For insect diversity comparisons, I plan to capture, count and identify all insects found/trapped. I haven't started with the counts yet, but are currently exploring the possibilities. I have read much about all different techniques to measure, compare, extrapolate, rarefy etc to analyse the data - which is great! The only problem is that I'll try to identify all individuals to species level, but probably won't be able to (therefore assigned it as precise as possible, for example to genus). As far as I know, all the methods (like Shannon entropy, Chao, Simpsons, Richness etc) are based on the fact that all the individuals are based on the same taxonomic level, right? Am I obligated to "downgrade" all my identification data to the lowest taxa available (for example pool all species to their associated genus level)? Or is it also possible to analyse diversity with OTU's of different levels? Thanks in advance!
I'd say it depends on what question you're trying to answer.
If you want to know how diverse a set of species you have, use species level. They don't have to be identified to a specific name, as long as you know which individuals belong to the same species (i.e. you can use morphospecies such as A. armata n.sp.).
If you can't divide your insects into species (named or not), then you'll probably have to pool the data to genus level. This then answers the question "How diverse a set of genera do I have?".
Mixing species and genera won't really work, because then you're answering the question "how diverse a set of species OR genera do I have, where it depends on my identification skills whether I used species or genus". Although you'd get a number as a result, it wouldn't really mean anything.
One option might be to identify some orders to species, and others to genus. For example, you could report the species diversity of Hymenoptera, and the genus diversity of Orthoptera. Then compare Orthoptera to Orthoptera and Hymenoptera to Hymenoptera.
If you register at https://www.inaturalist.org and submit very clear, close up photos of each of your insects to their website...they have a computer image id function that can probably get your insects to genus and maybe also to species--and then there are groups of experts that can confirm the id for you, so that each of your submissions become "research grade".
BEST method to id any living organism on the planet--give it a test try, then when you do your study, you will know how to work with their system.
The only thing you need to know is the Lat./Long. coordinates...of wherever you capture your specimens in digital format, and to a high degree, like 3-4 decimal places. Like for one site I work at, my coordinates are 37.4414 and -122.2536.
If you do not have GPS, download Google Earth and get the coordinates that way?
Hello Peter,
Can you use the morpho-species concept? e.g.: https://www.jstor.org/stable/pdf/2388960.pdf?refreqid=excelsior%3A2e8245bdab8ed8c86d8d0a4b25b426bb
Just try the iNaturalist method for ID...and at least get to genus that way. Then you can use whatever mathematics to work out the details?
Thank you for you suggestions. They are really helpful for identifying my samples more accurately and will definitely use them later on. I do understand that more accurate identification will aid more value to my results and analysis and my plan is to do so. However, my question is if community analyses are allowed if not all individuals are identified to the same taxonomic level. For example, converting the Shannon index to a true diversity is measured in units of (effective) number of species. If the calculation of this index is based on 50 species taxa en 10 genus taxa, I can image that we cannot say anything about the effective number of species after converting the index, because the it was also based on a few individuals which were not further identified then genus. Therefore, these 10 genus taxa could in reality be 30 distinct species taxa. So my question is how can I (statistically) adjust for the fact that my data will not only contain species, but also a few other taxonomic levels. One solution which I can think of is pooling all the species in a genus to one genus taxa, then do the calculations on genus taxa only and end up with a result measured in (effective) number of genera. But this would mean I have to through away my data of the species, ending up with less data (lets say the 50 species taxa are then pooled to 20 genus taxa). The data to illustrate the spadeR package (SimilarityPairData, http://chao.stat.nthu.edu.tw/wordpress/wp-content/uploads/software/SpadeR_Package_Introduction.pdf) seems to have many unidentified species combined with identified species in one dataset (see attached image, sp and spp). Therefore I would expect that you are allowed to perform community analyses on a dataset where not all individuals could be identified to species level, and thus ending up with different taxa in one dataset. Can anyone confirm this? And also, is the if the calculations are based on different taxa, in which unit of measure is my true diversity (converted Shannon index)? Hope this makes my question clearer.
See what you can do with the photos of each individual insect on iNaturalist first, and maybe try and get all of your specimens to genus first, then see where you need to go with the data after that? INaturalist is pretty good with plants and birds, getting them to species, but maybe only get your insects to genus for you?
You can apply statistics at your convenience, low or higher taxonomical level. I use to study OTUs in marine zooplankton and sometimes I have the same issue. Obviously, using the lowest taxonomic level is encouraged. Alternatively, you can use functional groups (assuming that it is interesting to you) instead of taxonomic levels.
I'd say it depends on what question you're trying to answer.
If you want to know how diverse a set of species you have, use species level. They don't have to be identified to a specific name, as long as you know which individuals belong to the same species (i.e. you can use morphospecies such as A. armata n.sp.).
If you can't divide your insects into species (named or not), then you'll probably have to pool the data to genus level. This then answers the question "How diverse a set of genera do I have?".
Mixing species and genera won't really work, because then you're answering the question "how diverse a set of species OR genera do I have, where it depends on my identification skills whether I used species or genus". Although you'd get a number as a result, it wouldn't really mean anything.
One option might be to identify some orders to species, and others to genus. For example, you could report the species diversity of Hymenoptera, and the genus diversity of Orthoptera. Then compare Orthoptera to Orthoptera and Hymenoptera to Hymenoptera.
Hi Peter,
Yes, whatever you are analyzing should all be at the same taxonomic level. Otherwise comparisons make no sense. You have two options if you can only identify a particular group of specimens to genus. 1. You can either view all the specimens in that particular genus as the same species, which means you would lose a lot of diversity information if there are multiple species within that group. 2. You can separate the individuals in that genus into subgroups based on their morphology. It's not uncommon with insects to have some specimens only identified to morphospecies because of the difficulty of identifying certain groups. You don't have to know the names, you just need to know they're different from others in that genus. We study native bee diversity and species in a couple genera are difficult to identify. So some of the species in that genus will be specifically identified to species and others only identified as, for example, Lasioglossum sp. 1, Lasioglossum sp. 2, etc.
And of course you could also identify all at the level of genera, or family, etc. Wouldn't have to be at the species level, but regardless of the taxonomic level decided on, all specimens being analyzed should be assessed at that common level of taxonomy.
There is also help program MorphoJ. It is designed for insects, but it is possible to work with any biological objects. The main thing is to choose the right matrix for the job. Regards, Pushkin Sergey Viktorovich
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