Biodiversity PDF

Diversity of Life Reading, Bio 2e, Chps 21-29 Optional, Freeman Chapters 26-33  Learning Goal Students should have a basic understanding of the major branches of the tree of life, to the extent that they can: 1) name attributes of major animal phyla and plant divisions...

Diversity of Life Reading, Bio 2e, Chps 21-29 Optional, Freeman Chapters 26-33  Learning Goal Students should have a basic understanding of the major branches of the tree of life, to the extent that they can: 1) name attributes of major animal phyla and plant divisions 2) identify key groups of non-animal eukaryotes, and 3) identify some major features of the groupings on the tree of life. Loading…  Tree of Life/Phylogenetic Tree/Taxonomic Groups a.k.a. eukaryotes (like you!) Node Common ancestor Bacteria, Archaea, Eucaryot a= domains  LUCA The last universal common ancestor, LUCA, was not the Loading… first form of life (because many forms went extinct early on and LUCA descended https://www.newscientist.com/article/2098564-universal-ancestor-of- from a survivor) all-life-on-earth-was-only-half-alive/ We have been able to infer a great deal about  Prokaryotes “Prokaryotes” are the most ancient, most abundant, and most metabolically diverse organisms. – This term describes a state of organization (no nucleus) rather than a taxonomic group. Prokaryotes include the: – Bacteria – Archaea  Bacteria Some major groups of bacterica include: Proteobacteria Cyanobacteria Gram-Positive Bacteria Chlamydias Spirochetes  Proteobacteria The proteobacteria are a large and diverse group that includes photoautotrophs, chemoautotrophs, and heterotrophs. – There is no taxonomic divide between “good” bacteria, those that are essential to the functioning of the biosphere, and “bad” bacteria, those that can kill us. Pathogenic bacteria occur within many different groups. www.biology.ed.ac.uk/.../microbes/myxococc.htm Among the proteobacteria are the myxobacteria, interesting gliding bacteria that produce “fruiting bodies” under conditions of starvation. Myxobacteria live in the soil, and “glide” along solid surfaces via a polysaccharide slime.  Among the proteobacteria are the ancestors of mitochondria. Also included are Rhizobium species that live in the roots of plants, and the rickettsias, tiny pathogens that live within the cells of animals bioinfo.bact.wisc.edu/.../Effects.html  These are among the most distinctive Spirochetes bacteria they move by a spiraling corkscrew motion. Loading… They can be free living or parasitic. Syphilis and Lyme’s disease are caused by spirochetes  Bacterial Photosynthesis Photosynthesis has evolved repeatedly in the bacteria. Cyanobacteria are the group best know for it, and their ecological importance is overwhelming. Other groups include purple sulfur bacteria, green sulfur bacteria, and certain heliobacteria. These groups can perform anoxogenic photosynthesis-they use molecules other than wate as an electron donor. For instance, H2S can be oxidized by purple sulfur bacteria, to granules of S  Chromantium sp, from a salt marsh near Woods Hole MA.  Archaea Although we know very little about them, the archaea are some of the most abundant, and important, organisms on the planet. – The group is very ancient-some bear a striking resemblance to fossils dated at more than two billion years old and many exploit ecological niches that were probably more important billions of years ago. – Though the majority live in ordinary habitats, the group includes many extremophiles. – These include, but are not limited to; methanogens-live in anerobic conditions and break down methane extreme thermophiles-live in incredibly hot environments extreme halophiles-live in extremely salty environments Unlike Bacteria, Archaea often have genetic sequences called introns. They have this in common with Eukarya. Also, like Eukarya, Archaea have histones,-proteins that wind DNA strands to manage their configuration. Like bacteria, they lack nuclei and membrane bound organelles. Unlike either-they have ether linked, rather than esther linked lipids in their cell membranes  Archaea Bacteria What’s an Intron? Below: A gene segment No nucleus or intro exon Have membrane n introns & intron bound histones organelles DOES DOES NOT code for code for amino amino acids/pr acids/protei otein n product product Image credit: - https://images.search.yahoo.com/search/images;_ylt=AwrhexOfqrpk09IIULZXNyoA;_ ylu=Y29sbwNiZjEEcG9zAzEEdnRpZAMyQURTQ0FURUdPUllfMQRzZWMDcGl2c w--?p=what+is+a+histone&fr2=piv- web&type=E210US739G0&fr=mcafee#id=4&iurl=http%3A%2F%2Fvignette3.wikia.n Histone= ocookie.net%2Fmmg-233-2014-genetics- genomics%2Fimages%2F6%2F60%2FFigure-1-Histones- 1024x1022.jpg%2Frevision%2Flatest%3Fcb%3D20141020193149&action=click - “spool” for https://images.search.yahoo.com/search/images;_ylt=AwrEt09HpLpkJIsIWchXNyoA;_ ylu=Y29sbwNiZjEEcG9zAzEEdnRpZAMyQURTQ0FURUdPUllfMQRzZWMDcGl2c w--?p=taxonomic+ranking+system&fr2=piv- web&type=E210US739G0&fr=mcafee#id=2&iurl=http%3A%2F%2Fthevenomintervie ws.com%2Fwp- content%2Fuploads%2F2019%2F06%2FTaxonomic_Rank_Graph.png&action=click -https://www.researchgate.net/profile/Sara-Heap- DNA 2/publication/241247131/figure/fig2/AS:718645441351682@1548349833366/Tree-of- Life-showing-the-three-domains-bacteria-archaea-and-eucaryota-The.png  Eukaryotes Eukaryotes, organisms with nuclei and nearly always possessing membrane-bound organelles, are a single branch on the tree of life. It is likely that the original eukaryote was an amalgam of prokaryote species, and possibly a viral component as well. – Modern studies of eukaryote taxonomy indicate there are probably between 11 and 20 eukaryote kingdoms. These kingdoms include many groups formerly classed simply as “protists”, such as diplomonads and parabasalids.  Endosymbiosis In 1966, Lynn Marguils developed an old hypothesis that the mitochondrial of eukaryotes evolved from bacteria that had lived, billions of years ago, as a mutualistic endosymbiosis with early eukaryotes. – These particular organelles are surrounded by a double cell membrane, suggesting a bacterium embedded in a membrane that encapsulated it. – These organelles also have DNA, and ribosomes that resemble those of bacteria Similarly, chloroplasts likely have analogous origins from cyanobacteria. At the time it was not accepted, and was considered a testable hypothesis. The invention of DNA sequencing and modern systematic analyses have provided overwhelming support.  In both cases, a prokaryote was an endosymbiont in an ancestral archaea (bacteria-probably a Rikketsia), or eukarya (cyanobacteria). Lateral gene transfer over hundreds of millions of years has moved much of the original genetic material to the nucleus. – It is possible that other such events have occurred, influencing the evolution of the nucleus and the flagella.  Viruses Whether a virus is “alive” or not is no great mystery-it simply depends on how life is defined. – Most viruses have DNA, some have RNA. – Viral genomes are typically small, they hijack the transcription and translation mechanisms of a host cell to produce more viruses. – Isolated, a virus has no metabolism, no need for an energy source. – All the living processes of a virus require a host. – Viruses require energy when infecting hosts, reproduce, and evolve.  Typically, a virus has a core of genetic material, – linear or circular, single or double stranded, sense or antisense, protected by a protein coat. – There may be a lipid envelope, and proteins that encourage a host cell to engage it by phagocytosis. – Once engulfed, the viral genes are translated by the host cell, “early expression” enabling the virus to replicate and take over, “late expression” Right-Ebola, a “stripped down” virus with only the essentials.  Viruses have no specific place on the tree of life because they have multiple origins. – Some are probably degenerate bacteria. – Others likely descend from plasmids or “selfish DNA. – There are many groups of viruses, classified by whether they have DNA or RNA, whether they have “sense” or “antisense” genetic material, Sputnik virophage-a whether the genetic material is virus that attacks single or double stranded, etc. viruses  Compared to prokaryotes, Eukaryotes have Domain 1) a nucleus, and usually a larger genome Eukarya 2) linear chromosomes 2) a much more sophisticated cytoskeleton 3) potential for sex in most Domain Eukarya consists of several “kingdoms”. Of these, the “protista” are not a natural biological grouping… – Protista - single celled (several kingdoms lumped for our convenience) – Plantae – multicellular – Fungi - multicellular – Animalia - multicellular You are here  “Protists” “Protists” are simply eukaryotes, most of which are are unicellular for most of their life cycle. – There are many groups of distantly related protists, which are now thought of as “kingdoms” in their own right. – Several groups have independently acquired photosynthesis, and become “algae”, others have evolved multicellularity. One group of multicellular protists evolved into animals. Another lineage evolved into fungi. There are several multicellular lineages, such as slime molds, that neither plant nor animal nor fungi.  Euglenozoa The Euglenozoa are a large and important group of flagellate protists (having flagella as opposed to cillia). Loading… – They branch off early in the eukaryote tree. – Many are free living, some are parasites. – Some are photosynthetic Trypanosoma brucei, mixotrophs, such as the well- the cause of African known Euglena gracilis. sleeping sickness  Alveolates This clade all have sacklike structures on the inner surface of their plasma membrane, and many common DNA sequences. The include Cilliates, Sporozoans, and Dinoflagellates – Stentor-a ciliate  Ciliates This group of unicellular eukaryotes moves by means of many small cillia, as opposed to one or more flagella. – Cillia are often used in feeding as well. They have a small diploid micronucleus for reproduction, and polyploid macronuclei for gene regulation. – Many are large, sophisticated organisms, rivaling small animals in their behavioral complexity and filling some of the same niches. Many are free living, many are parasites or commensals – Many can be seen with the naked eye  Dinoflagellates Dinoflagellates are a large group of unicellular eukaryotes that are very important producers, especially in marine environments. They have a distinctive arrangement of two flagellae, one lateral, one longitudinal, producing forward motion and turning force. Most are mixotrophic, combining photosynthesis with the ingestion of prey.  Dinoflagellates are known for the potent toxins produced by some species, and by their endosymbiotic associations. The “red tide’, seasonal blooms of phytoplankton that make seafood potentially deadly to ingest, are due to certain dinoflagellates, such as Pfiestieria. Dinoflagellate endosymbionts form associations with reef building corals, jellyfish, giant clams, and others.  Malaria-a Eukaryote Pathogen Plasmodium is a large genus of parasitic protozoa that parasitize birds, reptiles, and mammals, including humans. There is always a dipteran (Fly) vector which also hosts the parasite. – Sexual reproduction occurs in the insect host. – Many rounds of asexual reproduction occur in the vertebrate host. Plasmodium is a member of the Apicomplexa, a group derived from parasitic Dinoflagellates, thus, an Aveolate.  Malaria life history is complex. – A mosquito ingests blood containing malarial gametocytes. – These gametocytes unite in the mosquito midgut to form a zygote within the mosquito. – The zygote transforms into a mobile stage, moves, and releases sporozoites that migrate into the salivary glands. These Sporozoites are transferred during feeding, and enter the vertebrate bloodstream, where they move to the liver and invade, where they multiply, bud off from liver cells, and lodge in the lungs, where they have an opportunity to invade red blood cells. Once encysted in a red blood cell, the parasites transform several times, multiply, and explode the cell, releasing asexual progeny to invade other cells, or sexuals, to be picked up by mosquitoes.  Interestingly, the malaria parasite does not seem to harm the mosquito (it is more commensal rather than parasitic), but like nearly every parasite, it manipulates the behavior of its host. Female mosquitoes carrying malaria bite more often than mosquitoes not carrying malaria.  Stamenopiles This clade has certain pigments in common. – a yellow-brown pigment (which gives them their color). It is a carotenoid called fucoxanthin, and chlorophylls a and c It includes several important groups of producers, including; – Diatoms, Brown Algae, Red Algae – Some are multicellular, and called “seaweeds”, but not plants. – Macrocystis, on left, a brown alga  Diatoms Diatoms are a diverse and ecologically important group of unicellular eukaryotes. Most are non motile, and pelagic ones rely on turbulence to stay afloat. Common in fresh and salt water they are very important producers – (though there are hetrotrophic diatoms) – Their plastids have distinctive quadruple membranes encasing them, suggesting serial endosymbiosis.  Diatoms have distinctive silica cell walls, called frustrules, that encase them. – With each asexual division one daughter cell keeps each half of the box. Since the halves fit together, each daughter cell grows the new inside half, leading to a decline in size over time. – This decline in size is reversed by the formation of a sexual auoxspore, which gives rise to a much larger cell. Their use of silica means gives them a certain amount of character displacement from other unicellular algae, a possible key to their success.  Amebozoa This is a major taxonomic unit encompassing unicellular, or aggregate-multicellular eukaryotes often containing lobose pseudopods. These appendages serve many functions They contain slime molds, amebas, and foraminifera. They are a sister group to the Ophistokonts, which contains animals and fungi.  Cellular Slime Molds As the sister group to Ophistokonts, the amebozoa are interesting because the cellular slime molds have the capacity to organize themselves into multicellular structures. – Typically, these organisms are free living ameboids, till the food runs out. – Then they signal each other to organize into a multicellular structure for dispersal. Dog vomit slime mold common at UIC  Fungi Fungi are a kingdom of organisms that includes decomposers, parasites, and mutualisms. There are four major groups; Chytridomycots Zygomycots Ascomycots Basidiomycots  Characteristics of Fungi Fungi are a major clade (branch) or organisms on the tree of life. – They have cell walls containing chitin, a long chain polymer polysaccharide. – Fungi are heterotrophs-they typically digest food extracellularly, and absorb it, as opposed to animals, which typically ingest food. – Most are multicellular but many have reverted to unicellular forms called “yeasts”. Many ecological associations, including decomposers, parasites, mutualists, and commensals. Many fungi alternate between haploid and diploid multicellular phases.  Chytrids are usually aquatic and saprobes or parasites. – At least some of their cells have flagella, a primitive trait for fungi. Zygomycots usually live in the soil or decaying material. We encounter many of them as “molds” – Many live in a mycorryzal mutualistic symbiosis with terrestrial plants. – Zygosporangia are resistant to freezing and dessiccation. Ascomycots are usuallycomplex multicellular fungi that often produce spectacular fruiting bodies. – Their spores are held in saclike “asci” – About half live in mutualistic symbiotic associations called “lichens”, some are mycorryzal fungi. Basidiomycots are usually complex multicellular fungi, that often produce spectacular fruiting bodies called “mushrooms”. – Spores are arranged on a structure called a “basidium” – These fungi are often important decomposers of wood, others live in mycorrhyzal associations. EO Wilson’s Biodiversity again  Polling Question Which of the following organisms is a prokaryote? A) a mouse B) a yeast C) E. coli bacteria D) B and C E) None of the above  Some fungal diseases of humans. “Athletes foot” is a very common fungal infection caused by ascomycots in the genera Epidermophyton, Trichophyton and Microsporum. These are dermatophytes-fungi that prefer to live in layers of dead human skin, as parasites in the mold growth form. – “Ringworm” is usually caused by dermatophytes in the genera Trichophyton and Microsporum. – Candidiasis is caused by the over growth of an organism that is usually commensal, Candidia albicans, a unicellular ascomycot yeast.  Beer, wine, and bread use of the metabolic activity of domesticated yeasts, the ascomycots Saccharomyces cerevisiae and S. ovatus. – These species exist in the wild on the skins of ripe fruits. They require an insect vector, usually wasps, to move to new habitats. – In domestication, many strains have been selectively bred to ferment particular beverages. Ale yeasts-brew well at higher temperatures, their cells tend to sink. Lager yeasts-brew at lower temperatures, their cells tend to float.  Viridiplantae This group includes the green plants and the basal “bush” from which they originated. They have chlorophyls a and b, as well as certain other distinguishing characteristics. Green Algae-Chlorophytes Charophytes Plants  Green Algae The green algae are an informal grouping that includes the Chlorophyte and the Charophyte algae. – Land plants evolved from Chrophytes. Like land plants, they have chlorophylls a and b, giving them a green color. They move about with paired flagella (only present in charophyte gametes. – They include multicellular forms  True Plants These include several groups of multicellular, terrestrial photosynthesizers, including – Bryophytes-mosses, etc. – Pteridophytes-ferns. – Gymnosperms – Angiosperms-flowering plants  Adaptations to Life on Land Roots – intake water and minerals in soil Leaves – produce energy/sugar through photosynthesis Vascular tissue Xylem –transports water & minerals from roots to rest of plant (via evaporation from leaves, and adhesion of water in the column behind evaporating water). Phloem – pumps sugar/food/energy from leaves to rest of plant Cuticle Water and gas-tight; reduces water loss Stomata – pores in leaf cuticle; open to allow gas flow and close to reduces water loss  Plants Alternate Generations Reproductive cycle: alternation of generations. Sporophytes (2n) produce spores (n) by meiosis. Spores grow into gametophytes (n). Gametophytes make gametes (n) by mitosis, which fuse to become a fertilized zygote (2n). Zygotes grow into sporophytes. Fig. 29-5a Gametophyte Gamete from (n) another plant Mitosis Mitosis n n n n Spore Gamete MEIOSIS FERTILIZATION 2n Zygote Mitosis Sporophyte (2n) Table 29-1 * *  Nonvascular Plants Land plants evolved some time in the Silurian period, around 440 million years ago. By the early Devonian period, 415 mya, communities of plants had colonized the wet areas on land. The dry areas were still essentially barren.  Two early land plants, Rhynia and Psilophyton They grew in wet areas. The vascular tissue of Rhynia is primitive-thus, they are short. The sporophytes are shown. Psilophyton had vascular tissue and was a tracheophyte. Note the lack of true leaves, but the sporangium bearing structures.  Plants without sophisticated vascular tissue dominated terrestrial communities for 100 million years. As they proliferated, they altered terrestrial microenvironments, and created ecological niches for terrestrial animals, notably, arthropods. Animals did not colonize land out of manifest destiny- without food, in a punishing microenvironment, there was nothing there for them.  BUT they needed moist environments: No vascular system to take water up from soil! Sperm have to SWIM to egg So later, vascular plants gradually spread and became the dominant terrestrial producers Vascular tissue pumped water up from soil AND allowed them to grow TALL! The tree growth form had far-reaching effects on ecosystems. Many ecological niches opened up. Likely, the carbon pulled out of the atmosphere, and decomposing material from land sinking in oceans, caused a mass extinction. Archaeopteris, early tree.  Ferns vascular tissue spores, not seeds spores are sexual and haploid: not yet fertilized! Dominant sporophyte. Diverse - more than 12,000 species. Mostly tropical, some temperate Fig. 29-15d Seedless vascular plants Isoetes gunnii, a club “moss” a quillwort  Seed Plants A seed is an embryo and nutrients surrounded by a protective coat Their ecological importance cannot be overstated. – Gymnosperms, the “naked seed” plants, including the conifers, an informal grouping. – Angiosperms, the flowering plants  Gymnosperms Not a single lineage. Have vascular tissue, seeds, dominant sporophytes Gymnosperm means “naked seed” Conifer cone bearing trees: pine, fir, spruce. Most diverse and ecologically important group. – Cone - scaly structure produced by some seed plants; support either male or female reproductive structures; site of seed-production/ Cycads formerly very diverse. Others..such as Ginko bioloba (right)  Angiosperms Currently, the ecologically dominant group in most terrestrial environments. Produce flowers Seeds are enclosed in fruits Monocots are a distinct clade, the branch off early from within the” Dicots”.  Monocots vs. Eudicots Within the “Dicots”, the Eudicots are a true lineage.  Grasses One ecologically important group of monocots are grasses (family Poaceae) – They diversify and become widespread at the end of the Cretaceous period, eventually replacing ferns as the most important early-successional plants  In one way or another, most of our food calories come from grasses. Either domesticated edible grasses, called cereals,or up the food chain from grazing. – Their leaves grow from the base, making them tolerant of grazing. – Their leaves have parallel veins, and are alternate. – They are nearly always wind pollinated.  Animals Animals are a true lineage of multicellular organisms evolved from one line of protists (probably resembling a group called the choanocytes). Animals share a common ancestor with fungi, choanoflagellates, and some enigmatic groups to form a clade called the ophistokonts. – They have evolved many different body plans, each of which represents a phylum. There are about 35 present-day animal phyla, there were probably more in the distant past. – Collagen and mitochondrial genome reduction are common features of all animals.  Choanoflagellaes A group very similar to the common ancestor of all animals are the choanoflagellates. – They are free living or multicelular ophistokont protozoa with a distinctive feeding apparatus that resembles the collar cells of sponges. – Sponges, the most primitive animals, evolved form organisms like this.  Sponges Phylum Porifera Until recently sponges were thought to be the most basal animals. DNA analysis suggests that nearly all other animal life evolved from a dermosponge ancestor. Sponge fossils first appear in the Cambrian, but molecular fossils suggest they arose 600mya or earlier  Sponges (Porifera) Are multicellular, with tissues, but no true organs, nor organ systems like digestive, circulatory, nervous, and muscular. They are composed of a gel-like mesohyl sandwiched between two layers of cells. They lack symmetry Produce sperm  Sponges are filter feeders, that use flagellated collar cells to create a water current. Spicules in the mesohyl for an endoskeleton. – Some use silica, some calcium carbonate, some use spongin fibers. Their cells are undifferentiated and the entire animal can regenerate. The Ediacaran Fauna The first creatures resembling animals appear in the fossil record approximately 600 million years ago. – The Earth was recovering from massive glaciation. – This fauna is found worldwide, some forms having very large geographic ranges.  The Ediacaran fauna form distinct assemblages in deep water and shallow water. – Some were quite large. – Many have a “quilted” body plan. – Their existence seems to be tied to the presence of microbial mats, which were much more pervasive before the evolution of multicellular animals, and the bioturbation associated with them. – Their phylogenetic affinities, physiology, and natural history are currently a scientific mystery. Rangea sp. The Cambrian Explosion The Cambrian explosion was a relatively short lived adaptive radiation that happened at the beginning of the Cambrian period, 530 million years ago, and lasted appx 20 million years. Nearly all of the present-day animal phyla, and many extinct groups, originated during this time.  The Ediacaran fauna disappear completely at this time. – Bioturbation becomes widespread, and as the radiation progresses, food webs with multiple trophic levels evolve. – Many forms of life evolve complex features and become fairly common, but go extinct soon afterwards. Loading… Sequencing of the genes that code for 18s ribosomal RNA has enabled us to come up with a good phylogeny of animals. 18s ribosomal RNA is very evolutionarily conservative, and preserves info on deep branches. This one was our view in about 2001 Here is the current consensus. As genomic sequencing Techniques improved, note some surprises. This is science- incorrect hypotheses are rejected as new evidence comes in.  Ctenophores The “comb jellies” resemble cnidarians in several ways, This group was, until recently, thought to be close to the common ancestor of the bilateral metazoan animals. Recent evidence (Dunn, et al, 2014) has suggested that it is the outgroup to all other animals, including Porifera. Move by rows of cillia. – Tissues? – a “nerve net” – Most waste is regurgitated, but some come out anal pore.