Module 4 - Vertebrate Phylogeny
Vertebrate Phylogeny
Introduction
In 1835, a ship was anchored off the Galapagos Islands. Aboard that ship, the HMS
Beagle, was Charles Darwin, a man with a passion for natural history. He was about
to make an astonishing discovery while observing the island's wildlife, particularly
finches. These observations eventually led him to postulate that species evolve, that
is, they are derived from earlier species through transformation. It was in 1859 that
he presented in his book, “On the origin of species”, his theory of natural selection.
Darwin used the word ‘Phylogeny’ (created by Ernst Haeckel in 1866) for the first time
in the last edition (1872) of ‘On the origin of species’, and defined it as being the
"genealogical lineage of all organized' beings". Phylogenetic analysis is aimed at
determining the sequence and form of branching that occurred within the tree of
life. There has been tremendous progress in this area of research in the last thirty
years, due to the refinement of analytical methods and the appearance of new
databases (at the molecular level).
At present, phylogenetic research occupies a prominent position within the general
scope of evolutionary biology. This research is aimed at establishing the historic
framework governing the way living beings have descended from one another. Such
a historic framework is significant, because it promotes a better understanding of the
evolutionary processes responsible for today's biodiversity.
Your goal today will be to define what types of phylogenetic relationship link certain
species of vertebrates. These species are suitable representatives chosen from the
main groups of today's vertebrates. You will use the cladistic methodology to carry
out analysis. The purpose of this methodology is to define monophyletic groupings.
In order to establish monophyletism, the most convincing approach consists of
demonstrating that the members of a group share one or more characters that are
exclusive to them.
You must read and understand the appendices in this chapter before starting
the cladogram exercise. This exercise has been modified from a laboratory
approach to cladistic analysis by Brooks et al. (1994).
Methods
This module is divided into three phases:
1- You will make a series of morphological observations (12 characters) on nine
species.
1
,Module 4 - Vertebrate Phylogeny
2- You will code your observations of a matrix and use the lamprey as outgroup to
determine the polarization of characters (see Appendix A of this chapter for
explanations).
3- You will proceed with the phylogenetic analysis of your data. That is, based on the
information included in the coded matrix, you will construct a branching diagram
(cladogram).
1. Data Collection
One of the thrills of systematics is the discovery of characters that allow one to
explain parts of the tree of life. You will be assigned 12 characters that you will use in
your phylogenetic analysis. Your first task consists of finding the state of characters
in each of your nine assigned species. You will determine this information from
examining photographs of the specimens, reading the provided documents and
searching the internet.
Description of characters
The next paragraphs present the list of all characters included in our study. Each
character is briefly described, and the possible states for each character are
indicated (e.g. ‘Present’ and ‘Absent’).
Adult nephridial system (kidney type. In fish and amphibians, the functional
kidney (mesonephros or opistonephros) is found more posterior, draining via
tubules to a common mesonephric duct. In reptiles, birds and mammals, the adult
kidney (metanephros) is more posterior and empties via tubules into a common
ureter. Character states for this trait are: mesonephros (Ms) or metanephros (Mt).
Diagrams showing the different kidney types will be available in the laboratory.
Amnion. The amnion is an extra-embryonic membrane that forms the amniotic
cavity. Cells of the amnion secrete the amniotic fluid that provides the aquatic
environment necessary for the development of the embryo. Possible states for this
character are present (P) or absent (A).
Elimination of nitrogenous wastes. Vertebrates eliminate nitrogen mainly as 3
different forms: ammonia and ammonia salts, urea, or uric acid.
Ammonia excretion is common in aquatic vertebrates. Ammonia is soluble in water,
and a large quantity of water is required to eliminate it. On land, water conservation
is crucial, and nitrogenous waste is eliminated in a less toxic form requiring less
water: urea, or uric acid. Urea is the main product of nitrogen excretion in
amphibians and mammals but plays a role in osmoregulation of various other
species, such as sharks. In terrestrial turtles, lizards, snakes, crocodiles, and birds,
2
, Module 4 - Vertebrate Phylogeny
uric acid is the main nitrogenous excretion product. Compared to urea, uric acid can
be transformed into a salt that can be eliminated with very little water.
The states for this character are the following: ammonia (lamprey and bony fish),
urea (Chondrichthyes, amphibians, mammals) and uric acid (turtles, lizards, snakes,
crocodiles, birds).
Forelimbs modified for flight. The light bones of the anterior limbs are elongated,
reduced in number, resulting from fusion and always containing numerous air
cavities (pneumatized). Character states are modification present (P) or absent (A).
Gizzard. The stomach of some vertebrates has an area where food is broken down
by a thick muscular wall and by stones that it sometimes contains. Possible states for
this character are present (P) or absent (A).
Hair (or Fur). Possible states are: Present (P) or Absent (A).
Jaws. Jaws are used for biting, cutting and/or orienting a prey before it enters the
digestive tract. Vertebrates with jaws are gnathostomes; vertebrates without jaws are
agnathan. They may be either present (P) or absent (A).
Lungs and derived structures (swim bladder). In many vertebrates, the respiratory
exchanges occur mainly in the lungs, but some aquatic animals use structures
derived from the lungs (swim bladder) for flotation purposes. Character states for
lungs and derived structures are present (P) or absent (A).
Notochord (persistent or present at certain stage of development). An
elongated cellular and cartilaginous rod-like structure found dorsally in chordate
embryos. It sometimes persists into adulthood and provides axial skeletal support.
States are notochord present (P) or absent (A).
Number of digits on hind limb. Collect your information from diagrams and
specimens in the lab, as well as outside reference sources. If no hind limbs are
present, the number of digits is zero. Possible character states are 0, 4 or 5 digits.
Number of sacral vertebrae. The sacral vertebrae (the hip) act as an attachment
point for the pelvic girdle (posterior limbs). Possible states correspond to the
number of vertebrae: 0, 1, 2+.
Occipital condyle. A post-cranial protrusion (or bulge) that acts as the articulation
point for the spinal column. Animals that do not have a neck (no head movement in
relation to the thorax) do not have occipital condyles. Animals that do move or bend
their heads have one or two occipital condyles. Possible states for this character are:
0, 1 or 2 occipital condyles.
3
Vertebrate Phylogeny
Introduction
In 1835, a ship was anchored off the Galapagos Islands. Aboard that ship, the HMS
Beagle, was Charles Darwin, a man with a passion for natural history. He was about
to make an astonishing discovery while observing the island's wildlife, particularly
finches. These observations eventually led him to postulate that species evolve, that
is, they are derived from earlier species through transformation. It was in 1859 that
he presented in his book, “On the origin of species”, his theory of natural selection.
Darwin used the word ‘Phylogeny’ (created by Ernst Haeckel in 1866) for the first time
in the last edition (1872) of ‘On the origin of species’, and defined it as being the
"genealogical lineage of all organized' beings". Phylogenetic analysis is aimed at
determining the sequence and form of branching that occurred within the tree of
life. There has been tremendous progress in this area of research in the last thirty
years, due to the refinement of analytical methods and the appearance of new
databases (at the molecular level).
At present, phylogenetic research occupies a prominent position within the general
scope of evolutionary biology. This research is aimed at establishing the historic
framework governing the way living beings have descended from one another. Such
a historic framework is significant, because it promotes a better understanding of the
evolutionary processes responsible for today's biodiversity.
Your goal today will be to define what types of phylogenetic relationship link certain
species of vertebrates. These species are suitable representatives chosen from the
main groups of today's vertebrates. You will use the cladistic methodology to carry
out analysis. The purpose of this methodology is to define monophyletic groupings.
In order to establish monophyletism, the most convincing approach consists of
demonstrating that the members of a group share one or more characters that are
exclusive to them.
You must read and understand the appendices in this chapter before starting
the cladogram exercise. This exercise has been modified from a laboratory
approach to cladistic analysis by Brooks et al. (1994).
Methods
This module is divided into three phases:
1- You will make a series of morphological observations (12 characters) on nine
species.
1
,Module 4 - Vertebrate Phylogeny
2- You will code your observations of a matrix and use the lamprey as outgroup to
determine the polarization of characters (see Appendix A of this chapter for
explanations).
3- You will proceed with the phylogenetic analysis of your data. That is, based on the
information included in the coded matrix, you will construct a branching diagram
(cladogram).
1. Data Collection
One of the thrills of systematics is the discovery of characters that allow one to
explain parts of the tree of life. You will be assigned 12 characters that you will use in
your phylogenetic analysis. Your first task consists of finding the state of characters
in each of your nine assigned species. You will determine this information from
examining photographs of the specimens, reading the provided documents and
searching the internet.
Description of characters
The next paragraphs present the list of all characters included in our study. Each
character is briefly described, and the possible states for each character are
indicated (e.g. ‘Present’ and ‘Absent’).
Adult nephridial system (kidney type. In fish and amphibians, the functional
kidney (mesonephros or opistonephros) is found more posterior, draining via
tubules to a common mesonephric duct. In reptiles, birds and mammals, the adult
kidney (metanephros) is more posterior and empties via tubules into a common
ureter. Character states for this trait are: mesonephros (Ms) or metanephros (Mt).
Diagrams showing the different kidney types will be available in the laboratory.
Amnion. The amnion is an extra-embryonic membrane that forms the amniotic
cavity. Cells of the amnion secrete the amniotic fluid that provides the aquatic
environment necessary for the development of the embryo. Possible states for this
character are present (P) or absent (A).
Elimination of nitrogenous wastes. Vertebrates eliminate nitrogen mainly as 3
different forms: ammonia and ammonia salts, urea, or uric acid.
Ammonia excretion is common in aquatic vertebrates. Ammonia is soluble in water,
and a large quantity of water is required to eliminate it. On land, water conservation
is crucial, and nitrogenous waste is eliminated in a less toxic form requiring less
water: urea, or uric acid. Urea is the main product of nitrogen excretion in
amphibians and mammals but plays a role in osmoregulation of various other
species, such as sharks. In terrestrial turtles, lizards, snakes, crocodiles, and birds,
2
, Module 4 - Vertebrate Phylogeny
uric acid is the main nitrogenous excretion product. Compared to urea, uric acid can
be transformed into a salt that can be eliminated with very little water.
The states for this character are the following: ammonia (lamprey and bony fish),
urea (Chondrichthyes, amphibians, mammals) and uric acid (turtles, lizards, snakes,
crocodiles, birds).
Forelimbs modified for flight. The light bones of the anterior limbs are elongated,
reduced in number, resulting from fusion and always containing numerous air
cavities (pneumatized). Character states are modification present (P) or absent (A).
Gizzard. The stomach of some vertebrates has an area where food is broken down
by a thick muscular wall and by stones that it sometimes contains. Possible states for
this character are present (P) or absent (A).
Hair (or Fur). Possible states are: Present (P) or Absent (A).
Jaws. Jaws are used for biting, cutting and/or orienting a prey before it enters the
digestive tract. Vertebrates with jaws are gnathostomes; vertebrates without jaws are
agnathan. They may be either present (P) or absent (A).
Lungs and derived structures (swim bladder). In many vertebrates, the respiratory
exchanges occur mainly in the lungs, but some aquatic animals use structures
derived from the lungs (swim bladder) for flotation purposes. Character states for
lungs and derived structures are present (P) or absent (A).
Notochord (persistent or present at certain stage of development). An
elongated cellular and cartilaginous rod-like structure found dorsally in chordate
embryos. It sometimes persists into adulthood and provides axial skeletal support.
States are notochord present (P) or absent (A).
Number of digits on hind limb. Collect your information from diagrams and
specimens in the lab, as well as outside reference sources. If no hind limbs are
present, the number of digits is zero. Possible character states are 0, 4 or 5 digits.
Number of sacral vertebrae. The sacral vertebrae (the hip) act as an attachment
point for the pelvic girdle (posterior limbs). Possible states correspond to the
number of vertebrae: 0, 1, 2+.
Occipital condyle. A post-cranial protrusion (or bulge) that acts as the articulation
point for the spinal column. Animals that do not have a neck (no head movement in
relation to the thorax) do not have occipital condyles. Animals that do move or bend
their heads have one or two occipital condyles. Possible states for this character are:
0, 1 or 2 occipital condyles.
3
