Tag Archives: genetics

The genetic blueprint of an octopus reveals much about this amazing creature

The Conversation

Jan Strugnell, La Trobe University and Alvaro Roura, La Trobe University

Octopuses are among the most impressive of the invertebrates thanks to their ability to solve puzzles, camouflage perfectly with their surroundings, mimic other species, use tools and potentially predict world cup victories.

Now that scientists this month have published the first octopus genome we are a step closer to understanding how these feats are achieved in a lineage so divergent from our own.

The octopus genome was of the California two-spot (Octopus bimaculoides) and it may provide us with some leads on how the highly unusual octopod body plan evolved.

Interesting body plan

Octopods are contained within the group Cephalopoda, which literally means “head-footed”, as the foot (i.e. the octopus arms) are connected directly to the head.

One family of genes that is known to influence body plan in animals is called Hox. These genes usually occur together, clustered in groups, and the order of the genes directly corresponds to the order in which they are activated along the body during development.

In the octopus genome the scientists found the Hox genes are completely scattered, with no two of them occurring together. This scattered nature of the Hox genes across the genome may provide insights into octopod body plan development and why octopus have a much more unusual body plan than their cousins, such as snails and oysters.

Another big finding of this octopus genome project is actually something the authors did not find: whole genome duplication. That is, evidence that the entire genome was duplicated throughout history so that two copies of the genome were present.

It was previously believed that a whole genome duplication event in the octopus lineage may have driven the evolution of some of the remarkable characteristics present within octopus, such as complicated behaviours including the use of tools or vertebrate-like eyes.

The idea was that a whole genome duplication event frees up a set of genes, allowing these copies to take on new functions. But the lack of evidence for this suggests other mechanisms are at play.

Blended genome

One of these mechanisms appears to be the huge expansion in some gene families previously thought to be expanded only in vertebrates and not in other invertebrate lineages. One of these families is the protocadherins, which are cell adhesion molecules required to establish and maintain nervous system organisation.

The octopus genome boasts 168 protocadherin genes, which presumably play a crucial role in the highly modified octopus nervous system and complex brain. In contrast, these protocadherins are found in relatively small numbers (17 to 25) in organisms such as limpets and oysters, and are completely absent in several invertebrate model organisms including the fruit fly and nematodes.

The fact that protocadherin genes occur in large numbers in vertebrates and octopus but not in other animals, and that they are expressed in octopus neural and sensitive tissues (suckers and skin), suggests that they might play an important role in the evolution of cephalopod neural complexity.

Protocadherin diversity provides a mechanism to establish the synaptic connections needed to interpret the vast amount of stimuli, including touch and smell perceived through the suckers, and organise complex behavioural responses like camouflaging through the change in skin colour and texture/sculpture. It is interesting that the diversity in these genes has been generated by different mechanisms in octopus and vertebrates.

The genome also shows a lot of evidence for transposon activity. Transposons are DNA sequences that move locations around the genome (sometimes called “jumping genes”) and they can drive evolution.

In comparison to other genomes, the scientists note that the octopus genome looks like it has been “put into a blender and mixed”. They show that these transposons play an important role in driving this mixing of the genome.

They also found that transposons are highly expressed in neural tissues. They suggest that these may play an important role in memory and learning as shown in mammals and flies.

The ability of octopuses to learn and solve puzzles is something that is fascinating to us and so this will be a fruitful area for further research.

Why did it take so long?

It is more than 14 years since the human genome was published in Nature and Science, and numerous genomes have been published since then such as pandas, bees and recently 48 species of bird.

But this latest publication represents the first genome of any cephalopod and one of only a handful of molluscs, (the group containing cephalopods). Other molluscan genomes include the limpet (Lottia gigantea), oyster (Crassostrea gigas) and the sea hare (Aplysia californica).

This first octopus genome gives us great insight into the evolution and function of this fascinating group and will serve as a great catalyst for further research on cephalopod genetics.

Jan Strugnell is Associate professor at La Trobe University and Alvaro Roura is Postdoctoral fellow at La Trobe University

This article was originally published on The Conversation. (Reblogged by permission). Read the original article.

Leave a comment

Filed under Reblogs

Charles Darwin – where he was right and wrong

by Tim Harding, B.Sc.

(An edited version of this essay was published in The Skeptic magazine, June 2015, Vol 35 No 2, under the title ‘Darwin’s Missing Link’.  The essay is based on a talk presented to the Mordi Skeptics on Tuesday 5 May 2015).

Charles Darwin (1809-1882) is best known for his major contributions to evolutionary theory. In 1859, Darwin published his theory of natural selection as the mechanism of evolution in his revolutionary book On the Origin of Species. This book provided compelling evidence overcoming the scientific rejection of earlier concepts of transmutation of species. The basic principles of his theory have been shown to be correct and are now widely accepted as the basis of mainstream zoology, botany and ecology.

On the other hand, in a later book Darwin got it wrong with the mechanisms of inheritance.  The empirical rules of genetics, based solely on observational results, were largely understood since Gregor Mendel’s ‘wrinkled pea’ experiments in the 1860s. The postulated units of inheritance were called genes, but in Charles Darwin’s time it was not understood where genes were located in the body or what they physically consisted of. Darwin knew that there must have been a physical mechanism for inheritance, but his speculations about it – called pangenesis – were incorrect. Fortunately for the credibility of his theory of evolution by natural selection, he published these speculations later in a separate 1868 book titled Variation of Animals and Plants Under Domestication.

Darwin’s early career

Charles Robert Darwin was born in Shrewsbury, England, on 12 February 1809 at his family home, The Mount. He was the fifth of six children of wealthy society doctor and financier Robert Darwin, and Susannah Darwin (née Wedgwood).

Darwin went to Edinburgh University in 1825 to study medicine. In his second year he neglected his medical studies for natural history and spent four months assisting Robert Grant’s research into marine invertebrates. Grant revealed his enthusiasm for the concept of transmutation of species (the altering of one species into another), but Darwin initially rejected this concept (probably for religious reasons).

Ideas about the transmutation of species were controversial as they conflicted with theological beliefs that species were unchanging parts of a designed hierarchy and that humans were unique, unrelated to other animals. The political and religious implications were intensely debated, but transmutation was not accepted by the scientific mainstream until Darwin’s theory.

In December 1831, Darwin had joined the Beagle ship voyage as a gentleman naturalist and geologist.  In South America, he discovered fossils resembling huge armadillos, and noted the geographical distribution of modern species in hope of finding their ‘centre of creation’.  As the Beagle neared England in 1836, he began to think that species might not be immutable after all.

In March 1837, ornithologist John Gould announced that mockingbirds collected on the Galápagos Islands represented three separate species each unique to a particular island, and that several distinct birds from those islands were all classified as finches. Darwin began speculating, in a series of notebooks, on the possibility that ‘one species does change into another’ to explain these findings, and around July of that year sketched a genealogical branching of a single evolutionary tree.  Unconventionally, Darwin asked questions of fancy pigeon and animal breeders as well as established scientists.

Charles Darwin

Charles Darwin in 1860, aged 51

In late September 1838, Darwin started reading Thomas Malthus’s An Essay on the Principle of Population with its statistical argument that human populations, if unrestrained, breed beyond their means and struggle to survive. Darwin related this to the struggle for existence among wildlife and plants, so that the survivors would pass on their form and abilities, and unfavourable variations would be destroyed.  By December 1838, he had noted a similarity between the act of breeders selecting traits and a Malthusian nature selecting among variants thrown up by chance.

Darwin now had the framework of his theory of natural selection, but he was fully occupied with his career as a geologist and held off writing a sketch of his theory until his book on The Structure and Distribution of Coral Reefs was completed in May 1842.

Evolution by natural selection

Darwin continued to research and extensively revise his theory of natural selection while focusing on his main work of publishing the scientific results of the Beagle voyage.  He tentatively wrote of his ideas to the famous Scottish geologist Charles Lyell in January 1842; then in June he roughed out a 35-page pencil sketch of his theory. Darwin began correspondence about his theorising with the botanist Joseph Dalton Hooker in January 1844, and by July had rounded out his sketch into a 230-page essay, to be expanded with his research results and published if he died prematurely.

His famous 1859 book On the Origin of Species was written for non-specialist readers and attracted widespread interest upon its publication. As Darwin was already an eminent scientist, his findings were taken seriously.  The evidence he presented generated scientific, philosophical, and religious discussion. The debate over the book contributed to the campaign by Thomas Huxley and his fellow members of the X Club to secularise science by promoting scientific naturalism. Within two decades there was widespread scientific agreement that evolution, with a branching pattern of common descent, had occurred, but scientists were slow to give the mechanism of natural selection the significance that it deserved.

species divergence

Diagram representing the divergence of species, from Darwin’s Origin of Species

Darwin’s theory of evolution is based on some key facts (based on wild populations without human interference), which biologist Ernst Mayr has summarised as follows:

  • Every species is fertile enough that if all offspring survived to reproduce the population would grow.
  • Despite periodic fluctuations, populations remain roughly the same size.
  • Resources such as food are limited and are relatively stable over time.
  • Individuals in a population vary significantly from one another.
  • Much of this variation is heritable.

From these key facts, the following important inferences may be made, once again summarised by Ernst May:

  • A struggle for survival ensues.
  • Individuals less suited to the environment are less likely to survive and less likely to reproduce.
  • Individuals more suited to the environment are more likely to survive and more likely to reproduce and leave their heritable traits to future generations, which produces the process of natural selection.
  • This slow process gradually results in populations changing to adapt to their environments, and ultimately, these variations accumulate over time to form new species.

Natural selection provided a mechanism for variation and eventual speciation, but it did not explain the inheritance of variation.  Without some way to explain the inheritance of characteristics acted on by natural selection, his theory would be incomplete.

Mechanisms of inheritance

Before the advent of genetics, Hippokratic theories attempted to explain inheritance in terms of a blending of fluids extracted from all parts of both male and female bodies during intercourse.  It was thought that the characteristics of the offspring are determined by the relative amounts and strength of fluids from each part of the body of each parent.

On the other hand, ‘preformationist’ theories held that the new mammalian offspring is already preformed in miniature, either within the egg of its mother or in the semen of its father.  Both of these types of theories incorporated ‘encasement’, which was the thesis that God created all future organisms in miniature, and that reproduction was just the growth and development of these miniatures.

Hippokratic theories were very good at explaining inheritance but very bad at explaining growth and development; whilst preformationist theories were the opposite – very good at explaining growth and development but very bad at explaining inheritance.  To give some examples, Hippokratic theories were unable to adequately explain phenomena such as the regeneration of freshwater polyps; while preformationist theories were unable to adequately explain how the mating of a mare with a donkey produces a mule.

Darwin came to his hypothesis of pangenesis, from a different direction – to fill a gap left in his theory of evolution.  Darwin’s breeding experiments on domestic animals (mainly pigeons) in the 1850s and 60s were part of his attempts to complete his evolution theory.  He was attempting in these experiments to show just how quickly varying characteristics can be amplified by domestic breeding, and therefore how natural selection can operate.

Darwin called his explanation of inheritance ‘the hypothesis of Pangenesis’, which he published in 1868.  However, he provides a more succinct description of this hypothesis in an earlier unpublished manuscript on pangenesis sent to Thomas Huxley in 1865:

“Furthermore, I am led to believe from analogies immediately to be given that protoplasm or formative matter which is throughout the whole organisation, is generated by each different tissue and cell or aggregate of similar cells; – that as each tissue or cell becomes developed, a superabundant atom or gemmule as may be called of the formative matter is thrown off; – that these almost infinitely numerous and infinitely minute gemmules unite together in due proportion to form the true germ; – that they have the power of self-increase or propagation; and that they here run through the same course of development, as that which the true germ, of which they are to constitute elements, has to run through, before they can be developed into their parent tissues or cells. This may be called the hypothesis of Pangenesis”.


The Laws of Inheritance & Pangenesis

Darwin further proposed that his hypothesis would not only account for inheritance, but also for development:

“The development of each being, including all the forms of metamorphosis and metagenesis, as well as the so-called growth of the higher animals, in which structure changes, though not in a striking manner, depends on the presence of gemmules thrown off at each period of life, and on their development, at a corresponding period, in union with the preceding cells”.

Through these mechanisms, Darwin proposed that inheritance and development were tied together – not only in the generation of offspring and early stages of embryonic life, but throughout the life of the organism.  By giving ‘gemmules’ the power to be modified throughout the life of an organism and then be transferred to the next generation, he argued that inheritance should be viewed as a form of growth.

By means of this single hypothesis, Darwin attempted to not only fill a gap in his theory of evolution, but whether he meant to or not, he created an apparent synthesis between the then competing paradigms relating to inheritance and development.

After reading Variation Under Domestication, Francis Galton (a cousin of Darwin’s) arranged for a series of experiments to be conducted on rabbits initially housed in the Zoological Gardens of London and later at his Kensington home.  His intention was to demonstrate the transmission of ‘gemmules’ to succeeding generations via blood injected from one rabbit to another, using coat colour as a marker.  Galton ultimately found that not a single instance of induced variation of coat colour occurred in a total of 88 offspring from blood transfused parents, and in 1871 published his results in Nature.

In later editions of Variation Under Domestication, Darwin admitted in a footnote that he would have expected to find ‘gemmules’ in the blood, although their presence was not absolutely necessary to his hypothesis.  Darwin’s response is unconvincing, as he provides no alternative explanation as to how the ‘gemmules’ are transmitted from the parents’ somatic cells to the germ cells.  He made no real attempt to modify his hypothesis in response to Galton’s falsification of it, indicating a possible abandonment of commitment to his hypothesis.

After the rediscovery of Mendel’s work in the 1890s, scientists tried to determine which molecules in the cell were responsible for inheritance.  In 1910, Thomas Hunt Morgan argued that genes are on chromosomes, based on observations of a sex-linked white eye mutation in fruit flies.  In 1913, his student Alfred Sturtevant used the phenomenon of genetic linkage to show that genes are arranged linearly on the chromosome.  It was soon discovered that chromosomes consisted of DNA and proteins, but DNA was not identified as the gene carrier until 1944. Watson and Crick’s breakthrough discovery of the chemical structure of DNA in 1953 finally revealed how genetic instructions are stored inside organisms and passed from generation to generation.

In view of the fact that it took another 85 years after Darwin’s book Variation Under Domestication before the molecular mechanisms of inheritance to be discovered, Darwin can hardly be blamed for getting it wrong way back in 1868.  This was before even chromosomes had been discovered, let alone DNA.

On the plus side, Darwin’s theory of evolution by natural selection, with its tree-like model of branching common descent, has become the unifying theory of the life sciences. The theory explains the diversity of living organisms and their adaptation to the environment. It makes sense of the geologic record, biogeography, parallels in embryonic development, biological homologies, vestigiality, cladistics, phylogenetics and other fields, with unrivalled explanatory power; it has also become essential to applied sciences such as medicine, agriculture, conservation and environmental sciences.


Darwin, Charles (1859) The Origin Of Species. 6th ed. 1873. London: John Murray.

Darwin, Charles (1875) The Variation of Animals and Plants Under Domestication, Vol II London: John Murray.

Mayr, Ernst (1982) The Growth of Biological Thought: Diversity, Evolution, and Inheritance Harvard University Press.

Copyright notice: © All rights reserved. Except for personal use or as permitted under the Australian Copyright Act, no part of this website may be reproduced, stored in a retrieval system, communicated or transmitted in any form or by any means without prior written permission. All inquiries should be made to the copyright owner, Tim Harding at tim.harding@yandoo.com, or as attributed on individual blog posts.

If you find the information on this blog useful, you might like to consider supporting us.

Make a Donation Button

1 Comment

Filed under Essays and talks