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Lent term modules 2013-14


L1 Mammalian evolution and faunal history

Module Organiser: Dr Rob Asher

This course is similar in approach to the Michaelmas Term 'Topics in Vertebrate Evolution', but we make sure that it is possible to take 'Mammalian Evolution' without having done its Michaelmas Term relative. The course aims to familiarise you with the comparative morphology and functional biology, modes of life, distribution, evolutionary relationships and basic systematics of living and fossil mammals and their antecedents. Throughout, we attempt a synthesis of group-based and topic-based treatments.

The first block of lectures deals with the origin and radiation of the 'mammal-like reptiles', the origin of true mammals, and the diversity of so-called 'Mesozoic mammals'. Particular emphasis is placed on tracing the lineages leading to modern mammals; that is, the monotremes (duck-bill platypus and spiny anteater), marsupials, and placentals. In the following block of lectures, each of these modern groups is given more detailed attention.

The next block of lectures is devoted to aspects of the biology and evolution of mammals in the Tertiary, the period associated with the rise of modern mammals.

Finally, six lectures takes up the themes of mammalian evolution and faunal history in the Quaternary: that is, the biology of 'Ice Age' mammals, with an emphasis on the dating of events. The mammals in question have particularly complete fossil records, which makes possible an examination of processes of evolutionary change.

Lectures are backed-up by demonstration practical classes. Students may opt to be assessed on the material seen during these demonstrations in a practical assessment in the Easter Term. The assessment counts as the equivalent of one unit of project work. We do, however, recommend at least a look at demonstration material for all students, because that material helps to reinforce and illustrate the lectures.


L2 Responses to Global Change

Module Organisers: Dr Ed Tanner (Plant Sciences), Professor Bill Sutherland

(Inter-departmental Course)

The world is changing rapidly because of the growth of the world population and the increased us of resources by each individual, a result is changing climate and changing environments. Understanding what is happening and why it is happening will allow us to do something to mitigate the effects or acclimate to the changes.  Overall the course starts with detailed data-rich studies of various aspects of changes and moves on to using data to model what will happen in future. James Peace-Higgins starts with 4 lectures on the effects of climate change on bird populations; phenology and phenological mismatch; scaling up from population to distributions; finishing with managing climate change. Next is Pete Carey who will discuss plant distribution in a changing environment and how to assess plant populations and model their responses to climate. Then Howard Griffiths will address water limitation to plant growth, using examples from various parts of the world where water is limiting.  Ed Tanner will then discuss changes in nitrogen, phosphorus and salt (salinization). Then Louise Sime discusses global climate models. Lisa Wingate goes into detail of one aspect of climate modelling based in tree growth rings (touching on the ‘climategate’ controversy). Finally, Drew Purves will describe modelling forest growth and how it can be used to model the effects of climate change.


L3 Behavioural ecology

Module Organiser: Dr Rufus Johnstone

Behavioural ecology aims to provide a functional interpretation of variation in animal life histories and behaviour. The underlying theme is that individuals will behave in ways that promote their genetic contribution to future generations. The way in which they do so are constrained by their ecology and by social interactions with members of their own species.

The course aims to provide you with an understanding of:

1) the framework of evolutionary theory that is used to explain variation in life history patterns and animal behaviour;

2) the way in which ecology and social competition constrain and control evolutionary options;

3) the empirical evidence that supports functional interpretations of life history parameters and behaviour (including observation, comparative and experimental studies).

Lecture blocks deal with social evolution, communication, family life, vertebrate and insect societies and selfish genes.


L4 Applied ecology

Module Organiser: Dr David Aldridge

With ever increasing pressure on finite resources the world faces very serious environmental problems. This brand new course is about what ecological science can do to help. Sometimes we must accept that undesirable changes will occur, but ecologists often have the knowledge to give advice on how to minimize the harm.

While the focus of the course is very much on the application of ecological ideas and principles, we will take time to reinforce the crucial importance of understanding the fundamental science that underpins these concepts. Indeed, applied ecology helps us to test and develop basic ecological theory. For example, by studying the change in an ecosystem following the establishment of a non-native top predator we can gain unique insights into the way that community structure is affected through direct and indirect trophic cascades.

Case studies will be drawn from different fields and from different ecosystems. For example, we will consider how we can apply ecological concepts to control diseases or minimize the effects of pollution. We will ask how we can apply ecological theory to best manage water resources for different purposes. We will investigate how we can value the importance of different ecosystem services and biodiversity in deciding how best to manage conversion of rainforests.

This course promises to be accessible, thoughtprovoking and very topical. Debate will be encouraged through provision of seminars and supervisions.


L5 Genetics, development and animal diversity

Module Organiser: Dr Chris Jiggins

This course lies at the interface of whole organism biology and molecular genetics. The course looks both at how genomes themselves evolve, and also at how we can use genome information to understand more about whole organism biology. Recent advances in sequencing technology mean that genomic approaches are no longer limited to a few model species, but instead can be applied in many organisms of evolutionary or ecological interest.

The first part of the course looks at how genomes evolve and in particular the importance of conflict, both for genome evolution and the biology of the organism. A large proportion of many genomes consists of repetitive DNA, which replicates itself at the expense of the organism – a form of genomic parasitism. Other sources of conflict occur between the sexes, and between parents and offspring. We will look at the genetic basis of sex determination and how this can lead to conflict between chromosomes.

Molecular phylogenetics has revolutionised evolutionary biology by providing a wealth of data on the relationships between organisms. The second part of the course examines how we can reconstruct such relationships from DNA sequences, and how this can inform our understanding of character evolution. We also examine how patterns of sequence variation can be used to infer the influence of natural selection. For example, this approach has been used to identify genes likely to have been involved in the origin of language and cognition in humans.

Next we look at the genetic basis of adaptation. Do we expect evolutionary change to involve few or many genes, and how might we go about identifying the genes underlying a particular trait? What kinds of genes are likely to control recent evolutionary changes in morphological traits? Butterfly wing patterns are used as an example to illustrate these questions.

Finally, we will look at how the genetic ‘tool kit’ that controls the great diversity of animal body plans has arisen, and in particular the importance of both gene and genome duplication in the origins of diversity.


L6 Development: Cell differentiation and organogenesis

Module Organiser: Prof Helen Skaer

(Inter-departmental Course)

In this course we will examine the events in development, which follow the earlier steps of axies form covered in M8.

We have two main aims in this module: 1) to explore the mechanisms that are used to construct the complex functional units of cells, namely the establishment of groups of specialised, differentiated cells and the coordination of their shape and arrangement into organs, and 2) to examine how the basic developmental mechanisms found in simpler invertebrates have been elaborated in vertebrates to generate more complex structures. A series of topics will be presented, each using a particular tissue or organ to highlight particular developmental mechanisms. Thus, germ cells will reveal mechanisms of cell fate determination and stem cell renewal; the generation of epithelia addresses principles of cell polarity and tubulogenesis; neural crest and placodes illuminate mechanisms of cell allocation and migration; limb development will be used to illustrate how patterning mechanisms are coordinated with cell proliferation. Finally the coordination of these mechanisms on a more global scale will be addressed using the development of internal organs.

Throughout we will consider how the disruption of these mechanisms leads to congenital malformations and disease, including cancer. We will take a critical look at how our current ideas have become established and the current limitations in our knowledge.

This course is the second of two complementary modules (with M8), which can be taken together or on their own. Our aim is to provide a course that is accessible to anyone doing Part II Zoology whatever their previous background.

This is an interdepartmental course (with PDN). In addition to three lectures per week there are six journal club sessions, which provide an opportunity for interactive discussion of key references.


L7 Control of Cell Growth and Genome Stability

Module Organiser: Dr Philip Zegerman

The construction and maintenance of multicellular organisms requires precise control of cell numbers through cell proliferation and death. The course provides students with a broad understanding of the intracellular factors that govern how and when a cell divides and how the genetic material is conserved through cell division.

In the first part of the course, the lecturers examine the molecular mechanisms that regulate the mitotic cell division cycle, starting with the machinery of cell division in M phase. Moving on through the cell cycle, the molecular basis and regulation of DNA replication in S phase is discussed. The importance of coupling DNA replication to cell division is explained and the students hear how the cell ensures that the genome is only replicated once during each cell cycle. Finally, the involvement of chromatin structure in the control of DNA replication and transcription is considered.

The second part of the module describes how various types of DNA damage are repaired and explores the links between DNA repair factors and telomere maintenance. It then goes on to explain how the cell cycle is halted to allow sufficient time for repair to occur, thus ensuring that genomic integrity is maintained between a cell and its progeny.

The final block of lectures describes how the cell cycle goes awry in cancer and how apoptosis or programmed cell death contributes to the normal biological control of cancer cells and to regulating cell number during development.