Ecosystem• Ecosystem Level:• Ecological Area = number of species (species richness)• Taxonomic definition: Morphology & Life History differences• Molecular genetics

Phylogenetics tree construction • Maintain max. diversity of evolutionary lineages• Combining morphological and molecular tools can reveal historical

forces = possibly leading to conservation actions or evolutionary explanation of events.

• Example:Microbial communities

• Ecotones (between forest and savanna) generation of diversity

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Defining species

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Taxonomical Point of View

• Groups within a species defined as being of a taxon lower than a species

• Zoology = subspecies• Botany = variety, subvariety,form• Conservation Biology = Evolutionary

significant units (ESU) [species or smaller distinct population segments]

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Difficulty in defining "species" and identifying particular species

• Species = ?? • Before Evolution Concept:

Carl Linneaus invented classification system(religious concept, all creatures already exist)

• Hybrid = ??

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“Text book” definition• Species = individual organisms from a natural

population; generally interbreed and produces fertile offspring (Ernst Mayr)

• Exclude unusual or artificial mating: eg. horse to donkey = a mule (sterile) and only occur in captivity

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Species

• Previous definition relies on sexual reproduction

• Asexually reproducing organism eg. fungi or certain clone plants the previous definition would not apply

• Often difficult to tell based on morphology alone

• Natural or experimental hybridization6

Different way of thinking….• Barriers to create species

– Reproductive (Mating behaviour eg. aerial dance, song, physical trait selection)

– Geographical (Pangaea to current geography)Allopatric speciation

—Look for historical evidence for possible evolution events

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Different way of thinking…..• Be careful when sampling; possible Ring species eg.

D. Irwin’s study on Greenish warbler• Morphological differences pending source of samples• Possibly no obvious species boundary except at the

“end” …otherwise interbreed

West Siberia one bar on wing

East Siberia two bars

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Species side by side

• Species can diverge while living side by side

Sympatric speciation

• Cichlid (Amphilophus citrinellus) versus (A. zaliosus)

• A. citinellus = prey on snails

• A. zaliosus = prey on insect larvae

• Evolve different body shape and mating preferences

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Some examples of species definition

Species Definition

Textbook (Biological) Individual organism; generally interbreed; produce fertile offspring (E. Mayr)

Typological Classical; Fixed properties; Phenotypic based (Linnaeus)

Genetic (Phenetic) Similar DNA; DNA-DNA hybridization; Bar coding project (Current)

Evolutionary (Darwinian) Shares an ancestor; subspecies

Phylogenetics Shares an ancestor; not subspecies (Current)

Ecological Adapted to a particular niche

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Thoughts on species concept• No species concept are

entirely objective • Complexity of life the

likelihood of objective definition would be impossible

• Many disagreements in labeling a species or defining a species

• Biologist would settle for what works for them; mixture from different definitions would be ideal

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Example of species identification

• Example of defining different subspecies of Koala bears

• Due to dramatic local declines perhaps there are different Koala species

• Based on morphology there could be 3 subspecies• Minisatellites, mtDNA, RAPDs and SSRs failed to

identify differences• Data show strong North/South continuous cline• Morphological differences possibly due to

environment and not genetics (Sherwin et al 2000 Cons Biol 14:639-649)

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Example of species identification

• Sea bird (Petrel)• mtDNA revealed different

haplotypes for different morphological types

• 3 (B,C,D) for the dark species

• 5 (A,E,F,G,H) for the light species

• Assortative mating to maintain species differences (Brooke and Rowe, 1996 Ibis 138:420-432) (See Textbook p.78)

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Example of subspecies• Ursus americanus

kermodei (Kermode Bear)• White phase of the black

bear (mtDNA confirm) (Marshall and Ritland 2002 Molecular Ecology 11: 685-697)

• Possibly due to population isolation, assortative mating (SSR data)

• Due to a single nucleotide change (Ritland et al (2001) Tyr-to-Cys

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Hybrids

• Interbreeding of two separate species• Using maternal and paternal markers to

determine hybrid zones and extensiveness of the zone

• Conifer species in Abies (paternal cpDNA and maternal mtDNA)

• Using mtDNA, cpDNA and RAPD show hybrid saplings however little adult hybrids

Abies veitchii Abies homolepis

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Hybrids

• Detection of invasive species is very important and an important sign is the detection of hybrids between invasive and native species

• Use of molecular markers are especially important for species that lack many morphological differences

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Individuals• Identification of individuals to species can be difficult

pending on life stage (eg. non flowering plants or tadpoles) or lack of morphological characters

• To delimit a population, it is important to be able to identify individuals

• Biomonitoring by using larvaes is difficult without some kind of unique identifiers

• Barcoding of life project will greatly improve these problems but it will not work for many organisms eg. anaerobic organisms, many plant groups, prokaryotes

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• Forensic investigations calls for identification of suspect and victims

• Use of genetic markers great aid in the investigation

• Recall VNTR marker usage in previous lecture, can use RAPD, AFLP and now a suite of SNP markers to have compare evidential material with known samples (eg. saliva, hair, tree stumps etc.)

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Regions for barcoding of life

http://oceanexplorer.noaa.gov/explorations/04alaska/logs/summary/media/live_bamboo.html

http://micro.magnet.fsu.edu/optics/olympusmicd/galleries/brightfield/polysiphonia.html

http://www.destination360.com/central-america/costa-rica/costa-rica-animals

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Reproduction: determination of Sex• With immaturity and cryptic morphology the

identification of the sex of an individual is not always easy

• To calculate an effective population size the sex of breeding individuals needs to be identify

• Specific primers eg. SRY gene on the Y chromosome can help detect mammalian males

• Appropriate control is required to eliminate “false” females by using a housekeeping gene eg. actin

• Dart samples from whales to identify individuals and the sex of an individuals is an active area of molecular ecology (Barrett-Lennard, Van. Aquarium)

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Determination of Sex

• Exceptions in standard sexing of mammals such as bird (females = WZ, males = ZZ) there is the helicase DNA binding gene (CHD1) which produce different size products for the WZ chromosomes

• Even in plants there is an example of Y (male) specific PCR product eg. hops [diecous plants]

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Prey vs Predator• Predator-prey interactions, most commonly

look at the gut contents to study relationship

• Diet analysis eg. prey “crumbles”• Fecal content eg. coyote diet• Tracking predator eg. gut cells in fecal

matter• Identify individual prey using mtDNA eg.

COI gene, 12S rRNA • Multiple copies of mtDNA great chance of

prey amplification22

Prey vs Predator• Complication of possible secondary prey with PCR

techniques, there is a great chance of this problem with non-invasive sampling

• Some techniques are more problematic eg. RAPD. AFLP

• Usage of specific primers such as SSR will reduce generation of incorrect amplicons, dropout of specific alleles will bias genetic variation estimates

• No techniques are 100% error proof• Replication of 10% of samples will be important

and negative control when doing PCR must be done 23