Kin Recognition or Kin Discrimination in Single-Celled Organisms – Protists

EvoLiteracy News 04 04 2016

Can single-celled organisms distinguish between same (self or clone) and different (diverse clones)? Can they tell apart kin from non-kin? Can they “learn” to discriminate or recognize members of their own versus others’ cellular lineages? Answers to these questions are provided in three articles (first, second, and third) just published (early view) in the Journal of Eukaryotic Microbiology. The studies summarize outcomes of the symposium “Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications,” which took place at the VII European Congress of Protistology, organized last summer in partnership with the International Society of Protistologists (ECOP-ISOP 2015), and hosted by the University of Seville, Spain. I participated at this Symposium and co-authored two of the trilogy papers. But my purpose here is to bring attention to the topic “kin discrimination” or “kin recognition” in unicellular organisms, an area of research that has made much progress in the past fifteen years. There are some technicalities in the text below, but I ask the readers to make an effort and try to understand the broad themes, while being patient with the details. Enjoy! – Guillermo Paz-y-Miño-C.

Entamoeba invadens IP-1 Green-and-Red 3-hours - A Espinosa 2016

The unicellular eukaryote Entamoeba invadens (a protist) colored with Green or Red markers. When the Green and Red cells fully aggregate in mixed assemblages, they look yellow under the microscope, an indication that the amebas are able to distinguish members of the same clone, without being affected by the coloration. When grown in the laboratory with non-clone members, the amebas only aggregate with same-clone cells, an indication of preference to group with themselves. Photo courtesy of A. Espinosa 2016.

Readers unfamiliar with “protistan” biology might benefit from grasping some terminology (i.e. protist, prokaryote, eukaryote, clone, multicellularity, kin recognition/discrimination), which I explain next by answering simple questions. For those trained in biology, it might be fine to skip the first five subtitles, below, and move on directly to “From multicellular to unicellular: a round trip:”

What is a protist?

Remember that some organisms are made of single cells. Yes, the entire organism is a cell. For example, bacteria (like the E. coli that lives in the human gut) or amebas, which are also microscopic and can be found in a pond. However, one of the main differences between a bacteria and an ameba is that the former has no nucleus, in contrast to the latter that has it. For that reason, bacteria are called prokaryotes (pro = “before” or “prior to” or, in this case, no nucleus) and amebas are called eukaryotes (eu = “well” or “good” or, in this case, with nucleus). However, many other organisms have nucleated cells (and are, therefore, eukaryotes), like a frog, an orchid, a chimpanzee, a maple tree, or a Blue Whale. The term “protist” applies to unicellular eukaryotes, while the amphibian, the plant, or the aquatic mammal are called multicellular eukaryotes, since their bodies are made of billions of nucleated cells.

Now, the term “protist” is tricky because it includes extremely diverse organisms (which earliest ancestors likely emerged two billion years ago), and over the years scientists have realized that many exceptions exist of organisms that, although are not always unicellular in their life cycles, they are (or should be considered) protists. One of them is the social ameba (or amoeba), Dictyostelium, which forms multicellular assemblages (moving “slugs;” watch video) during its life stages, and also lives in nature as a single-celled, free ranging ameba. To learn more about the ambiguities intrinsic to the term “protist,” and for more examples, go here.

What is a clone?

Ameba cell division cartoon EvoLiteracyBecause unicellular organisms reproduce, in many cases, via simple cell divisions, the resulting progeny is often identical to the parental cell. A single ameba, for example, can give origin to 2 identical daughter cells, which, in turn, can generate 4 cells (i.e. 2, 4, 8… see cartoon on the right). The resulting thousands, or millions, of cells are “clones” (identical copies of each other). Now, during so many cell divisions, mutations that change the sequence of DNA can –and do– occur, making the descendant cells gradually different from the parental ones. Over time, maybe hundreds of years, a cell line could change enough to become a different clone. Moreover, after thousands or millions of years, different species of amebas can emerge, each distinctive from one another and from the species that gave them origin in the past, a phenomenon known as speciation.

What is multicellularity?

Volvox colonies

Volvox (a green-algae protist) forms large sphere-colonies made of hundreds, or thousands, of individual cells (see daughter colonies inside). Click on image for source.

Perhaps a more didactic question here is ‘where do multicellular organisms (i.e. frogs, orchids, chimps, maple trees, blue whales) come from’? A first, quick answer is that all multicellular organisms known today originated –at some point– in ancient assemblages of unicellular ancestors (traceable to billions of years ago). However, a more cautious answer is that we have a fragmentary understanding about how primitive single-celled eukaryotes took the path (here I mean driven by natural selection) toward permanent associations in immense cellular cooperatives, which we now call multicellular organisms (note that scientists consider the advent of multicellularity a “major evolutionary transition” in the history of Earth). And that is why studying modern protists, like gregarious amebas (in the genus Entamoeba), or facultative social amebas (i.e. not always social, but in response to environmental circumstances), like Dictyostelium, can give us hints about how multicellularity originated. This particular topic is discussed in the three articles published in JEUKMIC (first, second, and third), and to which I refer in this post. But before I get into that, take a look at the image of Volvox (inset). The organism Volvox is a green-algae protist, which forms large sphere-colonies made of hundreds, or thousands, of individual cells. Inside these spheres, daughter colonies develop and, when they mature, the parental spheres bursts and the descendant colonies are released into the aquatic environment, where they continue to grow and proliferate. Today’s multicellular aggregations of protists, like Entamoeba, Dictyostelium or Volvoxgive us clues about how multicellularity might have originated in ancient Earth. Moreover, they are good model-systems to study kin recognition or kin discrimination (which include an organism’s skills for grouping and cooperating with the right partners, and behaving altruistically toward them) in the context of the origin and evolution of multicellularity.

What is kin recognition or kin discrimination?

 “The ‘field of kin recognition’… has no consensus on definitions or proposed mechanisms, possibly due to the vast diversity of life histories across organisms and their phylogenetic complexities…”

NASA astronauts Scott Kelly and Mark Kelly Photo Tony Cenicola

NASA’s twin astronauts Scott, left, and Mark Kelly. Photo: Tony Cenicola. In humans, identical twins are the only natural “clones;” their genetic relatedness is equal to 100% (represented by r = 1.0). However, the rest of us are related to our siblings only by 50%, or r = 0.5. Our relatedness with our parents is the same, r = 0.5. Can the reader tell why? If so, here is a question: what would be your genetic relatedness with an uncle/aunt, or with a grand parent, or with a second cousin?

This topic can be a bit confusing. However, in one of the articles (the first one listed below), the authors explain why: “…The ‘field of kin recognition’… has no consensus on definitions or proposed mechanisms, possibly due to the vast diversity of life histories across organisms and their phylogenetic complexities (here, phylogeny means ancestry, somewhat analogous to genealogy, not of your own family, but rather of distinctive species or kinds of organisms grouped in distinctive categories). [The authors] refer to “recognition” as an organism’s ability to identify kin [family members] versus non-kin [members of another family]; in addition, [the authors] use the term “discrimination” as the capacity to distinguish one clone from another. Because [the authors] discuss instances of taxa- [taxa = in this particular case means species], clone-, and kin-discrimination/recognition in single-celled organisms capable of both discriminating between same and different, and discriminating/recognizing among clones of distinctive [degree of genetic relatedness, like, for example, values of r less than 1.0], [the authors] use these terms together…”

Why is it relevant to study kin recognition or kin discrimination in single-celled organisms?

To answer this question, I will borrow, again, text from the first article: “…Multicellularity is a major evolutionary transition in which single-celled organisms switched from living individually to permanent assemblages. It is possible that multicellularity originated —more than once— in clonality, via a gradual aggregation of closely related cells, capable of recognizing one another by means of chemical cues, and which lived consistently in intimate proximity and benefited from specialized division of labor (i.e. distinctive tissues and organs with given functions). Such specialization included the full allocation of soma-reproduction [soma = the entire body of an organism] to a small population of cells within the soma, the gametes [i.e. ovules, sperm]Protists are central to the reevaluation of the theoretical framework and concepts in the field of kin recognition, and to research about the origins and evolution of multicellularity...

From multicellular to unicellular: a roundtrip

The first article (by Paz-y-Miño-C and Espinosa) is a concise review on “Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards.” In it, the authors summarize the current understanding of the genetics of kin discrimination/recognition in unicellular Eukaryotes, and they do it historically by going back in time, to Darwin and his Origin of Species (1859; Darwin speculated* that selection may be applied to the family; kin discrimination/recognition rely on kin-selection theory), and the influential 1960s, when the modern field of kin recognition was, arguably, born. Here is a simplified version of the first article’s abstract:

During four decades (1960s to 1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly invertebrates and vertebrates, and some plants. This pioneering research had an animal behavior approach. During the 2000s, work on taxa-, clone- and kin-discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness (Table 1, below). Here we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity...”

[Click on Table 1, below, to enlarge]

Table 1 Kin-discrimination in Protists Paz-y-Mino-C Espinosa JEUKMIC 2016

Readers might find the following excerpts from this article quite intriguing, e.g. “learning” in unicellular organisms (is that possible?):

“…In 1899, H. S. Jennings wrote: ‘Paramecium… an animal that learns nothing, that exercises no choice in any respect, that is attracted by nothing and repelled by nothing, that reacts entirely without reference to the position of external objects, that has but one reaction [movement –watch video below] for the most varied stimuli… can hardly be said to have made the first step in the evolution of mind, and we are not compelled to assume consciousness or intelligence in any form to explain its activities.”

Above: movement behavior in Paramecium. This video is 13-min long and shows various types of Paramecium. If you watch it for a couple of minutes, it shall give you an idea about how these ciliates look like and move.

Except for mind, consciousness and intelligence, which are not prerequisites for kin discrimination or recognition (both can also operate in a reflex manner: stimulus-response), Jennings was mistaken about his entire characterization of Paramecium. Since the early 1900s, sensitization, trial-and-error learning, and classical or operant conditioning (relevant attributes among some of the multicellular eukaryotes that learn to recognize kin) have been documented in Paramecium; [including] micro-tube-escape swimming behavior via discrimination learning (1910s), habituation to approach baited and un-baited targets using bacteria as food-reinforcer (1950s), and swim-approach behavior toward mild-electrically-charged fields in learning discrimination tasks using positive and punishment reinforcements (2000s).”

And the authors add: “…But, to our knowledge, there is no direct, experimental evidence that protists can rely specifically on sensitization (i.e. the enhancement of a response to an incremental exposure to a stimulus, for example, the differential frequency exposure to kin versus non-kin during a life cycle), trial-and-error learning (i.e. repeated attempts to solve a task until success, for example, attempts to behave altruistically toward kin, and the benefits it entails, versus the costs of maladaptive altruism toward non-kin), or classical or operant conditioning to discriminate between kin and non-kin (i.e. learning to associate a behavioral or chemical cue with the advantages/disadvantages of aggregating, cooperating or reproducing with conspecifics of [diverse degree of relatedness]). All these topics, remain open areas of investigation and experimentation with protists since, like Paramecium, they possess basic sensory perception capabilities, which could have been co-opted [= adapted] during evolution to function in kin discrimination/recognition…”

Social amebas (or facultative social)

The second article (by Strassmann) is a another review, in this case on “Kin Discrimination in Dictyostelium Social Amoebae.” In it, the author recounts her research program on various species of social amebas, including Polysphondylium violaceum, D. purpureum and D. giganteum. Here is a simplified version of the abstract:

Evolved cooperation is stable only when the benefactor is compensated, either directly or through its relatives. Social amoebae cooperate by forming a mobile multicellular body in which about 20% of participants ultimately dies to form a stalk [watch video below]. This benefits the remaining individuals that become hardy spores at the top of the stalk, together making up [a] fruiting body. In studied species [of social ameba] with stalked migration, P. violaceum, D. purpureum, and D. giganteum, sorting based on clone identity occurs in laboratory mixes, maintaining high relatedness within the fruiting bodies. D. discoideum has unstalked migration where cell fate is not fixed until the slug forms a fruiting body. Laboratory mixes show some degree of both spatial and genotype-based sorting, yet most laboratory fruiting bodies remain chimeric. However, wild fruiting bodies are made up mostly of clonemates. A genetic mechanism for sorting is likely to be cell adhesion genes tgrB1 and tgrC1, which bind to each other. [These genes] are highly variable, as expected for a kin discrimination gene. It is a puzzle that these genes do not cause stronger discrimination between mixed wild clones, but laboratory conditions or strong sorting early in the social stage diminished by later slug fusion could be explanations.”

Above: the amazing videos of social behavior in amebas, by John Bonner, Professor of Biology at Princeton University. He obtained the images as an undergraduate student. This is a 2-min video of historical value, watch it to the end (it turns spectacular).

Gregarious amebas

The third article (by Espinosa et al.) is a multi-clone characterization of Entamoeba species; it is titled “Entamoeba Clone-recognition Experiments: Morphometrics, Aggregative Behavior, and Cell-signaling Characterization.” The authors discuss their laboratory trials with seven ameba varieties; here is a simplified version of the abstract:

Phylogeny of Entamoeba clones Espinosa et al JEUKMIC 2016

Schematic phylogeny based on ssrRNA sequences of the Entamoeba clones discussed in the Espinosa et al. article. Free-living: E. moshkovskii Laredo; commensal E. terrapinae and E. dispar; and parasitic E. invadens IP-1, E. invadens VK-1:NS, E. moshkovskii Snake and E. histolytica HM-1:IMSS.

Studies on clone- and kin-discrimination in protists have proliferated during the past decade. We report clone-recognition experiments in seven Entamoeba [varieties] (E. invadens IP-1, E. invadens VK-1:NS, E. terrapinae, E. moshkovskii Laredo, E. moshkovskii Snake, E. histolytica and E. dispar). First, we characterized morphometrically each clone (length, width, and cell-surface area) and documented how they differed statistically from one another (as per single-variable or canonical-discriminant analyses). Second, we demonstrated that amebas themselves could discriminate self (clone) from different (themselves versus other clones). In mix-cell-line cultures between closely-related (E. invadens IP-1 versus E. invadens VK-1:NS) or distant-phylogenetic clones (E. terrapinae versus E. moshkovskii Laredo), amebas consistently aggregated with same-clone members. Third, we identified six putative cell-signals secreted by the amebas and which known functions in Entamoeba spp. included: cell proliferation, cell adhesion, cell movement, and stress-induced encystation. To our knowledge, this is the first multi-clone characterization of Entamoeba spp. morphometrics, aggregative behavior, and cell-signaling secretion in the context of clone-recognition. Protists allow us to study cell-cell recognition from ecological and evolutionary perspectives. Modern protistan lineages can be central to studies about the origins and evolution of multicellularity.”


Again, I would like to quote the first article: “…because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge [to our current understanding of the origins and evolution of multicellularity].” – GPC – Evolution Literacy.

You can contact Guillermo Paz-y-Miño-C via email at

UniCellular Eukaryotes or Protists

Protists are among the most ancient organisms on Earth; they belong to multiple taxonomic groups and occupy all environments. Studies with protists can be central to generating new knowledge to our current understanding of the origins and evolution of multicellularity.

Suggested Readings and Note

JEUK-MICRO - COVER - May-June 2016Article I: Paz-y-Miño-C, G. & Espinosa A. 2016. Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards. Journal of Eukaryotic Microbiology 63: 367-377. DOI: 10.1111/jeu.12306.

Article II: Strassmann, J. E. 2016. Kin Discrimination in Dictyostelium Social Amoebae. Journal of Eukaryotic Microbiology 63: 378-383. DOI: 10.1111/jeu.12307.

Article III: Espinosa, A., Paz-y-Miño-C, G., Hackeya, M. & Rutherford, S. 2016. Entamoeba Clone-recognition Experiments: Morphometrics, Aggregative Behavior, and Cell-signaling Characterization. Journal of Eukaryotic Microbiology 63: 384-393. DOI: 10.1111/jeu.12313.

I also suggest to explore the paper that inspired the organization of the ECOP-ISOP 2015 symposium:

Espinosa, A. & Paz-y-Miño-C, G. 2014. Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications. Evolutionary Ecology DOI 10.1007/s10682-014-9721-z.

* Darwin (1859) speculated about the “puzzle of the sterile social insects,” in which female workers at a nest dedicate their lives to the persistence of the colony (structured around a large progeny), via assisting a fertile queen to reproduce with the available males. Darwin suggested that, in such cases of apparent sacrifice —by the workers— for the good of all, “selection may be applied to the family.” But, in the late 1800s, he could not offer a detailed mechanistic explanation for the latter. Fisher (1930) and Haldane (1932, 1955) wrestled with the genetics and mathematics of altruism and the anecdotic expression “I would lay down my life for two brothers or eight cousins” became legacy of their work. Hamilton (1964) and Maynard-Smith (1964) further reasoned that the ability to discriminate between close and distant genetic relatives could be directly linked to survival and reproductive success, and, ultimately, to kin selection (Maynard-Smith 1964, 1977). — For references, go to source.