we recently completed a phylogenomic analysis of genes encoding membrane transporters in the nuclear genomes of diatoms t. pseudonana and p. tricornutum . in addition to examples of long - term vertical inheritance of membrane transporters in these and other eukaryotes ( fig . 1a ) , we also found putative red and green algal origins ( fig . 25% ) of the 697 encoded membrane transporters were found to be of plantae origin . although 50 of these show an unresolved affiliation with red and/or green algae , interestingly , the majority ( 103 ) are of putative green algal provenance compared with 19 of putative red algal origin . to explain their long - term retention , we hypothesized that these genes , presumably derived from different algal secondary endosymbionts , contributed important membrane transport functions to diatoms . ( a ) maximum likelihood ( ml ) tree of a membrane transporter in diatoms and other  chromalveolates  that is widely shared among eukaryotes and appears to be vertically inherited . this protein encodes a member of the mitochondrial carrier family that , although of unknown function in diatoms , is annotated as a fe ( or potentially other cations ) transporter in yeast ( gi : 6322328 ) that is active under low - iron conditions . ( b ) ml phylogenetic tree of an endoplasmic reticulum nucleotide sugar transporter that has a history of e / hgt . this pan - eukaryote membrane transporter in a distinct group of  chromalveolates  is apparently of prasinophyte ( green algal ) origin . raxml and phyml bootstrap support values based on 100 pseudoreplicates (  50% ) are shown ( above and below the nodes , respectively ) . the unit of branch lengths is the number of substitutions per site ( see scale bars ) . red algae are shown in red text , green algae and plants in green text and  chromalveolates  in brown text . the ncbi gi number for each sequence the fluctuations of redox - sensitive transition metals over evolutionary timescales driven most notably by the rise of oxygen ca . 2.5 bya , would have introduced immense selective pressure for cell survival in aquatic environments . such environmental pressure is particularly relevant to the trafficking of molecules across cellular membrane , whether to acquire useful molecular compounds or to expel molecules that cause harm to the cell ( i.e. , cell detoxification ) . free - living unicellular algae are known to possess efficient transport systems , particularly of metal cations such as sodium and potassium , to maintain cell homeostasis with respect to the inter- and extra - cellular environments . therefore , the acquisition of red and/or green algal genes via e / hgt could have been a crucial selective force for the survival of ancient , and hence extant diatom lineages . our observations are also in general agreement with the hypothesis of a cryptic green algal endosymbiosis in diatoms , and likely more generally in  chromalveolates . and finally , these data suggest that the cryptic endosymbiont contributes gene functions that extend beyond photosynthetic capacity to roles related to cell adaptation to the external environment . a well - sampled phylogenetic tree of eukaryotes ( i.e. , the eukaryote tree of life ) is essential to understand the tempo and mode of endosymbiotic events that have occurred during algal evolution , and to test different hypotheses about the relationships between the major algal groups . the recent findings of extensive egt from putative serial endosymbioses , in combination with hgt events from diverse sources , stresses the significant impact that gene transfer has had on algal and eukaryote evolution in general . gene transfer events are not only of significance to cell evolution , but may also mislead inference of the tree of life . some of our previous studies were aimed at identifying genes that do not  follow  the presumed vertical ( e.g. , host lineage ) history of algal groups and their non - photosynthetic relatives ( e.g. , plantae , alveolata and stramenopiles ) to study the endosymbiotic origin of plastids , and , importantly , the impact of e / hgt on algal genome evolution . it has now become clear that the identification of bona fide cases of egt or hgt is often saddled by well - recognized stochastic errors ( e.g. , insufficient data ) and systematic biases ( e.g. , base composition , high mutation rates ) inherent to molecular phylogenetics that can lead to equivocal support for phylogenetic hypotheses . in spite of these difficulties , independent analyses using multiple single - locus phylogenetic trees provide support for the existence of egt during the evolution of eukaryotes , such as the cyanobacterial contribution to plantae genomes , the presence of red algal derived genes in diatoms and haptophytes , green algal genes in chlorarachniophytes , and cyanobacterial sequences in the nuclear genome of the photosynthetic filose amoeba paulinella chromatophora . once the existence of large - scale egt from putative serial endosymbioses and sporadic hgt events are recognized in diverse taxa , it is then fair to ask whether it remains feasible to reconstruct genealogical history of the host lineages that comprise major algal groups . the major challenge in this task is the successful exclusion of the vast collection of eukaryotic genes recruited via e / hgt that depict evolutionary histories that conflict with the vertical evolution of the host lineages . in principle , the presence of genes acquired by hgt should not impede reliable inference of genealogical history of eukaryotic lineages using molecular data . genes implicated in e / hgt could be excluded from phylogenetic analyses ( this is critical when using multi - gene concatenated alignments ) and , in some cases , used as a marker to unite lineages that share a common e / hgt event , such as a defined genetic exchange community . if appropriate phylogenetic methods and phylogenetic hypothesis - testing strategies are used to ameliorate or exclude the impact of e / hgt when inferring organismal evolution , then the representation of eukaryote evolution as a tree - like process is legitimate . as a complement to the widely used concatenated multi - gene analyses , we consider the exhaustive phylogenetic analyses of core biochemical pathways ; e.g. , the calvin cycle , the plastid tic / toc translocons , and the permeome to provide useful molecular markers to infer phylogenetic relationships between algal groups . at the same time , phylogenetic studies of single proteins involved in key biochemical processes , such as the plastid adp / atp translocator , carotenoid , and starch biosynthesis provide clear examples of genealogical relationships between major algal groups that are based on a history of shared e / hgts . these genes are of fundamental importance for understanding the evolution of key cellular functions but do not serve as markers of vertical evolution . in recent years , our understanding of algal evolution and diversification has benefited greatly from the availability of genome data from non - photosynthetic groups such as picobiliphytes and katablepharids . the inclusion of these data in phylogenetic analyses has necessitated the invocation of complex evolutionary scenarios to explain relationships between the major algal and protist lineages . the original idea of a united  chromalveolate  lineage is no longer tenable after the identification of the sar group and the finding of the intermingled positions of picobiliphytes , telonemids , and katablepharids with photosynthetic  chromalveolates .  genome - scale data from many of these algal and protist groups is still lacking . major sequencing efforts of key algal groups ( e.g. , red algae , glaucophytes , prasinophytes ) and non - photosynthetic taxa ( e.g. , picobiliphytes , telonemids , katablepharids ) are therefore required both for exploring the relationships between these lineages and for elucidating the number and tempo of endosymbiotic events that have generated the astonishing diversity of microbial eukaryotes .
the evolution of microbial eukaryotes , in particular of photosynthetic lineages , is complicated by multiple instances of endosymbiotic and horizontal gene transfer ( e / hgt ) resulting from plastid origin(s ) . 
 our recent analysis of diatom membrane transporters provides evidence of red and/or green algal origins of 172 of the genes encoding these proteins ( ca . 
 25% of the examined phylogenies ) , with the majority putatively derived from green algae . 
 these data suggest that e / hgt has been an important driver of evolutionary innovation among diatoms ( and likely other stramenopiles ) , and lend further support to the hypothesis of an ancient , cryptic green algal endosymbiosis in 
 chromalveolate 
 lineages . here , 
 we discuss the implications of our findings on the understanding of eukaryote evolution and inference of the tree of life .