Journal articles: 'Skinks Phylogeny Molecular aspects'

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Freitas, Elyse S., Aniruddha Datta-Roy, Praveen Karanth, L. Lee Grismer, and Cameron D. Siler. "Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae)." Zoological Journal of the Linnean Society 186, no. 4 (April 5, 2019): 1067–96. http://dx.doi.org/10.1093/zoolinnean/zlz001.

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AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.

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GARDNER, MICHAEL G., ANDREW F. HUGALL, STEPHEN C. DONNELLAN, MARK N. HUTCHINSON, and RALPH FOSTER. "Molecular systematics of social skinks: phylogeny and taxonomy of theEgerniagroup (Reptilia: Scincidae)." Zoological Journal of the Linnean Society 154, no. 4 (December 2008): 781–94. http://dx.doi.org/10.1111/j.1096-3642.2008.00422.x.

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Stuart-Fox, Devi M., Andrew F. Hugall, and Craig Moritz. "A molecular phylogeny of rainbow skinks (Scincidae: Carlia): taxonomic and biogeographic implications." Australian Journal of Zoology 50, no. 1 (2002): 39. http://dx.doi.org/10.1071/zo01051.

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The phylogenetic relationships amongst 29 species of Carlia and Lygisaurus were estimated using a 726-base-pair segment of the protein-coding mitochondrial ND4 gene. Results do not support the recent resurrection of the genus Lygisaurus. Although most Lygisaurus species formed a single clade, this clade is nested within Carlia and includes Carlia parrhasius. Due to this new molecular evidence, and the paucity of diagnostic morphological characters separating the genera, Lygisaurus de Vis 1884 is re-synonymised with Carlia Gray 1845. Our analysis is also inconsistent with a previous suggestion that Lygisaurus timlowi should be removed to Menetia, a genus that is distantly related relative to outgroups used here. Intraspecific variation in Carlia is, in several instances, greater than interspecific distance. The most strikingly divergent lineages are found within C. rubrigularis, which appears to be paraphyletic, with southern populations more closely related to C. rhomboidalis than to northern populations of C. rubrigularis. The two C. rubrigularis–C. rhomboidalis lineages form part of a major polytomy at an intermediate level of divergence. Lack of resolution at this level, however, does not appear to be due to saturation or loss of phylogenetic signal. Rather, the polytomy probably reflects a period of relatively rapid diversification that occurred sometime during the Miocene.

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Skinner, Adam, Mark N. Hutchinson, and Michael S. Y. Lee. "Phylogeny and divergence times of Australian Sphenomorphus group skinks (Scincidae, Squamata)." Molecular Phylogenetics and Evolution 69, no. 3 (December 2013): 906–18. http://dx.doi.org/10.1016/j.ympev.2013.06.014.

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Mirza, Zeeshan A., Andrey M. Bragin, Harshal Bhosale, Gaurang G. Gowande, Harshil Patel, and Nikolay A. Poyarkov. "A new ancient lineage of ablepharine skinks (Sauria: Scincidae) from eastern Himalayas with notes on origin and systematics of the group." PeerJ 10 (January 18, 2022): e12800. http://dx.doi.org/10.7717/peerj.12800.

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The Himalayas represent a renowned biodiversity hotspot and an important biogeographic realm that has influenced origin and diversification of multiple taxa. A recent herpetological investigation of the eastern Himalayas of the Indian state of Arunachal Pradesh led to the discovery of a unique lineage of ablepharine skink, which is herein described as a new genus along with a new species. The findings are based an integrated taxonomic approach incorporating data from external morphology, microCT scans of the skull and molecular data. The molecular phylogeny of ablepharine skinks is also presented that suggests taxonomic amendments. Discovery of this unique lineage of skinks further highlights the biogeographic importance of the eastern Himalayas as a source for origin of several relic biota.

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O'Connor, D., and C. Moritz. "A molecular phylogeny of the Australian skink genera Eulamprus, Gnypetoscincus and Nangura." Australian Journal of Zoology 51, no. 4 (2003): 317. http://dx.doi.org/10.1071/zo02050.

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Skinks from the genera Eulamprus, Gnypetoscincus and Nangura are a prominent component of the reptile fauna of the mesic forests of the east coast of Australia and have been the subject of numerous ecological studies. Highly conserved morphology and the retention of ancestral traits have limited our understanding of the relationships within and among these genera beyond an initial identification of species groups within Eulamprus. To address this deficit and to explore the relationships between Eulamprus and the monotypic genera Nangura and Gnypetoscincus, sections of two mitochondrial genes (ND4 and 16S rRNA) were sequenced and subjected to Bayesian phylogenetic analysis. This phylogenetic analysis supports recognition of the three species groups proposed for Eulamprus (murrayi, quoyii and tenuis) and indicates that this genus is paraphyletic, with Gnypetoscincus and Nangura being proximal to basal lineages of the tenuis group. To resolve these and broader problems of paraphyly, we suggest that each of the species groups from 'Eulamprus' should be recognised as a distinct genus. The phylogenetically and ecologically distinct water skinks of the quoyii group would be retained within Eulamprus and the diverse species of the tenuis group allocated to Concinnia. We suggest placing the monophyletic murrayi group, endemic to the rainforests of central eastern Australia, in a new genus (yet to be formally described). The sequencing data also revealed the existence of a genetically divergent but morphologically cryptic lineage within E. murrayi and substantial diversity within E. quoyii. There is evidence for two major habitat shifts from rainforest towards drier habitats, one leading to the quoyii group and the second defining a clade of three species within the tenuis complex. These ecological transitions may represent adaptations to general drying across eastern Australia during the late Miocene–Pliocene. Each of the major areas of east coast tropical or subtropical rainforest contains multiple phylogenetically diverse endemic species, reflecting the long-term persistence and high conservation value of wet forest habitats in each area.

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Honda, Masanao, Hidetoshi Ota, Robert W. Murphy, and Tsutomu Hikida. "Phylogeny and biogeography of water skinks of the genus Tropidophorus (Reptilia: Scincidae): a molecular approach." Zoologica Scripta 35, no. 1 (January 2006): 85–95. http://dx.doi.org/10.1111/j.1463-6409.2005.00215.x.

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Medina, Maria F., Aaron M. Bauer, William R. Branch, Andreas Schmitz, Werner Conradie, Zoltán T. Nagy, Toby J. Hibbitts, et al. "Molecular phylogeny of Panaspis and Afroablepharus skinks (Squamata: Scincidae) in the savannas of sub-Saharan Africa." Molecular Phylogenetics and Evolution 100 (July 2016): 409–23. http://dx.doi.org/10.1016/j.ympev.2016.04.026.

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Austin, Christopher C., Eric N. Rittmeyer, Stephen J. Richards, and George R. Zug. "Phylogeny, historical biogeography and body size evolution in Pacific Island Crocodile skinks Tribolonotus (Squamata; Scincidae)." Molecular Phylogenetics and Evolution 57, no. 1 (October 2010): 227–36. http://dx.doi.org/10.1016/j.ympev.2010.06.005.

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Rocco, Lucia, Innocenza Liguori, Domenico Costagliola, Maria A. Morescalchi, Fausto Tinti, and Vincenzo Stingo. "Molecular and karyological aspects of Batoidea (Chondrichthyes, Elasmobranchi) phylogeny." Gene 389, no. 1 (March 2007): 80–86. http://dx.doi.org/10.1016/j.gene.2006.09.024.

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Pepper, Mitzy, Joanna Sumner, Ian G. Brennan, Kate Hodges, Alan R. Lemmon, Emily Moriarty Lemmon, Garry Peterson, et al. "Speciation in the mountains and dispersal by rivers: Molecular phylogeny of Eulamprus water skinks and the biogeography of Eastern Australia." Journal of Biogeography 45, no. 9 (July 2, 2018): 2040–52. http://dx.doi.org/10.1111/jbi.13385.

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Quicke, Donald L. J., Hasan H. Basibuyuk, and Alexandr P. Rasnitsyn. "Morphological, palaeontological and molecular aspects of ichneumonoid phylogeny (Hymenoptera, Insecta)." Zoologica Scripta 28, no. 1-2 (January 1999): 175–202. http://dx.doi.org/10.1046/j.1463-6409.1999.00005.x.

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COLSTON, TIMOTHY J., R. ALEXANDER PYRON, and AARON M. BAUER. "A new species of African Snake-Eyed Skink (Scincidae: Panaspis) from Ethiopia." Zootaxa 4779, no. 2 (May 19, 2020): 190–200. http://dx.doi.org/10.11646/zootaxa.4779.2.2.

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A recent molecular phylogenetic revision of the snake-eyed skinks (genus Panaspis Cope, 1868) uncovered extensive cryptic diversity, including several new species from throughout sub-Saharan Africa. Here, we describe one of these from Ethiopia as Panaspis annettesabinae sp. nov. This description is based on a previous molecular phylogeny and morphological, scalation, and coloration data collected from the type specimen. Phylogenetic analyses place the species alone in what we term the P. annettesabinae species group from Ethiopia. This group forms the sister lineage to a large southern African radiation and suggests a potential northern origin for much of the extant diversity of Panaspis. Many new taxa have recently been discovered in the genus and region, and there are several historical records of Panaspis from elsewhere in Ethiopia. Thus, we suggest that the range of this new species (known only from a single specimen at present) may be much larger, and that additional undescribed species may exist in northern sub-Saharan Africa.

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Siler, Cameron D., Arvin C. Diesmos, Angel C. Alcala, and Rafe M. Brown. "Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification." Molecular Phylogenetics and Evolution 59, no. 1 (April 2011): 53–65. http://dx.doi.org/10.1016/j.ympev.2010.12.019.

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Jebram, Diethardt. "Ecological aspects of the phylogeny of the Bryozoa1." Journal of Zoological Systematics and Evolutionary Research 11, no. 1 (April 27, 2009): 275–83. http://dx.doi.org/10.1111/j.1439-0469.1973.tb00148.x.

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MELZER, SABINE, TRENT BELL, and GEOFF B. PATTERSON. "Hidden conservation vulnerability within a cryptic species complex: taxonomic revision of the spotted skink (Oligosoma lineoocellatum; Reptilia: Scincidae) from New Zealand." Zootaxa 4300, no. 3 (August 3, 2017): 355. http://dx.doi.org/10.11646/zootaxa.4300.3.2.

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The diverse skink fauna of New Zealand comprises 40 described species within the single genus Oligosoma Girard, 1857. Cryptic species are common among New Zealand skinks, leaving numerous species undescribed. We used molecular phylogeny together with morphological analyses to distinguish four species in the spotted skink, Oligosoma lineoocellatum (Duméril & Duméril 1851), species complex. These are O. lineoocellatum sensu stricto, which is confined to the centre of the South Island, O. prasinum sp. nov. from the Lake Tekapo region, O. elium sp. nov. from the northern half of the South Island, and O. kokowai sp. nov. from the northern South Island, Cook Strait, and the North Island. Despite significant genetic differences, the morphological similarity of these species made it challenging to resolve their taxonomic identity. Three of the four species previously recognised as a single, widespread taxon are now recognised as threatened with extinction by a combination of invasive predatory mammals and land use change.

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Smith, Sarah A., Ross A. Sadlier, Aaron M. Bauer, Christopher C. Austin, and Todd Jackman. "Molecular phylogeny of the scincid lizards of New Caledonia and adjacent areas: Evidence for a single origin of the endemic skinks of Tasmantis." Molecular Phylogenetics and Evolution 43, no. 3 (June 2007): 1151–66. http://dx.doi.org/10.1016/j.ympev.2007.02.007.

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Šmíd, Jiří, Marek Uvizl, Mohammed Shobrak, Al Faqih Ali Salim, Raed Hamoud M. AlGethami, Abdulaziz Raqi Algethami, Abdulkarim Saleh K. Alanazi, Saad Dasman Alsubaie, Salem Busais, and Salvador Carranza. "Swimming through the sands of the Sahara and Arabian deserts: Phylogeny of sandfish skinks (Scincidae, Scincus) reveals a recent and rapid diversification." Molecular Phylogenetics and Evolution 155 (February 2021): 107012. http://dx.doi.org/10.1016/j.ympev.2020.107012.

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Heim, Isabel, Michael Nickel, and Franz Brümmer. "Phylogeny of the genus Tethya (Tethyidae: Hadromerida: Porifera): molecular and morphological aspects." Journal of the Marine Biological Association of the United Kingdom 87, no. 6 (December 2007): 1615–27. http://dx.doi.org/10.1017/s0025315407058419.

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The genus Tethya represents a large cosmopolitan group of 81 recognized and a significant number of additional, still undescribed sponge species. The phylogenetic relationships within this old taxon are almost unknown. This is represented by the fact that several species are regarded as cosmopolitan. However, some of them might represent groups of closely related but distinct species. Using molecular and morphological characters, we aimed at a fundamental phylogenetic study for the genus Tethya, evaluating an existing morphological matrix and the cytochrome oxidase subunit I (COI) as a molecular marker. Intending to create a basic phylogenetic framework for the genus we selected a number of species from main biogeographic regions covered by Tethya species: from the Mediterranean Sea (T. citrina and T. aurantium), the northern European seas (T. citrina, T. norvegica and T. hibernica), the western Atlantic (T. actinia), the eastern Pacific (T. californiana), the Indo-Pacific (T. seychellensis) as well as three species of unknown biogeographical origin, originally described from aquarium habitats (T. wilhelma, T. gracilis and T. minuta). Both the morphological matrix, consisting of 29 characters and 131 character states, as well as the molecular matrices (COI nucleotide sequences of 658 bp as well as deduced amino acid sequence of 219 aa), resolved major biogeographical subgroups within the genus. However, the nucleotide based matrices revealed a higher resolution. Two major branches seem to have diverged early: an Indo-Pacific (T. seychellensis, T. wilhelma, T. minuta) and a Pan-European clade (T. citrina, T. norvegica, T. hibernica). For T. aurantium as well as a North-American group (T. californiana, T. actinia and T. minuta) our results are not conclusive. The morphological character set will have to be re-evaluated to gain a higher phylogenetic resolution. The addition of more species to our basal phylogenetic framework will allow analysing the evolution of the various biogeographical subgroups in the genus Tethya.

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Liu, Guo-Qing, Lian Lian, and Wei Wang. "The Molecular Phylogeny of Land Plants: Progress and Future Prospects." Diversity 14, no. 10 (September 21, 2022): 782. http://dx.doi.org/10.3390/d14100782.

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Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.

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Couper, Patrick J., Jessica Worthington Wilmer, Lewis Roberts, Andrew P. Amey, and George R. Zug. "Skinks currently assigned to Carlia aerata (Scincidae:Lygosominae) of north-eastern Queensland: a preliminary study of cryptic diversity and two new species." Australian Journal of Zoology 53, no. 1 (2005): 35. http://dx.doi.org/10.1071/zo04010.

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A preliminary investigation of genetic diversity in Carlia aerata, by sequencing the mitochondrial ND4 gene, revealed the presence of two cryptic species, described herein. The sequence data was added to an existing phylogeny to discern molecular relationships. Interestingly, genetic affinities lie not with C. aerata, the species to which they key. Instead, one has affinities with C. tanneri, the other with C. foliorum. This casts doubt on the validity of morphological characters alone to infer relationships within this genus. Despite low levels of genetic divergence from sister taxa, the new species can be diagnosed from these by morphological characters that exhibit little or no intraspecific variation. The addition of these new species to the gene tree did not enhance resolution of the phylogenetic relationships at the deeper nodes of the Carlia tree. The discovery of these two new cryptic species provides further support for a previously suggested rapid mid-Miocene diversification of Carlia that may have resulted from the successful expansion of a rainforest-dwelling ancestor into the expanding woodlands associated with Miocene climate fluctuations.

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KAY, GEOFFREY M., and J. SCOTT KEOGH. "Molecular phylogeny and morphological revision of the Ctenotus labillardieri (Reptilia: Squamata: Scincidae) species group and a new species of immediate conservation concern in the southwestern Australian biodiversity hotspot." Zootaxa 3390, no. 1 (July 17, 2012): 1. http://dx.doi.org/10.11646/zootaxa.3390.1.1.

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Ctenotus is the largest and most diverse genus of skinks in Australia with at least 97 described species. We generated largemitochondrial and nuclear DNA data sets for 70 individuals representing all available species in the C. labillardieri species-group to produce the first comprehensive phylogeny for this clade. The widespread C. labillardieri was sampled extensively toprovide the first detailed phylogeographic data set for a reptile in the southwestern Australian biodiversity hotspot. Wesupplemented our molecular data with a comprehensive morphological dataset for the entire group, and together these data areused to revise the group and describe a new species. The morphologically highly variable species C. labillardieri comprisesseven well-supported genetic clades that each occupy distinct geographic regions. The phylogeographic patterns observed inthis taxon are consistent with studies of frogs, plants and invertebrates, adding strength to emerging biogeographic hypothesesin this iconic region. The species C. catenifer, C. youngsoni, and C. gemmula are well supported, and despite limited samplingboth C. catenifer and C. gemmula show substantial genetic structure. The threatened C. lancelini from Lancelin Island and theadjacent mainland is the sister taxon to a new species from the Swan Coastal Plain, which we describe as C. ora sp. nov. Thisspecies is a habitat specialist, occurring primarily in sandy regions south of Perth that currently are under intense development. Ctenotus ora sp. nov. should be considered for conservation attention immediately.

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VAN DER LINDE, KIM, DAVID HOULE, GREG S. SPICER, and SCOTT J. STEPPAN. "A supermatrix-based molecular phylogeny of the family Drosophilidae." Genetics Research 92, no. 1 (February 2010): 25–38. http://dx.doi.org/10.1017/s001667231000008x.

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SummaryThe genus Drosophila is diverse and heterogeneous and contains a large number of easy-to-rear species, so it is an attractive subject for comparative studies. The ability to perform such studies is currently compromised by the lack of a comprehensive phylogeny for Drosophila and related genera. The genus Drosophila as currently defined is known to be paraphyletic with respect to several other genera, but considerable uncertainty remains about other aspects of the phylogeny. Here, we estimate a phylogeny for 176 drosophilid (12 genera) and four non-drosophilid species, using gene sequences for up to 13 different genes per species (average: 4333 bp, five genes per species). This is the most extensive set of molecular data on drosophilids yet analysed. Phylogenetic analyses were conducted with maximum-likelihood (ML) and Bayesian approaches. Our analysis confirms that the genus Drosophila is paraphyletic with 100% support in the Bayesian analysis and 90% bootstrap support in the ML analysis. The subgenus Sophophora, which includes Drosophila melanogaster, is the sister clade of all the other subgenera as well as of most species of six other genera. This sister clade contains two large, well-supported subclades. The first subclade contains the Hawaiian Drosophila, the genus Scaptomyza, and the virilis-repleta radiation. The second contains the immigrans-tripunctata radiation as well as the genera Hirtodrosophila (except Hirtodrosophila duncani), Mycodrosophila, Zaprionus and Liodrosophila. We argue that these results support a taxonomic revision of the genus Drosophila.

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Lachance, Marc-André, Ana Pupovac-Velikonja, Sabrina Natarajan, and Birgit Schlag-Edler. "Nutrition and phylogeny of predacious yeasts." Canadian Journal of Microbiology 46, no. 6 (June 1, 2000): 495–505. http://dx.doi.org/10.1139/w00-021.

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Yeast predation was studied with respect to the range of its distribution among ascomycetous yeasts, the range of yeast species that can be affected, and nutritional aspects of the phenomenon. The yeasts identified as predators belong to the Saccharomycopsis clade as defined on the basis of rDNA sequence relatedness. The 11 recognized species in the clade, plus three undescribed but related Candida species, were shown to be incapable of utilizing sulfate as sole source of sulfur, and all but two (Saccharomycopsis capsularis andSaccharomycopsis vini) were observed to penetrate and kill other yeasts under some conditions. Other unrelated sulfate transport-deficient yeasts (strains in the genera Pichia and Candida and the two known species of Starmera) are not predacious. The predacious species vary considerably as to the optimal environmental conditions that favour predation. Some are inhibited by the presence of rich nitrogenous nutrients, organic sulfur compounds, or higher concentrations of ammonium nitrogen, whereas other species may be stimulated under the same conditions. An attempt was made to correlate prey susceptibility to the excretion of substances that stimulate the growth of predators, but no correlation was detected between the two phenomena. The range of susceptible prey covers both ascomycetes and basidiomycetes, and includes Schizosaccharomyces pombe, which was previously thought to be immune. The achlorophyllous alga Prototheca zopfii is not killed by predacious yeasts, but the initial steps of penetration have been observed in some cases. Predacious species attack other predacious species, and in some cases, young cultures may penetrate older cultures of the same strain.Key words: predacious yeasts, sulfate transport deficiency, Saccharomycopsis.

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Shipunov, Alexey, Shyla Carr, Spencer Furniss, Kyle Pay, and José Rubens Pirani. "First Phylogeny of Bitterbush Family, Picramniaceae (Picramniales)." Plants 9, no. 2 (February 21, 2020): 284. http://dx.doi.org/10.3390/plants9020284.

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Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are rich in secondary metabolites; some species are known to be important for pharmaceutical purposes. Traditionally, Picramniaceae was classified as a subfamily of Simaroubaceae, but from 1995 on, it has been segregated containing two genera, Picramnia and Alvaradoa, with the recent addition of a third genus, Nothotalisia, described in 2011. Only a few species of the family have been the subject of DNA-related research, and fewer than half of the species have been included in morphological phylogenetic analyses. It is clear that Picramniaceae remains a largely under-researched plant group. Here we present the first molecular phylogenetic tree of the group, based on both chloroplast and nuclear markers, widely adopted in the plant DNA barcoding. The main findings are: The family and its genera are monophyletic and Picramnia is sister to two other genera; some clades corroborate previous assumptions of relationships made on a morphological or geographical basis, while most parts of the molecular topology suggest high levels of homoplasy in the morphological evolution of Picramnia.

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Fulton, Tara Lynn, and Curtis Strobeck. "Multiple markers and multiple individuals refine true seal phylogeny and bring molecules and morphology back in line." Proceedings of the Royal Society B: Biological Sciences 277, no. 1684 (November 25, 2009): 1065–70. http://dx.doi.org/10.1098/rspb.2009.1783.

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Despite decades of study, some aspects of Phocidae (Pinnipedia, Carnivora) phylogeny still remain unresolved. Using the largest novel dataset to date, including all extant phocids and comprising 15 nuclear and 13 mitochondrial genes, we illustrate the utility of including multiple individuals per species in resolving rapid radiations, and provide new insight into phocid phylogeny. In line with longstanding morphological views, Pusa is recovered as monophyletic for the first time with genetic data. The data are also used to explore the relationship between genetic distance and taxonomic rank. Intraspecific sampling also highlights the discrepancy between molecular and morphological rates of evolution within Phocidae.

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Cronin, Adam. "A molecular phylogeny and social behaviour of Japanese Ceratina (Hymenoptera, Apidae, Xylocopinae)." Insect Systematics & Evolution 35, no. 2 (2004): 137–46. http://dx.doi.org/10.1163/187631204788912418.

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AbstractPrimitively eusocial insect are often considered particularly useful for investigations into the processes underlying the origins of eusociality. Ceratinine bees have long been regarded as solitary, but sometimes exhibit oddly social traits for solitary species, while other species are known to be social, and social behaviour has been artificially induced in others still (Maeta & Sakagami 1995; Sakagami & Maeta 1995). Recent studies have had some success in elucidating aspects of the evolution of social behaviour in some groups using phylogenetics to infer historical changes in social behaviour (eg: Danforth 2002; Schwarz et al. 2003; Bull et al. 2003). Phylogenetic treatments of Ceratina have only recently been attempted in earnest (Terzo 2000) and behavioural data is lacking for many Ceratina species. Nonetheless, the Japanese fauna represents some of the most comprehensively studied Ceratina, and this study uses nucleotide data from mitochondrial COI and CytB and nuclear EF-1α regions to infer a phylogeny of Japanese Ceratina species. Data give good resolution for the subgeneric groups, and provide some support for the recent morphological phylogeny of Terzo (2000), but little resolution for higher relationships. Behavioural data suggest that sociality is variable within subgenera. The diversity and primitive nature of social behaviour in this group make it one of the most promising to provide insights into the process of social evolution, but more data are clearly needed.

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Schreiner, Mark E., Diana Fiur, Jiří Holátko, Miroslav Pátek, and Bernhard J. Eikmanns. "E1 Enzyme of the Pyruvate Dehydrogenase Complex in Corynebacterium glutamicum: Molecular Analysis of the Gene and Phylogenetic Aspects." Journal of Bacteriology 187, no. 17 (September 1, 2005): 6005–18. http://dx.doi.org/10.1128/jb.187.17.6005-6018.2005.

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ABSTRACT The E1p enzyme is an essential part of the pyruvate dehydrogenase complex (PDHC) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the E2p enzyme within the complex. We analyzed the Corynebacterium glutamicum aceE gene, encoding the E1p enzyme, and constructed and characterized an E1p-deficient mutant. Sequence analysis of the C. glutamicum aceE gene and adjacent regions revealed that aceE is not flanked by genes encoding other enzymes of the PDHC. Transcriptional analysis revealed that aceE from C. glutamicum is monocistronic and that its transcription is initiated 121 nucleotides upstream of the translational start site. Inactivation of the chromosomal aceE gene led to the inability to grow on glucose and to the absence of PDHC and E1p activities, indicating that only a single E1p enzyme is present in C. glutamicum and that the PDHC is essential for the growth of this organism on carbohydrate substrates. Surprisingly, the E1p enzyme of C. glutamicum showed up to 51% identity to homodimeric E1p proteins from gram-negative bacteria but no similarity to E1 α- or β-subunits of heterotetrameric E1p enzymes which are generally assumed to be typical for gram-positives. To investigate the distribution of E1p enzymes in bacteria, we compiled and analyzed the phylogeny of 46 homodimeric E1p proteins and of 58 α-subunits of heterotetrameric E1p proteins deposited in public databases. The results revealed that the distribution of homodimeric and heterotetrameric E1p subunits in bacteria is not in accordance with the rRNA-based phylogeny of bacteria and is more heterogeneous than previously assumed.

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Artyushin, I. V., S. V. Kruskop, V. S. Lebedev, and A. A. Bannikova. "Molecular Phylogeny of Serotines (Mammalia, Chiroptera, Eptesicus): Evolutionary and Taxonomical Aspects of the E. serotinus Species Group." Biology Bulletin 45, no. 5 (September 2018): 469–77. http://dx.doi.org/10.1134/s1062359018050035.

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Klussmann-Kolb, Annette. "Phylogeny of the Aplysiidae (Gastropoda, Opisthobranchia) with new aspects of the evolution of seahares." Zoologica Scripta 33, no. 5 (September 2004): 439–62. http://dx.doi.org/10.1111/j.0300-3256.2004.00158.x.

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Barry, A. F., R. Durães-Carvalho, E. F. Oliveira-Filho, A. A. Alfieri, and W. H. M. Van der Poel. "High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses." Infection, Genetics and Evolution 56 (December 2017): 8–13. http://dx.doi.org/10.1016/j.meegid.2017.09.024.

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Zhang, Xiufu, Jeremy J. Bruhl, Karen L. Wilson, and Adam Marchant. "Phylogeny of Carpha and related genera (Schoeneae, Cyperaceae) inferred from morphological and molecular data." Australian Systematic Botany 20, no. 2 (2007): 93. http://dx.doi.org/10.1071/sb06023.

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The limits, definitions and relationships of Carpha have been controversial and unclear. This study using cladistic analyses of morphological and combined morphological and molecular data indicates that: (1) Carpha sensu latu is paraphyletic and its species form two clades, consistent with the definitions of Carpha sensu stricto and Asterochaete respectively (i.e. the data support the division of Carpha sensu latu into two genera: Carpha sensu stricto and Asterochaete); (2) the morphological data show a high degree of homoplasy within Schoeneae; (3) Schoeneae is not a monophyletic tribe; (4) Schoenus and Tricostularia are polyphyletic; (5) it is better to place Schoenoides back in Oreobolus; (6) separation of Capeobolus brevicaulis from Costularia or Tetraria is supported; and (7) both genera Costularia and Tetraria should be maintained. The study resolves some phylogenetic relationships between Carpha and its relatives. Many aspects of these relationships are in agreement with previous studies, but some of these relationships have no support. The study also resolves the phylogenetic relationships of species of Carpha, although with lack of support for some clades, highlighting the need for other sources of data.

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HEDGES, S. BLAIR, WILLIAM E. DUELLMAN, and MATTHEW P. HEINICKE. "New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation." Zootaxa 1737, no. 1 (March 31, 2008): 1. http://dx.doi.org/10.11646/zootaxa.1737.1.1.

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New World frogs recently placed in a single, enormous family (Brachycephalidae) have direct development and reproduce on land, often far away from water. DNA sequences from mitochondrial and nuclear genes of 344 species were analyzed to estimate their relationships. The molecular phylogeny in turn was used as the basis for a revised classification of the group. The 882 described species are placed in a new taxon, Terrarana, and allocated to four families, four subfamilies, 24 genera, 11 subgenera, 33 species series, 56 species groups, and 11 species subgroups. Systematic accounts are provided for all taxa above the species level. Two families (Craugastoridae and Strabomantidae), three subfamilies (Holoadeninae, Phyzelaphryninae, and Strabomantinae), six genera (Bryophryne, Diasporus, Haddadus, Isodactylus, Lynchius, and Psychrophrynella), and two subgenera (Campbellius and Schwartzius) are proposed and named as new taxa, 13 subspecies are considered to be distinct species, and 613 new combinations are formed. Most of the 100 informal groups (species series, species groups, and species subgroups) are new or newly defined. Brachycephalus and Ischnocnema are placed in Brachycephalidae, a relatively small clade restricted primarily to southeastern Brazil. Eleutherodactylidae includes two subfamilies, four genera, and five subgenera and is centered in the Caribbean region. Craugastoridae contains two genera and three subgenera and is distributed mainly in Middle America. Strabomantidae is distributed primarily in the Andes of northwestern South America and includes two subfamilies, 16 genera, and three subgenera. Images and distribution maps are presented for taxa above the species level and a complete list of species is provided. Aspects of the evolution, biogeography, and conservation of Terrarana are discussed.

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Saunders, Gary W., and J. Craig Bailey. "Phylogenesis of pit-plug-associated features in the Rhodophyta: inferences from molecular systematic data." Canadian Journal of Botany 75, no. 9 (September 1, 1997): 1436–47. http://dx.doi.org/10.1139/b97-858.

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Small-subunit ribosomal RNA sequence data are presented for Rhodogorgon carriebowensis Norris et Bucher (Rhodogorgonales, Rhodophyta) and Galaxaura marginata (Ellis et Solander) Lamouroux (Nemaliales, Rhodophyta). Data for these species were included in a matrix consisting of small-subunit ribosomal RNA sequences for 70 taxonomically diverse red algal species. Distance, parsimony, and maximum-likelihood analyses of these data all strongly support (100% of bootstrap replicates for distance and parsimony) a close alliance between the Rhodogorgonales and Corallinales. Our alignment includes 19 species representing six florideophyte orders (Acrochaetiales, Batrachospermales, Corallinales, Nemaliales, Palmariales, Rhodogorgonales) in which pit plugs are characterized by two cap layers. Distance and parsimony analyses resolve a monophyletic lineage including all "two-cap-layer" species. Our parsimony-derived molecular phylogeny was used to test a published hypothesis of pit-plug evolution. Four aspects of Pueschel's hypothesis are consistent with the results of our molecular systematic study: (i) "naked" plugs represent the ancestral type, (ii) outer cap layers are homologous structures, (iii) domed outer caps are ancestral to plate-like outer caps, and (iv) cap membranes are a derived feature within the two-cap-layer lineage. Directions for future research are discussed. Key words: Acrochaetiales, Batrachospermales, Corallinales, molecular systematics, Nemaliales, Palmariales, phylogeny, pit plug, Rhodogorgonales, Rhodophyta.

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Schneider, Harald, Alan R. Smith, Raymond Cranfill, Terri J. Hildebrand, Christopher H. Haufler, and Tom A. Ranker. "Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants." Molecular Phylogenetics and Evolution 31, no. 3 (June 2004): 1041–63. http://dx.doi.org/10.1016/j.ympev.2003.09.018.

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KARNS, DARYL R., VIMOKSALEHI LUKOSCHEK, JENNIFER OSTERHAGE, JOHN C. MURPHY, and HAROLD K. VORIS. "Phylogeny and biogeography of the Enhydris clade (Serpentes: Homalopsidae)." Zootaxa 2452, no. 1 (May 12, 2010): 18. http://dx.doi.org/10.11646/zootaxa.2452.1.2.

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Previous molecular phylogenetic hypotheses for the Homalopsidae, the Oriental-Australian Rear-fanged Water Snakes indicate that Enhydris, the most speciose genus in the Homalopsidae (22 of 37 species), is polyphyletic and may consist of five separate lineages. We expand on earlier phylogenetic hypotheses using three mitochondrial fragments and one nuclear gene, previously shown to be rapidly evolving in snakes, to determine relationships among six closely related species: Enhydris enhydris, E. subtaeniata, E. chinensis, E. innominata, E. jagorii, and E. longicauda. Four of these species (E. subtaeniata, E. innominata, E. jagorii, and E. longicauda) are restricted to river basins in Indochina, while E. chinensis is found in southern China and E. enhydris is widely distributed from India across Southeast Asia. Our phylogenetic analyses indicate that these species are monophyletic and we recognize this clade as the Enhydris clade sensu stricto for nomenclatural reasons. Our analysis shows that E. chinensis is sister-species to a well-supported clade comprising the remaining species of the Enhydris clade (mean p distance between E. chinensis and other in-group taxa was 13.1%, range: 12.7-13.4%). Enhydris innominata, E. longicauda and E. jagorii also formed a strongly supported clade with very low interspecific p distances (mean 0.28%, range: 0–0.46%). We were unable to resolve relationships between E. enhydris and E. subtaeniata (mean divergence of 9.4%, range: 9.2-9.7%), and between these two species and E. innominata, E. longicauda and E. jagorii. We summarize classical morphological (scalation and coloration) characteristics of these species in the context of the molecular phylogeny. The Enhydris clade comprises a substantial portion of the vertebrate biomass of Southeast Asia and we discuss aspects of its biogeography, morphology and systematics.

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Forest, Félix, Keith A. Crandall, Mark W. Chase, and Daniel P. Faith. "Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1662 (February 19, 2015): 20140002. http://dx.doi.org/10.1098/rstb.2014.0002.

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Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science.

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GRISMER, L. LEE, PERRY L. ,. JR WOOD, EVAN S. H. QUAH, SHAHRUL ANUAR, NIKOLAY A. POYARKOV, NEANG THY, NIKOLAI L. ORLOV, PANUPONG THAMMACHOTI, and HUN SEIHA. "Integrative taxonomy of the Asian skinks Sphenomorphus stellatus (Boulenger, 1900) and S. praesignis (Boulenger, 1900) with the resurrection of S. annamiticus (Boettger, 1901) and the description of a new species from Cambodia." Zootaxa 4683, no. 3 (October 9, 2019): 381–411. http://dx.doi.org/10.11646/zootaxa.4683.3.4.

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Molecular phylogenetic analyses of the sister species Sphenomorphus stellatus and S. praesignis based on the mitochondrial genes 12S and 16S rRNA recover the former as paraphyletic with respect to the latter in that a specimen of S. stellatus from the type locality in Peninsular Malaysia is more closely related to S. praesignis than to Indochinese populations of S. stellatus. Furthermore, the phylogeny indicates that the Indochinese populations represent two species, thus resulting in four major lineages within this clade. These relationships are consistent with multivariate and univariate analyses of morphological and discrete color pattern data which statistically define and diagnose the four lineages and together with the molecular data, provide the foundation for robust, testable, species-level hypotheses. As such, S. stellatus is herein restricted to Peninsular Malaysia; S. annamiticus is resurrected for the circum-continental populations ranging through southeastern Thailand, southern Cambodia, and southern Vietnam; a new species—S. preylangensis sp. nov.—is described from an isolated mountain, Phnom Chi, from the Prey Lang Wildlife Sanctuary in central Cambodia; and the taxonomy of S. praesignis remains unchanged. The description of S. preylangensis sp. nov. underscores the necessity to conserve this remnant of lowland evergreen rainforest in the Prey Lang Wildlife Sanctuary.

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Papenbrock, Jutta. "Highlights in Seagrasses’ Phylogeny, Physiology, and Metabolism: What Makes Them Special?" ISRN Botany 2012 (December 10, 2012): 1–15. http://dx.doi.org/10.5402/2012/103892.

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The marine seagrasses form an ecological and therefore paraphyletic group of marine hydrophilus angiosperms which evolved three to four times from land plants towards an aquatic and marine existence. Their taxonomy is not yet solved on the species level and below due to their reduced morphology. So far also molecular data did not completely solve the phylogenetic relationships. Thus, this group challenges a new definition for what a species is. Also their physiology is not well understood due to difficult experimental in situ and in vitro conditions. There remain several open questions concerning how seagrasses adapted secondarily to the marine environment. Here probably exciting adaptation solutions will be detected. Physiological adaptations seem to be more important than morphological ones. Seagrasses contain several compounds in their secondary metabolism in which they differ from terrestrial plants and also not known from other taxonomic groups. Some of these compounds might be of interest for commercial purposes. Therefore their metabolite contents constitute another treasure of the ocean. This paper gives an introduction into some of the most interesting aspects from phylogenetical, physiological, and metabolic points of view.

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Wiens, John J., Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, Jack W. Sites, and Tod W. Reeder. "Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species." Biology Letters 8, no. 6 (September 19, 2012): 1043–46. http://dx.doi.org/10.1098/rsbl.2012.0703.

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Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.

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Dalbies-Tran, Rozenn, Véronique Cadoret, Alice Desmarchais, Sébastien Elis, Virginie Maillard, Philippe Monget, Danielle Monniaux, Karine Reynaud, Marie Saint-Dizier, and Svetlana Uzbekova. "A Comparative Analysis of Oocyte Development in Mammals." Cells 9, no. 4 (April 17, 2020): 1002. http://dx.doi.org/10.3390/cells9041002.

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Sexual reproduction requires the fertilization of a female gamete after it has undergone optimal development. Various aspects of oocyte development and many molecular actors in this process are shared among mammals, but phylogeny and experimental data reveal species specificities. In this chapter, we will present these common and distinctive features with a focus on three points: the shaping of the oocyte transcriptome from evolutionarily conserved and rapidly evolving genes, the control of folliculogenesis and ovulation rate by oocyte-secreted Growth and Differentiation Factor 9 and Bone Morphogenetic Protein 15, and the importance of lipid metabolism.

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Plieger, Tanja, and Matthias Wolf. "18S and ITS2 rDNA sequence-structure phylogeny of Prototheca (Chlorophyta, Trebouxiophyceae)." Biologia 77, no. 2 (December 2, 2021): 569–82. http://dx.doi.org/10.1007/s11756-021-00971-y.

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AbstractProtothecosis is an infectious disease caused by organisms currently classified within the green algal genus Prototheca. The disease can manifest as cutaneous lesions, olecranon bursitis or disseminated or systemic infections in both immunocompetent and immunosuppressed patients. Concerning diagnostics, taxonomic validity is important. Prototheca, closely related to the Chlorella species complex, is known to be polyphyletic, branching with Auxenochlorella and Helicosporidium. The phylogeny of Prototheca was discussed and revisited several times in the last decade; new species have been described. Phylogenetic analyses were performed using ribosomal DNA (rDNA) and partial mitochondrial cytochrome b (cytb) sequence data. In this work we use Internal Transcribed Spacer 2 (ITS2) as well as 18S rDNA data. However, for the first time, we reconstruct phylogenetic relationships of Prototheca using primary sequence and RNA secondary structure information simultaneously, a concept shown to increase robustness and accuracy of phylogenetic tree estimation. Using encoded sequence-structure data, Neighbor-Joining, Maximum-Parsimony and Maximum-Likelihood methods yielded well-supported trees in agreement with other trees calculated on rDNA; but differ in several aspects from trees using cytb as a phylogenetic marker. ITS2 secondary structures of Prototheca sequences are in agreement with the well-known common core structure of eukaryotes but show unusual differences in their helix lengths. An elongation of the fourth helix of some species seems to have occurred independently in the course of evolution.

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TAHER, MD ABU, AHMED SALAHUDDIN KABIR, SHAHED UDDIN AHMED SHAZIB, MIN SEOK KIM, and MANN KYOON SHIN. "Morphological Redescriptions and Molecular Phylogeny of Three Stentor Species (Ciliophora: Heterotrichea: Stentoridae) from Korea." Zootaxa 4732, no. 3 (February 13, 2020): 435–52. http://dx.doi.org/10.11646/zootaxa.4732.3.6.

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The morphologies of the three freshwater stentorid ciliates in Korea, Stentor coeruleus (Pallas, 1766); Stentor muelleri Ehrenberg, 1831, and Stentor tartari Murthy & Bai, 1974, were investigated based on live observations and protargol impregnation. The Korean population of S. tartari exhibits the following characteristics: body size 200–355 × 85–135 µm in vivo, 62–106 somatic kineties, 8–13 peristomial kineties, 110–180 adoral membranelles, mostly two macronuclear nodules and 5–18 micronuclei, reddish and colorless cortical granules and the presence of symbiotic algae. We identified S. tartari based on unique characteristics compared to close congeners. Korean populations of S. coeruleus and S. muelleri are congruent with previously described populations in most aspects of their morphologies. Here, for the first time, we report molecular gene sequence information for S. tartari. Small subunit (SSU) rRNA gene sequence-based phylogeny indicates that S. tartari, which has multiple macronuclei, forms a monophyletic group with other Stentor species having a single macronucleus. Our findings based on morphology and SSU rRNA gene sequence information corroborate the hypothesis that the elongated macronucleus evolved from the compact single or multi macronucleus state.

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Idris, Abeer Babiker, Hadeel Gassim Hassan, Maryam Atif Salaheldin Ali, Sulafa Mohamed Eltaher, Leena Babiker Idris, Hisham N. Altayb, Amin Mohamed Abass, Mustafa Mohammed Ahmed Ibrahim, El-Amin Mohamed Ibrahim, and Mohamed A. Hassan. "Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution." International Journal of Microbiology 2020 (October 27, 2020): 1–12. http://dx.doi.org/10.1155/2020/8825718.

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Background. Helicobacter pylori (H. pylori) is ubiquitous among humans and one of the best-studied examples of an intimate association between bacteria and humans. Phylogeny and Phylogeography of H. pylori strains are known to mirror human migration patterns and reflect significant demographic events in human prehistory. In this study, we analyzed the molecular evolution of H. pylori strains detected from different tribes and regions of Sudan using 16S rRNA gene and the phylogenetic approach. Materials and methods. A total of 75 gastric biopsies were taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was performed by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was applied, and the resulted sequences were matched with the sequences of the National Center for Biotechnology Information (NCBI) nucleotide database. The evolutionary aspects were analyzed using MEGA7 software. Results. Molecular detection of H. pylori has shown that 28 (37.33%) of the patients were positive for H. pylori and no significant differences were found in sociodemographic characteristics, endoscopy series, and H. pylori infection. Nucleotide variations were observed at five nucleotide positions (positions 219, 305, 578, 741, and 763–764), and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. These six mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites; 66.67% of them were located in the central domain of 16S rRNA. The phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. The presence of Sudanese H. pylori strains resembling Hungarian H. pylori strains could reflect the migration of Hungarian people to Sudan or vice versa. Conclusion. This finding emphasizes the significance of studying the phylogeny of H. pylori strains as a discriminatory tool to mirror human migration patterns. In addition, the 16S rRNA gene amplification method was found useful for bacterial identification and phylogeny.

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Vanbeselaere, Jorick, Chunsheng Jin, Barbara Eckmair, Iain B. H. Wilson, and Katharina Paschinger. "Sulfated and sialylated N-glycans in the echinoderm Holothuria atra reflect its marine habitat and phylogeny." Journal of Biological Chemistry 295, no. 10 (January 22, 2020): 3159–72. http://dx.doi.org/10.1074/jbc.ra119.011701.

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Among the earliest deuterostomes, the echinoderms are an evolutionary important group of ancient marine animals. Within this phylum, the holothuroids (sea cucumbers) are known to produce a wide range of glycoconjugate biopolymers with apparent benefits to health; therefore, they are of economic and culinary interest throughout the world. Other than their highly modified glycosaminoglycans (e.g. fucosylated chondroitin sulfate and fucoidan), nothing is known about their protein-linked glycosylation. Here we used multistep N-glycan fractionation to efficiently separate anionic and neutral N-glycans before analyzing the N-glycans of the black sea cucumber (Holothuria atra) by MS in combination with enzymatic and chemical treatments. These analyses showed the presence of various fucosylated, phosphorylated, sialylated, and multiply sulfated moieties as modifications of oligomannosidic, hybrid, and complex-type N-glycans. The high degree of sulfation and fucosylation parallels the modifications observed previously on holothuroid glycosaminoglycans. Compatible with its phylogenetic position, H. atra not only expresses vertebrate motifs such as sulfo– and sialyl–Lewis A epitopes but displays a high degree of anionic substitution of its glycans, as observed in other marine invertebrates. Thus, as for other echinoderms, the phylum- and order-specific aspects of this species' N-glycosylation reveal both invertebrate- and vertebrate-like features.

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PAXTON, HANNELORE. "Phylogeny of Eunicida (Annelida) based on morphology of jaws." Zoosymposia 2, no. 1 (August 31, 2009): 241–64. http://dx.doi.org/10.11646/zoosymposia.2.1.18.

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Eunicida have a complex jaw apparatus with a fossil record dating back to the latest Cambrian. Traditionally, Eunicidae, Onuphidae, and Lumbrineridae were considered closely related families having labidognath maxillae, whereas Oenonidae with prionognath type maxillae were thought to be derived. Molecular phylogenies place Oenonidae with Eunicidae/Onuphidae, and Lumbrineridae as the most basal taxon. Re-evaluation of the jaw types based on morphology and ontogeny demonstrated that the labidognaths Eunicidae and Onuphidae have a closer relationship to the prionognath Oenonidae than was previously thought. Lumbrineridae are neither labidognath nor prionognath; therefore a new type, Symmetrognatha, is proposed. Homologies of jaw elements and considerations of functional aspects of the jaw apparatus are explored to present a hypothesis of the Eunicida phylogeny. The earliest fossils are of placognath and ctenognath types, lacking maxillary carriers. While the former are extinct, the latter are represented by the extant Dorvilleidae. The interpretation of relationships between the carrier-bearing families depends on whether the carriers are thought to have evolved once only or twice independently. The similarity of the carrier structure and their associated muscles suggests the former, placing the Lumbrineridae as sister to Eunicidae/Onuphidae and Oenonidae. However, the ontogeny of the eunicid/onuphid apparatus as well as its adult structure differ greatly from those of lumbrinerids, indicating that the lumbrinerid carriers may have evolved independently and earlier than in eunicids/onuphids and oenonids.

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Campoccia, Davide, Lucio Montanaro, and Carla Renata Arciola. "Current Methods for Molecular Epidemiology Studies of Implant Infections." International Journal of Artificial Organs 32, no. 9 (September 2009): 642–54. http://dx.doi.org/10.1177/039139880903200914.

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Over the last few decades, the number of surgical procedures involving prosthetic materials has greatly multiplied, along with the rising medical and economic impact of implant-associated infections. The need to appropriately counteract and deal with this phenomenon has led to growing efforts to elucidate the etiology, pathogenesis and epidemiology of these types of infections, characterized by opportunistic pathogens. Molecular epidemiology studies have progressively emerged as a leading multitask tool to identify and fingerprint bacterial strains, unveil the complex clonal nature of important pathogens, detect outbreak events, track the origin of the infections, assess the clinical significance of individual strain types, survey their distribution, recognize associations of strain types with specific virulence determinants and/or pathological conditions, assess the role played by the specific components of the virulon, and reveal the phylogeny and the mechanisms through which new strain types have emerged. Despite the many advances that have been made thanks to these flourishing new approaches to molecular epidemiology, a number of critical aspects remain challenging. In this paper, we briefly discuss the current limitations and possible developments of molecular epidemiology methods in the investigation and surveillance of implant infections.

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Choudhary, K., A. Kumar Verma, S. Swaroop, and N. Agrawal. "A review on the molecular characterization of digenean parasites using molecular markers with special reference to ITS region." Helminthologia 52, no. 3 (September 1, 2015): 167–87. http://dx.doi.org/10.1515/helmin-2015-0031.

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Abstract The rDNA region of eukaryotes has the immense potential to resolve the evolutionary and phylogeny problems using molecular markers. As evident from the present review, ITS region data is considered for interpretation of inter and intra-specific variations of 136 studies of 33 families including 78 genus and 114 species affecting individuals worldwide. Along with ITS-1 and ITS-2 region in 29 studies 18S region, in 38 studies 28S region and in 43 studies mitochondrial genes (COI and NDI) were also analyzed. Three new genera (Allobilharzia gen. nov., Caulanus gen. nov., and Latuterus gen. nov.) and 49 new species were discovered. Only 47 studies expressed variations at intra-specific and inter-specific level in complete ITS region, ITS-1 and ITS-2 rDNA sequences due to differences in nucleotide positions. According to the findings ITS region is more reliable and precise marker for demarcation and identification of species in combination of other DNA markers. Major studies were involved around the parasites of families Fasciolidae, Schistosomatidae, Opisthorchidae, Paragonimidae and Paramphistomidae, Clinostomidae, Diplostomidae, Haploporidae, among others infecting humans, farm animals, birds, fishes, reptiles and amphibians on the clinical basis. In future, molecular and bioinformatics aspects based on genetic variations will lead to explore the untouched areas of trematodes.

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Libkind, Diego, Alejandra Ruffini, Maria van Broock, Leonor Alves, and Josï¿½ Paulo Sampaio. "Biogeography, Host Specificity, and Molecular Phylogeny of the Basidiomycetous Yeast Phaffia rhodozyma and Its Sexual Form, Xanthophyllomyces dendrorhous." Applied and Environmental Microbiology 73, no. 4 (December 22, 2006): 1120–25. http://dx.doi.org/10.1128/aem.01432-06.

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ABSTRACT Phaffia rhodozyma (sexual form, Xanthophyllomyces dendrorhous) is a basidiomycetous yeast that has been found in tree exudates in the Northern Hemisphere at high altitudes and latitudes. This yeast produces astaxanthin, a carotenoid pigment with biotechnological importance because it is used in aquaculture for fish pigmentation. We isolated X. dendrorhous from the Southern Hemisphere (Patagonia, Argentina), where it was associated with fruiting bodies of Cyttaria hariotii, an ascomycetous parasite of Nothofagus trees. We compared internal transcribed spacer (ITS)-based phylogenies of P. rhodozyma and its tree host (Betulaceae, Corneaceae, Fagaceae, and Nothofagaceae) and found them to be generally concordant, suggesting that different yeast lineages colonize different trees and providing an explanation for the phylogenetic distance observed between the type strains of P. rhodozyma and X. dendrorhous. We hypothesize that the association of Xanthophyllomyces with Cyttaria derives from a previous association of the yeast with Nothofagus, and the sister relationship between Nothofagaceae and Betulaceae plus Fagaceae correlates with the phylogeny of X. dendrorhous strains originating from these three plant families. The two most basal strains of X. dendrorhous are those isolated from Cornus, an ancestral genus in the phylogenetic analysis of the host trees. Thus, we question previous conclusions that P. rhodozyma and X. dendrorhous represent different species since the polymorphisms detected in the ITS and intergenic spacer sequences can be attributed to intraspecific variation associated with host specificity. Our study provides a deeper understanding of Phaffia biogeography, ecology, and molecular phylogeny. Such knowledge is essential for the comprehension of many aspects of the biology of this organism and will facilitate the study of astaxanthin production within an evolutionary and ecological framework.

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Schreiner, Mark E., Christian Riedel, Jiři Holátko, Miroslav Pátek, and Bernhard J. Eikmanns. "Pyruvate:Quinone Oxidoreductase in Corynebacterium glutamicum: Molecular Analysis of the pqo Gene, Significance of the Enzyme, and Phylogenetic Aspects." Journal of Bacteriology 188, no. 4 (February 15, 2006): 1341–50. http://dx.doi.org/10.1128/jb.188.4.1341-1350.2006.

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ABSTRACT Corynebacterium glutamicum recently has been shown to possess pyruvate:quinone oxidoreductase (PQO), catalyzing the oxidative decarboxylation of pyruvate to acetate and CO2 with a quinone as the electron acceptor. Here, we analyze the expression of the C. glutamicum pqo gene, investigate the relevance of the PQO enzyme for growth and amino acid production, and perform phylogenetic studies. Expression analyses revealed that transcription of pqo is initiated 45 bp upstream of the translational start site and that it is organized in an operon together with genes encoding a putative metal-activated pyridoxal enzyme and a putative activator protein. Inactivation of the chromosomal pqo gene led to the absence of PQO activity; however, growth and amino acid production were not affected under either condition tested. Introduction of plasmid-bound pqo into a pyruvate dehydrogenase complex-negative C. glutamicum strain partially relieved the growth phenotype of this mutant, indicating that high PQO activity can compensate for the function of the pyruvate dehydrogenase complex. To investigate the distribution of PQO enzymes in prokaryotes and to clarify the relationship between PQO, pyruvate oxidase (POX), and acetohydroxy acid synthase enzymes, we compiled and analyzed the phylogeny of respective proteins deposited in public databases. The analyses revealed a wide distribution of PQOs among prokaryotes, corroborated the hypothesis of a common ancestry of the three enzymes, and led us to propose that the POX enzymes of Lactobacillales were derived from a PQO.

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Journal articles on the topic 'Skinks Phylogeny Molecular aspects'

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