Ecology 3 Summative Review

HL - A3.2 Classification & Cladistics

discovering ancestries

what classifying organisms can help us

introgression

process by which hybrids form over many generations but, instead of having an equal share of the original two species’ genetic information, there is an unequal contribution from each species

how introgression is achieved

backcrossing: hybrid organisms breed with one of the original parent species to produce offspring; after many generations, organism resulting from introgression by backcrossing might only possess small percentage of the original species’ genes (which partly account for what we can see today)

backcrossing

hybrid organisms breed with one of the original parent species to produce offspring

molecular systematics

looking at molecular differences in protein sequences and DNA; more reliable method than than using morphological features to classify organisms

phylogeny

study of evolutionary past of a species, species that are more similar are more likely to be closely related

phylogenetic tree

shows evolutionary relationships between species by showing which developed from a common ancestor (advantage: not based on arbitrary, subjective, or contrived categories)

clades (monophyletic groups)

used when studying evolutionary relationships between species; comprising the most recent common ancestor of that group and all descendants; comprising just one species or can be made up of multiple

common descent

concept crucial to deciding into which groups are organisms classified

primitive traits (plesiomorphic traits)

inherited from a distant common ancestor and have remained relatively unchanged over time (ex: leaves with vascular tissue, presence of backbone in vertebrates, pentadactyl limb)

derived traits (apomorphic traits)

evolved more recently and not present in distant ancestor; modifications or innovation unique to a particular lineage (ex: feathers in birds are derived from reptile scales, opposable thumbs in humans and primates are not present in other mammals)

accumulate gradually

differences in polypeptide sequences … because mutations happen randomly and over time

DNA hybridization

• one strand taken from species A, and a homologous strand (sequence from the same position in the same gene) taken from species B

• both strands fused together using enzymes

• there’s a match where bases connect

• difference where they’re repelled and no match

homologous strand

sequence from the same position in the same gene

molecular clock

uses quantitative biochemical data to estimate the time of speciation events; a scientific technique used to estimate the timing of evolutionary events (lineage-splitting) by measuring the accumulated, relatively constant rate of genetic mutations in DNA or protein sequences over millions of years

cladogram

represents cladistics in a visual way (contains: node, sister group, outgroup, root, terminal branches)

node

place where the speciation event happened and the relative position of the common ancestor

sister group

group of closest relatives

outgroup

less closely related to others in the cladogram

root

base of the cladogram

terminal branches

tip of the cladogram

monophyletic

sharing recent common ancestors

paraphyletic

different common ancestors

circumscription

process of placing taxa where they clearly show monophyletic groups, indicating common ancestor

domains

3 largest groupings for organisms

archaea

• single-celled organisms that are different from bacteria

• very ancient

• discovered in extreme conditions such as hydrothermal vents and hot springs, but also in other habitats (ex: ocean, soil, guts)

• main types include extremophiles, which includes thermophile (methane-loving), and halophiles (salt-loving)

eubacteria

domain where most bacteria we know belong (ex: bacteria in gut, bacteria that produces disease)

eukarya

domain where we find the rest of all the species, membrane-bound organelles and membrane-bound nucleus

justification for the separation of archaea from bacteria

• differences in subunit of ribosomes called 16S rRNA

• metabolic reactions carried out by archaea that no bacteria can perform, like producing methane or even some can use hydrogen as a source of energy

• the ways in which archaea read DNA to produce RNA, and the way they produce proteins from RNA, share some characteristics with eukaryotes than prokaryotes

• some physical features are different, such as the type of molecules used to build cell membrane and cell wall

open systems

what ecosystems are since they exchange energy and matter with their surroundings

thermodynamics

energy cannot be created nor destroyed, it is transformed

conservation of mass

matter cannot be destroyed nor created

closes system

matter does not enter/leave, it must be recycledl energy can still enter/leave

systems theory

provides explanation of how systems interact with each other and environment

photosynthetic

• organisms that take carbon dioxide and convert it into energy-rich sugar

• the addition of minerals allow them synthesize complex molecules such as cellulose, proteins and lipids to build other structures like stems, leaves, fruits, and seeds

• sunlight energy transformed into chem energy, stored inside bonds of organic molecules

chemosynthesis

• ecosystems that exist in total darkness (ex: deep ocean water, dark caves, deep underground) rely on this to provide energy

• bacteria and archaea use chemical energy instead of sunlight

• they oxidize inorganic compounds (ex: H₂S hydrogen sulfide, methane, or iron compounds) to generate energy

• hydrothermal vents are an example: mineral dissolved in seawater infiltrate cracks in the ocean floor and are warmed by magma, rise to the ocean floor surface and provide organisms with minerals to perform chemical reaction

decomposers (saprotrophs and detritivores)

• essential part of ecosystems

• break down non-living food sources (ex: feces, entire dead bodies, fallen leaves, skin shed from other organisms)

• not considered partof the food chain

saprotrophs

secrete enzymes onto dead (ex: fallen trees) and absorb the nutrients (external digestion) (ex: mushrooms and molds)

detritivores

• have mouth parts to ingest dead matter and digest inside body

• digestive enzymes convert organic matter into a more usable form for themselves and other organisms

• ex: proteins from dead organisms broken down into ammonia, and nitrogen in ammonia can be converted into useful nitrates by bacteria; earthworms; dung beetles; roly poly

primary production

biomass generated by activity of producers (photosynthetic organisms fix carbon to make carbon compounds for food), measured g m^-2 y^-1

secondary production

• conversion of one form of carbon molecule to another inside consumers

• due to loss of biomass when carbon compounds are converted to CO₂ and water in cell respiration, it’s always lower than primary production

carbon source

organism that is a net producer of CO₂ (ex: tree burning)

carbon sink

holds and absorbs more carbon that released (ex: when photosynthesis exceeds respiration there’s a net uptake of CO₂)

peat

formed from partially decomposed organic matter under aerobic and acidic conditions in waterlogged soil

greenhouse gas effect

short wave radiation hits Earth’s surface → surface reflects back in the form of long wave radiation → greenhouse gas traps long wave radiation → global warming

requirements for stability in ecosystems

sufficient supply of energy, nutrient recycling, genetic diversity, response to climatic change

deforestation of the Amazon rainforest

example of a possible tipping point in ecosystem sustainability, when the forest loses the ability to re-establish itself

tippint point

critical threshold at which a small change in human activities cause a drastic and irreversible shift in ecosystem structure, function, stability

mesocosm

self-contained system that provides a living environment for organisms

Winogradsky columns

frequently used to create environment that encourages bacteria growth in layers

keystone species

organisms that play an important role in the biodiversity of their ecosystem; have a disproportionately large impact on the environment relative to its abundance; its loss leads to ecosystem collapse (ex: wolf at Yellowstone)

roles of keystone species

1. predators: exert pressure on lower trophic levels to prevent them from monopolising certain resources

2. mutualism: they can support life cycle of variety of species within a community (ex: pollinators/seed dispersal)

3. engineers: they can refashion the env in a manner that promotes the survival of other species

removal experiment

one way to find out if a species is a keystone species

trophic cascade

changes in the population of one species (usually the top predator) cause indirect effects that ripple through the entire food chain, affecting multiple trophic levels

Chilean sea bass (example of sustainable harvesting)

• In the 1970s, fish from Chile started to become famous due to its delicious taste.

• by 1900, the wild pop of this species was collapsing due to overfishing with longlining, which also damages the ecosystem.

• nowadays, there are many regulations that promote sustainable fishing in term of how to catch them, age of the fish, and the season of the year when fishing is permitted

• allows replacement to occur

black cherry trees (example of sustainable harvesting)

• usually found in hardwood forests mixed with other species

• color of its wood (light red) makes it desirable for furniture/cabinet making

• in some areas, large areas were clear-cut to make farming fields

• nowadays more sustainable

• since trees grow very slowly, the selective logging needs to occur at a pace that does not exceed the growth of the remaining trees

• the logging of back cherry trees only sustainable if:

  • selective logging used (not clear-cut)

  • trees selected, rather than cut down randomly

  • enough trees are left to produce fruits/seeds

  • data collected to compare the quantity of wood being removed with current growth

  • processes should follow guidelines made by sustainable harvesting orgs

soil erosion

• loss of upper solid layer of a field greatly reduces productivity

• upper layer (topsoil) should be rich in organic nutrients

• excess of rainwater and wind can cause erosion of the topsoil, and this is particularly problematic in areas with no crops, b/c there are no roots to hold on to the soil

solution for soil erosion

• sometimes, farmer plant simple plants such as rye and clover (named cover crops) just to cover the soil and prevent erosion when weather is not suitable for other crops.

• by planting other species, these reduce the penetrating force or heavy rainfall and their roots hold the spoil in place.

• later, cover crops ploughed back into solid to increase organic matter in the topsoil

leaching of nutrients

• nutrients needed by plants must be water soluble for the plants to make use of dissolved nutrients

• leaching occurs when rain/irrigation water dissolves nutrients (usually from nitrogen and phosphorus compounds) in the soil and then carries them away from the root zone of a crop

• dissolved chemicals often end up in the water supply of the area. while leaching cannot be prevented, it can be minimized by applying appropriate amounts of fertilizer and irrigation water at optimum times, considering seasons and crop requirements

fertilizer supply

• farms use chemical fertilizers to enrich their soils w/ nitrogen, potassium, and phosphorus compounds

• sources of fertilizers are limited and demand often exceeds supply

• since fertilizers are expensive to produce, the final cost of products are usually higher too

• some farmers minimize the use of chemical fertilizers by planting crops of beans or clover (legumes) that have nitrogen-fixing bacteria within their roots

pollution from agrochemicals

• water runoff and the leaching of both fertilizers and chemical pesticides results in pollution of water bodies

• this is especially true when crops are over fertilized and excessive pesticide chemicals are applied

carbon footprint

• C footprint = total amount of GHG (including CO2 and methane) that is generated by an activity

• currently, est % of GHG from ag is 12%

• C footprint in ag:

  • use of petroleum products to run farm machinery

  • addition of fertilizers, often made from petroleum products

  • clearing natural forest land and other ecosystems to create farmland

  • transport of crops grown in one area of the world to another

eutrophication

1. irrigation and rainwater leach phosphates and nitrates into bodies of water

2. influx of fertilizers stimulate excessive algae growth

3. greatest growth occurs at the top (most sunlight available for algae to perform photosynthesis)

4. thick layer across the water’s surface

5. sunlight blocked by excessive growth → algae lower down dies → bacteria decomposes

6. decomposition uses dissolved oxygen (biochemical oxygen demand/bod)

consequences of eutrophication

• rapid growth in algal pop will occur (algal blooms) as a result of the increased availability of nutrients

• as the algae die, there will be a subsequent spike in saprotrophic microbes (decomposers)

• high decomp rate = + bod by saprotrophic bacteria

• saprotrophs will consume available quantities of dissolved oxygen, leading to deoxygenation of the water supply

• eutrophication will also increase turbidity of the water, which will reduce oxygen production by photosynthetic seaweeds

• this stresses survival of marine orgs→ - biodiversity in ecosystem

biomagnification

phenomenon that occurs when harmful substances in the env build up in the organisms towards the top of a food chain

• each trophic level typically consumes many orgs from the previous trophic level.

• if the organisms that are consumed contain a toxin that does not break down, then the substance becomes more concentrated in the living tissues of the organism that eat them

• 2 relevant examples include mercury and DDT Dichloro-Diphenyl-Trichloroethane (microplastics too)

mercury

• source: burning of coal and production of cement

• released by these processes enter the atmosphere and are then washed into the oceans

• microorganisms convert it into methylmercury

• compound moves up the food chain → more concentrated in the tissue of animals

• humans are exposed to high levels of this toxin by eating fish that are at or near the top of a food chain

• accumulation can have severe health effects, mainly related to neurological damage.

DDT

• synthetic insecticide developed in the 1940s.

• inexpensive, effective, and long lasting

• beneficial insects were being killed and mosquitoes were becoming resistant to it

• the chemical entered bodies of water in water runoff.

• water: absorbed by phytoplankton, and it increase its concentration in higher trophic levels.

• greatest documented effect was on brown pelicans and bald eagles (calcium metabolism was altered, and they produced thin-shelled eggs that could not withstand the weight of the parent bird during incubation)

• Regulatory actions began in 1950s and by 1972 the EPA (Environmental Protection Agency) in the US banned its use, and the population of predatory birds largely recovered.

microplastics

plastic smaller than 5mm

gyres

formed by winds and ocean currents, and creates a swirling mass of debris that is funnelled towards a center; plastics in the oceans tend to get caught up here

Great Pacific Garbage Patch

greatest gyre, 2 vortex centers (one off California, other off Japan)

effect of microplastic and macroplastic pollution

• Sea turtles sometimes eat plastic bags thinking they are jellyfish

• Plastic rings from six-pack of canned drinks entrap seabirds and other wildlife

• Albatrosses pick up plastics from the ocean surface and feed it to their chicks

• Plastic fishing nets are often lost by fishing boats and are a death trap for fish, sea turtles, and marine mammals

• Microplastic are filling the stomachs and intestines of marine organisms after accidental ingestion

rewilding activities

conservation efforts aimed at restoring and protecting the natural processes and wilderness areas. 

examples of rewilding activities

• Reintroduction of apex predators and other keystone species

• Establishing wildlife corridors, to connect habitats over larger areas

• Stopping agriculture and resource harvesting such as logging and hunting

• Minimizing human influences on an ecosystem, including using ecological management techniques

Hinewai Reserve (rewilding case study)

• 30-year-old rewilded area on the South Island of New Zealand. The reserve started as 109 hectares of land that used to be farmland.

• The reserve has been expanded and is privately owned by a trust, but is freely open to the public via many walking paths.

• The goal is to foster regeneration of native vegetation and wildlife. The strategy is to allow nature to take its course, so that native vegetation can repopulate the area, along with many native species of animals. It is an example of rewilding success.

primary succession

new land is created and a series of communities emerge, any one community prepares the land for the next type of community.

1. first living organisms (pioneer species) appear (usually lichens/mosses), they’re photosynthetic and do not grow root systems

2. over a long period of time, rowth and death of multiple generations of lichens and moss help build up a soil that can be used by other producers.

3. emergence of thin soil allows plants to grow (typically small shrubs with root systems) → more volcanic rock broken → more soil

4. bacteria begins colonizing, forms the basis of more complex food chains

5. deepened and enriched soil allows grasses, larger shrubs, and trees to grow

6. more animals join, after many hundreds of years, climax community develops

secondary succession

existing ecosystem is drastically altered by, for example, fire, flood, or human interference, and the remains of the previous ecosystem are used as a starting point for further changes.

pioneer species

first living organisms in ecological succession

characteristics of primary succession over time

• Increasing species diversity

• Increasing size of plants in the community

• Increasing primary production

• More complex food webs

• Increasing nutrient cycling

compare and contrast primary succession and secondary succession

Similarities

1. both see change over time in the species that live in the area (some species gradually replace others in a particular area)

2. both triggered by changes in the abiotic and biotic factors of the ecosystem

Differences

1. Primary succession begins with no life, whereas secondary succession follows a disturbance

2. Primary succession takes place in a new area (e.g. volcanic island), while secondary succession takes place in an old area (e.g. following a forest fire)

3. Primary succession involves lichen and mosses that begin to grow on rocks, whereas secondary succession involves seeds and roots that are already present.

4. Primary succession begins in an area without soil, secondary succession begins in one where soil is present.

5. In primary succession, biomass and production are low. In contrast, secondary succession sees high biomass and production.

climax community

final community in ecological succession, tends to be ecologically stable and will not change unless the environmental conditions change of there is human interference.

arrest

Sometimes, human activity can alter the process of succession, like removing forests for livestock grazing and draining wetlands for development. Therefore, human activities can … the natural development of an ecosystem and reset the succession timeline to an earlier stage.

forest browning

With less water, photosynthesis cannot occur as much as before, and the primary production in the forest is reduced (less carbon dioxide will be removed from the air).

When this happens, the needles of the coniferous trees will lose the green pigment, turning brown and falling off.

can lead to death of all trees

legacy carbon

carbon locked up in the soil, from very ancient past ecosystems

emperor penguin (example of polar habitat change)

• live along the coasts of Antarctica and migrates many kilometers over the ice to reach its breeding grounds each winter.

• prefer to breed on sea ice (ice formed when oceans freeze).

• sheets of ice start to break up in the summer, but by then the eggs have hatched and the chicks are big enough to get their own food.

• With global climate change, some zones of icea are exposed to warmer temperatures and start to break up earlier than the breeding season, making impossible for them to raise their young.

• Some colonies have move to ice found on land, but there are concerns about the future of the emperor penguin population.

walruses (example of polar habitat change)

• look for ice shelves as breeding grounds and a place to raise their youngs.

• When the mother needs to get food, it is very convenient for them, since they can easily go for food and it does not take long until they are back.

• with melting ice, the breeding grounds are reduced and many populations need to move closer to the pole.

• Mothers are not as close to the water and have to leave the babies for longer periods of time.

• This makes the young more vulnerable to attack by predators such as polar bears, but also struggle finding food.

Coriolis effect

caused by the rotation of Earth on its axis

nutrient upwelling

Movement of nutrient-rich water from deeper parts of the ocean towards the surface, plays an important role in bringing nutrients to the food webs along the coasts.

• Cold water is nutrient-rich because it originates from the deep ocean, where organic matter—such as dead marine organisms and waste—sinks, decomposes, and releases nutrients.

• These nutrients accumulate over time in deep waters, making them an essential reservoir for oceanic life.

El Niño

climate phenomenon that occurs when warm ocean waters in the central and eastern Pacific disrupt normal weather patterns

• happens due to the weakening or reversal of trade winds, preventing the usual upwelling of cold, nutrient-rich water along the South American coast.

• leads to heavy rainfall and flooding in South America, droughts in Australia and Southeast Asia, and warmer global temperatures.

• affects marine life, reduces fish populations, disrupts agriculture, and influences hurricane activity worldwide.

range shifts

changes in the geographic distribution of species in response to environmental factors

poleward range migration of trees

• what prevents tree populations from expanding its upper northern range limit is extreme cold, since many seeds or saplings cannot tolerate the cold.

• Due to global warming and winters becoming less harsh, it is hypothesized that some tree populations are spreading poleward (like it happened when the Earth warmed after the most recent ice age, which is demonstrated by fossil record).

upslope range migration of birds

• Papua New Guinea is a mountainous country, in which some habitats are temperate and others tropical. There are several types of birds, and in the 1960s, detailed surveys of montane bird species were carried out, showing the altitudes where they lived.

• This survey was conducted again 50 years later, and some changes were appreciated, especially for the species Penoethello sigillatus (white-winged robin).

phenology

study of the timing of biological events

photoperiod

number of hours in a day when sunlight is shining. In temperate zones, the photoperiod changes through the year. Although different plants have different thresholds, they will all produce flowers when a certain length of daylight is reached. 

bud setting

process by which a plant uses current stores of energy to prepare leaf and flower buds for the next season.