Searcharxiv⌕ Search

arXiv · 0707.0329

Expected Anomalies in the Fossil Record

Abstract

The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of `gaps' (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. Traditionally, gaps have often been explained by the improbability of fossilization and the discontinuous selection of found fossils. Here we take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found. Using a simple null model, we show mathematically that the question of whether a taxon sampled from some time in the past is likely to be morphologically intermediate to other samples (dated earlier and later) depends on the shape and dimensions of the underlying phylogenetic tree that connects the taxa, and the times from which the fossils are sampled.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Mareike Fischer, Mike Steel. 2008-08-26. Expected Anomalies in the Fossil Record. https://arxiv.org/abs/0707.0329

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

Cultural evolution shaped human's uniquely sensitive disgust avoidance

Disgust is an emotion that serves to avoid contaminants, and is central to the behavioural immune system. While disgust-motivated avoidance occurs in bonobos and chimpanzees, humans show uniquely high levels of contamination sensitivity. There is some disagreement over to what extent human disgust avoidance is a genetic adaptation or shaped through social transmission, and whether parental modelling plays a role in the latter. Here, we address this debate by simulating 100,000 years of cultural and biological evolution in various scenarios. We modelled disgust as a trait that governed the extent to which individuals forewent potentially contaminated nutrition. This lowered their risk of gastrointestinal illness, at the cost of increasing starvation risk and birth-interval. As environmental levels and costs of contamination rose, so did relative fitness of high disgust-avoidant individuals. Evolutionary shifts in disgust as polygenic trait occurred as a consequence of germ-cell mutations, but were most prominent in populations with high initial genetic variance. Crucially, cultural transmission between generations operated at a higher rate, even if parental modelling was eliminated. These results underscore the plausibility of cultural evolution's role in shaping human's uniquely sensitive disgust avoidance, and serves as an illustration of emerging theories that paint affective and cognitive mechanisms as socially transmitted rather than genetic adaptations.

q-bio.PE↗

On estimating the effective sample size of phylogenetic trees in an autocorrelated chain

Estimating the effective sample size (ESS) is fundamental in Bayesian phylogenetic inference to account for autocorrelation in MCMC samples. While methods for continuous parameters are well established, the discrete and high-dimensional nature of treespace poses substantial challenges. In this paper, we introduce a new approach based on Conditional Clade Distributions (CCDs) to emulate MCMC chains with known ESS bounds. We compare existing tree ESS estimators with novel approaches that utilize CCDs as tractable tree distributions, as well as a new probabilistic estimator based on differences in clade frequencies between independent chains. Using our emulated chains from both simulated and real datasets, we assess estimators for their ability to recover the true ESS (accuracy), their insensitivity to the removal of autocorrelated samples from the chain (stability), and their tolerance to combining multiple chains together (robustness). We further examine how multimodality and poor inter-mode chain mixing can compromise the reliability of tree ESS estimates. These findings indicate that our new CCD-based estimators perform comparably to existing approaches with respect to accuracy, stability, and robustness. In contrast, the probabilistic estimator and two previously recommended methods incur prohibitive computational costs for long chains. Together, these results establish a new framework for evaluating tree ESS estimators using CCD-based emulated MCMC chains and demonstrate their performance and current limitations in practical phylogenetic analyses. The expanded suite of tree ESS estimators is available in the user-friendly TreeStat2 software package for BEAST 2.

q-bio.PE↗

Leaky protection reveals three patterns in the relative advantages of vaccination strategies across transmission intensity

Targeted vaccination often prioritizes individuals who contribute most to transmission. However, this rationale may change under leaky protection, whereby vaccination reduces susceptibility at each exposure rather than fully preventing infection. Here, we use a survey-derived individual-level exposure framework for 2,279 residents to simulate infection dynamics across ranges of transmission intensity and vaccine efficacy. We compare two vaccination strategies: the high-exposure strategy (prioritizing highly exposed individuals) and the oldest-first strategy (prioritizing older individuals). As transmission intensity changes, we identify three patterns in the relative advantages of these two strategies. At low transmission, the high-exposure strategy outperforms the oldest-first strategy in reducing both epidemic peak size and final infection proportion. At intermediate transmission, it lowers epidemic peak size but increases final infection proportion, revealing a trade-off between these metrics. At high transmission, differences between the strategies narrow, and the oldest-first strategy has a slight advantage for both metrics. Overall, our findings highlight the importance of considering vaccine failure mode when evaluating vaccination policies under different transmission dynamics.

q-bio.PE↗