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Most people use genetic relatedness when constructing phylogenies today. People in the field understand species labels are just discrete terms. Some fields like

Most people use genetic relatedness when constructing phylogenies today. People in the field understand species labels are just discrete terms. Some fields like metagenomics don’t even consider the species much and group things by genus or some higher level instead because of the difficulty of defining this stuff. Not to mentioned most of what you sample using metagenomics is going to be a population pool (think someone extracting dna out of soil or stool, there’s billions of organisms you are sampling potentially in that one sample). You start to think less of “do i have this organism and what does this mean” and more “what gene sequences am I detecting out of this pool and what does this mean for the resulting proteins being released in the environment and what that does”

ak217 3y ago
Yep - metagenomics/phylogenomics practitioners have learned the hard way that trying to focus on species definitions gets you nowhere (if you think defining a species in multicellular sexually reproducing eukaryotes is hard, wait till you see what bacteria do - it's basically a free-for-all; and on top of that, short read metagenetic DNA sequencing gives you a soup of DNA that is very hard to precisely partition by source). I consider the focus on species and speciation to be a science social phenomenon more than anything else, a lot of it attributable to the prestige of being the one to "discover" the species (a.k.a. describe it in a way that sticks). The flipside is that the science of phylogenomics is incredibly fruitful, in that as we collect more complete information about genomes and their diversity and patterns of conservation, we are able to better understand life in all of its forms. It's also very data intensive and computationally complex - some of the most sophisticated data compression, suffix tree construction, hashing, and clustering algorithms are used in this field. An unsung group of heroes in the face of this insane complexity is the scientists at NCBI whose job it is to organize all of the taxonomic and reference genetic/genomic sequence information (they are the ones who build the GenBank, RefSeq, and NCBI Taxonomy databases). Their work is as close as it comes to the source of truth on this. While the GenBank FTP server is easily overwhelmed by modern workloads trying to ingest this data, AWS and GCP provide high throughput mirrors (https://aws.amazon.com/opendata/ https://aws.amazon.com/opendata/, s3://ncbi-blast-databases, gs://blast-db).

ak217 3y ago

Yep - metagenomics/phylogenomics practitioners have learned the hard way that trying to focus on species definitions gets you nowhere (if you think defining a species in multicellular sexually reproducing eukaryotes is hard, wait till you see what bacteria do - it's basically a free-for-all; and on top of that, short read metagenetic DNA sequencing gives you a soup of DNA that is very hard to precisely partition by source). I consider the focus on species and speciation to be a science social phenomenon more than anything else, a lot of it attributable to the prestige of being the one to "discover" the species (a.k.a. describe it in a way that sticks). The flipside is that the science of phylogenomics is incredibly fruitful, in that as we collect more complete information about genomes and their diversity and patterns of conservation, we are able to better understand life in all of its forms. It's also very data intensive and computationally complex - some of the most sophisticated data compression, suffix tree construction, hashing, and clustering algorithms are used in this field. An unsung group of heroes in the face of this insane complexity is the scientists at NCBI whose job it is to organize all of the taxonomic and reference genetic/genomic sequence information (they are the ones who build the GenBank, RefSeq, and NCBI Taxonomy databases). Their work is as close as it comes to the source of truth on this. While the GenBank FTP server is easily overwhelmed by modern workloads trying to ingest this data, AWS and GCP provide high throughput mirrors (https://aws.amazon.com/opendata/ https://aws.amazon.com/opendata/, s3://ncbi-blast-databases, gs://blast-db).