Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies

Wishkerman, Asher; Hamilton, Paul B.

doi:10.1002/aps3.1204

Cited by 23 publications

(17 citation statements)

References 45 publications

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“…Additional descriptive morphological data investigated in previous studies on N. palea were also recorded (Trobajo & Cox, 2006). For analysis of shape outlines, we used Elliptic Fourier Analysis (EFA) which is also implemented in diatom morphometric tools such as DiaOutline (Wishkerman and Hamilton 2018) and SHERPA (Kloster et al 2014). We extracted valve outlines from SEM images using the “Quick Selection” tool of Adobe Photoshop CC 2019 and exported these on a white background.…”

Section: Methodsmentioning

confidence: 99%

Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex

Çiftçi

Alverson

Bodegom

et al. 2022

Preprint

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In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically based taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear-lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Subsequent gene-tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies and a resulting putative recent hybrid. Our study shows that phylogenomic analyses of many unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.

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Section: Methodsmentioning

confidence: 99%

Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex

Çiftçi

Alverson

Bodegom

et al. 2022

Preprint

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“…In the simulation with removing the 1 st PC of global variation from PCA scores of NEFD data, we found the subsequent PCs a bit more equalized in the amount of reflected variation (see S1 Appendix ). In general, the success of automated identification depends on the range of variation in the data [ 62 ]. Therefore, we argue it is essential not to focus on a bold number but rather to be able to disentangle the contribution of separate descriptors to the discriminant model.…”

Section: Discussionmentioning

confidence: 99%

Geometric morphometric analysis of spore shapes improves identification of fungi

2021

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Morphology of organisms is an essential source of evidence for taxonomic decisions and understanding of ecology and evolutionary history. The geometric structure (i.e., numeric description of shape) provides richer and mathematically different information about an organism’s morphology than linear measurements. A little is known on how these two sources of morphological information (shape vs. size) contribute to the identification of organisms when implied simultaneously. This study hypothesized that combining geometric information on the outline with linear measurements results in better species identification than either evidence alone can provide. As a test system for our research, we used the microscopic spores of fungi from the genus Subulicystidium (Agaricomycetes, Basidiomycota). We analyzed 2D spore shape data via elliptic Fourier and principal component analyses. Using flexible discriminant analysis, we achieved the highest species identification success rate for a combination of shape and size descriptors (64.7%). The shape descriptors alone predicted species slightly better than size descriptors (61.5% vs. 59.1%). We conclude that adding geometric information on the outline to linear measurements improves the identification of the organisms. Despite the high relevance of spore traits for the taxonomy of fungi, they were previously rarely analyzed with the tools of geometric morphometrics. Therefore, we supplement our study with an open access protocol for digitizing and summarizing fungal spores’ shape and size information. We propagate a broader use of geometric morphometric analysis for microscopic propagules of fungi and other organisms.

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“…However, they used discriminant analysis as a dimensionality reduction tool and above its result applied other classification techniques. Authors of [66] evaluated their analyses of diatom cell shapes visually, i.e. as strength of separation of observations in the space of discriminant functions.…”

Section: Discussionmentioning

confidence: 99%

Quantitative analysis of spore shapes improves identification of fungi

Ordynets

Keßler

Langer

2021

Preprint

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Morphology of organisms is an important source of evidence for biodiversity assessment, taxonomic decisions, and understanding of evolution. Shape information about zoological and botanical objects is often treated quantitatively and in this form improves species identification. In studies of fungi, quantitative shape analysis was almost ignored. The disseminated propagules of fungi, the spores, are crucial for their taxonomy – currently in the form of linear measurements or subjectively defined shape categories. It remains unclear how much quantifying spore shape information can improve species identification. In this study, we tested the hypothesis that shape, as a richer source of information, overperforms size when performing automated identification of fungal species. We used the fungi of the genus Subulicystidium (Agaricomycetes, Basidiomycota) as a study object. We analysed 2D spore shape data via elliptic Fourier and Principal Component analyses. With flexible discriminant analysis, we achieved a slightly higher species identification success rate for shape predictors (61.5%) than for size predictors (59.1%). However, we achieved the highest rate for a combination of both (64.7%). We conclude that quantifying fungal spore shapes is worth the effort. We provide an open access protocol which, we hope, will stimulate a broader use of quantitative shape analysis in fungal taxonomy. We also discuss the challenges of such analyses that are specific to fungal spores.

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Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies

Cited by 23 publications

References 45 publications

Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex

Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex

Geometric morphometric analysis of spore shapes improves identification of fungi

Quantitative analysis of spore shapes improves identification of fungi

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