Phylogeny and the Tree of Life

Phylogeny and the Tree of Life: Overview

• Definition of Phylogeny: Phylogeny refers to the evolutionary relationship and history of a species or group of organisms.

• The Global Tree of Life: Biologists use highly resolved, automatically generated trees of life based on completely sequenced genomes to understand the history of all living things.

• Method of Categorization: Biologists distinguish and categorize the millions of species on Earth by using traits shared due to common ancestry. These classifications reflect evolutionary history.

• Interpreting Evolutionary History on a Tree:

  • Branch Points: A branch point represents the common ancestor of all the groups shown beyond that point.

  • Shared Characters: A hatch mark on a tree represents a character shared by the groups to the right of that mark.

  • Character Loss: Ancestors may possess a trait that is subsequently lost in specific lineages. For example, a common ancestor possessed limbs (as seen in geckos and iguanas), but these limbs were lost in lineages leading to snakes and glass lizards.

  • Sister Groups: Taxa that are each other's closest relatives (e.g., humans and chimpanzees) form a sister group.

Evolutionary Relationships and Convergent Evolution

• Basis of Phylogeny: Phylogenies are increasingly based on $DNA$ sequence data.

• Independent Evolution: DNA reveals that similar body forms can evolve independently from different ancestors. This is known as convergent evolution.

• Example (Fig. 26.1): Legless body forms evolved independently from legged ancestors in the lineages leading to both glass lizards and snakes.

• Homology vs. Analogy:

  • Homology: Similarities due to common ancestry. Classification is primarily based on these homologous traits.

  • Analogy: Similarities due to common adaptation or convergent evolution, rather than shared ancestry.

Problems with Common Names and the Binomial Solution

• Ambiguity of Common Names: The use of common names is inconsistent and confusing because:

  • A single organism can have different names across various languages, cultures, and geographical locations.

  • Example: The Puma ($Puma \, concolor$): This big cat has numerous names, including: puma, cougar, mountain lion, catamount, panther, painter, ghost cat, red tiger, poltroon tiger, sneak-cat, tiger, gray tiger, bender, mountain tiger, silver lion, Brazilian cat, Pampas-cat, deer tiger, Leon Bayo, Onca Parda, red lion, leopard, painther, tigre, ghost walker, purple panther, Rocky Mountain lion, Mexican lion, leon, California lion, yuma puma, gray lion, swamp devil, swamp screamer, white lion, southern panther, tall grass creeper, slough walker, night crier, tyger, carcajou, quincuajou, Carolina panther, and red panther.

  • Casual Group Names: Names like monkey, finch, bug, insect, butterfly, grass, trees, and big cats are too broad.

  • Inaccurate Names: Some names are biologically misleading, such as jellyfish (a cnidarian), crayfish (a crustacean), silverfish (an insect), and seahorses.

• The Universal Naming System: Proposed in $1753$ by Carolus Von Linnaeus ($1707$-$1778$), a Swedish naturalist.

  • Binomial Nomenclature: A system of latinized names consisting of two parts.

  • The Genus: The first part of the name (e.g., $Homo$); always starts with a capital letter.

  • The species/epithet: The second part of the name (e.g., $sapiens$); written in lowercase.

  • Formatting Rules: The name must be italicized when typing and underlined individually when handwriting.

Examples of Scientific Names and Subspecies

• Standard Binomial Examples:

  • Tiger: $Panthera \, tigris$

  • Lion: $Panthera \, leo$

  • Human: $Homo \, sapiens$

  • Orangutan: $Pongo \, abelii$

  • Northern Cardinal: $Cardinalis \, cardinalis$

• Elephants of the World:

  • African Elephants:

    • Forest Elephant ($Loxodonta \, cyclotis$)

    • Savannah Elephant ($Loxodonta \, africana$)

  • Asian Elephant: $Elephas \, maximus$

• Subspecies: Scientists recognize "regionally distinct groups" (morphologically and genetically) within a single species as subspecies. These are denoted by a third epithet (the subspecies name).

  • Asian Elephant Subspecies:

    1. Indian Elephant ($Elephas \, maximus \, indicus$): Widest range; accounts for the majority of remaining Asian elephants.

    2. Sumatran Elephant ($Elephas \, maximus \, sumatrensis$): The smallest subspecies.

    3. Sri Lankan Elephant ($Elephas \, maximus \, maximus$): The largest and darkest in color.

  • Northern Cardinal Subspecies: There are $19$ recognized subspecies of $Cardinalis \, cardinalis$ throughout its range.

Hierarchical Classification (The Linnaean Hierarchy)

• Linnaean System: Created by Carolus Von Linnaeus, this system places species into increasingly inclusive groups or "ranks."

• Taxon (plural, taxa): The named group at any level of the hierarchy.

• Hierarchy Levels (Least Inclusive to Most Inclusive):

  1. Species

  2. Genus

  3. Family

  4. Order

  5. Class

  6. Phylum

  7. Kingdom

  8. Domain

• Mnemonic: "Look, Did King Phillip Come Over For Green Salad?"

• Linking Classification and Phylogeny: The Linnaean hierarchy corresponds to the branching patterns seen in a phylogenetic tree.

• Limitations of Linnaean Classification:

  • It is based primarily on morphological characteristics.

  • Species in the same genus might not actually be closely related.

  • Unrelated species may be grouped together due to superficial similarities.

  • Related species might be separated if they have lost shared features.

  • Modern classifications rely more on precise characters, such as $DNA$ sequences, to produce better phylogenies.

Structural Components of Phylogenetic Trees

• Evolutionary Hypothesis: A phylogenetic tree is a hypothesis regarding evolutionary relationships.

• Terminology:

  • Evolutionary Lineage: A branch on the tree representing the history of a taxon.

  • Branch Point: Represents the divergence of two evolutionary lineages from a common ancestor.

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

  • Basal Taxon: A lineage that diverges from all other members of its group early in the history of that group.

• Tree Formats: Trees can be drawn horizontally, vertically, or diagonally without changing the relationships conveyed.

• Rotation of Branch Points: Rotating branches around a branch point does not change the evolutionary relationships. The order of taxa at the tips is not significant; the branching pattern (order of divergence) is what matters.

Evidence for Constructing Phylogenies

• Multisource Data: Information is gathered from morphology, genes, and biochemistry.

• Focus on Homology: Similarities due to shared ancestry are the only reliable basis for trees.

• Dangers of Analogy: Analogies arise from convergent evolution (similar adaptations to similar environments).

  • Example: The Australian mole (a marsupial) and the African golden mole (a placental) look very similar due to convergent evolution despite different lineages (Fig. 26.7).

  • Example: Bat and bird wings are homologous as forelimbs (sharing bone structure), but analogous as functional wings (since flight evolved independently); insect wings are entirely analogous to both.

Cladistics and Types of Taxonomic Groups

• Cladistics: The primary method for inferring phylogeny using common ancestry as the criterion.

• Clade: A group of species consisting of an ancestral species and all its descendants. Clades are nested within larger clades.

• Types of Groups (Fig. 26.10 & 26.11):

  • Monophyletic Group (Clade): Consists of an ancestral species and all its descendants.

  • Paraphyletic Group: Consists of an ancestral species and some, but not all, of its descendants. (e.g., a group excluding cetaceans from even-toed ungulates).

  • Polyphyletic Group: Includes distantly related species but does not include their most recent common ancestor.

Character Types and Tree Inference

• Shared Ancestral Character: A trait found in a clade that originated in an ancestor of the taxon (e.g., the backbone in mammals; it does not distinguish mammals from other vertebrates).

• Shared Derived Character: An evolutionary novelty unique to a particular clade (e.g., body hair in mammals, which distinguishes them from other vertebrates).

• Study Groups:

  • Ingroup: The species or group being studied.

  • Outgroup: A species or group closely related to the ingroup but not part of it, used as a basis for comparison to determine ancestral versus derived characters.

Branch Length Meaning and Phylogenetic Hypotheses

• Proportional Branch Lengths:

  • Genetic Change: In some trees, branch length represents the number of changes in a specific $DNA$ sequence. Longer branches indicate lineages where the gene evolved more rapidly (Fig. 26.13).

  • Geologic Time: Branches can be scaled to represent the time of existence or intervals of time based on fossil data. In these trees, all lineages have the same total length from the base to the tip, indicating equal time since divergence from a common ancestor (Fig. 26.14).

• Continual Revision: Phylogenies are hypotheses subject to modification based on new data.

• Avian Evolution Example (Fig. 26.16):

  • Hypothesis 1: Birds descended from theropods (bipedal dinosaurs). Supported.

  • Hypothesis 2: The closest living relatives of birds are crocodiles. Supported.

Questions & Discussion

• Q: What is the name of the big cat widely distributed in North and South America?

• A: It has dozens of names, including Puma, Cougar, and Mountain Lion, leading to the necessity of the scientific name $Puma \, concolor$.

• Q: How many sister taxa are shown in the horizontal, vertical, and diagonal trees?

• A: The transcript presents various tree forms and tasks the student with identifying sister groups, noting that the branching pattern remains identical regardless of orientation.

• Q: In which vertebrate lineage has the studied gene evolved most rapidly in Figure 26.13?

• A: This depends on identifying the longest branch length in a tree where length is proportional to the number of changes in a $DNA$ sequence.

• Q: What is the outgroup of the vertebrates in the tree in Figure 26.12?

• A: This requires identifying the lineage that diverged before the characters defining the vertebrate clade evolved.