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Molecular Phylogenetics and Evolution

Chuan Xie, Deng-Feng Xie, Yan Zhong, Xian-Lin Guo, Qing Liu, Song-Dong Zhou, Xing-Jin He
Exploring the effects of orographic events and climatic shifts on geographic distribution of organism in the Hengduan Mountains Region (HMR) and its eastern adjacent area is crucial to the understanding of the environmental changes to organismal evolution. To gain further insight into these processes, we reconstruct evolutionary history of ten species in Allium section Sikkimensia, distributed across regions abovementioned. Using chloroplast and nuclear sequence variation of 79 populations of these ten Allium species with known morphological preferences, we elucidate the phylogenetic relationship, divergence time, ancestral area and genetic structures...
September 18, 2018: Molecular Phylogenetics and Evolution
Ma Chiela M Cremen, Frederik Leliaert, John West, Daryl W Lam, Satoshi Shimada, Juan M Lopez-Bautista, Heroen Verbruggen
The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders - Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes...
September 15, 2018: Molecular Phylogenetics and Evolution
Aglaia Antoniou, Alexandros Frantzis, Paraskevi Alexiadou, Nefeli Paschou, Nikos Poulakakis
Natural interspecific hybridization might be more important for the evolutionary history and speciation of animals than previously thought, considering several demographic and life history traits as well as habitat disturbance as factors that promote it. In this aspect, cetaceans comprise an interesting case in which the occurrence of sympatric species in mixed associations provides excellent opportunities for interspecific sexual interaction and the potential for hybridization. Here, we present evidence of natural hybridization for two cetacean species commonly occurring in the Greek Seas (Stenella coeruleoalba and Delphinus delphis), which naturally overlap in the Gulf of Corinth by analyzing highly resolving microsatellite DNA markers and mitochondrial DNA sequences in skin samples from 45 individuals of S...
September 13, 2018: Molecular Phylogenetics and Evolution
Pengcheng Wang, Hongyan Yao, Kadeem J Gilbert, Qi Lu, Yu Hao, Zhengwang Zhang, Nan Wang
Organisms are unevenly distributed on earth and the evolutionary drivers of that have puzzled ecologists and evolutionary biologists for over a century. Even though many studies have focused on the mechanisms of unevenly distributed fauna and flora, there remains much to learn about the evolutionary drivers behind biodiversity hotspots. In the Tibetan Plateau and Hengduan Mountains, a biodiversity hotspot in the Palearctic realm, alpine uplift cannot be the driver for recent speciation (<two million years ago), researchers broadly refer to climatic oscillations driven biodiversity, however, the specific individual roles of glaciation and inter-glaciation periods in promoting biodiversity is unclear...
September 12, 2018: Molecular Phylogenetics and Evolution
Andrea González Marín, Melisa Olave, Luciano J Avila, Jack W Sites, Mariana Morando
During the speciation process sibling lineages accumulate differences in time (e.g. genetic, morphological, and/or ecological). Phenotypic traits such as size or shape, however, could experience rapid changes or show stasis depending on their role in survival and reproduction. The clade Phymaturus patagonicus includes 26 species characterized by a conservative morphology, and all inhabit rock crevice microhabitats in arid environments. In this study we quantify levels of morphological divergence (size and shape) among the multiple species relative to interspecific molecular divergence, and show that most species have not diverged significantly in size and/or shape to permit unambiguous species diagnosis with morphological data alone...
September 8, 2018: Molecular Phylogenetics and Evolution
De Chen, Edward L Braun, Michael Forthman, Rebecca T Kimball, Zhengwang Zhang
Next-generation DNA sequencing (NGS) offers a promising way to obtain massive numbers of orthologous loci to understand phylogenetic relationships among organisms. Of particular interest are old museum specimens and other samples with degraded DNA, where traditional sequencing methods have proven to be challenging. Low coverage shotgun sequencing and sequence capture are two widely used NGS approaches for degraded DNA. Sequence capture can yield sequence data for large numbers of orthologous loci, but it can only be used to sequence genomic regions near conserved sequences that can be used as probes...
September 7, 2018: Molecular Phylogenetics and Evolution
Zhi-Yao Ma, Jun Wen, Stefanie M Ickert-Bond, Ze-Long Nie, Long-Qing Chen, Xiu-Qun Liu
The application of whole-genome resequencing based on next-generation sequencing technologies provides an unprecedented opportunity for researchers to resolve long-standing evolutionary problems. Taxa belonging to the grape genus (Vitis L.) represent important genetic resources for the improvement of cultivated grapes. However, it has been challenging to resolve the deep phylogenetic relationships within Vitis, limiting the current understanding of the evolutionary history of Vitis and preventing the use of valuable wild grape resources...
September 6, 2018: Molecular Phylogenetics and Evolution
Vera S Bogdanova, Anatoliy V Mglinets, Natalia V Shatskaya, Oleg E Kosterin, Vladimir I Solovyev, Gennadiy V Vasiliev
Organellar genomes may shed light on complicated patterns of plant evolution at inter- and intraspecies level. Primary structure of plastid genomes sequenced in this study and taken from public databases was characterised and compared in 22 diverse, mostly wild representatives of the genus Pisum (peas). Phylogenetic trees reconstructed via Bayesian approach on the basis of entire plastid genomes resembled those reconstructed on the basis of a nuclear gene His5 coding for a minor histone H1 subtype. They reveal Pisum fulvum as an early divergence of the genus but do not support other taxonomical subdivisions...
September 6, 2018: Molecular Phylogenetics and Evolution
Scott A Schneider, Akiko Okusu, Benjamin B Normark
The armored scale insect tribe Aspidiotini comprises many pest species that are globally invasive and economically damaging. The taxonomy of scale insects is based almost solely upon morphological characters of adult females, and little prior work has been done to test the classification of aspidiotines against molecular evidence. To address these concerns, we reconstruct a molecular phylogeny for aspidiotine armored scales that expands greatly upon taxonomic and character representations from previous studies...
September 6, 2018: Molecular Phylogenetics and Evolution
Aaron Floden, E E Schilling
Polygonatum is a widespread temperate genus with approximately 75 species centered in the Eastern Himalaya and Indo-Burma biodiversity hotspots. A complete assessment of the remarkable diversity of Polygonatum in these areas requires an accurate circumscription of the genus, as well as a clear understanding of generic and infrageneric relationships, both of which have been problematic in the past. In this study, we reconstruct phylogenetic relationships within Polygonatum and test its monophyly using a phylogenomic approach...
September 5, 2018: Molecular Phylogenetics and Evolution
Thomas J Near, Daniel J MacGuigan, Elyse Parker, Carl D Struthers, Christopher D Jones, Alex Dornburg
Notothenioids are a clade of ∼120 species of marine fishes distributed in extreme southern hemisphere temperate near-shore habitats and in the Southern Ocean surrounding Antarctica. Over the past 25 years, molecular and morphological approaches have redefined hypotheses of relationships among notothenioid lineages as well as their relationships among major lineages of percomorph teleosts. These phylogenies provide a basis for investigation of mechanisms of evolutionary diversification within the clade, and have enhanced our understanding of the notothenioid adaptive radiation...
September 5, 2018: Molecular Phylogenetics and Evolution
Hollis A Dahn, Jason L Strickland, Alejandra Osorio, Timothy J Colston, Christopher L Parkinson
Accurate representation of lineage diversity through complete taxon sampling is crucial to understanding the evolution of biodiversity, particularly when using molecular phylogenetics to estimate evolutionary relationships. In this interest, taxonomic diversity is often used as a proxy for lineage diversity even though the two concepts are not synonymous. We explore this within the snake tribe Lampropeltini which includes some of the most conspicuous and heavily studied snakes in North America. Both the taxonomy and hypothesized relationships within this tribe have been in flux...
September 3, 2018: Molecular Phylogenetics and Evolution
Almir R Pepato, Teofânia H D A Vidigal, Pavel B Klimov
The family Halacaridae comprises more than one thousand mostly marine or rarely freshwater species. Many are predacious, but among marine mites, some genera evolved the ability to feed on macroalgae. We inferred a time-calibrated phylogeny based on 18S rDNA, 28S rDNA, and Cytochrome oxidase I (5,143 nt aligned) and all non-monotypic halacarid subfamilies plus a representative outgroup set (72 taxa). The family Halacaridae was rendered as the sister-group of Parasitengona, diverging 321.5, 264.0-381.3 Ma and radiating 271...
August 29, 2018: Molecular Phylogenetics and Evolution
Carlos J Pavón-Vázquez, Uri O García-Vázquez, Robert W Bryson, Manuel Feria-Ortiz, Norma L Manríquez-Morán, Adrián Nieto-Montes de Oca
Integrative taxonomy has been generally considered as a goal in systematics for more than a decade. Here, we employed environmental, molecular, and morphological data to evaluate the species boundaries within the short-nosed skink Plestiodon brevirostris from south-central Mexico, one member of the morphologically conservative P. brevirostris group. Our molecular dataset includes one mitochondrial and two nuclear loci. The mitochondrial fragment includes the full length of the gene coding for the NADH dehydrogenase subunit 1 protein, a segment of the gene coding for 16S ribosomal RNA, and flanking tRNAs...
August 29, 2018: Molecular Phylogenetics and Evolution
Bohumil Mandák, Karol Krak, Petr Vít, Maria N Lomonosova, Alexander Belyayev, Farzaneh Habibi, Lei Wang, Jan Douda, Helena Štorchová
Hybridization and polyploidization represent an important speciation mechanism in the diploid-polyploid complex of the Chenopodium album aggregate. In the present study we successfully reconstructed the evolutionary histories of the majority of Eurasian representatives of the C. album aggregate, resulting in the most comprehensive phylogenetic analysis of this taxonomically intricate group of species to date. We applied a combination of classical karyology for precise chromosome number determination, genomic in-situ hybridization for the determination of genomic composition, flow cytometry for the estimation of genome size and sequencing of plastid (cpDNA) and nuclear (ribosomal internal transcribed spacer - ITS and the introns of the FLOWERING LOCUS T LIKE genes - FTL) markers for a phylogenetic reconstruction and the identification of parental genomes in polyploid taxa...
August 29, 2018: Molecular Phylogenetics and Evolution
Jin-Hua Ran, Ting-Ting Shen, Hui Wu, Xun Gong, Xiao-Quan Wang
Pinaceae comprises 11 genera, and represents the largest family of conifers with an extensive wild distribution in the Northern Hemisphere. Intergeneric relationships of Pinaceae have been investigated using many morphological characters and molecular markers, but phylogenetic positions of four genera, including Cathaya, Cedrus, Nothotsuga and Pseudolarix, remain controversial or have not been completely resolved. To completely resolve the intergeneric relationships of Pinaceae, we conducted a comparative transcriptomic study of 14 species representing all Pinaceae genera...
August 25, 2018: Molecular Phylogenetics and Evolution
Brajogopal Samanta, James M Ehrman, Irena Kaczmarska
In 1983, Hasle and colleagues removed cymatosiroid diatoms from the pennates, and erected a new centric diatom family, the Cymatosiraceae, mainly to accommodate for their newly discovered mode of sexual reproduction. The new family consisted of two subfamilies differing in frustule structure. The family was later elevated to the rank of Order Cymatosirales Round and Crawford. We revisited intra-ordinal relationships within Cymatosirales using combined genetic (DNA sequences), morphological (valve and frustule structure), and reproductive (auxospore type) characters...
August 25, 2018: Molecular Phylogenetics and Evolution
Sergei Volis, Keren Fogel, Tieyao Tu, Hang Sun, Marianna Zaretsky
Mandragora L. (Solanaceae) is the only genus of the tribe Mandragoreae, one of the two tribes of the cosmopolitan nightshade family, which occur exclusively in Eurasia and northern Africa. The genus occurs discontinuously in the Mediterranean region, Turanian region, and on the Tibetan Plateau, representing a classical disjunction pattern in the biogeography of the Old World flora. In this study, we reconstructed the genus phylogeny using AFLP, eight plastid DNA regions and one nuclear (ITS) gene, and evaluated the taxonomic value of quantitative traits time to flowering, fruit and seed size...
August 25, 2018: Molecular Phylogenetics and Evolution
V K Anoop, Neelesh Dahanukar, Siby Philip, Liju Thomas, Rajeev Raghavan
Rivers draining the Western Ghats (WG) mountain ranges in peninsular India harbor an exceptionally diverse, unique and evolutionarily distinct assemblage of lower vertebrates with high levels of endemism, attributed to their evolution and potentially long history of isolation during the Late Cretaceous or Early Tertiary. A molecular phylogeny of hillstream loaches of the genus Mesonoemacheilus endemic to the WG revealed the presence of four clades which we designate as 'species groups'. A consensus of various species delimitation methods indicates the likelihood of 'at least' seven more undescribed species within Mesonoemacheilus...
August 25, 2018: Molecular Phylogenetics and Evolution
Craig D Osborne, Victoria S Haritos
The critical role that bacterial methanotrophs have in regulating the environmental concentrations of the potent greenhouse gas, methane, under aerobic conditions is dependent on monooxygenase enzymes which oxidise the substrate as both a carbon and energy source. Despite the importance of these organisms, the evolutionary origins of aerobic methane oxidation capability and its relationship to proteobacterial evolution is not well understood. Here we investigated the phylogenetic relationship of proteobacterial methanotrophs with related, non-methanotrophic bacteria using 16S rRNA and the evolution of two forms of methane monooxygenase: membrane bound (pMMO and pXMO) and cytoplasmic (sMMO)...
August 24, 2018: Molecular Phylogenetics and Evolution
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