Arxiu d'etiquetes: tree of life

Photosynthesis and vegetal life

In this article we will talk about photosynthesis and about the first kinds of vegetal life. In the current systematic, the term plant fits primarily to terrestrial plants, while the term vegetal is an old term of Aristotelian connotation that refers to organisms with photosynthetic functions. But, as with everything, there are exceptions.

The term plant has existed for many years. But, previously, Aristotle was who classified the living organisms into three mainly groups:

  • Vegetals (vegetative soul): can perform nutrition and reproduction.
  • Animals (sensitive soul): nutrition, reproduction, perception, movement and desire.
  • Humans: can do all these things and also have the ability to reason.
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Aristotle (Public domain)

This simplistic way of perceiving the living world has lasted for a long time, but has varied due to different studies by several authors like Linnaeus or Whittaker, among others.

A very current classification was proposed in 2012, The Revised Classification of Eukaryotes. J. Eukariot. Microbiol. 59 (5): 429-493; this one reveals a true tree of life.

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Sina ;. Adl, et al. (2012) The revised classification of Eukaryotes.  J Eukaryot Microbiol.; 59 (5): 429-493

WHAT IS PHOTOSYNTHESIS? IS IT A UNIQUE PROCESS?

Photosynthesis is a metabolic process that allows to use light energy to transform simple inorganic compounds into organic complexes. To do this, they need a number of photosynthetic pigments that capture these light rays and that through a series of chemical reactions allow to perform internal processes that give rise to organic compounds.

This nutritious option has been developed by many organisms in multiple groups and branches of the tree of life of eukaryotes. And among them appears  the Archaeplastida, the lineage of organisms that has led to land plants.

Terrestrial plants (Embryophyta) are easily definable, but what about the algae? Usually, they are defined as eukaryotic organisms living primarily in the aquatic environment and with a relatively simple organization, but this is not always true. For this reason, all Archaeplastida groups falling outside the concept of land plants (a small group within Archaeplastida) are called “algae“.

There are also photosynthetic prokaryotes into Eubacteria domain, and it is in these where photosynthesis is highly variable. While in eukaryotes is unique, oxygenic photosynthesis.

The Eubacteria domain is very broad, and among its branches there are up to 5 large groups of photosynthetic organisms: Chloroflexi, Firmicutes, Chlorobi, Proteobacteria and Cyanobacteria. The latter are the only eubacterial performing an oxygenic photosynthesis; with release of oxygen from water molecules and using hydrogen from water as electron donor. The rest performs an anoxygenic photosynthesis: the electron donor is sulfur or hydrogen sulfide and, during this process, oxigen is never released, since water rarely intervenes; which is why they are known as purple sulfur bacteria.

Photosynthesis is probably older than life itself. Oxygenic photosynthesis, which is tightly related to this group of bacteria, the cyanobacteria, probably occurs later. But it was crucial for the development of life on our planet, since transformed the atmosphere in a more oxygenated one and, due to this, life on Earth had become more diverse and has evolved.

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Amazon, the lungs of the Earh (Author: Christian Cruzado; Flickr)

WHAT PIGMENTS ARE USED?

Cyanobacteria share pigments with terrestrial plants and other photosynthetic eukaryotes. These pigments are primarily chlorophylls a and b (the universal ones); c and d are only present in some groups. There are two more pigments that are univeral: carotenes, these ones act as antennas that transfer the captured energy to chlorophylls and also protect the reaction center against autoxidation, and phycobiliproteins (phycocyanin, phycoerythrin, etc.), which appear in both cyanobacteria and other eukaryotic groups photosynthetic and are responsible for capturing light energy.

But, why exist this variability of accessory pigments? because each pigment have a different absorption spectrum, and the fact to present different molecules allows to collect much better the wavelenght of sunlight; i.e., energy capture is much more efficient.

On the other hand, the anoxygenic photosynthetic bacteria don’t present chlorophylls and, instead, have specific molecules of the prokaryotes, the bacteriochlorophylls.

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Absorption spectrum of different pigments (Reference: York University)

Where are pigments located?

In the organisms with oxygenic photosynthesis, that is, in cyanobacteria and photosynthetic eukaryotes, pigments are located into complex structures. In cyanobacteria, there are various concentric flattened sacs called thylakoids in the peripheral cytoplasm, which are only surrounded by a membrane. And it is in the lumen of the thylakoid where pigments are located. In eukaryotes, however, we found chloroplasts, which are intracellular organelles full of thylakoids with at least two membranes and they are particular of photosynthetic eukaryotes. In these chloroplasts is where photosynthesis takes place. Both groups, therefore, perform oxygenic photosynthesis within the thylakoids; the difference is that in eukaryotes, the thylakoids are located into the chloroplasts.

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Plant cells where we can see chloroplasts (Author: Kristian Peters – Fabelfroh)

On the other hand, in organisms with anoxygenic photosynthesis there are different options. The purple bacteria contain pigments in chromatophores, a kind of vesicles in the center or periphery of the cell. In contrast, the green bacteria (Chlorobi and Chloroflexi) present several flattened vesicles at the periphery of the cell, on the plasma membrane, where bacteriochlorophyll are located. In Heliobacterium, the pigment is attached to the inner surface of the plasma membrane. They are generally not complex structures, and often this structures have simple membranes.

ORIGIN OF THE PHOTOSYNTHETIC ORGANISMS

The fossil evidence of the earliest photosynthetic organisms are the stromatolites (3.2 Ga ago). They are structures formed by overlapping thin layers of organisms together with their own calcium carbonate deposits. These occurs in shallow waters, in warm and well-lit seas. Although many seem straight columns, deviations are observed because they try to be oriented towards the sunlight to perform photosynthesis. In the past they had a crucial importance in building reefs-like formations and they also participated into the atmospheric composition changes. Currently, there are some which are still alive.

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Stromatolites (Author:Alessandro, Flickr)

REFERENCES

  • Notes from the Environmental Biology degree (Universitat Autònoma de Barcelona) and the Master’s degree in Biodiversity (Universitat de Barcelona).
  • Font Quer, P. (1953): Diccionario de Botánica. Editorial Labor, Barcelona.
  • Izco, J., Barreno, E., Brugués, M., Costa, M., Devesa, J. A., Fernández, F., Gallardo, T., Llimona, X., Parada, C., Talavera, S. & Valdés, B. (2004) Botánica 2.ªEdición. McGraw-Hill, pp. 906.
  • Willis, K.J. & McElwain, J.C. (2014) The Evolution of Plants (second edition). Oxford University Press, 424 pp.

Difusió-anglès

Classification and phylogeny for beginners

In this blog, we usually use therms related with the classification of living beings and their phylogeny. Due to the difficulty of these therms, in this post we will explain them for those who are introducing to the topic. 

INTRODUCTION

Before introducing in the topic, it is necessary to explain two concepts, which are usually confused: systematics and taxonomy.

Systematics is the science of the classification and reconstruction of phylogeny, it means that is responsible for reconstructing the origin and diversification of a taxon (unit that we want to classify, such as a species, a family or an order).

On the other hand, taxonomy is the study of the principles of scientific classification, the order and the name of organisms.

In other words, while systematics is responsible for creating systems of classification, which are represented by trees, taxonomy establishes the rules and methods to identify, name and classify each species in the different taxonomic categories based on systematics.

ABOUT SPECIES AND BEYOND

We cannot begin to talk about how to classify species without knowing what is a species and other classification levels of organisms.

WHAT IS A SPECIES?

Along history, it has been given several definitions to the concept species with different approaches.

  • Morphological concept of species: a species is a group of organisms with fix and essential features that represent a pattern or archetype. This concept is totally discarded nowadays, despite morphological features are used in guides to identify species.
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Despite all guides use morphological features to identify species, morphological concept of species is not used (Picture: Revista Viva).
  • Biological concept of species: a species is a group of natural populations which reproduce among them and reproductively isolated and have their own niche in nature. So, a species has common ancestry and share traits of gradual variation.  This definition has some problems: it is only applicable in species with sexual reproduction and it is not applicable in extinct species.
  • Evolutionary concept of species: a species is a single lineage of ancestor-descendent populations that maintains its identity in front of other lineages and has its evolutionary tendencies and historical destination. This approach and the biological one are, in fact, complementary because they are talking about different phenomenons.
  • Phylogenetic concept of species: according to this point of view, a species is an irreducible group of organisms, diagnostically distinguishable from other similar groups and inside which there is a parental pattern of ancestry and descendants.  This point of view covers sexual and asexual reproduction.
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According to the phylogenetic definition of species, A, B and C are different species. In the C group, all of them are the same species with different types (Picture: Sesbe).

BEYOND SPECIES

Species are classified into a hierarchical system based on more taxonomical categories. From the highest to the lowest category, organisms can be classified in: Domain> Kingdom> Phylum> Class> Order> Family> Genus> Species> Subspecies> Variety> Form. 

We are giving an example: imagine dogs.  Dogs, like wolf, are included in the same species: Canis lupus, but dog is the subspecies Canis lupus familiaris. The naming of a species is its genus (Canis) followed by the specific epithet (lupus). The other taxonomical categories of dogs are: Eukarya Domain, Animal Kingdom, Chordata Phylum, Vertebrata Subphylum, Mammalia Class, Carnivora Order and Canidae Family.

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Dogs and wolfs are included in the same species, but they are different subspecies (Picture: Marc Arenas Camps).

HOW IS TREE OF LIFE RECONSTRUCTED?

To reconstruct tree of life, it is the relationships between living and extinct species (phylogeny), we use traits. Traits are features of organisms that are used to study the variation inside a species and among them.

To reconstruct the phylogeny, it is used the shared traits among different taxa. We have to distinguish two types of similarity: when similarity of traits is a result of a common lineage is called homology, while when it is not the result of common ancestry is known as homoplasy.

Probably, it will be easier to understand it with an example. The wings of owls and quails are similar because they have the same origin (homology), but the wings of insects, birds and bats, despite they have the same function, they do not have the same origin (homoplasy).

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The wings of insects, birds and bats are an homoplasy (Picture: Natureduca).

There are three types of homoplasy:

  • Parallelism: the ancestral condition of a variable trait (plesiomorphic) is present in the common ancestor, but the derived state (apomorphic) has evolved independently. An example is the development of a four-cavity heart in birds and mammals.
  • Convergence: in this case, the homoplastic trait is not present in the common ancestor. The structures originated by convergence are called analogy. An example is the wings of insects and birds.
  • Secondary loss or reversion: consist on the reversion of a trait to a state that looks ancestral. So, it looks and old state but, in fact, is derived.
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Biological parallelism, convergence and reversion (Picture: Marc Arenas Camps).

There are different types of traits that are used to order living beings: morphological, structural, embryological, palaeontological, ethological, ecological, biochemical and molecular.

Species that share derived states of a trait constitute clades and the trait is known as synapomorphy. Synapomorphies are traits that were originated in a common ancestor and are present in that ancestor and all its descendants. So, mammary glands are a synapomorphy of mammals.

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Mammary glands are a synapomorphy of mammals (Picture: Tiempo de éxito).

After the selection of traits, the several classification schools use them in different ways to get the best relationship between living beings.

REFERENCES

  • Notes of the subject Advanced Biology Basics, Degree in Biology (University of Barcelona).
  • Hickman, Roberts, Larson, l’Anson & Eisenhour (2006). Principios integrales de zoología. Ed. McGraw Hill (13 ed).
  • Izco (2004). Botánica. Ed. McGraw Hill (2 ed).
  • Shnek & Massarini (2008). Biología. Ed. Médica Panamericana (7 ed).
  • Vargas (2009). Glosario de Cladística: Introducción a la sistemática filogenética.
  • Cover picture: Tree of life mural, Kerry Darlington

Difusió-anglès

Evolution for beginners

Biological evolution is still not well understood by general public, and when we speak of it in our language abound expressions that confuse even more how mechanisms that lead to species diversity work. Through questions you may have ever asked yourself, in this article we will have a first look at the basic principles of evolution and debunk misconceptions about it.

IS EVOLUTION REAL? IT IS NOT JUST A THEORY OR AN IDEA WITHOUT EVIDENCES?

Outside the scientific field, the word “theory” is used to refer to events that have not been tested or assumptions. But a scientific theory is the explanation of a phenomenon supported by evidence resulting from the application of the scientific method.

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The scientific method. Image by Margreet de Heer.

Theories can be modified, improved or revised if new data don’t continue to support the theory, but they are always based on some data, repeatable and verifiable experiments by any researcher to be considered valid.

So few people (sic) doubts about the heliocentric theory (the Earth rotates around the Sun), or the gravitational theory of Newton, but in the popular imagination some people believe that the theory of evolution made by Charles Darwin (and Alfred Russell Wallace) is simply a hypothesis and has no evidence to support it. With new scientific advances, his theory has been improved and detailed, but more than 150 years later, nobody has been able to prove it wrong, just the contrary.

WHAT EVIDENCE WE HAVE THAT EVOLUTION IS TRUE?

We have many evidences and in this post we will not delve into them. Some of the evidence available to us are:

  • Paleontological record: the study of fossils tell us about the similarities and differences of existing species with others thousands or millions old, and to establish relationships respect each other.
  • Comparative anatomy: comparison of certain structures that are very similar between different organisms, can establish whether they have a common ancestor (homologous structures, for example, five fingers in some vertebrates) if they have developed similar adaptations (analogous structures, for example, the wings of birds and insects), or if they have lost their function (vestigial organs, such as the appendix).
Homologous organs in humans, cats, whales and bats
Homologous organs in humans, cats, whales and bats
  • Embryology: the study of embryos of related groups shows a strong resemblance in the earliest stages of development.
  • Biogeography: The study of the geographical distribution of living beings reveals that species generally inhabit the same regions as their ancestors, although there are other regions with similar climates.
  • Biochemistry and genetics: chemical similarities and differences allow to establish relationships among different species. For example, species closely related to each other have a structure of their DNA more similar than others more distant. All living beings share a portion of DNA that is part of your “instructions”, so there are also found in a fly, a plant or a bacterium, proof that all living things have a common ancestor.

IS IT TRUE THAT ORGANISMS ADAPT TO THE ENVIRONMENT AND ARE DESIGNED FOR LIVING IN THEIR HABITAT?

Both expressions, frequently used, mean that living beings have an active role to adapt to the environment or “someone” has designed them to live exactly where they are. It is a typical example of Lamarck and giraffes: as a result of stretching the neck to reach the higher leaves of the treescurrently giraffes have this neck for giving it this use. They have a necessity, they change their bodies to success. It is precisely upside down: it is the habitat that selects the fittest, nature “selects” those that are most effective to survive, and therefore reproduce. It is what is known as natural selection, one of the main mechanisms of evolution. It needs three requirements to act:

  • Phenotypic variability: there must be differences between individuals. Some giraffes necks were slightly longer than others, just as there are taller people than others, with blue or brown eyes.
  • Biological fitness: this difference has to suppose an advantage. For example, giraffes with a slightly longer neck could survive and reproduce, while the others don’t.
  • Heredity: these characters must be transmitted to the next generation, the offspring will be slightly different to that feature, while “short neck” feature transmits less and less.
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The variability in the population causes individuals with favorable characteristics to reproduce more and pass on their genes to the next generation, increasing the proportion of those genes. Image taken from Understanding evolution

Over the years these changes are accumulated until the genetic differences are so big that some populations may not mate with others: a new species has appeared.

If you thought that this is similar to artificial selection that we do with the different breeds of dogs, cows who give more milk, trees bearing more fruit and larger, congratulations, you think like Darwin as it was inspired by some of these facts. Therefore, living beings are mere spectators of the evolutionary process, depending of changes in their habitat and their genetic material.

WHY ORGANISMS ARE SO DIVERSE?

Genetic variability allows natural selection act. Changes in the genetic material (usually DNA) are caused by:

  • Mutations: changes in the genome that may be adverse or lethal for survival, indifferent or beneficial to survival and reproduction. If they have benefits, they will pass to the next generations.
  • Gene flow: is the motion of genes between populations (migration of individuals allows this exchange when mate with others in a different population).
  • Sexual reproduction: allows recombination of genetic material of different individuals, giving rise to new combinations of DNA.

Populations that have more genetic variability are more likely to survive if happen any changes in their habitat. Populations with less variability (eg, being geographically isolated) are more sensitive to any changes in their habitat, which may cause their extinction.

Evolution can be observed in beings with a very high reproduction rate, for example bacteria, since mutations accumulate more quickly. Have you ever heard that bacteria become resistant to our antibiotics or some insects to pesticides? They evolve so quickly that within a few years were selected the fittest to survive our antibiotics.

ARE WE THE MOST EVOLVED ANIMALS?

Theory of Evolution has various consequences, such as the existence of a common ancestor and that therefore, that we are animals. Even today, and even among the young ones, there is the idea that we are something different between living beings and we are in a special podium in the collective imagination. This anthropocentric thinking caused Darwin mockery and confrontations over 150 years ago.

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Caricature of Darwin as an orangutan. Public domain image first published in 1871

We use our language to be “more evolved” as a synonym for more complex, and we consider ourselves one species that has reached a high level of understanding of their environment, so many people believe that evolution has come to an end with us.

The question has a mistake of formulation: actually evolving pursues no end, it just happens, and the fact that millions of years allows the emergence of complex structures, it does not mean that simpler lifeforms are not perfectly matched in the habitat where they are. Bacteria, algae, sharks, crocodiles, etc., have remained very similar over millions of years. Evolution is a process that started acting when life first appeared and continues to act in all organisms, including us, although we have changed the way in which natural selection works  (medical and technological breakthroughs, etc.).

SO IF WE COME FROM MONKEYS, WHY DO STILL MONKEYS EXIST?

The truth is that we don’t come from monkeys, we are monkeys, or to be more rigorous, apes. We have not evolved from any existing primate. As we saw in a previous post, humans and other primates share a common ancestor and natural selection has been acting differently in each of us. That is, evolution has to be viewed as a tree, and not as a straight line, where each branch would be a species .

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First scheme of the evolutionary tree of Darwin in his notebook (1837). Public domain image.

Some branches stop growing (species become extinct), while others continue to diversify. The same applies to other species, in case you have asked yourself, “if amphibians come from fish, why are there still fish?”. Currently, genetic analyzes have contributed so much data that they make so difficult to redesign the classical Dariwn’s tree.

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Classification of live organisms based on the three domains Archaea, Bacteria and Eukarya, data of Carl R. Woese (1990). Included in Eukarya there are the Protista, Fungi, Plantae and Animalia kingdoms. Image by Rita Daniela Fernández.

Evolution is a very broad topic that still generates doubts and controversies. In this article we have tried to bring to uninitiated people some basics, where we can delve into the future. Do you have any questions about evolution? Are you interested into a subject that we have not talked about? You can leave your comments below.

REFERENCES

MIREIA QUEROL ALL YOU NEED IS BIOLOGY