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Chapter 27

Unit 5 - Chapter 27 Bio 1M03 .docx

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McMaster University
James S Quinn

Bio 1M03 1 Unit Five: Evolutionary Processes and Patterns Chapter 27: Phylogenies and the History of Life 27.1 Tools for Studying History: Phylogenetic Trees  Phylogeny – the evolutionary history of a group of organisms  Phylogenetic tree – shows ancestor descendant relationships among populations or species and may be interpreted as depicting the evolutionary history for the group o Branch – represents a population through time o Node – represents the point in time when an ancestral group split into two or more descendant groups o Tip – represents a group living today or extinct  Monophyletic group (clade) – a set of individuals that contains all descendants of their most recent common ancestor Key Concepts  Adaptive Radiations are an important pattern in the history of life o They are instances of rapid diversification associated with new ecological opportunities and/or new morphological innovations  Phylogenies and the fossil record are major tools that biologists use to study the history of life  The Cambrian explosion was a rapid morphological and ecological diversification of animals that occurred during the Cambrian period  Mass extinction have occurred repeatedly throughout the history of life  Sister Groups – closest relative o Eg/ Humans and chimps are sister groups How Do Researchers Estimate Phylogenies?  Researchers analyze characteristics of species (genetic, morphological, behavioural etc.) to infer phylogenetic relationships among species  There are four general strategies for using data to estimate trees: the phenetic (distance), cladistics (maximum parsimony), maximum likelihood and Bayesian o Phenetic (Distance) – based on computing a statistic that summarizes the overall similarity among taxa  Compute “genetic distance” between two populations  Average percentage of bases in a DNA sequence that differs  A computer program compares the statistics for different populations and builds a tree that clusters the most similar populations together  Data  Distance Matrix (distance between each individual)  Phylogeny o Cladistic (Maximum Parsimony) – based on the realization that relationships among species can be reconstructed by identifying synapomorphies, the shared derived characters of the species under study  Attempts to minimize the number of changes on a tree that are needed to explain the observed data  Data  Consider trait evolution on many phylogenies  Select the phylogeny with the least number of changes  Synapomorphy – a trait that certain groups of organisms have that exist in no others; allow biologists Bio 1M03 2 to recognize monophyletic groups; characteristics that are shared because they are derived from traits that existed in their common ancestor Distinguishing Homology from Homoplasy  Homology – occurs when traits are similar due to shared ancestry  Homoplasy – occurs when traits are similar for reasons other than common ancestry  Problems can arise with both phenetic and cladistics analyses because similar traits can evolve independently in two distant species rather than from a trait present in a common ancestor  Evidence That Species Are Related: Structural Homology  How Do We Know That Hox Genes of Humans and Fruit Flies are Homologous? o Similar DNA sequence (including homeobox domain – the polypeptide encoded by the homeobox binds to DNA and regulates expression of other genes) o Similar genomic organization o Similar expression patterns during development o Similar function o Other species closely related to fruit flies and humans also have HOX genes with these features  Convergent evolution – occurs when natural selection favours similar solutions to the problems posed by a similar way of life, as shown by the dolphin and ichthyosaur  Convergent Evolution is a common cause of Homoplasy Bio 1M03 3 Convergence of Placental and Marsupial Mammals  Reversion back to ancestral state can occur – may causes you to make incorrect inferences  Maximum Parsimony – an assumption that the most likely explanation or patterns is the one that implies the least amount of change  Convergent evolution and other causes of Homoplasy should be rare compared to similarity due to shared ancestry, so the tree that implies the fewest overall evolutionary changes should be the one that most accurately reflects what happened during evolution Whale Evolution: A Case Study  Traditionally, cladograms based on morphological data places whales outside of the artiodactyls – mammals that have hooves, an even number of toes and an unusually pulley-shaped ankle bone (astragalus)  DNA sequence data, however, suggest a close relationship between whales and hippos  Recent data on gene sequences called short interspersed nuclear elements (SINEs) show that whales and hippos share several SINE genes (4, 5, 6, 7) that are absent in other artiodactyl groups Bio 1M03 4  These SINEs are shared derived traits (synapomorphies) and support the hypothesis that whales and hippos are indeed closely related Cryptic Species  Many species are not easily distinguished by morphology  Animal and plant parts also are sometimes not easily identified  Most diverse parts of the world are also the least known DNA Barcoding  Barcoding high throughout classification of diversity based on a variable gene  Based on DNA sequences of one gene (cytochrome oxidase I (CO1)) for animals and internal transcribed spacer 2 (ITS2) of the small subunit ribosomal RNA gene for plants  Useful for assessment of biodiversity, and wildlife forensics, tracking food, import/exports, endangered species, species discovery, species identification, identification of cryptic species, disease outbreaks  Criticisms of DNA barcoding: oversimplification of the science of taxonomy, may not distinguish recently diverged species, may not identify hybrid species, could draw funding away from traditional taxonomy Bio 1M03 5  Current dogma is that barcoding should contribute to or enhance traditional taxonomic studies, not replace them  Goals of DNA Barcoding o Inventory biodiversity o Automate and expedite species identification 27.4 Adaptive Radiations  Adaptive Radiations – when a single lineage produces many descendant species that live in a wide diversity of habitats and find food in a variety of ways o Instances of rapid diversification of a lineage accompanied by ecological diversification  Can be triggered by ecological opportunity and morphological innovation  May include high diversity of species, spectacular divergence or specialization or both  “The differentiation of a single ancestor into an array of species that inhabit a variety of environments and that differ in traits used to exploit those environments”  Criteria to detect adaptive radiation: 1. Common Ancestry 2. Phenotype-Environment Correlation 3. Trait Utility 4. Rapid Speciation Ecological Opportunity as a Trigger  One of the most consistent triggers of adaptive radiations is ecological opportunity, meaning the availability of new types of resources  Eg/ Biologists have documented adaptive radiations of the Anolis lizards of the Caribbean islands o Lineage includes 150 species o There is a strong correspondence between the size and shape of each species and the habitat it occupies o Species of Anolis vary in leg length and tail length; some species are ground dwelling; others live in distinct regions of shrubs or trees – suggests that lizard species have diversified in a way that allows them to occupy many different habitats o Biologists estimates the phylogeny of Anolis from DNA sequence data, then compared the habitats occupied by each species with their relationships on the phylogenetic tree  Found that the original colonist on each island belonged to a different ecological group – from different evolutionary starting points, an adaptive radiation occurred on both islands o On both islands, the same four ecological types eventually evolved – new species arose on each island independently, but both islands have similar varieties of habitats so each island ended up with a complement of species Bio 1M03 6  Frog Species Diversity in the Philippines is higher than Sulawesi for most groups o Frogs of the genus Platymantis occurs in the Philippines but not in Sulawesi o But in Sulawesi, there is extraordinary variation of fanged frogs, suggestive of “ecotypes” Bio 1M03 7 o Comparison to Philippines o Multiple sympatric species o Variation in modes of reproduction, body size Morphological Innovation as a Trigger  Morphological innovation can also be a trigger for adaptive radiation  The evolution of key innovations allow descendants to live in new areas, exploit new food sources, or move in new ways Eg/ Cichlid Fish Underwent Multiple Adaptive Radiations  Cichlids are a family of teleost fishes that include ~3000 species – about 10% of extent teleost diversity  Great Lakes of Tanganyika, Malawi and Victoria have ~250-800 species in each lake  Adaptations for feeding, variation in social behaviours, size and morphology  Cichlid fishes have a functionally decoupled set of jaws – oral and pharyngeal  Frees up jaws to independently specialize in food collection and processing  Exploit new niches 27.5 Mass Extinction Mass Extinctions vs. Background Extinctions  Mass Extinction – refers to the rapid extinction of a large number of lineages scattered throughout the tree of life o Periods with extreme levels of biodiversity loss o Result from extraordinary, sudden and temporary changes in the environment; they cause extinction randomly with respect to individuals fitness under normal conditions o When at least 60 percent of the species present are wiped out within 1 million years  Background Extinctions – refers to the lower, average rate of extinction observed when a mass extinction is not occurring o Typically occur when normal environmental change, emerging diseases, or competition reduces certain populations to zero o Result primarily from natural selection o The “background rate” or extinction refers to the level of extinction during periods when mass extinctions are not occurring Bio 1M03 8  What Killed the Dinosaurs o Impact Hypothesis – proposed that a meteorite struck Earth 65 mya and caused the extinction of an estimated 60-80% of the multicellular species alive, including dinosaurs o Evidence – all dates to ~65 mya  Iridium – sedimentary rocks that formed at the Cretaceous Paleogene boundary were found to contain extremely high quantities of Iridium, which is rare in Earth rocks but abundant in asteroids and meteorites  Abundant amounts of Shocked Quarts and Microtektites (only found at documented meteor impact sites) discovered in abundance in rock layers dates to 65 million years ago  Shocked Quartz – formed when shock waves from an asteroid impact alter the structure of sand grains  Microtektites found in rock layers – form when minerals are melted at an impact site and then cool and re-solidify  A huge crater off Mexico’s Yucatan peninsula Selectivity  Some evolutionary lineages were better able than others to withstand the environmental change brought on by the meteorite impact  For example, among vertebrates, the dinosaurs, pterosaurs (flying reptiles) and large marine reptiles perished, while the mammals, crocodilians, amphibians, and turtles survived  Size Selectivity Hypothesis – the extended darkness and cold would affect large organisms disproportionately because they require more food o Extensive data on the survival and extinction of marine clams and snails have shown no hint of size selectivity and small bodied dinosaurs perished along with the large  Organisms that were capable of inactivity for long period – by hibernating or resting as long lived seeds or spores, were able to survive the catastrophe Recovery  Recovery was slow  Terrestrial Ecosystems around the world were radically simplified o After the K-P extinction, fern fronds and fern spores dominate the plant fossil record from North America and Australia – suggest that extensive stands and ferns replaced diverse assemblages of cone-bearing and flowering plants after the impact o In marine environments, some invertebrate groups do not exhibit normal levels of species diversity in the fossil record until 4-8 million years past the K-P boundary  Mammalia that had consisted largely of rat-sized predators and scavengers exploded and took the place of the dinosaurs Bio 1M03 9 6 Mass Extinction: Now  Global diversity has undergone a progressive decline over the last 30,000 years  Current rate of extinction is 100-1000 times background rate of extinction  Most human colonization (past and present) is associated with environmental degradation  As of Jan 2010, only 842 extinctions are documented by the IUCN  Most extinctions are undocumented  Ancient Extinction  Historical Extinction  Mass Extinction  Island Fauna Extinction  Extinction of once abundant fauna  Disease related extinction  Extinction of biological phenomena Case Study of Extinction: Cichlid Fish in Lake Victoria  Nile perch (Lates noloticus) was introduced from Lake Albert into the Uganda portion of Lake Victoria in 1950s and 1963 o Was recorded in Tanzania in 1964 and Kenya in 1970’s  Explosive increase in Nile perch population was observed in the 1980’s Nile Perch Ecology o Reaches sexual maturity in 3 years, mature females can produce 16 million eggs; no parental care o Voracious predator with a wide diet (polyphagous); can eat other fish cannibalism o Can reach huge sizes – up to 230 kg, but it is typically about 3-6 kg  Consequences of Introduction of Nile Perch o Introduction of Nile Perch caused the largest mass extinction of contemporary vertebrates o Within a decade, about 200 endemic species of haplochromine cichlids went extinct in Lake Victoria o Some species of cichlids ate algae; now algae is growing unchecked o Because of the increased amount of algae, more plant material settles on the bottom of the lake before decomposing o Increased decomposition of plant material at the lake bottom decreases oxygen in water – forces fish to live on the surface where oxygen is more plentiful or go extinct o Introduction of Nile perch resulting in a 5-fold increase in the amount of fish protein available to local communities and increased income and employment opportunities o But, unlike indigenous fishes, perch must be dried over a fire, and this requires large amounts of wood o And now fish are smaller than before and overfished, so many fish processing centers have closed o Species replacement – loss of some cichlids led to expansion of other species with similar ecological roles  Extinction of detritivorous cichlids may have provided an ecological niche for the expansion of the native prawn Caridina nilotica o Nila perch also feeds on this prawn but switched only after many of the cichlids went extinct o Cichlid predators of this prawn were eradicated too Bio 1M03 10 27.2 Tools for Studying History: The Fossil Record  Fossil – the physical trace left by an organism that lived in the past  Fossil Record – the total collection of fossils that have been found throughout the world  The foss
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