Question

Since brain does not fossilize, and behaviors can't be interpreted from fossils, there is a drive to exclusively use extant species in analyzing the evolution of language. Could it be useful to incorporate some information found in extinct hominin species in addition to comparing living species? Beyond looking at the fossil record, could genomics help provide insights?

Answer 1

Brain does not fossilize, brain endocast (i.e., replica of the inner surface of the braincase, constitutes the only direct evidence for reconstructing hominin brain evolution. In this context, paleoneurology has suffered from strong limitations due to the fragmentary nature of the fossil record and the absence of any information regarding subcortical elements in extinct taxa.

When developing and evaluating these cause-and-effect hypotheses, caution must be exercised,. For one, such hypotheses need to specify the taxonomic level at which the effect is observed because evolutionary patterns are scale-dependent. Evolution is hierarchical, and trends at lower taxonomic levels can look very different when combined at higher taxonomic levels (i.e. Simpson's paradox) Furthermore, different taxonomic levels imply different evolutionary mechanisms. Patterns within lineages (i.e. hypothesized ancestor-descendant sequences) are determined by microevolutionary, population-level processes (i.e. anagenesis). The most popular hypotheses related to hominin ECV increase. Patterns observed at the clade level, on the other hand, are the result of processes operating across multiple lineages and therefore can also be shaped by macroevolutionary processes (i.e. origination by lineage-splitting and extinction) in addition to microevolutionary ones. For example, from one time period to the next, the mean ECV of a clade can increase because (i) existing lineages evolve larger brains anagenetically, (ii) a new lineage originates with a brain size greater than the pre-existing clade mean or (iii) a lineage with a brain size smaller than the clade mean goes extinct. We must first understand how hominin brain size has increased across taxonomic scales in order to properly infer the evolutionary processes and potential drivers involved.

To date, most explanations for hominin brain size increase have focused on microevolutionary mechanisms. These hypotheses can explain anagenetic patterns but may not be relevant for patterns caused by origination and extinction. For example, some researchers argue extinction is an emergent phenomenon because species do not go extinct for the same reasons individual organisms die. ECV increase via anagenesis and lineage splitting are likely different enough processes that it makes sense to understand how each independently influenced ECV increase. Our results emphasize that origination and extinction were also important in shaping ECV patterns at the clade level, and both micro- and macroevolutionary change influenced hominin brain size to different extents at different times. Therefore, we must construct new, comprehensive theories to explain potential influences on hominin brain size evolution.

Periods when macroevolutionary processes drove clade-level ECV increase were, by definition, characterized by a combination of factors promoting origination and extinction. These factors may have included large-scale climate and environmental change, habitat fragmentation and vicariance, interspecific interactions, etc. It is worth repeating here that inferred periods of macroevolutionary importance were estimated using observed first and last appearance dates of lineages' cranial specimens, and these dates are very likely to shift as new fossil specimens are discovered (specifically, first appearances would become older, and last appearances would become younger)

It is noteworthy that almost all the first and last appearances are associated with an increase in average clade-level brain size, and the importance of each is staggered in time. The connection between first brain size and larger brain size is an example of directional speciation where there is a consistent, biased shift in the phenotypes of daughter lineages relative to that of their ancestral lineages. Directional speciation may be caused by developmental or evolutionary constraints that bias phenotypic change towards larger ECV, or selection for larger brains in peripatric populations, The association between last brain size and smaller-brained species may signal some kind of extinction selectivity, either directly or indirectly related to ECV (e.g. extinction rates may be correlated with geographic range size which in turn is correlated with body and brain size). This result is corroborated by smaller-brained species having shorter lineage durations.If species with larger ECVs are found to have higher diversification rates (origination minus extinction rates), this may suggest that species sorting also caused clade-level ECV to increase. Just as natural selection operates via differential birth/death of individuals associated with a given trait, species sorting operates via differential origination/extinction of species, in this case, associated (directly or indirectly) with brain size. Species sorting is implied by the increased variation in brain size, generated by the addition of larger-brained lineages via directional speciation; this increased variation was later culled by selective extinction of smaller-brained lineages. If species sorting is borne out, it would suggest that all three mechanisms known to influence phenotypic evolution within a clade (i.e. anagenesis, directional speciation and species sorting) were acting in concert at multiple taxonomic scales to produce the directional ECV trend observed at the hominin clade level. Moreover, the potential influence of species sorting requires a reorientation of how we think about hominin brain size evolution, since oft-proposed microevolutionary mechanisms are not necessary and may not be sufficient to generate higher-level sorting.

Inferring the potential drivers for periods of anagenetic change is more difficult. Within-lineage trends are typically explained as being caused by only directional selection. However, the observed rate of within-lineage ECV increase is too slow to be consistent with uniform directional selection, given our knowledge from empirical microevolutionary studies and theoretical models. One would need to decrease the mean-standardized selection gradient by 50% from 0.28 to 0.14 (if evolvability is held constant). In their compilation of mean-standardized selection gradients, Hereford et al. found that such low estimates are so small as to not be significantly different from zero.The potential prevalence of genetic drift should perhaps not be surprising given the rarity of hominins in the fossil record which implies small population sizes, but drift is difficult to reconcile with the strongly directional ECV pattern within hominin lineages.

Microevolutionary studies have shown that populations can respond rapidly to selection pressures on generational timescales (i.e. populations rapidly climb the adaptive peak and stay at the summit). Such high rates, however, need not characterize the tempo at which the adaptive peak itself moves over geological time. Therefore, selection was for larger ECV on average but must have fluctuated and included episodes of stasis and/or drift. All of this occurs on too fine a timescale to be resolved by the current hominin ECV fossil record, resulting in emergent directional trends within lineages.

Beyond looking at the fossil record, could genomics help provide insights?

Comparative genomic can help in providing further insights. Comparative genomic is a field of biological research in which the genome sequences of different species — human, mouse, and a wide variety of other organisms from bacteria to chimpanzees — are compared. By comparing the sequences of genomes of different organisms, researchers can understand what, at the molecular level, distinguishes different life forms from each other. Comparative genomics also provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give each organism its unique characteristics.

Although living creatures look and behave in a myriad of ways, all of their genomes consist of DNA, the chemical chain that harbors the genes that code for thousands of different kinds of proteins. Within DNA are the instructions sufficient to make an organism and the means by which organisms pass information along to their offspring. Remarkably, this information is coded by only four nucleotides: adenosine (A), cytosine (C), guanine (G), and thymine (T). Understanding the order of these nucleotides in linear DNA molecules has been an active pursuit since the discovery of DNA’s double-helical structure (Watson et al. 1953). As such, DNA sequencing has emerged as a fundamental approach to molecular biology research. The power of DNA sequencing as a research tool has spurred the dramatic advancement of DNA sequencing technology, which is allowing ever more genomes to be sequenced and making comparative genomics an accessible focal point for the study of any form of life.

A simple comparison of the general features of genomes such as genome size, number of genes, and chromosome number presents an entry point can highlight some striking findings. For example, while the tiny flowering plant Arabidopsis thaliana has a smaller genome than that of the fruit fly Drosophila melanogaster (157 million base pairs v. 165 million base pairs, respectively) it possesses nearly twice as many genes (25,000 v. 13,000). In fact A. thaliana has approximately the same number of genes as humans (~25,000). Thus, a very early lesson learned in the "genomic era" is that genome size does not correlate with evolutionary status, nor is the number of genes proportionate to genome size.

Similar genomes separated by about 5 million years of evolution (such as human and chimpanzee) are particularly useful for finding the sequence differences that may account for subtle differences in biological form. These are sequence changes under directional selection, a process whereby natural selection favors a single phenotype and continuously shifts the allele frequency in one direction. Comparative genomics is thus a powerful and promising approach to biological discovery that becomes more and more informative as genomic sequence data accumulate.

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