scholarly journals What does mitogenomics tell us about the evolutionary history of the Drosophila buzzatii cluster (repleta group)

2019 ◽  
Author(s):  
Nicolás N. Moreyra ◽  
Julián Mensch ◽  
Juan Hurtado ◽  
Francisca Almeida ◽  
Cecilia Laprida ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Biology ◽  
Large Scale ◽  
South American ◽  
Phylogenetic Studies ◽  
Drosophila Buzzatii ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Tree Topologies ◽  
American Clade

AbstractThe Drosophila repleta group is an array of more than 100 cactophilic species endemic to the “New World”. The acquisition of the ability to utilize decaying cactus tissues as breeding and feeding sites is a key aspect that allowed the successful diversification of the repleta group in the American deserts. Within this group, the Drosophila buzzatii cluster is a South American clade of seven cactophilic closely related species in different stages of divergence, a feature that makes it a valuable model system for evolutionary research. However, even though substantial effort has been devoted to elucidating the phylogenetic relationships among members of the D. buzzatii cluster, the issue is still controversial. In effect, molecular phylogenetic studies performed to date generated ambiguous results since tree topologies depend on the kind of molecular marker employed. Curiously, even though mitochondrial DNA has become a popular marker in evolutionary biology and population genetics, none of the more than twenty Drosophila mitogenomes assembled so far belongs to this cluster. In this work we report the assembly of six complete mitogenomes of five species: D. antonietae, D. borborema, D. buzzatii, D. seriema and two strains of D. koepferae, with the aim to revisit the phylogenetic relationships and divergence times by means of a mitogenomic approach. The recovered topology using complete mitogenomes gives support to the hypothesis of the monophyly of that the D. buzzatii cluster and shows two main clades, one including D. buzzatii and D. koepferae (both strains) and the other the remaining species. These results are in agreement with previous reports based on a few mitochondrial and/or nuclear genes but in conflict with the results of a recent large-scale nuclear phylogeny, suggesting that nuclear and mitochondrial genomes depict different evolutionary histories.

On the status of the snake genera Erythrolamprus Boie, Liophis Wagler and Lygophis Fitzinger (Serpentes, Xenodontinae)

Zootaxa ◽  
2009 ◽  
Vol 2173 (1) ◽  
pp. 66-68 ◽  
Author(s):  
FELIPE F. CURCIO ◽  
VÍTOR DE Q. PIACENTINI ◽  
DANIEL S. FERNANDES
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Evidence ◽  
South American ◽  
Phylogenetic Studies ◽  
The Status ◽  
Molecular Phylogenetic ◽  
Recent Debate ◽  
The Subject

The genus Erythrolamprus Boie (1826) comprises six species of Central and South American false coral snakes (Peters & Orejas-Miranda 1970; Zaher 1999; Curcio et al. 2009). It is traditionally allocated in the tribe Xenodontini (subfamily Xenodontinae), along with the genera Liophis, Lystrophis, Umbrivaga, Waglerophis and Xenodon (sensu Dixon 1980; Cadle 1984; Myers 1986; Ferrarezzi 1994; Zaher 1999). Although Xenodontini is supported by morphological and molecular evidence, phylogenetic relationships and classification within the tribe have been the subject of recent debate. Molecular phylogenetic studies have recovered clades with Erythrolamprus nested within some representatives of the genus Liophis (Vidal et al. 2000; Zaher et al. 2009), partly corroborating previous hypotheses based on morphology (e.g. Dixon 1980).

scholarly journals Biogeography and ecology: towards the integration of two disciplines

2011 ◽  
Vol 366 (1576) ◽  
pp. 2438-2448 ◽  
Author(s):  
Robert E. Ricklefs ◽  
David G. Jenkins
Keyword(s):  
Evolutionary Biology ◽  
Plate Tectonics ◽  
Large Scale ◽  
Open Systems ◽  
Ecological Factors ◽  
Future Research ◽  
Ecological Communities ◽  
History Of ◽  
Future Research Directions ◽  
Synthetic Approaches

Although ecology and biogeography had common origins in the natural history of the nineteenth century, they diverged substantially during the early twentieth century as ecology became increasingly hypothesis-driven and experimental. This mechanistic focus narrowed ecology's purview to local scales of time and space, and mostly excluded large-scale phenomena and historical explanations. In parallel, biogeography became more analytical with the acceptance of plate tectonics and the development of phylogenetic systematics, and began to pay more attention to ecological factors that influence large-scale distributions. This trend towards unification exposed problems with terms such as ‘community’ and ‘niche,’ in part because ecologists began to view ecological communities as open systems within the contexts of history and geography. The papers in this issue represent biogeographic and ecological perspectives and address the general themes of (i) the niche, (ii) comparative ecology and macroecology, (iii) community assembly, and (iv) diversity. The integration of ecology and biogeography clearly is a natural undertaking that is based on evolutionary biology, has developed its own momentum, and which promises novel, synthetic approaches to investigating ecological systems and their variation over the surface of the Earth. We offer suggestions on future research directions at the intersection of biogeography and ecology.

scholarly journals A molecular phylogenetic analysis of the genera of fruit doves and allies using dense taxonomic sampling

2019 ◽  
Vol 42 ◽  
pp. 2019001
Author(s):  
Jennifer Nowak ◽  
Andrew Sweet ◽  
Jason Weckstein ◽  
Kevin Johnson
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Large Fraction ◽  
Nuclear Gene ◽  
Data Sets ◽  
Foraging Mode ◽  
Biogeographic Patterns ◽  
Reconstruction Methods ◽  
Molecular Phylogenetic ◽  
History Of

Fruit doves and their allies are a diverse group within the pigeon and dove family (Aves: Columbidae). Progress towards subfamilial classification of Columbidae relies on identifying major groups and the phylogenetic relationships within these groups. One such recently proposed group is the Raphinae based on previous evidence that the extinct dodo is potentially within what was formerly recognized as the Treroninae (fruit doves and allies). Although several studies have explored the phylogenetic relationships within Columbidae, most have focused either on broad-scale, familial level relationships or finer scale, species level relationships. Here we use mitochondrial and nuclear gene sequences from a diverse taxonomic sample to identify relationships among the genera and species of fruit doves and their allies. In particular our goal is to identify which of these genera should be included within Raphinae (the name which has taxonomic priority over Treroninae), focusing on an inclusive, well-supported monophyletic group. We also use dense taxon sampling to explore relationships among genera and species in this group, expanding on previous studies. In addition, we use resulting phylogenetic hypotheses to reconstruct the ancestral evolutionary history of foraging mode and biogeographic patterns of dispersal within the group. We used two data sets for our phylogenetic analysis: the first consisting of novel sequences generated for this project and the second with additional, previously published sequences from the fruit dove genus (Ptilinopus). Our analyses found support for the monophyly of a clade that contains a large fraction of the genera currently classified within Raphinae and also found several well-supported clades within this group of pigeons and doves. Character reconstruction methods based on the resulting phylogeny recover multiple transitions from a terrestrial to an arboreal foraging mode and evidence for multiple dispersal events from Asia to Africa throughout the history of the clade.

scholarly journals The tribe Scrophularieae (Scrophulariaceae): A Review of Phylogenetic Studies

Hacquetia ◽  
2019 ◽  
Vol 18 (2) ◽  
pp. 337-347 ◽  
Author(s):  
Mehrshid Riahi ◽  
Farrokh Ghahremaninejad
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Morphological Data ◽  
Hybrid Speciation ◽  
The North ◽  
Phylogenetic Studies ◽  
Phylogenetic Reconstructions ◽  
Data Collection And Analysis ◽  
History Of ◽  
Review Reports

Abstract Molecular data have been increasingly used to study the phylogenetic relationships among many taxa, including scrophs. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review reports of the recent knowledge of the phylogenetic relationships within Scrophularieae (2011–2017). The results of these analyses led to the following conclusions. (1) Species of Scrophularia have undergone one or more Miocene migration events occurred from eastern Asia to the North America with subsequent long dispersal and diversification in three main directions. (2) Allopolyploid and aneuploid hybrid speciation between Scrophularia species can occur, so hybridization and polyploidy have an important role for history of diversification. (3) The ancestral staminode type for the genus Scrophularia seems to be a large staminode. (4) Monophyly of the genus Verbascum with respect to the genus Scrophularia is strongly supported. (5) Oreosolen, is not monophyletic, because all accessions of Oreosolen were nested within Scrophularia. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies.

Morphological and molecular phylogenetic studies in South American Cortinarius species

2003 ◽  
Vol 107 (10) ◽  
pp. 1143-1156 ◽  
Author(s):  
Sigisfredo Garnica ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
South American ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic

scholarly journals The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition

2019 ◽  
Author(s):  
Sebastian S Groh ◽  
Paul Upchurch ◽  
Paul M Barrett ◽  
Julia J Day
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Morphological Characters ◽  
Late Triassic ◽  
Continuous Data ◽  
Comprehensive Review ◽  
Phylogenetic Studies ◽  
History Of ◽  
First Time

Abstract Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.

scholarly journals Preserving and vouchering butterflies and moths for large-scale museum-based molecular research

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2160 ◽  
Author(s):  
Soowon Cho ◽  
Samantha W. Epstein ◽  
Kim Mitter ◽  
Chris A. Hamilton ◽  
David Plotkin ◽  
...  
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Primary Source ◽  
University Of Florida ◽  
University Of Maryland ◽  
Phylogenetic Studies ◽  
Wing Patterns ◽  
Molecular Phylogenetic ◽  
The University ◽  
Specimen Identification

Butterflies and moths (Lepidoptera) comprise significant portions of the world’s natural history collections, but a standardized tissue preservation protocol for molecular research is largely lacking. Lepidoptera have traditionally been spread on mounting boards to display wing patterns and colors, which are often important for species identification. Many molecular phylogenetic studies have used legs from pinned specimens as the primary source for DNA in order to preserve a morphological voucher, but the amount of available tissue is often limited. Preserving an entire specimen in a cryogenic freezer is ideal for DNA preservation, but without an easily accessible voucher it can make specimen identification, verification, and morphological work difficult. Here we present a procedure that creates accessible and easily visualized “wing vouchers” of individual Lepidoptera specimens, and preserves the remainder of the insect in a cryogenic freezer for molecular research. Wings are preserved in protective holders so that both dorsal and ventral patterns and colors can be easily viewed without further damage. Our wing vouchering system has been implemented at the University of Maryland (AToL Lep Collection) and the University of Florida (Florida Museum of Natural History, McGuire Center of Lepidoptera and Biodiversity), which are among two of the largest Lepidoptera molecular collections in the world.

scholarly journals Combining the small South American genus Androtrichum into Cyperus (Cyperaceae)

2020 ◽  
Vol 153 (3) ◽  
pp. 446-454
Author(s):  
Luciana Pereira-Silva ◽  
Rafael Trevisan ◽  
Ana Claudia Rodrigues ◽  
Isabel Larridon
Keyword(s):  
The Other ◽  
Distribution Data ◽  
South American ◽  
Kranz Anatomy ◽  
Phylogenetic Studies ◽  
Code Of Nomenclature ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Taxonomic Changes ◽  
Complex Relationships

Background and aims – Molecular phylogenetic studies have provided a clearer understanding of the complex relationships within the family Cyperaceae. These studies have consistently shown that 12 allied genera are nested in the genus Cyperus. However, early Sanger sequencing-based phylogenies that included the two species of the small South American genus Androtrichum were inconclusive in placing this genus either as sister to Cyperus or as part of its early divergent lineages. A recent phylogenetic analysis however conclusively placed the two species of Androtrichum within the C3 Cyperus Grade. In this study, we investigate if the morphology and anatomy of Androtrichum species provide additional evidence for their placement in the genus Cyperus. In addition, we provide descriptions and distribution data for the species.Material and methods – Herbarium material from FLOR, FURB, GENT, ICN, and K has been studied. Samples of the culm and leaf were studied using histological methods. Taxonomic changes and typifications of names were performed according to the International Code of Nomenclature for algae, fungi, and plants. Key results – The morphology and the non-Kranz anatomy observed in the Androtrichum species confirm their placement among the other C3  Cyperus species. Androtrichum is combined into Cyperus. For one species, a combination in Cyperus is already available: Cyperus trigynus. For the other species, a new name in Cyperus is published: Cyperus byssaceus. Two typifications are established and morphological descriptions and distribution data are provided. Conclusion – By integrating recent molecular phylogenetic data with additional evidence from morphology and anatomy, Androtrichum is combined into Cyperus. As a result of this taxonomic change, a single monophyletic genus Cyperus is now recognised in the Cyperus Clade of tribe Cypereae.

THE EVOLUTIONARY HISTORY OF DROSOPHILA BUZZATII. III. CYTOGENETIC RELATIONSHIPS BETWEEN TWO SIBLING SPECIES OF THE BUZZATII CLUSTER

Genetics ◽  
1982 ◽  
Vol 101 (3-4) ◽  
pp. 503-518 ◽  
Author(s):  
A Ruiz ◽  
A Fontdevila ◽  
M Wasserman
Keyword(s):  
Salivary Gland ◽  
Sibling Species ◽  
Related Species ◽  
Evolutionary History ◽  
South American ◽  
Closely Related Species ◽  
Drosophila Buzzatii ◽  
Repleta Group ◽  
Chromosomal Data ◽  
History Of

ABSTRACT Drosophila buzzatii has been found sympatric in Argentina with a closely-related sibling species, D. serido. The biogeographical, reproductive and chromosomal data allow us to combine these species into an evolutionary unit, the buzzatii cluster. Salivary gland chromosomes also have been used to determine their phylogenetic relationships with other closely related species, showing that the buzzatii cluster species share two inversions—2d  2 and 2s  6—with the species of the martensis cluster. Both clusters arose from South American populations of the ancestor of the mulleri complex, and we propose to include D. buzzatii and D. serido in the mulleri complex of the repleta group.

scholarly journals Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene

2005 ◽  
Vol 86 (10) ◽  
pp. 2849-2858 ◽  
Author(s):  
H. Bourhy ◽  
J. A. Cowley ◽  
F. Larrous ◽  
E. C. Holmes ◽  
P. J. Walker
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Pcr Amplification ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Degenerate Primers ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Vector Borne

RNA viruses of the family Rhabdoviridae include arthropod-borne agents that infect plants, fish and mammals, and also include a variety of non-vector-borne mammalian viruses. Herein is presented a molecular phylogenetic analysis, the largest undertaken to date, of 56 rhabdoviruses, including 20 viruses which are currently unassigned or assigned as tentative species within the Rhabdoviridae. Degenerate primers targeting a region of block III of the L polymerase gene were defined and used for RT-PCR amplification and sequencing. A maximum-likelihood phylogenetic analysis of a 158-residue L polymerase amino acid sequence produced an evolutionary tree containing the six recognized genera of the Rhabdoviridae and also enabled us to identify four more monophyletic groups of currently unclassified rhabdoviruses that we refer to as the ‘Hart Park’, ‘Almpiwar’, ‘Le Dantec’ and ‘Tibrogargan’ groups. The broad phylogenetic relationships among these groups and genera also indicate that the evolutionary history of rhabdoviruses was strongly influenced by mode of transmission, host species (plant, fish or mammal) and vector (orthopteran, homopteran or dipteran).

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