Thanks for all the great comments and/or publications. Following is a list of all the comments and publications. If this list spurs more thoughts, comments and recommended publications, awesome! -- Ed
It seems like you are talking about a statistically rare species with respect to a sample. I would recommend looking at McCune and Grace's Analysis of Ecological Communities. Of course, there are many cases (eg. calculation of species richness, evenness or diversity measures) when you would not want to delete any rare species. The removal of rare taxa, at least in my view, is more a statistical thing than an ecological thing. What I mean is the taxa are removed to avoid skewing a site based on a small number of taxa. There are different ways to define rare. In my own work, some species are legitimately rare, others are made rarer by disturbance, and some are database-rare, meaning that we simply didn't identify or encounter it often. What do these things mean? In practice, maybe much the same, but the question is whether you're trying to detect rare things or not. If so, dropping them from analysis makes little sense. I use ordination a lot, and that technique does really poorly with zeros (non-occurrence records) in the dataset. I frequently will combine taxa to a higher level (genera) or maybe even functional type. That frequently helps with my analyses by making fewer analytical objects (columns in the database). I don't have any great references for this, but Bruce McCune has talked about this I know. I define rare as <1% relative read abundance in any one sample (speaking in OTU language). In microbiome research, singletons or taxa <1% relative read abundance probably aren't having a huge effect on the function of the bacterial community, but then again, some are finding that rarer taxa do have influence on community function... generally speaking they are talking those organisms not "rare" as I define above, but "rarer" meaning not in the "core" microbiome... but there again, everyone defines a core differently... Personally, I say it is context dependent and you have to defend your rationale. ; ) Now that I have thoroughly muddied the waters.... 1.Cao, Y., Williams, D. D. & Williams, N. E. How important are rare species in aquatic community ecology and bioassessment? Limnol. Oceanogr. 43, 1403–1409 (1998). 2.Marchant, R. How important are rare species in aquatic community ecology and bioassessment? A comment on the conclusions of Cao et al. Limnol. Oceanogr. 44, 1840–1841 (1999). 3.Cao, Y. & Williams, D. D. Rare species are important in bioassessment (Reply to the comment by Marchant). Limnol. Oceanogr. 44, 1841–1842 (1999). Cao, Y., Larsen, D. P. & Thorne, R. S.-J. Rare species in multivariate analysis for bioassessment: some considerations. Journal of the North American Benthological Society 20, 144–153 (2001). Jain, M. et al. The importance of rare species: a trait-based assessment of rare species contributions to functional diversity and possible ecosystem function in tall-grass prairies. Ecology and Evolution 4, 104– 112 (2014). Ostermiller, J. D. & Hawkins, C. P. Effects of Sampling Error on Bioassessments of Stream Ecosystems: Application to RIVPACS-Type Models. Journal of the North American Benthological Society 23, 363–382 (2004). Poos, M. S. & Jackson, D. A. Addressing the removal of rare species in multivariate bioassessments: The impact of methodological choices. Ecological Indicators 18, 82–90 (2012). Dorado, J., et al. (2011). "Rareness and specialization in plant– pollinator networks." Ecology 92(1): 19-25. Hopkins, G. W., et al. (2002). "Identifying rarity in insects: the importance of host plant range." Biological Conservation 105(3): 293- 307. Kunin, W. E. and K. J. Gaston, Eds. (1997). The biology of rarity: causes and consequences of rare-common differences. London, Chapman & Hall. Lesica, P., et al. (2006). "Rare plants are common where you find them." Am. J. Bot. 93(3): 454-459. Rabinowitz, D. (1981). Seven forms of rarity. The Biological Aspects of rare Plant Conservation. H. Synge. New York, Wiley: 205-217. Molina, R., Horton, T. R., Trappe, J. M. & Marcot, B. G. Addressing uncertainty: How to conserve and manage rare or little-known fungi. Fungal Ecology 4, 134–146 (2011). Ramirez, K. S. et al. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology 3, 189–196 (2018). Shade, A. & Gilbert, J. A. Temporal patterns of rarity provide a more complete view of microbial diversity. Trends in Microbiology 23, 335–340 (2015). Shade, A., McManus, P. S. & Handelsman, J. Unexpected Diversity during Community Succession in the Apple Flower Microbiome. mBio 4, e00602-12 (2013). Shade, A. et al. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity. mBio 5, e01371-14 (2014).
