scholarly journals Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

2017 ◽  
Vol 13 (9) ◽  
pp. 20170393 ◽  
Author(s):  
Jeffrey W. Streicher ◽  
John J. Wiens
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Species Tree ◽  
Sister Relationship ◽  
Weak Support ◽  
Terrestrial Vertebrates ◽  
Squamate Reptiles ◽  
Tree Methods ◽  
Nuclear Loci ◽  
Phylogenomic Analyses

Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.

scholarly journals Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

2012 ◽  
Vol 8 (6) ◽  
pp. 1043-1046 ◽  
Author(s):  
John J. Wiens ◽  
Carl R. Hutter ◽  
Daniel G. Mulcahy ◽  
Brice P. Noonan ◽  
Ted M. Townsend ◽  
...  
Keyword(s):  
Large Scale ◽  
Sister Group ◽  
Molecular Data ◽  
Base Pairs ◽  
Terrestrial Vertebrates ◽  
Squamate Reptiles ◽  
Tree Methods ◽  
Molecular Dataset ◽  
Diverse Groups ◽  
First Time

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.

scholarly journals Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

2020 ◽  
Author(s):  
Daniel M Portik ◽  
John J Wiens
Keyword(s):  
Missing Data ◽  
Molecular Phylogenetics ◽  
Species Tree ◽  
Sequence Length ◽  
Data Sets ◽  
Full Data ◽  
Tree Methods ◽  
Phylogenomic Analyses ◽  
Alignment Errors ◽  
The Impact

Abstract Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($\sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several “best practices” for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming]

scholarly journals Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

2020 ◽  
Vol 70 (1) ◽  
pp. 49-66 ◽  
Author(s):  
Paul M Hime ◽  
Alan R Lemmon ◽  
Emily C Moriarty Lemmon ◽  
Elizabeth Prendini ◽  
Jeremy M Brown ◽  
...  
Keyword(s):  
Tree Species ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Strong Support ◽  
Species Tree ◽  
Tree Of Life ◽  
Lineage Sorting ◽  
Sister Relationship ◽  
Gene Tree Discordance

Abstract Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]

scholarly journals Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12691
Author(s):  
Jiajia Wang ◽  
Yu Bai ◽  
Haifeng Zhao ◽  
Ruinan Mu ◽  
Yan Dong
Keyword(s):  
Positive Selection ◽  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Taxon Sampling ◽  
And Topology ◽  
Tree Inference ◽  
Abundant Taxon ◽  
New Perspective ◽  
Phylogenomic Analyses

Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda—Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes’ identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.

scholarly journals An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Alexandros Vasilikopoulos ◽  
Bernhard Misof ◽  
Karen Meusemann ◽  
Doria Lieberz ◽  
Tomáš Flouri ◽  
...  
Keyword(s):  
Sister Group ◽  
Molecular Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Character State ◽  
Terrestrial Environment ◽  
Weak Support ◽  
Sequencing Technologies ◽  
Phylogenomic Analyses ◽  
Key Aspects

Abstract Background The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations. Results Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera. Conclusion Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.

Molecular phylogeny of the Annelida

2000 ◽  
Vol 78 (11) ◽  
pp. 1873-1884 ◽  
Author(s):  
Damhnait McHugh
Keyword(s):  
Molecular Analysis ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Nuclear Gene ◽  
Sister Group ◽  
The Body ◽  
Sister Group Relationship ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Sister Relationship

Traditionally, the Annelida has been classified as a group comprising the Polychaeta and the Clitellata. Recent phylogenetic analyses have led to profound changes in the view that the Annelida, as traditionally formulated, is a natural, monophyletic group. Both molecular and morphological analyses support placement of the Siboglinidae (formerly the Pogonophora) as a derived group within the Annelida; there is also evidence, based on molecular analysis of the nuclear gene elongation factor-1α, that the unsegmented echiurids are derived annelids. While monophyly of the Clitellata is well-supported by both molecular and morphological analyses, there is no molecular evidence to support monophyly of the polychaete annelids; the Clitellata fall within a paraphyletic polychaete grade. Relationships among groups of polychaete annelids have not yet been resolved by molecular analysis. Within the Clitellata, paraphyly of the Oligochaeta was indicated in a phylogenetic analysis of cytochrome c oxidase I, which supported a sister relationship between the leeches, including an acanthobdellid and a branchiobdellid, and two of the four oligochaetes in the analysis. There is some evidence from analysis of 18S rRNA sequences for a sister-group relationship between the clitellates and the taxon Aeolosoma. There is no agreement regarding the body form of the basal annelid, and while molecular analyses provide strong support for the Eutrochozoa, the identity of sister-group to the Annelida among the Eutrochozoa remains enigmatic. It is recommended that future investigations include additional conserved gene sequences and expanded taxon sampling. It is likely that the most productive approach to resolving annelid phylogeny, and thus increasing our understanding of annelid evolution, will come from combined analyses of several gene sequences.

The Demand For Money in Pakistan: Reply (Notes and Comments)

1975 ◽  
Vol 14 (3) ◽  
pp. 370-375
Author(s):  
M. A. Akhtar
Keyword(s):  
Interest Rates ◽  
Money Demand ◽  
Strong Support ◽  
Physical Capital ◽  
Careful Examination ◽  
Demand For Money ◽  
Weak Support ◽  
Complementarity Hypothesis ◽  
The Difference ◽  
The One

I am grateful to Abe, Fry, Min, Vongvipanond, and Yu (hereafter re¬ferred to as AFMVY) [1] for obliging me to reconsider my article [2] on the demand for money in Pakistan. Upon careful examination, I find that the AFMVY results are, in parts, misleading and that, on the whole, they add very little to those provided in my study. Nevertheless, the present exercise as well as the one by AFMVY is useful in that it furnishes us with an opportunity to view some of the fundamental problems involved in an empi¬rical analysis of the demand for money function in Pakistan. Based on their elaborate critique, AFMVY reformulate the two hypo¬theses—the substitution hypothesis and the complementarity hypothesis— underlying my study and provide us with some alternative estimates of the demand for money in Pakistan. Briefly their results, like those in my study, indicate that income and interest rates are important in deter¬mining the demand for money. However, unlike my results, they also suggest that the price variable is a highly significant determinant of the money demand function. Furthermore, while I found only a weak support for the complementarity between money demand and physical capital, the results obtained by AFMVY appear to yield a strong support for that rela¬tionship.1 The difference in results is only a natural consequence of alter¬native specifications of the theory and, therefore, I propose to devote most of this reply to the criticisms raised by AFMVY and the resulting reformulation of the two mypotheses.

scholarly journals Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae)

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 561
Author(s):  
Gavin J. Martin ◽  
Sarah E. Lower ◽  
Anton Suvorov ◽  
Seth M. Bybee
Keyword(s):  
Positive Selection ◽  
Transient Receptor Potential ◽  
Strong Support ◽  
Model Organism ◽  
Receptor Potential ◽  
Guanine Nucleotide Binding Protein ◽  
Weak Support ◽  
Niche Adaptation ◽  
Ideal System ◽  
Phototransduction Pathway

Most organisms are dependent on sensory cues from their environment for survival and reproduction. Fireflies (Coleoptera: Lampyridae) represent an ideal system for studying sensory niche adaptation due to many species relying on bioluminescent communication; as well as a diversity of ecologies. Here; using transcriptomics; we examine the phototransduction pathway in this non-model organism; and provide some of the first evidence for positive selection in the phototransduction pathway beyond opsins in beetles. Evidence for gene duplications within Lampyridae are found in inactivation no afterpotential C and inactivation no afterpotential D. We also find strong support for positive selection in arrestin-2; inactivation no afterpotential D; and transient receptor potential-like; with weak support for positive selection in guanine nucleotide-binding protein G(q) subunit alpha and neither inactivation nor afterpotential C. Taken with other recent work in flies; butterflies; and moths; this represents an exciting new avenue of study as we seek to further understand diversification and constraint on the phototransduction pathway in light of organism ecology.

Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

2014 ◽  
Vol 81 ◽  
pp. 221-231 ◽  
Author(s):  
R. Alexander Pyron ◽  
Catriona R. Hendry ◽  
Vincent M. Chou ◽  
Emily M. Lemmon ◽  
Alan R. Lemmon ◽  
...  
Keyword(s):  
Species Tree ◽  
Tree Methods

Generations and Aging: A Longitudinal Study

1975 ◽  
Vol 6 (2) ◽  
pp. 85-101 ◽  
Author(s):  
Jay Meddin
Keyword(s):  
Longitudinal Study ◽  
Survey Data ◽  
Age Differences ◽  
Secondary Analysis ◽  
Strong Support ◽  
Weak Support ◽  
Theories Of Aging ◽  
Longitudinal Investigation ◽  
Values And Beliefs ◽  
The Relationship

This study is a longitudinal investigation of the relationship between age and subjective outlook. Over the years, a number of theoretical positions have been introduced to either account for or to minimize age differences in attitudes, values and beliefs. The author has organized these theories of aging into three basic sociological frameworks or models: the “generations” model, the “age status” model and the “illusion of differences” model. Using a relatively simple methodological design, hypotheses derived from these models were tested through secondary analysis of survey data. Strong support was found for the “generations” hypothesis, weak support for the “age status” hypothesis, and no support at all for the “illusion of differences” hypothesis.

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