scholarly journals Phylogeny of Paullinia L. (Paullinieae: Sapindaceae), a diverse genus of lianas with rapid fruit evolution

2019 ◽  
Author(s):  
Joyce G. Chery ◽  
Pedro Acevedo-Rodríguez ◽  
Carl J Rothfels ◽  
Chelsea D. Specht
Keyword(s):  
Molecular Phylogeny ◽  
Visual Display ◽  
Single Copy ◽  
Wind Dispersal ◽  
Fruit Morphology ◽  
Nuclear Markers ◽  
Evolutionary Transitions ◽  
Neotropical Forest ◽  
Fruit Evolution ◽  
Animal Dispersed Seeds

AbstractPaullinia L. is a genus of c. 220 mostly Neotropical forest-dwelling lianas that displays a wide diversity of fruit morphologies. Paullinia resembles other members of the Paullinieae in being a climber with stipulate compound leaves and paired inflorescence tendrils. However, it is distinct in having capsular fruits with woody, coriaceous, or crustaceous pericarps. While consistent in this basic plan, the pericarps of Paullinia fruits are otherwise highly variable—in some species they are winged, whereas in others they are without wings or covered with spines. With the exception of the water-dispersed indehiscent spiny fruits of some members of Paullinia sect. Castanella, all species are dehiscent, opening their capsules while they are still attached to the branch, to reveal arillate animal-dispersed seeds. Here we present a molecular phylogeny of Paullinia derived from 11 molecular markers, including nine novel single-copy nuclear markers amplified by microfluidics PCR. This is the first broadly sampled molecular phylogeny for the genus. Paullinia is supported as monophyletic and is sister to Cardiospermum L., which together are sister to Serjania Mill + Urvillea Kunth. We apply this novel phylogenetic hypothesis to test previous infrageneric classifications and to infer that unwinged fruits represent the ancestral condition, from which there were repeated evolutionary transitions and reversals. However, because the seeds of both winged and unwinged fruits are all dispersed by animals, we conclude that the repeated transitions in fruit morphology may relate to visual display strategies to attract animal dispersers, and do not represent transitions to wind dispersal.

scholarly journals Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 38 ◽  
Author(s):  
Dehuai Luo ◽  
Yanping Li ◽  
Qingyuan Zhao ◽  
Lianpeng Zhao ◽  
Arne Ludwig ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Single Copy ◽  
Species Trees ◽  
Degenerate Primers ◽  
Nuclear Markers ◽  
Gene Markers ◽  
Fossil Species ◽  
Living Fossil ◽  
Molecular Clock Model ◽  
Extant Species

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.

scholarly journals Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e76957 ◽  
Author(s):  
Carl J. Rothfels ◽  
Anders Larsson ◽  
Fay-Wei Li ◽  
Erin M. Sigel ◽  
Layne Huiet ◽  
...  
Keyword(s):  
Single Copy ◽  
Nuclear Markers

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Transcriptome phylogenies support ancient evolutionary transitions in bioluminescence traits of cypridinid ostracods

2021 ◽  
Author(s):  
Emily A. Ellis ◽  
Jessica A. Goodheart ◽  
Nicholai M. Hensley ◽  
Vanessa L. González ◽  
Nicholas J. Reda ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Molecular Phylogeny ◽  
Divergence Times ◽  
Evolutionary Transitions ◽  
Single Origin ◽  
Molecular Phylogenetic ◽  
The Caribbean ◽  
Character Mapping ◽  
Molecular Phylogenetic Data ◽  
Relaxed Clock

AbstractBioluminescence evolved many times independently, leading to dramatic effects on ecosystems by influencing communication both within and between species. One origin of bioluminescence is within cypridinid ostracods. Bioluminescent cypridinids probably all use light as an anti-predator display, while a subset that diversified in the Caribbean also use light for courtship signaling. Despite their importance for understanding the evolution of bioluminescence, very little molecular phylogenetic data are available for cypridinids and the timing of evolutionary transitions of luminous traits is poorly understood. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. Our results strongly support previous hypotheses of a single origin of bioluminescent courtship signaling, nested within a single origin of bioluminescence, and the secondary loss of courtship signaling in Vargula tsujii. We propose the name Luminini for the Tribe of bioluminescent cypridinids and Luxorina for the Sub-tribe of cypridinids with courtship signaling. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved at least 151 Million Years Ago (MYA) and cypridinid bioluminescence originated at least 197 MYA, making it one of the oldest documented origins of bioluminescence. The molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2463 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V. Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

An EPIC journey to locate single-copy nuclear markers in sea anemones

2018 ◽  
Vol 47 (6) ◽  
pp. 756-776 ◽  
Author(s):  
Mercer R. Brugler ◽  
Ricardo E. González-Muñoz ◽  
Michael Tessler ◽  
Estefanía Rodríguez
Keyword(s):  
Single Copy ◽  
Sea Anemones ◽  
Nuclear Markers

scholarly journals Molecular phylogeny of Culex subgenus Melanoconion (Diptera: Culicidae) based on nuclear and mitochondrial protein-coding genes

2018 ◽  
Vol 5 (5) ◽  
pp. 171900 ◽  
Author(s):  
Carolina Torres-Gutierrez ◽  
Tatiane M. P. de Oliveira ◽  
Kevin J. Emerson ◽  
Eduardo Sterlino Bergo ◽  
Maria Anice Mureb Sallum
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Phylogenetic Signal ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Single Copy ◽  
Neotropical Region ◽  
Nuclear Genes ◽  
Morphological Identification ◽  
Protein Coding

The subgenus Melanoconion of the mosquito genus Culex is taxonomically diverse and is widely distributed in the Neotropical Region, with 10 species occurring in the Nearctic Region. Species of this subgenus pose a taxonomical challenge because morphological identification is based largely on anatomical characters of the male genitalia. We addressed the monophyly of the Spissipes and Melanoconion Sections of the subgenus Melanoconion and some of the informal groups in each section. Our sample taxa included 97 specimens representing 43 species, from which we analysed fragments of two single-copy nuclear genes ( CAD , HB ) and one mitochondrial gene ( COI ). Phylogenetic relationships within the subgenus are presented based on results of maximum-likelihood and Bayesian analyses using a multi-locus matrix of DNA sequences. We show a molecular phylogeny of Melanoconion in which both sections were recovered as monophyletic groups. The monophyly of the Atratus and Pilosus groups was confirmed. Within each section, other monophyletic groups were recovered highlighting the potential need for future nomenclature rearrangement. The phylogenetic signal contained in nuclear genes, when analysed together, was more informative than each gene analysed separately, corroborating monophyly of Melanoconion relative to Culex ( Culex ) species included in the analyses, the Melanoconion and Spissipes Sections and some species groups. Our results provide new information for the classification of the subgenus and additional data that can be used to improve species identification when a more representative taxon sampling is available.

Sign in / Sign up

Export Citation Format

Share Document