Evolution & Phylogeny

The first amniote vertebrates appear in Pennsylvanian coal-measure deposits (~312–310 Mya). Within a few million years the lineage bifurcated into the two crown clades that dominate terrestrial tetrapod biology:

• Synapsida — a single temporal fenestra low on the skull; eventually leads through Therapsida and Cynodontia to modern Mammalia.
• Sauropsida (Reptilia sensu lato) — two temporal fenestrae (diapsid) or none (anapsid); includes all modern reptiles and birds.

The fenestrae are not ornamental; they are structural correlates of jaw-adductor geometry. Laurin & Reisz 1995 used skull fenestration together with vertebral and pelvic characters to anchor the sauropsid-synapsid split at roughly 312 Mya, close to Hylonomus and Paleothyris from the Joggins fossil forest (Nova Scotia).

Four extant reptile orders, plus the avian crown, are the descendants that survived the Permo-Triassic and K-Pg mass extinctions:

The turtle position was debated for decades. Molecular phylogenomics (Chiari 2012, Crawford 2015, Field 2014) now place Testudines as sister to Archosauria (crocodiles + birds), with their anapsid skull a secondary loss of fenestration.

Phylogenetically, birds are theropod dinosaurs. Any clade that excludes Aves but includes all other reptiles is therefore paraphyletic — it leaves out some descendants of the common ancestor. Cladistic convention demands monophyletic groups (all descendants of a common ancestor), so modern authors either:

• Use “Reptilia” in the traditional paraphyletic sense and note that it is not a clade.
• Redefine Reptilia to include Aves (the modern cladistic convention — Modesto & Anderson 2004).
• Use “Sauropsida” instead for the monophyletic birds + reptiles clade.

\[ \text{Amniota} \to \{\text{Synapsida},\ \text{Sauropsida}\},\quad \text{Sauropsida} \supset \text{Aves} \]

Throughout this course we use “reptile” to mean non-avian sauropsid, while acknowledging the cladistic nesting. M1–M8 focus on traits where non-avian reptiles differ substantially from birds: ectothermy, scales, squamate locomotion, and TSD.

The Mesozoic (252–66 Mya) is the classic “Age of Reptiles”: pseudosuchian archosaurs dominate the Triassic; dinosaurs (Ornithischia + Saurischia) take over by the Jurassic; pterosaurs radiate in the air; marine reptiles (ichthyosaurs, plesiosaurs, mosasaurs) dominate the seas; lepidosaurs (lizards + snakes) begin their own explosive radiation. The Chicxulub impact terminates non-avian dinosaurs, pterosaurs, ammonites, and most marine reptiles at 66.0 Mya (Schulte 2010, Renne 2013).

Survivors (Testudines, Squamata, Crocodylia, Sphenodon, Aves) share traits associated with small body size, burrowing or aquatic refugia, and broad dietary flexibility. Meredith 2011 phylogenomic timing confirms that the squamate crown radiated rapidly across the K-Pg boundary, recovering diversity within ~10 My.

Reptile genomes range from ~1.1 Gb (green anole, Alfoldi 2011) to ~3 Gb (crocodile, Green 2014), with chromosome numbers from 2n = 16 (some geckos) to 2n = 68 (some turtles). Micro- and macrochromosomes coexist; sex-determination systems vary widely across orders and sometimes within genera:

• ZW (female heterogamety) in most snakes and some lizards.
• XY (male heterogamety) in many skinks and geckos.
• TSD (temperature-dependent) in most turtles, all crocodilians, Sphenodon, and some lizards (M6).

This diversity makes reptiles the premier vertebrate group for studying sex- chromosome turnover, neofunctionalisation of sex-determining genes (DMRT1, SOX9, CIRBP), and the relationship between genetic and environmental sex determination.