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Evolutionary Origin of the Turtle Shell


This intro is lightly adapted from thelogicofscience.com

Many people mistakenly believe that there are two fundamentally different types of evolution: microevolution and macroevolution. They argue that microevolution does actually occur, but only produces small changes within a species or “kind” of animal. For example, they’re okay with the concept that all finches evolved from a common ancestor, all crows evolved from a common ancestor, all ducks evolved from a common ancestor, etc.

However, they draw the line roughly at the taxonomic level of family (e.g., ducks are in the Anatidae family), and they argue that evolution beyond that level (what they call macroevolution) is impossible and has never and can never happen. Thus, they dismiss the notion that finches, crows, and ducks all share a common ancestor.

However, this distinction is completely arbitrary and meaningless: the exact same evolutionary mechanisms that caused the evolution of finch species could (and indeed did) cause the evolution of all birds. In other words, macroevolution is simply the accumulation of microevolutionary steps, and one inherently leads to the other.

Here is a visual explanation. The image below shows a hypothetical pathway through which turtles could have evolved from their lizard-like ancestors.

Several of these images are renderings of actual fossils: B6 = Milleretta, A15 = Eunotosaurus, C22 = Odontochelys, B30 = Proganochelys, D37 = Chelydra [modern turtles]; these are just screen shots from Dr. Tyler Lyson’s excellent video.

This full progression is, of course, what creationists would consider to be macroevolution, and creationists are adamant that today’s turtle families were uniquely created and did not evolve from a lizard-like ancestor. However, because they accept microevolution, most creationists would have no problem with any particular pair of images, and they would accept that A1 could evolve into B1, B1 could evolve into C1, etc.

In other words, each pair of images shows “microevolution” (which creationists almost universally accept), but when we string all of those steps together, we get “macroevolution” (which they say is impossible).

You can probably see where I am going with this, but just to be sure, I will state it explicitly. If you are going to say that macroevolution is impossible and turtles could not have evolved from lizard-like ancestors, then which step do you think is impossible?

Please show me which step could not have occurred, and justify that claim. Additionally, please explain the obvious transitional fossils. Remember, B6, A15, C22, B30, and D37 are actual fossils, and they perfectly match the expectations for what a transitional fossil should look like (details here). So, if turtles and their lizard like ancestors were uniquely created kinds, then at what point in this progression do lizard-like reptiles end and turtles begin?

Image from “Evolutionary Origin of the Turtle Shell” by Tyler Lyson









And here is the amazing video

Continued from “The Logic of Science”

Some people will likely be inclined to ignore my questions and harp instead on the fact that this pathway is hypothetical, but that argument completely misses the point in several ways. First, this pathway is only partially hypothetical because B6, A15, C22, B30, and D37 are actual fossils that we have found.

Additionally, of course the pathway is partially hypothetical. We will never find every single one of these steps, and we don’t need to: Evolution is very much like the visible light spectrum. Each color gradually fades into the next color without a clear breaking point. In other words, there is a point along the spectrum that is clearly red, and there is a point that is clearly blue, and there is a point that is clearly violet, but there is a spectrum of change in between those points – and it is not possible to pick an exact point where the blue ends and violet begins, just as you cannot pinpoint the exact step at which the reptile becomes a turtle as we know it.


Evolutionary Origin of the Turtle Shell
Tyler R. Lyson, Gabe S. Bever, Torsten M. Scheyer, Allison Y. Hsiang, Jacques A. Gauthier
Current Biology, Published Online: May 30, 2013
DOI: https://doi.org/10.1016/j.cub.2013.05.003




Is evolution a theory or a fact

Is evolution a theory or a fact?

“evolution” has 2 different uses:
‘facts’ of evolution, and the ‘theory’ of evolution.

Here are observable facts

* Many forms of life that used to exist, no longer exist today.
(We’ve found many fossils; more are discovered every day)

* Many forms of life exist now, that did not exist in the past.
(Many modern animals and plants are obviously different from fossils)

* DNA exists.

* Every time an organism reproduces, random changes (mutations) in DNA happen. (We actually explicitly see these with gene-sequencing)

* Some mutations help an organism survive – those genes pass on to the next generation.
(We actually see organisms survive and reproduce. We can sequence the DNA of the parent and of the offspring. We literally see the genes.)

* Some mutations don’t help an organism survive; those genes die out.
(We actually see that some organisms die before they reproduce. Their genes literally die with them.)

* Millions of different DNA samples show a relationship between all forms of life.

* As time goes by, some genes become more common, some become less common. (This has been directly observed in bacteria, some plants and some animals)

Here is the theory that connect such facts

1. Organisms produce more offspring than can survive to adulthood and reproduce.

2. All organisms have random mutations.

3a. Mutations that allow an organism to survive are passed on to their offspring.

3b. Mutations that don’t allow an organism to survive die off.

4. So over time, some mutations become more common.

The “theory” of evolution is the relationship between observations (“facts.”)

In this sense, the theory is just as true as the theory of gravity, or the theory of electricity.



Evolution 101. Univ of California Museum of Paleontology



Teaching about evolution

So, we’re supposed to teach our students about evolution – but where to start? What topics to cover? And in what order should we cover them? And for each topic, what are the relevant learning standards? This sequence works for me:

Chicken or the egg

Abiogenesis & spontaneous generation

Abiogenesis – modern discoveries

Charles Darwin’s Voyage of Discovery and Darwin’s notebook

Darwin’s finches

Fossils: Evidence of evolution over time and Dating of fossils

Convergent evolution and Homologous and analogous structures

Natural selection

Artificial selection

clades & phylogenies

clades rotate = equivalent phylogenies

Gradualism vs. Punctuated Equilibrium

Examples of evolution

Evolution of our kidneys

Evolution of humans

Evolution of whales

Where did the idea of evolution develop? How has the idea of evolution changed over time?

Advanced topics

Evolution of the first animals

Ontogeny and Phylogeny: Addressing misconceptions

Did nerves evolve twice?

Horizontal Gene Transfer and Kleptoplasty

Evolution and the 2nd law of thermodynamics

Scars of evolution

Evolution of the first animals

Animals probably evolved from marine protists, although no group of protists has been identified from an at-best sketchy fossil record for early animals.

Cells in primitive animals (sponges in particular) show similarities to collared choanoflagellates as well as pseudopod-producing amoeboid cells.

Multicellular animal fossils and burrows (presumably made by multicellular animals) first appear nearly 700 million years ago, during the late precambrian time….

All known Vendian animal fossils had soft body parts: no shells or hard (and hence preservable as fossils) parts.

Animals in numerous phyla appear at (or in many cases before) the beginning of the Cambrian Period ( 540 million years ago)

from http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookDiversity_7.html

Nicole King explains “All animals, from sponges to jellyfish to vertebrates [animals with a backbone], can be traced to a common ancestor. So far, molecular and fossil evidence indicate that animals evolved at least 600 million years ago. The fossil record does not reveal what the first animals looked like or how they lived. Therefore, my lab and other research groups around the world are investigating the nature of the first animals by studying diverse living organisms….. Choanoflagellates are a window on early animal evolution. Both cell biological and molecular evidence indicate that choanoflagellates are the closest living relatives of multicellular animals.




Between 620 and 550 million years ago (during the Vendian Period) relatively large, complex, soft-bodied multicellular animals appear in the fossil record for the first time. While found in several localities around the world, this particular group of animals is generally known as the Ediacaran fauna, after the site in Australia where they were first discovered.

The Ediacaran animals are puzzling in that there is little or no evidence of any skeletal hard parts i.e. they were soft-bodied organisms, and while some of them may have belonged to groups that survive today others don’t seem to bear any relationship to animals we know. Although many of the Ediacaran organisms have been compared to modern-day jellyfish or worms, they have also been described as resembling a mattress, with tough outer walls around fluid-filled internal cavities – rather like a sponge.


A new study mapping the evolutionary history of animals indicates that Earth’s first animal–a mysterious creature whose characteristics can only be inferred from fossils and studies of living animals–was probably significantly more complex than previously believed… the comb jelly split off from other animals and diverged onto its own evolutionary path before the sponge. This finding challenges the traditional view of the base of the tree of life, which honored the lowly sponge as the earliest diverging animal. “This was a complete shocker,” says Dunn. “So shocking that we initially thought something had gone very wrong.”

But even after Dunn’s team checked and rechecked their results and added more data to their study, their results still suggested that the comb jelly, which has tissues and a nervous system, split off from other animals before the tissue-less, nerve-less sponge.

The presence of the relatively complex comb jelly at the base of the tree of life suggests that the first animal was probably more complex than previously believed, says Dunn.



Is this possible? for this to be true, it would seem that complex structures – neurons – have evolved twice! Independently? See here for more amazing details:

Did neurons evolve twice? The curious case of comb jellies

Chicken or the egg

Which came first, the chicken or the egg?

At first glance, this seems like a reasonable question. But most questions have hidden assumptions, and this question has tons of them. And as it turns out, most of the assumptions are incorrect – meaning that the question – as it is usually asked or understood – is actually meaningless.

The question assumes that (a) chickens and eggs have existed continuously, without change, for a long period of time (b) that chickens (vaguely defined!) lay eggs (also vaguely defined!), and (c) that eggs hatch into chickens.

Problem? None of these assumptions are true. They only appear to be true because people only look at chickens and eggs over a very short period of time (perhaps weeks, a year, or when reading books, thinking back over the last 5000 years.)

But birds and their ancestors have been continuously changing for millions of years – and so has the way that their ancestors reproduced. The first chickens… may not even have been chickens, but rather some other form of bird that no longer exists.  And those earlier birds are descendants of a branch of the dinosaur family tree; and those early dinosaurs are a branch of the reptile family tree.  And over very long, deep periods of time, the way that these organisms reproduced has actually changed!

In fact, the first eggs developed millions of years before anything we even know as birds existed.

chicken or the egg

Also see:

Evolution of bird eggs Image by D Anduza

Evolution of bird eggs, Image by D Anduza

FIGURE 7. Simplified phylogeny showing hypothesized stages in the evolution of reproductive traits toward modern birds. Exact locations of stages 1 and 4 are unclear, given the complex distribution of traits in basal theropods and the lack of information for basal Aves and Ornithuromorpha.

Synapomorphies: Stage 1, pre-maniraptoran theropods—bilaminar eggshell with a mammillary and second layer composed of narrow shell units, irregularly distributed squamatic.

Stage 2, oviraptor-grade maniraptorans – increase in relative egg size, more elongate egg shape, slight asymmetry, monoautochronic ovulation, iterative laying, eggshell with more pronounced continuous layer and well-developed squamatic ultrastructure, prominent surface ornamentation, large and highly organized clutches, incubation involving nearly full burial with attendant adult, possibly paternal care.

Stage 3, troodontidgrade paravians—loss of surface ornamentation, increasing asymmetry, low porosity, potential for third (external) layer in eggshell, clutches of ‘‘planted’’ and near vertical eggs, improved contact incubation with tighter clutch configuration, and exposed upper portions of eggs.

Stage 4, Enantiornithes—loss of function in right ovary and oviduct, increasing relative egg size, reduction in egg elongation, incubation as in troodontids or as singleton eggs fully buried in sandstone.

Stage 5, basal Neornithes—eggs show further increase in relative size, more variable and less elongate egg shape, clutch free of sediment cover, egg rotation, chalazae with potentially greater incubation efficiency.

Source: Reproduction in Mesozoic birds and evolution of the modern avian
reproductive mode. Authors – David J. Varricchio and Frankie D. Jackson
The Auk: Ornithological Advances Volume 133 p.654–684, 2016 American Ornithologists’ Union

Genetic variation, classification and race

Genetic variation, classification and ‘race’
Lynn B Jorde & Stephen P Wooding
Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

Nature Genetics 36, S28 – S33 (2004)  Published online: ; | doi:10.1038/ng1435


New genetic data has enabled scientists to re-examine the relationship between human genetic variation and ‘race’. We review the results of genetic analyses that show that human genetic variation is geographically structured, in accord with historical patterns of gene flow and genetic drift. Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations. Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. Therefore, ancestry, or even race, may in some cases prove useful in the biomedical setting, but direct assessment of disease-related genetic variation will ultimately yield more accurate and beneficial information.

Figure 1: A neighbor-joining network of population similarities, based on the frequencies of 100 Alu insertion polymorphisms.

The network is rooted using a hypothetical ancestral group that lacks the Alu insertions at each locus. Bootstrap values are shown (as percentages) for main internal branches. (Because of the relatively small sample sizes of some individual populations, bootstrap values for terminal branches within main groups are usually smaller than those of the main branches, indicating less statistical support for terminal branches.) The population groups and their sample sizes are as follows: Africans (152): Alur, 12; Biaka Pygmy, 5; Hema, 18; Coriell Mbuti Pygmy, 5; a second sample of Mbuti Pygmy from the Democratic Republic of the Congo, 33; Nande, 17; Nguni, 14; Sotho/Tswana, 22; Kung (San), 15; Tsonga, 14. East Asians (61): Cambodian, 12; Chinese, 17; Japanese, 17; Malay, 6; Vietnamese, 9. Europeans (118): northern Europeans, 68; French, 20; Poles, 10; Finns, 20. South Indians (365): upper caste Brahmin, Kshatriya and Vysya, 81; middle caste Kapu and Yadava, 111; lower caste Relli, Mala and Madiga, 74; tribal Irula, Khonda Dora, Maria Gond and Santal, 99.

Figure 2

A neighbor-joining tree of individual similarities, based on 60 STR polymorphisms, 100 Alu insertion polymorphisms, and 30 restriction site polymorphisms.  The percentage of shared alleles was calculated for all possible pairs of individuals, and a neighbor-joining tree was formulated using the PHYLIP software package. African individuals are shown in blue, European individuals in green and Asian individuals in orange.

Figure 3

(a) Results of applying the structure program to 100 Alu insertion polymorphisms typed in 107 sub-Saharan Africans, 67 East Asians and 81 Europeans. Individuals are shown as dots in the diagram. Three clusters appear in this diagram; a cluster membership posterior probability of 100% would place an individual at an extreme corner of the diagram.

(b) A second application of the structure program, using the individuals shown in a as well as 263 members of caste populations from South India. Adapted from ref. 32.

Figure 4

A neighbor-joining tree formulated using the same methods as in Figure 2, based on polymorphisms in the 14.4-kb gene AGT.

A total of 246 sequence variants, including 100 singletons, were observed. The 368 European, Asian and African individuals are described further in ref. 54.

Author’s conclusion: “Race remains an inflammatory issue, both socially and scientifically. Fortunately, modern human genetics can deliver the salutary message that human populations share most of their genetic variation and that there is no scientific support for the concept that human populations are discrete, nonoverlapping entities. Furthermore, by offering the means to assess disease-related variation at the individual level, new genetic technologies may eventually render race largely irrelevant in the clinical setting. Thus, genetics can and should be an important tool in helping to both illuminate and defuse the race issue.”

Note by RK ” there is no scientific support for the concept that human populations are discrete, nonoverlapping entities.” – Outside of racist groups, no one, let alone scientists, make such a claim. This article does not debunk the idea that biological groups/races/clades for humans exists: It clearly proves that such groups exists, and shows it in precise detail. However, this data can also debunk racial claims made from people using non-scientific definitions of the word “race”.

When scientists use words like “race”, “populations” or “clades”, these words have precise meanings. Every discovery in biology and evolution over the last 200 years has clearly shown that the basic concept of biological groups has to exist. All forms of life have family trees that develop in ways that can be represented by cladograms, and those cladograms show evolutionary phylogenies.

“A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.”

See Clades and phylogenies and clades rotate = equivalent phylogenies.

Evolution of cereals and grasses

Evolution of cereals and grasses

Intro (TBA)

Paper 1: “Wheat: The Big Picture”, The Bristol Wheat Genomics site, School of Biological Sciences, University of Bristol

Wheat: The Big Picture – the evolution of wheat

Evolution wheat barley sorghum rice

Figure 2. Phylogenetic tree showing the evolutionary relationship between some of the major cereal grasses. Brachypodium is a small grass species that is often used in genetic studies because of its small and relatively simple genome.


Paper 2: Increased understanding of the cereal phytase complement for better mineral bio-availability and resource management

Article (PDF Available) in Journal of Cereal Science 59(3) · January 2013 with 244 Reads
DOI: 10.1016/j.jcs.2013.10.003

Fig-1-Phylogenetic tree of cereals selected grasses PAPhy gene copy numbers

Fig. 1. Phylogenetic tree of cereals and selected grasses. PAPhy gene copy numbers are given for each species and key evolutionary events are indicated.

Paper 2
Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences.
Peng Z, Lu T, Li L, Liu X, Gao Z, Hu T, Yang X, Feng Q, Guan J, Weng Q, Fan D, Zhu C, Lu Y, Han B, Jiang Z – BMC Plant Biol. (2010)

Phylogeny of grasses inferred from concatenated alignment of 43 putative orthologous cDNA sequences

Figure 2: Phylogeny of grasses inferred from concatenated alignment of 43 putative orthologous cDNA sequences. (A) Tree inferred from maximal likelihood method. Bayes inference yielded the same topology. (B) Tree inferred from neighbor joining method. Branch length is proportional to estimated sequence divergence measured by scale bars. Numbers associated with branches are bootstrap percentages. Arabidopsis was used as outgroup. Subfamily affiliation of the grasses is indicated at right.

Paper 3 Evolution of corn

The evolution of maize (corn)

Figure 1: The evolutionary stages of domestication and diversification.
Evolution of crop species: genetics of domestication and diversification
Rachel S. Meyer & Michael D. Purugganan
Nature Reviews Genetics 14, 840–852 (2013) doi:10.1038/nrg3605


Paper 4 text

Brachypodium distachyon: making hay with a wild grass
Magdalena Opanowicz, Philippe Vain, John Draper, David Parker, John H. DoonanEmail the author John H. Doonan
DOI: http://dx.doi.org/10.1016/j.tplants.2008.01.007

Phylogenetic Brachypodium and cereals