Biol 1030 Midterrm

What is taxonomy, and what are the taxa?

The scientific study and system of naming, classifying, and organizing species based on their shared characters, also showing how species are related to each other.

The taxa are kingdom, phylum, class, order, family, genus, and species.

Phylogeny

A graphical representation of relationships between organisms.

What do(es) a branching point, a pair of branches themselves, and any line in a phylogenic tree represent?

• A branching point reps a node, where the common ancestor is found.

• A pair of branches reps a dichotomy, repping speciation and divergence.

• A line reps traces of gradual change during evolutionary history of a sub-populations.

When you mix the systems of phylogeny and taxonomy together, where do smaller taxa appear and what do larger taxa contain? What are sister taxa?

• Smaller taxa are found at the fingertips, while bigger taxa can be akin to a hand with those fingertips.

• Sister taxa are taxa that share a recent common ancestor.

What are cladistics, and what are clades?

Method of organizing species into clades based on common characteristics, with the clades being groups of related organisms.

There are four important features of cladograms you oughta know, name ‘em and define ‘em.

• Outgroup, which is a closely related taxon but outside of the clade and where the clade diverged from.

• Basal taxon, which is the first of the clade to diverge.

• Shared ancestral characters, which are characters present in the clade and the outgroup.

• Shared derived characters, which are characters present in the clade but not the outgroup.

What are three common groups that can be grouped in clados? What does each consist of?

• Monophyletic groups, consisting of all related species and their common ancestor. (The whole hand.)

• Paraphyletic groups, consisting of a common ancestor and some of its descendants. (Some of the hand.)

• Polyphyletic groups, consisting of the descendants only. (Just the fingertips.)

What’s the diff. between clades and grades?

• Clades show common ancestry between species. Clades are tied to the concepts of homologous structures and divergent evolution.

• A pair of grades are similar shared derived characters between species that have no shared ancestral trait relationship between them. Grades are tied to the concepts of analogous structures and convergent evolution.

Each node represents a dichotomy if there is enough evidence. What is false about a polytomy?

A. The relationship between taxa within a polytomy is not well understood.

B. Species in a polytomy have shared evolutionary lineage.

C. Multiple species (taxa) diverge from a common ancestor.

D. There would be two taxa that diverge from a common ancestor.

D.There would be two taxa that diverge from a common ancestor.

Which of the following is true regarding the interpretation of phylogenetic trees?

A. We can't interpret any relationships.

B. The order of the taxa can be displayed (redrawn) multiple ways.

C. The order of nodes is not important.

D. The tips of the branches is important and can't be displayed in other ways.

B. The order of the taxa can be displayed (redrawn) multiple ways.

Regarding character (traits) in a phylogenetic trees, which of the following is false?

A. Characters are shared by all organisms in the phylogenetic tree.

B. Characters can be shared with ancestors.

C. Characters can be shared with other extant species.

D. Characters that are only found in the group you are interested in are in referred to as derived characteristics.

E. Characters that are found in the group you are interested in and in the common ancestor are referred to as ancestral characteristics.

A. Characters are shared by all organisms in the phylogenetic tree.

When adding traits to phylogenies, which of the following is true?

Question options:

A. Traits are only placed at the root of the tree.

B. The trait can only apply to one taxon.

C. All descendants after the tick mark, share the characteristic.

D. The location of character (trait) is not linked to the evolution of the trait.

C. All descendants after the tick mark, share the characteristic.

What are the 10 major phyla in the kingdom Animalia? Fun fact, Kingdom Animalia was once called Metazoa, due to multicellularity.

• Porifera

• Cnidaria

• Chordata

• Echinodermata

• Platyhelminthes

• Brachiopods

• Annelida

• Mollusca

• Nematoda

• Arthropoda

In the beginning, the eukaryotes diverged into two taxa, one being the animals and the other being the . . . ? What was the structure of this taxon, and what makes it different from animals?

Choanoflagellates, which were organisms that had a flagellum sticking through the collar-like structure composed of microvilli. They’re diff. from animals in a sense that they only had one cell, while animals had multiple cells.

Because choanoflagellates only had one cell, what do these choanoflagellates come in as a group? What’s the group called, rather?

A group of choanoflagellates is called a colony.

Cleavage

A series of mitotic cell divisions without cell growth between the divisions.

Blastulation

Multicellular stage in embryonic development to which the cleavage leads, wherein many animals take the form of a hollow ball.

Blastula

The hollow ball surrounding a fluid-filled cavity called the blastocoel.

Gastrulation

The next stage of embryonic development after blastulation wherein the blastula transforms into a gastrula.

Gastrula

The multilayered structure of cells, following gastrulation.

Archenteron

The pouch formed by gastrulation.

Blastopore

The first opening in the embryo and the point of invagination during gastrulation.

Organogenesis

The stage of embryonic development starting at the end of gastrulation and ending at birth, wherein the three germ layers form internal organs of organism.

Neurogenesis

The process wherein neurons are produced by neural stem cells that occurs heavily during embryonic development but continues after birth.

What two sets of traits help us organize and differentiate phyla? Provide the traits in each set.

• Morphological set of traits, which include symmetry, tissues, and body cavities.

• Developmental set of traits, which include cleavage and blastopore fate.

Animals with assymetry

Animals that do not have any internal plane of symmetry.

Animals with radial symmetry

Animals with multiple internal planes of symmetry; usually dipoblastic.

Animals with bilateral symmetry

Animals that have only one internal plane of symmetry; usually tripoblastic.

In animals with bilateral symmetry, what are the different sides of different axes?

• For the first axis, we have the anterior (front) side and the posterior (back) side.

• For the second axis, we have a right and left side.

• For the third axis, we have the dorsal (top) side and the ventral (bottom) side.

Cephalization

Evolutionary trend wherein sensory organs are concentrated to the head, present in nearly all animals with bilateral symmetry.

In animals with radial symmetry, what does the structure of multiple neurons look like? How about in animals with bilateral symmetry?

In radial symmetry, we have a network of neurons. In bilateral symmetry, we still get a network, but now we have clusterings of neurons, one small (ganglia) and one big (brains).

Why do animals with radial symmetry have a network of individual neurons, while animals with bilateral symmetry have a network of clustered neurons?

Animals with radial symmetry, i.e. cnidarians, have a network of individual neurons because, at the time and until now, it was advantageous and did not have any environmental pressure to make a network of clustered neurons. Meanwhile, animals with bilateral symmetry have the network of clustered neurons because they needed it at the time and until now.

What’s the advantage of having cephalization for bilaterally symmetric animals?

Shorter distance, faster response, more integration of body parts.

True tissue

A group of cells working towards a specialized goal and separated by protein membranes, wherein each cell needs each other to make this thang work.

Germ layer

Layer of cells formed after gastrulation, later transforming into various tissues and organs of the body.

Ectoderm

Outer germ layer covering the embryo, later on growing and remaining as the outer layer of animal and, in some phyla, the central nervous system.

Endoderm

Inner germ layer, lining the archenteron and giving rise to the lining of the digestive tract and organs such as the liver and lungs of vertebrates.

Mesoderm

Middle germ layer in between the endoderm and the ectoderm, giving rise to the muscles and most organs between the digestive tract and the outer covering of the animal.

Dipoblastic animals

Animals with two germ layers.

Tripoblastic animals

Animals with three germ layers.

Cavity

Fluid-filled spaces located between different tissue layers, supporting structure of body and a transport mechanism.

Coelom

Cavity between endoderm and ectoderm.

Hemocoel

Cavity between the endoderm and the mesoderm.

Acoelomates

Animals with no cavity, but using diffusion across their body’s surface as their transport mechanism.

The two main patterns of developmental traits are protostome development and deuterostome development. What’s the difference between ‘em?

Protostome development has the blastopore becoming the mouth, while deuterostome development has the blastopore becoming the anus.

There are two types of cleavage, one for each pattern of developmental traits in animals. Define both of ‘em, and tell me in which can you find each.

• Determinate cleavage refers to the cleavage wherein the functions of the cells have been set.

• Indeterminate cleavage refers to cleavage wherein the functions of the cells have not yet been set.

You can find determinate cleavage in protostomes, while you can find indeterminate cleavage in deuterostomes.

What is spiral cleavage, and what type of developmental cleavage is it tied to?

The geometrical cleavage tied to determinate cleavage, wherein the planes of cell division are diagonal to the vertical axis of the embryo.

What is radial cleavage, and what type of developmental cleavage is it tied to?

The geometrical cleavage tied to indeterminate cleavage, wherein the planes are either parallel or perpendicular to the vertical axis of the embryo.

You can skip this card, but I tried making a mnemonic for geo. cleavage, dev. cleavage, and what clade each are in. Ready?

Patron Silver Double! (Protostome → Spiral → Determinate)

Double Rum with lots of Ice! (Deuterostome → Radial → Indeterminate)

Segmentation

The repetition of body units present as an analogous character in the 3 of 10 phyla: chordata, annelida, arthropoda.

Dividing the Metazoa: Does it have true tissues?

If yes, Eumatozoa.

If no, Parazoa.

Dividing the Eumetazoa: Does it have radial symmetry?

If yes, “Radiata.”

If no, “Bilateria.”

Dividing the Bilateria: Is it a deuterostome?

If yes, Deuterostomia.

If no, Protostomia.

Dividing the Deuterostomia: Does it have a water vascular system?

If yes, Echinodermata.

If no, Chordata.

Dividing the Protostomia: Does it have continuous growth?

If yes, Lophotrochozoa.

If no, Ecdysozoa.

Dividing the Lophotrochozoa: What are its four phyla?

Platyhelminthes, Mollusca, Annelida, and Barchiopoda.

Dividing the Ecdysozoa: What are its two phyla?

Nematoda and Arthropoda.

Phylum Porifera

Also called the sponges, the basal taxon of the Metazoa, charactered by having two layers of cells but not true tissues. They exhibit random growth, and most are thus assymetrical.

Choanoderm

A type of cell layer composed of choanocytes.

What are choanocytes, what is their main function, and what does this tell us regarding the evolution and speciation of sponges?

Flagellated collar cells filtering food particles. These tell us that the sponges evolved from choanoflagellates.

Ostia

Pores for water to get in and out of the sponge.

Spongocoel

Large cavity at the centre of the sponges wherein water is placed after entry and is taken for exit.

Mesohyl

The gelatinous middle layer between the epidermis and choanoderm, consisting of cells and a skeleton.

Spicules

Tiny needles produced by amoeboid cells, serving as the skeleton.

Amoebocytes

Cells taking nutrients from food vacuoles of choanocytes, taking nutrients to other cells within sponge.

Porocytes

Cells helping water pass through ostia.

Phylum Cnidaria

Phylum charactered by radial symmetry, dipoblasticity, and presence of cnidocytes.

Cnidocyte

Explosive cells containing stinging organelles called nematocysts, acting like a harpoon.

In the Phylum Cnidaria, there are two clades. What are these two clades and what are the differences between the two?

• Clade Medusozoa, which can be in polyp and medusa form, with the latter meaning that their oral surface is down. They’re usually swimmers.

• Clade Anthozoa, with species always in polyp form, meaning their oral surface is up. They’re usually crawlers.

How do cnidarians reproduce?

Asexually by fission.

Gastrodermis

Inner layer of cells lining the gastrovascular cavity.

Mesoglea

Extracellular matrix functioning as a hydrostatic skeleton.

Phylum Echinodermata

Phylum charactered by being spiny-skinned deuterostomes with a water vascular system, bearing larvae exhibiting bilateral symmetry but most adults exhibiting pentaradial symmetry.

Ring canal

Circular water-filled tube, connecting to radial canals, functioning as a central hub for nutrient distribution and waste expulsion.

Water vascular system

System of tube feet, canals, smooth muscle generating water pressure, and chemical glue attaching to substrate.

Tube feet

Hydraulic structures functioning for locomotion, with each tube foot containing an ampulla, a small bulb-like structure.

How do echinoderms move?

Ampullae sucks water into the tube foot, stretching the tube foot, and muscles in the tube foot contract to shorten them, pulling the animal along.

What’s a madreporite? And what is the order of how water enters the echinoderm?

Tiny plate at the centre of the echinoderm, allowing water inside.

Water flows to the madreporite, to the stone canal, to the ring canal, to the radial canal, and to the tube feet.

Stone canal

Tubular structure connecting madreporite to ring canal.

Hepatic caeca

Literally meaning “liver-like gut,” they are the digestive glands of echinoderms.

Echinoderm’s cardiac stomach

Part of digestive system turning inside out through its mouth to engulf and digest prey.

Echinoderm’s pyloric stomach

Part of digestive system where food is transferred after its placement in cardiac stomach.

How do echinoderms eat, digest, and expel waste?

Food enters mouth, goes to hepatic caeca for breakdown, and waste is expelled out the anus.

How do echinoderms reproduce?

Sexually and asexually by fission.

There are 3 clades within the phylum Echinodermata. Name them and differentiate them.

• Clade Asteroidea, wherein Ec looks like a star.

• Clade Echinoidea, wherein Ec looks like a spiney sphere.

• Clade Holothuroidea, wherein Ec has modified tube feet for physical intimidation. They don’t use it much for physical defense.

Phylum Chordata

Phylum charactered by their notochord, dorsal hollow nerve chord, pharyngeal gill slits, and post-anal tail.

What’s the difference between the gills, the gill slits, and the gill arches?

• Gills are respiratory organs found in aquatic animals that extract oxygen from water and release carbon dioxide.

• Gill slits are individual openings to gills.

• Gill arches are skeletal structures, supporting the gills.

Define each of the four anatomical features in chordates.

• The notochord provides skeletal support, developing into the vertebral column in vertebrates.

• The dorsal hollow nerve cord develops into the central nervous system.

• The gill slits are openings in the pharynx that, commonly: (a) in invertebrate aquatic chordates, filters water; (b) in vertebrate aquatic chordates, develop into gill arches, such as in bony fish, and; (c) in terrestrial animals, develops into the jaw and inner ear bone.

• The post-anal tail is a muscular region of the body aiding locomotion and balance.

Pharynx

The region leading from the mouth and nose to the esophagus and larynx.

Cephalochordata

Chordata clade made of the lancelets, they are small, fish-like animals that are the only chordates retaining the big four throughout their life.

Urochordata

Chordata clade made of the tunicates or “sea squirts,” they possess the big four during their larval stage but only keep the gill slits during their adult stage, modifying the slits into a pharyngeal basket to filter water and food particles.

Vertebrata

Chordata clade composing most of the phylum, charactered by a vertebral column and cranium.

What are cyclostomes? Provide 2 examples of a cyclostome.

Basal vertebrate clade, possessing a circular mouth with no jaws, capability of producing slime through slime glands as defence mechanism, and capability of absorbing nutrients using their skin. E.g. hagfish and lampreys.

Gnathostomes

Vertebrate clade possessing hinged jaws from gill arches to capture prey.

Chondrichthyans

Basal gnathostome clade, possessing skeletons made of cartilage, e.g. ratfishes, rays, and sharks.

Osteichthyans

Gnathostome clade with bones and lungs, with the first forming a skeleton hardened with calcium phosphate and the latter evolving to take oxygen from air when it was scarce in water.

Actinopterygians

Basal osteichthyan clade with fishes that have rayed and upgraded, membranous fins.

Sarcopterygians

Osteichthyan clade with fishes that have lobed and fleshy fins.

Tetrapods

Osteichthyan paraphyletic group, possessing four limbs, composed of the amphibians, reptiles, and mammals

Amphibians

Basal tetrapod clade that walked on land but still needed water in which to deposit their eggs.