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How many eukaryotes are there on Earth?

How many eukaryotes are there on Earth?


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I have been reading:

William B. Whitman, David C. Coleman, and William J. Wiebe, "Prokaryotes: The unseen majority", Proc. Natl. Acad. Sci. USA 95, pp. 6578-6583, June 1998. [Full Text] [PDF]

wherein they estimate the number of prokaryote cells on Earth to be of the order of $10^{31}$.

I can't seem to find any equivalent data for eukaryote one-celled life. Are there any estimates for the number of one-celled eukaryotic living things on Earth? Do any other estimates confirm or tell against the reference I have cited above?


Could not fit in a comment…

To make sure we all understand your question…

Is your questionhow many (eukaryote) species are currently living?orHow many (eukaryote) cells are currently living??

Just a hint to answer the question

Micheal Lynch, in his book (On the Origin of Genome Architecture) at page 3, Box 1.1 tries to answer the questionHow much DNA is there on earth?. He ends up with an estimation of a total length of DNA on earth of $10^{24}$ km for procaryotes, $10^{25}$ km for eukaryote (of which $frac{1}{1000}$% is accounted to humans). This sums up to a total DNA length of $10^{12}$ light-years, or 10 times the diameter of the known universe!

In his calculations, he estimates that the total number of procaryote cells at $10^{30}$ (citing Whitman et al. 1998 as you did). He estimates the total number of eukaryote species to $10^7$, i.e. 6 times the number of known eukaryote species. However, he doesn't directly give any reference for this estimate but he refers to different chapters in the book that contain lots of references.

… I hope that helps…


How many eukaryotes are there on Earth? - Biology

Eukaryotes are very diverse in phylogenic terms, the common feature being a membrane bound nucleus.

Learning Objectives

Assess the phylogeny of Eukarya

Key Takeaways

Key Points

  • Eukaryotes are broadly determined by the prescence of a membrane bound nucleus, though many eukaryotes have other membrane bound structures.
  • The domain of eukarya are broadly grouped into six kingdoms: Excavata, Amoebozoa, Opisthokonta, Rhizaria, Chromalveolata, and Archaeplastida.
  • The exact nature of the relationships (i.e. common ancestors) of the the eukarya domain are still debated.

Key Terms

  • crown group: In phylogenetics, the crown group of a collection of species consists of the living representatives of the collection together with their ancestors back to their last common ancestor as well as all of that ancestor’s descendants. It is thus a clade, a group consisting of a species and all its descendents.
  • cristae: Cristae (singular crista) are the internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes.

Phylogeny of the Eukarya

A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria, chloroplasts, and the Golgi apparatus. All large complex organisms are eukaryotes, including animals, plants, and fungi. The group also includes many unicellular organisms.

rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved crown group, which was usually divided by the form of the mitochondrial cristae. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive. But this is now considered an artifact of a divergent evolutionary line, and they are known to have lost them secondarily.

Eukaryotes are split into 6, subdivisions, referred to as kingdoms. They include:

The Six Kingdoms: This is one hypothesis of eukaryotic relationships. The Opisthokonta group includes both animals (Metazoa) and fungi. Plants (Plantae) are placed in Archaeplastida.

1. Excavata – Various flagellate protozoa

2. Amoebozoa – Most lobose amoeboids and slime moulds

3. Opisthokonta – Animals, fungi, choanoflagellates

4. RhizariaForaminifera – Radiolaria, and various other amoeboid protozoa

5. ChromalveolataStramenopiles (or Heterokonta) – Haptophyta, Cryptophyta (or cryptomonads), and Alveolata

6. Archaeplastida (or Primoplantae) – Land plants, green algae, red algae, and glaucophytes

There is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizara is not one of the main eukaryote groups. The Amoeboza and Opisthokonta are each monophyletic and form a clade, often called the unikonts. There is debate about the true constituents of the animal kingdoms.

Beyond this, there does not appear to be a consensus. It has been estimated that there may be 75 distinct lineages of eukaryotes. Most of these lineages are protists. The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000 to 220,050 Mb in the dinoflagellate Prorocentrum micans. This suggests that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. The last common ancestor of all eukaryotes is believed to have been a phagotrophic protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis), a dormant cyst with a cell wall of chitin, cellulose, and peroxisomes. Later endosymbiosis led to the spread of plastids in some lineages.


The Levels of Classification

Taxonomy (which literally means “arrangement law”) is the science of naming and grouping species to construct an internationally shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist) uses a hierarchical model. A hierarchical system has levels and each group at one of the levels includes groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups. An analogy is the nested series of directories on the main disk drive of a computer. For example, in the most inclusive grouping, scientists divide organisms into three domains : Bacteria, Archaea, and Eukarya. Within each domain is a second level called a kingdom . Each domain contains several kingdoms. Within kingdoms, the subsequent categories of increasing specificity are: phylum , class , order , family , genus , and species .

As an example, the classification levels for the domestic dog are shown in [Figure 2]. The group at each level is called a taxon (plural: taxa). In other words, for the dog, Carnivora is the taxon at the order level, Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, such as domestic dog, or wolf. Each taxon name is capitalized except for species, and the genus and species names are italicized. Scientists refer to an organism by its genus and species names together, commonly called a scientific name, or Latin name. This two-name system is called binomial nomenclature . The scientific name of the wolf is therefore Canis lupus. Recent study of the DNA of domestic dogs and wolves suggest that the domestic dog is a subspecies of the wolf, not its own species, thus it is given an extra name to indicate its subspecies status, Canis lupus familiaris.

[Figure 2] also shows how taxonomic levels move toward specificity. Notice how within the domain we find the dog grouped with the widest diversity of organisms. These include plants and other organisms not pictured, such as fungi and protists. At each sublevel, the organisms become more similar because they are more closely related. Before Darwin’s theory of evolution was developed, naturalists sometimes classified organisms using arbitrary similarities, but since the theory of evolution was proposed in the 19 th century, biologists work to make the classification system reflect evolutionary relationships. This means that all of the members of a taxon should have a common ancestor and be more closely related to each other than to members of other taxa.

Recent genetic analysis and other advancements have found that some earlier taxonomic classifications do not reflect actual evolutionary relationships, and therefore, changes and updates must be made as new discoveries take place. One dramatic and recent example was the breaking apart of prokaryotic species, which until the 1970s were all classified as bacteria. Their division into Archaea and Bacteria came about after the recognition that their large genetic differences warranted their separation into two of three fundamental branches of life.

Art Connection

Figure 2: At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit “plant”: modification of work by “berduchwal”/Flickr credit “insect”: modification of work by Jon Sullivan credit “fish”: modification of work by Christian Mehlführer credit “rabbit”: modification of work by Aidan Wojtas credit “cat”: modification of work by Jonathan Lidbeck credit “fox”: modification of work by Kevin Bacher, NPS credit “jackal”: modification of work by Thomas A. Hermann, NBII, USGS credit “wolf” modification of work by Robert Dewar credit “dog”: modification of work by “digital_image_fan”/Flickr)

In what levels are cats and dogs considered to be part of the same group?

[reveal-answer q=�″]Show Answer[/reveal-answer]
[hidden-answer a=�″]Cats and dogs are part of the same group at five levels: both are in the domain Eukarya, the kingdom Animalia, the phylum Chordata, the class Mammalia, and the order Carnivora.[/hidden-answer]


The Three Domains of Life

When scientists first started to classify life, everything was designated as either an animal or a plant. But as new forms of life were discovered and our knowledge of life on Earth grew, new categories, called ‘Kingdoms,’ were added. There eventually came to be five Kingdoms in all – Animalia, Plantae, Fungi, Protista, and Bacteria.

The five Kingdoms were generally grouped into two categories called Eukarya and Prokarya. Eukaryotes represent four of the five Kingdoms (animals, plants, fungi and protists). Eukaryotes are organisms whose cells have a nucleus — a sort of sack that holds the cell’s DNA . Animals, plants, protists and fungi are all eukaryotes because they all have a DNA -holding nuclear membrane within their cells.

The cells of prokaryotes, on the other hand, lack this nuclear membrane. Instead, the DNA is part of a protein-nucleic acid structure called the nucleoid. Bacteria are all prokaryotes.

However, new insight into molecular biology changed this view of life. A type of prokaryotic organism that had long been categorized as bacteria turned out to have DNA that is very different from bacterial DNA . This difference led microbiologist Carl Woese of the University of Illinois to propose reorganizing the Tree of Life into three separate Domains: Eukarya, Eubacteria (true bacteria), and Archaea.

Archaea look like bacteria – that’s why they were classified as bacteria in the first place: the unicellular organisms have the same sort of rod, spiral, and marble-like shapes as bacteria. Archaea and bacteria also share certain genes, so they function similarly in some ways. But archaeans also share genes with eukaryotes, as well as having many genes that are completely unique.

Archaea are so named because they are believed to be the least evolved forms of life on Earth (‘archae’ meaning ‘ancient’). The ability of some archaea to live in environmental conditions similar to the early Earth gives an indication of the ancient heritage of the domain.

The early Earth was hot, with a lot of extremely active volcanoes and an atmosphere composed mostly of nitrogen, methane, ammonia, carbon dioxide, and water. There was little if any oxygen in the atmosphere. Archaea and some bacteria evolved in these conditions, and are able to live in similar harsh conditions today. Many scientists now suspect that those two groups diverged from a common ancestor relatively soon after life began.

Millions of years after the development of archaea and bacteria, the ancestors of today’s eukaryotes split off from the archaea. So although archaea physically resemble bacteria, they are actually more closely related to us!

If not for the DNA evidence, this would be hard to believe. The archaea that live in extreme environments can cope with conditions that would quickly kill eukaryotic organisms. Thermophiles, for instance, live at high temperatures – the present record is 113°C (235°F). In contrast, no known eukaryote can survive over 60°C (140°F). Then there are also psychrophiles, which like cold temperatures – there’s one in the Antarctic that grows best at 4°C (39°F). As a group, these hard-living archaea are called “extremophiles.”

There are other kinds of archaea extremophiles, such as acidophiles, which live at pH levels as low as 1 pH (that’s about the same pH as battery acid). Alkaliphiles thrive at pH levels as high as that of oven cleaner. Halophiles, meanwhile, live in very salty environments. But there are also alkaliphilic, acidophilic, and halophilic eukaryotes. In addition, not all archaea are extremophiles. Many live in more ordinary temperatures and conditions.

Many scientists think the thermophilic archaea – the heat-loving microbes living around deep-sea volcanic vents – may represent the earliest life on Earth. But NAI member Mitchell Sogin, a microbiologist with the Marine Biological Laboratory, says that instead of being the Earth’s first life form, they could be the sole survivors of a catastrophe that occurred early in the Earth’s history. This catastrophe could have killed off all other forms of life, including the universal ancestor from which both archaea and bacteria arose.

“Some have argued that the occurrence of thermophilic phenotypes in the deepest archaeal and bacterial lineages suggests that life had a hot origin,” says Sogin. “However, there are other equally compelling arguments which suggest that this distribution of phenotypes on the tree of life reflects survival of heat-loving organisms during times of major environmental upheaval.”

Such environmental upheavals include asteroid and comet bombardments, which we know happened frequently during the Earth’s earliest years. Although our geologically active planet has erased much of the evidence of these cataclysmic events, the Moon bears witness to the amount of asteroid and comet activity that occurred in our neighborhood. Because the Moon is geologically inactive, its surface is still littered with scars from these early impacts.

Large impacts can create severe global environmental changes that wipe out life at the planet’s surface. It is believed, for instance, that the dinosaurs fell victim to the environmental effects of a large asteroid impact. Among other effects, impacts throw a lot of dust and vaporized chemicals up into the atmosphere. This blocks sunlight, impairing photosynthesis and altering global temperatures.

But thermophilic archaeans are not dependent on the Sun for their energy. They harvest their energy from chemicals found at the vents in a process called chemosynthesis. These organisms are not greatly impacted by surface environmental changes. Perhaps the only organisms that were able to survive the large, frequent impacts of Earth’s early years were the thermophilic organisms that lived around deep-sea volcanic vents.

“Certainly the discovery of the archaea pointed out microbial diversity – particularly in extreme environments – that was previously unrecognized,” says Sogin. “As to what this data has to say about the origins of life, I am of the opinion that we still do not know where the root lies within the three kingdom tree.”

Woese is currently working to unearth that root. But he says the search for the universal ancestor is a far more subtle and complex problem than most people realize.

“The problem is not merely a case of identifying some original cell or cell line that gave rise to it all,” says Woese. “The universal ancestor may not be a single lineage at all.”

Instead, says Woese, lateral gene transfer – a process where genes are shared between microorganisms – may have been so prevalent that life did not evolve from one individual lineage.

“At the universal ancestor stage, horizontal gene transfer may have been so dominant that the ancestor may in effect have been a community of cell lineages that evolved as a whole. We will be able to trace all life back to an ancestor, but that state will not be some particular cell lineage.”

The transfer of bacterial genes seems to have been a vital part of the evolution of archaeans and eukaryotes. In fact, it is believed that such a transfer was responsible for the development of the first eukaryotic cell. As oxygen accumulated in the atmosphere through the photosynthesis of blue green algae, life on Earth needed to quickly adapt. When a cell consumed aerobic (oxygen-using) bacteria, it was able to survive in the newly oxygenated world. Today, the aerobic bacteria have evolved to become mitochondria, which helps the cell turn food into energy.

Modern-day archaea and eukarya seem to rely on such bacterial intervention in their metabolisms. This points to the possibility that bacterial genes may have replaced other genes in the two lineages over time, erasing some features of the last common ancestor. But Woese says there are certain molecular similarities among all three domains that still may point to a universal ancestor.

“Although there are differences in the information-processing systems, there are many universal features in translation and core similarities in transcription that link all three domains,” says Woese. “But this is a very complex and hard to understand area. These early interactions were almost certainly between entities the like of which no longer exist. They were primitive entities that were on their way of becoming one of the three modern cell types, but were definitely not modern cells. Their interactions were peculiar to that particular era in evolution, before the modern cell types arose.”

Perhaps the universal ancestor is not to be found on Earth. Because life on Earth seems to have appeared very soon after the planet became habitable, many scientists think that life could have arrived from outer space, via the asteroids and comets that bombarded the Earth in its earliest years.

In addition, because some Martian rocks that have arrived on our planet seem to contain fossilized microbes, some have speculated that life on Earth might originally have come from Martian meteorites. However, Woese believes that if we find evidence for life on Mars, it will either be unrelated to Earth-based life, or be the result of contamination of Mars by rocks from Earth.

Sogin also doesn’t think that the first microbes were brought to Earth by a Martian asteroid or comet. However, he does believe that microbial life may be a common feature of the Galaxy.

“Life at extreme environments as represented principally by the archaea forces us to consider the possibility of living organisms on other solar system bodies under conditions that we would not have deemed possible just ten or fifteen years ago,” says Sogin. “For example, we can imagine life under the ice on Europa and even the possibility of subsurface life on Mars. Certainly microbial life is far more robust and can survive and even thrive under conditions that are likely to be found elsewhere in the solar system and certainly in the galaxy.”

Woese, on the other hand, hasn’t yet made up his mind about the occurrence of life elsewhere.

“Life in Universe – rare or unique? I walk both sides of that street,” says Woese. “One day I can say that given the 100 billion stars in our galaxy and the 100 billion or more galaxies, there have to be some planets that formed and evolved in ways very, very like the Earth has, and so would contain microbial life at least. There are other days when I say that the anthropic principal, which makes this universe a special one out of an uncountably large number of universes, may not apply only to that aspect of nature we define in the realm of physics, but may extend to chemistry and biology. In that case life on Earth could be entirely unique.”

Whether or not Earth-like life is common or unique, Sogin says it will be a long time before we can answer that question with any certainty.

“I think that life occurs elsewhere in the universe,” says Sogin. “However, I am not sure we will ever be able to obtain conclusive evidence of life elsewhere given today’s technology, or even tomorrow’s technology.”

The development of the Three Domains concept has, in Woese’s opinion, dramatically altered the way scientists view life on Earth. He says the concept has highlighted the shared traits – as well as the differences – among all three groups.

“Most biologists still speak of prokaryotes versus eukaryotes, but now they discuss their similarities, says Woese. “In the old days, they focused mainly if not solely on their differences. I often analogize the conceptual climate before and after the discovery of the archaeas to changing from monocular to binocular vision.”

By finding out what he can about the similarities among all three domains, Woese says he is “studying the two interrelated fundamental biological problems of the nature of the universal ancestor and the evolutionary dynamic of horizontal gene transfer.”

Sogin, meanwhile, is exploring the evolution of biological complexity in microbial ecosystems.

“Life is very old – appearing on Earth at least 3.5 billion years ago and possibly 3.9 or 4 billion years ago,” says Sogin. “It was microbial and continued in that mode for the first 70 to 90 percent of Earth’s history. Complex multicellularity in the form of differentiated tissue is a relatively recent event. Throughout time the microbes ruled and continue to govern all biological processes on this planet.”

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Where Did Eukaryotes Come From?

According to various archeological evidences, eukaryotic cells have started to exist more than 0.6 billion years ago. Up until now, their evolution is viewed by many as one of the most unusual events in biological history.

To explain such a bizarre event, scientist Lynn Margulis proposed the so-called “Endosymbiotic Theory“.

  • This theory states that the mitochondria (the powerhouse of the cell), and the chloroplasts (structure for photosynthesis) were once single-celled organisms that have been engulfed by “proto-eukaryotic” cells.
  • The eukaryotic mitochondria and chloroplasts have a different set of genetic materials as compared to the cell itself. Hence it proves that they were once bacterial cells.
  • Their continuous and maintained symbiosis required both cells to reproduce at the same rate and not to digest each other.
  • As a result, the resulting cells could now produce their energy and fix carbon through the use of light.

Materials and Methods

Taxon Sampling and Sequencing

Forty-six species were used to infer the plastid phylogeny including 32 red algae including the chromists, 12 green algae and land plants, the glaucophyte Cyanophora paradoxa, and a cyanobacterium (Nostoc sp. PCC7120) as the outgroup (for strain identifications and GenBank accession numbers, see table 1 in the Supplementary Material online). A total of 42 new plastid sequences were determined in this study. Our sequencing strategy was to focus on red algae and chromists that span the known diversity of these lineages. In particular, we included a broad diversity of extremophilic Cyanidiales, including two mesophilic taxa that we have recently discovered (Cyanidium sp. Sybil, Cyanidium sp. Monte Rotaro), and members of the other genera in this early-diverging red algal order. Our data set included, therefore, key early-diverging red and green (e.g., Mesostigma viride) algae and land plants (e.g., Anthoceros formosae), a glaucophyte, and a cyanobacterium.

To prepare DNA, the algal cultures were frozen in liquid nitrogen and ground with glass beads using a glass rod and/or Mini-BeadBeater (Biospec Products, Inc., Bartlesville, Okla.). Total genomic DNA was extracted with the DNeasy Plant Mini Kit (Qiagen, Santa Clarita, Calif.). Polymerase chain reactions (PCR) were done using specific primers for each of the plastid genes (see Yoon, Hackett, and Bhattacharya 2002 Yoon et al. 2002). Four degenerate primers were used to amplify and sequence the photosystem I P700 chlorophyll a apoprotein A2 (psaB) gene: psaB500F 5′-TCWTGGTTYAAAAATAAYGA-3′, psaB1000F 5′-CAAYTAGGHTTAGCTTTAGC-3′, psaB1050R 5′-GGYAWWGCATACATATGYTG-3′, psaB1760R 5′-CCRATYGTATTWAGCATCCA-3′. Because introns were found in the plastid elongation factor Tu (tufA) and photosystem I P700 chlorophyll a apoprotein A1 (psaA) genes of some red algae (most likely indicating gene transfer to the nucleus [H. S. Y., D. B. unpublished data]), the reverse transcriptase (RT)-PCR method was used to isolate cDNA. For the RT-PCR, total RNA was extracted with the RNeasy Mini Kit (Qiagen, Santa Clarita, Calif.). To synthesize cDNA from total RNA, M-MLV Reverse Transcriptase (GIBCO BRL, Gaithersburg, Md.) was used according to the manufacturer's protocol. The PCR products were purified with the QIAquick PCR Purification kit (Qiagen), and were used for direct sequencing with the BigDye Terminator Cycle Sequencing Kit (PE-Applied Biosystems, Norwalk, Conn.) and an ABI-3100 at the Center for Comparative Genomics at the University of Iowa. Some PCR products were cloned into pGEM-T vector (Promega, Madison, Wis.) prior to sequencing.

Phylogenetic Analyses

Sequences were manually aligned with SeqPup ( Gilbert 1995). The alignment used in the phylogenetic analyses is available on request from D. B. We prepared a concatenated data set of 16S rRNA (1,309 nt), psaA (1,395 nt), psaB (1,266 nt), photosystem II reaction center protein D1 (psbA) (957 nt), ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL 1,215 nt), and tufA (969 nt) coding regions (a total of 7,111 nt) from photosynthetic eukaryotes and the cyanobacterium Nostoc sp. PCC7120 as the outgroup. Because the rbcL gene of the green and glaucophyte algae are of cyanobacterial origin, whereas those in the red algae and red-algal-derived plastids are of proteobacterial origin (e.g., Valentin and Zetsche 1990), the evolutionarily distantly related green and glaucophyte rbcL sequences were coded as missing data in the phylogenetic analyses. The highly divergent and likely nonfunctional tufA sequence in Chaetosphaeridium globosum ( Baldauf, Manhart, and Palmer 1990) and the nuclear-encoded land plant tufA genes ( Baldauf and Palmer 1990) were also excluded from the analysis.

Trees were inferred with Bayesian inference and the minimum evolution (ME) and maximum parsimony (MP) methods. To address the possible misleading effects of nucleotide bias or mutational saturation at third codon positions in the DNA data set (e.g., for rbcL, see Pinto et al. 2003), we excluded third codon positions from the phylogenetic analyses (leaving a total of 5,177 nt). In the Bayesian inference of the DNA data (MrBayes, version 3.0b4 Huelsenbeck and Ronquist 2001), we used the general time reversible (GTR) + Γ model with separate model parameter estimates for the three data partitions (16S rRNA, first, and second codon positions in the protein-coding genes). Metropolis-coupled Markov chain Monte Carlo (MCMCMC) from a random starting tree was initiated in the Bayesian inference and run for 2 million generations. Trees were sampled each 1,000 cycles. Four chains were run simultaneously of which three were heated and one was cold, with the initial 200,000 cycles (200 trees) being discarded as the “burn-in.” Stationarity of the log likelihoods was monitored to verify convergence by 200,000 cycles (results not shown). A consensus tree was made with the remaining 1,800 phylogenies to determine the posterior probabilities at the different nodes. In the ME analyses, we generated distances using the GTR + I + Γ model (identified with Modeltest version 3.06, [ Posada and Crandall 1998] as the best-fit model for our data) with the PAUP*4.0b8 software ( Swofford 2002). Ten heuristic searches with random-addition-sequence starting trees and tree bisection-reconnection (TBR) branch rearrangements were done to find the optimal ME trees. Best scoring trees were held at each step. In addition, we attempted to correct for mutational saturation and base composition heterogeneity in the DNA data by recoding first and third codon positions as purines (R) and pyrimidines (Y [see Phillips and Penny 2003 Delsuc, Phillips, and Penny 2003]). The 16S rDNA and second codon position data were maintained as the original nucleotides in this analysis. A starting tree was generated with the RY-recoded data set using the ME method and the HKY-85 evolutionary model. This tree was used as input in PAUP* to calculate the parameters for the GTR + I + Γ model. These parameters were then used in a ME-bootstrap analysis (2,000 replications) with the settings described above.

Unweighted MP analysis was also done with the DNA data, using heuristic searches and TBR branch-swapping to find the shortest trees. The number of random-addition replicates was set to 10 for each tree search. To test the stability of monophyletic groups in the ME and MP trees, we analyzed 2,000 bootstrap replicates ( Felsenstein 1985) of the DNA data set. We also did a Bayesian analysis in which all three codon positions were included in the data set (7,111 nt). The settings implemented in this inference were the same as described above (i.e., ssgamma), except for the use of a four-partition evolutionary model (i.e., 16S rRNA, first, second, and third codon positions).

In addition to the DNA analyses, we also inferred trees using the five proteins in our data set (i.e., excluding 16S rRNA). An ME tree was inferred with the “Fitch” program (PHYLIP version 3.6 Felsenstein 2002) using the WAG + Γ evolutionary model with 10 random sequence additions and global rearrangements to find the optimal trees. PUZZLEBOOT version 1.03 (http://hades.biochem.dal.ca/Rogerlab/Software/software.html) and Tree-Puzzle V5.1 ( Schmidt et al. 2002) were used to generate the distance matrix. The gamma value was calculated using Tree-Puzzle. Protein bootstrap analyses using the ME method were done using the settings described above and 500 replicates. A quartet-puzzling–maximum likelihood analysis of the five-protein data set was done with Tree-Puzzle and the WAG + Γ model (50,000 puzzling steps).

Molecular Clock Analyses

We used the maximum likelihood method to infer the divergence times of different plastid lineages. Seven different constraints were used in this analysis (see fig. 1A and table 2 in the Supplementary Material online). To date divergences in the best Bayesian tree and in the pool of credible Bayesian trees (see fig. 1 in the Supplementary Material online), we used the r8s program ( Sanderson 2003) and the Langley-Fitch (LF) method with a “local molecular clock” and the Nonparametric rate smoothing (NPRS, Sanderson [1997]) method, both with the Powell search algorithm. In the LF method, local rates were calculated for 12 different clades (e.g., for each of the chromist plastid lineages, six for non-Cyanidiales red algae, one for the Cyanidiales, one for the Streptophyta [charophytes and land plants], and one for the chlorophyte green algae). Ninety-five percent confidence intervals on divergence dates were calculated using a drop of two (s = 2) in the log likelihood units around the estimates ( Cutler 2000). Three different starting points were used in each molecular clock analysis to avoid local optima. We chose methods that relax the assumption of a constant molecular clock across the tree because the likelihood ratio test showed significant departure, in our data set, from clock-like behavior (P < 0.005).


New theory suggests alternate path led to rise of the eukaryotic cell

As a fundamental unit of life, the cell is central to all of biology. Better understanding how complex cells evolved and work promises new revelations in areas as diverse as cancer research and developing new crop plants.

But deep thinking on how the eukaryotic cell came to be is astonishingly scant. Now, however, a bold new idea of how the eukaryotic cell and, by extension, all complex life came to be is giving scientists an opportunity to re-examine some of biology’s key dogma.

All complex life — including plants, animals and fungi — is made up of eukaryotic cells, cells with a nucleus and other complex internal machinery used to perform the functions an organism needs to stay alive and healthy. Humans, for example, are composed of 220 different kinds of eukaryotic cells — which, working in groups, control everything from thinking and locomotion to reproduction and immune defense.

Thus, the origin of the eukaryotic cell is considered one of the most critical evolutionary events in the history of life on Earth. Had it not occurred sometime between 1.6 and 2 billion years ago, our planet would be a far different place, populated entirely by prokaryotes, single-celled organisms such as bacteria and archaea.

For the most part, scientists agree that eukaryotic cells arose from a symbiotic relationship between bacteria and archaea. Archaea — which are similar to bacteria but have many molecular differences — and bacteria represent two of life’s three great domains. The third is represented by eukaryotes, organisms composed of the more complex eukaryotic cells.

Eukaryotic cells are characterized by an elaborate inner architecture. This includes, among other things, the cell nucleus, where genetic information in the form of DNA is housed within a double membrane mitochondria, membrane-bound organelles, which provide the chemical energy a cell needs to function and the endomembrane system, which is responsible for ferrying proteins and lipids about the cell.

Prevailing theory holds that eukaryotes came to be when a bacterium was swallowed by an archaeon. The engulfed bacterium, the theory holds, gave rise to mitochondria, whereas internalized pieces of the outer cell membrane of the archaeon formed the cell’s other internal compartments, including the nucleus and endomembrane system.

“The current theory is widely accepted, but I would not say it is ‘established’ since nobody seems to have seriously considered alternative explanations,” explains David Baum, a University of Wisconsin–Madison professor of botany and evolutionary biologist who, with his cousin, University College London cell biologist Buzz Baum, has formulated a new theory for how eukaryotic cells evolved. Known as the “inside-out” theory of eukaryotic cell evolution, the alternative view of how complex life came to be was published recently (Oct. 28, 2014) in the open access journal BMC Biology.

The inside-out theory proposed by the Baums suggests that eukaryotes evolved gradually as cell protrusions, called blebs, reached out to trap free-living mitochondria-like bacteria. Drawing energy from the trapped bacteria and using bacterial lipids — insoluble organic fatty acids — as building material, the blebs grew larger, eventually engulfing the bacteria and creating the membrane structures that form the cell’s internal compartment boundaries.

“The idea is tremendously simple,” says David Baum, who first began thinking about an alternate theory to explain the rise of the eukaryotic cell as an Oxford University undergraduate 30 years ago. “It is a radical rethinking, taking what we thought we knew (about the cell) and turning it inside-out.”

From time to time, David Baum dusted off his rudimentary idea and shared it with others, including the late Lynn Margulis, the American scientist who developed the theory of the origin of eukaryotic organelles. Over the past year, Buzz and David Baum refined and detailed their idea, which, like any good theory, makes predictions that are testable.

“First, the inside-out idea immediately suggested a steady stepwise path of evolution that required few cellular or molecular innovations. This is just what is required of an evolutionary model,” argues Buzz Baum, an expert on cell shape and structure. “Second, the model suggested a new way of looking at modern cells.”

“The current theory is widely accepted, but I would not say it is ‘established’ since nobody seems to have seriously considered alternative explanations.”

Modern eukaryotic cells, says Buzz Baum, can be interrogated in the context of the new theory to answer many of their unexplained features, including why nuclear events appear to be inherited from archaea while other features seem to be derived from the bacteria.

“It is refreshing to see people thinking about the cell holistically and based on how cells and organisms evolved,” says Ahna Skop, a UW–Madison professor of genetics and an expert on cell division. The idea is “logical and well thought out. I’ve already sent the paper to every cell biologist I know. It simply makes sense to be thinking about the cell and its contents in the context of where they may have come from.”

The way cells work when they divide, she notes, requires the interplay of molecules that have evolved over many millions of years to cut cells in two in the process of cell division. The same molecular functions, she argues, could be repurposed in a way that conforms to the theory advanced by the Baums. “Why spend the energy to remake something that was made thousands of years ago to pinch in a cell? The functions of these proteins just evolve and change as the organism’s structure and function change.”

Knowing more about how the eukaryotic cell came to be promises to aid biologists studying the fundamental properties of the cell, which, in turn, could one day fuel a better understanding of things like cancer, diabetes and other cell-based diseases aging and the development of valuable new traits for important crop plants.

“I have no idea if it is right or wrong, but they’ve done a good job of pulling in detail and providing testable hypotheses. That, in itself, is incredibly useful.”

One catch for fleshing out the evolutionary history of the eukaryotic cell, however, is that unlike many other areas of biology, the fossil record is of little help. “When it comes to individual cells, the fossil record is rarely very helpful,” explains David Baum. “It is even hard to tell a eukaryotic cell from a prokaryotic cell. I did look for evidence of microfossils with protrusions, but, not surprisingly, there were no good candidates.”

A potentially more fruitful avenue to explore, he suggests, would be to look for intermediate forms of cells with some, but not all, of the features of a full-blown eukaryote. “The implication is that intermediates that did exist went extinct, most likely because of competition with fully-developed eukaryotes.”

However, with a more granular understanding of how complex cells evolved, it may be possible to identify living intermediates, says David Baum: “I do hold out hope that once we figure out how the eukaryotic tree is rooted, we might find a few eukaryotes that have intermediate traits.”

“This is a whole new take (on the eukaryotic cell), which I find fascinating,” notes UW–Madison biochemistry Professor Judith Kimble. “I have no idea if it is right or wrong, but they’ve done a good job of pulling in detail and providing testable hypotheses. That, in itself, is incredibly useful.”


In general, there are 8 types of main organelles in a cell: chromosomes, mitochondria, Golgi apparatus, endoplasmic reticulum, ribosome, microtubules, microfilaments and lissome.

Structure of cell organelles.

If we are talking about animal cells, then animal cell organelles include centrioles and microfibrils (besides organelles mentioned above).

How many organelles are in a plant cell? Plant cell organelles include the plastids (besides organelles mentioned above). In general, the composition of organelles in the cells may vary significantly depending on the type of the cell itself.


4.3 Eukaryotic Cells

In this section, you will explore the following questions:

  • How does the structure of the eukaryotic cell resemble as well as differ from the structure of the prokaryotic cell?
  • What are structural differences between animal and plant cells?
  • What are the functions of the major cell structures?

Connection for AP ® Courses

Eukaryotic cells possess many features that prokaryotic cells lack, including a nucleus with a double membrane that encloses DNA. In addition, eukaryotic cells tend to be larger and have a variety of membrane-bound organelles that perform specific, compartmentalized functions. Evidence supports the hypothesis that eukaryotic cells likely evolved from prokaryotic ancestors for example, mitochondria and chloroplasts feature characteristics of independently-living prokaryotes. Eukaryotic cells come in all shapes, sizes, and types (e.g. animal cells, plant cells, and different types of cells in the body). (Hint: This a rare instance where you should create a list of organelles and their respective functions because later you will focus on how various organelles work together, similar to how your body’s organs work together to keep you healthy.) Like prokaryotes, all eukaryotic cells have a plasma membrane, cytoplasm, ribosomes, and DNA. Many organelles are bound by membranes composed of phospholipid bilayers embedded with proteins to compartmentalize functions such as the storage of hydrolytic enzymes and the synthesis of proteins. The nucleus houses DNA, and the nucleolus within the nucleus is the site of ribosome assembly. Functional ribosomes are found either free in the cytoplasm or attached to the rough endoplasmic reticulum where they perform protein synthesis. The Golgi apparatus receives, modifies, and packages small molecules like lipids and proteins for distribution. Mitochondria and chloroplasts participate in free energy capture and transfer through the processes of cellular respiration and photosynthesis, respectively. Peroxisomes oxidize fatty acids and amino acids, and they are equipped to break down hydrogen peroxide formed from these reactions without letting it into the cytoplasm where it can cause damage. Vesicles and vacuoles store substances, and in plant cells, the central vacuole stores pigments, salts, minerals, nutrients, proteins, and degradation enzymes and helps maintain rigidity. In contrast, animal cells have centrosomes and lysosomes but lack cell walls.

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 1, Big Idea 2, and Big Idea 4 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 1 The process of evolution drives the diversity and unity of life.
Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry
Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Science Practice 7.2 The student can connect concepts in and across domains to generalize or extrapolate in and/or across enduring understandings
Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life and how these shared, conserved core processes and features support the concept of common ancestry for all organisms.
Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis.
Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments.
Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 2.13 The student is able to explain how internal membranes and organelles contribute to cell functions.
Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.
Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively.
Learning Objective 2.14 The student is able to use representations and models to describe differences in prokaryotic and eukaryotic cells.
Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties.
Enduring Understanding 4.A Interactions within biological systems lead to complex properties.
Essential Knowledge 4.A.2 The structure and function of subcellular components, and their interactions, provide essential cellular processes.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 4.5 The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions.

Teacher Support

Divide students into groups of 4–5 and assign each group either a bacterial, plant or animal cell and ask each group to draw the cell and its components on a large sheet of paper. Groups will use a separate sheet of paper to list all the structures and their respective functions. Ask each group to present its cell model to the rest of the class. Post the drawings on the wall of the class. Update the models with corrections as needed.

Many students reason that plant cells do not need mitochondria because the chloroplasts within plant cells convert light energy into chemical energy, and, therefore, mitochondria are not needed. Stress that all eukaryotic cells (with only few exceptions) contain mitochondria.

Emphasize that the diagrams in the textbook represent generalizations. Cells vary enormously in shapes and functions. Some internal structures may be predominant according to the type of cell. For instance, liver cells that detoxify chemicals and synthesize lipids have an extensive smooth endoplasmic reticulum.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 1.15] [APLO 2.5][APLO 2.25][APLO 1.16]

Have you ever heard the phrase “form follows function?” It’s a philosophy practiced in many industries. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should be built with several elevator banks a hospital should be built so that its emergency room is easily accessible.

Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells (Figure 4.8). Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others and 3) several, rod-shaped chromosomes. Because a eukaryotic cell’s nucleus is surrounded by a membrane, it is often said to have a “true nucleus.” The word “organelle” means “little organ,” and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body have specialized functions.

At this point, it should be clear to you that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Before turning to organelles, let’s first examine two important components of the cell: the plasma membrane and the cytoplasm.


UCMP Phylogeny Wing:The Phylogeny of Life

Life! It's everywhere on Earth you can find living organisms from the poles to the equator, from the bottom of the sea to several miles in the air, from freezing waters to dry valleys to undersea thermal vents to groundwater thousands of feet below the Earth's surface. Over the last 3.7 billion years or so, living organisms on the Earth have diversified and adapted to almost every environment imaginable. The diversity of life is truly amazing, but all living organisms do share certain similarities. All living organisms can replicate, and the replicator molecule is DNA. As well, all living organisms contain some means of converting the information stored in DNA into products used to build cellular machinery from fats, proteins, and carbohydrates.

Three Domains of Life

Click on a domain to begin exploring.

Until comparatively recently, living organisms were divided into two kingdoms: animal and vegetable, or the Animalia and the Plantae. In the 19th century, evidence began to accumulate that these were insufficient to express the diversity of life, and various schemes were proposed with three, four, or more kingdoms. The scheme most often used currently divides all living organisms into five kingdoms: Monera (bacteria), Protista, Fungi, Plantae, and Animalia. This coexisted with a scheme dividing life into two main divisions: the Prokaryotae (bacteria, etc.) and the Eukaryotae (animals, plants, fungi, and protists).

Recent work, however, has shown that what were once called "prokaryotes" are far more diverse than anyone had suspected. The Prokaryotae are now divided into two domains, the Bacteria and the Archaea, as different from each other as either is from the Eukaryota, or eukaryotes. No one of these groups is ancestral to the others, and each shares certain features with the others as well as having unique characteristics of its own.

Within the last two decades, a great deal of additional work has been done to resolve relationships within the Eukaryota. It now appears that most of the biological diversity of eukaryotes lies among the protists, and many scientists feel it is just as inappropriate to lump all protists into a single kingdom as it was to group all prokaryotes. Although many revised systems have been proposed, no single one of them has yet gained a wide acceptance.

A fourth group of biological entities, the viruses, are not organisms in the same sense that eukaryotes, archaeans, and bacteria are. However, they are of considerable biological importance.

In all cladograms in our exhibits, if there is a picture within a box, that means we have an exhibit on the taxon. If your favorite organisms aren't here yet, keep trying: since there may be as many as 100 million living and fossil species of organism, it may take us a little while to cover all the highlights. For more information on finding your way around in our phylogeny exhibit, read the navigation page.


Watch the video: Ευκαρυωτικό κύτταρο - Βιολογία Βκαι ΓΓυμνασίου (December 2022).