# Presentation: 074255

## Using molecular approachesto identify biodiversity attributesin theNorth American aridlands

- Brett R. Riddle
- University of Nevada Las Vegas

## Biodiversity why Molecular?

## Conference onMolecular BiodiversityMarch 2004 DanBIFDanish Biodiversity Information Facility

## Biodiversity

- Molecular (genes)
- DNA
- RNA
- proteins

- Organismal (species)
- distribution
- phylogeny
- identification

- Ecological (ecosystem)
- composition
- structure
- function

## molecular biodiversity: several objectives

-   Intrinsic interest in biodiversity at the molecular level
- genomics
- proteomics
- etc.

## molecular biodiversity: several objectives

-   Intraspecific population structure
- 	genetic diversity
- 	gene flow

## molecular biodiversity: several objectives

-   Molecular identification of ESUs and species
- DNA taxonomy
- DNA bar-coding

## molecular biodiversity: several objectives

-   Molecular phylogeny
- ESUs
- species
- higher taxa

## molecular biodiversity: several objectives

-   Molecular phylogeography and biogeography
- 	geography of speciation
- 	evolution of biotas
- 	historical responses of species and biotas to
- 		ecological changes

## Most definitions of biodiversity

- have at least these 3 components:
-   genetic diversity
-   species diversity
-   ecosystem diversity

## More complex and realistic concepts of biodiversity integrate patterns and processes across hierarchies:

- e.g., Noss’s conceptual framework

- STRUCTURAL

- COMPOSITIONAL

- FUNCTIONAL

- genes

- landscapes

- landscapes

- landscapes

## Biodiversity issues at smaller (local) scales:

- characterizing population genetic structures
- characterizing and mapping evolutionarily significant units (ESUs) and species
- prioritizing and managing populations, ESUs, species, and habitats with high value

## Biodiversity issues at larger (regional) scales:

- 	assessing distribution and evolution of
- 	ESUs and species
- 	biotas
- 	prioritizing hot spots of
- 	endemism
- 	rarity
-     		complementarity
-  	        phylogenetic diversity (PD)
- 	predicting responses to
- 		habitat fragmentation and loss
- 		global climate change

## Biodiversity at smaller (local) scales

- 		 mitochondrial DNA
- 		 nuclear DNA
-  microsatellites
-  SNPs

- Biodiversity at smaller (local) scales

- Biodiversity at larger (regional) scales

- molecular
- approaches

## Population, species, and biotic

- histories and futures at regional and
- larger scales—why does it matter?

- *

## 	regional to continental

- Spatially large scales
- 	regional to continental
- Temporally broad scales
- 	millions to thousands of years

## Comparative phylogeography, biogeography, and biodiversity in the warm deserts of northwestern Mexico and the southwestern USA

## North American warm deserts

## The geography of speciation and assembly of biotas in the warm deserts of North America

*Chaetodipus*
- 	coarse-haired pocket mice
*Dipodomys merriami* species group
- 	Merriam’s kangaroo rat and related species
*Peromyscus eremicus* species group
- 	cactus mouse and related species
*Ammospermophilus*
- 	antelope ground squirrels
*Bufo punctatus*
*	**red spotted toad*

## Slide 20

## Slide 21

## Slide 22

## Slide 23

## Slide 24

## Slide 25

## Historical biogeographic approaches				(Crisci 2000)

- Center of origin and dispersal
- Panbiogeography
- Phylogenetic biogeography
- Ancestral areas
- Cladistic biogeography
- Event-based methods (DIVA)
- Phylogeography
- Parsimony analysis of endemicity
- Experimental biogeography

**Notes:**
Many different approaches have become available for discerning the geographical histories of taxa, areas, and biotas.

## “...the geographic distributions of 
genealogical lineages, especially those 
within and among closely related species” 
(Avise, 2000)

*genealogical lineages**, especially those *
*within and among closely related** **species**” *
- (Avise, 2000)

- Why phylogeography?

## Why phylogeography?

- Why phylogeography?

**Notes:**
While it shares the basic goals of unraveling historical vicariance and dispersal, Phylogeography has emerged essentially as a geographical extension of modern molecular genetics and lays claim to a broader set of goals. 

Avise, in his book titled Phylogeography, considered this field unique in providing a bridge between more traditional micro and macroevolutionary disciplines...

## Earth history in western North America

- 				mountain building, rifting, etc.				(many millions of years)
- to
- 				climatic oscillations
- 				(several million to a few 					thousand years)

- 0

- 2

- 6

- 10

- millions of years ago

## Biotic responses 

- to complex earth history
- are diverse and
- include:
- Several modes of Speciation
- Extinction
- Jump dispersal
- Geo-dispersal
- Range shifts

## Earth history is long and complex

- Many opportunities for:
- dispersal
- vicariance
- extinction
- range shifting

- 0

- 2

- 6

- 10

- mya

## Why phylogeography?

- sampling multiple individuals to delineate 		evolutionary lineages (phylogroups / ESUs)
- sampling multiple localities to delineate
- 	geographic distributions

## This sampling strategy often: 

-   Reveals *cryptic (hidden)** **species or *
*	**evolutionary lineages*
-   Reveals *cryptic (hidden)** biogeographic **	**structure*
- Examples...

## Slide 34

## Slide 35

## Slide 36

## Slide 37

## Slide 38

## Slide 39

## 	Traditional historical (cladistic) biogeography 

**taxon **
**histories**

**summary **
**area**
**history**

**vicariant events**

**+**

**+**

**=**

*	*Traditional historical (cladistic) biogeography
- search for recurring patterns in co-distributed taxa

## 2 recurring patterns

- suggest a history of
- vicariance involving the
- Baja California peninsular
- biota...

## Peromyscus eremicus group

*Peromyscus eremicus *group
*Chaetodipus baileyi*
*Bufo punctatus*

## 2. sister-taxa in Southern Peninsular and

- Northern Peninsular (+ Sonoran) deserts

*Ammospermophilus leucurus*
*Peromyscus eremicus *group
*Chaetodipus baileyi *group
*Chaetodipus arenarius*
*Dipodomys merriami* group

## Recurring patterns suggest a

*history of vicariance*:
- Any evidence for vicariant events
- in the earth history record?
- YES
- example:
- evolution of Baja California peninsula

## Slide 45

## A partial model of Vicariance across Peninsular 

**V****z****P****t****V**
**V****izcaino ****P****leistocene**** V****icariance**

- A partial model of Vicariance across Peninsular
- and Continental deserts...

**ILPPV**
**I****sthmus of ****L****a**** P****az**** P****liocene**** V****icariance**

**NPV**
**N****orthern **
**P****liocene**** **
**V****icariance**

## Does this model have predictive power?

- Birds

|  | ILPPV | VzPtV | NPV |  |
| --- | --- | --- | --- | --- |
| Auripaurus flaviceps |  | x |  | Zink et al. 2000b |
| Campylorhynchus 
  brunneicappilus |  | 
x |  | 
Zink et al. 2000b |
| Callipepla squamata grp. |  |  | x | Zink et al. 2001 |
| Pipilo fuscus grp. |  |  | x | Zink et al. 2001 |
| Polioptila melanura grp. |  |  | x | Zink et al. 2001 |
| Toxostoma curvirostre grp. |  |  | 
x | 
Zink et al. 2001 |
| Toxostoma lecontei grp. |  | x |  | Zink et al. 2001 |

## Does this model have predictive power?

- Reptiles

|  | ILPPV | VzPtV | NPV |  |
| --- | --- | --- | --- | --- |
| Cnemidophorus tigris |  |  | x | Radkey et al. 1997 |
| Sauromalus obesus grp. |  | x |  | Petren and Case 2002 |
| Phrynosoma coronutum grp. | x | x |  | 
Montanucci 2004 |
| 
Pituophis melanoleucus |  | x |  | Rodriguez-Robles and
DeJesus-Escobar 2000 |
| Urosaurus nigricaudus | x | x |  | Aguirre et al. 1999 |
| Uta stansburiana grp. | x |  |  | Upton and Murphy 1997 |

## Does this model have predictive power?

- Invertebrates

| Taxon | ILPPV | VZPtV | NPV |  |
| --- | --- | --- | --- | --- |
| Centruroides exilicauda |  |  | x | Gantenbein et al. 2001 |
| Drosophila pachea |  |  | x | Hurtado et al. 2004 |

## Does this model have predictive power?

- Plants

| Taxon | ILPPV | VzPtV | NPV |  |
| --- | --- | --- | --- | --- |
| Lophocereus schottii |  |  | x | Nason et al. 2002 |

## ?

- continental deserts?

## 3. sister-taxa in Gulf of California region and

- Chihuahuan Desert of the Mexican Plateau

*Ammospermophilus*
*Peromyscus eremicus *group
*Chaetodipus penicillatus *group
*Chaetodipus nelsoni* group
*Bufo punctatus*

## At this point, good qualitative support for vicariance, but:

- Not tested within a rigorous analytical framework yet,
*and...*

## ...remember, we expect more complexity than just vicariance:

- Several Modes of Speciation
- Extinction
- Jump dispersal
- Geo-dispersal
- Range shifts

## 	More realistic historical 

**taxon **
**histories**

**summary **
**area**
**history**

**vicariant events**

**post-speciation **
**dispersal event**

**sympatric speciation event**

**+**

**+**

**=**

*	*More realistic historical
- (phylogenetic) biogeography
- search for recurring *and* unique
- patterns in co-distributed taxa

## Sampling taxa from the “core” warm deserts biota:

-   9 mammalian cladograms
-   7 avian cladograms
-   4 reptilian cladograms
-   1 amphibian cladograms
-   1 plant cladograms
-   Totals: 	22 cladograms
- 		64 terminal phylogroups

## Riddle and Hafner, Figure 2

## North American warm deserts

## 4 “core” areas of endemism from

- A

- B

- C

- D

- E

- F

- G

- H

- I

- J

- K

- L

- M

- N

- O

- P

- Continental
- East

- Peninsular
- South

- Continental
- West

- Peninsular
- North

- 4 “core” *areas of endemism* from
- Parsimony Analysis of Endemicity:

## Timeframe of vicariance and earth history events

- from primary Brooks Parsimony Analysis:

- Continental East

- Continental West

- Peninsular North

- Peninsular South

- middle Pleistocene Vizcaino seaway

- Pliocene marine transgressions

- Mio-Pliocene uplifting

- 1 of 2 trees:

## 1 of 2 trees from

- secondary Brooks
- Parsimony Analysis

## Connecting the large spatial and

- older patterns with scales and
- issues of more immediate
- biodiversity concern

##  1:

-  1:
- Embedded Pleistocene histories within
- the core warm deserts?

## Dipodomys merriami       Nested Clade Analysis

*Dipodomys merriami*       Nested Clade Analysis

## Dipodomys merriami  

*Dipodomys merriami*
- embedded Pleistocene structure?

- Rio Nazas –
- Sierra Parras

- Mesa
- Huatamote

## 2:

- Testing hypotheses of
- historical responses
- to ecological / geological changes
- Approach:
- Statistical phylogeography

## Peninsular North + Peninsular South

- _13 widespread phylogroups:_
*Peromyscus fraterculus*
*Neotoma intermedia*
*Pipilo crissalis*
*Callipepla californica*
*Polioptila californica*
*Toxostoma cinereum*
*Campylorhynchus brunneicapillus*
*Bufo punctatus*
*Lophocereus schottii*

## predictions from phylogeographic theory

-   _recent range expansion_         or          _ancestrally widespread_
*mismatch distribution*
-    unimodal						ragged
*isolation-by-distance*
-    significant					non-significant
*gene diversity*
*   *decreases along gradient			otherwise
- 				*cladogram shape*
-     serially nested along gradient		otherwise

## Initial phylogeographic tests of hypotheses in

- BPA trees:

*?**	**Peromyscus fraterculus*
*?**	**Neotoma intermedia*
*?**	**Pipilo crissalis**	**	**	*
*?**	**Callipepla californica*
- Yes	*Polioptila californica (Zink et al. 2000)**	*
*?**	**Toxostoma cinereum*
*?**	**Campylorhynchus brunneicapillus*
*?**	**Bufo punctatus*
- Yes	*Lophocereus schottii (Nason et al. 2002**	*

- Biotic range expansion (geo-dispersal) from Peninsular South to Peninsular North?

## 3:

- Specific biodiversity applications:
-   locating hot spots of diversity
-   evaluating history of biotic diversification
-    deciphering contribution of endemic
-    divergence and range expansion to spatial
-    measures of diversity
-    (e.g., phylogenetic diversity, PD)

## 4:

- Ecological modeling of species/phylogroup niches
- 	GARP, BIOCLIM
- Reconstruction of past species distributions
- 	PMIP models:
- 		  6,000 years ago
- 		21,000 years ago
- Testing paleodistribution predictions with
- 	Phylogeographic data
- Predicting distributional shifts with climate change

## collaborators:

- Dr. David J. Hafner
- Lois Alexander
- Jef Jaeger
- funding:
- National Science Foundation