Paper Details: S0123 / S.Y.B.Sc. (Choice Base) Sem IV / S2015

Life Science: Paper III Date: 02-05-2018

Time:02:00 pm - 05:00 pm Q.P.CODE 34686

Answer Key

Q. 1. A). Define/Explain: 1. Phylogram- A phylogram is a branching diagram (tree) that is assumed to be an estimate of a phylogeny. The branch lengths are proportional to the amount of inferred evolutionary change. A cladogram is a branching diagram (tree) assumed to be an estimate of a phylogeny where the branches are of equal lengths.

2. Outgroup-In cladistics or phylogenetics, an outgroup is a group of organisms that serves as a reference group when determining the evolutionaryrelationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny

3. ORF-In molecular genetics, an (ORF) is the part of a reading frame that has the ability to be translated. An ORF is a continuous stretch of codons that contain a start codon (usually AUG) and a stop codon (usually UAA, UAG or UGA).

4. Nodes-The tips of the tree represent groups of descendent taxa (often species) and the nodes on the treerepresent the common ancestors of those descendants.

5. Duplicate - duplication (or chromosomal duplication orgene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene

6. Homologous sequences-Sequence homology is the biological homology between or DNAsequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry either because of a speciation event (orthologs), or because of a duplication event (paralogs).

7.Common Ancestor-All species share a common descent. In evolutionary biology, a group of organisms share common descent if they have a common ancestor. There is strong quantitative support for the theory that all living organisms on Earth are descended from a common ancestor.

Q. 1. B) Match the Column: a) - v);b) - vi);c) - i);d) - ii) ; e) - iii); f) - vii); g) – iv)

Q.1.C) 1. FALSE 2. FALSE 3. FALSE 4. TRUE 5. TRUE 6. TRUE

Q.2.A. 1. Concept of Allopatric and Sympatric Speciation:

The key to speciation is the evolution of genetic differences between the incipient species. For a lineage to split once and for all, the two incipient species must have genetic differences that are expressed in some way that causes matings between them to either not happen or to be unsuccessful. These need not be huge genetic differences. A small change in the timing, location, or rituals of mating could be enough. But still, some difference is necessary. This change might evolve by natural selection or genetic drift. Reduced gene flow probably plays a critical role in speciation. Speciation can take place in two general ways. A single species may change over time into a new form that is different enough to be considered a new species. This process is known as anagenesis. More commonly, a species may become split into two groups that no longer share the same gene pool. This process is known as cladogenesis. There are several ways in which anagenesis and cladogenesis may take place. In all cases, reproductive isolation occurs. Sympatric Speciation Sympatric speciation occurs when populations of a species that share the same habitat become reproductively isolated from each other. This speciation phenomenon most commonly occurs through polyploidy, in which an offspring or group of offspring will be produced with twice the normal number of chromosomes. Where a normal individual has two copies of each chromosome (diploidy), these offspring may have four copies (tetraploidy). A tetraploid individual cannot mate with a diploid individual, creating reproductive isolation. Sympatric speciation is rare. It occurs more often among plants than animals, since it is so much easier for plants to self-fertilize than it is for animals. A tetraploidy plant can fertilize itself and create offspring. For a tetraploidy animal to reproduce, it must find another animal of the same species but of opposite sex that has also randomly undergone polyploidy.

Allopatric Speciation Allopatric speciation, the most common form of speciation, occurs when populations of a species become geographically isolated. When populations become separated, gene flow between them ceases. Over time, the populations may become genetically different in response to the natural selection imposed by their different environments. If the populations are relatively small, they may experience a founder effect: the populations may have contained different allelic frequencies when they were separated. Selection and genetic drift will act differently on these two different genetic backgrounds, creating genetic differences between the two new species.

2. Social and Behavioral Characteristics of Hunting Societies:

Hunter gatherer societies cover a wide range of characteristics, from really simple to reasonably complex ones. Hunter-gatherers are often grouped together based on kinship and band (or tribe) membership. Prehistoric hunter-gatherers lived in groups that consisted of several families resulting in a size of a few dozen people. The general opinion among anthropologists seems to be that as of some 40,000 years ago they were egalitarian. Not only did they indulge in food sharing, but they shared virtually all consumer goods, even down to some personal items such as smoking pipes. Most hunter-gatherers have a symbolically structured sexual division of labour. However, it is true that in a small minority of cases, women hunt the same kind of quarry as men, sometimes doing so alongside men. In addition to social and economic equality in hunter-gatherer societies, there is often, though not always, sexual parity as well.

Egalitarianism was apparently an intentional policy enforced by leveling behavior from the bottom up. This ensured that leaders who exhibited “big man” behavior were kept in check by various means, including ridicule and even disobedience. Egalitarianism was thus a deliberate policy by the ordinary group members. Members who did not share according to the standards of the group were subjected to open criticism, gossip and eventually ostracism.

The sharing behavior of such societies should not be understood as the more successful one sharing their resources with less successful ones - the haves sharing with the have-nots. The really interesting thing is that sharing is a practice whereby everybody gives and everybody receives. It is a demonstration of goodwill, solidarity and camaraderie. The social effects of sharing are apparently not, according to researchers, foremost in the minds of the sharers.

But the result of the sharing practice is that of making equal that which is not equal through deliberate activity. People’s hunting and gathering skills are not naturally equal. But sharing makes the within-group results reasonably equal.

These characteristics are probably the most fundamental ones of hunter gatherers, especially so during the formative millennia of the Pleistocene, when much of the human psyche was formed.

Q.2.B)

1. Selective Factors that lead to altruistic behaviour:

The importance of social interactions in developing behaviour and communication skills is seen throughout primate groups in panoply of calls, grimaces, gestures and activities used to indicate social positions, needs and means of survival.

In evolutionary biology, an organism is said to behave altruistically when its behaviour benefits other organisms, at a cost to itself. The costs and benefits are measured in terms of reproductive fitness, or expected number of offspring. So by behaving altruistically, an organism reduces the number of offspring it is likely to produce itself, but boosts the number that other organisms are likely to produce. This biological notion of altruism is not identical to the everyday concept. In everyday parlance, an action would only be called ‘altruistic’ if it was done with the conscious intention of helping another. But in the biological sense there is no such requirement. Indeed, some of the most interesting examples of biological altruism are found among creatures that are (presumably) not capable of conscious thought at all, e.g. insects. For the biologist, it is the consequences of an action for reproductive fitness that determine whether the action counts as altruistic, not the intentions, if any, with which the action is performed. Altruistic behaviour is common throughout the animal kingdom, particularly in species with complex social structures. For example, vampire bats regularly regurgitate blood and donate it to other members of their group who have failed to feed that night, ensuring they do not starve. In numerous bird species, a breeding pair receives help in raising its young from other ‘helper’ birds, who protect the nest from predators and help to feed the fledglings. Vervet monkeys give alarm calls to warn fellow monkeys of the presence of predators, even though in doing so they attract attention to themselves, increasing their personal chance of being attacked. In social insect colonies (ants, wasps, bees and termites), sterile workers devote their whole lives to caring for the queen, constructing and protecting the nest, foraging for food, and tending the larvae. Such behaviour is maximally altruistic: sterile workers obviously do not leave any offspring of their own—so have personal fitness of zero—but their actions greatly assist the reproductive efforts of the queen. From a Darwinian viewpoint, the existence of altruism in nature is at first sight puzzling, as Darwin himself realized. Natural selection leads us to expect animals to behave in ways that increase their own chances of survival and reproduction, not those of others. But by behaving altruistically an animal reduces its own fitness, so should be at a selective disadvantage vis-à- vis one which behaves selfishly. 2. Social Evolution:

Social evolution is a sub-discipline of evolutionary biology that is concerned with social behaviors that have fitness consequences for individuals other than the actor. Social behaviors can be categorized according to the fitness consequences they entail for the actor and recipient.

• Mutually beneficial – a behavior that increases the direct fitness of both the actor and the recipient • Selfish – a behavior that increases the direct fitness of the actor, but the recipient suffers a loss • Altruistic – a behavior that increases the direct fitness of the recipient, but the actor may suffer a loss • Spiteful – a behavior that decreases the direct fitness of both the actor and the recipient This classification was proposed by W. D. Hamilton, arguing that natural selection favors mutually beneficial or selfish behaviors. Hamilton's insight was to show how kin selection could explain altruism and spite. Social evolution is also often regarded (especially, in the field of social anthropology) as evolution of social systems and structures. In 2010, Harvard biologist E. O. Wilson, a founder of modern sociobiology, proposed a new theory of social evolution. He argued that the traditional approach of focusing on eusociality had limitations, which he illustrated primarily with examples from the insect world 3. Eugenics: Eugenics is a movement that is aimed at improving the genetic composition of the human race. Historically, eugenicists advocated selective breeding to achieve these goals. Today we have technologies that make it possible to more directly alter the genetic composition of an individual. However, people differ in their views on how to best (and ethically) use this technology.

History of Eugenics In 1883, Sir Francis Galton, a respected British scholar and cousin of Charles Darwin, first used the term eugenics, meaning “well-born.” Galton believed that the human race could help direct its future by selectively breeding individuals who have “desired” traits. This idea was based on Galton’s study of upper class Britain. Following these studies, Galton concluded that an elite position in society was due to a good genetic makeup. While Galton’s plans to improve the human race through selective breeding never came to fruition in Britain, they eventually took sinister turns in other countries. The eugenics movement began in the U.S. in the late 19th century. However, unlike in Britain, eugenicists in the U.S. focused on efforts to stop the transmission of negative or “undesirable” traits from generation to generation. In response to these ideas, some US leaders, private citizens, and corporations started funding eugenical studies.

4. Development of vocalization in primates:

Communication has been the means through which a stimulus from one individual can trigger a response in others. The methods include signals transmitted through any of the sensory channels, scent, touch, vision and sound in primates. Non-human primates emphasize the use of body language. The oral sounds of some apes and monkeys are somewhat discrete at times as well. Unlike us, however, their communication does not involve displacement. That is, they apparently do not "talk" about things and events that are not here and now. People discuss such things as what the world was like two centuries ago. There is no evidence that non-human primates do this. At the broadest level, vocalizations can be described as the result of tissue vibrations generated by the passage of air through a constriction in an animal’s vocal tract. In most tetrapods (excluding birds) the principal oscillator is the vocal folds within the larynx. During phonation, air from the lungs passes between the vocal folds, setting them into oscillation and producing a rich spectrum of vibrations that provide the acoustic power for vocalization. When the pattern of vocal fold vibration is approximately periodic, the resulting spectrum is harmonic and we perceive a voice pitch related to its fundamental frequency (‘F0’), which corresponds to the rate of one open/close cycle of vocal fold motion. These laryngeal “source” vibrations are propagated into the air in the supralaryngeal vocal tract, whose resonances act as acoustic “filters”, imposing a second distinct set of resonant frequencies called formants on the laryngeal spectrum.

Q.3.A) 1. 1. Stating Null Hypothesis and alternative Hypothesis (2 M) 2. For decision of performing paired T test (1 M) 3. Writing down Group 1, Group 2, calculating difference between (1 M) 4. Calculating S.D of differences (2M) (3.559) 5. Calculating mean of difference (1M) (5/-5) 6. Writing down correct formula (1 M) 7. Substitution of all values and correct answer (1M) The absolute value of the calculated t exceeds the critical value (4.4426>2.262), so the means are significantly different. 8. Correct conclusion – based on t and p value whether to accept null hypothesis or not (1 M)

2. 1. Stating Null Hypothesis and alternative Hypothesis (2 M) 2. For decision of performing unpaired T test (1 M) 3. Mean of group 1 – mean of group 2 is 1.500 (1 M) 4. Writing down correct formula (2M) 6. Correct Substitution and calculation (3 M) SEM 1 :0.333 SEM 2: 0.144 SE : 0.374T statistic : -4.015 The two-tailed P value equals 0.0005 By conventional criteria, this difference is considered to be extremely statistically significant. 7. Correct decision – based on calculations? (1M) reject Null Hypothesis. Q.3.B) (5M each)

1. Stating Null Hypothesis and alternative Hypothesis (1 M) 2. For decision of performing annovaand Writing down correct formula (1M) 6. Correct Substitution and calculation (2 M) 7. Correct decision – based on calculations? (1M) Accept Null Hypothesis.

FIELD1 FIELD 2 FIELD3 FIELD 4 A 12 18 14 16 B 19 17 15 13 C 14 16 18 20 n 3 3 3 3 X 15.000 17.000 15.667 16.333 s 3.606 1.000 2.082 3.512

Xave 16.000

source df SS MS F P-value treatments 3 6.667 2.222 0.2899 0.8317 error 8 61.333 7.667 total 11 68.000

2.

1. Stating Null Hypothesis and alternative Hypothesis (1 M) 2. For decision of performing annova and Writing down correct expected frequency values (1M) 6. Correct formula and Substitution and calculation (2 M) 7. Correct decision – based on calculations? (1M) Accept Null Hypothesis. Results Died Survived Row Totals Placebo 12 (6.76) [4.06] 25 (30.24) [0.91] 37 Drug 7 (12.24) [2.24] 60 (54.76) [0.50] 67

104 (Grand Column Totals 19 85 Total)

The chi-square statistic is 7.7157. The p-value is .005474. The result is significant at p < .05.

3. 1. Stating Null Hypothesis and alternative Hypothesis (1 M) 2. for decision of performing Z TEST Writing down correct formula (1M) 6. Correct Substitution and calculation (2 M) 7. Correct decision – based on calculations? (1M) Reject Null Hypothesis.

Z Score Calculations Z = (M - μ) / √(σ2 / n) Z = (147 - 180) / √(27.5 / 13) Z = -33 / 1.45444 Z = -22.6892< 1.96 at P= 0.05

4.explain what the test is with formula 2 M assumptions and uses 3 M The assumptions of the one-sample Z test focus on sampling, measurement, and distribution. The assumptions are listed below. One-sample Z tests are considered "robust" for violations of normal distribution. This means that the assumption can be violated without serious error being introduced into the test. The central limit theorem tells us that, if our sample is large, the sampling distribution of the mean will be approximately normally distributed irrespective of the shape of the population distribution. Knowing that the sampling distribution is normally distributed is what makes the one- sample Z test robust for violations of the assumption of normal distribution. • Interval or ratio scale of measurement (approximately interval) • Random sampling from a defined population • Characteristic is normally distributed in the population

Q. 4. A) Answer Any One of the following: 10mks 1. Gene Annotation and its types: DNA annotation or annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. An annotation (irrespective of the context) is a note added by way of explanation or commentary. Once a genome is sequenced, it needs to be annotated to make sense of it. For DNA annotation, a previously unknown sequence representation of genetic material is enriched with information relating genomic position to - boundaries, regulatory sequences, repeats, gene names and protein products. This annotation is stored in genomic databases such as , FlyBase, and WormBase. Educational materials on some aspects of biological annotation from the 2006 annotation camp and similar events are available at the Gene Ontology website. The National Center for Biomedical Ontology (www.bioontology.org) develops tools for automated annotation of database records based on the textual descriptions of those records. As a general method, dcGO has an automated procedure for statistically inferring associations between ontology terms and protein domains or combinations of domains from the existing gene/protein-level annotations. Genome annotation consists of three main steps:.identifyingportions of the genome that do not code for

1. Identifying elements on the genome, a process called , and 2. attaching biological information to these elements. Automatic annotation tools try to perform all this by computer analysis, as opposed to manual annotation (a.k.a. curation) which involves human expertise. Ideally, these approaches co-exist and complement each other in the same annotation pipeline.Thesimpliest way to perform gene annotation relies on homology based search tools, like BLAST, to search for homologous genes in specific databases, the resulting information is then used to annotate genes and .[6] However, nowadays more and more additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. Ensembl) rely on both curated data sources as well as a range of different software tools in their automated genome annotation pipeline. Structural annotation consists of the identification of genomic elements.

• ORFs and their localization • • coding regions • location of regulatory motifs Functional annotation consists of attaching biological information to genomic elements.

• biochemical function • biological function • involved regulation and interactions • expression These steps may involve both biological experiments and insilico analysis. based approaches utilize information from expressed proteins, often derived from mass spectrometry, to improve annotations. A variety of software tools have been developed to permit scientists to view and share genome annotations. Genome annotation remains a major challenge for scientists investigating the , now that the genome sequences of more than a thousand human individuals and several model organisms are largely complete.[9][10] Identifying the locations of genes and other genetic control elements is often described as defining the biological "parts list" for the assembly and normal operation of an organism.[6] Scientists are still at an early stage in the process of delineating this parts list and in understanding how all the parts "fit together".Genome annotation is an active area of investigation and involves a number of different organizations in the life science community which publish the results of their efforts in publicly available biological databases accessible via the web and other electronic means. Here is an alphabetical listing of on-going projects relevant to genome annotation: • Encyclopedia of DNA elements (ENCODE) • Entrez Gene • Ensembl • GENCODE • Gene Ontology Consortium • GeneRIF • RefSeq • Uniprot • Vertebrate and Genome Annotation Project (Vega)

Q. 4. A.

2. Phylogenetic Trees and their Significance: A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities— their phylogeny—based upon similarities and differences in their physical or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor. Phylogenetic trees are central to the field of phylogenetics. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of the descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetic comparative methods. Unrooted trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred. Rooted Tree: A rooted phylogenetic tree (see two graphics at top) is a directed tree with a unique node — the root — corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. The root node does not have a parent node, but serves as the parent of all other nodes in the tree. The root is therefore a node of degree 2 while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges). The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.Eg/Diagram

Unrooted tree: An unrooted phylogenetic tree for myosin, a superfamilyof proteins.Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred. Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis. Eg/Diagram Bifurcating tree Both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either labeled or unlabeled. A rooted bifurcating tree has exactly two descendants arising from each interior node (that is, it forms a binary tree), and an unrooted bifurcating tree takes the form of an unrooted binary tree, a free tree with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrootedmultifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating trees, more labeled than unlabeled trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For labeled bifurcating trees, there are:Rooted trees and unrooted trees Special types of trees

• A dendrogram is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of a phylogenetic tree . • A cladogram is a phylogenetic tree formed using cladistic methods. This type of tree only represents a branching pattern; i.e., its branch spans do not represent time or relative amount of character change . • A phylogram is a phylogenetic tree that has branch spans proportional to the amount of character change • A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch spans. • A spindle diagram (often called a Romerogram after the American palaeontologist Alfred Romer) is the representation of the evolution and abundance of the various taxa through time. • A Dahlgrenogram is a diagram representing a cross section of a phylogenetic tree • A phylogenetic network is not strictly speaking a tree, but rather a more general graph, or a directed acyclic graph in the case of rooted networks. They are used to overcome some of the limitations inherent to trees.

Q. 4. B. Describe Any Two of the following: 10 mks

1. Orthologues and Paralogues:

Homolog

• A gene related to a second gene by descent from a common ancestral DNA sequence. The term, homolog, may apply to the relationship between genes separated by the event of speciation (see ortholog) or to the relationship betwen genes separated by the event of genetic duplication (see paralog). Ortholog

• Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution. Identification of orthologs is critical for reliable prediction of gene function in newly sequenced genomes. (See also Paralogs.). Speciation

• Speciation is the origin of a new species capable of making a living in a new way from the species from which it arose. As part of this process it has also aquired some barreir to genetic exchage with the parent species. Paralog

• Paralogs are genes related by duplication within a genome. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one.

2.Nucleic Acid Sequence Comparison Ans: Give any one method of Comparing DNADNA hybridization, Repetitive sequence comparison or any other suitable studied by student ( ref: Molecular phylogenetics by Strickburger)

3.Six Frame Translation and its significance: In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.A single strand of a nucleic acid molecule has a phosphoryl end, called the 5′- end, and a hydroxyl or 3′-end. These define the 5'→3' direction. There are three reading frames that can be read in this 5'→3' direction, each beginning from a different nucleotide in a triplet. In a double stranded nucleic acid, an additional three reading frames may be read from the other, complementary strand in the 5'→3' direction along this strand. As the two strands of a double-stranded nucleic acid molecule are antiparallel, the 5'→3' direction on the second strand corresponds to the 3'→5' direction along the first strand. One needs to consider six reading frames when considering the potential of DNA to protein (three frames for each strand). But only one strand is transcribed into RNA — the so- called coding strand. It would therefore seem to me that there are actually only three reading frames to consider. Explain with suitable example. Of +1,+2,+3 and -1,-2,-3 frames.

Q. 4 B. 4.What is Parsimony Principle? Explain with suitable example. Parsimony Principle

The principle of parsimony argues that the simplest of competing explanations is the most likely to be correct. Developed by the 14th-century logician William of Ockam, the theory is also known as Occam's Razor.Biologists use the principle of parsimony when drawing phylogenetic trees. To draw a phylogenetic tree you must first determine which species in a group are most closely related to each other. Biologists generally compare the DNA or physical characteristics of species in the group and look for differences. The principle of parsimony as applied to biology says the phylogenetic tree that requires the fewest evolutionary changes is the one you should assume is correct. Examples

The simplest example involves a physical characteristic like feathers. Let's say you're comparing three species called A, B and C; A and B have feathers and C does not. Based on the principle of parsimony, you would conclude the two species with feathers are more closely related (i.e., share a more recent common ancestor), since in that case the feather trait would only need to have evolved once. The alternative would imply that a common ancestor gave rise to A and another species that now became the common ancestor of C and B. In that case, the feather trait would need to have evolved twice; the principle of parsimony would argue this is not the correct history. Computer Algorithms

To create the most parsimonious phylogenetic trees, biologists usually take into consideration multiple characteristics and DNA sequences from multiple genes. If only a few species are involved you can do this analysis by eye; but as the number of species grows, so too does the number of possible evolutionary trees that could connect them all. Determining the correct tree based on parsimony can quickly become a very complicated problem. Nowadays biologists often use computer algorithms that quickly sort through a large number of possible trees and assign each a score based on how many evolutionary changes it would require. Assumptions: The principle of parsimony is an assumption that is probably true for most situations but need not always be true. It's possible that the actual evolutionary history of a group of species is not the one that involved the fewest changes -- because evolution is not always parsimonious. Another approach to determining relationships is so-called maximum likelihood analysis, which uses statistical analysis to determine which evolutionary tree is most likely or most probable. Both parsimony and maximum likelihood have their own advocates and critics. Explain any suitable example studied by student.

Q.5. Write Short Notes on Any four of the following: 20mks 1. Advantages of Bipedalism: Walking upright distinguishes humans from other primates, and this distinction is expressed anatomically in many of the unique skeletal and other features of the human form. Bipedalism formed the backdrop for our divergence form the rest of the apes. Changes in the locomotion (movement) of primate species had already led to a more upright posture .Primates also developed the tendency to sit upright. While only humans are habitually bipedal, apes and monkeys will even stand on two legs under certain circumstances. For instance, some monkeys will stand to look over tall grass in order to spot potential food sources, predators and other monkeys. Many primates stand when fighting or displaying dominance, they do this because standing makes them appear larger. Some monkeys and apes will even stand up for short periods of time in order to carry things of throw something. This tendency toward a more upright posture was the foundation that allowed for the fully upright, bipedal ape to emerge. However, it was an environmental change that finally triggered the divergence of the Hominin lineage (our direct ‘human’ ancestors) The relatively rapid divergence of new species such as the Hominin branch is known as an '''adaptive radiation'''. This often occurs when there is a significant environmental change and new species rapidly evolve to take advantage of an unoccupied niche It's believed the earliest Hominins emerged in Eastern Africa approximately 5-6 million years ago when this region of Africa experienced considerable environmental changes. Africa became much dryer and the forest, which was home to the apes, became a wooded savannah (grassland). This massive shift forced some of the apes / early Hominins out of the trees in search of alternate food sources. It also meant that movement throughout a continuous tree canopy was no longer possible. As climate and habitats changed, bipedalism had considerable advantages. First and foremost bipedalism was more energy efficient. Even a small reduction in the energy used for movement would be a huge selective advantage. This energy could be invested into rearing young / increases the chances of survival. Bipedalism also made it easier to regulate body temperature (thermoregulation). Being able to see over tall grass or simply see further over the horizon may have helped early Hominins to locate food or avoid predation. Early Hominins would have been scavengers, being able to collect food and carry it to a home base is a selective advantage especially since it reduces the threat from competing scavengers. Freeing up of the hands allowed the further development of tools and weapons. Whilst tools are a definite selective advantage, they are probably a consequence of bipedalism rather than a cause. Specialization of tasks done with the hands would have contributed to the social interaction and cultural evolution of early Hominins.It also helped to see over the grass''' may have helped to spot predators or locate carcasses at a distance. “Holding tools and weapons” (probably a consequence of bipedalism, rather than a cause). “Carrying food” to a ‘home- base’ / position of safety. “Thermoregulation”: Smaller surface area presented to the sun at midday (60% less)& greater air flow across the body when lifted higher off the ground. “Efficient Locomotion”: Energy efficient method that favors low speed, long distance movement – walking. In a sense bipedalism is an extension of a tendency shown by most primates towards a more upright posture. Monkeys sit semi-upright, apes brachiate with the body suspended vertically, and nearly all primates suckle their young sitting upright. However humans are the only primates that habitually walk on two legs. In evolutionary terms bipedalism actually developed very rapidly (over approx 2.2 million years). We have already looked at some of the advantages of a bipedal lifestyle, however, these may not fully explain the speed at which bipedalism developed. As Africa became warmer and drier, walking up-right also meant that less of the body was exposed to direct sun-light from above, aiding thermoregulation. Standing upright also increased air-flow across the body, making it easier to cool down (thermoregulation). This also explains why selection favoured the reduction in body hair and an increase in the number of sweat glands. However, infant chimps and gorillas hang onto their mothers’ long hair using not only their hands, but prehensile (grasping) feet. Human babies do not have prehensile feet, and moreover their hands have no hairy maternal body to cling to. Thus they have to be carried by their mother. This may have resulted in self-accelerating push towards bipedalism. Partially bipedal hominins, with a big toe tending to face slightly forward, would have less prehensile feet. As infants they would therefore be less able to grasp the mother, who would have to use her arms to carry them. Since her arms would be less available for walking, she would depend more on her legs, thus increasing the advantage of having a forward facing big toe. This may have resulting in a ‘positive feedback’ cycle. A greater dependency on the mother to carry the infant may also have influenced the social behaviour of our early ancestors. Most primates do not share food (except with relatives). However, if females were forced to carry their young their hands may not have been free to forage for food. Thus males may have played a greater role in gathering food and carrying it back to a home base to be shared. Later the freeing up of the hands would also allow for the development of tools, which would in turn result in a better diet that would in turn allow for the development of a larger brain. This would in turn result in better tools, a better diet and so forth. Another positive feedback cycle that led to the rapid expansion of the brain.

2.Morphological Species: Morphological species means the assemblage of individuals with morphological features in common and separable from other, such assemblage by correlated morphological discontinuities in a number of features. Morphological species have evolved with the taxonomical identification of characters. Taxonomists classify the characters in which taxonomic distinctions are present using numerical methods. Species are correlated using statistical means considering many identical characters and such species are grouped together.The species with variations in identical characters exhibit low correlation and are grouped differently.

3. (5 M each) Elaborate any 4 points 4M , explain definition 1 M • Definition: A statistical test, in which specific assumptions are made about the population parameter is known as parametric test. A statistical test used in the case of non-metric independent variables, is called non-parametric test. • Basis for comparison for parametric test nonparametric test • Basis of test statistic: Distribution Vs Arbitrary • Measurement level: Interval or ratio Vs Nominal or ordinal • Measure of central tendency: Mean Vs Median • Information about population: completely known Vs Unavailable • Applicability: Variables Vs Variables and Attributes • Example Correlation test Pearson Vs Spearman

4. Elaboration of table 3M with examples 2M

Examples of type I errors include a test that shows a patient to have a disease when in fact the patient does not have the disease, a fire alarm going on indicating a fire when in fact there is no fire, or an experiment indicating that a medical treatment should cure a disease when in fact it does not.

Examples of type II errors would be a blood test failing to detect the disease it was designed to detect, in a patient who really has the disease; a fire breaking out and the fire alarm does not ring; or a clinical trial of a medical treatment failing to show that the treatment works when really it does.

5. Evolutionary Clocks and their significance:

Evolutionary clocks are genetic sequences within genes that can help determine when in the past species diverged from a common ancestor. There are certain patterns of nucleotide sequences that are common among related species that seem to change at a regular time interval. Knowing when these sequences changed in relation to the Geologic Time Scale can help determine the age of the species' origin and when speciation occurred.Evolutionary clocks were discovered in 1962 by Linus Pauling and Emile Zuckerkandl. While studying the amino acid sequence in hemoglobin of various species. They noticed that there seemed to be a change in the hemoglobin sequence at regular time intervals throughout the fossil record. This led to the assertion that the evolutionary change of proteins was constant throughout geologic time.Using this knowledge, scientists can predict when two species diverged on the phylogenetic tree of life. The number of differences in the nucleotide sequence of the hemoglobin protein signifies a certain amount of time that has passed since the two species split from the common ancestor. Identifying these differences and calculating the time can help place organisms in the correct place on the phylogenetic tree in respect to closely related species and the common ancestor.There are also limits to how much information an evolutionary clock can give about any species.Most of the time, it cannot give an exact age or time when it was split off of the phylogenetic tree. It can only approximate the time relative to other species on the same tree. Often, the evolutionary clock is set according to concrete evidence from the fossil record. Radiometric dating of fossils can then be compared to the evolutionary clock to get a good estimation of the age of the divergence.A study in 1999 by FJ Ayala came up with five factors that combine to limit the functioning of the evolutionary clock. Those factors are as follows:

• Changing the amount of time between generations • Population size • Differences specific to a certain species only • Change in the function of the protein • Changes in the mechanism of natural selection

6. Different Types of Phylogenetic Tree Building Methods:

Algorithmic methods: defined only on the basis of the algorithm. Accomplish the goal of estimating a phylogeny by defining a specific sequence of steps that lead to the determination of a tree. Methods that use algorithms include: Cluster analysis (UPGMA) and Neighbor-joining. These methods are also fall under the category of phenetic methods because they rely on measures of overall similarity. You may recall that one major criticism of phenetic techniques is the inability to distinguish between homology and homoplasy, AND being able to even identify support for specific relationships. A second complaint of Cluster analysis (but not Neighbor-joining) refers to the ultrametric properties of the generated trees. Ultrametric distances are defined by satisfying the three point criteria.

Neighbor-joining (Saitou and Nei, 1987) is similar to cluster analysis but removes the assumption that the data are ultrametric. In this method the raw data are provided as a distance matrix, and the initial tree is a star tree (completely unresolved). A modified distance matrix is then created in which the separation between each pair of nodes is adjusted (normalized) on the basis of their average divergence from all other nodes. The tree is constructed by linking the least distant pair of nodes in the modified matrix. When two nodes are linked, their common ancestral node is then added to the tree and the terminal nodes and their branches are removed. At each stage in the process two terminal nodes are replaced by one node until only two nodes remain, separated by a single branch.

Maximum Likelihood methods (Cavalli-Sforza and Edwards, 1967; Felsenstein, 1981; 1993) evaluate hypotheses about evolutionary history in terms of the probability that a proposed model of the evolutionary process and the hypothesized history would give rise to the observed data. The hypothesis with the higher probability of giving rise to the observed data is preferred to one with a lower probability. Likelihood was defined by Edwards (1972) in the following way: "The likelihood, L(H|R), of the hypothesis H given the data R and a specific model, is proportional to P(R|H)...."

Parsimony methods

While likelihood methods require an a-priori model of evolution as part of tree construction parsimony methods are considered to be comparatively model free. Several methods based upon the parsimony optimality criterion have been developed and are summarized below.