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Common descent

From Wikipedia, the free encyclopedia

Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. According to modern evolutionary biology, all living beings could be descendants of a unique ancestor commonly referred to as the last universal common ancestor (LUCA) of all life on Earth.[1][2][3][4]

Common descent is an effect of speciation, in which multiple species derive from a single ancestral population. The more recent the ancestral population two species have in common, the more closely are they related. The most recent common ancestor of all currently living organisms is the last universal ancestor,[3] which lived about 3.9 billion years ago.[5][6] The two earliest pieces of evidence for life on Earth are graphite found to be biogenic in 3.7 billion-year-old metasedimentary rocks discovered in western Greenland[7] and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia.[8][9] All currently living organisms on Earth share a common genetic heritage, though the suggestion of substantial horizontal gene transfer during early evolution has led to questions about the monophyly (single ancestry) of life.[3] 6,331 groups of genes common to all living animals have been identified; these may have arisen from a single common ancestor that lived 650 million years ago in the Precambrian.[10][11]

Universal common descent through an evolutionary process was first proposed by the British naturalist Charles Darwin in the concluding sentence of his 1859 book On the Origin of Species:

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.[12]

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Transcription

This episode of State Clearly was only possible with support from our viewers, and from Brain-Tools.org a company dedicated to developing and delivering to patients, new treatments for Alzheimer's. Stated Clearly presents: What is Natural Selection? Natural selection is one of several key concepts contained within the theory of evolution. To understand exactly what natural selection is and why it's so important let's first take a quick look at two other evolutionary concepts: Descent with Modification and the overarching idea of Common Descent. Descent with Modification is the observable fact that when parents have children, those children often look and behave slightly different than their parents, and slightly different than each other. They descend from their parents with modifications. The differences found in offspring are partially due to random genetic mutations. Common Descent is the idea that all life on Earth is related. We descended from a common ancestor. through the gradual process of descent with modification over many many generations, a single original species is thought to have given rise to all the life we see today. the common descent of all life on earth is not a directly observable fact. We have no way of going back in time to watch it happen. Instead, Common Descent as a conclusion based on a massive collection of observable facts. Facts found independently in the study of fossils genetics comparative anatomy mathematics biochemistry and species distribution. Because the evidence for common descent is so overwhelming, the concept has been around since ancient times. In the past however, it was rejected by many philosophers and scientists for one main reason: You cannot get order and complexity from random chaos alone. The bodies and behaviors of living things are extremely complex and orderly. Descent with Modification simply produces random variation. All through history no one could explain how complex life arose from simple life through random variation, until Charles Darwin discovered Natural Selection. Charles Darwin, who lived from 1809 to 1882 was a naturalist: someone who studies nature. At the start of his career he traveled the world by ship, collecting and documenting plants and animals. During his travels, Darwin became very interested in the idea of common descent. He noticed that islands contain species of plants and animals unique to those islands, they can't be found anyplace else on earth, but they often look and behave surprisingly similar to creatures found on nearby continents. Tortoises on the Galapagos islands can be distinguished from those of Africa, meanwhile, with the exception of size, they're almost identical to a species found nearby in South America. Darwin believed the similarities could be best explained through Common Descent. Long ago a tortoise from the mainland may have drifted to the islands, possibly on a raft of storm debris, and once arriving, laid her eggs. Random changes caused by Descent with Modification over thousands of years, eventually transformed the island creatures and the mainland creatures so much, that they could no longer be considered the same species. This idea made good sense to Darwin except for one thing: the island creatures he found were not just randomly different from their mainland cousins, they were specially adapted for island life. the Galapagos is a collection of 18 main islands, many of which are home to tortoises. The larger islands have lots of grass and vegetation. Tortoises there grow extra heavy and have dome like shells. Some of the smaller islands have very little grass, forcing the tortoises to feed on island cactus. the best cactus pads grown the tops of these plants. Fortunately, tortoises on these islands are equipped with expanded front legs and saddle like shells allowing them to stretch their necks extra long to reach their food. It's almost as if these island creatures have been perfectly sculpted to survive within their unique environments. How did this sculpting take place? Random Descent with modification alone could never do such a thing. Darwin drew upon his knowledge of selective breeding to answer this question. For thousands of years, farmers have been taking wild plants and animals, and through the process of selective breeding, have sculpted the original wild forms into new domestic forms, much better suited for human use and consumption. The process is slow but simple if a single plant produces a hundred seeds, most will grow to be nearly identical to the parent plant. A few however, will be slightly different. Some variations are undesirable: smaller size, bitter taste, vulnerability to disease and so on. Other variations are highly valued! Thicker sweeter leaves for example. If a farmer only allows the best plants to reproduce and creates seeds for the next crop, small positive changes will add up over multiple generations, eventually producing a dramatically superior vegetable. You might be surprised to hear that broccoli cauliflower, kale, brussels sprouts, and cabbages, are all just different breeds of a single type of weed commonly found along the shores of the English Channel. The evolution of this original plant into all the varieties we see today was carefully guided by different farmers around the world, who simply selected for different traits. It's important to note, that the farmer doesn't actually create anything. Random Descent with Modification creates new traits. The farmer simply chooses which of those new creations are allowed to reproduce, and which are not. Darwin proposed that nature itself is also capable of selection. It may not have an intelligent brain like a farmer, but nature is an extremely dangerous place in which to live. There are germs which can kill you. Animals that can eat you. You could die of heat exhaustion. You could die of exposure to the cold. When parents produce a variety of offspring, nature, simply by being difficult to survive in, decides which of those variations get to live in reproduce, and which do not. Over multiple generations, creatures became more and more fit for survival and reproduction within their specific environments. Darwin called this process Natural Selection. Since Darwin first put forth his idea in the mid 1800s Natural Selection has been studied and witnessed numerous times in nature and in the science lab. What started out as a mere idea is now officially an observable fact! Darwin's discovery has greatly expanded our understanding of the natural world it has lead to amazing new breakthroughs, and it finally allowed scientists to seriously consider the idea of Common Descent. So to sum things up, What exactly is natural selection? Natural Selection is the process by which random evolutionary changes are selected for by nature in a consistent orderly non random way. Through the process of descent with modification, new traits are randomly produced. Nature then carefully decides which of those new traits to keep. Positive changes add up over multiple generations, negative traits are quickly discarded. Through this simple ongoing process, nature, even though it may not have a thinking mind, is capable of producing incredibly complex and beautiful creations. I'm Jon Perry, and that's Natural Selection stated clearly! that's it for this episode if you enjoyed it, subscribe to us on youtube and follow us on out face book page. if needed, I can be contacted directly from our website at statedclearly.com

History

The idea that all living things (including things considered non-living by science) are related is a recurring theme in many indigenous worldviews across the world.[13] Later on, in the 1740s, the French mathematician Pierre Louis Maupertuis arrived at the idea that all organisms had a common ancestor, and had diverged through random variation and natural selection.[14][15]

In 1790, the philosopher Immanuel Kant wrote in Kritik der Urteilskraft (Critique of Judgment) that the similarity[a] of animal forms implies a common original type, and thus a common parent.[16]

In 1794, Charles Darwin's grandfather, Erasmus Darwin asked:

[W]ould it be too bold to imagine, that in the great length of time, since the earth began to exist, perhaps millions of ages before the commencement of the history of mankind, would it be too bold to imagine, that all warm-blooded animals have arisen from one living filament, which the great First Cause endued with animality, with the power of acquiring new parts attended with new propensities, directed by irritations, sensations, volitions, and associations; and thus possessing the faculty of continuing to improve by its own inherent activity, and of delivering down those improvements by generation to its posterity, world without end?[17]

Charles Darwin's views about common descent, as expressed in On the Origin of Species, were that it was probable that there was only one progenitor for all life forms:

Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.[18]

But he precedes that remark by, "Analogy would lead me one step further, namely, to the belief that all animals and plants have descended from some one prototype. But analogy may be a deceitful guide." And in the subsequent edition,[19] he asserts rather,

"We do not know all the possible transitional gradations between the simplest and the most perfect organs; it cannot be pretended that we know all the varied means of Distribution during the long lapse of years, or that we know how imperfect the Geological Record is. Grave as these several difficulties are, in my judgment they do not overthrow the theory of descent from a few created forms with subsequent modification".

Common descent was widely accepted amongst the scientific community after Darwin's publication.[20] In 1907, Vernon Kellogg commented that "practically no naturalists of position and recognized attainment doubt the theory of descent."[21]

In 2008, biologist T. Ryan Gregory noted that:

No reliable observation has ever been found to contradict the general notion of common descent. It should come as no surprise, then, that the scientific community at large has accepted evolutionary descent as a historical reality since Darwin's time and considers it among the most reliably established and fundamentally important facts in all of science.[22]

Evidence

Common biochemistry

All known forms of life are based on the same fundamental biochemical organization: genetic information encoded in DNA, transcribed into RNA, through the effect of protein- and RNA-enzymes, then translated into proteins by (highly similar) ribosomes, with ATP, NADPH and others as energy sources. Analysis of small sequence differences in widely shared substances such as cytochrome c further supports universal common descent.[23] Some 23 proteins are found in all organisms, serving as enzymes carrying out core functions like DNA replication. The fact that only one such set of enzymes exists is convincing evidence of a single ancestry.[3][24] 6,331 genes common to all living animals have been identified; these may have arisen from a single common ancestor that lived 650 million years ago in the Precambrian.[10][11]

Common genetic code

Amino acids nonpolar polar basic acidic Stop codon
Standard genetic code
1st
base
2nd base
T C A G
T TTT Phenyl-
alanine
TCT Serine TAT Tyrosine TGT Cysteine
TTC TCC TAC TGC
TTA Leucine TCA TAA Stop TGA Stop
TTG TCG TAG Stop TGG Tryptophan 
C CTT CCT Proline CAT Histidine CGT Arginine
CTC CCC CAC CGC
CTA CCA CAA Glutamine CGA
CTG CCG CAG CGG
A ATT Isoleucine ACT Threonine  AAT Asparagine AGT Serine
ATC ACC AAC AGC
ATA ACA AAA Lysine AGA Arginine
ATG Methionine ACG AAG AGG
G GTT Valine GCT Alanine GAT Aspartic
acid
GGT Glycine
GTC GCC GAC GGC
GTA GCA GAA Glutamic
acid
GGA
GTG GCG GAG GGG

The genetic code (the "translation table" according to which DNA information is translated into amino acids, and hence proteins) is nearly identical for all known lifeforms, from bacteria and archaea to animals and plants. The universality of this code is generally regarded by biologists as definitive evidence in favor of universal common descent.[23]

The way that codons (DNA triplets) are mapped to amino acids seems to be strongly optimised. Richard Egel argues that in particular the hydrophobic (non-polar) side-chains are well organised, suggesting that these enabled the earliest organisms to create peptides with water-repelling regions able to support the essential electron exchange (redox) reactions for energy transfer.[25]

Selectively neutral similarities

Similarities which have no adaptive relevance cannot be explained by convergent evolution, and therefore they provide compelling support for universal common descent. Such evidence has come from two areas: amino acid sequences and DNA sequences. Proteins with the same three-dimensional structure need not have identical amino acid sequences; any irrelevant similarity between the sequences is evidence for common descent. In certain cases, there are several codons (DNA triplets) that code redundantly for the same amino acid. Since many species use the same codon at the same place to specify an amino acid that can be represented by more than one codon, that is evidence for their sharing a recent common ancestor. Had the amino acid sequences come from different ancestors, they would have been coded for by any of the redundant codons, and since the correct amino acids would already have been in place, natural selection would not have driven any change in the codons, however much time was available. Genetic drift could change the codons, but it would be extremely unlikely to make all the redundant codons in a whole sequence match exactly across multiple lineages. Similarly, shared nucleotide sequences, especially where these are apparently neutral such as the positioning of introns and pseudogenes, provide strong evidence of common ancestry.[26]

Other similarities

Biologists often[quantify] point to the universality of many aspects of cellular life as supportive evidence to the more compelling evidence listed above. These similarities include the energy carrier adenosine triphosphate (ATP), and the fact that all amino acids found in proteins are left-handed. It is, however, possible that these similarities resulted because of the laws of physics and chemistry - rather than through universal common descent - and therefore resulted in convergent evolution. In contrast, there is evidence for homology of the central subunits of transmembrane ATPases throughout all living organisms, especially how the rotating elements are bound to the membrane. This supports the assumption of a LUCA as a cellular organism, although primordial membranes may have been semipermeable and evolved later to the membranes of modern bacteria, and on a second path to those of modern archaea also.[27]

Phylogenetic trees

BacteriaArchaeaEukaryotaAquifexThermotogaBacteroides–CytophagaPlanctomyces"Cyanobacteria"ProteobacteriaSpirochetesGram-positivesChloroflexiThermoproteus–PyrodictiumThermococcus celerMethanococcusMethanobacteriumMethanosarcinaHaloarchaeaEntamoebaeSlime moldsAnimalsFungiPlantsCiliatesFlagellatesTrichomonadsMicrosporidiaDiplomonads
A phylogenetic tree based on ribosomal RNA genes implies a single origin for all life.

Another important piece of evidence is from detailed phylogenetic trees (i.e., "genealogic trees" of species) mapping out the proposed divisions and common ancestors of all living species. In 2010, Douglas L. Theobald published a statistical analysis of available genetic data,[3] mapping them to phylogenetic trees, that gave "strong quantitative support, by a formal test, for the unity of life."[4]

Traditionally, these trees have been built using morphological methods, such as appearance, embryology, etc. Recently, it has been possible to construct these trees using molecular data, based on similarities and differences between genetic and protein sequences. All these methods produce essentially similar results, even though most genetic variation has no influence over external morphology. That phylogenetic trees based on different types of information agree with each other is strong evidence of a real underlying common descent.[28]

Objections

2005 tree of life shows many horizontal gene transfers, implying multiple possible origins.

Gene exchange clouds phylogenetic analysis

Theobald noted that substantial horizontal gene transfer could have occurred during early evolution. Bacteria today remain capable of gene exchange between distantly-related lineages. This weakens the basic assumption of phylogenetic analysis, that similarity of genomes implies common ancestry, because sufficient gene exchange would allow lineages to share much of their genome whether or not they shared an ancestor (monophyly). This has led to questions about the single ancestry of life.[3] However, biologists consider it very unlikely that completely unrelated proto-organisms could have exchanged genes, as their different coding mechanisms would have resulted only in garble rather than functioning systems. Later, however, many organisms all derived from a single ancestor could readily have shared genes that all worked in the same way, and it appears that they have.[3]

Convergent evolution

If early organisms had been driven by the same environmental conditions to evolve similar biochemistry convergently, they might independently have acquired similar genetic sequences. Theobald's "formal test" was accordingly criticised by Takahiro Yonezawa and colleagues[29] for not including consideration of convergence. They argued that Theobald's test was insufficient to distinguish between the competing hypotheses. Theobald has defended his method against this claim, arguing that his tests distinguish between phylogenetic structure and mere sequence similarity. Therefore, Theobald argued, his results show that "real universally conserved proteins are homologous."[30][31]

RNA world

The possibility is mentioned, above, that all living organisms may be descended from an original single-celled organism with a DNA genome, and that this implies a single origin for life. Although such a universal common ancestor may have existed, such a complex entity is unlikely to have arisen spontaneously from non-life and thus a cell with a DNA genome cannot reasonably be regarded as the origin of life. To understand the origin of life, it has been proposed that DNA based cellular life descended from relatively simple pre-cellular self-replicating RNA molecules able to undergo natural selection. During the course of evolution, this RNA world was replaced by the evolutionary emergence of the DNA world. A world of independently self-replicating RNA genomes apparently no longer exists (RNA viruses are dependent on host cells with DNA genomes). Because the RNA world is apparently gone, it is not clear how scientific evidence could be brought to bear on the question of whether there was a single origin of life event from which all life descended.

See also

Bibliography

Notes

  1. ^ Now called homology.

References

  1. ^ Weiss, Madeline C.; Sousa, Filipa L.; Mrnjavac, Natalia; Neukirchen, Sinje; Roettger, Mayo; Nelson-Sathi, Shijulal; Martin, William F. (2016-07-25). "The physiology and habitat of the last universal common ancestor". Nature Microbiology. 1 (9): 16116. doi:10.1038/nmicrobiol.2016.116. ISSN 2058-5276. PMID 27562259. S2CID 2997255.
  2. ^ Forterre, Patrick; Gribaldo, Simonetta; Brochier, Céline (October 2005). "[Luca: the last universal common ancestor]". Médecine/Sciences. 21 (10): 860–865. doi:10.1051/medsci/20052110860. ISSN 0767-0974. PMID 16197904.
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  12. ^ Darwin 1859, p. 490
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  15. ^ Treasure 1985, p. 142
  16. ^ Kant 1987, p. 304: "Despite all the variety among these forms, they seem to have been produced according to a common archetype, and this analogy among them reinforces our suspicion that they are actually akin, produced by a common original mother."
  17. ^ Darwin 1818, p. 397 [§ 39.4.8]
  18. ^ Darwin 1859, p. 484
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  21. ^ Kellogg, Vernon L. (1907). Darwinism To-Day. Henry Holt and Company. p. 3
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