3.S: Unit 3 Summary

Unit 3.2

Scientists continually obtain new information that helps to understand the evolutionary history of life on Earth. Historically, organisms were organized into a taxonomic classification system. Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others and, based on morphologic and genetic evidence, scientists attempt to map the evolutionary pathways of all life on Earth. However, today many scientists build phylogenetic trees to illustrate evolutionary relationships; the taxonomic classification system is expected to reflect evolutionary relationships.

To build phylogenetic trees, scientists must collect character information that allows them to make evolutionary connections between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes. Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths (analogies). After homologous information is identified, scientists use cladistics to organize these events as a means to determine an evolutionary timeline.

Many disciplines within the study of biology contribute to understanding how past and present life evolved over time, and together they contribute to building, updating, and maintaining the “tree of life.” Information gathered may include data collected from fossils, from studying morphology, from the structure of body parts, or from molecular structure, such as the sequence of amino acids in proteins or DNA nucleotides. By considering the trees generated by different sets of data scientists can put together the phylogeny of a species. Scientists continue to discover new species of life on Earth as well as new information about already identified species. Thus, phylogenetic trees change as new data arrive.

Unit 3.3

The geological time scale is a result of hundreds of years of investigation and remains very much a work in progress. The Earth has gone through periodic cycles of increases and decreases in temperature. During the past 2000 years, the Medieval Climate Anomaly was a warmer period, while the Little Ice Age was unusually cool. Both of these irregularities can be explained by natural causes of changes in climate, and, although the temperature changes were small, they had significant effects. Natural drivers of climate change include Milankovitch cycles, changes in solar activity, and volcanic eruptions. None of these factors, however, leads to rapid increases in global temperature or sustained increases in carbon dioxide. The burning of fossil fuels is an important source of greenhouse gases, which plays a major role in the greenhouse effect. Long ago, global warming resulted in the Permian extinction: a large-scale extinction event that is documented in the fossil record. Currently, modern-day climate change is associated with the increased melting of glaciers and polar ice sheets, resulting in a gradual increase in sea level. Plants and animals can also be affected by global climate change when the timing of seasonal events, such as flowering or pollination, is affected by global warming.

The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common ancestor of today’s Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.

Unit 3.4

Acellular Entities

Viruses are tiny, acellular entities that can usually only be seen with an electron microscope. Their genomes contain either DNA or RNA—never both—and they replicate using the replication proteins of a host cell. Viruses are diverse, infecting archaea, bacteria, fungi, plants, and animals. Viruses consist of a nucleic acid core surrounded by a protein capsid with or without an outer lipid envelope. The capsid shape, presence of an envelope, and core composition dictate some elements of the classification of viruses. The most commonly used classification method, the Baltimore classification, categorizes viruses based on how they produce their mRNA. Viral replication within a living cell always produces changes in the cell, sometimes resulting in cell death and sometimes slowly killing the infected cells. There are six basic stages in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release. A viral infection may be productive, resulting in new virions, or nonproductive, which means that the virus remains inside the cell without producing new virions.

Prions are infectious agents that consist of protein, but no DNA or RNA, and seem to produce their deadly effects by duplicating their shapes and accumulating in tissues. They are thought to contribute to several progressive brain disorders, including mad cow disease and Creutzfeldt-Jakob disease. Viroids are single-stranded RNA pathogens that infect plants. Their presence can have a severe impact on the agriculture industry.

Kingdoms Bacteria and Archaea

Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular DNA in the nucleoid area of the cell. Most prokaryotes have a cell wall that lies outside the boundary of the plasma membrane. Some prokaryotes may have additional structures such as a capsule, flagella, and pili. Bacteria and Archaea differ in the lipid composition of their cell membranes and the characteristics of the cell wall. In archaeal membranes, phytanyl units, rather than fatty acids, are linked to glycerol. Some archaeal membranes are lipid monolayers instead of bilayers.

The cell wall is located outside the cell membrane and prevents osmotic lysis. The chemical composition of cell walls varies between species. Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan, but they may have pseudopeptidoglycan, polysaccharides, glycoproteins, or protein-based cell walls. Bacteria can be divided into two major groups: Gram-positive and Gram-negative, based on the Gram stain reaction. Gram-positive organisms have a thick cell wall, together with teichoic acids. Gram-negative organisms have a thin cell wall and an outer envelope containing lipopolysaccharides and lipoproteins.

Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans. The very broad range of environments that prokaryotes occupy is possible because they have diverse metabolic processes.

Protists

Protists are extremely diverse in terms of their biological and ecological characteristics, partly because they are an artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are motile, but these organisms use diverse structures for transportation.

Kingdom Fungi

Fungi are eukaryotic organisms that appeared on land more than 450 million years ago. They are heterotrophs and contain neither photosynthetic pigments such as chlorophyll nor organelles such as chloroplasts. Because fungi feed on decaying and dead matter, they are saprobes. Fungi are important decomposers that release essential elements into the environment. External enzymes digest nutrients that are absorbed by the body of the fungus, which is called a thallus. A thick cell wall made of chitin surrounds the cell. Fungi can be unicellular as yeasts or develop a network of filaments called a mycelium, which is often described as mold. Most species multiply by asexual and sexual reproductive cycles and display an alternation of generations. Another group of fungi do not have a sexual cycle.

Kingdom Animalia

The most rapid diversification and evolution of animal species in all of history occurred during the Cambrian period of the Paleozoic Era, a phenomenon known as the Cambrian explosion. Until recently, scientists believed that there were only very few tiny and simplistic animal species in existence before this period. However, recent fossil discoveries have revealed that additional, larger, and more complex animals existed during the Ediacaran period, and even possibly earlier, during the Cryogenian period. Still, the Cambrian period undoubtedly witnessed the emergence of the majority of animal phyla that we know today, although many questions remain unresolved about this historical phenomenon.

The remainder of the Paleozoic Era is marked by the growing appearance of new classes, families, and species, and the early colonization of land by certain marine animals. The evolutionary history of animals is also marked by numerous major extinction events, each of which wiped out a majority of extant species. Some species of most animal phyla survived these extinctions, allowing the phyla to persist and continue to evolve into species that we see today.

Animals constitute an incredibly diverse kingdom of organisms. Although animals range in complexity from simple sea sponges to human beings, most members of the animal kingdom share certain features. Animals are eukaryotic, multicellular, heterotrophic organisms that ingest their food and usually develop into motile creatures with a fixed body plan. A major characteristic unique to the animal kingdom is the presence of differentiated tissues, such as nerve, muscle, and connective tissues, which are specialized to perform specific functions. Most animals undergo sexual reproduction, leading to a series of developmental embryonic stages that are relatively similar across the animal kingdom. A class of transcriptional control genes called Hox genes directs the organization of the major animal body plans, and these genes are strongly homologous across the animal kingdom.

Organisms in the animal kingdom are classified based on their body morphology and development. True animals are divided into those with radial versus bilateral symmetry. Generally, the simpler and often non-motile animals display radial symmetry. Animals with radial symmetry are also generally characterized by the development of two embryological germ layers, the endoderm and ectoderm, whereas animals with bilateral symmetry are generally characterized by the development of a third embryological germ layer, the mesoderm. Animals with three germ layers, called triploblasts, are further characterized by the presence or absence of an internal body cavity called a coelom. The presence of a coelom affords many advantages, and animals with a coelom may be termed true coelomates or pseudocoelomates, depending on which tissue gives rise to the coelom. Coelomates are further divided into one of two groups called protostomes and deuterostomes, based on a number of developmental characteristics, including differences in zygote cleavage and method of coelom formation.

Scientists are interested in the evolutionary history of animals and the evolutionary relationships among them. There are three main sources of data that scientists use to create phylogenetic evolutionary tree diagrams that illustrate such relationships: morphological information (which includes developmental morphologies), fossil record data, and, most recently, molecular data. The details of the modern phylogenetic tree change frequently as new data are gathered, and molecular data has recently contributed to many substantial modifications of the understanding of relationships between animal phyla.

Kingdom Plantae

Land plants acquired traits that made it possible to colonize land and survive out of the water. All land plants share the following characteristics: alternation of generations, with the haploid plant called a gametophyte, and the diploid plant called a sporophyte; protection of the embryo, formation of haploid spores in a sporangium, formation of gametes in a gametangium, and an apical meristem. Vascular tissues, roots, leaves, cuticle cover, and a tough outer layer that protects the spores contributed to the adaptation of plants to dry land. Land plants appeared about 500 million years ago in the Ordovician period.

Seedless nonvascular plants are small, having the gametophyte as the dominant stage of the lifecycle. Without a vascular system and roots, they absorb water and nutrients on all their exposed surfaces. Collectively known as bryophytes, the three main groups include the liverworts, the hornworts, and the mosses. Liverworts are the most primitive plants and are closely related to the first land plants. Hornworts developed stomata and possess a single chloroplast per cell. Mosses have simple conductive cells and are attached to the substrate by rhizoids. They colonize harsh habitats and can regain moisture after drying out. The moss sporangium is a complex structure that allows the release of spores away from the parent plant.

The pterophytes are seedless, vascular plants. Vascular systems consist of xylem tissue, which transports water and minerals, and phloem tissue, which transports sugars and proteins. With the development of the vascular system, there appeared leaves to act as large photosynthetic organs, and roots to access water from the ground. Small uncomplicated leaves are microphylls. Large leaves with vein patterns are megaphylls. Modified leaves that bear sporangia are sporophylls. Some sporophylls are arranged in cone structures called strobili.

Seed plants appeared about one million years ago, during the Carboniferous period. Two major innovations—seed and pollen—allowed seed plants to reproduce in the absence of water. The gametophytes of seed plants shrank, while the sporophytes became prominent structures and the diploid stage became the longest phase of the lifecycle. Gymnosperms became the dominant group during the Triassic. In these, pollen grains and seeds protect against desiccation. The seed, unlike a spore, is a diploid embryo surrounded by storage tissue and protective layers. It is equipped to delay germination until growth conditions are optimal. Angiosperms bear both flowers and fruit. The structures protect the gametes and the embryo during its development. Angiosperms appeared during the Mesozoic era and have become the dominant plant life in terrestrial habitats.