Inference of higher-order conifer relationships from a multi-locus plastid data setThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 658-669 ◽  
Author(s):  
Hardeep S. Rai ◽  
Patrick A. Reeves ◽  
Rod Peakall ◽  
Richard G. Olmstead ◽  
Sean W. Graham
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Bootstrap Support ◽  
Sister Group Relationship ◽  
Ribosomal Protein Genes ◽  
Conifer Species ◽  
Noncoding Regions ◽  
Selection Of

We reconstructed the broad backbone of conifer phylogeny from a survey of 15–17 plastid loci and associated noncoding regions from exemplar conifer species. Parsimony and likelihood analyses recover the same higher-order relationships, and we find strong support for most of the deep splits in conifer phylogeny, including those within our two most heavily sampled families, Araucariaceae and Cupressaceae. Our findings are broadly congruent with other recent studies, and are inferred with comparable or improved bootstrap support. The deepest phylogenetic split in conifers is inferred to be between Pinaceae and all other conifers (Cupressophyta). Our current gene and taxon sampling does not support a relationship between Pinaceae and Gnetales, observed in some published studies. Within the Cupressophyta clade, we infer well-supported relationships among Cephalotaxaceae, Cupressaceae, Sciadopityaceae, and Taxaceae. Our data support recent moves to recognize Cephalotaxus under Taxaceae, and we find strong support for a sister-group relationship between the two predominantly southern hemisphere conifer families, Araucariaceae and Podocarpaceae. A local hotspot of indel evolution shared by the latter two conifer families is identified in the coding portion of one of the plastid ribosomal protein genes. The removal of the most rapidly evolving plastid characters, as defined using a likelihood-based classification of substitution rates for the taxa considered here, is shown to have little to no effect on our inferences of higher-order conifer relationships.

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

scholarly journals On a remarkable new species of <i>Tharsis</i>, a Late Jurassic teleostean fish from southern Germany: its morphology and phylogenetic relationships

Fossil Record ◽  
2019 ◽  
Vol 22 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Gloria Arratia ◽  
Hans-Peter Schultze ◽  
Helmut Tischlinger
Keyword(s):  
New Species ◽  
Late Jurassic ◽  
Strong Support ◽  
Sister Group ◽  
Common Species ◽  
Upper Jurassic ◽  
Morphological Characters ◽  
Morphological Description ◽  
Sister Group Relationship ◽  
Southern Germany

Abstract. A complete morphological description, as preservation permits, is provided for a new Late Jurassic fish species (Tharsis elleri) together with a revision and comparison of some morphological features of Tharsis dubius, one of the most common species from the Solnhofen limestone, southern Germany. An emended diagnosis of the genus Tharsis – now including two species – is presented. The new species is characterized by a combination of morphological characters, such as the presence of a complete sclerotic ring formed by two bones placed anterior and posterior to the eye, a moderately short lower jaw with quadrate-mandibular articulation below the anterior half of the orbit, caudal vertebrae with neural and haemal arches fused to their respective vertebral centrum, and parapophyses fused to their respective centrum. A phylogenetic analysis based on 198 characters and 43 taxa is performed. Following the phylogenetic hypothesis, the sister-group relationship Ascalaboidae plus more advanced teleosts stands above the node of Leptolepis coryphaenoides. Both nodes have strong support among teleosts. The results confirm the inclusion of Ascalabos, Ebertichthys and Tharsis as members of this extinct family. Tharsis elleri n. sp. (LSID urn:lsid:zoobank.org:act:6434E6F5-2DDD-48CF-A2B1-827495FE46E6, date: 13 December 2018) is so far restricted to one Upper Jurassic German locality – Wegscheid Quarry near Schernfeld, Eichstätt – whereas Tharsis dubius is known not only from Wegscheid Quarry, but also from different localities in the Upper Jurassic of Bavaria, Germany, and Cerin in France.

scholarly journals Placozoa and Cnidaria are sister taxa

2017 ◽  
Author(s):  
Christopher E. Laumer ◽  
Harald Gruber-Vodicka ◽  
Michael G. Hadfield ◽  
Vicki B. Pearse ◽  
Ana Riesgo ◽  
...  
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Large Dataset ◽  
Animal Evolution ◽  
Phylogenetic Placement ◽  
The Matrix ◽  
Show Evidence ◽  
Animal Phylogeny ◽  
Reduced Forms

AbstractThe phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria (=Planulozoa), also seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that the support for Planulozoa can be assigned to this source of systematic error. In interpreting this placozoan-cnidarian clade, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.

A Phylogenetic Analysis and Taxonomic Revision of Bartonia (Gentianaceae: Gentianeae), Based on Molecular and Morphological Evidence

2009 ◽  
Vol 34 (1) ◽  
pp. 162-172 ◽  
Author(s):  
Katherine G. Mathews ◽  
Niall Dunne ◽  
Emily York ◽  
Lena Struwe
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Species Boundaries ◽  
Morphological Evidence ◽  
Phylogenetic Study ◽  
Sister Group Relationship ◽  
Internal Transcribed Spacer Region ◽  
Test Species

A phylogenetic study and taxonomic revision of the four currently accepted species of Bartonia (Gentianaceae, subtribe Swertiinae) were conducted in order to test species boundaries and interspecific relationships. Species boundaries were examined based on measurements of key quantitative and qualitative morphological characters as given in the original descriptions. Phylogenetic analyses were performed using molecular data from the nuclear internal transcribed spacer region and chloroplast DNA (trnL intron through the trnL-F spacer), separately and combined using parsimony and Bayesian methodologies, incorporating outgroups from subtribes Swertiinae and Gentianinae. The morphological study revealed that characters of one species, B. texana, represent a subset of the morphological variation found within B. paniculata, but that B. paniculata, B. verna, and B. virginica could all be separated from one another. The molecular phylogenetic analyses all found B. texana to nest in a clade with the two recognized subspecies of B. paniculata (subsp. paniculata and subsp. iodandra), making the latter paraphyletic. Bartonia texana is here reduced to subspecific rank, as Bartonia paniculata subsp. texana. Also, the phylogenetic analyses showed strong support for a sister group relationship between B. verna and B. virginica, as opposed to between B. paniculata and B. virginica as has been previously suggested.

scholarly journals Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

2003 ◽  
Vol 17 (4) ◽  
pp. 605 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Recent Common Ancestor ◽  
Bootstrap Support ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

scholarly journals Phylogenetic evidence suggests a later origin of the DRD2l and DRD4rs dopamine receptor gene lineages

2018 ◽  
Author(s):  
Juan C Opazo ◽  
Kattina Zavala ◽  
Soledad Miranda-Rottmann ◽  
Roberto Araya
Keyword(s):  
Dopamine Receptors ◽  
Phylogenetic Relationships ◽  
Receptor Gene ◽  
Strong Support ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Dopaminergic Neurotransmission ◽  
Tree Topologies ◽  
The Central Nervous System ◽  
Time Of Origin

Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric disorders. From an evolutionary standpoint, phylogenetic relationships among the DRD1 class of dopamine receptors are still a matter of debate as in the literature different tree topologies have been proposed. In contrast, phylogenetic relationships among the DRD2 group of receptors are well understood. Understanding the time of origin of the different dopamine receptors is also an issue that needs further study, especially for the genes that have restricted phyletic distributions (e.g. DRD2l and DRD4rs). Thus, the goal of this study was to investigate the evolution of dopamine receptors, with emphasis on shedding light on the phylogenetic relationships among the D1 class of dopamine receptors and the time of origin of the DRD2l and DRD4rs gene lineages. Our results recovered the monophyly of the two groups of dopamine receptors. Within the DRD1 group the monophyly of each paralog was recovered with strong support, and phylogenetic relationships among them were well resolved. Within the DRD1 class of dopamine receptors we recovered the sister group relationship between the DRD1C and DRD1E, and this clade was recovered sister to a cyclostome sequence. The DRD1 clade was recovered sister to the aforementioned clade, and the group containing DRD5 receptors was sister to all other DRD1 paralogs. In agreement with the literature, among the DRD2 class of receptors, DRD2 was recovered sister to DRD3, whereas DRD4 was sister to the DRD2/DRD3 clade. According to our phylogenetic tree, the DRD2l and DRD4rs gene lineages would have originated in the ancestor of gnathostomes between 615 and 473 mya. Conservation of sequences required for dopaminergic neurotransmission and small changes in regulatory regions suggest a functional refinement of the dopaminergic pathways along evolution.

A new phylogeny and phylogenetic classification for the Canthyloscelidae (Diptera: Psychodomorpha)

2000 ◽  
Vol 78 (6) ◽  
pp. 1067-1077 ◽  
Author(s):  
Dalton de Souza Amorim
Keyword(s):  
Phylogenetic Analysis ◽  
Middle Jurassic ◽  
Sister Group ◽  
Head Capsule ◽  
Sister Group Relationship ◽  
Phylogenetic Classification ◽  
The Family

A new phylogeny and phylogenetic classification for the Canthyloscelidae (Diptera: Psychodomorpha) is presented. A phylogenetic analysis of the Scatopsoidea is performed. A sister-group relationship between the Canthyloscelidae and Scatopsidae is accepted and the monophyly of the Canthyloscelidae is corroborated, including the genera Exiliscelis, Synneuron, Hyperoscelis, and Canthyloscelis. An earlier phylogenetic analysis of the group is considered, in which Synneuron was accepted as the sister-group of the Scatopsidae and Exiliscelis was considered the sister-group of Synneuron + Scatopsidae. Some apomorphic similarities between the larvae of all genera of Canthyloscelidae, especially the reduction of the head capsule, are considered true synapomorphies. Exiliscelis is considered the sister-group of the rest of the family and is placed in a new subfamily, Exiliscelinae. In the Canthyloscelinae, Synneuron is the sister-group of Hyperoscelis + Canthyloscelis. A phylogenetic classification of the group is proposed. Prohyperoscelis rohdendorfi Kovalev, 1985, from the Middle Jurassic in Russia, is accepted as the sister-group of Canthyloscelis.

scholarly journals Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Christopher E Laumer ◽  
Harald Gruber-Vodicka ◽  
Michael G Hadfield ◽  
Vicki B Pearse ◽  
Ana Riesgo ◽  
...  
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Compositional Bias ◽  
Sister Group Relationship ◽  
Large Dataset ◽  
Animal Evolution ◽  
The Matrix ◽  
Show Evidence ◽  
Animal Phylogeny ◽  
Reduced Forms

The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria as seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that support for the Cnidaria + Bilateria clade can be assigned to this source of systematic error. In interpreting these results, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.

scholarly journals Evolution of dopamine receptors: phylogenetic evidence suggests a later origin of the DRD2l and DRD4rs dopamine receptor gene lineages

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4593 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala ◽  
Soledad Miranda-Rottmann ◽  
Roberto Araya
Keyword(s):  
Dopamine Receptors ◽  
Phylogenetic Relationships ◽  
Receptor Gene ◽  
Strong Support ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Dopaminergic Neurotransmission ◽  
Tree Topologies ◽  
The Central Nervous System ◽  
Time Of Origin

Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric disorders. From an evolutionary standpoint, phylogenetic relationships among the DRD1 class of dopamine receptors are still a matter of debate as in the literature different tree topologies have been proposed. In contrast, phylogenetic relationships among the DRD2 group of receptors are well understood. Understanding the time of origin of the different dopamine receptors is also an issue that needs further study, especially for the genes that have restricted phyletic distributions (e.g., DRD2l and DRD4rs). Thus, the goal of this study was to investigate the evolution of dopamine receptors, with emphasis on shedding light on the phylogenetic relationships among the D1 class of dopamine receptors and the time of origin of the DRD2l and DRD4rs gene lineages. Our results recovered the monophyly of the two groups of dopamine receptors. Within the DRD1 group the monophyly of each paralog was recovered with strong support, and phylogenetic relationships among them were well resolved. Within the DRD1 class of dopamine receptors we recovered the sister group relationship between the DRD1C and DRD1E, and this clade was recovered sister to a cyclostome sequence. The DRD1 clade was recovered sister to the aforementioned clade, and the group containing DRD5 receptors was sister to all other DRD1 paralogs. In agreement with the literature, among the DRD2 class of receptors, DRD2 was recovered sister to DRD3, whereas DRD4 was sister to the DRD2/DRD3 clade. According to our phylogenetic tree, the DRD2l and DRD4rs gene lineages would have originated in the ancestor of gnathostomes between 615 and 473 mya. Conservation of sequences required for dopaminergic neurotransmission and small changes in regulatory regions suggest a functional refinement of the dopaminergic pathways along evolution.

The evolution of fruit in Scandiceae subtribe Scandicinae (Apiaceae)

2001 ◽  
Vol 79 (11) ◽  
pp. 1358-1374 ◽  
Author(s):  
Krzysztof Spalik ◽  
Aneta Wojewódzka ◽  
Stephen R Downie
Keyword(s):  
Phylogenetic Trees ◽  
Sister Group ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Bootstrap Support ◽  
Sister Group Relationship ◽  
Vascular Bundles ◽  
Fruit Morphology ◽  
The Family ◽  
Fruit Characters

Evolutionary relationships among 66 representatives of the family Apiaceae, including 37 species of tribe Scandiceae subtribe Scandicinae, were inferred from separate and combined analyses of fruit morphology and anatomy and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences. Phylogenetic trees inferred from analysis of 35 fruit characters were not congruent to those derived from molecular data and, overall, had much lower bootstrap support values than the latter. Contrary to molecular data, fruit characters did not support the monophyly of subtribe Scandicinae. Fruit data do, however, corroborate the monophyly of nearly every genus within Scandicinae, the affinity of members of the "crown" clade—Anthriscus, Kozlovia (including Krasnovia and Neoconopodium), Geocaryum, Myrrhis, and Osmorhiza—that had been identified in previous molecular analyses, and the sister group relationship between the "crown" clade and the genus Scandix. Phylogenies derived from the analysis of combined ITS and fruit characters were congruent to those inferred from molecular data alone. Reconstructions of ancestral character states using the results of the combined analysis suggest that among extant Scandicinae, the fruits of Athamanta have retained the most plesiomorphic characters. Evolutionary tendencies that have occurred in the fruits of Scandicinae include the broadening of the vascular bundles and vittae, the thickening of the cuticle and epidermal cell wall, the origin of bristles from hairs, the appearance of a pedicel-like appendage, the development of a long beak, and lateral wings. These changes are interpreted as adaptations to fruit dispersal and seed defense.Key words: Apiaceae, Scandiceae subtribe Scandicinae, ITS, fruit morphology.

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