Biodiversity and the Tree of LifeBiodiversity and the Tree of Life

Brent D. MishlerBrent D. Mishler Dept. of Integrative BiologyDept. of Integrative BiologyUniversity and Jepson HerbariaUniversity and Jepson Herbaria

Berkeley Natural History MuseumsBerkeley Natural History Museums

• What is biodiversity and why is it important?What is biodiversity and why is it important?• The importance of the Tree of Life: two big The importance of the Tree of Life: two big

ideas for students!ideas for students!• A quick run-through of major branches of the A quick run-through of major branches of the

Tree, with emphasis on plants.Tree, with emphasis on plants.• Introduction to teaching phylogenetic Introduction to teaching phylogenetic

reconstruction.reconstruction.• A brief introduction to comparative genomics.A brief introduction to comparative genomics.

Summary of talkSummary of talk

What is biodiversity? What is biodiversity? It is the whole tree of life!It is the whole tree of life!A single, magnificent genealogy connecting all organisms alive today. A single, magnificent genealogy connecting all organisms alive today. Two main lessons for students:Two main lessons for students:

1. 1. We are We are allall related related -- not just in the John Muir sense of all being part of -- not just in the John Muir sense of all being part of the same worldwide ecosystem, but literally genealogically related !the same worldwide ecosystem, but literally genealogically related ! **** This should inform our moral treatment of other living things.This should inform our moral treatment of other living things.

2. 2. We are not all that specialWe are not all that special -- just one tiny twig on a strange, gigantic -- just one tiny twig on a strange, gigantic tree that took root on one little planet in an infinite universe.tree that took root on one little planet in an infinite universe.

You are hereYou are here

What is the value of biodiversity?What is the value of biodiversity?• ethical:ethical: each lineage is a thread in an heirloom each lineage is a thread in an heirloom

fabric that we have the responsibility to pass on to fabric that we have the responsibility to pass on to future generations. future generations.

• intellectual: intellectual: we have a basic need to understand the we have a basic need to understand the world, how it came to be, and where we fit in it.world, how it came to be, and where we fit in it.

• ecological:ecological: biodiversity is needed for proper biodiversity is needed for proper function of ecosystems, and as the raw material for function of ecosystems, and as the raw material for natural selection (future evolutionary potential).natural selection (future evolutionary potential).

• economic:economic: natural lineages are a potential source natural lineages are a potential source for a myriad of products of direct economic benefit for a myriad of products of direct economic benefit (medicines, food, esthetics, shelter, etc.).(medicines, food, esthetics, shelter, etc.).

Valley Life Sciences BuildingValley Life Sciences Building

•University and Jepson HerbariaUniversity and Jepson Herbaria  •Museum of Vertebrate ZoologyMuseum of Vertebrate Zoology•Essig Museum of EntomologyEssig Museum of Entomology  •Phoebe A. Hearst Museum of AnthropologyPhoebe A. Hearst Museum of Anthropology•University of California Botanical GardenUniversity of California Botanical Garden  •University of California Museum of PaleontologyUniversity of California Museum of Paleontology

http://bnhm.berkeley.museum/index.shtmlhttp://bnhm.berkeley.museum/index.shtml

The Berkeley Natural History Museums is a consortium of six The Berkeley Natural History Museums is a consortium of six museums, which together encompass some of the world's most museums, which together encompass some of the world's most valuable natural history and anthropology collections. Their unique valuable natural history and anthropology collections. Their unique synthesis of research, teaching, outreach and collections allows in-synthesis of research, teaching, outreach and collections allows in-depth insights into the history and evolution of life. depth insights into the history and evolution of life.

Courtesy of Sogin Lab -- MBL

Metazoa (animals) Metazoa (animals)

Fungi (mushrooms, molds, yeast) Fungi (mushrooms, molds, yeast)

Green Plants (green algae, land plants)Green Plants (green algae, land plants)

Rhodophyta (red algae)Rhodophyta (red algae)

Alveolates (dinoflagellates, ciliates) Alveolates (dinoflagellates, ciliates)

Stramenopiles (brown algae, diatoms, Stramenopiles (brown algae, diatoms, oomycetes, chrysophytes) oomycetes, chrysophytes)

Crown Eukaryotes:Crown Eukaryotes:

How can we discover How can we discover phylogenetic history?phylogenetic history?

• You can’t actually see phylogeny, so You can’t actually see phylogeny, so how do you make inferences about it?how do you make inferences about it?

• Think of a huge oak tree buried in a Think of a huge oak tree buried in a sand dune, with only the tips of the sand dune, with only the tips of the twigs showing -- what would you do?twigs showing -- what would you do?

• The concept of historical markers -- The concept of historical markers -- characterscharacters

• Need to find something that changed its Need to find something that changed its condition along a lineage, and survived condition along a lineage, and survived in recognizable form to the present.in recognizable form to the present.

http://ib.berkeley.edu/courses/bio1b/evolutionfall06/evolutionf06.htmlhttp://ib.berkeley.edu/courses/bio1b/evolutionfall06/evolutionf06.html

period of period of shared historyshared history

Phylogenetic Reconstruction:Phylogenetic Reconstruction:Need to find markers that can be hypothesized to have changed Need to find markers that can be hypothesized to have changed their state on some shared branch in the past, and to have retained a their state on some shared branch in the past, and to have retained a recognizable record of the derived state to the present.recognizable record of the derived state to the present.

a marker a marker changing statechanging state

Phylogenetics explained:Phylogenetics explained:

homologyhomology -- a feature shared by two lineages because of -- a feature shared by two lineages because of descent from an ancestor that had the feature.descent from an ancestor that had the feature.

transformationtransformation - a heritable change in a homology along a - a heritable change in a homology along alineage from a lineage from a priorprior state to a state to a posteriorposterior state state

divergencedivergence -- the splitting of one lineage into two lineages -- the splitting of one lineage into two lineages

reticulationreticulation - the blending of two lineages into one lineage - the blending of two lineages into one lineage

monophylymonophyly -- all and only descendants of a common ancestor -- all and only descendants of a common ancestor