Introduction to Cladistics, the Vertebrata (Cuvier 1812)

Classification Methods By ecology By form By ancestry

Karl von Linné Carolus Linnaeus (1707-1778) In the dress of a native Sami of northern Scandinavia Linne is reference to a large lime tree near his ancestral home Latinized his name to Carolus Linnaeus

Linnaean System Created hierarchical system of classification Species defined as a binomial Systema Naturae (1735) first edition, began to use the binomial to delineate a species Species Plantarum (1753) is the starting point for all plant taxonomy

Hierarchical Taxonomy of Linnaeus THE RANKS OF OUR SPECIES KINGDOM: ANIMALIA (all living things that develop from a blastula) PHYLUM: VERTEBRATA (all animals that have articulated vertebrae) CLASS: MAMMALIA: (all vertebrates that have hair and feed their young with milk, have a single dentary and three bones in the middle ear) ORDER: PRIMATES (all mammals that have opposable thumbs, forward-facing eyes) FAMILY: HOMINIDAE (all primates that are large, >30-40 kg, tailless, and omnivorous, the Great Apes) GENUS: Homo (hominids that are bipedal with very fine body hair) SPECIES: Homo sapiens (a species of Homo that has a chin and small face)

Animal Kingdom

Vertebrates

Mammals

Primates

Hominidae Tree

Hominini Tree

Types of Clades Used in the Phylocode

Traditional organization of Vertebrate Taxonomy AGNATHA -Jawless Fishes CHONDRICHTHYES -Sharks, skates, rays and chimeras OSTEICHTHYES -Bony Fishes AMPHIBIA -Amphibians REPTILIA -Reptiles MAMMALIA -Mammals AVES -Birds

The cladistic interpretation is much more complicated than the Linnaean taxonomy would suggest. 1. Animals with a hollow dorsal nerve cord, notochord, and pharyngeal gill slits. 2. Brain encapsulated, or at least partially so, by a cartilaginous or bony cranium. Vertebrae, associated with or replace notochord. First duplication of genome (1R). 3. Loss of vertebrae. 4. Mineralized bone. Second duplication of the genome (2R). 5. Head shield of dermal bone; bony scales. 6. Paired spines or fins. 7. Neurocranium encloses brain dorsally. 8. Mouth formed by articulated jaws. 9. Teeth erupt from dental lamina. 10. Paired fin radials barely extend beyond body. 11. Gills covered by an operculum. 12. Pectoral and pelvic girdles anchored to vertebral column. 13. Digits reduced to 5 or fewer; radius as long as the ulna. Operculum lost. 14. Premaxilla less than 2/3 skull width. 15. Egg with an outer amnion membrane. 16. One temporal fenestra formed by the squamosal and jugal bones. 17. Large post-temporal fenestra; suborbital foramen in palate. 18. Two temporal fenestrae; upper one formed by the squamosal and postorbital bones. 19. Trunk ribs single-headed, end of humerus robust.

Cladistic definition of Vertebrata Vertebrates include all animals that possess a vertebral column and their descendants.

Common characters of Vertebrata Skeleton composed of cartilage or mineral tissue composed of hydroxyapatite in form of bone (with collagen matrix), dentine, and enamel Bilateral symmetry Head with multiple sense organs Brain and spinal cord (CNS, central nervous system) Skeleton supporting base of brain and body axis, usually elaborated more fully Segmented body axis with muscles Paired appendages1 Mouth, stomach, and gut Heart and circulatory system ventral to CNS Pharyngeal pouches with aortic arches (gill apparatus2) 1 in all jawed vertebrates and some extinct agnathans 2 gill apparatus in embryonic stages of amniotes David Polly (2013)

Vertebrates span the entire Phanerozoic Eon Era Period ended (MYA): began (MYA): P h a n e r o z o i c Cenozoic Holocene 0.0115 Pleistocene 1.806 Pliocene 5.332 Miocene 23.03 Oligocene 33.9 Eocene 55.8 Paleocene 65.5 Mesozoic Cretaceous 65.5 ± 0.3 145.5 ± 4.0 Jurassic 199.6 ± 0.6 Triassic 251.0 ± 0.4 Paleozoic Permian 299.0 ± 0.8 Carboniferous 359.2 ± 2.5 Devonian 416.0 ± 2.8 Silurian 443.7 ± 1.5 Ordovician 488.3 ± 1.7 Cambrian 542.0 ± 1.0 Vertebrates span the entire Phanerozoic

Origin of Vertebrates? From a chordate group that underwent whole genome duplication (WGD), a theory proposed by Susumu Ohno (1970), a Japanese- American (1928-2000). HOX clusters and their apparent duplications support the Ohno hypothesis (Soshnikova et al. 2013). Urochordates (sister-group to Vertebrata) have a single HOX cluster. Mice have 4 sets. Evolution of vertebrate Hox clusters and their functional specificities. In chordates, Hox genes are essential for the patterning of the neural tube and somites. In vertebrates, duplication of the ancestral Hox cluster led to the emergence of proximal appendages and nephrogenic structures. Furthermore, recruitment ofHoxA/B cluster is a key step in the development of complex vertebrate heart.

Cyclostomata (Dumeril 1806) Superclasses of the Cyclostomata are monophyletic as supported by molecular evidence (Stock and Whitt 1992, Kuraku et al. 1999, Delarbre et al. 2002, Furlong and Holland 2002, Mallatt and Sullivan 2002, and Heimberg et al. 2010) and morphological/developmental studies (Ota et al. 2007 and 2011, and Oisi et al. 2013). They lack jaws and paired appendages.   Myxinomorphi (Nelson 2006) Petromyzontomorphi (Nelson 2006)

4. Mineralized bone. Second duplication of the genome (2R). 1. Animals with a hollow dorsal nerve cord, notochord, and pharyngeal gill slits. 2. Brain encapsulated, or at least partially so, by a cartilaginous or bony cranium.  Vertebrae, associated with or replace notochord. First duplication of genome (1R). 3. Loss of vertebrae. 4. Mineralized bone. Second duplication of the genome (2R). 5. Head shield of dermal bone; bony scales. 6. Paired spines or fins. 7. Neurocranium encloses brain dorsally. 8. Mouth formed by articulated jaws. 9. Teeth erupt from dental lamina. 10. Paired fin radials barely extend beyond body. 11. Gills covered by an operculum. 12. Pectoral and pelvic girdles anchored to vertebral column. 13. Digits reduced to 5 or fewer; radius as long as the ulna.  Operculum lost. 14. Premaxilla less than 2/3 skull width. 15. Egg with an outer amnion membrane. 16. One temporal fenestra formed by the squamosal and jugal bones. 17. Large post-temporal fenestra; suborbital foramen in palate. 18. Two temporal fenestrae; upper one formed by the squamosal and postorbital bones. 19. Trunk ribs single-headed, end of humerus robust.

Stem gnathostomes, ‘Ostracoderms’ Paraphyletic group of 5 superclasses, all extinct Late Cambrian to Triassic, very diverse during the Devonian Nested taxa, mainly bottom- dwelling forms Most heavily armored with dermal bone Likely sifted the bottom mud for small animals Evolution of paired appendages Tails heterocercal, hypocercal, epicercal, diphycercal

Origin of the articulating jaw Mallatt (1996) Janvier (1996 & 2007) (Above) A sequence of events as presented by Janvier 1996a and 2007c.  The cartilaginous support for the velar skeleton as seen in the lamprey (and likely also occurring in the extinct armored agnathans) expanded forward in the mouth.  Muscles attached to the cartilaginous bars served to ventilate the gills and, perhaps to force more water over the gills to be filtered.  That structure then became co-opted as moveable jaws. (Right) A sequence of events as presented by Mallatt (1996) which shows the more classical theory of the development of the first gill arch to become the jaws (both upper and lower.  The internal gill arches typical of the more derived agnathans and the gnathostomes are segmented.  Mallatt suggests that the first gill arch moved forward in the mouth with muscles attached to bend the gill arch in order to serve as a more efficient gill ventilator than the velum.  The red is Meckel's cartilage.

Class Osteichthyes (Huxley 1880) The primitive condition in the Osteichthyes is the occurrence of a lung and a bony skeleton in the paired fins, producing a lobe-like base from which rays emerge.  The class is formed of two unequal clades (presented here as subclasses) defined by the structure of their paired fins: Actinopterygii (the ray-finned fishes) and the Sarcopterygii (the lobe-finned fishes).  Image from http://www.boundless.com

Class Osteichthyes (Huxley 1880) The teleost fishes seem to have undergone a third genome duplication (Glasauer and Neuhauss 2014; Volff 2005), which has driven their remarkable diversity Figure from Volff 2005

Class Osteichthyes (Huxley 1880) Sarcopterygii, the lobe-finned fishes Lobe-fin vs ray-fin appendicular skeletal structure

Class Osteichthyes (Huxley 1880) Lineage of late Devonian Sarcopterygii and transition to tetrapods A cladogram taken from Clack (2009).  The analysis was based on characters of the skull, axial and appendicular skeletons.  The structure of the tree is consistent with other analyses (e.g. Ruta et al. 2003 and Laurin 2002).  The presence of digits on the manus (hand) and pes (foot) marks the boundary between the sarcopterygian fishes and tetrapods.  That boundary was crossed between Tiktaalik and Ventastega.

The Devonian World

Class Stegocephali (Cope 1868) The name is derived from two Greek roots that mean roofed or covered head [roof -stege (στέγη); and head -kephale (κεφαλή)].  The basal tetrapods No defining structural synapomorphy other than digits Many species have gills, fish-like tails, fish-like teeth (on the palate) A drawing of Acanthostega (in the foreground) and Ichthyostega (background).  Acanthostega had legs that could not support its weight out of water and likely was a fully aquatic "fish with legs".   Image from: http://www.bertsgeschiedenissite.nl/geschiedenis%20aarde/devoon2.htm A drawing of Pederpes, one of the first tetrapods to be found in Romer's Gap (~360-345 MYA).  Its hind legs were situated so that the feet rested fully on the ground and pointed forward.  It was one of the first 'terrestrial tetrapods", though it likely spent most of its time in the water. Image by: DiDgd- Wikipedia