Phylogenetic research

(Including the non-cellular life forms)

What is the Tree of Life?

In his 1859 masterpiece On the Origin of Species, Charles Darwin included

just one illustration a tree depicting branching and extinction through
time.
With this he crystallized the idea that species share common ancestors at various points back
in time. He referred to the genealogical relationships among all living things as the great Tree
of Life.

Throughout the late 19th century there were many attempts to portray evolutionary
relationships with tree-like diagrams. These were based on overall appearances shared
similarities in the form and structure of organisms.
However, it was not until the middle of the 20th century, especially through the work of the
German entomologist Willi Hennig in the mid-1960s that the analytical methods used by
scientists today to study phylogenetic relationships began to be developed and modern
research on the Tree of Life began.

This basic logic, together with extraordinary advances in computer science and molecular
biology, prepared the way for the reconstruction of the entire Tree of Life. Owing to an
exponential rise in phylogenetic research around the globe, we can now discern the branching
pattern of the entire Tree. This mega-science effort has revolutionized our understanding of our
own place in nature, and the resulting knowledge has already been put to an amazing variety
of scientific and practical uses.
 What is a Phylogenetic Relationship?

In evolutionary biology the word relationship has a particular meaning,

which is key to understanding and using the Tree of Life.

Phylogenetic trees come about through successive events of speciation

(branching), in which one species gives rise to two.

Phylogenetic relationship refers to the relative times in the past that species shared common
ancestors. Two species (B & C) are more closely related to one another than either one is to a
third species (A) if, and only if, they share a more recent common ancestor with one another
(at Time 2) than they do with the third species (at Time 1).
The model below shows that crocodiles and birds (the owl) are more closely related to one
another than either is to mammals (the Gorilla). Why? Because scientists have inferred that the
crocodiles and birds share a more recent common ancestor! Notice that no matter how you
swivel the branches of this tree, the same relationships hold:

The information about relationships is not in where the species sit relative to one another at
the tips of the branches; we dont read trees across the top from left to right. Instead, we read
trees downward from the tips, moving backward in time, or upward from the bottom, moving
forward in time.
Starting from the bird, for instance, we can move back in time and ask whether the bird branch
connects first to the crocodile branch or to the mammal branch. Starting from the bottom, we
can ask which branching event occurred first, and which occurred later. The entire Tree of Life
is made of small trees like this one.

Some relationships seem obvious: a cow and a sheep are more closely related than either one
is to a sunflower. Others are not nearly so obvious. Is a mushroom closer to a human or to a
water lily? Surprisingly, mushrooms are closer to us than they are to plants.

Organisms that look very different can be quite closely related, while very similar organisms,
might be very distantly related. Remember, phylogenetic relationship refers not to the
similarities and differences among organisms, but to the relative times that they shared
common ancestors in the past.

Evolution Along the Branches of the Tree of Life

Our conclusions about phylogenetic relationships rely on what Darwin called descent with
modification. As time passes, the traits of species undergo evolutionary change along the
branches of the phylogenetic tree. We use these changes to understand how species are related.
All else being equal, species that share a trait that evolved within a lineage will be more closely
related to one another than they are to species that lack this derived trait.
 Going Back In Time
We can also use knowledge of phylogenetic relationships to work backward to infer where in
the tree various evolutionary changes occurred. Knowing the relationships and the traits of the
species at the tips of the tree, we can reconstruct what ancestral species looked like.

For example, the tree to the right implies

that the ancestor of species B and C
probably had the evolutionarily derived
character (represented by black boxes)
shared by B and C today. That is, the
change to this derived condition
(represented by the short black bar)
probably occurred along the branch just
below the node (at Time 2) that connects
B and C. The ancestor of species A, B, and
C, had the ancestral character (represented by the white box).

We can make such inferences one at a time (character by character), or we can consider entire
suites of characteristics, which provide us with a unique perspective on the evolution of a
lineage through time.

Ancestral Arachnids

Some animation techniques of ancestral character state reconstruction is used to infer the
evolution of the shape, size and number of body parts of the arachnids (the branch of the Tree
of Life that includes spiders, scorpions, mites and ticks) and their relatives such as the
horseshoe crabs. To see how their different body forms evolved, we can trace up the branches
from an ancestor at the base to any tip of the tree and watch the evolutionary changes that are
reconstructed along the way.

Notice that the ancestor of two descendants seldom looks like either descendant, because
change usually happens along both paths. In fact, phylogenetic trees show that it is misguided
to say, for example, that humans evolved from chimps; rather, both humans and chimpanzees
evolved from a common ancestor that differed from both.

The common ancestor of all arachnids probably resembled the now extinct eurypterids or sea
scorpions, fearsome aquatic predators that lived some 250 to 500 million years ago.

While arachnids share basic body parts, these have diverged in fascinating ways.

The chelicerae in spiders, for example, are fangs that evolved the ability to inject venom; in
pseudo scorpions they evolved to produce silk; and in solpugids they became massive jaws that
rip apart prey.
In scorpions, the rear of the abdomen evolved
into a poisonous stinger; in spiders, into a silk-
producing organ for making webs; and in whip
scorpions, a feeler for targeting a cannon that
fires nasty chemicals at its enemies.

Giant Whip Scorpion

Also known as uropygids or vinegaroons, whip scorpions dig burrows in the moist soil of
tropical and subtropical areas in the New World and Asia. Whip scorpions have no venom, but
when disturbed spray a noxious chemical that smells like vinegar. They leave their burrows at
night to feed on insects, spiders, and other invertebrates. The giant whip scorpion
(Mastigoproctus giganteus) is one of the largest species, and is found in southwestern North
America.
 Flat Rock Scorpion

The flat rock scorpion (Hadogenes troglodytes) comes from dry, rocky habitats in South Africa.
Like other scorpions, its stinger is venomous, but this species relies more on its powerful
pincers for hunting and defense. The bodies of these scorpions are adapted to fit in narrow
rocky crevices, where they capture and eat snails and other invertebrates.

Extreme Divergence!
Would you guess that the tiny Ruby-throated
Hummingbird (Archilocus colubris) and the
giant tyrannosaur Albertosaurus libratus are
related? Sometimes organisms that look
radically different turn out to be closely
related. Such extreme divergence can evolve
quite naturally, especially when lineages
move into new environments.

Did you know that crocodilians are the

nearest living relatives of birds? Although they dont look very much alike, there is abundant
evidence for their close common ancestry, at least among living reptiles. Crocodilians and birds
both sing to defend their territories and attract mates, build nests for their eggs, and care for
their young. And, when we add our knowledge of extinct reptiles, the differences between
crocodilians and birds are much less striking.

Albertosaurus was a fierce carnivore; a hummingbird may be no less fierce, but its diminutive
size and taste for nectar are unusual for a dinosaur. Albertosaurus probably sported feathers,
just like living birds. Birds, it turns out, are just a highly divergent branch in the dinosaur tree,
the rest having disappeared long ago. Birds are the dinosaurs that took to the air, dodged the
great extinction 65 million years ago and, with some 10,000 species alive today, have been so
successful ever since.
 A Case of Extreme Divergence in Plants

The water lotus (Nelumbo) was long thought to be closely related to the water lilies
(Nymphaeaceae). Surprisingly, the water lotus turns out to be closely related to the sycamore
tree (Platanus). This idea was first suggested on the basis of pollen structure, but has now been
strongly supported by DNA sequences.

The case of the water lotus illustrates both extreme divergence (water lotus relative to the
sycamore) and convergent evolution (water lotus relative to the water lily). The water lotus
lineage has undergone extreme evolution of its form in adapting to life in calm, freshwater
habitats, and has converged to look like a water lily.

Convergent Evolution: Recurrence of Form

 Organisms that look remarkably alike are sometimes the result of convergent evolution
although they look similar, they evolved not from an immediate common ancestor with their
traits, but within separate lineages that initially lacked them.

Compare the torpedo-shaped body of a fish with the body of a swimming mammal, like a
dolphin or a whale. The first mammals were terrestrial and walked on four limbs. As the
ancestors of the cetaceans adapted to swimming, their limbs were reduced and their body shape
converged on the typical fish shape.

Sometimes convergent evolution modified different body parts to look the same and perform
the same function: insect wings were derived from the exoskeleton, while bird wings were
derived from forelimbs with an internal skeleton. In other cases, modification of the same basic
part occurred independently in separate lineages: the wings of both birds and bats are modified
forelimbs, though modified in quite different ways.

The Tree of Life contains many remarkable examples of convergent evolution, which attest to
the great power of natural selection to adapt different organisms to similar environments. Such
cases are discovered as we study how species are related finding that similar organisms are
actually distantly related and must have evolved their similar traits independently. Sometimes
convergent similarities are so striking that they have fooled biologists for decades before being
revealed through careful phylogenetic research.
 Convergent Insect Eaters: Pitcher Plants

Plants that digest insects have evolved

independently in several distantly related
lineages, apparently as an adaptation to low-
nitrogen soils.

The production of pitchers tubular

leaves that insects have a hard time escaping
occurs in several plant groups that until
recently were thought to be closely related.

Now there is compelling evidence that they are quite separate the pitcher plants of the New
World (Sarraceniaceae) are closer to blueberries and kiwi fruits, while those of the Old World
(Nepenthaceae) are related to other insectivores (the Venus fly-trap and the sundews), and in
turn to knotweeds and carnations.
 A Succulent Convergence

Thick succulent stems, adapted to conserve water, evolved independently in several lineages
of desert flowering plants.

Both the familiar Latin American cacti and the African euphorbias lost their leaves and
transferred photosynthesis to their enlarged stems, whose specialized anatomy provides water
storage and support.

Although their stems are similar, their flowers (and fruits) are very different from one another.

Cacti (Cactaceae) belong within a major branch of flowering plants that includes carnations
and ice-plants, while the euphorbs (Euphorbiaceae) are members of a very distantly related
branch that includes violets and willows.

Leaf-bearing relatives of the stem-succulent forms have now been identified. Pereskia, with its
large leaves, is actually a cactus! And, Crown-of-Thorns is a euphorb.
 Big Surprises in the Tree of Life

Has the explosion of phylogenetic research confirmed or overturned our

ideas on relationships? The answer is: both!
This research has provided overwhelming support for many long-recognized groups, among
them insects, mammals and birds, as well as seed plants and flowering plants. It has also
confirmed earlier suspicions that some groups do not form a single branch of the Tree of Life.
Brown algae, for example, are only very distantly related to the red algae, and crocodiles and
dinosaurs are more closely related to birds than they are to lizards or turtles.

Phylogenetic studies are also uncovering

totally unexpected relationships. This is
especially true for microorganisms, where
little visible structural evidence is available.
Here, DNA sequences are providing data
that are fundamentally changing our
understanding of relationships.

Only over the last few decades have we

realized that there are three major branches
of the Tree of Life the Bacteria, the
Archaea and the Eukaryotes. The Archaea,
single-celled organisms that often live in
extreme environments, had been put
together with the Bacteria, but molecular
evidence reveals that they are widely
separated. The Archaea are probably more
closely related to the Eukaryotes, the branch
that includes humans and most other
familiar organisms.

We have also discovered that fungi are more closely related to animals than to plants, and that
within the animals the segmented worms (annelids) are more closely related to the
unsegmented mollusks (snails, clams and squids) than they are to segmented arthropods
(spiders, lobsters, millipedes and insects).
Major new discoveries are being made even in the best-known organisms, including mammals
and flowering plants. In this exhibit we feature two totally unexpected results, both showing
that really big organisms can be very closely related to really small ones the Afrotheria
lineage within mammals, connecting elephant shrews with elephants, and the story of Rafflesia,
the plants that produce the worlds largest flowers.

The Black and Rufous Giant Elephant Shrew

This pair of brothers were born at the Smithsonians National Zoo in Washington, D.C., on
February 4, 2007. Active most of the day, they spend their time foraging and gathering leaf
litter for nests. In the wild, each elephant shrew can build six or seven nests in its home range,
where it sleeps, cares for offspring and evades predators.

Elephant shrews eat beetles, termites, spiders and ants, and supplement their diet with fruits
and seeds. In captivity they are fed crickets, mealworms and dry cat food supplemented with
peanut oil.

Elephant Shrew Diversity

Elephant shrews are neither elephants nor shrews. The 16 living species of elephant shrew all
have relatively large ears and eyes, a rat-like hairless tail, and long, thin legs that make them
speedy runners.

Individuals of the four species of giant elephant shrew weigh in at about one pound (540
grams), while those of the other species are much smaller the short-eared elephant shrew
weighs less than two ounces (about 35 grams). Elephant shrews get their common name from
their long, mobile trunk-like nose, with which they explore the world. Biologists also refer to
these animals by their African Bantu name, sengis.

The Distribution of Elephant Shrews

Elephant shrews are found throughout the forests, savannas, scrublands and deserts of southern
Africa and parts of North Africa. The Black and Rufous Giant Elephant Shrew lives only in
forests and dense woodlands of eastern Kenya and Tanzania, habitat that is rapidly
disappearing because of human activity. As a result, this extraordinary animal is at high risk of
extinction in the wild.
 Afrotheria: Unexpected Relatives!
These animals are all members of the same mammal lineage, the Afrotheria. With about 80
extremely varied species, this group includes such unlikely companions as the tiny elephant
shrews and the worlds largest land mammal, the elephants. However, in-depth DNA analyses
show that these animals are all of the descendants of a single common ancestor. So, even though
the golden mole looks very much like a mole, and has a similar subterranean lifestyle, it is more
closely related to the aardvark! While scientists agree that the Afrotheria evolved in Africa
(unlike some African mammals, such as lions and zebras, which originated elsewhere), there
is debate as to exactly when. Some evidence suggests that it was as far back as 100 million
years ago in the Cretaceous Period, while other studies indicate that it may have been around
the time that the non-avian dinosaurs became extinct, some 65 million years ago.

The Afrotheria Tree

Phylogenetic relationships among the different animals that make up the Afrotheria have been
vigorously debated, and are currently the subject of a major international research effort. Here
we present a current hypothesis that is being tested using additional molecular and
morphological evidence:
 Floral Giants From Humble Beginnings

One fascinating recent phylogenetic discovery concerns Rafflesia, a group of

plants that live in the tropical forests of Southeast Asia.
These bizarre organisms produce the worlds
largest flowers. Leafless, stemless, rootless and
nonphotosynthetic, these plants live as parasites
inside a host plant, a woody vine related to
grapes. Their bodies have been reduced to
something that resembles the thread-like
filaments of a fungus, which allows it to steal its
nutrition as it grows through the host stem.
Lacking almost all recognizable structural
features other than their extraordinary
flowers, which look and smell like a rotting
animal carcass Rafflesias closest relatives
have remained a mystery for nearly 200 years.
It has even been proposed that they are not flowering plants at all, but fungi. Despite the use
of DNA sequences, this riddle has proven difficult to solve. The problem is confounded by
drastic reduction of the chloroplast DNA in Rafflesia and the transfer of some genes from the
host plant directly into the genome of the parasite. It was not until 2007 that a definitive study
in the journal Science reported the findings of botanist Charles Davis of Harvard University
and his colleagues. Rafflesia and its closest relatives, Rhizanthes and Sapria are nested
squarely within a large flowering plant group (with over 6,000 species) known as the
Euphorbiaceae, the euphorbs or spurges. This group contains some familiar plants, including
the poinsettia, the rubber tree, the castor bean and the cassava, or yuca root. What is striking
about this discovery is that related plants in the Euphorbiaceae (such as Ditaxis) have small or
even tiny flowers, which implies an astounding rate of increase in flower size along the line
leading to Rafflesia. The remarkable size of these smelly giants may help lure pollinating flies
to their blossoms by better mimicking decaying animals on the forest floor.
 The World's Largest Flower
Rafflesia arnoldii produces the largest
known individual flowers, nearly three
feet (one meter) across and weighing up
to 15 pounds (7 kilograms).

The individual flowers of Rafflesia

arnoldii are either male (pollen bearing)
or female (seed bearing), and may be
pollinated by bluebottle carrion flies
attracted by the color and the smell of
tainted beef.

A fly enters the chamber of a male flower and is guided to the anthers, where a sticky mass of
pollen is deposited on its back for transport to a female flower.

Successful pollination is rare, however, because Rafflesia populations are few and far between.
The flowers open only rarely and then only for about five days.

The flowers offer no reward to the flies, who are fooled into looking for food or a place to lay
eggs. The distinctive projections on top of the disk in the center of the flower may help to
radiate heat and spread the carrion odor.
 Rafflesia and its Relatives
There are 13 species of Rafflesia living in southeast Asia. These differ in size, coloration, and
the number of various flower parts.

The closest relatives of Rafflesia are Rhizanthes and Sapria, each with two species. These are
also Asian parasitic plants with smaller but equally bizarre flowers.

The magnificent flowers of Rafflesia arnoldii have become a symbol of Borneo. Tragically,
Rafflesia and its relatives are now all threatened with extinction from destruction of their
rainforest habitats. It has not been possible to cultivate them.
 A Monumental Scientific Challenge

Just how big is the Tree of Life?

There are around 1,750,000 known
species on Earth, with countless more
awaiting discovery. Most students of
biodiversity believe that the real number
may be over 10 million. And these are
just the species alive today.

The Tree of Life contains all the species

that have ever lived adding extinct
species would push the number to over
100 million! The sheer size of the Tree
of Life makes reconstructing it one of the
most challenging scientific problems
ever undertaken.

How much of the Tree of Life

has been reconstructed?

Some 100,000 species have been included in formal phylogenetic analyses so far, between 5%
and 10% of the known living species, but perhaps only 1% of the real total, and a fraction of a
percent of the species that have ever existed. However, even if not formally analyzed, virtually
all known species can now be assigned provisionally a place in the Tree.

This tree contains 3,000 species representing the lineages of some 30,000 flowering plants:
Shown below are 100 trees, each with 3,000 species (see above), to represent
a total of 300,000 species:

This is approximately the number of flowering

plant species on Earth today. The shaded trees
represent the number of species of flowering
plants that have been included in phylogenetic
analyses to date. So far, approximately 21,000
species, or 7%, have been included.

Computational Complexity

Reconstructing the Tree of Life

One key issue in reconstructing the Tree of Life is the development of algorithms and
computational infrastructure to allow scientists around the world to apply the same methods.

A common approach is to identify the simplest hypothesis of relationships that explains as

much different evidence as possible. Increasingly, however, scientists prefer the tree that
renders the observed species data the most likely, given an underlying model of the
evolutionary process.

But finding the simplest or the most likely hypothesis can be very challenging. As phylogenetic
datasets grow larger, it becomes more difficult to analyze them properly. With more and more
species under study, the number of alternative phylogenetic hypotheses that must be considered
to select the best tree increases dramatically.

For example, for 3 species there are just 3 possible phylogenetic trees, and for 5 species there
are 105. From there the number of possible trees grows amazingly quickly. For 50 species there
are more possible trees than the number of atoms in the universe. For 100 species there are
more trees than the volume of the entire universe measured in the smallest possible units,
assuming expansion at the speed of light since the big bang 20 billion years ago.
No computer, no matter how powerful, can examine every possible tree for even a moderate
number of species. Therefore, computer scientists have had to devise clever strategies to avoid
examining every possible tree; so-called heuristic search algorithms.

One method quickly builds a starting tree

and then rapidly swaps branches around
to find better trees.

Another strategy breaks large problems

down into smaller ones, solves these, and
then puts them back together again.

Much remains to be done to improve the

performance of phylogenetic methods.
 Why Study the Tree of Life?
Click on the link to watch a video on this topic!

https://www.youtube.com/watch?v=ooLr8d_pDBc

By providing a chronicle of past evolutionary events, phylogenetic trees have become central
to understanding the process of evolution, and therefore to the interpretation of all biological
information.

The Tree of Life is of great scientific interest, but does it have immediate
practical value? The answer is a definite Yes!

Phylogenetic comparisons with model organisms (such as the chimpanzee, mouse, zebra fish
and yeast) are providing major insights into the structure and function of the human genome,
knowledge that will enable us to address a wide variety of human disorders.

Medical journals routinely publish phylogenetic trees, which have proven to be critical in
identifying and tracing the origins of emerging infectious diseases such as HIV, the Ebola and
West Nile viruses, anthrax, and influenza.

HIV

In the case of HIV (the virus responsible for AIDS, now the leading infectious cause of death
worldwide), phylogenetic studies have revealed multiple sources of the disease in nonhuman
primates and have also helped trace its transmission through human populations.
 Rabies
Rabies, which is transmitted through blood and saliva, is the tenth leading cause of human
death from infectious disease. As it spreads from host to host the viral strain accumulates
mutations in its genetic material, and from these we can recover its phylogenetic history.
The map below shows a phylogeny of a rabies virus strain that spread across Europe starting in the
1930s. This strain originated in African dogs, but then jumped host species into the red fox in
southern Europe and later into the raccoon dog in north eastern Europe. The tree shows a
characteristic transmission wave as the virus spread westward across Europe starting in the 1950s.

Agriculture
Knowledge of phylogenetic relationships also

plays a key role in agriculture, especially by

identifying the wild relatives of domesticated
plants and animals (potatoes from South America,
chickens from Southeast Asia, wheat from the
Middle East), guiding genetic improvements
(engineering resistance to drought and pathogens)
and locating potential biological control agents.
For example, the discovery that the Mexican grass
teosinte is the wild ancestor of cultivated maize has
led to an understanding of the genes that could
enhance desirable key attributes of the cultivated
plant.
 Phylogenetic Predictions
Phylogenetic trees predict the characteristics of species that have not yet been carefully studied.
This can guide the search for useful natural products, including bioprospecting for new drugs.
For example, the drug taxol, which is used to treat breast cancer, was first isolated from the
Pacific yew plant. A focus on related plants turned up a similar chemical in a more widespread
species, which greatly enabled the production of the drug.

Treating Snake Bites

In Australia, which has more poisonous snakes than any other continent, phylogenetic analysis
is used to help identify antivenins. Venin properties correlate strongly with evolutionary
relationships. Therefore, for example, the anitvenin for the red-bellied black snake can also be
used for the closely related (although very different looking) king brown snake
 The Poison in Poison Ivy
Some people who are sensitive to poison
ivy discover that they have a similar
reaction to the skin of mango fruits.
Phylogeny provides the answer to this
puzzling phenomenon. Mangos and poison
ivy turn out to be related.

They both belong to the Cashew family, the

Anacardiaceae. Many members of this
branch of the Tree of Life produce urushiol,
the oil that is the poison in poison ivy.

And what about the cashew itself? Urushiol is

found in the shell of completely raw cashew nuts,
as well as the leaves. However, virtually all raw
nuts that are sold have been steamed to release
the resin and make them safe to eat.

Another plant that belongs to the Anacardiaceae

is the Japanese lacquer tree, which is used to
make exquisite traditional lacquerware. The tree
sap also contains urushiol and there have been
cases of similar allergic reactions, particularly
among laquerware craftsmen.
 Live Elephant Shrews at the Yale Peabody Museum!

This pair of brothers were born at the Smithsonians National Zoo in Washington, D.C., on
February 4, 2007.

Active most of the day, they spend their time foraging and gathering leaf litter for nests. In the
wild, each elephant shrew can build six or seven nests in its home range, where it sleeps, cares
for offspring and evades predators.

See link:

https://www.youtube.com/watch?v=1ntSuzTJw8o

Elephant shrews eat beetles, termites, spiders and ants, and supplement their diet with fruits
and seeds. In captivity they are fed crickets, mealworms and dry cat food supplemented with
peanut oil.

See link:

https://www.youtube.com/watch?v=9R8hpPY_9kY

Morphing Arachnids - Using Phylogenies for Time Travel

Each feature of the living species at the tips of a tree can be mapped onto the tree to determine
where evolutionary changes likely occurred.

Then, at each internal node, the features can be blended together to form an overall picture of
the ancestral species.

On the left of the animation above is a phylogenetic tree of selected arachnids (such as spiders
and scorpions); on the right is an animation showing what ancestral species may have looked
like at different points in the tree.

See link:

More about the tree of life:

See link:

http://www.ucmp.berkeley.edu/exhibits/historyoflife.php

https://www.youtube.com/watch?v=fObmcBGMm9I
Here is a close-up view of the tree from the animation above:
 This is part of Chapter 1 of the book:
The Demoncratic Version Volume II
By Victor E Rosez

The study of the Tree of life is a new science

Since 1837, the famous Charles Darwin, made a

summer sketch of a kind of tree in his notebook, many
Biologists, Botanists, Zoologists, Ichthyologists,
Bacteriologists, Herpetologist, Ornithologists,
Anthropologists, Paleontologists and more were trying to
expand it as illustrating metaphors of the history of life.
Since that time all these scientists started to add names
to that simple sketch of Darwin and finally a group of
them expanded it to a real tree which showed a
genealogy of some two and an half million of species that
would include all life that exists. This was an amazing
work but their conclusion should have been limited to the
more humble pretention that it concerned only the
lifeforms that were sequenced until now.
But there is more. Their genealogical studies and
paradigms amplified these kind of forms of life that were
well known to all of us. Mammals, birds, fishes and other
animals represented almost half of what was suddenly
called The tree of Life giving a lesser space for plants,
fungi and algae and a small area reserved for bacteria
and microbes. It was a nice evolution, as we look back
to the primitive I think sketch of Darwin to what was
shown a century later. Slowly the tree of life became
more realistic when the world of microorganisms was
discovered and it became clear that this world dominated
in number all life on Earth. But many Earth and Planetary
Sciences scholars were still not satisfied with it. Their
research showed indeed that the Tree of Life was much
more complicated than that.
 Darwins I think
Tree of Life sketch

Another sketch from 1868

 Tree of life: Red - Eukaryotes
Green - archaea
Blue - bacteria
However, it would last until the 21st century before
scientist became aware that the number of living species
on earth was much higher as presumed and that a
subdivision in three groups was not correct. A new
version emerged, showing five groups of phyla instead
of three. The expansion occurred in the area of bacteria
and other microorganisms. The section of animals and
plants became suddenly very narrow. Nevertheless, new
questions arose. The last tree of life, as shown below,
needed to be expand by some groups of phyla which are
much older and higher in number (with at least a factor
between x10 and x 100). (The phyla of the non-cellular
life forms). Another issue was that the number of two and
an half million living species was an underestimating.
The real number could probably been a thousand times,
even a million times higher. The estimation of the
number of living species since the origin of times became
or is becoming a new challenge.
 21the century tree of life
Credit: Jillian Fiona (Jill) Banfield

The new estimated total number of species on Earth

-- The most precise calculation ever offered
With 6.5 million species on land and 2.2 million in oceans.

Researchers find that Earth may be home to one trillion species

And again: how many lifeforms since the beginning of time, including
the possible restarts when all life forms were eradicated?
In addition, how many times science will discover a new missing link?
Moreover, the end is not in sight yet because the real origin of life, the
non-cellular RNA life forms were ignored until now, in other words the
world of Viruses, Virions and Viroids (and we have to include self-
replicating molecules, RNA, Prions, Proteins and Enzymes).

* https://phys.org/news/2016-05-earth-home-trillion-species.html
* see also missing Link Lokiarchaeota
 We are not only talking about the New Origin of Species
but also about the real mechanics that made evolution
possible, because there is evidence enough that once
there was a world dominated by RNA lifeforms.
The non-cellular RNA life forms are two major things:
- They are the last common ancestor of Life.
- They are the major driver of human and all other
evolutions of lifeforms, much more than natural selection,
changing ecological environments due to sudden
cataclysms or mass extinction.

Citation: The constant battle between pathogens and their

hosts has long been recognized as a key driver of
evolution, but until now scientists have not had the tools
to look at these patterns globally across species and
genomes. In a new study, researchers apply big-data
analysis to reveal the full extent of viruses' impact on the
evolution of humans and other mammals.*

Phylogeny or the study of the origin and evolution of all

species became indeed a multidisciplinary science.
It includes all kinds of technology and the branch of
physical anthropology that deals with the evolutionary
biology, its origin and the diversity of primates or
Hominidae.
* Links:
https://phys.org/news/2016-07-viruses-revealed-major-driver-human.html#jCp
https://www.newscientist.com/article/mg21128251-300-first-life-the-search-for-the-
first-replicator/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873004/
https://www.nature.com/articles/nmicrobiol201648#f1
http://news.berkeley.edu/2015/06/15/newfound-groups-of-bacteria-are-mixing-up-the-
tree-of-life/
http://phenomena.nationalgeographic.com/2011/03/18/glimpses-of-the-fourth-domain/
letter of Darwin: not created by a beneficent and omnipotent God
Looking back to On the Tendency of Species to form Varieties
and on the Perpetuation of Varieties and Species by Natural
Means of Selection and On the Origin of Species by Means of
Natural Selection, or the Preservation of Favored Races in the
Struggle for Life, and the first trees of life, like the I Think
and other sketches of Charles Darwin, one cannot deny that
they were contaminated by creationists influences.
The separated creation of man (and animals), the plants
and the lower life forms in his Life Trees were based on
morphological similarities and that was it.
But the more he visited remote and isolated areas on earth,
circumnavigating all continents of the world, the more he
became convinced that life couldnt have been created by
a beneficent and omnipotent God, and his faith in biblical
creation faded away. Darwin and the young Wallace
developed each almost simultaneously essentially a similar
explanation for the evolution of species. The raw material
for this theory was already known for decades, but the
books of Darwin were the first to be successfully published.
He became in fact the undisputed founder of a new branch
of science: The Evolution or The evolutionary theory.
However his books, especially The descend of man and
Selection in Relation to Sex, contained some popular
expressions. These would create a few other sciences
including domains such as Eugenics, inferior and superior
races. And of course on top we will see the undisputed
superiority of the British Race dominating the world and
placing the African on the bottom-line, not as an inferior
race but rather as a sub-species closer to the ape than to
modern man), and craniometry (later on developed in NAZI
Germany).
http://anthro.palomar.edu/evolve/evolve_2.htm : Darwins short biography
http://creation.com/darwin-and-eugenics
Anthropology at War: World War I and the Science of Race in Germany
 Darwin was not always very scientific in his pretentions,
because he was not really a biologist nor anthropologist. We
can discover many speculations in his work without any
evidence. We can see that Darwin's hypothetical theory of
pangenesis was completely debunked by his nephew
Francis Galton, whom did extended research in hereditary
matters. However, it was the monk Gregor Mendel, who had
the right answers, but no one was aware of him at that time.*
Physical and behavioral changes which are at the origin of
natural selection only occurred at the level of genes and DNA
and genes. We know them as mutations. This was the main
difference between Darwin and Lamarck whose own theory
of transmutation of species which was rejected by the former.
However, the CUMC or Columbia University Medical
Center scientists discovered new evidences showing that
once traits are obtained, they can be transmitted or inherit
without the involvement of DNA, debunking at the same time
DNA related theories about Human races. A discovery,
which also confirms that Alfred Russel Wallace was not that
wrong. As well, biological evolution, as the discontinuity of
culture is both due to extreme ecological and climate
fluctuations. This can happen in a relatively short time.
The incorporation of genetics in Darwin's theory known as
the "modern evolutionary synthesis" is closing the gap
between classic Darwinism and the evolution of several
sciences unknown in Darwins time. New technology and
observation with satellites of our atmosphere and the sun,
are giving complementary answers on the illusion of skin
color.*
*
The modern evolutionary synthesis
http://www.pbs.org/wgbh/evolution/library/06/1/l_061_01.html
http://www.dnaftb.org/6/bio.html
http://www.dnaftb.org/14/ Eugenics
Thermodynamics on the origin of life?
https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/
Professor Nina Jablonski shows this on a very simple way
in one of her video seminaries. *
Darwin's theories of evolution by natural selection were
used to try to show that women's place in society was the
result of nature just alike races with an emphasis on skin
color. In the Descent of Man, Darwin wrote that by choosing
tools and weapons over the years, "man has become
ultimately superior to woman. This was strongly denied by
Blackwell. His arguments for women's equality went largely
ignored until the 1970s when feminist scientists and
historians began to explore Darwin. Despite that Darwin did
not speech about Man in his Origin of the Species it was
clear that all Human species had the animals as ancestors.
In his following writings, such as the third book The
Expression of Emotions in Man and Animal, from 1872, he
wrote down his racist ideas. He wanted to give evidence
that there was something like superior and inferior races. It
was not surprising that this had some horrible
consequences as hordes of headhunters started their
gruesome work to get specimen skulls of Tasmanian and
Australian owners, no matter if they were still in use or not.
The new science of head measuring gave a full
employment job to many unscrupulous hunters. In a short
time, more than 90% of the aboriginal communities
disappeared and the museums of the civilized Western
countries were proud to show the world their own proof of
the evolution. The skulls of the Herero people of Namibia
are still silent witnesses of what Germany did in Africa.
Paradoxically, Darwin was an outspoken opponent of
slavery, something he considered degrading.

*https://www.ted.com/talks/nina_jablonski_breaks_the_illusion_of_skin_color

*darwin-c-the-descent-of-man-and-selection-in-relation-to-sex.
His prediction that the inferior races of the earth would be
swept by the superior race was also wrong, as far as it is
possible to speak about inferior and superior races of
course. We clearly can see in comparison that all non-
Western populations are showing a much larger
demographic growth.