Chapter 26

Concept 26.1

  • Phylogeny → Evolutionary history of a species of an species or group.

  • Systematics → Discipline focused on classifying organs and determining their evolutionary relationships.

Binomial Nomenclature & Hierarchical Class

  • Binomial (two-part format) → Created by Carolus Linnaeus, it provides a first genus name (plural) followed by specific epithet, unique to the species it belongs to.

    • Example → Panthera pardus (the scientific name for the leopard), demonstrates how this system simplifies the naming of organisms and reduces confusion in taxonomy.

    • First letter is capitalized and the entire binomial is italicized.

  • Linnaean System of Classification

    • Family → Related genera.

    • Orders → Related families.

    • Classes → Related orders.

    • Phyla → Related classes.

    • Kingdoms → Related phyla.

    • Domains → Related kingdoms.

  • Taxon → Named group at any level of biological classification, including but not limited to species, genus, family, order, class, phylum, kingdom, and domain.

Linking Classification and Phylogeny

  • Phylogenetic tree → Branching pattern which matches evolutionary history of organisms by illustrating how different groups have diverged from common ancestors over time.

  • Branch points → represent common ancestor of two evolutionary lineages diverging from it.

    • Length of the branch represents the quantity of genetic changes.

  • Evolutionary lineage → sequence of ancestral organisms leading to a particular descendant taxon.

  • Sister Taxa → Groups of organisms which share an immediate common ancestor not shared by any other group.

  • Rooted phylogenetic tree → Phylogenetic tree which has a branch point within the tree that represents the most recent common ancestor of all taxa within the tree.

  • Basal taxon → a lineage that diverges early in the history of a group and lies on a branch that does not share a more recent common ancestor with any other taxa.

Concept 26.2

Morphological and Molecular Homologies

  • Homologies → Phenotypic and genetic similarities due to shared ancestry.

  • Homologies can be great and both small:

    • Hawaiian silversword plants are tall, twiggy trees, while their close relatives, the California sunflower species, are typically shorter and bushier, illustrating how homological traits can manifest differently in response to environmental pressures.

  • Analogy → Similar phenotypic traits due to convergent evolution, where an species develops similar function despite lack of shared ancestor.

  • Identification of genetic and phenotypic structures allows determination in a homologous versus analogous traits.

Molecular Homologies/Analogies

  • Molecular Homologies are difficult due to the many different bases at many sites over different lengths.. due to insertions and deletions over time.

  • These insertions and deletions pose a challenge, however morphological similarities and computer programs can help to analyze genetic sequences and identify potential homologous relationships despite the variability.

    • Australian “mole” and golden moles → look similar but genetic differences are present.

    • Silversword plants → Morphologically different but genetically homologous.

  • “Distant” homologies versus coincidental matches → Another posed issue with molecular identification as bases can coincidentally align due to chance rather than shared ancestry.

Concept 26.3

Cladistics

  • Cladistics → Approach to systematics where common ancestry is primary criterion used to classify organisms.

    • Clades → groups of organisms that include a common ancestor and all its descendants, often represented in a branching tree-like diagram.

  • Monophyletic → a group of organisms that includes an ancestor and all of its descendants, forming a complete branch on the tree of life.

  • Paraphyletic (“beside the tribe”) → a group of organisms that includes a common ancestor but not all of its descendants, resulting in an incomplete branch on the tree of life.

    • Most common recent ancestor of all members of the group is part of the group.

    • Group consisting of even-toed ungulates and their common ancestor is paraphyletic because it does include cetaceans, which descended from the ancestor.

  • Polyphyletic (“many tribes”) → a group of organisms that does not include a common ancestor, instead comprising members from multiple evolutionary lineages, leading to an artificial grouping on the tree of life.

    • Group consisting of seals and cetaceans (based on similar morphologic features) is polyphyletic because it lacks a common ancestor, as seals and cetaceans evolved from different lineages despite exhibiting similar adaptations to aquatic environments.

Shared Ancestral and Shared Derived Characters

  • Shared ancestral character → Phenotypic character which originated in a ancestor of the taxon.

    • All mammals have backbones, but a backbone does not distinguish mammals from vertebrates.

  • Shared derived character → Phenotypic character that is unique to a particular clade and not found in other groups.

    • Hair is a an phenotypic character shared by all mammals but not found in their ancestors.

    • Shared derived character can also refer to an loss of a feature itself.

  • Outgroup → Species or group of species from evolutionary lineage closely related to but not part of the group of species being studied.

  • Ingroup → A group of species that are studied and are more closely related to each other than to any outgroup.

Maximum and Maximum Likelihood

  • Principle of Maximum Parsimony → We should investigate simplest explanation that is consistent with the facts.

    • Also called “Occam’s razor” after William of Occam, who shaved away unnecessary complications.

  • Principle of Maximum Likelihood → This principle suggests that the best model for the data is the one that maximizes the likelihood function, effectively providing the highest probability of observing the given data under the specified model.

  • Phylogenetic Trees are Hypotheses with ones with Maximum Likelihood to be most accurate.

    • Phylogenetic bracketing → method of predicting by parsimony, that features shared by two groups of closely related organisms are present in their common ancestor, thus enabling the inference of characteristics in extinct species based on their living relatives.

      • Dinosaurs!

Concept 26.4: Organism’s evolutionary history is documented in its genome.

  • Comparative anatomy → the study of similarities and differences in the anatomy of different species, which can reveal relationships between organisms and provide insights into their evolutionary paths.

  • Different genes can evolve at different rates, even in same evolutionary lineage. Meaning, molecular trees can represent long and short times.

    • DNA which encodes for ribosomal RNA (rRNA) changes slowly, therefore molecular trees using rRNA as a molecular marker would be long-term.

    • DNA which encodes for mitochondrial DNA (mtDNA) changes rapidly, therefore molecular trees using mtDNA are more recent.

Gene Duplication and Gene Families

  • Gene duplication can play important role in evolution due to it increasing genetic diversity by increased genes in genome.

  • Gene families → Groups of related genes within an organism’s genome.

    • Orthologous genes → Homology is result of speciation events and occurs within genes of different species.

      • Differences among orthologous genes reflect history of speciation events, making them powerful for phylogeny.

      • Cytochrome c genes in humans and dogs share same function.

    • Paralogous genes → Homology results from gene duplication that produces multiple copies of a gene within the same species, which may evolve new functions over time.

      • Example is Olfactory genes within rice and humans, which have duplicated several times to reach 380 functional gene receptors in humans.

Gene Evolution

  • Two forms of evolutionary lineages have emerged through genetic evolution.

  • First through Orthologous evolution, many species have diverged while sharing common genetic characters:

    • Humans and mouse lineages have separated about 65 million years ago, despite 99% of genes of human and mice being orthologous.

  • Second through Paralogous evolution, where gene duplications occur within a species, resulting in various functions and roles for the duplicated genes.

    • Humans have about four times as many genes as yeast and many human genes can encode multiple proteins at once.

Concept 26.5: Molecular clocks help track evolutionary time.

  • Molecular clock → an approach for measuring absolute time of evolutionary change based on observations that genes and proteins evolve at a constant rate over time.

  • Number of nucleotide substitutions in orthologous genes is proportional to he time that has elapsed since genes branched from their common ancestor.

  • Number of nucleotide substitutions in paralogous genes is proportional to time since ancestral gene was duplicated.

  • These average rates of genetic change can help fill in the gaps lacking in the fossil record.

  • Only show smooth average rate of change, deviations are frequent and these are never precise.

Differences in Clock Speed

  • Differences arise from the fact that some mutations are selectively neutral while others are beneficial or detrimental.

    • Harmful mutations are eliminated quickly while neutral (or little impact) mutations lack a significant impact on the organism's fitness, allowing them to persist in the population over time.

  • Clock rate is indicative of gene mutation’s significance in evolutionary processes; harmful/impactful ones have shorter clock rates.

Potential Issues with Molecular Clocks

  • Irregularities by natural selection in which DNA changes are favored over others can impact the accuracy of molecular clocks, leading to discrepancies in estimating evolutionary timelines.

    • Drosphila species, D. simulans and D. yakuba all have genes which were spurred by natural selection, despite having long clock rates.

  • Molecular clocks can over-span the fossil record and yield ages that do not align with the physical evidence of species emergence, further complicating our understanding of evolutionary relationships.

  • Problems can be avoided by calibrating molecular clocks with data on rates which genes have evolved in different taxa. In some cases, using many genes can help.

  • Despite broad period and problems mentioned, many molecular clocks do line up with fossil-based estimates.

Applying Molecular Clock to Origins of HIV

  • Most widespread strain in humans is HIV-1 M; Using samples collected from various times from 1959, molecular clocks have been established.

  • It appears when extrapolating backward in time, HIV-1 M first spread to humans around 1930 with another piece of suggesting 1910.

Concept 26.6

From Two Kingdoms to Three Domains

  • Original classification was: plants and animals; this changed late 1960s with five recognized kingdoms:

    • Monera (prokaryotes)

    • Protista (diverse kingdom consisting of mostly unicellular organisms)

    • Plantae → Plants

    • Fungi → eukaryotic organisms that decompose organic matter and include yeasts, molds, and mushrooms

    • Animalia → multicellular eukaryotic organisms that are typically motile and consume organic material for energy.

  • Three primary domains are present however:

    • Bacteria → contains majority of unicellular prokaryotic organisms.

    • Archaea → Diverse group of prokaryotic organisms which inhabit most of Earth.

    • Eukarya → Contains all organisms which contain a true nuclei such as plants, fungi and animals.

  • Modern systematists have completely voided recognition of Monera and Protista as separate kingdoms, favoring a more simple three kingdom system.

Horizontal Gene Transfer

  • Reconstruction of the tree of life is based in part on sequence comparisons of rRNA genes, which encode RNA components for ribosomes.

  • Horizontal gene Transfer → process in which genes are transferred from one genome to another through mechanisms such as:

    • Transformation: the uptake of naked DNA from the environment by a bacterium, allowing it to acquire new genetic traits.

    • Transduction: the process by which bacterial DNA is transferred from one bacterium to another by a virus (bacteriophage), which can lead to genetic variation in the recipient bacterium.

    • Conjugation: a method where genetic material is transferred directly between bacteria through physical contact, often via a pilus, enabling the sharing of plasmids.

  • Transferring specific genes can assist in survival of certain eukaryotes. Example is G. sulphuraria, which through transferred genes have acquired the ability to thrive in extreme environments.