ch ecology

Flashcards cover phylogeny basics (taxa, in-group/out-group, monophyly, derived vs ancestral traits, nodes, sister taxa) and ecology basics (turnover, photic zones, autotrophs, energy transfer, and food webs) as described in the notes.

1. What is a Taxon in biological classification?

A taxon (plural: taxa, from Greek for 'arrangement group') is a formal name for any grouping of organisms at a specified level within the hierarchical system of biological classification. This system, originally developed by Carl Linnaeus, organizes biological diversity into ranks, providing a universal language for scientists. While the original Linnaean ranks included Kingdom, Phylum, Class, Order, Family, Genus, and Species, the higher rank of Domain was later added to reflect a more ancient split in the tree of life (e.g., Bacteria, Archaea, Eukaryota). Each taxon at any rank is intended to represent a meaningful evolutionary group, though this has evolved with our understanding of phylogeny.

2. What is Binomial Nomenclature?

Binomial nomenclature is the formal system for naming species, established by Carl Linnaeus. This system assigns a unique, two-part scientific name (a binomial) to every recognized species, ensuring clarity and universal recognition across different languages and regions. Its components are:

1. The Genus name (always capitalized), which describes the broader group to which the species belongs.
2. The specific epithet (never capitalized), which distinguishes the particular species within its genus.

For example, Homo sapiens refers to humans, where 'Homo' is the genus and 'sapiens' is the specific epithet. This system prevents confusion caused by common names and establishes a standardized scientific identity for each species, crucial for communication in taxonomy and biology.

3. What is Phylogeny?

Phylogeny is the study of the evolutionary history and relationships among groups of organisms. It serves as the conceptual framework and a set of analytical tools used to reconstruct the 'tree of life,' illustrating how different species and lineages have diverged from common ancestors over geological time. By analyzing shared characteristics (genetic, morphological, behavioral), phylogenetic studies aim to:

• Determine the ancestral relationships between species.
• Understand the timing and patterns of evolutionary diversification.
• Inform taxonomic classifications to better reflect evolutionary history.

Ultimately, phylogeny provides insights into the processes and products of evolution, connecting all life forms through shared ancestry.

4. What is the difference between an In-group and an Out-group in phylogenetic reconstruction?

In phylogenetic reconstruction (the process of building phylogenetic trees to understand evolutionary relationships), two key concepts are:

• In-group: This is the primary designated study group—the set of taxa (species or other taxonomic units) whose evolutionary relationships are the main focus of the phylogenetic analysis. The internal branches and nodes within the in-group reveal the evolutionary history and diversification of that specific group.
• Out-group: This is a strategically chosen taxon or set of taxa known to be distantly related to, but outside of, the in-group. The out-group is crucial because it serves as an external reference point. By understanding where the out-group branches off, researchers can reliably root the phylogenetic tree (determining the most ancient common ancestor of the in-group) and infer character state polarity (distinguishing between ancestral and derived traits within the in-group by comparison).

5. What is an Ancestral (Plesiomorphic) Trait and why is it not used for diagnosing monophyly?

An ancestral (plesiomorphic) trait is a character state that is shared with the out-group and is presumed to have been present in the last common ancestor of both the in-group and the out-group. It represents an older, primitive characteristic that has been inherited largely unchanged over long evolutionary periods.

An ancestral trait is not typically informative for defining specific relationships within the in-group or for diagnosing a unique monophyletic group (clade) because:

• It is a general characteristic shared across a broad evolutionary span.
• It does not represent a novel evolutionary event unique to the specific clade of interest.

For example, having five digits (pentadactyly) is an ancestral trait for amphibians, reptiles, and mammals. While they all possess it, it doesn't uniquely define the mammals; it was present in their much older common ancestor.

6. What is a Derived (Apomorphic) Trait and its crucial role in phylogeny?

A derived (apomorphic) trait is a character state that evolved within the in-group (or its immediate ancestor) and is not present in the out-group. These traits are evolutionary novelties—new characteristics that have arisen at a specific point in a lineage's history.

Derived traits are fundamental for defining monophyletic groups (also known as clades) because they:

• Indicate a shared, unique evolutionary history among the descendants of a particular common ancestor.
• Function as synapomorphies (shared derived characters) when present in two or more taxa within the in-group, providing strong evidence that these taxa share a more recent common ancestor with each other than with other groups.

For instance, the presence of mammary glands is a derived trait that defines mammals as a monophyletic group, as this characteristic evolved within the mammalian lineage and is exclusive to it among vertebrates.

7. Define Monophyly in phylogenetics and its significance.

Monophyly describes a group of organisms that accurately reflects true evolutionary history. A monophyletic group, also known as a clade, consists of:

• A Most Recent Common Ancestor (MRCA)
• All of its descendants, and only those descendants.

This means that every member of a monophyletic group shares a unique common ancestor that is not an ancestor to any organism outside the group. Monophyletic groups are considered the only natural groupings in phylogenetic classification because they represent complete evolutionary units. Classifying organisms into monophyletic groups ensures that our taxonomic system accurately mirrors the branching patterns of the tree of life, making it a cornerstone for understanding biodiversity and evolutionary relationships. The conceptual test for monophyly involves 'cutting' a single branch on a phylogenetic tree: if all organisms that 'fall off' form the group, and no others, it is monophyletic.

8. What is Non-monophyly in phylogenetics, and what are its types?

Non-monophyly refers to any grouping of organisms that does not accurately reflect true evolutionary history because it fails the complete descendant criterion of monophyly. These groups are considered artificial or unnatural in a phylogenetic context. Non-monophyletic groups are categorized into two main types:

1. Paraphyletic groups: These groups consist of a common ancestor but exclude some, but not all, of its descendants. A classic example is the traditional classification of 'Reptilia,' which includes most reptiles but excludes birds, even though birds evolved directly from reptilian ancestors. Because birds are descendants of the MRCA of reptiles, 'Reptilia' as traditionally defined is paraphyletic.
2. Polyphyletic groups: These groups consist of descendants from multiple different ancestors, often grouped together by superficial similarities (e.g., convergent traits) but do not include their true most recent common ancestor. An example might be 'warm-blooded animals,' which would include mammals and birds, but their immediate common ancestor was cold-blooded. This grouping does not reflect a shared, unique evolutionary origin for the 'warm-bloodedness' trait.

9. What are Sister Taxa?

Sister taxa are two taxa (or groups of taxa) that are each other's closest evolutionary relatives within a phylogenetic tree. They share an immediate common ancestor that is derived from a single speciation event and is not an ancestor to any other group depicted on that particular tree diagram. This means that a specific branching point (node) on the tree leads directly and exclusively to these two sister groups.

For example, if species A and species B diverge from a common ancestor that does not lead to any other depicted species, then A and B are sister taxa. This relationship indicates their particularly close and recent evolutionary divergence, making them invaluable for comparative studies aimed at understanding recent evolutionary changes, adaptations, and the mechanisms of speciation.

10. Why is choosing an Out-group important in phylogenetic analysis?

The careful selection of a strategically chosen out-group is critically important in phylogenetic analysis for several reasons:

1. Roots the phylogenetic tree: The out-group provides an external reference point, allowing researchers to determine the point of divergence between the in-group and a closely related, but distinct, lineage. This 'roots' the tree, establishing the true direction of evolutionary time and identifying the deepest split within the in-group.
2. Infers character state polarity: By comparing traits (characters) between the out-group and the in-group, researchers can distinguish between ancestral (plesiomorphic) traits (characteristics inherited from a distant common ancestor, shared with the out-group) and derived (apomorphic) traits (evolutionary novelties that originated within the in-group). This distinction is fundamental for identifying synapomorphies (shared derived traits) which are essential for defining monophyletic groups (clades) and reconstructing accurate evolutionary relationships.

Without a properly chosen out-group, it would be difficult to confidently interpret the evolutionary direction of character changes or to unambiguously root the phylogenetic tree, potentially leading to inaccurate hypotheses about evolutionary history.

11. In the vertebrate example, how are 'backbone' and 'lacking a backbone' classified as traits?

In the context of understanding the evolution of vertebrates:

• Having a backbone is considered a derived (apomorphic) trait for the vertebrate lineage. This is because the vertebral column is an evolutionary novelty that arose within this specific group, uniquely characterizing all vertebrates (fish, amphibians, reptiles, birds, mammals) and distinguishing them from all invertebrate groups. It represents a significant evolutionary innovation.
• Conversely, lacking a backbone is considered an ancestral (plesiomorphic) trait when considering the broader animal kingdom. This characteristic was present in the common ancestors of both vertebrates and all invertebrates long before the evolution of the vertebral column. Since it is a widespread, older characteristic shared by a vast array of life forms (including the out-group relative to vertebrates), it does not provide specific information to define or diagnose the vertebrate clade itself.

12. What does a Node on a phylogenetic tree represent?

A node on a phylogenetic tree is a critical interpretative element that represents a hypothesized Most Recent Common Ancestor (MRCA) of all the lineages that diverge from that specific point. It signifies a pivotal event in evolutionary history:

• A hypothetical ancestral population from which new lineages arose.
• A speciation event where one ancestral lineage split into two or more distinct descendant lineages (e.g., population subdivision leading to reproductive isolation).

Essentially, each node marks a point in the geological past where a common ancestor existed, and significant evolutionary divergence initiated. The placement and relationships of nodes illustrate the branching pattern of evolution. Time is generally understood to progress from the root of the tree (the oldest node, representing the deepest common ancestor of all taxa on the tree) outwards toward the tips or leaves (representing more recent or extant (living) taxa, or terminal extinct groups).

13. In simple terms, what are Apomorphies and Plesiomorphies?

In simple terms, when analyzing evolutionary traits:

• Apomorphies are derived traits—these are new characteristics or features that evolved within a specific lineage. They are unique to a particular group of organisms or to its immediate ancestor and are not found in more distant ancestors (or the out-group). Apomorphies are very useful for identifying and defining specific, younger evolutionary branches or clades, as they represent novel evolutionary events that unify a group of descendants.
• Plesiomorphies are ancestral traits—these are old characteristics or features that were inherited largely unchanged from a distant common ancestor. They are broadly shared across many different lineages, including the out-group, and thus they do not provide unique information to define or diagnose a particular, more recent evolutionary group. While they show shared ancestry, they don't delineate recent divergences.

14. How is a Monophyletic Group determined using a conceptual 'cut test' on a phylogenetic tree?

A monophyletic group (or clade), which includes a Most Recent Common Ancestor (MRCA) and all of its descendants, can be conceptually identified using a simple 'cut test' on a phylogenetic tree:

1. Imagine making a single 'cut' on any branch within a phylogenetic tree. This cut should isolate a single ancestral branch.
2. Observe which organisms 'fall off' as a result of that single cut.
3. If all the organisms that 'fall off' form the entire group you are considering, and no other organisms are included that did not 'fall off' with that cut (meaning no descendants of your MRCA are left behind), then the group is truly monophyletic.

This intuitive test ensures that the group is a complete, natural evolutionary unit, encompassing all lineages that trace back to an exclusive common ancestor without arbitrarily excluding any descendants or including unrelated groups. It directly verifies the fundamental definition of monophyly.

15. What is the significance of Sister Taxa in a phylogenetic tree for evolutionary studies?

The significance of sister taxa in a phylogenetic tree extends beyond simply knowing they are close relatives. Their importance lies in:

• Highlighting recent evolutionary events: Sister taxa represent the most recent divergence event from a unique common ancestor, making them ideal subjects for studying recent speciation processes, early adaptive radiations, and the initial stages of evolutionary change between closely related lineages.
• Facilitating comparative studies: Because sister taxa have shared a very recent common ancestor and have accumulated differences over a relatively short evolutionary time, comparing them can help pinpoint recent evolutionary changes (e.g., in morphology, genetics, behavior). This allows researchers to infer the sequence of character evolution and the mechanisms driving diversification more accurately.
• Testing evolutionary hypotheses: By examining sister group relationships, biologists can test hypotheses about character evolution, biogeography, co-evolutionary patterns, and the ecological factors that might have driven their divergence.

They serve as crucial reference points for understanding the fine-scale details of life's branching history.

16. Explain the Time Component of Phylogenetic Trees.

The time component of phylogenetic trees illustrates the evolutionary timeline, depicting the historical sequence of divergence events and the progression of life through geological time:

• Root to Tips Progression: Time is conventionally depicted as progressing from the root of the tree (representing the most ancient common ancestor of all taxa included in the tree) outwards towards the tips or leaves (representing current or most recent taxa, which may be extant species or terminal extinct groups).
• Nodes as Divergence Points: Each node on the tree signifies a specific point in the past where a common ancestor existed and a speciation event occurred, leading to the divergence of new lineages.
• Relative vs. Absolute Time: While all phylogenetic trees show the relative order of divergence events (which split happened before another), some trees are additionally scaled to show absolute geological time. These 'timetrees' use molecular clock calibrations and fossil evidence to place divergence events into a specific chronological framework (e.g., millions of years ago), providing a more precise historical perspective on evolutionary events.

17. What is the Linnaean Hierarchy?

The Linnaean Hierarchy is a foundational system of biological classification developed by Carl Linnaeus in the 18th century. It organizes organisms into a nested series of ranks, from broad, inclusive categories to more specific, exclusive ones, creating a structure that reflects presumed relationships (though modern phylogenetics has refined these views to reflect actual evolutionary history). The primary ranks in this hierarchy, from most inclusive to most exclusive, are:

• Domain (a later addition)
• Kingdom
• Phylum (or Division for plants/fungi)
• Class
• Order
• Family
• Genus
• Species

Each rank contains taxa that share certain common characteristics. This hierarchical structure provides a standardized way to categorize and understand the immense diversity of life on Earth, facilitating scientific communication and the organization of biological knowledge.

18. What are Terrestrial Organisms and what primarily determines their distribution?

Terrestrial organisms are living beings (plants, animals, fungi, microbes) that primarily inhabit and derive their resources from land environments. Their distribution at large geographical scales, and the characteristics of the communities they form (e.g., forests, grasslands, deserts), are primarily determined by climate. Specifically, the interaction of ambient temperature and precipitation levels are the most significant factors. These climatic factors dictate fundamental ecological conditions such as:

• The availability of water.
• The rate of evapotranspiration.
• The growing season length.
• The physiological stresses organisms face.

This strong dependence on climate means that terrestrial biomes, and the life within them, are often structured along climatic gradients.

19. What is Climate and its profound role as an abiotic determinant for terrestrial organisms?

Climate refers to the long-term, characteristic meteorological patterns (such as temperature, precipitation, humidity, wind) of a region over extended periods (typically 30 years or more). For terrestrial organisms, climate is a primary abiotic determinant—a non-living environmental factor—that profoundly shapes their distribution and the structure of ecological communities. Its role includes:

• Defining Biomes: The specific combinations of long-term temperature and precipitation dictate the formation of major terrestrial biomes (e.g., tropical rainforests, deserts, tundras, temperate forests). Each biome supports characteristic plant and animal communities uniquely adapted to those conditions.
• Influencing Physiological Processes: Climate directly impacts organismal physiology, affecting metabolic rates, reproductive cycles, and survival strategies.
• Resource Availability: It controls the availability of essential resources like water and influences soil characteristics, thus dictating which plant types can thrive, which in turn supports specific animal populations.

Therefore, understanding regional climate is essential for predicting species occurrences and ecosystem functions on land.