Post-molecular systematics and the future of phylogenetics

Pyron, R. Alexander

doi:10.1016/j.tree.2015.04.016

Cited by 94 publications

(77 citation statements)

References 85 publications

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“…However, in many cases, the backbone of phylogenetic trees may be less resolved or poorly supported, perhaps due to evolutionary processes such as recombination, hybridization, or a lack of critical phylogenetic signal at varying depths within the evolutionary history of the organisms being investigated. Therefore, many single‐ or low‐copy nuclear genes harboring phylogenetic signals useful at different phylogenetic depths are required to represent underlying evolutionary patterns and processes (Salichos and Rokas, ; Wickett et al., ; Pyron, ; Zimmer and Wen, ).…”

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confidence: 99%

Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

et al. 2018

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Premise of the StudyThe development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts.MethodsUsing 30 transcriptomes, we compared Hyb‐Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation‐ and coalescent‐based methods.ResultsHyb‐Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony‐informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics.ConclusionsMethods differed across criteria important for phylogenetic marker development. We recommend Hyb‐Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community‐driven efforts to reconstruct the legume tree of life.

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Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

et al. 2018

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“…Considering the paucity of anatomical studies, the importance of anatomy to performance (Herrel et al. ), and the continued need for detailed morphological data (Pyron, ), investigations describing and especially quantifying the musculature of snakes are desperately needed to better understand their evolution, function, and diversity.…”

Section: Introductionmentioning

confidence: 99%

Quantitative axial myology in two constricting snakes:Lampropeltis holbrookiandPantherophis obsoletus

Penning

2018

Journal of Anatomy

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A snake's body represents an extreme degree of elongation with immense muscle complexity. Snakes have approximately 25 different muscles on each side of the body at each vertebra. These muscles serially repeat, overlap, interconnect, and rarely insert parallel to the vertebral column. The angled muscles mean that simple measurements of anatomical cross-sectional area (ACSA, perpendicular to the long-axis of the body) serve only as proxies for the primary determinant of muscle force, physiological cross-sectional area (PCSA, area perpendicular to the muscle fibers). Here, I describe and quantify the musculature of two intraguild constrictors: kingsnakes (Lampropeltis holbrooki) and ratsnakes (Pantherophis obsoletus) whose predation performance varies considerably. Kingsnakes can produce significantly higher constriction pressures compared with ratsnakes of similar size. In both snakes, I provide qualitative descriptions, detail previously undescribed complexity, identify a new lateral muscle, and provide some of the first quantitative measures of individual muscle and whole-body PCSA. Furthermore, I compare measurements of ACSA with measurements of PCSA. There was no significant difference in PCSA of muscles between kingsnakes and ratsnakes. There is, however, a strong relationship between ACSA and PCSA measurements. I could not identify a significant difference in musculature between kingsnakes and ratsnakes that explains their different levels of constriction performance. Unmeasured components of muscle function, such as endurance and force production, might account for differences in performance between two species with similar muscle structure.

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“…It is possible that one nuclear and five chloroplast 628 markers are not enough to detect coalescent speciation events, at 629 least in Otatea. However, the use of morphology in combination 630 with molecular data for the non-parametric analysis increased 631 the nodal support for the phylogenetic tree(Pyron, 2015). In the 632 other hand, the morphological approaches should be necessary633 for the description of new species(Fujita et al, 2012).…”

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confidence: 99%

Parametric and non-parametric species delimitation methods result in the recognition of two new Neotropical woody bamboo species

Ruíz-Sánchez

2015

Molecular Phylogenetics and Evolution

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Post-molecular systematics and the future of phylogenetics

Cited by 94 publications

References 85 publications

Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

Quantitative axial myology in two constricting snakes:Lampropeltis holbrookiandPantherophis obsoletus

Parametric and non-parametric species delimitation methods result in the recognition of two new Neotropical woody bamboo species

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