Phylogeny of Halgerda (Mollusca : Gastropoda) based on combined analysis of mitochondrial CO1 and morphology

2003 ◽  
Vol 17 (5) ◽  
pp. 617 ◽  
Author(s):  
Shireen J. Fahey
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Signal ◽  
Optimality Criteria ◽  
Retention Indices ◽  
Species Level ◽  
Combined Analysis ◽  
Length Difference ◽  
Incongruence Length Difference

A phylogeny of the nudibranch Halgerda Bergh, 1880 is presented based on mitochondrial CO1 and compared with a previously published morphology-based phylogeny. Incongruence length difference (ILD) tests indicated possibly conflicting phylogenetic signals. Both separate and combined analyses resulted in trees that were very similar in topology, both to each other and to the morphology-based tree (albeit with lower consistency and retention indices). Some differences are noted in the topology based on the optimality criteria used: parsimony and maximum likelihood. Results of this study indicate that the CO1 gene contains sufficient phylogenetic signal for inferring species-level phylogeny in the Nudibranchia and also supports many of the clades in the morphological phylogeny. Specifically, the more basal clades of the morphology-based phylogeny are supported with differences noted at the most terminal taxa.

scholarly journals Behaviour of cranes (family Gruidae) mirrors their phylogenetic relationships

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nela Nováková ◽  
Jan Robovský
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Species Level ◽  
Monophyletic Group ◽  
Molecular Tree ◽  
Behavioural Repertoire ◽  
Over Time

Abstract Background The behavioural repertoire of every species evolved over time and its evolution can be traced through the phylogenetic relationships in distinct groups. Cranes (family Gruidae) represent a small, old, monophyletic group with well-corroborated phylogenetic relationships on the species level, and at the same time they exhibit a complex and well-described behavioural repertoire. Methods We therefore investigated the evolution of behavioural traits of cranes in a phylogenetic context using several phylogenetic approaches and two types of trait scoring. The cranes exhibit more than a hundred behavioural displays, almost one third of which may be phylogenetically informative. Results More than half of the analysed traits carry a significant phylogenetic signal. The ancestor of cranes already exhibited a quite complex behavioural repertoire, which remained unchanged in Balearicinae but altered greatly in Gruinae, specifically by the shedding of traits rather than their creation. Trait scoring has an influence on results within the Gruinae, primarily in genera Bugeranus and Anthropoides. Conclusions Albeit the behavioural traits alone cannot be used for resolving species-level relationships within the Gruidae, when optimized on molecular tree, they can help us to detect interesting evolutionary transformations of behaviour repertoire within Gruiformes. The Limpkin (Aramus guarauna) seems to be the most enigmatic species and should be studied in detail for its behavioural repertoire, which may include some precursors of crane behavioural traits.

scholarly journals Identifying the North American Plum Species Phylogenetic Signal Using Nuclear, Mitochondrial, and Chloroplast DNA Markers

2016 ◽  
Vol 141 (6) ◽  
pp. 623-644 ◽  
Author(s):  
Dario J. Chavez ◽  
Thomas G. Beckman ◽  
José X. Chaparro
Keyword(s):  
Chloroplast Dna ◽  
Prunus Persica ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Species Relationships ◽  
The North

Prunus phylogeny has been extensively studied using chloroplast DNA (cpDNA) sequences. Chloroplast DNA has a slow rate of evolution, which is beneficial to determine species relationships at a deeper level. The chloroplast-based phylogenies have a limitation due to the transfer of this organelle by interspecific hybridization. This creates difficulties when studying species relationships. Interspecific hybrids in Prunus occur naturally and have been reported, which creates a problem when using cpDNA-based phylogenies to determine species relationships. The main goal of this project was to identify nuclear gene regions that could provide an improved phylogenetic signal at the species level in Prunus. A total of 11 species in Prunus and within section Prunocerasus were used. Two peach (Prunus persica) haploids were used to test the reliability of the molecular markers developed in this project to amplify single-copy genes. A total of 33 major genes associated with vernalization response, 16 with tree architecture, and 3 with isozymes, were tested. Similarly, 41 simple sequence repeat (SSR) markers, seven cpDNA regions, and the internal transcribed spacer (ITS) region, were used. Multiple gene regions were identified and provided the greatest number of characters, greatest variability, and improved phylogenetic signal at the species level in Prunus section Prunocerasus. Out of those, trnH-psbA, PGI, MAX4, AXR1, LFY, PHYE, and VRN1 are recommended for a phylogenetic analysis with a larger number of taxa. The use of potentially informative characters (PICS) as a measure of how informative a region will be for phylogenetic analyses has been previously reported beneficial in cpDNA regions and it clearly was important in this research. This will allow selecting the region(s), which can be used in phylogenetic studies with higher number of taxa.

Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution

1998 ◽  
Vol 46 (5) ◽  
pp. 419 ◽  
Author(s):  
D. J. Colgan ◽  
A. McLauchlan ◽  
G. D. F. Wilson ◽  
S. P. Livingston ◽  
G. D. Edgecombe ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Histone H3 ◽  
Gc Content ◽  
Length Difference ◽  
Partitioned Data ◽  
Cladistic Analyses ◽  
Group Relationships ◽  
Incongruence Length Difference ◽  
Significant Support ◽  
Basal Position

The range of DNA sequences used to study the interrelationships of the major arthropod groups (chelicerates, myriapods, hexapods and crustaceans) is limited. Here we investigate the value of two genes not previously employed in arthropod phylogenetics. Histone H3 data were collected for 31 species and small nuclear ribonucleic acid U2 data for 29 species. The sequences provided a total of 460 sites and 192 parsimony-informative characters. H3 analyses showed substantial codon usage bias, but had a low consistency index (0.26). Consistency indices were higher for the U2 data (0.49), suggesting that the class of snRNAs may provide several phylogenetically useful genes. The present data are not by themselves sufficient to clarify major arthropod group relationships. Partitioned data for H3 and U2 are incongruent according to Incongruence Length Difference tests. Although the most parsimonious trees, based on combined analyses of all taxa, differ substantially from morphology-based trees, anomalous groupings are weakly supported with only one exception. The trees uphold monophyly of Onychophora, Branchiopoda, and Malacostraca (rather than the rival Phyllopoda). Cladistic analyses constraining the monophyly of morphologically defined classes do not significantly distinguish between the main rival hypotheses of major clade relationships. Combined (‘spliced’) analysis of both genes improves topological congruence with morphological groupings relative to that of either partition. Character congruence between H3, U2, and morphology is increased by downweighting (but not excluding) transitions and third codons. Analyses of four-taxon statements using PHYLTEST found significant support for the basal position of the Crustacea among the euarthropods. This support may be due to the similarity of chelicerates, myriapods and hexapods in percentage GC content.

scholarly journals A Comprehensive Analysis of the Phylogenetic Signal in Ramp Sequences in 211 Vertebrates

2020 ◽  
Author(s):  
Lauren M. McKinnon ◽  
Justin B. Miller ◽  
Michael F. Whiting ◽  
John S.K. Kauwe ◽  
Perry G. Ridge
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Signal ◽  
Comprehensive Analysis ◽  
P Value ◽  
Chi Square ◽  
Random Chance ◽  
Binary Character ◽  
Chi Square Analysis ◽  
Translational Speed ◽  
Speed And Accuracy

AbstractBackgroundRamp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented.MethodsRamp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene.ResultsParsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a p-value of approximately zero as compared to random chance.DiscussionRamp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.

scholarly journals Phylogenetics analysis of TP53 gene in humans and its use in biosensors for breast cancer diagnosis

2020 ◽  
Author(s):  
Sara da Silva Nascimento ◽  
Pierre Teodósio Félix
Keyword(s):  
Breast Cancer ◽  
Maximum Likelihood ◽  
Cancer Diagnosis ◽  
Direct Detection ◽  
Phylogenetic Signal ◽  
Neighbor Join ◽  
Breast Cancer Diagnosis ◽  
Tp53 Gene ◽  
Indirect Detection ◽  
Human Populations

AbstractBiosensors are small devices that use biological reactions to detect target analytes. Such devices combine a biological component with a physical transducer, which converts bio-recognition processes into measurable signals. Its use brings a number of advantages, as they are highly sensitive and selective, relatively easy in terms of development, as well as accessible and ready to use. Biosensors can be of direct detection, using a non-catalytic ligand, such as cell receptors and antibodies, or indirect detection, in which there is the use of fluorescently marked antibodies or catalytic elements, such as enzymes. They also appear as bio-affinity devices, depending only on the selective binding of the target analyte to the ligative attached to the surface (e.g., oligonucleotide probe). The objectives were to evaluate the levels of genetic diversity existing in fragments of the TP53 gene deposited in molecular databases and to study its viability as a biosensor in the detection of breast cancer. The methodology used was to recover and analyze 301 sequences of a fragment of the TP53 gene of humans from GENBANK, which, after being aligned with the MEGA software version 6.06, were tested for the phylogenetic signal using TREE-PUZZLE 5.2. Trees of maximum likelihood were generated through PAUP version 4.0b10 and the consistency of the branches was verified with the bootstrap test with 1000 pseudo-replications. After aligning, 783 of the 791 sites remained conserved. The maximum likelihood had a slight manifestation since the gamma distribution used 05 categories + G for the evolutionary rates between sites with (0.90 0.96, 1.00, 1.04 and 1.10 substitutions per site). To estimate ML values, a tree topology was automatically computed with a maximum Log of −1058,195 for this calculation. All positions containing missing gaps or data were deleted, leaving a total of 755 sites in the final dataset. The evolutionary history was represented by consensus trees generated by 500 replications, which according to neighbor-join and BioNJ algorithms set up a matrix with minimal distances between haplotypes, corroborating the high degree of conservation for the TP53 gene. GENE TP53 seems to be a strong candidate in the construction of Biosensors for breast cancer diagnosis in human populations.

scholarly journals A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lauren M. McKinnon ◽  
Justin B. Miller ◽  
Michael F. Whiting ◽  
John S. K. Kauwe ◽  
Perry G. Ridge
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Signal ◽  
P Value ◽  
Chi Square ◽  
Random Chance ◽  
Binary Character ◽  
The Mean ◽  
Presence And Absence ◽  
Chi Square Analysis ◽  
Translational Speed

AbstractRamp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals.

scholarly journals Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets

2017 ◽  
Author(s):  
Xiaofan Zhou ◽  
Xingxing Shen ◽  
Chris Todd Hittinger ◽  
Antonis Rokas
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Signal ◽  
Single Gene ◽  
Gene Tree ◽  
Species Tree ◽  
Data Matrix ◽  
Systematic Evaluation ◽  
Data Sets ◽  
Tree Inference ◽  
Data Matrices

AbstractPhylogenetics has witnessed dramatic increases in the sizes of data matrices assembled to resolve branches of the tree of life, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these four programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets from diverse animal, plant, and fungal lineages with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation–based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the relative performance of the programs. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses.

scholarly journals Unraveling the Olfactory Biases of Male Euglossine Bees: Species-Specific Antennal Responses and Their Evolutionary Significance for Perfume Flowers

2021 ◽  
Vol 9 ◽  
Author(s):  
Katharina Brandt ◽  
Stefan Dötterl ◽  
Santiago R. Ramírez ◽  
Florian Etl ◽  
Isabel Cristina Machado ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Chemical Compounds ◽  
Species Level ◽  
Evolutionary Significance ◽  
Euglossine Bees ◽  
Specific Chemical ◽  
Antennal Response ◽  
Euglossine Bee ◽  
Species Specific ◽  
Antennal Responses

Male euglossine bees exhibit unique adaptations for the acquisition and accumulation of chemical compounds from “perfume flowers” and other sources. During courtship display, male bees expose perfume mixtures, presumably to convey species-specific recognition and/or mate choice signals to females. Because olfaction regulates both signal production (in males) and signal detection (in females) in this communication system, strong selective pressures are expected to act on the olfactory system, which could lead to sensory specialization in favor of an increased sensitivity to specific chemical compounds. The floral scents of euglossine-pollinated plants are hypothesized to have evolved in response to the preexisting sensory biases of their male euglossine bee pollinators. However, this has never been investigated at the peripheral olfactory circuitry of distinct pollinating genera. Here, we present a comparative analysis using electroantennography (EAG) of males across the phylogeny of 29 euglossine bee species, among them Euglossa and Eulaema species. First, we tested whether antennal responses differ among different euglossine genera, subgenera and species. Secondly, we conducted a comparative phylogenetic analysis to investigate the macroevolutionary patterns of antennal responses across the euglossine bee phylogeny. We found that antennal response profiles are very unique on the species level and differ on the subgenus and the genus level. The differences can be explained by chemical compounds typically found in the floral scent bouquets of perfume flowers and specific compounds of species either pollinated by Euglossa (e.g., ipsdienol) or Eulaema bees (e.g., (−)-(E)-carvone epoxide). Also, we detected a phylogenetic signal in mean antennal responses and found that especially at the species level of our simulation the overall antennal responses exhibit greater disparity relative to a null model of pure Brownian-motion across the phylogeny. Altogether, our results suggest that (1) euglossine bee species exhibit species-specific antennal responses that differ among euglossine genera and subgenera, (2) antennal responses diverge early after speciation events, and (3) scent composition of perfume flowers evolved in response to pollinator-mediated selection imposed by preexisting sensory biases in euglossine bees.

scholarly journals Extinction rates of non-avian dinosaur species are uncorrelated with the rate of evolution of phylogenetically informative characters

2020 ◽  
Vol 16 (6) ◽  
pp. 20200231 ◽  
Author(s):  
Nicholas M. A. Crouch
Keyword(s):  
Species Diversity ◽  
Temporal Variation ◽  
Environmental Conditions ◽  
Morphological Evolution ◽  
Phylogenetic Signal ◽  
Species Level ◽  
Common Mechanism ◽  
Phenotypic Evolution ◽  
Extinction Rates ◽  
Prior Expectation

Determining the factors that shape temporal variation in species diversity is an ongoing challenge. One theory is that species exhibiting lower rates of phenotypic evolution should be more likely to go extinct as they are more susceptible to changing environmental conditions. However, little work has been done to assess whether this process shapes comparatively few lineages, or is a common mechanism shaping changes in species diversity. Here, I analyse the correlation between rates of morphological evolution and extinction at the species level using six published morphological matrices of non-avian dinosaurs. I find no correlation between the two rates at different taxonomic scales, suggesting that extinction in these groups is better described by other factors. As there is a strong prior expectation of correlated rates, I suggest that traditional morphological matrices are inappropriate for addressing this question and that the characters governing lineage persistence are independent of those with high phylogenetic signal. This may be comprehensively determined with continued development of phenomic matrices.

scholarly journals The Utility of the Incongruence Length Difference Test

2002 ◽  
Vol 51 (4) ◽  
pp. 625-637 ◽  
Author(s):  
F. Keith Barker ◽  
François M. Lutzoni
Keyword(s):  
Length Difference ◽  
Difference Test ◽  
Incongruence Length Difference
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