spanning the native range of golden perch, Macquaria ambigua (Teleostei; Percichthyidae)...
March 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28347888/on-the-importance-of-geographic-and-taxonomic-sampling-in-phylogeography-a-reevaluation-of-diversification-and-species-limits-in-a-neotropical-thrush-aves-turdidae
#20
Jorge Enrique Avendaño, Enrique Arbeláez-Cortés, Carlos Daniel Cadena
Phylogeographic studies seeking to describe biogeographic patterns, infer evolutionary processes, and revise species-level classification should properly characterize the distribution ranges of study species, and thoroughly sample genetic variation across taxa and geography. This is particularly necessary for widely distributed organisms occurring in complex landscapes, such as the Neotropical region. Here, we clarify the geographic range and revisit the phylogeography of the Black-billed Thrush (Turdus ignobilis), a common passerine bird from lowland tropical South America, whose evolutionary relationships and species limits were recently evaluated employing phylogeographic analyses based on partial knowledge of its distribution and incomplete sampling of populations...
March 24, 2017: Molecular Phylogenetics and Evolution
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