biogeography expands: of the species · shown here - and is consistent with the fossil record....

Biogeography expands:

• Phylogeography

• Ecobiogeography

Phylogeography — Historical Biogeographyof the Species

Due to advances in DNA sequencing andfingerprinting methods, historicalbiogeography has recently begun tointegrate relationships of populationswithin species and the areas they occupy

Historical biogeography traditionallydeals with relationships among species,genera, and higher taxonomic groupsand the areas they occupy


John Avise, animal geneticist at University of Georgia, coined the termed“phylogeography” to describe “the history and formation of species” from ageographical perspective


The classic phylogeographicanalysis by Avise and his studentsinvolved the identification of astrong geographical signal withinspecies separating populationsfrom the Atlantic seacoast from theGulf of Mexico seacoast.

The presence of two quite distinctgenotypes within all theseunrelated species has beenexplained by Pleistocene glacialand inter-glacial events


One of the most debated, and still unresolved, issues inphylogeography is the geographical origin of Homosapiens - the “Eve hypothesis” as maternally inheritedmitochondrial DNA (mtDNA) is often used


The “out-of-Africa” scenario is often supported - asshown here - and is consistent with the fossil record.However, different ways of analyzing DNA support an“out-of-Asia” scenario as well.


Steps in a phylogeographic study

1. Sample populations widely acrossgeographical range of species

3. Identify and quantify genotypes foreach population [haplotypes if cpDNAor mtDNA]

2. Sample multiple individuals fromeach population to access levels ofvariation in cpDNA, mtDNA, or nucleargenes

Map of the populations and distribution ofhaplotypes of Cedrela odorata (Spanish cedar)across Mesoamerica (Cavers et al. 2003)


Steps in a phylogeographic study

4. Construct minimum spanning tree forthe haplotypes

5. Overlay geographical distributionsonto the tree (or use Nested CladeAnalysis in complicated studies)

Minimum spanning tree of five haplotypes andtheir geographic locations for Cedrela odorata(Spanish cedar) (Cavers et al. 2003)


Example 1: Cryptic invasion of a non-native genotype of Phragmites australis(common reed) into North America (Saltonstall 2002)

Native population in Great Lakes Invasive population in Great Lakes


Minimum spanning tree for all genotypes

Europe, Australasia,Africa, South America

North American

Invasive form

Note that the native NorthAmerican genotypes are closelyrelated and they are unrelated tothe invasive form from the OldWorld


A few populations scatteredfrom Connecticut toMaryland prior to 1910 alsoexhibited the invasivegenotype

Genotyping of common reedfrom herbarium specimensprior to 1910 indicates thewidespread presence of 11native genotypes and 1southern genotype also seenin South America and Asia


However, the invasivegenotype has dramaticallyspread across NorthAmerica since 1910

Genotyping of common reedfrom modern populations(both herbarium specimensafter 1960 and extantpopulations) indicates thesame distributions ofgenotypes


The “invasive” nature of theintroduced common reed ismore dramatically seen inthe time sequence ofgenotyping of pre-1900 tomodern populations

The native North Americangenotypes are systematicallyreplaced by the invasiveform along the easternseaboard of Connecticut,Rhode Island, andMassachusetts


Example 2: History of the North Atlantic during the Pleistocene - differentiationin refugia (nunataks) or recent (Holocene) migration? (Brochmann et al. 2003)


Example 2: History of the North Atlantic during the Pleistocene - differentiationin refugia (nunataks) or recent (Holocene) migration? (Brochmann et al. 2003)


Nodding saxifrage, Saxifraga cernua

1. North Atlantic populations do not showendemic genotypes

2. Migration of several genotypes into (mixed)populations of North Atlantic regions


Levels of species endemism in the NorthAtlantic - black pie sections indicate proportionof endemism

3. Lack of endemic genotypes issupported by the general lack of endemicspecies in the glaciated North Atlanticregion. Genotype and species endemism,however, is high in “refugia” south ofglaciated regions.

Clavija

Historical Biogeography:New Approaches – Interfacing with Ecology

1. Community assembly – timing?

2. Community assembly – species come from where?

3. Community assembly – phylogenetic structure?

When did our modern tropical forests arise?

Clavija

Historical Biogeography:Rise of our Modern Forests

Orders Ericales and Malpighiales

Clavija

• they include 62% of the total stems in an average tropicalforest


• DNA phylogenetic treeof the order Ericales –time calibrated with fossildates (Sytsma et al. 2005)

Evolution in time

• Major rapid radiation ofEricales diversity(“backbone”) occurs from105-95 mya in Albian -early Cenomanian ofCretaceous

• Corresponds to origin ofimportant tropical treefamilies

Evolution in time

• DNA phylogenetic treeof the order Malpighiales– time calibrated withfossil dates (Davis et al.2005)• Major rapid radiation ofthe order is earlyCretaceous

When did they arise? Summary of phylogenetic methods:

Clavija

• Major floristic elements in place by mid-early Cretaceous

• Most species arose recently in Pliocene - Pleistocene


• Examined speciation eventswithin Southern Hemispherecontinental biome types

Michael Crisp et al. (2009) Nature

Historical Biogeography:Biome Relationships

Only 356 shifts occurred in10,800 speciation events

1. Most speciation events oftrees (and herbs) occur withinsame biome type OR betweensimilar biome types

within same biomebetween two biomes

Historical Biogeography:Biome Relationships

• Examined speciation eventswithin Southern Hemispherecontinental biome types

Michael Crisp et al. (2009) Nature

2. Most transoceaniccolonizations occur within samebiome type

3. Niche conservatism NOTadaptive radiation is seen in S.Hemisphere diversification

Historical Biogeography:Phylogenetic vs. Geographic Distance

• Examined phylogenetic andbiogeographical relationshipswithin Seasonally Dry TropicalForests

Toby Pennington et al.(2009) Ann Rev Ecol Syst


• Most species are of recentorigin

• Speciation events involvedaughter species in similarcommunities in similargeographical area

— niche conservatism

Chronogram of legume tribe

Historical Biogeography:Phylogenetic vs. Geographic Distance


• Strong correlation ofgeographic distance andphylogenetic distance!

Mantel test

Historical Biogeography:In situ and recent evolution of Cerrado

• When did the Cerrado originate?

• Did the Cerrado species come invia dispersal of dry adaptedspecies? (niche conservatism)

• Did the Cerrado species arise insitu from surrounding wet adaptedspecies? (adaptive radiation)

PNAS 2009

• Cerrado species arose in last10my

• All arose in situ fromsurrounding wet adapted species

• Convergent evolution for arid,fire system in many groups!

— adaptive radiations!

biogeography expands: of the species · shown here - and is consistent with the fossil record....

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