When asked for an example of “paraphyly”, the easiest case to give is that of reptiles. The clade “Reptilia” classically comprises the turtles, lizards, snakes, crocodiles, and dinosaurs, and leaves birds out – even though birds are dinosaurs. So unless you explicitly state that you count birds as reptiles, you’re talking of a paraphyletic taxon. The correct name for the clade, Reptilia including birds, is Sauropsida (although they are nowadays used synonymously).
The sister group to the Sauropsida is the Synapsida (extant members are the mammals), both clades making up the Amniota (the vertebrates with an amniotic egg). The fundamental split between them occurred in the mid-Carboniferous (see here for the context), with the earliest fossil representative of a divergence being the 313 Ma (Upper Carboniferous) Hylonomus (Benton & Donoghue, 2007).
The Sauropsida itself is conclusively monophyletic thanks to several cranial autapomorphies and a variety of physiological characteristics (Benton, 1990); some autapomorphies are listed below:
- Reduced tabular bone (in skull).
- Reduced supratemporal bone (in skull).
- Anterior crista on the supraoccipital bone (in skull).
- Temporal opening beneath the eye.
- Single coronoid in the lower jaw.
- First two vertebrae fused.
- Muscles of the iris are striated, not smooth.
As the cladogram above (modified from Benton, 2005) shows, the Sauropsida consists of the Diapsida (extant members are lizards, snakes, dinosaurs, crocs…) and Anapsida (extant members are the turtles), and a whole range of Permian species, both belonging on the stems and representatives of now-extinct clades. The fossil record shows that the anapsids are more ancestral, as the earliest sauropsidan fossils have the anapsid skull – i.e. lacking the typical temporal openings. Diapsids have two temporal openings, synapsids have one.
The importance of these temporal openings in the evolution of the amniotes, and especially the diapsids, shouldn’t be underestimated: these are spaces for muscles and nerves to go through, and are responsible for the diversification of the amniotes by giving them the ability to exploit more diverse sources of food.
The position of the turtles is one of the greater controversies in higher-level vertebrate phylogenetics. Nobody doubts that they are sauropsids – this was proposed as early as Goodrich (1916), based on the characteristic morphology of the heart and on the hooked fifth metatarsal. Given that, like the earliest sauropsidan fossils, they’re anapsids, they’re placed as the sister to the rest of the sauropsids; this is also supported by developmental biology (Werneburg & Sánchez-Villagra, 2009). However, another hypothesis states that turtles specifically lost their temporal openings secondarily, making them a taxon within the diapsids. As far as I know, no consensus has yet been reached on this matter and it’s still an open question.
The crown-group of the Diapsida is known from as early as the Permian (270 Ma), and is split into two clades: the Lepidosauria (snakes, lizards) and the Archosauria (crocs, dinos). Another big question mark concerns the extinct swimming reptiles – ichthyosaurs, plesiosaurs, placodonts, and nothosaurs, and their position within the diapsid system. They all returned secondarily to the oceans, but they are so derived that no synapomorphies with any of the known groups of diapsid can be conclusively determined.
The Lepidosauria include the Squamata, a monophyletic clade that includes lizards, snakes and amphisbaenians, and characterised by a highly-modified flexible skull. It originated in the Jurassic, and the modern diversity is extremely interesting from a comparative viewpoint: limbs have become lost 25 times independently in the squamates (Wiens et al., 2006), viviparity’s evolved convergently over 100 times (Lee & Shine, 1998), with some lizards even having a sort of placental system going (Flemming & Blackburn, 2003).
The only living members of the Archosauria are the birds and the crocodiles, a definite reduction in diversity compared to their past dominance.
A proper look at this clade would have involved the entire fossil record and stem species, but this post is nothing more than an expansion from a conversation where I was explaining the concept of paraphyly :)
Benton MJ. 1990. Phylogeny of the major tetrapod groups: Morphological data and divergence dates. Journal of Molecular Evolution 30, 409-424.
Benton MJ. 2005. Vertebrate Palaeontology.
Benton MJ & Donoghue PCJ. 2007. Paleontological Evidence to Date the Tree of Life. Molecular Biology and Evolution 24, 26-53.
Flemming AF & Blackburn DG. 2003. Evolution of placental specializations in viviparous African and South American lizards. Journal of Experimental Zoology A 299, 33-47.
Goodrich ES. 1916. On the Classification of the Reptilia. Proc. R. Soc. B 89, 261-276.
Lee MSY & Shine R. 1998. Reptilian Viviparity and Dollo’s Law. Evolution 52, 1441-1450.
Werneburg I & Sánchez-Villagra MR. 2009. Timing of organogenesis support basal position of turtles in the amniote tree of life. BMC Evolutionary Biology 9, 82.
Wiens JJ, Brandley MC & Reeder TW. 2006. WHY DOES A TRAIT EVOLVE MULTIPLE TIMES WITHIN A CLADE? REPEATED EVOLUTION OF SNAKELINE BODY FORM IN SQUAMATE REPTILES. Evolution 60, 123-141.