Difficulty: Intermediate | Prerequisites: Part 1 (Fundamentals) and Part 2 (Character Traits and Matrix)
This is the third and final part of the B130 Plant Diversity lab notes. It covers the construction of a phylogenetic tree from the character matrix, how to trace evolutionary trends across the tree, and the end-of-lab questions about correlated traits, convergent evolution, and adaptations to terrestrial life. You need Parts 1 and 2 sorted before tackling this.
The character matrix from Part 2 is fed into Mesquite to generate the most parsimonious phylogenetic tree. The tree shows green algae as the outgroup, with land plants forming a clade united by the cuticle and embryo retention. Within land plants, vascular tissue separates the bryophytes (liverworts, mosses) from the vascular plants (lycophytes, ferns, gymnosperms, angiosperms). Several traits evolved in correlated clusters, and heterospory is a classic example of convergent evolution in this dataset.
Phylogenetic tree
A branching diagram showing the inferred evolutionary relationships among a set of organisms. Each branching point (node) represents a common ancestor, and the tips represent the organisms being studied.
Most parsimonious tree
The tree that explains the observed character data with the fewest total evolutionary changes. Mesquite's heuristic search algorithm finds this tree.
Outgroup
The taxon placed outside the group of interest to root the tree. In this lab, green algae are the outgroup. Re-rooting the tree on the algae branch makes all other relationships fall into place relative to the ancestral condition.
Correlated traits
Two or more characters that change state at the same point on the tree. They may be functionally linked (for example, pollen and pollen tube sperm delivery evolve together because one enables the other).
Convergent evolution
The independent origin of similar traits in separate lineages. In this lab, heterospory is the primary example, having evolved independently in lycophytes, ferns, and the ancestor of seed plants.
Ancestral state
The character state present in the common ancestor. Determined by comparison with the outgroup. For most traits in this lab, the algal condition (0) is ancestral.
Derived state
A character state that differs from the ancestral condition. Shared derived states (synapomorphies) are the evidence used to group organisms together on a tree.
The tree is built from the character matrix (Part 2) using Mesquite's heuristic parsimony search. The steps:
Enter the character values for traits 1 to 14 into the Mesquite matrix editor.
Run the tree search: Taxa & Trees > Tree Inference > Tree Search > Mesquite Heuristic.
Re-root the resulting tree on the branch leading to green algae, making algae the outgroup.
Use Analysis > Trace Character History > Parsimony Ancestral States to map each character's evolutionary history onto the tree.
The most parsimonious tree typically groups the seven plant types as follows:
Green algae sit as the outgroup (the most distantly related to all land plants).
Liverworts branch off first among land plants.
Mosses branch off next.
Lycophytes and ferns form a group of seedless vascular plants (though their exact branching order can vary depending on character coding).
Gymnosperms and angiosperms group together as seed plants.
Algae from land plants: The cuticle (trait 1) and embryo care (trait 10) separate all land plants from green algae. All land plants retain and protect the developing sporophyte embryo inside the parent plant. Gas exchange regulation (trait 2) also changes at this node, from none to at least pores.
Non-vascular from vascular plants: Vascular tissue (trait 3) separates liverworts and mosses from lycophytes, ferns, gymnosperms, and angiosperms. Correlated with this: height greater than 5 cm (trait 5) and sporophyte dominance (trait 7) tend to appear alongside vascular tissue.
Seedless vascular from seed plants: Pollen (trait 6), pollen tube sperm (trait 11), spore retention (trait 12), always-present heterospory (trait 13 = 2), and seeds (trait 14) all appear together in the ancestor of gymnosperms and angiosperms. This is a heavily correlated cluster of traits.
Traits are correlated when they change at the same node on the tree. Key correlations from this lab:
Pollen (6), pollen tube sperm (11), spore retention (12), obligate heterospory (13 = 2), and seeds (14) all arise together at the base of seed plants. These traits are functionally linked: retaining spores inside the sporophyte is a prerequisite for seeds; pollen eliminates the need for free water; heterospory produces distinct male and female gametophytes.
Vascular tissue (3) and height greater than 5 cm (5) correlate: lignified xylem provides both transport and structural support.
Cuticle (1) and embryo care (10) correlate at the land plant node.
Heterospory (trait 13) is the clearest case of convergent evolution in this dataset. It appears "sometimes" (coded as 1) in lycophytes and ferns independently, and "always" (coded as 2) in seed plants. Because lycophytes and ferns are not each other's closest relatives, and neither is sister to seed plants in the simplest tree, heterospory likely evolved at least twice.
The end-of-lab questions ask you to connect specific traits to the challenges of living on land. Here is the mapping:
Challenge | Adaptation | How It Helps |
|---|---|---|
Water loss from exposed tissues | Cuticle (trait 1) | Waxy waterproof layer reduces evaporation |
Gas exchange blocked by cuticle | Stomata with guard cells (trait 2) | Adjustable pores let CO2 in and O2 out without excessive water loss |
Internal transport of water and nutrients | Vascular tissue (trait 3) | Xylem carries water/minerals, phloem carries sugars over long distances |
Structural support without buoyancy | Lignin in xylem cell walls | Rigid support allows upright growth on land |
Reproduction without standing water | Pollen and pollen tubes (traits 6, 11) | Sperm delivery without free water |
Embryo vulnerability in open air | Embryo retention (trait 10), seeds (trait 14) | Protection, nourishment, and dispersal of offspring |
Dispersal to new habitats | Seeds (trait 14) | Packaged embryo + nutrient store can survive transit and germinate in new locations |
Students often read a phylogenetic tree as a ladder of progress, with algae as "primitive" and angiosperms as "advanced." Every living group is equally evolved; they have simply adapted to different conditions. The tree shows relatedness, not a ranking.
Students sometimes think correlated traits must be caused by the same gene. Correlation on a tree means the traits changed at the same evolutionary node. They may be functionally linked, but the correlation could also be coincidental.
Students confuse "convergent" with "correlated." Correlated traits change at the same node on the tree. Convergent traits change at different, independent nodes to reach a similar state.
Students sometimes assume every trait on the tree evolved only once. Heterospory is the clear counterexample: it appears in multiple unrelated lineages.
True or false: On the phylogenetic tree, green algae are the ingroup. False. Green algae are the outgroup.
Fill in the blank: The principle of ___ states that the tree requiring the fewest evolutionary changes is preferred. Parsimony.
True or false: Heterospory evolved only once in plant evolution. False. It evolved independently multiple times (convergent evolution).
Fill in the blank: Traits that change at the same node on a phylogenetic tree are called ___ traits. Correlated.
True or false: Seeds, pollen, and pollen tube sperm all appear at the same node on the tree. True. They are correlated at the seed plant node.
Q: What characteristic(s) separate land plants from algae on the phylogenetic tree?
A: The cuticle (trait 1) and embryo care (trait 10) are the key synapomorphies uniting all land plants to the exclusion of algae. Gas exchange regulation (trait 2, from 0 to at least 1) also changes at this node.
Q: Name a set of correlated traits and explain why they might be functionally linked.
A: Pollen (6), pollen tube sperm (11), spore retention (12), obligate heterospory (13), and seeds (14) all appear at the seed plant node. They are functionally linked: retaining spores allows gametophytes to develop inside the sporophyte; separate male and female gametophytes (heterospory) are needed for pollen to work; pollen tubes deliver sperm without water; and seeds package the embryo for dispersal.
Q: Why is heterospory considered convergent rather than a single evolutionary event?
A: Heterospory appears in some lycophytes, some ferns, and all seed plants. These groups are not a single clade on the tree: lycophytes and ferns branch off separately from seed plants. The simplest explanation is that heterospory evolved independently at least twice.
Q: List three challenges that the transition from water to land posed for plants, and name the adaptation that addresses each.
A: (1) Water loss, addressed by the cuticle. (2) Gas exchange blocked by the cuticle, addressed by stomata with guard cells. (3) Reproduction without standing water, addressed by pollen and pollen tubes.
Q: Why do gymnosperms and angiosperms group together on the tree? Name the shared derived traits.
A: They share pollen (6), pollen tube sperm (11), spore retention (12), obligate heterospory (13 = 2), and seeds (14). These synapomorphies define the seed plant clade.
⚠️ The end-of-lab questions map directly to exam material. Be prepared to name which traits separate algae from land plants, which traits are correlated, and which trait(s) evolved convergently.
⚠️ The adaptations-to-challenges table is a high-value study target. Expect a question asking you to match a terrestrial challenge to the plant trait that solves it.
⚠️ Understand the difference between correlated and convergent. Correlated = same node. Convergent = different nodes, same outcome.
Phylogenetic tree construction connects to the earlier lab on building trees with Mesquite (character matrices, parsimony analysis). The reproductive traits covered here are explored in much greater detail in the Plant Reproduction lab, which walks through complete life cycles for mosses, ferns, gymnosperms, and angiosperms. The concept of convergent evolution recurs throughout B130 wherever analogous structures are discussed.
Phylogenetic tree, parsimony, most parsimonious tree, Mesquite, character matrix, outgroup, ingroup, re-rooting, ancestral state, derived state, synapomorphy, convergent evolution, correlated traits, B130, BIOL 130, plant diversity, green algae, liverwort, moss, lycophyte, fern, gymnosperm, angiosperm, seed plants, vascular plants, non-vascular plants, bryophytes, cuticle, stomata, vascular tissue, pollen, seeds, heterospory, terrestrial adaptations, selective pressures, land plants, alternation of generations, sporophyte, gametophyte