What is the species hypothesis?

[Y Soun]

What is the species hypothesis? Is it a new hypothesis or an old one?

[Fazil Hussein]

Here is an answer from Bard:

The Species Hypothesis as Operational Taxonomic Unit (OTU) is a relatively recent approach in ecology and environmental studies that uses DNA sequences to group organisms into putative species. Here’s how it works:

– DNA Sequencing: Researchers collect environmental samples, such as soil or seawater, and extract DNA from all the organisms present (without necessarily knowing what they are).
– Clustering: They then sequence a specific DNA region (often a “barcode” gene) for each organism and use computer algorithms to cluster these sequences based on their similarity.
– OTU Definition: A threshold of similarity is chosen (e.g., 97% for bacteria, 95% for fungi). Sequences that are more similar than this threshold are grouped into the same OTU, which is assumed to represent a single species under the species hypothesis.
– Species Inference: While acknowledging limitations, researchers interpret each OTU as a potential species, even if it hasn’t been formally described or confirmed through traditional taxonomic methods.

This approach has several advantages:

– Speed and Scalability: It allows researchers to quickly and efficiently assess species diversity in complex environments with many unknown organisms.
– Standardization: OTUs provide a standardized way to compare data across different studies and ecosystems, even when dealing with unidentified species.
– Hypothesis Generation: By identifying distinct OTUs, the species hypothesis can guide further research efforts to formally describe and characterize these potential new species.

[K. Raji]

The Species Hypothesis (SH) is a concept used in the field of biology, particularly in the study of Eukaryotes. It refers to any species-level group of individuals that share a given set of observed characters. In the context of DNA sequencing, these are sequences that share a given level of similarity, also known as operational taxonomic units (OTUs).

Each Species Hypothesis has a unique accession code, for example, SH037970.06FU, where SH translates into Species Hypothesis and is followed by a unique number, full stop, version number, and taxon acronym (FU for Fungi). The full name of the Species Hypothesis includes the Latin (or other) name given to the sequence, the SH accession code, the similarity level at which the SH was designated, and the INSDC/UNITE (nucleotide/fungal databases) accession number of the representative/reference sequence.

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