genetic diversity - keep populations of species as genetically diverse as possible -measured by...

Genetic Diversity

- keep populations of species as genetically diverse as possible

-measured by number of polymorphic alleles (how many alleles a gene has) and heterozygosity (presence of two different alleles)

- _____ (RFLP) can be used to detect differences in DNA sequences

How Restriction Fragments Reflect DNA Sequence

• RFLPs

– Reflect differences in the sequences of DNA samples

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DNA from chromosomes

CCGG

GGCC

ACGG

TGCC

CCGG

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Plant 1 Plant 3

Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

• After digestion by restriction enzymes

– The fragments are run through a gel

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Longerfragments

Shorterfragments

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Plant 1 has three polymorphic alleles -xwy

Plant 2 has two polymorphic alleles and is heterozygous z/w

Plant 3 has two polymorphic alleles and is heterozygous z/y

New alleles in sexually reproducing organisms can result from crossing over, independent assortment, and gene flow.

Mutations can also produce new alleles.

High polymorphic alleles and heterozygosity confer a genetic advantage as they have more alleles and thus are better adapted.

Low genetic diversity indicates possible inbreeding.

• Sequence for plant 1-CCGG…CCGG

• Sequence for plant 3-ACGG…CCGG

• Plants 1 & 3 have a different allele

w

x

y y

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DNA from chromosomes

CCGG

GGCC

ACGG

TGCC

CCGG

GGCC

CCGG

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Plant 1 Plant 3


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Because the state has a diverse climate andgeology, its biodiversity is rich. Correll andJohnston(1979) summed up the size andvariability of the state in the following,“Texas is 860 miles north to south and 773miles east to west. Enclosed within the4,137 mile perimeter of the state are 267,339square miles. Brewster County, alone, islarger than Connecticut. Texas has a 624mile coastline and 90 peaks in the Trans-Pecos a mile or more high. Each year about56 inches of rain fall in the pine-hardwoodforests along the Sabine River, which formspart of the state’s eastern boundary. Lessthan eight inches fall in the ChihuahuanDesert in the extreme west. This is likenedto Miami and Phoenix, respectively.”

The biodiversity of a region is further enriched by those flora and fauna that are endemic, or found only in a particular region. There are about 5000 plant taxa in Texas and it is estimated that between 400 and 500 of these are endemic to the state. Texas shares affinities with the Great Plains to the north, eastern deciduous forest to the east, mountain forest and desert to the west, and subtropical biomes to the south.



Appendix Three Pg 1358-1359 SMIFNCT

Piney Woods



Piney Woods-primarily rolling pine-hardwood forest -hardwood trees include members of the Fagaceae (_____), Juglandaceae (_____), Magnoliaceae, and Ulmaceae (_____)-understory species include beautyberry (Verbenaceae), flowering dogwood, hollies, and species of greenbrier (Smilacaceae). -members of the family ______ include Longleaf (Pinus palustris), shortleaf (P. echinata), and loblolly (P. taeda). -along river margins are members of the Salicaceae like willowand Cupressaceae like bald cypress. Swamps and bogs with bryophytes such as Sphagnum moss, various Cyperaceae (sedges), carnivorous plants, and orchids occur in low areas.

Commercial timber harvesting, ranching, farming, and urban sprawl are the primary factors threatening the Piney Woods.

Four Ecosystems are threatened:American Beech-Southern Magnolia (Fagaceae-Magnoliaceae) and American Beech-White Oak (Fagaceae) communities arethreatened because of their limited distribution in Texas, abusive forestry practices such as clearcutting, and the fact that cattle grazing reduces re-growth. Longleaf pine-beakrush (Rhynchospora spp.) (Pinaceae-Cyperaceae) and longleaf pine-little bluestem (Pinaceae-Poaceae) communities are also threatened because of clearcutting, conversion to pasture, overgrazing, lack of prescribed burning, and urbanization.

Endemism is low to moderate.

Gulf Prairies and Marshes



The Gulf Prairies and Marshes is a gently rolling, treeless prairie interspersed with marshes. Grasses dominate with forbs and scattered shrubs including mesquite (Family ____) and and pricklypear (Family _____). Deep sands are dominated bylive oak-little bluestem (Families _____ and _____ , respectively). In marshes are members of the Alismataceae like arrowhead and burhead and moisture-loving grasses and sedges. In deeper marshes or lakes there are some of the same species and, in addition, marsh pennywort (Hydrocotyle) (Apiaceae), waterlily (Nymphaceae), large sedges (Cyperaceae) and cat-tail (Typhaceae).

Halophytic vegetation dominates the coast in salty soils.

One ecosystem in the Gulf Prairies and Marshes is threatened.

Live oak (Q. virginiana)-red bay Persea borbonia) communities in the Coastal Prairies and Marshes are threatened by residential, industrial, and agricultural development.

Endemism is moderate.



The Oak Woods and Prairies is ecotonal between the eastern deciduous forest and the Great Plains. Today, brush and tree densities increase due to overgrazing and control of fire. Farming, ranching and urbanization have affected the natural vegetation of this region. The region is divided into the western and eastern Cross Timbers and the Oak Woodlands (Post Oak Savannah). Live oak-little bluestem (Fagaceae and Poaceae) communities are common in the uplands of the western Cross Timbers. The eastern Cross Timbers has more developed forest while the Oak Woodlands contains thebest developed oak-hickory forest in Texas. Post oak and black hickory (Fagaceae and _____) dominate the woody vegetation of the eastern Cross Timbers and the Oak Woodland. Sugarberry-Elm (Family _____) communities occur in all three subregions. Mesquite (Family _____) is invading parts of these areas that have been overgrazed.

Communities within the Oak Woods and prairies are considered to be relatively stable and are not listed as watched, threatened, or endangered.

Though endemism is relatively low, there are a number of endemics occurring within this region and they are listed in Appendix Three of Shinners and Mahler’s Illustrated Flora of North Central Texas.



Blackland Prairie- Low to moderate endemism



The Blackland Prairies is found adjacent to and as ecotones with the Oak Woods and Prairies. The Blackland Prairie subregion contains deep soils and tall grasses in areas not under cultivation. Some of the dominant grasses include little bluestem, Indiangrass and big bluestem.Occasional woody plants include hackberry (Family _____), post oak (Fagaceae), and Mesquite (Fabaceae).

Three tall grass communities are endangered or threatened in this biome. Gammagrass-switchgrass communities have a very limited distribution and are considered endangered due to conversion of habitat to farmland, changes in drainage patterns, overgrazing, and fire suppression. Little bluestem (LB)-brownseed paspalum and LB-Indian-grass, and Silveanus dropseed communities are considered threatened.

South Texas Plains (South Texas Brushlands) is in large cattle ranches with farming and urbanization increasing southward. The area originally supported grasslands or savannahs but overgrazing and control of fires has increased the amount of brush in the area dramatically and recently. Prior to brush invasion, seacoast bluestem and Paspalum, were two of the dominant grasses on sands. A chaparral of shrubs and small trees of a kind occurring over large areas of semiarid northeastern Mexico occurs on well drained and usually calcareous soils. The more frequent species included guajillo (Acacia berlandieri), blackbrush (A. rigidula) (Family ______), cenizo (Family ______), mescalbean (Sophora secundiflora) (Family _____), Morman tea (Ephedraceae), granjeno or spiny hackberry (Family _____), and many other shrub species. Mesquite and pricklypear have increased due to overgrazingand control of fire.

In the subtropical zone of the South Texas Brushland, three ecosystems are threatened or endangered: Texas palmetto (Arecaceae) and Texas Ebony-Anacua communities are endangered while the Texas Ebony-Snake Eyes community is threatened because of their limited distribution, conversion to crop land and pastures, and urbanization.

Endemism is moderate in the South Texas Brushlands.



The Edwards Plateau area comprises or Texas “Hill Country” is bounded by spectacular canyons on the east and south while in the north and west, it becomes ecotonal with other regions. The area is primarily rangeland but urbanization is beginning to affect the vegetation. A few of the common grasses include little bluestem, Indiangrass, grama grasses, and buffalo grass (Poaceae).Oaks (Fagaceae) and junipers (Cupressaceae) dominate the woody vegetation. Bald cypress (Family _____) occurs along most of the streams and rivers. Mesquite (Fabaceae) and junipers are common invaders of overgrazed sites.

Because of its variation in topography, the Edwards Plateau is an area of high endemism in the state. A number of communities are watch-listed and are being monitored but none are T&E. The primary concern is with urban sprawl and subsequent lowering of the water table.



The Rolling Plains and High Plains are part of the Great Plains region of the central United States and most of these areas are used for rangeland though cultivation is increasing in some areas. A few of the grasses common to these two regions include little bluestem, grama grasses, buffalo grass, and other short grass species. Mesquite (Fabaceae), redberry juniper (Cupressaceae), and sand sage (Family _____) are woody dominants common to both regions. Shinnery oak (Fagaceae) is common in the Rolling Plains while Yucca (Family _____) and cactus (Cactaceae) are common in the High Plains.

The cottonwood-tallgrass (Populus deltoides) (Salicaceae) community in the High Plains is very limited in distribution and threatened by lowered groundwater tables, overgrazing, and lack of prescribed burning.

Endemism is low.



The Trans Pecos lies west of the Pecos River and includes mountains and arid valleys that are part of the Chihuahuan Desert. Diverse habitats include desert valleys and plateaus as well as wooded mountainsides. Most of the land is used as native rangeland. The Sand Hills subregion consists of mostly shin oak (Fagaceae) and mesquite (Fabaceae) on windblown dunes and grasslands dominated by little bluestem (Poaceae). The Stockton Plateau consists of flat-topped plateaus intersected by canyons. Salt basins are dominated by halophytes and desert scrub by xerophytes. Cresote bush, mesquite (Fabaceae), ocotillo, cacti(Cactaceae), lechuguilla and Yucca spp. (Agavaceae), redberry juniper (Juniperus pinchoti) (Cupressaceae), and Morman tea (Ephedra spp.) are some of the common species in the desert.

Cresote bush. Photo by James Manhart, TAMU

Ocotillo

Dominants in mountain habitats include oneseed and alligator Juniper (Cupressaceae), Pinon, Ponderosa, and Limber pine(Family _____), Graves and Gray oak (Fagaceae) as well as quaking aspen (Salicaceae).

Two ecosystems are T&E: Within the salt basins, the saltgrass-Olney Bulrush (Poaceae-Cyperaceae) community is threatened by its limited distribution in Texas and the lowering of the water table in the area. In mesic canyons and along streams, the velvet ash-willow (Salicaceae) community is threatened because of its limited distribution in Texas, changes in stream flow due to dams and channelization, as well as overgrazing.

Because of the variability of environments found within the Trans Pecos, this is another region of high endemism in the state.

Biodiversity is declining at a rapid rate in Texas and all overthe world

-some estimates indicate that 40% of all species living on planet will be gone in 40 years

-E. O. Wilson conservatively estimates 27,000 extinctionsper year (74 per day or 3/hour) compared to a rate of 27 per year in earth’s past

According to Center for Plant Conservation

http://www.centerforplantconservation.org/

- One quarter of the native plants in the United States are of conservation concern. That’s 5,000 different species.

-More than 200 native plant species in the United States have gone extinct

- More than 730 plant species in the U.S. are federally listed as endangered or threatened

Three Greatest Threats to Plant Biodiversity

1. Loss of habitat-protected natural areas like parks and wildlife refuges attemptto counter this problem

2. Overcollecting-conservation organizations have produced informational materials such as The Gardener’s Guide to Plant Conservation (World Wildlife Fund), and laws have been created to prohibit the sale of endangered species.

3. Introduced plants that become naturalized-outcompete natives and take over their habitat-attempts are made to eradicate them from protected natural areas

http://www.abdn.ac.uk/ecosystem/bioecofunc/intro.htm

Is biodiversity important to ecosystem function?-currently worldwide studies are testing three hypotheses

1. Rivet Popper Hypothesissuggests ecosystems are like airplane wings where flight (ecosystem functioning) may or may not be compromised depending upon which rivets (species) are lost

2. Redundancy Hypothesiscertain species may drive ecosystem functioning, while other so-called 'redundant' (= 'insurance' or 'passenger') species contribute little in the way of functioning. This isnot to say that redundant species in terms of function can be lost, since loss may result in decreased resilience should the environment change

3. Idiosyncratic Hypothesisecosystem function changes as the number of species changes, but the magnitude and direction of change is unpredictable (= 'idiosyncratic') due to the complex and varied roles of individual species

Currently 100s of studies (http://www.abdn.ac.uk/ecosystem/bioecofunc/intro.htm)

underway to test these hypotheses. To illustrate one early study that supported the rivet popper hypothesis, consider thefollowing:Tilman, D. and Downing, J.A. (1994) Biodiversity and stability in grasslands. NATURE 367: 363-365.University of Minnesota-207 four meter squared plots distributed among one nativeprairie and three abandoned fields of different ages-each year, they clipped a different quadrat of each plot andanalyzed its species diversity and biomass-during a drought in 1987-88, productivity fell in plots drastically-drop in productivity of species-rich plots was about 1/4 of species-poor plots and species-rich plots recovered to their pre-drought levels of biomass about four times faster

Regardless of whether biodiversity is essential to ecosystem function, ecological services and species economics make biodiversity essential

Ecological Services-millions of species and their symbioses interact with environment to clean air and water, and to form fertile soilsA few examples:PhotosynthesisCarbon cycleNitrogen cycleWater cycle

Species economics-use of tens of thousands of species by people everywhereto provide food, shelter, health, and other commodities amounting to trillions of dollars in agricultural, forestry, fisheriespharmaceutical, and textile products as well as nature tourism

Two Examples of pharmaceuticals of which 40% come from biotaincluding 25% from plants alone1. Rosy periwinkle (Catharanthus roseus)-native to Madagascar where there are 13,000 species of plantsand 85% are endemic-85% island’s habitat has been lost due slash & burn agriculture-studies discovered two drugs (vinblastine and vincristine)used in leukemia treatment. Childhood leukemia survival rates have increased from 10 to 95%

2. Pacific yew (Taxus brevifolia)-drug taxol reduces incidence of ovarian and breast cancer-took bark of three trees to provide sufficient taxol for a singlecancer patient. Because of our understanding of phylogenetic relationships, a close relative, T. bacatta, which contains taxolin the leaves is used at less cost and without harming naturalpopulations

What if these and hundreds of other organisms had not been discovered by taxonomists?

Two examples of improvements in agriculture because ofknowledge about biodiversity

1. 1962- baling hay in the Andes

-Dr. Hugh Iltis (University Wisconsin) and Dr. Don Ugent (Southern Illinois University) collected 1000 specimens for the herbarium from Andes

-seeds from a wild tomato discovered in these collections wereused to grow plants that were crossed with cultivated tomatoesincreasing the value of tomato fruits eight million dollars per year

2. Late 70’s- Western Mexico

-Stimulated by a drawing of wild corn on a poster by Dr. Hugh Iltis and sent to herbaria round the world as a New Years Day card, Dr. Luz Maria Villareal de Puga (University Guadalajara) asked her undergraduate students to try and find this plant that had last been seen in the wild in 1921 at its only location, in Western Mexico

-Rafael Guzman found Zea diploperrennis in cloud forestsof Jalisco, Mexico. This wild species hybridizes with Z. mayes and is resistant to seven types of viral disease that infect cultivated corn (which has annual worldwide value of 60 billion)-today, few remaining populations would be extinct but the cloud forest in that region has become a biosphere preserve

Herbaria, botanic gardens, arboreta, seed banks, and protectednatural areas all play a role in protecting biodiversity

HerbariaFunctions:1. Reference collection-aids in identification-depository for type specimens and voucher specimens taken during research projects

2. Teaching and training aid

3. Body of data for research

Three types of Herbaria

1. National or International (Major)-type and voucher specimens from all over the world-assist in identifying the world’s flora-examples would include Botanical Research Institute of Texas, Plant Resources Center at University of Texas, Missouri Botanical Garden, New York Botanical Garden, Field Museum of Chicago, and Kew Gardens in London

2. Regional Herbaria-concentrates on regional floristic studies -examples would include Texas A&M University Herbarium and Robert Bebb Herbarium at University of Oklahoma

3. Working or teaching herbarium-smaller collections used for identification of local flora-3/4 of listings in Index Herbariorum (Holmgren, P.K. and N. H. Holmgren. 1998 onwards (continuously updated). Index Herbariorum. New York Botanical Garden.http://sciweb.nybg.org/science2/IndexHerbariorum.asp)-many national parks and small colleges and universities-examples include Tarleton State University Herbarium (TAC), Texas A&M University-Kingsville Herbarium (TAIC),and Rocky Mountain Research Station, USDA, Forest Service (FPF), Fort Collins, CO

Botanic Gardens and Arboreta (1300 worldwide)-maintain living collections of herbaceous and woody (arboreta)plantsFunctions1. Research-larger ones associated with research institutions and provide material for experiments in plant propagation, reproductivebiology, breeding and hybridization studies, and studies to examine genetic variation2. Teaching and training using greenhouses, garden plots, and some conserve natural habitat3. Public service by identifying plants and information on propagation4. Centers for conservation of rare and endangered plants

Seed banks-700 in the worldNational Center for Genetic Resources Preservation in Fort Collins, COhttp://www.ars.usda.gov/main/site_main.htm?modecode=54020500

Seed Bank Advantages 1. Readily Available to geneticists and crop breeders

Seed Bank Disadvantages

1. Storage and grow-out costs are high so that only the most useful food, forage, and forestry crops are maintained2. USDA has had 160,000 samples stored since 1898 but only 5-10% are still alive today- National Center for Genetic Resources Preservation is using tubesfilled with liquid nitrogen in deep freezes that will only have a 1%loss in germination over a hundred billion years3. Evolution is stopped. As pests evolve new virulence, the storedcrops are not co-evolving with them

Botanical gardens and arboreta (BGA)BGA Advantages

1. May allow some evolution to occur

BGA Disadvantages

1. There are few cases of plants being conserved for long periods of time-only one case where botanic garden saved plant from extinctionFranklinia altamana-originally collected by royal botanist John Bartram in late 1760s-planted in garden of his 112 acre farm in Philadelphia-today farm is only 44 acres but shrub survived there but went extinct in wild

2. Populations in botanical gardens are too small and catastrophes like freezes, hurricanes, and disease can decimatepopulations

Ex. Rancho Santa Anna Botanical GardenAgave utahensis-wild relative of fiber and tequila cultivars-botanical garden received 204 plants in 1936 (enough to maintain genetic variation for hundreds of years)-1951-50 plants remained, 1980-16 plants-the small remaining population is suffering from inbreeding and has lost most of its former variation

Protected Natural Areas (PNAs)-greater than 10,000 national parks and marine sanctuaries-National Wildlife Refuge System is in all states and includes about 500 refuges-currently about 6% of earth in PNAs. If this could be increased to 15%, conservation biologists estimate that 85% of earth’sbiodiversity could be conserved

Advantages PNAs

1. Protects ecosystem and large numbers of species in their natural habitat allowing co-evolution to occur

Advantages PNAs

2. Multimillion dollar benefit of ecotourism-PNAs for California Grey whale have increased their numbers from a few thousand to 24,000 and it has been removed fromendangered species list and 300,000 tourists per year

Disadvantages PNAs

1. Plants are not readily available to geneticists and crop breeders 2. Few parks are managed for their genetic resources and inundeveloped countries are abandoned due to funding or changes in government3. Large parts of tropics have no PNAs

genetic diversity - keep populations of species as genetically diverse as possible -measured by...

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different alleles

high polymorphic alleles

number of polymorphic

polymorphic alleles

heterozygous zynew alleles

pearson education

plant taxa

low genetic diversity