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Mollusk family tree

Cladograms and Evolution

Molluscs are invertebrate animals with a three part body plan that includes

(a) mantle = large body mass, with internal organs. Mantle is usually wholly or partly enclosed in a calcium carbonate shell.

(b) radula = fleshy structure used for feeding, sometimes compared to a tongue. Covered in very tiny denticles (miniature teeth.) Only found in molluscs. In all molluscs (except the bivalves.)

(c) a nervous system (almost all animals have a nervous system)

Several categories

Gastropods- “stomach foot”. Includes snails, slugs, limpets, and sea cucumbers.

Cephalopods- “head foot”. Includes octopi, squid, cuttlefish, and nautilus.

Bivalves- foot projects from shell. Includes clams, oysters, scallops, mussels

(there are a few other smaller categories)


Phylogenomics reveals deep molluscan relationships Cladogram

Image from Phylogenomics reveals deep molluscan relationships, by Kocot et al.

Nature volume 477, pages 452–456 (22 September 2011) doi:10.1038/nature10382

Learning Standards

Massachusetts Science and Technology/Engineering Curriculum FrameworkLife

Science (Biology), Grades 6–8.
Classify organisms into the currently recognized kingdoms according to characteristics that they share. Be familiar with organisms from each kingdom.

Biology, High School
5.2 Describe species as reproductively distinct groups of organisms. Recognize that species are further classified into a hierarchical taxonomic system (kingdom, phylum, class, order, family, genus, species) based on morphological, behavioral, and molecular similarities.

Benchmarks for Science Literacy, American Association for the Advancement of Science

Students should begin to extend their attention from external anatomy to internal structures and functions. Patterns of development may be brought in to further illustrate similarities and differences among organisms. Also, they should move from their invented classification systems to those used in modern biology… A classification system is a framework created by scientists for describing the vast diversity of organisms, indicating the degree of relatedness between organisms, and framing research questions.

SAT Biology Subject Area Test

Evolution and diversity: Origin of life, evidence of evolution, patterns of evolution, natural selection, speciation, classification and diversity of organisms.

Teaching About Evolution and the Nature of Science, National Academy Press (1998)

Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification.




MCAS Evolution

MCAS Evolution

Feb 2016 MCAS.  Scientists often compare fossils of extinct organisms with living organisms to help determine evolutionary relationships. What is the primary information that scientists use when comparing fossils with living organisms?

A. the types of minerals that formed the fossils
B. the size of the rocks that contained the fossils
C. the cause of death for the fossilized organisms
D. the physical characteristics of the fossilized organisms


Feb 2016 MCAS .

The pictures below show the shells of some species of land snails found on a Pacific island. Each species was found on a different hill on the island. Based on the snails’ shell shapes, scientists made hypotheses about the evolutionary relationships among the snails. Which of the following would be the best characteristic to compare in order to test these hypotheses?

Snail shells 16

A. the size of the snails
B. the diet of the snails
C. the DNA of the snails
D. the average age of the snails


Scientists hypothesized that several species of frogs called tiger frogs evolved from a recent common ancestor. The hypothesis was based on fossil evidence and on physical similarities among living species.

Which of the following provides the best additional support for the scientists’ hypothesis?

A. Tiger frogs have longer life spans than other frog species.
B. Tiger frogs have the same diet and all use enzymes to digest food.
C. Tiger frogs live near each other and are all preyed upon by the same predator species.
D. Tiger frogs have similarities in their mitochondrial DNA that are not shared by other frog species.


Spring 2017

Some populations of Atlantic tomcod fish have an allele that makes the fish resistant to toxic pollutants called PCBs. Tomcod populations in several rivers were analyzed for the presence of this allele. Each river had varying levels of PCB pollution. Which of the following results would best support the conclusion that natural selection is influencing the presence of this allele in the tomcod populations?

A. All of the tomcod in each of the rivers have this allele.

B. The percentage of tomcod with this allele remains the same from year to year in each river.

C. The rivers with high PCB levels have larger percentages of tomcod with this allele than the rivers without PCBs.

D. Eggs from tomcod without this allele can hatch in rivers with or without PCBs, and eggs from tomcod with this allele can only hatch in rivers without PCBs.


Spring 2017.

A researcher observed army ants, which form colonies with one queen ant and many worker ants. The researcher observed worker ants moving from place to place to hunt and collect a variety of food for the colony. The queen ant was observed mating with a male ant from another ant colony. The queen produced many eggs after this mating. Which of the following could help increase the genetic diversity in the colony of army ants?

A. the queen ant mating with the ant from a different colony
B. the worker ants collecting the food for the colony to eat
C. the worker ants moving from place to place
D. the queen ant eating a variety of food


Scientists discovered a 375-million-year old fossil in Canada. The diagram below shows the top and side views of the fossil.

Transitional form fossil amphibian
Which observation would best support the hypothesis that this organism was
a transitional form between amphibians and fish?



A. The fossil has a long body, which both modern amphibians and modern fish have.
B. The fossil is larger than most modern amphibians, but smaller than most ancient fish.
C. The fossil has some body structures that are similar to amphibians and some body structures that are similar to fish.
D. The fossil was discovered near a lake, which shows that the organism
needed water to reproduce, as do amphibians and fish.


Some plants in an area produce a toxin that protects them from being eaten by a variety of insect species. The toxin decreases reproductive rates in insects. Because of a genetic mutation, some fruit flies can detect the plant toxin and therefore avoid eating the plant.

a. Describe how the number of fruit flies in the population that can detect the toxin will most likely change over the next 25 years.

b. According to the mechanism of natural selection, explain how the change you described in part (a) will occur.

c. Based on the changes in the fruit fly population, describe what will most likely happen to the plants’ production of the toxin. Explain your answer.


Sperm whales have vestigial hip bones, and a small percentage of sperm whales
also have vestigial hind limbs. Which of the following statements best explains
the presence of these vestigial structures in sperm whales?

A. Sperm whales evolved from ancestors that walked on land.
B. Sperm whales are in the process of evolving into land mammals.
C. These structures are acquired by each individual sperm whale during its lifetime.
D. These structures resulted from sperm whales having a long period of embryonic development.


2014 MCAS Open response question

An elephant shrew and a shrew are pictured below.

Elephant Shrew and shrew

For many years, scientists had classified elephant shrews in the same family as shrews. In the 1990s, however, scientists gathered evidence for the evolutionary tree below and reclassified elephant shrews into a different family from shrews.

MCAS Elephant Shrew cladogram phylogeny

a. Describe the most likely reason why scientists originally classified elephant shrews with shrews.

b. Using the evolutionary tree, identify the groups to which elephant shrews are most closely related.

c. Identify and explain the evidence scientists most likely used to build the evolutionary tree and reclassify elephant shrews.

d. Identify one other type of evidence that scientists use to determine evolutionary relationships and build evolutionary trees.


Scientists measured and recorded the average body size in a bird population over time. One year, a period of cold weather killed many of the birds. A few generations later, the scientists observed that the average body size in the population was larger than it had been before the cold weather. The scientists concluded that the population had evolved through natural selection. Which of the following would provide the best evidence to support the scientists’ conclusion?

A. The size of the bird eggs also increased over time.
B. The birds with the largest body size were the males.
C. The frequency of alleles for body size changed in the bird population.
D. The number of birds in the population had decreased by 50% or more.


The three-spined stickleback is a species of fish. It lives in the ocean and in streams that flow into the ocean. Some scientists think that the ocean populations and stream populations may be evolving into separate species. Which of the following statements describes how speciation of these fish would most likely occur?

A. Fish from stream populations would start to reach maturity at the same time as fish from ocean populations.

B. Fish from stream populations would sometimes swim into the ocean but fish from ocean populations would stop swimming into streams.

C. Ocean populations and stream populations would each mate fewer times per year and would have decreased birth rates over time.

D. Ocean populations and stream populations would each adapt differently to their environments and would accumulate enough differences over time to prevent interbreeding


In a certain insect species, body color varies from very light gray to very dark gray. These insects are eaten by birds that find their prey by sight. A brush fire occurs, blackening the ground where one population of this insect species lives. Which of the following is most likely to occur over the next few years?

A. The body color in the population will mutate to black.
B. The percentage of very dark gray individuals will increase.
C. The distribution of body color in the population will not change.
D. The very light gray individuals will learn how to reproduce at a later age.





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