John A. Finarelli

Acanthodes and shark-like conditions in the last common ancestor of modern gnathostomes

Acanthodians, an exclusively Palaeozoic group of fish, are central to a renewed debate on the origin of modern gnathostomes: jawed vertebrates comprising Chondrichthyes (sharks, rays and ratfish) and Osteichthyes (bony fishes and tetrapods). Acanthodian internal anatomy is primarily understood from Acanthodes bronni because it remains the only example preserved in substantial detail, central to which is an ostensibly osteichthyan braincase. For this reason, Acanthodes has become an indispensible component in early gnathostome phylogenies. Here we present a new description of the Acanthodes braincase, yielding new details of external and internal morphology, notably the regions surrounding and within the ear capsule and neurocranial roof. These data contribute to a new reconstruction that, unexpectedly, resembles early chondrichthyan crania. Principal coordinates analysis of a character–taxon matrix including these new data confirms this impression: Acanthodes is quantifiably closer to chondrichthyans than to osteichthyans. However, phylogenetic analysis places Acanthodes on the osteichthyan stem, as part of a well-resolved tree that also recovers acanthodians as stem chondrichthyans and stem gnathostomes. As such, perceived chondrichthyan features of the Acanthodes cranium represent shared primitive conditions for crown group gnathostomes. Moreover, this increasingly detailed picture of early gnathostome evolution highlights ongoing and profound anatomical reorganization of vertebrate crania after the origin of jaws but before the divergence of living clades.

Brain-size evolution and sociality in Carnivora

Increased encephalization, or larger brain volume relative to body mass, is a repeated theme in vertebrate evolution. Here we present an extensive sampling of relative brain sizes in fossil and extant taxa in the mammalian order Carnivora (cats, dogs, bears, weasels, and their relatives). By using Akaike Information Criterion model selection and endocranial volume and body mass data for 289 species (including 125 fossil taxa), we document clade-specific evolutionary transformations in encephalization allometries. These evolutionary transformations include multiple independent encephalization increases and decreases in addition to a remarkably static basal Carnivora allometry that characterizes much of the suborder Feliformia and some taxa in the suborder Caniformia across much of their evolutionary history, emphasizing that complex processes shaped the modern distribution of encephalization across Carnivora. This analysis also permits critical evaluation of the social brain hypothesis (SBH), which predicts a close association between sociality and increased encephalization. Previous analyses based on living species alone appeared to support the SBH with respect to Carnivora, but those results are entirely dependent on data from modern Canidae (dogs). Incorporation of fossil data further reveals that no association exists between sociality and encephalization across Carnivora and that support for sociality as a causal agent of encephalization increase disappears for this clade.

Graphite and carbonates in the 3.8 Ga old Isua Supracrustal Belt, southern West Greenland

We present a systematic study of abundance, isotopic composition and petrographic associations of graphite in rocks from the ca. 3.8 Ga Isua Supracrustal Belt (ISB) in southern West Greenland. Most of the graphite in the ISB occurs in carbonate-rich metasomatic rocks (metacarbonates) while sedimentary units, including banded iron formations (BIFs) and metacherts, have exceedingly low graphite concentrations. Regardless of isotopic composition of graphite in metacarbonate rocks, their secondary origin disqualifies them from providing evidence for traces of life stemming from 3.8 Ga. Recognition of the secondary origin of Isua metacarbonates thus calls for reevaluation of earlier interpretations that suggested the occurrence of 3.8 Ga biogenic graphite in these rocks. Thermal decomposition of siderite; 6FeCO3 = 2Fe3O4 + 5CO2 + C, is the process seemingly responsible for the graphite formation. The cation composition (Fe, Mg, Mn, and Ca) of the carbonate minerals, carbon isotope ratios of carbonates and associated graphite and petrographic assemblages of a suite of metacarbonates support the conclusion that multiple pulses of metasomatism affected the ISB, causing the deposition of Fe-bearing carbonates and subsequent partial disproportionation to graphite and magnetite. Equilibrium isotope fractionation between carbonate and graphite in the rocks indicates peak metamorphic temperatures between 500 and 600 ◦ C, in agreement with other estimates of metamorphic temperature for the ISB.

The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness from Low Coverage Homozygous Genomes

Thomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison’s grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent’s DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as “forced homozygote approach”. The results were confirmed using simulated data for different relatedness classes. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.

Diversity dynamics of Miocene mammals in relation to the history of tectonism and climate

Continental biodiversity gradients result not only from ecological processes, but also from evolutionary and geohistorical processes involving biotic turnover in landscape and climatic history over millions of years. Here, we investigate the evolutionary and historical contributions to the gradient of increasing species richness with topographic complexity. We analysed a dataset of 418 fossil rodent species from western North America spanning 25 to 5 Ma. We compared diversification histories between tectonically active (Intermontane West) and quiescent (Great Plains) regions. Although diversification histories differed between the two regions, species richness, origination rate and extinction rate per million years were not systematically different over the 20 Myr interval. In the tectonically active region, the greatest increase in originations coincided with a Middle Miocene episode of intensified tectonic activity and global warming. During subsequent global cooling, species richness declined in the montane region and increased on the Great Plains. These results suggest that interactions between tectonic activity and climate change stimulate diversification in mammals. The elevational diversity gradient characteristic of modern mammalian faunas was not a persistent feature over geologic time. Rather, the Miocene rodent record suggests that the elevational diversity gradient is a transient feature arising during particular episodes of Earths history.

Congruence of morphologically-defined genera with molecular phylogenies

Morphologically-defined mammalian and molluscan genera (herein “morphogenera”) are significantly more likely to be monophyletic relative to molecular phylogenies than random, under 3 different models of expected monophyly rates: ≈63% of 425 surveyed morphogenera are monophyletic and 19% are polyphyletic, although certain groups appear to be problematic (e.g., nonmarine, unionoid bivalves). Compiled nonmonophyly rates are probably extreme values, because molecular analyses have focused on “problem” taxa, and molecular topologies (treated herein as error-free) contain contradictory groupings across analyses for 10% of molluscan morphogenera and 37% of mammalian morphogenera. Both body size and geographic range, 2 key macroevolutionary and macroecological variables, show significant rank correlations between values for morphogenera and molecularly-defined clades, even when strictly monophyletic morphogenera are excluded from analyses. Thus, although morphogenera can be imperfect reflections of phylogeny, large-scale statistical treatments of diversity dynamics or macroevolutionary variables in time and space are unlikely to be misleading.

THE EVOLUTION OF ENCEPHALIZATION IN CANIFORM CARNIVORANS

Abstract A weighted-average model, which reliably estimates endocranial volume from three external measurements of the neurocranium of extant taxa in the mammalian order Carnivora, was tested for its applicability to fossil taxa by comparing model-estimated endocranial volumes to known endocast volumes. The model accurately reproduces endocast volumes for a wide array of fossil taxa across the crown radiation of the Carnivora, three stem carnivoramorphan taxa, and Pleistocene fossils of two extant species. Applying this model to fossil taxa without known endocast volumes expanded the sample of fossil taxa with estimated brain volumes in the carnivoran suborder Caniformia from 11 to 60 taxa. This then allowed a comprehensive assessment of the evolution of relative brain size across this clade. An allometry of brain volume to body mass was calculated on phylogenetically independent contrasts for the set of extant taxa, and from this, log-transformed encephalization quotients (logEQs) were calculated for all taxa, extant, and fossil. A series of Mann–Whitney tests demonstrated that the distributions of logEQs for taxa early in caniform evolutionary history possessed significantly lower median logEQs than extant taxa. Median logEQ showed a pronounced shift around the Miocene–Pliocene transition. Support tests, based on likelihood ratios, demonstrated that the variances of these distributions also were significantly lower than among modern taxa, but logEQ variance increased gradually through the history of the clade, not abruptly. Reconstructions of ancestral logEQs using weighted squared-change parsimony demonstrate that increased encephalization is observed across all major caniform clades (with the possible exception of skunks) and that these increases were achieved in parallel, although an “ancestor-descendant differencing” method could not rule out drift as a hypothesis. Peculiarities in the estimated logEQs for the extinct caniform family Amphicyonidae were also investigated; these unusual patterns are likely due to a unique allometry in scaling brain to body size in this single clade.

Basin-wide magnetostratigraphic framework for the Bighorn Basin, Wyoming

New paleomagnetic data from six different sections in the Bighorn Basin are combined with previously published results to construct a basin-wide magnetostratigraphic framework. Geomagnetic polarity reversals between chrons C26r, C26n, C25r, C25n, C24r, and C24n have been identifi ed among multiple stratigraphic sections in different parts of the basin. Using the new magnetostratigraphic framework, paleontological, paleobotanical, and isotopic information from these varied locations in the basin can now be correlated and compared to similar records from elsewhere in the world. These new data resolve previous uncertainty concerning the timing of an important episode of faunal turnover known as Biohorizon B, which is slightly below the chron C24r-C24n boundary, close to the position of the Elmo isotope excursion in marine records. Backstripping analysis using these new magnetostratigraphic data helps defi ne the time-transgressive onset of basin formation and shows the different subsidence histories of the northern and southern parts of the basin.

A dynamic global equilibrium in carnivoran diversification over 20 million years

The ecological and evolutionary processes leading to present-day biological diversity can be inferred by reconstructing the phylogeny of living organisms, and then modelling potential processes that could have produced this genealogy. A more direct approach is to estimate past processes from the fossil record. The Carnivora (Mammalia) has both substantial extant species richness and a rich fossil record. We compiled species-level data for over 10 000 fossil occurrences of nearly 1400 carnivoran species. Using this compilation, we estimated extinction, speciation and net diversification for carnivorans through the Neogene (22–2 Ma), while simultaneously modelling sampling probability. Our analyses show that caniforms (dogs, bears and relatives) have higher speciation and extinction rates than feliforms (cats, hyenas and relatives), but lower rates of net diversification. We also find that despite continual species turnover, net carnivoran diversification through the Neogene is surprisingly stable, suggesting a saturated adaptive zone, despite restructuring of the physical environment. This result is strikingly different from analyses of carnivoran diversification estimated from extant species alone. Two intervals show elevated diversification rates (13–12 Ma and 4–3 Ma), although the precise causal factors behind the two peaks in carnivoran diversification remain open questions.

Estimating body mass in New World "monkeys" (Platyrrhini, Primates), with a consideration of the Miocene platyrrhine, Chilecebus carrascoensis

Abstract Well-constrained estimates of adult body mass for species of fossil platyrrhines (New World “monkeys”) are essential for resolving numerous paleobiological questions. However, no consensus exists as to which craniodental measures best correlate with body mass among extant taxa in this clade. In this analysis, we analyze 80 craniodental variables and generate predictive equations applicable to fossil taxa, including the early platyrrhine Chilecebus carrascoensis. We find mandibular length to be the best craniodental predictor of body mass. There is no significant difference in predictive value between osteological and dental measures. Variables associated with the mandible and lower dentition do significantly outperform the cranium and upper dentition. Additionally, we demonstrate that modern platyrrhines differ, morphometrically, from early fossil forms. Chilecebus possesses unusual cranial proportions in several key features, as well as proportionally narrow upper incisors and wide upper cheek teeth. These variables yield widely divergent body mass estimates for Chilecebus, implying that the correlations observed in a crown group cannot be assumed a priori for early diverging fossils. Variables allometrically consistent with those in extant forms yield a body mass estimate of slightly less than 600 grams for Chilecebus, nearly a factor of two smaller than prior preliminary estimates. Scaled to body mass, the brain of Chilecebus is markedly smaller than those of modern anthropoids, despite its lowered body mass estimate advocated here. This finding, in conjunction with a similar pattern exhibited by fossil catarrhines, suggests that increased encephalization arose independently in the two extant subgroups of anthropoids (platyrrhines and catarrhines).