BIO&212 PDF - Evolution and Scientific Method

Evolution and Scientific Method Convergent evolution: species that are not closely related, that independently evolve similar features or behaviors Zoology: the scientific study of animals Phylogenetic tree: a diagram depicting the history of animal life → each...

Evolution and Scientific Method Convergent evolution: species that are not closely related, that independently evolve similar features or behaviors Zoology: the scientific study of animals Phylogenetic tree: a diagram depicting the history of animal life → each branch represents evolutionary lineages → each branching event represents the historical splitting of an ancestral species to form new ones Major Goals of the Study of Animal Diversity Phylogeny of Hawaiian honeycreepers 1) studying animal diversity is to locate the origins of major characteristics such as multicellularity a coelom spiral cleavage vertebrae homeothermy 2) Understanding historical processes that generate and maintain diverse species and adaptations Invertebrae (no backbone) vs. Vertebrae (backbone) Ectothermic (cold-blooded) vs. Endothermic (warm-blooded) Steps of the Scientific Method 1) Observation → a critical step in evaluating animal populations 2) Question 3) Hypothesis formation → can be done via the hypothetic- deductive method, experimental method, or the comparative method 4) Empirical test 5) Controlled experiment (including at least 2 groups; test and control) 6) Conclusions (either accept or reject your hypothesis) 7) Publication Basis for Hypothesis Formation must be derived from prior observations of nature from theories derived in such observations ideally constitute general statements about nature that may explain a large number of diverse obser vations MUST be testable → Rule of thumb: "if my hypothesis correctly explains past obser vations, then future observations must match specific expectations." - hypothetic-deductive method: a scientific process of making a conjecture and then seeking empirical tests that potentially lead to its rejection - experimental method: hypotheses of proximate causes are tested that includes explanations for how animals perform their metabolic, physiological, and behavioral functions at a molecular, cellular, organismal, and population levels Steps to use the Experimental Method 1) Predict from a tentative explanation to explain how system being studied would respond to treatment 2) Making the treatment 3) Comparing obser ved results to predicted ones - comparative method: hypotheses of ultimate causality to identify patterns of variation and evolutionary relatedness of different species by comparing their molecular biology, cell biology, organismal structure, development, and ecology → heavily relies on the results of experimental science The Darwinian Evolutionary Theory Charles Dar win established that evolutionary changes are based in differences that occur among organisms within a population Evolution occurs at the level of a population, with the frequency of favorable traits increasing over generations Darwin's Discoveries Dar win's Great Voyage of Discovery consisted of extensive collections and observations that took 5 years (1831-1836 ), on the H.M.S Beagle → mostly surveying the South American coast and Galápagos Islands Darwin's Observations Dar win primarily noted the similarities in climate and topography of the islands, and that each island often had a unique species that resemble those of the South American mainland → each island had a unique species that resembled forms on other islands Dar win concluded that Galapágos life must have originated in continental South America, and that the islands were once colonized but separated by the rare occurrence of trans-oceanic dispersal; which led to each species to undergo modifications in various environmental conditions on different islands Diagram displaying various different beaks acquired through evolution, in favor of what is best suited for their diets per each respective island G rN (E) =. Pre-Darwinian Evolutionary Ideas Early Greek philosophers Xenophanes, Empedocles, and Aristotle, recorded the idea that life has a long history of evolutionary change; but failed to establish an evolutionary concept that could guide a meaningful study of life’s history. → recognized fossils as evidence of former life Lamarckism: the first complete hypothesis of evolution created in 1809; by Jean Baptiste de Lamarck, which proposed an evolutionary mechanism known as transformational evolution; meaning acquired traits were inherited. → made a convincing case that fossils were the remains of extinct animals Transformational evolution theories are rejected because genetic studies show that traits acquired during an organism’s lifetime, are not transmitted to offspring. → differs from Dar win’s evolutionary theory, since his was interpreted as variational; rather than transformational Uniformitarianism: the scientific study of the history of nature, created by geologist, Charles Lyell Lyell’s Conclusions 1) The laws of physics and chemistry have not changed throughout the Earth's history 2) Past geological events occurred by natural processes like those obser ved today 3) Earth's age must be measured in millions of years Variational Evolution Transformational Evolution True Doberman What Lamarck thought would result Peppered moths displaying variational evolution, by What actually resulted adapting to hide better within their environments Doberman after modification (cropped ears and tail) Development of Dar win’s Ideas (After the Voyage of Discovery) Dar win read the works of Thomas R. Malthus’ works, including his publication, An Essay of the Principle of Population, which provided him with key insights to include every organism Main Points from Malthus’ Works 1) Populations have the reproductive capacity to expand beyond environmental capacity. 2) While human populations tend to increase geometrically, the capacity for humans to feed this population only grows arithmetically; meaning that the human population will outgrow food production. What Darwin Concluded 1) All organisms have the capacity to overproduce 2) Only a limited number of offspring survive and produce the next generation, which results in favorable characteristics being passed down, such as certain physical, behavioral, other other various attributes to help them live in their environments Natural Selection natural selection: a process where populations accumulate favorable characteristics throughout long periods of evolutionary time → adaptions tend to be anatomical structures, physiological processes, or behavioral traits Dar win referred to natural selection as the “survival of the fittest” → Dar winian fitness does NOT always refer to the biggest or strongest organisms → Fitness refers to organisms who survive more often and leave more offspring, due to their characteristics Darwin’s Initial Foundation of Natural Selection 1) Favorable characteristics are specific to an environment, where they can be favored in one but not in another 2) Organisms whose characteristics are best suited to their particular environment sur vive more often and leave more offspring Darwin’s Evidence 1) Fossils of extinct organisms resemble those of living organisms 2) Geographical patterns suggest that organismal lineages change gradually as individuals move into new habitats 3) Islands have diverse animals and plants that are related, yet different from their mainland sources Darwin’s Finches Dar win believed that all the finches he discovered on the Galápagos had evolved from a single ancestor, into individual species who specialized in particular foods. He termed this as “descent with modification. “ → This ended up being an example of adaptive radiation, which is when a cluster of species change to occupy a series of different habitats within a region, known as niches → niche: the representation of how a species interacts biologically and physically within its environment to sur vive → Each different habitat offers different niches; species will evolve to adapt to each niche Studies that Backed Darwin’s Finches David Lack researched finches in the Galápagos in 1938, and found that different species fed on the same kinds of seeds, depending on the season and food available In 1977, Peter and Rosemary Grant studied medium ground finches during a drought on the island, Daphne Major, in the Galápagos. → Part of their study included measuring the finches’ beak shape over a span of many years, and recording their feeding preferences → Their findings were that: 1) Finches preferred to feed on small, tender seeds 2) Finches would switch to larger, harder-to-crack seeds when small seeds were difficult to find 3) Beak depth would increase when large, tough seeds were only available 4) Average beak depth increased after the drought ended 5) Only the large-beaked finches that could crack the bigger seeds, would survive to make the next generation, 6) When the wet periods returned to Daphne Major, smaller-beaked finches were able to feed on the plentiful amount of small seeds; meaning that the average beak depth decreased The Grants’ study was able to provide an example of evolution in action, which means adaptations were made in real time Evidence of Evolution fossils: preser ved remains, tracks, or traces of once-living organisms Fossils are the most direct evolution of macroevolution, which are large scale evolutionary changes over a long period of time Examples of Macroevolution homologous structures: the same body part that is present in an ancestor → eg: Related species that have the same bones, but might have different uses for them analogous structures: similar looking structures in unrelated lineages → also known as convergent evolution, where unrelated organisms independently evolve similar traits to adapt to similar necessities or environments An organism’s evolutionary past is also evident at the molecular level, usually seen at protein levels → These evolutionary changes accumulate at a constant rate, which allows us to date changes in individual genes across various organisms based on their time of divergence bet ween evolutionary lineages; known as a “molecular clock” → eg: changes have accumulated in the cytochrome c gene, at a constant rate Organisms that are more distantly related should have accumulated a greater number of evolutionary differences, than t wo species that are closely related Geological Time Geologists divided Earth’s history into a table of succeeding events based on ordered layers of sedimentary rock The Law of Stratigraphy 1) Oldest layers are at the bottom, while younger layers are higher 2) Radiometric dating: a method for determining the absolute age of rocks 3) Radioactive decay of naturally occurring elements is independent of heat and pressure Potassium-Argon (K-Ar) dating allows us to determine the age range of a fossil or deposits, by using the known half-life of K-40 (1.3 billion years) to find out how long it took to decay into Ar-40 → Half of a sample will be gone at the end of 1.3 billion years → Half of the remaining sample will be gone at the end of the next 1.3 billion years This correlates to fossils by allowing scientists to track the evolution of a species over time, showing the progression of simpler life forms to more complex ones Animal Ecology Ecology: the study of the relationship of organisms to their environments. organism: an individual living thing → Physiological and behavioral mechanisms of organisms must be understood in order to understand their ecological relationships population: organisms of the same species that coexist as reproductive units → properties within a population can't be discovered by studying individuals alone → populations of many species live together in complex ecological communities → the number of different species present in a community is measured as species richness demography: the study of the age, sex ratio, and growth rate of a population population growth: the difference bet ween rates of birth and death → unrestricted growth is not prevalent in nature → growing populations eventually exhaust food or space; food production cannot keep pace with exponential growth indefinitely → Sigmoid growth is a depiction of the growth of a population or organism overtime, and occurs when population density exerts negative feedback; known as density dependence deme: a geographically and genetically cohesive population that is separable from other populations, sharing a gene pool stable deme (source deme): a population that is able to successfully interbreed to supply less stable demes (sink demes) sink deme: a population that cannot sustain itself, and relies on immigrants from stable demes → movement among demes provide some evolutionary cohesion among species → interactions among demes is called metapopulation dynamics → unpredictable changes to local environments can cause demes to become depleted or eliminated Human Population Growth about 5 million around 8000 BC, before Agricultural Revolution Human population rose to 500 million by 1650 1 billion by 1850 2 billion by 1927 4 billion by 1974 6 billion by October 1999 8.2 billion on January 10th, 2025 Predicted to reach 9.7 billion by 2050 Ecological Interactions niche: the role an organism play in its ecosystem, including the conditions it needs to survive and how they interact with other organisms → survival conditions include an animal's limits of temperature, moisture, food, salinity, or pH → niches of specific species undergo evolutionary changes over successive generations fundamental niche: an animal's potential role to live within a wider range of conditions → animals in a fundamental niche are deemed to be generalists, due their ability to survive in a wide range of conditions (eg: raccoons) realized niche: a narrower subset of suitable environments that an animal actually experiences → animals in a realized niche are deemed to be specialists, due to having highly restricted requirements and have limited tolerance to various things like temperature changes (eg: red pandas) habitat: physical space where an animal lives and is defined by the animal's normal activity biosphere: land, water, and atmosphere that supports all life on Earth resources: environmental factors that an animal uses directly → some resources are expendable, an example of this is food, due to the fact that it must be continuously replenished once eaten → other resources are nonexpendable, meaning that it is not consumed when used; this can be space or energy forms → competition will occur when resources become limited abiotic factors (nonliving): space or energy forms such as heat, wind, water, soil, air, chemicals → abiotic factors can reduce a population by killing members, regardless of size; but are unrelated to population size, meaning that they're density-independent (eg: fires, storms, fluids, severe climate fluctuations, eye.) biotic factors (living): competitive organisms, predators, host, parasites, and prey → biotic factors respond to population increases, and as individuals live closer together; resulting in their effects being more severe, this makes them density-dependent Community Ecology mutualism: when species benefit from their interactions with each other → some mutualistic relationships are obligatory for survival facultative mutualism: interactions that are not required for a species to survive Types of Interactions Prey Defenses predator-prey: predators benefit while prey is harmed cryptic defenses: bodies match some aspect of the environment parasitism: parasites benefit while hosts are harmed aposematic defenses: bright colors or behaviors to warn predators of inedibility → parasites don't kill hosts to continue benefiting from them Bayesian mimicry: harmless species that mimic models that have toxins or stings → parasitoids kill their hosts Müllerian mimicry: different species with noxious or toxic factors, that evolve to resemble each other herbivory: animals benefit while plants are harmed commensalism: one species benefits and the other neither benefits or is harmed Trophic Levels 1) primary producers: green plants and algae use carbon, nitrogen, and photosynthesis, to produce energy for all other organisms 2) herbivores: first level of consumer that eat plants 3) carnivores; eat herbivores or other carnivores 4) decomposers: organisms like bacteria or fungi, that feed on dead plants or animal matter to break down and release nutrients back into the environment Ecological Pyramids ecological pyramid: represent food chains in terms of numbers or biomass eltonian pyramid: a representation of the numerical amount of organisms pyramid of biomass: a display of the total bulk or "standing crop" of organisms at each trophic level energy pyramid: a depiction of the rates of energy flow bet ween levels, and gives the best overall picture of community structure since it is based on production → energy transferred from each level is less than what what entered it Law of Thermodynamics in Ecology 1) more than 90% of the energy in an animal's food is lost as heat 2) less than 10% is stored as biomass 3) each trophic level contains only 10% of the energy of the trophic level below it → while the energy budget of every animal is infinite, it is only available after satisfying maintenance needs Community Ecology (cont.) keystone species: organisms that have a large impact on ecosystems, and can have drastic and crucial impacts if absent → keystone species reduce competition and allow more species to exist on the same resource, and allows them to coexist in diverse communities Parasites ectoparasites: parasites that tend to live on or in the skin of a host to obtain nutrition and disperse to other potential hosts (eg: lice, ticks, etc.) endoparasites: parasites that live inside the tissues and organs of a host, and are transferred through contaminated food and water that has been in contact with parasite-egg infested feces (eg: giardia lambila, tapeworms, etc.) Reproduction and Population Growth modularity: genetically identical organisms that reproduce via fragmentation and asexual cloning (eg: sponges, coral, and bryozoans) parthenogenesis: the development of an embryo from an unfertilized egg or from one in which the male and female nuclei fail to unite following fertilization; known as the virgin origin → widespread across ecology and taxonomically in the animal kingdom semelparity: the condition in which an organism reproduces only once during its life history iteroparity: the condition in which an organism reproduces multiple cohorts of offspring → offspring are able to mature and reproduce while their parents are alive and still actively reproduce Survivorship Curves survivorship cur ve: the survivorship pattern of a species from birth to death of the last member of a generational cohort Type I: generally a convex curve display of the high probability of survival throughout early and middle life stages, with a sharp decline in older stages → rarely occurs in nature Type II: a diagonal line that displays a constant mortality rate throughout a population → common among birds and mice → humans can fall in bet ween Type I or II, depending on nutrition and medical care Type III: a cur ve that displays a high death rate immediately after birth, with fewer individuals surviving into adulthood → can explain the need of high reproductive output from many animals → common among fish, invertebrates, and small mammals Introduction to Sponges fossil records of sponges date back to the early Cambrian (around 550 million years ago) and possibly Pre-Cambrian period Multicellularity has occurred in unicellular lineages at least 25 times → one such lineage included multicelled animals, such as phylum Porifera, commonly known as sponges → most evidence points to choanoflagellates as the ancestors to animals Ecological Relationships there are approximately 5,000 species of sponges, mainly marine → there are about 150 species of freshwater sponges sponges grow on a variety of other living organisms, such as barnacles, coral, and mollusks → contrary to this, other animals can live as commensals or parasites both in and on sponges; including crabs, fish, etc. sponges have very few predators, due to their elaborate skeletal structures, aposematic coloration, and ability to produce a noxious odor the growth pattern of sponges is dependent on the shape of substrate, available space, and both the direction and speed of water currents General Features of Phylum Porifera Porifera means “pore-bearing,” which is a feature among sponges, since they have many pores and canals the skeleton of sponges are composed of spicules in size many species are brightly colored due to pigments in dermal cells some sponges appear radically symmetrical, but many are irregular in shape and have no symmetry the majority of sponges are filter feeders living sponges are assigned to 3 classes: 1) Calcarea 2) Hexactinellida 3) Demospongiae → a 4th class called, Homoscleromorpha, was a former subgroup of Demospongiae Sponge Structures and their Functions dermal ostia (ostium): small incurrent pores on the outside of a sponge that allows water to enter oscula: a large water outlet at the top of a sponge that allows water and waste to exit mesohyl: an extracellular matrix made up of a collagen-like gel, that provides structural support in sponges and transports nutrients Types of Sponge Cells choanocytes (collar cells): ovoid cells that line flagellated canals and chambers, that have various functions such as maintaining flows of water throughout the a sponge, digestion, and reproduction → one end is embedded in the mesohyl, while the exposed end contains the central flagellum and is surrounded by a collar of microvilli → flagella beat to pump water through the sponge, while the microvilli acts as a filter to strain food out from the water → particles too large to enter the collar of microvilli are trapped in mucus, then phagocytized by choanocytes; which later is moved to archaeocytes for digestion archaeocytes: ameboid cells that move within the mesohyl, and phagocytize particles in the external epithelium → archaeocytes are able to differentiate into other types of cells: 1) sclerocytes: cells that secrete spicules, which provide structure to the skeleton of sponges and some protection 2) spongocytes: cells that secrete spongin, which is a flexible protein that makes up the body wall and encases spicules to hold them together 3) collencytes: cells that secret fibrillar collagen to help form the mesohyl pinacocytes: flat epithelial-like cells that form a pinacoderm layer to cover exterior surfaces and some interior surfaces, which help provide minor protection against abrasions → some pinacocytes can transform into contractile myocytes to help regulate the flow of water porocytes: tubular cells that pierce the body wall, and remain contractile to control the water flow Types of Skeletons Fibrous Skeletons Rigid Skeletons all sponges with fibrous skeletons contain rigid skeletons are mostly comprised fibrils of collagen throughout the of spicules that can be made from extracellular matrix (ECM) either silica or calcium carbonate, which usually is a variation that → different varieties of collagen occur (eg: important to taxonomy Demospongiae species secret spongin, while → Demospongiae and glass sponges secrete Homoscleromorphs are the only sponges that make type IV collagen that is usually and in siliceous spicules, while calcareous sponges other animals) secrete calcium carbonate spicules Sponge Physiology sponges consume detritus, plankton, and bacteria → digestion is intracellular freshwater sponges have contractile vacuoles that have filtering capabilities → larger sponges can filter up to 1,500 liters of water per day some sponges can crawl up to 4 millimeters per day Adaptive Diversification diversification among sponges centers on their unique water-current system and its degree of complexity new methods of feeding have evolved for a family of carnivorous sponges that are found in deep water caves → some characteristics of these sponges include: tiny hook-like spicules that cover the body, that is used to entangle crustaceans and grows over them they lack choanocytes and internal canals Classes of Sponges Calcarea sponges in this class have spicules made of calcium carbonate, that are straight and tend to have 3 or 4 rays most sponges in this class are small with tubular or vase shapes many are lacking in color, but can sometimes be bright yellow, green red, and lavender sponges in this class can have any of the 3 canal systems, asconoid, syconoid, and leuconoid Hexactinellida (Hyalospongiae) sponges in this class are known as glass sponges, that have spicules made up of silica and have 6 rays most are radially symmetrical nearly all sponges in this class are deep-sea forms glass sponges have a unique tissue structure known as, syncytial tissue → the trabecular reticulum is the largest continuous syncytial tissue among animals, and is bilayered with choanoblasts and other cells → collar bodies of choanoblasts line chambers bet ween the bilayers of the trabecular reticulum to collect food Demospongiae sponges of this class have both siliceous spicules and/or spongin this class makes up 80% of all living sponge species, and have the leuconoid canal system almost all sponges in this class are marine, except for Spongillidae, which are freshwater sponges freshwater sponges inhabit well-oxygenated ponds and springs, and flourish in summer → when they die in late autumn, they leave behind gemmules freshwater sponges have siliceous spicules, and have spongin skeletons; making them more suitable for use as a bath sponge marine sponges can highly vary in colors and shapes Homoscleromorpha a subgroup of sponges that were formerly part of the Demospongiae class these marine sponges live in cryptic habitats and come in a range of colors a unique feature is that their pinacoderm have a basal lamina, which is not a true tissue, known as incipient epithelium → these sponges are the link bet ween having non-tissue and true tissue (eg: Collegen IV vs. incipient epithelium) Types of Canal Systems asconoid: the simplest body form of a sponge where they appear small and tube shaped, and are lined with choanocytes * refer to Sponge Structures and their Functions and Types of Sponge Cells, for how asconoid channel systems work → all ascanoid sponges are in the calcarea class syconoid: sponges that resemble asconoids, but are larger and have thicker body walls that are lined with epithelial cells instead of choanocytes → water enters through dermal ostia which lead to incurrent canals, then move to radial canals through prosopyles, which then exit through apopyles that lead to spongocoel leuconoids: channel systems that are larger and have many oscula; sponges with this channel system are the most complex, with spongocoel → like other channels, chambers are lined with choanocytes and water enters through incurrent canals, then are discharged to current canals that lead to oscula the leuconoid system evolved independently many times among sponges, where the system increased flagellated surfaces compared volume, since more collar cells can meet food demands → most sponges are leucanoids Reproduction and Development sponges are able to regenerate lost parts and repair injuries, along with reproducing asexually most sponges are monoecious, meaning they have both male and female sex cells → sperm arise from transformed choanocytes → oocytes develop from choanocytes or archaeocytes sperm released from one individual enters the canal system of another individual, where it gets taken in through choanocytes which become carrier cells, to carry sperm through mesohyl to oocytes → some sponges are oviparous, meaning they release both oocytes and sperm into water parenchymula: a free-swimming larvae of a sponge, that is an asexual reproductive bud → once larvae settle on a substrate, out wardly directed flagellated cells on the larval surface migrate inwards to become choanocytes in flagellated chambers all sponges form external buds that can remain or detach to form colonies, known as fragmentation sponges also have internal buds known as gemmules, that are dormant masses of encapsulated archaeocytes → gemmules can sur vive harsh environmental conditions such as drought, freezing, lack of oxygen, etc.