Despite recent advances, key events in snake evolution have remained difficult to resolve, including their position in the squamate tree and several ingroup relationships. Comparative genomics has unrealised potential for phylogenetic inference and may advance understanding of snake evolution. This chapter reviews the history of snake molecular phylogenetics up to the current genomics revolution. This work has often corroborated phylogenetic inferences from morphology but also discovered relationships not previously considered or supported. We discuss properties of snake nuclear genomes, considering their potential for phylogenetic inference. Using data from 30 available squamate genomes, we provide preliminary examples applying both cumulative and non-cumulative frequency coding to genome size, GC content, and 14 repetitive element characteristics. Cumulative frequency coding outperforms non-cumulative coding and recovers most, but not all, well-known snake clades. We describe how the relationships of some snake lineages remains poorly supported despite their inclusion in large genomic-scale datasets, and suggest possible avenues of future research using comparative genomics.

This chapter assesses morphological characters proposed to support the Pythonomorph Hypothesis— a purported close relationship between snakes and mosasaurians. With an emphasis on early diverging (non-mosasaurid) mosasaurians and mosaurids, new morphological data (including from high-resolution CT) for well-preserved dolichosaurid and mosasaurid fossils are presented. Details of the skull and mandibles are interpreted as supporting the monophyly of Mosasauria as the proximal outgroup of Varanoidea, to the exclusion of snakes. However, mosasaurians do deviate from the typical varanoid condition in aspects of their infraorbital foramen, ventral part of the lacrimal and its relationship with the prefrontal, anterior ramus of the ectopterygoid and its contact with the maxilla and jugal, lack of plicidentine, and (at least in early diverging mosasaurians) anguinoidean tooth replacement. We consider most characters previously reported as supporting the Pythonomorph Hypothesis to be problematic, because of incomplete fossil preparation, artefacts of taphonomy, limited comparisons, misinterpretations of anatomy, incomplete taxon sampling, or inadequate character formulation and/or scoring.

Mosasaurian phylogenetics has been one of the most controversial topics in squamate systematics, with various studies and authors arguing in favor of a varanoid affinity (the Varanoid Hypothesis), a snake affinity (the Pythonomorph and Ophidiomorph Hypotheses) or only distant affinities to these lineages (the Stem-scleroglossan Hypothesis). We review the classification history of mosasaurians over the past two centuries, focusing on non-mosasaurid mosasaurians (dolichosaurs and aigialosaurs). A reappraisal is provided based on a new phylogenetic analysis. Our results clearly support the Varanoid Hypothesis. The Pythonomorph and Ophidiomorph Hypotheses are reviewed, and characters traditionally inferred to support these hypotheses are discussed and reinterpreted. Taxonomic sampling and fossil completeness likely play a major role—our (hopefully improved) phylogenetic hypothesis being based on denser taxon sampling and more complete character scoring resulting from additional studies, including the application of modern imaging techniques. Based on current data, our interpretation is that a particularly close phylogenetic relationship between mosasaurians and snakes can be rejected.

Pachyophiidae fossils are among the most complete known for snakes, and include the earliest snakes with fully developed hindlimbs. Pachyophiids have been historically seen as suitable morphological intermediates between lizards and extant snakes, supporting the hypothesis that snakes originated in a marine setting from a macrophagous common ancestor with mosasaurian lizards. Pachyophiids have been subject to conflicting interpretations of their anatomy, fuelling renewed debate on snake origins and early diversification. We revisit pachyophiid cranial anatomy, providing additional evidence from new preparations, high resolution CT scans, and Synchrotron images. We address challenges posed by fossil (in)completeness to the study and interpretation of these specimens, and reassess phylogenetic affinities. We critically reassess morphological evidence supporting the Marine Hypothesis, concluding that (i) snakes are not especially closely related to mosasaurians, and (ii) pachyophiids are relatively deeply nested within the snake crown, so that they are of greater importance for understanding early crown-snake evolutionary history than they are for understanding snake origins.

Our young and originally tropical species Homo sapiens has spread, in an amazingly short period of time, to occupy more areas of our planet than any other animal species has ever contrived to do. Human beings reside on all five continents, and in virtually every environment that those continents have to offer.

Like every one of the many millions of other organisms with which we share our planet, the species Homo sapiens is the product of a long evolutionary history. The first very simple cellular organisms spontaneously arose on Earth close to four billion years ago, and their descendants have since diversified to give us forms as different as streptococci, roses, sponges, anteaters, and ourselves.

A description of some of the methods used in racial genetics and genomics is essential if we are to understand why claims have been made that modern genomics establishes the existence of race.

As scientific knowledge increased, the outward physical variation of humans on this planet posed a mystery to natural historians, and begged explanation. Why were there so many different “kinds” of people on the planet? If scientists could understand how this variation worked in nature, then perhaps, the reasoning went, we could understand why people appear different.

Why do some researchers care so much about race in their experimental designs? It is easy to understand why a racist forced by inherent bias would take this approach. But why would a nonracist biologist insist on doing racial science? As far as we can tell, there are two major reasons for this: medical expediency and the discovery of the genetic basis of complex traits. We would suggest that the first of these is a red herring, and the second a brick wall.

Research prior to human genomics opened several doors to race-focused research, but the availability of genomes was a game-changer. As we pointed out in Chapter 4, there is nothing inherently wrong in using racial or ethnic boundaries as research tools for trying to discover biological patterns within the human species – if they are justified.

A big part of the story of our species, and of how variation is apportioned within it, involves how our ancestors spread over the globe. After all, if we had simply stayed in our place of origin in Africa and not ventured out, there would be no question that we are a single entity. That is because if our species had been restricted to a single location (as many others are), two things would have ensured that differentiation into separate entities would not have occurred.

Humans have been roaming around the planet since the very beginning, encountering other humans in the process and doubtless forming opinions about them. And since human beings seem to have an innate urge to classify everything – doing which, after all, lies at the core of our way of mentally organizing and understanding the world around us – there is little doubt that, from the earliest days, our symbolic forebears categorized each other in some way.

As the nineteenth century dawned, the idea that species might not forever remain as the Creator had made them was no longer unthinkable. At one end of the range of possibilities was Buffon’s limited notion of within-species change; at the other was Lamarck’s vision of lineages transforming themselves through inner impulse.

Compared to other primate groups, molecular genetic data for colobines are still limited and much of their phylogenetic relationships, particularly within genera, remain unknown. In recent years, however, more molecular genetic work has been done and revealed interesting and unexpected insights into colobine evolution. In this chapter, we review the current knowledge about colobine phylogeny and phylogeography, and present and discuss results from published and unpublished mitochondrial sequence data.