Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule, with replacement rates established (calibrated) using paleontological age estimates from textbooks (e.g., Dodson 1960). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology. To capitalize on these opportunities, increasingly sophisticated divergence dating methods have been, and continue to be, developed. In contrast, comparatively, little attention has been devoted to critically assessing the paleontological and associated geological data used in divergence dating analyses. The lack of rigorous protocols for assigning calibrations based on fossils raises serious questions about the credibility of divergence dating results (e.g., Shaul and Graur 2002; Brochu et al. 2004; Graur and Martin 2004; Hedges and Kumar 2004; Reisz and Müller 2004a, 2004b; Theodor 2004; van Tuinen and Hadly 2004a, 2004b; van Tuinen et al. 2004; Benton and Donoghue 2007; Donoghue and Benton 2007; Parham and Irmis 2008; Ksepka 2009; Benton et al. 2009; Heads 2011).

Significance: Melanin is a widespread pigment that provides black to reddish brown hues to organisms. Recent evidence has shown that melanin is retained in exceptionally preserved fossils, including feathered dinosaurs, allowing the reconstruction of ancient color patterns. However, little is known about the chemical preservation of melanin or its distribution in the fossil record. Here, we show that melanin is preserved in a number of soft-bodied fossils, but its burial under high pressure and temperature for millions of years alters its original chemistry. The widespread occurrence of melanin substantiates the applicability of reconstructing aspects of original color patterns and allows us to dismiss the alternative suggestion that these structures are microbial in origin.

New elasmosaurid plesiosaur specimens are described from the Early Maastrichtian of Angola. Phylogenetic analyses reconstruct the Angolan taxon as an aristonectine elasmosaurid and the sister taxon of an unnamed form of similar age from New Zealand. Comparisons also indicate a close relationship with an unnamed form previously described from Patagonia. All of these specimens exhibit an ostensibly osteologically immature external morphology, but histological analysis of the Angolan material suggests an adult with paedomorphic traits. By extension, the similarity of the Angolan, New Zealand and Patagonian material indicates that these specimens represent a widespread paedomorphic yet unnamed taxon.

An interdisciplinary study of the archaeological landscape of the Trieste area (northeastern Italy), mainly based on airborne light detection and ranging (LiDAR), ground penetrating radar (GPR), and archaeological surveys, has led to the discovery of an early Roman fortification system, composed of a big central camp (San Rocco) flanked by two minor forts. The most ancient archaeological findings, including a Greco–Italic amphora rim produced in Latium or Campania, provide a relative chronology for the first installation of the structures between the end of the third century B.C. and the first decades of the second century B.C. whereas other materials, such as Lamboglia 2 amphorae and a military footwear hobnail (type D of Alesia), indicate that they maintained a strategic role at least up to the mid first century B.C. According to archaeological data and literary sources, the sites were probably established in connection with the Roman conquest of the Istria peninsula in 178–177 B.C. They were in use, perhaps not continuously, at least until the foundation of Tergeste, the ancestor of Trieste, in the mid first century B.C. The San Rocco site, with its exceptional size and imposing fortifications, is the main known Roman evidence of the Trieste area during this phase and could correspond to the location of the first settlement of Tergeste preceding the colony foundation. This hypothesis would also be supported by literary sources that describe it as a phrourion (Strabo, V, 1, 9, C 215), a term used by ancient writers to designate the fortifications of the Roman army.

Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for theMus/Rattussplit or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of theKarnimataclade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludesRattusand its relatives. Combining the new interpretation with the widely accepted hypothesis that theProgonomysclade includesMus, the lineage separation event in the Siwalik fossil record represents theMus/Arvicanthissplit. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating.