On calibrating the completometer for the mammalian fossil record

We know that the fossil record is incomplete. But how incomplete? Here we very coarsely estimate the completeness of the mammalian record in the Miocene, assuming that the duration of a mammalian species is about 1 Myr and the species diversity has stayed constant and is structurally comparable to the taxonomic diversity today. The overall completeness under these assumptions appears to be around 4%, but there are large differences across taxonomic groups. We find that the fossil record of proboscideans and perissodactyls as we know it for the Miocene must be close to complete, while we might know less than 15% of the species of artiodactyl or carnivore fossil species and only about 1% of primate species of the Miocene. The record of small mammals appears much less complete than that of large mammals.

Geologically calibrated mammalian tree and the corresponding global events, including birth of human

The robust timetree could be constructed using a calibration function of BEAST v1. X released in 2018 simply by applying times of the most recent (= the latest) common ancestors (tMRCAs) for specific monophyletic species groups (clades). The present research is probably the first trial to fully use the calibration function in BEAST X. The specific node age (child tMRCA) in BEAST X = “minimum age” in conventional MCMCTree, but the “maximum age” in MCMCTree can be equivalent to, e.g., the parent node age (parent tMRCA) in BEAST X. We applied 19 mammalian fossil calibration ages considering Benton et al. (2015; solely their minimum ages), including those of fossil Gorilla and Pan + one geologic event calibration age for otters (= Quaternary isolation time of the Ryukyu islands and start of vicariant speciation), and we estimated our targeted splitting age of Homo and Pan at 5.69 Ma (calibration dates by Benton et al., 2015 were incorrect). After the initial rifting at 120 Ma, the Atlantic Ocean spread over 500 km on Chron 34 (84 Ma), and Afrotheria (Africa) and Xenarthra (South America) started vicariant speciation at this time (~ 70 Ma), reflecting the progressed continental isolation. Ordinal-level differentiations started just after the K-Pg boundary (66.0 Ma), and this timing reconfirmed that mammalian radiation occurred by rapidly filling the niches left vacant by the non-avian dinosaurs. In addition, we made a base substitution rate vs age diagram using the BEAST X function and showed that the rate exponentially increased and accelerated toward the Holocene, other than having the 55 Ma mild peak reflecting the post K-Pg mammalian explosion. The increased rate might have consequently increased the biodiversity, and extensive adaptive radiation might have ultimately birthed Homo sapiens. The basic factor of radiation might be the generation and spreading of C4 grasses since 20 Ma, which has been linked to increasing carbon fixation, decreasing atmospheric CO2 concentrations, cooling Earth, and triggering the Quaternary (2.58 Ma ~) glacier-inter glacier cycle and severe climatic change. Note that Perissodactyla and Cetartiodactyla (Laurasiatheria) feed on C4 grasses (savanna), and Carnivora (also Laurasiatheria) is the predator, also suggesting coevolutions since 20 Ma.

Doma: a new multi-technological lithic occurrence in the Lower Son Valley (north-central India) and its regional context

The Lower Son Valley is generally overlooked despite a lengthy history of archaeological and geological studies in the adjacent Middle Son Valley. However, recent explorations in the former have yielded a large number of Palaeolithic and microlithic sites. This paper provides an initial report on Doma, a newly discovered site with the first-known stratified bifaces in this part of the valley. The site preserves multi-period technologies in different contexts including terminal Acheulean/early Middle Palaeolithic, and Upper Palaeolithic (all tentatively assigned based on respective typologies). Preliminary field observations are presented on the sedimentary sequence, archaeological surveys, topographical mapping, raw material, and the overall palaeoanthropological assessment of Doma. The raw material utilised at the site is primarily porcellanite, derived from exposures of the Semri Group of the Vindhyan Supergroup. The oldest Palaeolithic evidence at Doma broadly resembles Late Acheulean sites dated to ∼140-120 ka in the nearby Middle Son Valley. The Pleistocene sediments here also yielded mammalian fossil specimens such as long bone fragments, dental specimens and antler fragments. Along with the lithics and fossils, the site also preserves datable sedimentary sequence with calcrete, all key proxies to develop a testable model of technological transitions within a palaeoenvironmental framework, in the future.

Trehalase Gene as a Molecular Signature of Dietary Diversification in Mammals

Diet is a key factor in determining and structuring animal diversity and adaptive radiations. The mammalian fossil record preserves phenotypic evidence of many dietary shifts, whereas genetic changes followed by dietary diversification in mammals remain largely unknown. To test whether living mammals preserve molecular evidence of dietary shifts, we examined the trehalase gene (Treh), which encodes an enzyme capable of digesting trehalose from insect blood, in bats and other mammals with diverse diets. Bats represent the largest dietary radiation among all mammalian orders, with independent origins of frugivory, nectarivory, carnivory, omnivory, and even sanguivory in an otherwise insectivorous clade. We found that Treh has been inactivated in unrelated bat lineages that independently radiated into noninsectivorous niches. Consistently, purifying selection has been markedly relaxed in noninsectivorous bats compared with their insectivorous relatives. Enzymatic assays of intestinal trehalase in bats suggest that trehalase activity tends to be lost or markedly reduced in noninsectivorous bats compared with their insectivorous relatives. Furthermore, our survey of Treh in 119 mammal species, which represent a deeper evolutionary timeframe, additionally identified a number of other independent losses of Treh in noninsectivorous species, recapitulating the evolutionary pattern that we found in bats. These results document a molecular record of dietary diversification in mammals, and suggest that such molecular signatures of dietary shifts would help us understand both historical and modern changes of animal diets.

Advances in Quaternary Studies: The Contribution of the Mammalian Fossil Record

Explaining the multifaceted, dynamic interactions of the manifold factors that have modelled throughout the ages the evolutionary history of the biosphere is undoubtedly a fascinating and challenging task that has been intriguing palaeontologists, biologists and ecologists for decades, in a never-ending pursuit of the causal factors that controlled the evolutionary dynamics of the Earth’s ecosystems throughout deep and Quaternary time. [...]

Signal or noise? A null model method for evaluating the significance of turnover pulses

Patterns of turnover in the mammalian fossil record have been interpreted as reflecting “pulses” of originations and extinctions hypothesized to be driven by climate change. However, criteria for determining what constitutes a meaningful pulse have been idiosyncratic, and investigations of turnover patterns in mammals have yielded mixed results.This study presents simple simulations of fossil records in which origination and extinction probabilities for each lineage are held constant. Nonetheless, the total number of turnover events per time bin varies stochastically, producing statistical “noise.” Various simulation and analytical assumptions are examined to determine their impact on the type I error rate (i.e., how often “pulses” are detected in a purely stochastic process).Results suggest that simple analytical parameters (length of time bins and turnover-pulse criterion) have predictable and straightforward effects on false-positive rates. Furthermore, “pulses” of turnover of a magnitude similar to that observed in the terrestrial mammalian fossil record may be quite common under realistic analytical conditions.The null turnover model offers a practical way to evaluate the significance of observed turnover events in future empirical studies of the fossil record. In evaluating the significance of a “pulse” of fossil origination or extinction events, analytical parameters can be explored using this null model to determine the approximate type I error rate for a set of parameters. Because false-positive rates are shown to be quite high, functional trait-based approaches may offer more reliable indicators of the impact of climate change on turnover dynamics.