A single origin of plastids and the monophyly of three "primary" plastid-containing groups -the Chloroplastida (or Viridiplantae; green algae+land plants), Rhodophyta, and Glaucophyta -are widely accepted, mainstream hypotheses that form the basis for many comparative evolutionary studies. This "Archaeplastida" hypothesis, however, thus far has not been unambiguously confirmed by phylogenetic studies based on nucleocytoplasmic markers. In view of this as well as other lines of evidence, we suggest the testing of an alternate hypothesis that plastids of the Chloroplastida are of secondary origin. The new hypothesis is in agreement with, or perhaps better explains, existing data, including both the plastidal and nucleocytoplasmic characteristics of the Chloroplastida in comparison to those of other groups.Keywords: Archaeplastida; Chloroplastida; glaucophytes; green algae; plastids; primary plastids; red algae; secondary plastids; Viridiplantae Polish Botanical Society Elektronicznie podpisany przez Polish Botanical Society DN: c=IE, st=Warszawa, o=ditorPolish Bot, ou=Standard Certificate, ou=anical SocietySupport, serialNumber=PT2110520970.1, title=Managing E, sn=Otreba, givenName=org.plPiotr, email=p.otreba@pbsociety., cn=Polish Botanical Society Data: 2014.12.31 14:57: Kim and Maruyama / Secondary origin of green algal plastids is similar to the hypothesis pertaining to the evolutionary origin of primary plastids proposed by Stiller [12,13], that the Archaeplastida hypothesis may be fundamentally flawed because "primary plastids" as we understand it are of mixed, serial endosymbiotic origins. If this proposed hypothesis is indeed correct, we suggest that, of the three archaeplastidan groups, plastids of the Chloroplastida (or Viridiplantae) are most likely to be of secondary origin. This is based on several lines of observation as elaborated below.Multi-gene based phylogenetic approaches thus far have not been able to unambiguously support the Archaeplastida hypothesis Analyses of plastid genomes and other plastid-associated features significantly support the monophyly of plastids to the exclusion of cyanobacteria, thereby suggesting that the plastids originated from a single cyanobacterium-like ancestor [3,4,[14][15][16][17]. This, together with the assumption of a primary origin for the plastids of green algae (plus their land plant descendants), glaucophytes, and red algae, form the basis of the Archaeplastida hypothesis. This posits that the three archaeplastidan groups form a clade and originated from a single plastid-generating endosymbiosis [5]. Corroborating this, some of the earlier phylogenetic studies that utilized nucleus-encoded proteins seemed, at least partially, to support the Archaeplastida hypothesis with moderate to strong bootstrap support values (e.g. [18][19][20][21]). However, as more taxa or protein data (or both) were included, archaeplastidan monophyly dropped in support, or was not recovered at all (e.g. [10,11,[22][23][24][25][26][27][28][29][30][31]). One recent study repre...