Constructing Phylogeny TreesUsing Synamorphies

IntroductionPhylogeny trees are a graphical tool used to reconstruct evolutionary history. These trees can be constructed by comparing the morphological or genetic similarities among a group of organisms. While genetic analysis is considered more reliable, morphology is often a quicker method to do an initial analysis and can be very useful in working with fossils that lack DNA for analysis.

When using morphology, the anatomical structures of the organisms are compared to find similarities. Morphological traits that are similar in structure among species are called synamorphies or homologous structures. Synamorphies are inferred to be the result of the species descending from a common ancestor that had the original trait. For example, if two organisms have a vertebrate column, it is likely because they are both descended from a common ancestor who had a spinal column.

Figure 1:Humans and gorillas share a large number of synamorphies (e.g. their skeletal structures). This suggests that humans and gorillas are related species and inherited these synamorphies from a common ancestor.Image source: https://commons.wikimedia.org/wiki/File:Primatenskelett-drawing.jpg

However synamorphies that have evolved from a common ancestor often look very different if they are examined superficially. This is because the structures have been adapted through evolution for a different function, environment or niche. An example of this is the forelimb of primates and birds.

Primate forelimbs are adapted for grasping whereas birds forelimbs are adapted for flying. Consequently the forelimbs of primates and birds look very different externally. However an internal examination of their limbs illustrates that they are composed of the same set of bones and muscles. Furthermore the embryonic development of these organisms show that their forelimbs are developed from the same embroyonic cell masses and involve similar gene sets.

Figure 2:The Forelimbs of all tetrapods (birds, reptiles, amphibians, mammals) develop from the same embryonic cell mass and involve the expression of similar development genes.Image source: https://embryology.med.unsw.edu.au/embryology/index.php/File:Stage14_somites_limbbuds.png

Synamorphies (homologous structures) that are adapted to different functions are inferred to be the result of divergent evolution. In divergent evolution, populations of a species evolve along different pathways leading to new species. In order for this speciation to occur, the populations of the species must have become reproductively isolated from each other.

Figure 3:The Forelimbs of primates and birds are homologous structures. Due to divergent evolution, the limb they inherited from their common ancestor has been adapted to very different functions.Edited Images from: http://evolution.berkeley.edu/evolibrary/search/imagedetail.php?id=390&topic_id%3D%26keywords%3D

When constructing phylogeny trees, the degree of relatedness among organisms is inferred by the number of homologous structures that they share. The more traits that are shared between two organisms, the more recent in time the two organisms shared a common ancestor. For example, the Table 1 illustrates that Humans share two of the studied traits with wolves but only one with salmon. Therefore it can be inferred that Humans are more closely related to wolves than salmon.

Table 1: Morphology of Compared Organisms

Human Tuna Horse

Forward Foramen Magnum

Present Absent Absent

Placenta Present Absent Present

Vertebrate column Present Present Present

Thus the inferred evolutionary relationship between humans, salmon and wolves can be illustrated on the following phylogeny tree (Figure 3):

Figure 3:This phylogeny tree shows that all three organisms are descended from a common ancestor (A) that had a backbone. However horses and humans are more closely related to each other than to tuna because they are both share a common ancestor (B). This can be inferred from the fact that they both have a placenta. It was assumed that tuna must have divergent from the horse and human lineages before the evolution of the placenta because tuna lack a placenta.

In a phylogeny tree descended species are the tips of the branches; synamorphies are shown by solid square boxes or dashes along the branches, and common ancestors that mark divergent evolution events are illustrated by open circles at the branching points in the tree.

Method1. Research the taxonomic breakdown of each of the following organisms:

Ambystoma maculatumChelydra serpentineEuplectella aspergillumHomo sapienLithobates catesbeianus

Macaca mulattaMacropus rufusPetromyzon marinusThunnus alalunga

2. Based on the taxonomic information you researched, determine which of the following structures are likely to exist in your each of your organisms given the following descriptions of various morphological traits:

An AmnionAn amnion is a membrane that forms around the embryo. It fills with fluid and contains a yolk sac to provide the developing fetus with nutrition in a protected environment. The evolution of the amnion was key in allowing tetrapods (four limbed creatures) to adapt to terrestrial habitats would otherwise have dehydrate their incubating fetuses.

The amnion is found in Mammals, Reptiles and Birds.

Figure 4:The aminon around Amniota fetuses provide them with protection and nutrition.Images source: https://upload.wikimedia.org/wikipedia/commons/thumb/2/20/Chicken_egg_diagram.svg/1200px-Chicken_egg_diagram.svg.png

Paired AppendagesPaired appendages include fins and limbs that show bilateral symmetry on either side of the spinal column of most extant Chordates. This arrangement of appendages has allowed the evolution of more controlled and effective mechanisms of motion (swimming, running, flying, etc.)Paired appendages are found in Gnathostomata which are the jawed vertebrates. Gnathostomata includes all most of the Chordates except hagfish and lampreys.

Figure 5:Gnathostomata have paired fins or limbs.Edited Images from:http://www.science20.com/news_articles/hox_gene_research_and_new_data_how_fish_grew_feet

Dorsal Nerve CordThe dorsal nerve cord is a hollow cord that develops early in embryonic development along the dorsal side of the embryo. In vertebrates this cord eventually develops into the spinal column and brain.

The dorsal nerve cord is unique to Chordates.

Figure 6:The dorsal nerve cord of vertebrates delevops into their brain and spinal cord.Images source:https://manoa.hawaii.edu/exploringourfluidearth/biological/invertebrates/phylum-chordata

Foramen Magnum Forward (near centre of skull)The foramen magnum is the hole through which the spinal column enters the skull. For most organisms the foramen magnum is at the back of the skull, however in fully erect bipedal organisms the foramen magnum is shifted to the centre of the bottom of the skull in order to allow the head to be held directly above a vertical spine.

The foramen magnum is forward in the Family Hominidae.

Figure 7:The foramen magnum is at the back of the skull in quadrupeds. It is under the skull but closer to the back in knuckle-walkers and neat the centre under the skull in bipedal creatures.Images source: http://www.biology-pages.info/P/Primates.html

Tetrapod LimbsThe tetrapod limbs are composed of four appendages: two upper limbs and two lower limbs. The internal structure of the limb is composed of a single long bone (the humerus) attached to two long bones (the radius and ulna) and followed by a series of smaller bones that form 5 digits in embryonic forms. The limb may be modified in the adult form of the organism (e.g. fewer digits).

Tetrapod limbs are found in the Classes Amphibian, Birds, Mammals reptiles Reptiles.

Figure 8:Tetrapod limbs are very diverse in their adaptations to various functions. However they show a similar skeletal structure suggesting that they have evolved from a common ancestor that possessed this limb design.Images source: http://evolution.berkeley.edu/evolibrary/article/homology_02

Mammary glandsMammary glands produce milk that allows organisms with this structure to feed their young after birth.

Mammary glands are unique to Mammals.

Figure 9:Mammals have specialized glands that produce milk for feeding their young offspring.Images source:http://www.hopkinsmedicine.org/healthlibrary/test_procedures/gynecology/mammogram_procedure_92,P07781/

NotochordThe notochord is a flexible cord that runs along from the head to the tail of the organism during fetal development. The notochord is important for the organization and attachment of muscles during fetal development in chordates. However, it is often not present in adult vertebrates because it becomes incorporated into the intervertebral discs that cushion the spinal column vertebrae.

The notochord is unique to Chordates.

Figure 10:The nortochord in vertebrates often becomes incorporated into the Intervertebral disc.Images source: https://commons.wikimedia.org/wiki/File:716_Intervertebral_Disk.jpg

PlacentaThe placenta is a temporary organ in most extant mammals that connects the fetus to the uterine wall. The primary function of this organ is to allow the diffusion of gases, nutrients and wastes between the fetus and the mother’s circulatory system.

Mammals that complete fetal development in an internal uterus have a placenta. These mammals do not lay eggs, nor do they have a pouch. Mammals with a placenta belong to the Mammalian Infraclass Placentalia.

Figure 11:The placenta is a highly vascularized organ that nourishes the fetus in the uterus of most mammals.Images source: https://embryology.med.unsw.edu.au/embryology/index.php/Placenta_Development

Vertebral ColumnThe vertebrate column is a series of bones that runs from the head to the tail of most chordate organisms. It encases and protects the spinal column.

The vertebral column is unique to vertebrates (a subphylum of chordates). Vertebrates include the Classes Amphibia, Birds (Aves), Fish, Mammalia and Reptilia.

Figure 12:The vertebral column of chordates runs from the base of the skull to the tail along the dorsal side of the organism. The vertebral column is composed of set of smaller bones called vertebrae.Images source: https://www.geol.umd.edu/~tholtz/G104/lectures/104anat.html

3. Finally, using your data, construct a phylogeny tree to illustrate the most plausible evolutionary relationship among your studied organisms.

Results

Table 2: Taxonomic Information Various Species

Ambystoma maculatum Chelydra serpentine Euplectella aspergillum

Kingdom

Phylum

Class

Order

Family

Genus

Species

Table 2: Taxonomic Information Various Species (Continued)

Homo sapienLithobates

catesbeianusMacaca mulatta

Kingdom

Phylum

Class

Order

Family

Genus

Species

Macropus rufus Petromyzon marinus Thunnus alalunga

Kingdom

Phylum

Class

Order

Family

Genus

Species

Table 3: Presence of Synamorphies in Organisms Studied

Scientific Name

Am

byst

oma

mac

ula

tum

Chel

ydra

se

rpen

tine

Eupl

ecte

lla

aspe

rgil

lu

Hom

o sa

pien

Lith

obat

es

cate

sbei

anus

Mac

aca

mul

atta

Mac

ropu

s ru

fus

Pet

rom

yzon

m

arin

us

Thu

nnu

s al

alu

nga

Common Name

Amnion present around embryo

Dorsal Nerve Cord

Foramen magnum forward(at centre of skull)

Mammary glands

Notochord

Paired appendages

Placenta

Tetrapod limbs

Vertebral column

Analysis

Figure 13: The Likely Evolutionary Relationship Among Organisms Studied

Research the taxonomic breakdown of Crotalus cerastes

Crotalus cerastes

Common name:

Kingdom

Phylum

Class

Order

Family

Genus

Species

Based on its taxonomic breakdown sketch the most likely position of Crotalus cerastes on your tree in Figure 13.

Based on its position on the tree, what expected morphological trait is missing from Crotalus cerastes?

Below is a fossil of an extinct snake species Tetrapodophis amplectus. Based on your analysis of this image, propose an explanation as to why Crotalus cerastes is missing an expected morphological trait.

Figure 14:Tetrapodophis amplectus fossil.Edited Images from: http://www.nature.com/news/four-legged-fossil-snake-is-a-world-first-1.18050