Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness

Kuang, Tingyun; Tornabene, Luke; Li, Jingyan; Jiang, Jiamei; Chakrabarty, Prosanta; Sparks, John S.; Naylor, Gavin J. P.; Li, Chenhong

doi:10.1016/j.ympev.2018.07.018

Cited by 37 publications

(35 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S7). Additionally, when compared to other studies, evidence suggests that filtering efficacy is highly idiosyncratic to the data and evolutionary scenarios, and corroborates the difficulty of finding a single method that outperforms the others under all circumstances (Doyle et al 2015;Hosner et al 2016;Meiklejohn et al 2016;Blom et al 2017;Gilbert et al 2018;Kuang et al 2018;Molloy and Warnow 2018).…”

Section: Performance Of Filtering Strategiessupporting

confidence: 60%

“…Based on this observation, it could be argued that filtering the data solely by locus length or %GC is a simpler approach to increase the ratio of phylogenetic to non-phylogenetic signal. However, the relationship between these measures and higher congruency or nodal support is not straightforward, which indicates that different filtering criteria have additional effects, particularly when accounting for saturation or homoplasy (Kuang et al 2018).…”

Section: Performance Of Filtering Strategiesmentioning

confidence: 99%

“…Filtering genes prior to species tree estimation is commonplace in both concatenation and coalescent-based phylogenomic analyses (Doyle et al 2015;Hosner et al 2016;Meiklejohn et al 2016;Streicher et al 2016;Blom et al 2017;Dornburg et al 2017a;Gilbert et al 2018;Kuang et al 2018;Molloy and Warnow 2018). In general, the rationale for these screening criteria is to maximize phylogenetic information while minimizing noise.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting

et al. 2018

Self Cite

View full text Add to dashboard Cite

Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously-and commonly-proposed hypothesis, where the family Apteronotidae was found as the sister group to all other gymnotiform families. In contrast, coalescent-based analyses suggested a novel hypothesis where families producing pulse-type (viz., Gymnotidae, Hypopomidae and Rhamphichthyidae) and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were reciprocally monophyletic.Nodal support for this second hypothesis increased when analyzing loci with the highest phylogenetic information content and further increased when data were pruned using targeted filtering methods that maximized phylogenetic informativeness at the deepest nodes of the Gymnotiformes. Bayesian concordance analyses and topology tests of individual gene genealogies demonstrated that the difficulty of resolving this radiation was likely due to high gene-tree incongruences that resulted from incomplete lineage sorting. We show that data filtering reduces gene tree heterogeneity and increases nodal support and consistency of species Downloaded from https://academic.oup.com/sysbio/advance-article-abstract/doi/10.1093/sysbio/syy085/5232148 by Bukkyo University user on 06 December 20183 trees using coalescent methods; however, we failed to observe the same effect when using concatenation methods. Furthermore, the targeted filtering strategies applied here support the use of "gene data interrogation" rather than "gene genealogy interrogation" approaches in phylogenomic analyses, to extract phylogenetic signal from intractable portions of the Tree of Life.

show abstract

Section: Performance Of Filtering Strategiessupporting

confidence: 60%

Section: Performance Of Filtering Strategiesmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…All five native Hawai'ian freshwater goby species are in the sub‐order Gobioidei and four are in the family Oxudercidae (Kuang et al ., ). Surveys indicate that Lentipes concolor (Kinzie, ) inhabit higher elevation stream reaches, which are achievable because modified pelvic fins allow it to climb waterfalls as high as 100 m (Englund & Filbert, ; Fitzsimmons & Nishimoto, ).…”

Section: Methodsmentioning

confidence: 97%

Migratory flexibility in native Hawai'ian amphidromous fishes

Heim-Ballew

Moody

Blum

et al. 2019

Journal of Fish Biology

View full text Add to dashboard Cite

We assessed the prevalence of life history variation across four of the five native amphidromous Hawai'ian gobioids to determine whether some or all exhibit evidence of partial migration. Analysis of otolith Sr.: Ca concentrations affirmed that all are amphidromous and revealed evidence of partial migration in three of the four species. We found that 25% of Lentipes concolor (n = 8), 40% of Eleotris sandwicensis (n = 20) and 29% of Stenogobius hawaiiensis (n = 24) did not exhibit a migratory lifehistory. In contrast, all individuals of Sicyopterus stimpsoni (n = 55) included in the study went to sea as larvae. Lentipes concolor exhibited the shortest mean larval duration (LD) at 87 days, successively followed by E. sandwicensis (mean LD = 102 days), S. hawaiiensis (mean LD = 114 days) and S. stimpsoni (mean LD = 120 days). These findings offer a fresh perspective on migratory life histories that can help improve efforts to conserve and protect all of these and other at-risk amphidromous species that are subject to escalating anthropogenic pressures in both freshwater and marine environments.

show abstract

“…More sophisticate filtering methods could be developed for controlling the quality of alignments, such as removing loci that are randomly aligned. 25,26 Filtering loci based on whether their gene tree agrees with widely accepted phylogenetic relationship (eg, known monophyletic groups) or other criteria (eg, fit a molecular clock) 27 may also be helpful.…”

Section: Introductionmentioning

confidence: 99%

Assexon: Assembling Exon Using Gene Capture Data

Yuan

Atta

Tornabene

et al. 2019

Evol Bioinform Online

Self Cite

View full text Add to dashboard Cite

Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide phylogenetic spectrum; thus, de novo assembling methods are more generally applied. Current approaches for assembling targeted exons from short reads are not particularly optimized as they cannot (1) assemble loci with low read depth, (2) handle large files efficiently, and (3) reliably address issues with paralogs. Thus, we present Assexon: a streamlined pipeline that de novo assembles targeted exons and their flanking sequences from raw reads. We tested our method using reads from Lepisosteus osseus (4.37 Gb) and Boleophthalmus pectinirostris (2.43 Gb), which are captured using baits that were designed based on genome sequence of Lepisosteus oculatus and Oreochromis niloticus, respectively. We compared performance of Assexon to PHYLUCE and HybPiper, which are commonly used pipelines to assemble ultra-conserved element (UCE) and Hyb-seq data. A custom exon capture analysis pipeline (CP) developed by Yuan et al was compared as well. Assexon accurately assembled more than 3400 to 3800 (20%-28%) loci than PHYLUCE and more than 1900 to 2300 (8%-14%) loci than HybPiper across different levels of phylogenetic divergence. Assexon ran at least twice as fast as PHYLUCE and HybPiper. Number of loci assembled using CP was comparable with Assexon in both tests, while Assexon ran at least 7 times faster than CP. In addition, some steps of CP require the user’s interaction and are not fully automated, and this user time was not counted in our calculation. Both Assexon and CP retrieved no paralogs in the testing runs, but PHYLUCE and Hybpiper did. In conclusion, Assexon is a tool for accurate and efficient assembling of large read sets from exon capture experiments. Furthermore, Assexon includes scripts to filter poorly aligned coding regions and flanking regions, calculate summary statistics of loci, and select loci with reliable phylogenetic signal. Assexon is available at https://github.com/yhadevol/Assexon .

show abstract

Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness

Cited by 37 publications

References 79 publications

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting

Migratory flexibility in native Hawai'ian amphidromous fishes

Assexon: Assembling Exon Using Gene Capture Data

Contact Info

Product

Resources

About