Download 10. Genetic & Ecosystem - Faculty Sites

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
Plant 1 Plant 3
w
Cut
C
C
G
G
G
G
C
C
z
A
C
G
G
T
G
C
C
C
C
G
G
G
G
C
C
x
Cut
y
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
C
C
G
G
G
G
C
C
Cut
y
DNA from chromosomes
• After digestion by restriction enzymes
– The fragments are run through a gel
1
–
3
2
Longer
fragments
z
z
x
w
Shorter
fragments
+
y
w
y
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
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
Plant 3
Plant 1
w
Cut
C
C
G
G
G
G
C
C
z
A
C
G
G
T
G
C
C
C
C
G
G
G
G
C
C
x
Cut
y
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
C
C
G
G
G
G
C
C
Cut
y
DNA from chromosomes
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Because the state has a diverse climate and
geology, its biodiversity is rich. Correll and
Johnston(1979) summed up the size and
variability of the state in the following,
“Texas is 860 miles north to south and 773
miles east to west. Enclosed within the
4,137 mile perimeter of the state are 267,339
square miles. Brewster County, alone, is
larger than Connecticut. Texa s has a 624
mile coastline and 90 peak s in the TransPecos a mile or more high. Ea ch year about
56 inches of rain fall in the pine-hardwood
forests along the Sabine River, which forms
part of the state’s eastern boundary. L ess
than eight inches fall in the Chihuahuan
Desert in the extreme west. This is likened
to Miami and Pho enix, 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
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Piney Woods
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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 willow
and 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 are
threatened 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.) (PinaceaeCyperaceae) and longleaf pine-little bluestem (PinaceaePoaceae) 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
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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 by
live 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.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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 the
best 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.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Blackland Prairie- Low to moderate endemism
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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 overgrazing
and 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 EbonySnake 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.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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 ashwillow (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 over
the 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 extinctions
per 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 attempt
to 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
Is biodiversity important to ecosystem function?
-currently worldwide studies are testing three hypotheses
1. Rivet Popper Hypothesis
suggests ecosystems are like airplane wings where
flight (ecosystem functioning) may or may not be
compromised depending upon which rivets (species)
are lost
http://www.abdn.ac.uk/ecosystem/bioecofunc/intro.htm
2. Redundancy Hypothesis
certain species may drive ecosystem functioning, while
other so-called 'redundant' (= 'insurance' or 'passenger')
species contribute little in the way of functioning. This is
not 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 Hypothesis
ecosystem 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 the
following:
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 native
prairie and three abandoned fields of different ages
-each year, they clipped a different quadrat of each plot and
analyzed 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 soils
A few examples:
Photosynthesis
Carbon cycle
Nitrogen cycle
Water cycle
Species economics
-use of tens of thousands of species by people everywhere
to provide food, shelter, health, and other commodities
amounting to trillions of dollars in agricultural, forestry, fisheries
pharmaceutical, and textile products as well as nature tourism
Two Examples of pharmaceuticals of which 40% come from biota
including 25% from plants alone
1. Rosy periwinkle (Catharanthus roseus)
-native to Madagascar where there are 13,000 species of plants
and 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 single
cancer patient. Because of our understanding of phylogenetic
relationships, a close relative, T. bacatta, which contains taxol
in the leaves is used at less cost and without harming natural
populations
What if these and hundreds of other organisms had not been
discovered by taxonomists?
Two examples of improvements in agriculture because of
knowledge 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 were
used to grow plants that were crossed with cultivated tomatoes
increasing 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 forests
of 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 protected
natural areas all play a role in protecting biodiversity
Herbaria
Functions:
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)
plants
Functions
1. Research
-larger ones associated with research institutions and provide
material for experiments in plant propagation, reproductive
biology, breeding and hybridization studies, and studies to
examine genetic variation
2. Teaching and training using greenhouses, garden plots, and
some conserve natural habitat
3. Public service by identifying plants and information on
propagation
4. Centers for conservation of rare and endangered plants
Seed banks
-700 in the world
National Center for Genetic Resources Preservation in Fort Collins, CO
http://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 maintained
2. 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 tubes
filled with liquid nitrogen in deep freezes that will only have a 1%
loss in germination over a hundred billion years
3. Evolution is stopped. As pests evolve new virulence, the stored
crops 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 extinction
Franklinia 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 decimate
populations
Ex. Rancho Santa Anna Botanical Garden
Agave 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’s
biodiversity 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 from
endangered 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 in
undeveloped countries are abandoned due to funding or
changes in government
3. Large parts of tropics have no PNAs