Innovative advances in deoxyribonucleic acid (DNA) technologies over the past few decades have brought about remarkable changes in the ancient DNA research which is the game changer of molecular phylogenetic analysis. The field of ancient DNA research which has a history of 28 years, involves the retrieval, amplification, sequencing and analysis of DNA sequences from archaeological and paleontological remains to unravel the evolutionary relationship between extant and extinct species (Millar, Huynen, Subramanian, Mohandesan & Lambert, 2008). Ancient DNA research has undergone major phases of development through improvements in DNA sequencing techniques, provided new insights and holds a great promising future in the field of molecular phylogenetics.
The first ancient DNA study was performed in the year 1984, which involved the retrieval of small DNA sequences from the skin of a quagga (Equus quagga) that was extinct for nearly 100 years (Higuchi, Bowman, Freiberger, Ryder & Wilson, 1984). The extracted mitochondrial DNA (mtDNA) was amplified via molecular cloning and subjected to phylogenetic analysis. The phylogenetic analysis showed that quagga was the extinct subspecies of the plains zebra. Another study on ancient Egyptian mummies demonstrated that DNA can be extracted from the well-preserved soft tissue remains and sequenced through molecular cloning (Pääbo, 1985). These studies highlighted the feasibility of using ancient DNA in elucidating the evolution of extinct species. However, the studies were spectacular with flaws such as the lack of reproducibility as the recovery of DNA from post-mortem was of very low concentration and short sequences, low cloning efficiencies and cloning artifacts. This places limitations i...
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...ning, involves converting of aligned sequences into distances to represent pairwise differences between sequences. UPGMA (unweighted pair group method with arithmetic mean) uses the assumption of a molecular clock to generate a rooted tree that has all branches ending at the same time point. On the other hand, Neighbour-Joining generates an unrooted tree, which is used in building of guide trees in CLUSTAL. Character-based methods such as parsimony and maximum likelihood, involves examining of each nucleotide position in the MSA dataset. Parsimony method involves selection of a tree with the minimum number of evolutionary changes while the maximum likelihood method involves selection of a tree that maximizes the probability of the observed data. Phylogenetic trees are useful in illustrating the inferred evolutionary relationship between extinct and extant species.
A study performed by Martin Hausler and Peter Schmid of the University of Zurich, Switzerland, appeared in the October 1995 issue of Journal of Human Evolution, igniting controversy over the 1974 Australopithecus discoveries in Hadar, Ethiopia. The most famous of the Hadar specimens is the 3-million-year-old skeleton, “Lucy,” who was recovered by paleoanthropologist, Donald Johanson. In his article, Shreeve presents the methods and findings of Hausler and Schmid’s study as well as some counter arguments from other scientists in the field.
...kman, J. (2001).Earliest Hominid Discovery Not the Missing Link—But Close [online].Energy Science News. Available from: www.pnl.gov/energyscience.com [Accessed 30 March 2004].
Vigilant, Linda. Stoneking, Mark. Harpending, Henry. et al. 1991. African Populations and Evolution of Human Mitochondrial DNA. Science 253: 1503-1507.
Neves, A. M., & Serva, M. (2012). Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans. Plos ONE, 7(10), 1-10. doi:10.1371/journal.pone.0047076
Australopithecus afarensis who existed 3.5 million years ago and a 4.4 million year old skeleton of an Ardipithecus ramidus are the closest science has come to discovering the human lineage. Shattered Ancestry an article written by Katherine Harmon discusses the remains of two hominids found within Ethiopia. These skeletal remains have created a huge controversy within the topic of evolution questioning many assumptions that have been made referencing the human lineage. The skeleton of the Australopithecus afarensis was named Lucy and was discovered in 1974. The evidence of her walking upright on her two feet essentially guaranteed her a spot in the human lineage line. Lucy was a chimplike ape that was said to walk upright making scientists believe the human ancestry was simple. The complete skeleton found in Ethiopia of an Ardipithecus ramidus named Ardi completely changed all assumptions made from scientists about the complexity of the human lineage. These remains have encouraged researches that the human line is not the only lineage to have evolved but the chimpanzee line has undergone drastic changes as well. There are many traits that researchers have always directly linked to the human lineage however since these discoveries occurred researchers are reconsidering. The recent discoveries that have shattered what has always suggested what linked a species to the human lineage have changed the certainty of whether it is possible to confidently identify the human’s last common ancestor. Majority of scientist had forgotten that there would have been many hominid species living together at one time. New theories have been suggested since scientists revealed that the foot of a hominid found called the Burtele site was found ju...
vii[7] White, T.D. et al. Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature.423, 742-747 (2003)
Grens, Kerry. "Lost Colony DNA." Scientist 26.1 (2012): 16. MasterFILE Complete. Web. 23 Oct. 2013.
As time progress on the phylogeny, Australopithecus africanus and Australopithecus afarensis were considered to be direct descendants of Proconsul heseloni. However it was decided that A. afarensis branched off and became extinct with no other descendants. Reasons for branching A. africanus and A. afarensis include the data taken from the brain vs....
Wonder of DNA. Design(er) Conference. Answers in Genesis, 10 Apr. 2014. Web. 17 Apr. 2014
Paabo’s team, from Leipzig, Germany, used a method of amino acid content as a way of measuring extractible DNA from the bones. The amino acid method was a...
Noonan, James P. Neanderthal genomics and the evolution of modern humans. Journal List Genome Res, v.20(5); May 2010
The concept of transitional species is an important and complex notion in evolutionary biology. To begin with, there is no such thing as transitional species since all living things were always evolving in the past, not stopping at one stage or another, and they will continue to evolve in the future. In terms of evolutionary biology, we use the concept of transitional species as a way to dim ambiguity. Much like the use of the Linnean taxonomic system of species, we come up with concepts like transitional species to organize and classify species in order to understand their evolutionary roots and how those species changed through life’s history to become what they are today. “In the same way that the concept of species can be provisionally meaningful to describe organisms at a single point in time, the concept of transitional species can be provisionally meaningful to describe organisms over a length of time, usually quite a long time, such as hundreds of thousands or millions of years” (111). Though it can be difficult to distinguish what can be considered an ancestral species from another, the fossil record can show us how species change through time as they develop ways to adapt to stresses found in their environments. “In the modern sense, organisms or fossils that show intermediate stages between ancestral and that of the current state are referred to as transitional species” (222). The concept of transitional species is, in essence, fairly straight forward. This paper will outline the concept of transitional (or sometimes termed intermediate) species and the latter’s role in evolutionary biology, as well as go in depth about several common transitional species: Tiktaalik, an animal at the cusp between life in the water and ...
... tested hairs and other parts for DNA and concluded that they fit into our family tree. “ Those hair samples that could not be identified as known animal or human were subsequently screened using DNA testing, beginning with sequencing of mitochondrial DNA followed by sequencing nuclear DNA to determine where these individuals fit in the tree of life” (Ketchum 2013).
DNA Timeline: DNA Science from Mendel to Today. (2014). Retrieved May 29, 2014, from http://www.dnai.org/timeline/
Common Summary: This study focuses on the evolution and of an organism’s genetics over time. In this study, Rebekah Rogers and Montgomery Slatkin from the University of California, Berkley compared the genetic sequences between two specimens of woolly mammoths, from two different environments and population sizes to test the genome evolution theory that small isolated populations of animals will cause an accumulation of detrimental genetic mutations and defects. To identify the shifts in the mammoth’s genetics, Rebekah et al. used ancient DNA sequences to identify the differences in heterozygous and hemizygous shifts in the DNA. Here the scientist were able to observe the deletions, retrogenes, premature stop codons, and point mutations that differed between the two mammoths. Through comparing SNPs, the scientist saw that the Wrangel mammoths had 318 genes with premature stop codons and that some of those stop codons affected the gene codes for the olfactory system and the structure of the odorant binding receptors that give mammals the ability to smell. Also through the comparisons, the scientists found that the Wrangel mammoth had 27,228 deletions compared to the 21,346 deletions in the mainland mammoths. The deletions in the Wrangel DNA effected 1628 bases that coded for synapse functions, urinary protein production, pheromones; and, the deletions on the FOXQI locus in the Wrangel mammoths caused the development of translucent hairs and a satin coat. These deletions had an increase of heterozygosity in the Wrangel mammoths and showed that there were defects in the mammal’s DNA repairing mechanisms. And by using genetic ontology, the results showed that the Wrangel mammoths had 1.3x as many retrogenes as the mainland mammoths. The increase of retrogenes included genes that affected transcription, translation, cell division, DNA repair, and the chaperones of protein