This easter I have spent on thinking / writing / editing of an introduction to the paper about smudgeplot - a tool for predicting ploidy and visualization of genome structure. I collaborated on this tool for my own data, I have not really thought through how far it goes, so I started to wonder how many polyploid species are out there. So I asked on Twitter and guess what, so many people have responded to the tweet that I have decided to compile the answers in a blogpost.
polyploidy in exant species
When I originally posted the question. The I actually meant the distribution among extant species. So here is a list of different taxonomical groups (they are bit random, sorry for that):
- Flowering plants
- Meyers & Levin 2007: “Over 70% of all angiosperm species have a ploidal level increase somewhere in their evolutionary histories”
- Red algae
- Varela-Álvarez et al. 2018: Study of three species of Porphyra. “Multiple ploidy levels and genome sizes were found in Porphyra Porphyra species.” and apparently it’s not a simple polyploidy, but it’s a bit messier: “In P. linearis, genetic differentiation was found among three polyploid lineages: triploid, tetraploid and mixoploids, representing different evolutionary units.”
- Novikova et al 2019: three indipendent polyploid species of Australian burrowing frogs in the genus Neobatrachus (9 species seuqenced)
- Goldman and LoVerde 1981: Hybrid origin of polyploidy in freshwater snails from genus Bulinus. Species of Bulinus complex are naturally in diploid, tetraploid, hexaploid and octoploid states.
- Campbell et al. 2016
- Jackson et al. 2018 They have done a whole-genome sequencing of 1,011 Saccharomyces cerevisiae isolates, mixture of wild and domesticated samples. Domesticated isolates exhibit high variation in ploidy, aneuploidy: 11.4% were polyploid (various ploidy levels) and 24.3% of the strains exhibited aneuploidy of at least one chromosome.
- Todd et al. 2016
- Demin et al. 2018 Amoeba proteus and A. borokensis shows something called “Cyclic polyploidy”
- Chen 1940: Polyploidy commonly found in Paramecium bursaria is probably resulting from fusion of more than two pronuclei during conjugation.
- Soppa 2011: “Euryarchaea are typically oligoploid or polyploidy and their genome copy numbers are tightly regulated in response to growth phase and/or growth rate.”
Polyploidy was the ancestral state of many big taxonomical groups we focused on - like two rounds of whole genome duplications1 in vertebrates, bony fishes, vast majority of land plants and likely lot more.
- Li at al. 2017: “evidence for 18 ancient WGDs and at least six other bursts of gene duplication during the evolution of insects.”
- General (two recent reviews):
- Van de Peer et al. 20172
- Blischak et al. 2018: ”In this review, we discuss the prevalence of polyploidy across the tree of life”
consequences of polyploidy
Here the topic is too complex, so I will just provide paper titles and links:
Contributions by The Tattooed Future Fellow
polyploidy within organisms
Reviewed in Edgar and Orr-Weaver 2001: In many animal some cells undergo endoreplication and generate somatic polyploid cells:
- neurons, cardiac and skeletal muscle cells, megakaryocytes, trophoblast and other extra-embryonic cells (placenta) are polyploid. Hepatocytes are tetraploid.
- Ciliates (Alveolata) carry a diploid micronucleus (the germline of the cell) but also a polyploid macronucleus (the somatic nucleus; the one that carries all the gene expression and regulation).
- There is the ever popular insect salivary gland polytene cells.
- C. elegans have polyploid intestine cells.
Contributions by Wallace Marshall, Benoit Bruneau, Amy Shaub Maddox, Cami Rosso and Erika Anderson. Since it’s bit off my own interest I have not tried to look up for sources of the individual statements.
I use here whole genome duplication for consistency with literature, however I dislike it very much because it sort of suggest that the ancestor was autopolyploid. However we have no information about the origin of duplication, the ancestral polyploid could be as well of a hybrid origin - allopolyploid. ↩
They call polyploidy an evolutionary dead. I find that strange since there are so many lineages with polyploid ancestors. Perhaps I am missing something, but if nothing else it’s very confusing notation. ↩