Linnaean Taxonomy and Phylogenies

Linnaean Taxonomy

• The basic Linnaean taxonomy and its system of scientific names used for nearly 3 centuries is not based on evolutionary thinking.
• Carolus Linnaeus developed the taxonomic system where organisms can be arranged in a hierarchical classification.
• Species and subspecies can be assigned to groups of highly similar organisms, which can then be arranged into larger groups of moderately similar organisms.

Darwin and Phylogenetic Systematics

• Darwin explained that the patterns seen were through the evolutionary process of branching descent, which with modification, created natural nested hierarchies of similarity which are consequences of phylogenetic history.
• Darwin's approach resulted in species, genus and family classifications changes.
• Hennig's phylogenetic systematics: emphasizes that phylogenetic trees document evolutionary history to classify the world.

Phylogenies and Evolutionary History

• Phylogenies aim to reconstruct and understand common descent patterns to understand the evolutionary events in life's history.
• Phylogeny studies branching relationships of populations when giving rise to descendant populations over evolutionary time.
• Phylogeny allows for reconstructing the tree of life by understanding major events and historical relationships that connect all living things.
• Phylogenies are used to understand the descent history and relationships between genera within a family or among species within a genus.
• Understanding the evidence of common ancestry requires taking a historical perspective, giving insight into population relationships.
• Pedigrees and phylogenies both represent ancestry patterns using treelike branching.
• Pedigrees show individual ancestry while phylogenies show that of species, genre, and families.
• Pedigree nodes are individuals, but phylogeny nodes represent populations.
• Each individual of a sexual species has two parents, therefore each pedigree node has two ancestors and can leave many descendants.
• Conventional phylogeny assumes species split in two and never recombine.
• Phylogeny results from character observations, (anatomical features, behavior patterns, genetic sequences etc).
• Traits have character states, specific character values, and possible character traits.
• Traits assist phylogeny studies to infer ancestry patterns and population descent to graphically represent them as a tree.
• Traits can also study sequencing and evolutionary event timing by mapping additional traits onto phylogenies.
• Reconstructing trees and mapping events onto trees generates hypotheses.
• A phylogenetic tree is a hypothesis about relationships, the location, and evolutionary events order.
• Hypotheses are tested and are subject to refinement or refutation with new data
• Existing phylogenetic trees concerning evolutionary events are tested or inferences compared against new evidence to test consistency, and modified if needed via the new data.
• Predicting common ancestry based on phylogenetic relatedness can be done even without understanding genes, DNA, or heredity/mechanisms.
• Darwin's ancestry pattern hypothesis made a prediction that became testable later.
• If descent with modification is correct, DNA sequence similarity patterns should reflect the inferred ancestry patterns from other evidence.
• Special creation hypothesis or lineages formed via acquired characteristics inheritance would not produce such DNA similarity patterns.

Reading Phylogenetic Trees

• Each branch tip represents a group of related organisms (taxon).
• Phylogenies show relationships among taxa through tree, ladder, and circular formats.
• These formats are interchangeable and with no orientation relevance.
• Nodes represent common ancestors to taxa after the splitting in branching points.
• Branch tips from a given node are descendants of the ancestor at that node.
• The tree can be traced backward until it converges with the branches to find the most recent common ancestor of two or more species.
• The base of the tree(root) represents the common ancestors to every species on the tree.
• Each interior node in a phylogenetic tree represents a population at some time in the past, rather than in the present day.
• Evolutionary relationships can be depicted in multiple ways, for example, a phylogeny remains unchanged if rotated around a node.
• Relative positions from left to right of the branch tips do not relay information about how closely related two species are.
• What matters is distance to the most recent common ancestor when tracing down.
• Both clades and monophyletic groups, each phylogeny shows the relationships between organism groups; along with squamate organisms as an outgroup-taxon related to groups of interest before an earlier branch.
• Sister Taxa are taxa from the same node and more distantly related to one another than they are to each other.
• A polytomy is a node with uncertainty that has more than two branches arising from it.
• A phylogenetic tree can determine natural organism groupings that are monophyletic groups.
• These groups are a taxonomic group including the descendants of the group's common ancestor.
• A clade always comprises a group that shares a single recent common ancestor.
• All species from this ancestor are in the clade, and all species not descended are not members of the clade.
• Polyphyletic groups do not represent clades and lack a common ancestor of it's members, and/or all descendants of the common ancestor.
• Paraphyletic groups contain the group's common ancestor but not all descendants.
• Rooted trees show the common lineage for the species derived on the tree.
• As a result, in rooted trees the indicated direction show the passage of time.
• Unrooted trees lack a full indication of the time direction.
• Character data or DNA sequences form unrooted trees as most algorithms show branch tips representing more recent species than nodes.
• Rooted and unrooted trees can "root" any points or branches onto the tree.
• An unrooted tree with "k" branches will have k corresponding rooted trees.
• Branch lengths convey relationship patterns among various species.
• Branch lengths represent the amount of evolutionary change (measured as DNA sequence or characters changes) that occurred in a given branch.
• Cladograms are trees without different branch lengths and phylograms trees that represent evolutionary change with branch lengths.
• Chronograms branch lengths represent real time opposed to evolutionary change.

Phylogenies and Hypothesis Testing

• Evolutionary relationships can be generated and tested through phylogenetic tree structures, as well as via branch lengths on phylogenetic trees.
• Biologists theorize that species that have shorter generation times may experience faster rates of evolution, as measured by DNA sequence changes.
• Germ-line cells pass through the same number of replication rounds despite of lifespan and have the same chance of change, as primary reasoning.
• Short-lived species may have greater mutual change in the germ line per year as they have shorter lifetimes than long-lived species.

Traits on Trees

• Hypotheses concerning the time and manner in traits evolve can be generated with their structures.
• Opsins facilitate color vision and have a evolutionary history of cone opsins of tetrapod vertebrates.
• Representative tetrapod groups which include squamate reptiles, birds, rodents, platyrrhine primates, baboons, and humans can be located at the tree tips.
• Each kind of opsin presence or absence is a character that can be mapped onto the tree.
• Branch tips are displayed with cone opsins with each group's presence.
• Humans and baboons are trichomats that have 3 different cone opsins.
• Rodents and platyrrhine primates are generally tetrachromats and have four cone opsins.
• Common ancestry of these groups can be seen at the base of the tree with hypothesized states.
• Birds and lizards with a common that are ancestor where indicates they were most likely tetrachromat.
• Traits can be indicated at the root and tips and branches that suggest where traits have arose or have been lost.
• The mammalian clade indicates that two medium- wavelength opsins along the branch leading from the common ancestor are lost.
• These losses were possibly joined with early mammals nocturnal lifestyles due to low color vision use.
• Platyrrhine and catarrhine primates evolved with the subsequent divergence and duplication of the gene long-wavelength opsin.
• It's possible the addition was favored due to primates better detection for ripe fruit or young leaves.
• Previously obstructed traits on tree provide a hypothesis about the evolution history of traits.
• Similarity is a consequence of shared ancestry while others of natural selection on divergent organism groups.
• Distinguishing species based on similarities determines their relationships.
• Homologous traits occur when two or more species inherited their qualities from one ancestor.
• Analogous traits occur when two or more species possess a characteristic due to similar evolutionary, and selective pressure.

Divergent and Convergent Evolution

• A trait can be homologous or analogous depending on its ancestral history.
• The presences of homologous traits is evidence that the species have shared ancestry.
• Convergent evolution reveals similarly structured or functioning solutions to similar problems.
• Divergent evolution occurs when similar species diverge since natural selection operates differently on them, example being coat color in oldfield mouse.
• Convergent evolution occurs when species become more similar from similar selective conditions, example being poison frogs.

Hypotheses and Evolutionary Relationships

• Evolutionary trees generate new hypotheses about historical relationships among origins.
• Phylogenies facilitate new hypotheses which can be tested through information about relationships and descent.
• Arthropod venom evolution shows that spiders and centipedes contain HAND toxins derived from neuropeptide hormones ITP/CHH.
• Hormones found in spiders is hypothesized to be about 375 mya and weaponized into toxins.
• Peptide data mapped onto a spider phylogeny showed spider and centipede HAND toxins share 22% sequence similarity.
• Convergent evolution of HAND toxins suggests, 3D folding structures appears almost identical, although.

Phylogenies in Predicting Pharmaceuticals

• Phylogenetic analysis helps in the search for new phytochemicals for new pharmaceuticals.
• 2859 had anti-infective properties while the remaining 13,213 lacked known anti-infective characteristics.
• Data mapped on species that produces with anti-infective properties or lack phylogeny of seed plant on Java.
• 26 clades that produced more anti- infective properties than expected and 24 fewer properties, were then found.
• Promising species to target with “hot clades” have then be suggested.

Vestigial Traits

• Rudimentary characteristics have past function in evolution.
• Traits remain in place for cases when they serve no function due to the traits not harming the organism and/or no path of natural selection present.
• A vestigial trait maybe linked, so eliminating the traits affects a connected aspect.
• Some function is still present in the trait, but remains to be identified.
• Common descent can be traced by comparing functionless traits in species to functional forms in other species, as part of limblessness traits.
• Shared evolution can be a vestigial traits test.
• Common ancestors by descent from one or few indicates we will see shared vestigial traits in species that share the that trait.

Timeframes of Earth's Ecological Events

• The Earth is 4.6 billion years old with a cooled outer layer and molten inner layer.
• There was originally no water when the Earth was formed with the atmosphere finally cooling enough to allow for it.
• Collections of surrounded chemicals most likely represented the first life with the protobionts evolving RNA to DNA for the double helix structure.
• The presence of unicellular organisms like prokaryotes started in the archaean eon around 3.9-3.5 billion years ago.
• Unicellular organisms started an oxygen revolution that increased the amount of oxygen in Earth's atmosphere.
• Cyanobacteria created the oxygen revolution which was a major instance of living organisms causing massive change leading to eukaryotes.
• A prokaryote parasitizing another is the simple explanation of how parasitic relation led to eukaryotic organelles.
• Multi-cellular evolution and more complexity were byproducts of unicellular endosymbiosis.
• Animals diversified in the Cambrian explosion around 535 million years ago.
• Organisms like plants, animals, and fungi began colonizing land.
• Fossils that form plant life increased and formed fossil fuels as a result in the Carboniferous period.
• Extinction and the lack of information makes it difficult to determine mass extinction events.
• The most substantial mass extinction, Permian-Triassic, extinguished 96% of marine and 70% of terrestrial life due to methane volcanic explosions, oceans changes, and a long recovery.

Coevolution and Life Evolution

• Extinction is followed by filling of available niches which often spurs new organism groups evolution.
• Coevolution is the response and interactions between organisms that affect the evolution.
• Mammals became more dominant after the dinosaurs went extinct.
• The speed of evolution which is changed and impacted by what humans favor, artificial selection, and speciation, occurs in Anthropocene or age or man.
• Anthropogenically factors including climate change, human population, and increased temperature affect which species decline.
• Prokaryotics are 3.5 - 3.8 billion years ago.
• Stromatolies formed microbial mats into layers starting 3.45 billion years ago.
• Photosynthetic evolution is tied to the Great Oxygenation event (2.4-2.1 billion years ago).
• Eukaryotes are around 2 billion years old and sexually producing individuals of those are between 1-2 billion years ago.
• Vertebrates emerged and diversified during the Cambrian Explosion around 500 million years ago.

Patterns of Extinction

• Numerous extinction events occurred throughout the time periods since, causing various groups to either diversify or be eliminated.
• The Holocene extinction period is caused mainly by human activity including deforestation
• Organisms adapt to new environment and those remaining filled the niches from extinction at different point.

Chapter 12: Major Transitions

• Cellular slime molds radically transform from single cells to a multicellular slug formation providing an excellent model organism.
• D. discoideum begins as a single-celled amoeba that consumes soil-borne bacteria, when nutrients deplete, 800,000 fuse into a slug to reproduce.
• This slug migrates then form a fruiting body composed of supporting stalk and spore creating cells.
• Maturation of spores recreates amoebas again, in the form of independent and multicellular creatures.
• Transformation of amoeba in slugs provides a hint as to the processes of transformation during the change during evolution.
• Nothing intrinsically entails complexity buildup, sometimes it can be lost.

Major Evolutionary Transitions

• Transitions to the origin of life involves a shift to the processes included such as:
  • The origin of heredity
  • A shift to proteins
  • The emergence of eukaryotic cells and sex
  • The increasing complexity towards an eventual social existence
• Some major transitions were singular, whereas others evolved independently.
• Regardless, there is now the common theme of lost ability to reproduce as individuals, which enhances the ability to perform tasks as a group.
• They can also be locked in to details that prevent reversion and leads to cooperation with policing as the key to maintain cooperation.
• The division of labor between reproduction and maintenance leads to the germ-soma distinction.

Eukaryotic Cell Evolution

• Membrane bound organelles and a distinct nucleus are an evolutonary hallmark of the eukaryotic cell.
• Endosymbiosis and evolutionary models explain the source of eukaryotics.
• Lynn Margulis' Endosymbiotic theory proposed ancestors of a few such structures have been parasitic.
• The long term symbiotic relationship causes energy, food and protection and merges the entities into a shared fate.

Models of Evolutionary History

• The transfer of genes or symbiotic events cannot be simplified easily on an evolution tree.
• While 3 domain is traditionally accepted , two - domain suggests Archaea clade is nested within the eukaryota.
• Asgard Archaea support by identifying that it codes for many eukaryotic signature proteins.
• The nucleus likely came before and organelles after in regards to ancestry.
• There have also been cases were genes have transferred to the nucleus after the organelles and nuclei were created, to maintain proper working.

Mulicellular Evolution

• Independent but convergent evolution is the driver for multicellular evolution.
• A common understanding of such can be by either coming together or staying together.
• Single cells will merge to become multicellular or unicellular organisms could fail to be separated to perform the task.
• Genetic similarity can explain why the latter method is more successful as greater commonality causes lesser conflict.
• Yeast and experimental conditions can demonstrate staying through yeast experiments where one tries to promote change.
• Settling selects toward yeast to settle better, and cell clusters are more successful as a result indicating multicellularity
• Mutations produce snowflake clusters, this causes these mutations to prevent breaking.
• Snowflake clusters show death at break points, these clusters of cells leads to greater apoptosis.

Slime Molds

• Slime molds and the slug provide the basis for joining together for multicellularity.
• Communication and navigation via cAMP, are needed.
• Cells emitted cAMP causes signaling, and aggregation proteins support cell structure of the slug.
• Nutrients like temperature and light allows for communication, it allows the slug to orient and use resources.
• Slugs can therefore use information that a single cell cannot, this means an economy of scale.
• It is also able to form slime sheath protecting it from nematode predators with the collective ability to traverse over dangerous soils to produce spores.

Evolution of Individuality Models

• It is an evolutionary challenge of when a group of cells become an individual because these entities pass on heritable traits and processes.
• Gradual processes improve an organization with transferring fitness to greater levels.
• The division and evolution is critical to separate the role between germs and somatic activity, leading toward separate lineages.
• Natural selection favors smaller individuals due to the likelyness of mutation and cheat. This leads to a restriction on individuals who can spread.
• As division between somatic and germ lines increases, there is less cheating and genes can be divided accordingly.

Volvocine algae

• These help understand the differentiation between the groups of specialization.
• Volvox, species show specialization for 2000 somatic or 16 flagella reproductive cells.
• SOmatic motility is critical for survival.

RegA gene

• The gene is expressed to supress the development for chloroplast and is reliant to cell division for which traits are somatic.
• Expression is influenced the rsl1 gene during cell division.
• Ancestor lineages to create 750 generations in which cells were tested against predation to promote multicellularity.
• This is the basis to create the theory behind the evolution of individuality by which the process of what happens to certain members to create better opportunities for success and evolution.

Solitary to Group Living: Major Transitions

• Living in groups has been a theme for the evolution, rather than on their own.
• It is a measure to be safer from scale effects and predatory groups that increase benefit for living the group.
• Coordination and the relationship influences the degree of group living.

Group Definition

• Affecting various groups in any way including ungulates in the tight and coordinated.
• Group Foraging benefits are linked to economies of scale.
• Blue gulls that look in aqua insects increase success greatly for those in numbers by having a flushing effect.
• Passive foraging creates aggregate impacts which create aggregate behavior between action and animals benefitting as a result.
• Many passive processes involve complex action that leads into coordination and communication.
• Chimps will hunt together, creating different hunting roles which has evidence of cooperation.
• Bees are also highly successful as they work together as the waggle worker bee is able to find and then convey those findings.

Group Costs

• Proximity effects when individuals take away food or parasites during group living.
• Group size comes with certain benefits but has its own form of costs.

What About Major Transitions?

• In the cases the evolution with complex species leads to:
  • Multicellularity
  • Specialization
  • Groups
  • Origins
  • Transitions to the first cell