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J Phycol. 2018 Oct;54(5):703-719. doi: 10.1111/jpy.12767. Epub 2018 Aug 28.

Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1.

Author information

1
Section Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
2
British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
3
División Ficología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n (B1900FWA), La Plata, Argentina.
4
Research School of Earth Sciences, The Australian National University, Jaeger Building 4, 142 Mills Road, Acton, ACT, 2601, Australia.
5
Departamento de Geología, Universidad de Salamanca, 37008, Salamanca, Spain.
6
UMR-CNRS 5805 EPOC, Université de Bordeaux, Allée Geoffroy Saint Hilaire, 33615, Pessac Cedex, France.
7
Section Marine Geology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
8
Department of Earth & Environmental Sciences, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, 990-8560, Japan.
9
Bioinformatics, University of Applied Sciences, Constantiaplatz 4, 26723, Emden, Germany.
10
Geology Department, Colgate University, Hamilton, New York, 13346, USA.
11
School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK.
12
Área de Paleontología, Departamento de Geología, Universidad de Salamanca, 37008, Salamanca, Spain.

Abstract

Semiautomated methods for microscopic image acquisition, image analysis, and taxonomic identification have repeatedly received attention in diatom analysis. Less well studied is the question whether and how such methods might prove useful for clarifying the delimitation of species that are difficult to separate for human taxonomists. To try to answer this question, three very similar Fragilariopsis species endemic to the Southern Ocean were targeted in this study: F. obliquecostata, F. ritscheri, and F. sublinearis. A set of 501 extended focus depth specimen images were obtained using a standardized, semiautomated microscopic procedure. Twelve diatomists independently identified these specimen images in order to reconcile taxonomic opinions and agree upon a taxonomic gold standard. Using image analyses, we then extracted morphometric features representing taxonomic characters of the target taxa. The discriminating ability of individual morphometric features was tested visually and statistically, and multivariate classification experiments were performed to test the agreement of the quantitatively defined taxa assignments with expert consensus opinion. Beyond an updated differential diagnosis of the studied taxa, our study also shows that automated imaging and image analysis procedures for diatoms are coming close to reaching a broad applicability for routine use.

KEYWORDS:

SHERPA ; Bacillariophyta; automatic diatom identification; high throughput microscopy; image analysis; morphometrics; taxonomic agreement

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