The Neanderthal Project

Neanderthals: when we hear the word, we think of someone as uncivilized or caveman-like. Why is that? A Neanderthal was someone that lived long ago and is more primitive than the modern human being today. Is that entirely true though? Just how different is a Neanderthal from a Homo sapiens sapiens? It is considered to either to be a separate species under the genus Homo or a subspecies of Homo sapiens. They are an extinct lineage that lived in areas now known as Europe, Northern Africa, and Western Asia. With larger skulls, a more prominent brow, and a shorter stature, Neanderthals do resemble a very primitive form of modern humans.

Why do we want to know about these old relatives from the past? We are currently the only living species under Homo on this planet, but discoveries of our previous ancestors can answer many questions about us. Looking at morphological similarities, genetic similarities, and anthropological similarities can help shape our modern human history.

The Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, is dedicated to research in evolutionary genetics and human evolution. It would make sense that a team led by Svante Pääbo, head of the department of Evolutionary Genetics at the institute, would tackle the challenge of completing the entire Neanderthal Genome.

According to the new results based on the analysis of four billion base pairs of Neanderthal DNA, the team showed there is genetic contribution of about 1% to 4% to non-African modern humans. It also resulted in the discovery of a new group of extinct humans, the Denisovans, who were related to Neanderthals and who contributed genes to present-day people in Oceania.

The sequences presented from Neanderthal and Denisovan DNA can lead to powerful insight on interbreeding between the hominid groups. Comparing the genome can lead to analysis results of the most recent common ancestor to the three groups. To quote the paper, “In addition, the Denisovan genome differs from the Neanderthal genome in that it contains about 2.7 to 5.8% of the genome of an unknown archaic hominin.”

The project could also help determine the origin of Homo sapiens. There are currently two hypothesis: the Out of Africa states ancient Homo sapiens evolved into the modern human solely in Africa. Once evolved, that is when humans began to migrate throughout the continents and eventually replace other hominid species such as Homo erectus and Neanderthal. The multiregional origin of modern humans suggest that Homo erectus was throughout the world and eventually evolved into archaic Homo sapiens , which evolved into modern humans. There was no replacement of the former by the latter, and the origin would essentially be each continent. Genetic testing of hominid specimens can answer the questions of inbreeding, which therefore prove they were two distinct species during the same time period. As the project states, remnants of Neanderthal DNA and Denisovan DNA remain in some modern humans today, which could only be possible if Homo sapiens sapiens evolved solely in Africa and migrated outward to interact with other hominid species.

It’s so fascinating what a toe bone that is 50,000 years old can tell us.

Article in Nature


From water to land.. back to water

Whales are quite extraordinary animals. The Blue Whale is the largest animal to date, and whales inhabit all of the oceans. With long lifespans, great migratory patterns, and complex social behaviors, whales are remarkable ocean dwellers. What is even more peculiar is the fact that whales are mammals. Along with a few other species of mammals, whales have truly adapted an aquatic lifestyle. It’s common knowledge that whales are mammals, but do we actually stop and think what it takes for a terrestrial organism to become aquatic?

Whales have completely reduced hind limbs, fused cervical vertebrae, and a nostril that has moved from the front of the head to the top. The forelimbs have also been modified into flippers, and all of this from a regular, land mammal. It is known that the closest living relative animal to the whale is the hippopotamus, and the hippopotamus belongs to the family Artiodactyl (the even toed undulates). So an even toed, four legged animal is our starting character. This ancestor would go on to become the hippo and whale, but what we’d like to know is exactly how that journey happened. Luckily, the whale’s ancestors left a wonderful fossil record. Each newer fossil exhibits characters that are more and more like the common whale we see today. The trend shows shorter hind limbs throughout time, a larger rib cage and nostrils that moved throughout the skull. Skeletal changes became evident due to great fossils. Testing of saltwater oxygen isotopes proved early ancestors could drink salt water, something other mammals cannot do. Here is a good phylogeny from University of California, Berkeley: whale_evo

You can see the transformation, and now get an understanding of how something this can happen in life’s history. For more information, check out the website

and check out a good animation of this

A Turtle’s Place in Life

It has been a long standing question as to what Testudines (or more commonly known as turtles) are most closely related to. Are they more closely related to crocodilians and bird  or to lizards and tuataras? Current research is underway for the answer. Wang et. al states that genetic evidence suggests they are more closely related to Archosauria, which comprise of crocodilians, birds, and the extinct dinorsaurs. However, there is no consensus yet in the scientific community because morphologists propose that they are either more closely related to Lepidosauria, which comprise of lizards, snakes and tuataras, or perhaps they are at the base of the Reptilia tree altogether.

Turtles have such a unique body shape and seem different from any other reptile. The base of their shell is actually a part of the skeleton with the vertebrae integrated into the bones. In face, their body shape has been pretty consistent and derived since their origin in the Triassic period (with the oldest fossil dating back to 220 million years ago), with the turtle coexisting with certain dinosaurs as well! This makes turtles the oldest extant reptiles, even older than lizards and crocodiles. As you can see, it is quite difficult to suspect the relationship between turtles and their reptile relatives.

Another team of scientists did a genomic analysis of one thousand loci from reptiles in each major lineage. Using humans as an outlier to the phylogenetic tree, they compared genetic elements from a chicken and a finch, a crocodile and an alligator, a lizard and a snake, a tuatara, and two turtles. The phylogenetic tree constructed showed turtles were in fact the sister taxon to crocodilians and birds. They found no support for the turtle-lepidosaur relationship.

Read More…

Orchid: The Most Devious Plant?

There are approximately 24,000 species of flowers in the family Orchidaceae, and to put it into perspective, that is about 4 times the number of mammal species on this planet. Orchids can be found all over the planet, excluding glacial areas, with more genera being found in tropic areas. Some synapomorphies (or dervied traits for these flowers that differentiate it between other flowers) for this family include bilaterally symmetric flowers, resupinate flowers (positioned upside down), a nearly always highly modified petal (labellum), fused stamens and carpels, and extremely small seeds.

Orchids are pollinated by insects, and in order to attract pollinators, orchids “dupe” them by deceiving them with food or sexual promise. As other flowers that provide nectar, orchids also do something quite deceiving. They promise sexual gratification with visual chemicals or even pheromones as well. Males sense these stimuli and are very attracted to heading to the source, i.e. the flower. Once inside the flower, the pick up the pollen before they realize they have been duped. One benefit of sexual deception as opposed to food deception is that insects will be more likely to outcross the orchid’s genes, rather than being self-pollinated. With nectar, an insect will simply hop to the next flower on the same plant and self-pollination occurs. On the other hand, insects will be more likely to leave the plant once they realized there is no sex for them. They’ll leaving carrying pollen and then come across a different plant of the same species and fall for the same trap! Insects are not terribly smart, and orchids have evolved to take advantage of them as means of mating. Taking advantage of it has boggle great minds such as Charles Darwin, who in fact wrote a book about it. To read more about the evolution of deception in orchids, read this article written by Salvatore Cozzolino and Alex Widmer.

Mathematics and Biology.. How the Two Collide

Did you know that a matrix can lead us to a possible solution in conservation ecology? Or that celluar automata can help predict forest fires or spread of illnesses? Mathematical modeling is quite an important contribution in biological research, and models can really help us see the bigger picture of the phenomenon we are trying to understand.

Dr. Nina Fefferman is currently a researcher at Rutgers University. Her lab studies epidemiology and evolutionary sociobiology. She earned her Ph.D from Tufts University. in Mathematical Biology, and she has a knack to create models in her mind for different sorts of systems. Daughter of Charles Fefferman, she has inherited the gift of mathematics, and her application of it in the field of biology has allowed her to contribute over 32 publications in the past 10 years.

In the paper “Deviations in influenza seasonality” , the paper discusses the emergence of new influenza strains how it is not entirely known too well, making each year a new curveball for scientists. Many people believe that flu often strikes in the winter because it is cold, which causes the illness. However, that is not case. Dr. Fefferman states that even in areas like Texas, where temperature is constant year-round, influenza still peaks during the months of typical winter season. She worked on the paper with biostaticians and immunologists, which I think celebrates the unity between mathematics and biology. Using modeling to prove how the influenza virus is constantly evolving and using it to predict what it may possibly become helps to develop new vaccines and control outbreaks.

There is a whole realms of research when biology can be utilized with mathematical modeling; it is important to know that math and science are not two separate fields that are not meant to interact with one another, but rather they two should work together to paint bigger pictures and concepts on the way we tackle life’s mysteries.



Our Inner Fish Walking Through Life


Neil Shubin earned a Ph.D. in organismic and evolutionary biology from Harvard University in 1987. He is a paleontologist and evolutionary biologist with a special interest in fish paleontology. He has studied at Columbia University as well as University of  California,Berkeley. He currently teaches organismal biology and human anatomy for the medical school at the University of Chicago and serves as Associate Dean of Organismal Biology and Anatomy and Professor on the Committee of Evolutionary Biology. Shubin is also Provost of the Field Museum of  Natural History. Now one might be wondering how a paleontologist is teaching anatomy, but Shubin says the knowledge of the anatomy of fish actually helps him understand human anatomy easier. He states that the understanding of the roadmap to fish can lead to a better understand of the more complex roadmaps of humans. His goal, in fact, was to discover the organism that transitioned from the ocean to land; one that retained parts of fish                                                             while wielding parts of tetrapods. He came very close and because of his discovery and experiences, he decided to write Your Inner Fish.

Your Inner Fish: A Journey Into the 3.5-Billion-Year History of the Human Body Published in 2008 by Pantheon Books, each page in this 201-page novel raises a question, proposes the answer, tells a charming experience, or does all three! His passion for evolution and paleontology is evident through his story, and he challenges the way we have thought about ourselves to a higher level. What makes a human similar to a chicken, a shark, or even a jellyfish? What do teeth, hair, feathers, and breasts have in common? Shubin explores the questions regarding earth’s rich, life history. Each chapter focuses on a different aspect of biology, with the first two chapters explaining his field experience and anatomy. To understand what the transition from fish to tetrapod may have looked like, it is important to recognize the uniqueness between the two different groups. Fish have few bones in their fins, with no sign of digits, a wrist, two forearm bones, and a humerus attached to a shoulder. Fish tend to have conical shaped skulls, while tetrapods have adopted a more flattened skull. Shubin explains the transition of fins to limbs so simply, and he gives credit to past scientists that have come up with discoveries in the field of anatomy.

He led his first expedition in 1986 and since then has been on many more. Shubin, along with his team, discovered the genus Tiktaalik , an extinct organism that is a fish but shares many characteristics of tetrapods. It has scales, a flattened skull, and a wrist within its fins. It is understood that organisms under this genus explain the evolutionary transition from fish to amphibians. With each topic, he asks common questions that can leave the general public wondering what is the answer. Shubin then provides a clear and logical explanation of what the process and answer are most likely to be. An excellent read for those who are curious on vertebrate evolution.

Why are Birds Dinosaurs? Because of Cladistics

Would you believe someone if he or she told you that birds are dinosaurs? Would you believe that same person if he or she said that birds and crocodiles were more closely related to one another than a crocodile and a lizard? Skepticism is always healthy in science, but according to current phylogeny, both statements are true.

What exactly is cladistics? It is a biological approach to the classification of living organisms. What groups organisms together is uniqueness among them. Each branch is a clade containing creatures that share the same derived trait. As you travel the tree further back in time, you see what traits are derived, and eventually, you’ll see more and more common traits between more clades of organisms. For example, Amphibians are creatures that have four limbs and can survive on land. You can clearly tell them apart from fish. But fish and amphibians both have jaws. Their most recent common ancestor (MRCA) would go on to give birth (so to speak) to the jawed fish and amphibians. They are more closely related to one another than a jawed fish and a jawless fish. The lamprey and jawed fish have a MRCA that is OLDER than the MRCA of jawed fish and amphibians.. confusing? Let’s take a look at a phylogenetic tree of the tetrapods:



Looking at the base of the tree, you can see every branch after lungs are organisms that contain lungs. As you move along the tree, you’ll find new, unique characteristics that define the new clades and differentiate them from their ancient ancestors. You can see that these differences, along with molecular testing, places crocodiles and birds as sister taxa. Those two clades, named Archosauria, are the sister taxa to snakes and lizards. Therefore, crocodiles and birds share more in common with one another than a crocodile shares with a lizard. Now here is a tree for Archosauria:


Using what you’ve now learned, can you see why birds are dinosaurs?




The Mathematics Behind Epidemiology

Epidemiology studies the patterns, behaviors, causes and effects of a particular disease or health condition in a certain population. The main purpose is to identify risk factors for diseases and consequently determine ways to minimize risk factors, thereby decreasing an outbreak or high numbers of the health condition. In order to calculate what sort of parameters are involved, we have to look at a big picture, i.e. a model.

For an infectious disease, epidemiologists use differential equations to map out the behavior of infections. They follow an SIR model, where S is the susceptible population, I is the infectious population, and R is the removed population. Generally the susceptible population is any person that is able to get the disease, a person in the I population can transmit the disease to people in S, and the removed population include those that have developed an immunity and recovered.


Differential equations are useful because they define the change of a curve. If we refer to these populations as curves on a graph, then studying the change in numbers of each population is what we want to know (how many people are being infected, which would be people moving from S to I). The change in each curve is simply its corresponding differential equation. Beta typically represents transmission rate, which is how likely it is for an infectious person to infect a susceptible person. The negative sign indicates a negative change on the curve (the population is decreasing). In the I differential equation, the people that left the S population (-beta*S*I) would in fact be the people entering the I population, hence a positive beta*S*I. Delta (or gamma) typically refers to recovery rate. Same principle applies: the negative indicates the people no longer belonging to the I population, but rather the R population. Using this basic principle, further complex models can be determined to map out more complicated diseases. Information regarding vaccines and preventative measures can also affect the Beta value, which in turn affects the change of the population. Fascinating stuff, huh?


Here is a PDF from the Biomathematics journal regarding epidemiological models.

IPM is a safer alternative to continual pesticide application

Agriculture is a very important business that is essential to all humans. Earth houses approximately 7 billion people on this planet, and in order to feed all of these consumers, the planet must sustain more producers. Pesticides were introduced and became commonly used since 1945. However, misuse, and even use of pesticides are responsible for soil pollution, water pollution, atmospheric pollution, and crop pollution because degraded products of pesticides flow into soil, groundwater, rivers and bodies of water. Not only that, but they are a very serious concern for human health as well. There is an estimated 26 million human pesticide poisoning and 220,000 deaths per years worldwide. Because of this, pesticides should only be a temporary solution, and instead of spending time and money on something harmful, researchers should spend time using integrated pest management (IPM) strategies that effectively care for crops in a safe way.

The main goal of IPM is to “maximize control efficacy, efficiency, sustainability and output, while minimizing negative environmental effects.” There are different alternatives to pesticides that show effectiveness against pests. Much research deals with semiochemicals (such as attractants, like pheromones, and repellents) associated with insects. A push-pull strategy is implemented to help “push” unwanted pests from the crops, and “pull” them towards a diversion, where they do no harm. using pheromones can easily attract insects to some other source to prevent them from destroying the essential crop. Other strategies include decoy crops, where a certain plant is used as a decoy for pests to attack. Certain IPM strategies have introduced predators and parasitoids of particular insects to control the population.


Exploring these methods will lead to a greener planet.

Axolotl numbers are dwindling in its only Natural Habitat


The axolotl appears to be an adorable “walking fish” (as it’s sometimes called), but it is a salamander that remains in its aquatic environment for its entire life, unlike other amphibians. Axolotl have the uncanny ability to regenerate many of its body parts, making it very valuable for scientific research. Unfortunately, it is becoming more difficult to find them in their natural habitat in Mexico. Axolotl lived in Lake Xochimilco and Lake Chalco, but Lake Chalco was ultimately drained by the Mexican government, limiting these salamanders to Lake Xochimilco and stemming canals. A team of scientists have spent three months trying to locate the organism in this area with no results. Lead Biologist Luis Zambrano states another three month survey will be attempted, hopefully with more luck since this time of year is breeding season for the axolomeh (plural). Surveys conducted by the Mexican Academy of Sciences have shown the numbers of axolotl have diminished over the past decade. While they are not yet extinct, they are considered a critically endangered species by the International Union for Conservation of Nature (IUCN). To help their survival rate, researchers have attempted to create clean areas in Lake Xochimilco to protect axolotl from polluted water, predators, and competitors.

Hopefully this is not the end for these interesting creatures of Mexico. They have played a role in Aztec folklore and they have many unique biological characteristics, which is why they are model organisms to study. Along with regenerating limbs easily, axolotl have accepted transplants from other axolomeh with ease, and these organs are completely functional. Think of the answers these organisms can provide for researchers!

If the shelters do their job correctly, perhaps many more axolomeh will be spotted walking along the bottom of Lake Xochimilco.

Link to original article