Rapid evolution of the cerebellum in humans and other great apes

Humans’ unique cognitive abilities are usually attributed to a greatly expanded neocortex, which has been described as “the crowning achievement of evolution and the biological substrate of human mental prowess” [1]. The human cerebellum, however, contains four times more neurons than the neocortex [2] and is attracting increasing attention for its wide range of cognitive functions. Using a method for detecting evolutionary rate changes along the branches of phylogenetic trees, we show that the cerebellum underwent rapid size increase throughout the evolution of apes, including humans, expanding significantly faster than predicted by the change in neocortex size. As a result, humans and other apes deviated significantly from the general evolutionary trend for neocortex and cerebellum to change in tandem, having significantly larger cerebella relative to neocortex size than other anthropoid primates. These results suggest that cerebellar specialization was a far more important component of human brain evolution than hitherto recognized and that technical intelligence was likely to have been at least as important as social intelligence in human cognitive evolution. Given the role of the cerebellum in sensory-motor control and in learning complex action sequences, cerebellar specialization is likely to have underpinned the evolution of humans’ advanced technological capacities, which in turn may have been a preadaptation for language.

Speciation and bursts of evolution

A longstanding debate in evolutionary biology concerns whether species diverge gradually through time or by rapid punctuational bursts at the time of speciation. The theory of punctuated equilibrium states that evolutionary change is characterised by short periods of rapid evolution followed by longer periods of stasis in which no change occurs. Despite years of work seeking evidence for punctuational change in the fossil record, the theory remains contentious. Further there is little consensus as to the size of the contribution of punctuational changes to overall evolutionary divergence. Here we review recent developments which show that punctuational evolution is common and widespread in gene sequence data.

Chaos of Wolbachia Sequences Inside the Compact Fig Syconia of Ficus benjamina (Ficus: Moraceae)

Figs and fig wasps form a peculiar closed community in which the Ficus tree provides a compact syconium (inflorescence) habitat for the lives of a complex assemblage of Chalcidoid insects. These diverse fig wasp species have intimate ecological relationships within the closed world of the fig syconia. Previous surveys of Wolbachia, maternally inherited endosymbiotic bacteria that infect vast numbers of arthropod hosts, showed that fig wasps have some of the highest known incidences of Wolbachia amongst all insects. We ask whether the evolutionary patterns of Wolbachia sequences in this closed syconium community are different from those in the outside world. In the present study, we sampled all 17 fig wasp species living on Ficus benjamina, covering 4 families, 6 subfamilies, and 8 genera of wasps. We made a thorough survey of Wolbachia infection patterns and studied evolutionary patterns in wsp (Wolbachia Surface Protein) sequences. We find evidence for high infection incidences, frequent recombination between Wolbachia strains, and considerable horizontal transfer, suggesting rapid evolution of Wolbachia sequences within the syconium community. Though the fig wasps have relatively limited contact with outside world, Wolbachia may be introduced to the syconium community via horizontal transmission by fig wasps species that have winged males and visit the syconia earlier.

Evolution of late glacial ice-marginal lakes on the northwestern Canadian Shield and their influence on the location of the Dubawnt Lake palaeo-ice stream

During deglaciation of the North American Laurentide Ice Sheet large proglacial lakes developed in positions where proglacial drainage was impeded by the ice margin. For some of these lakes, it is known that subsequent drainage had an abrupt and widespread impact on North Atlantic Ocean circulation and climate, but less is known about the impact that the lakes exerted on ice sheet dynamics. This paper reports palaeogeographic reconstructions of the evolution of proglacial lakes during deglaciation across the northwestern Canadian Shield, covering an area in excess of 1,000,000 km(2) as the ice sheet retreated some 600 km. The interactions between proglacial lakes and ice sheet flow are explored, with a particular emphasis on whether the disposition of lakes may have influenced the location of the Dubawnt Lake ice stream. This ice stream falls outside the existing paradigm for ice streams in the Laurentide Ice Sheet because it did not operate over fined-grained till or lie in a topographic trough. Ice margin positions and a digital elevation model are utilised to predict the geometry and depth of proglacial takes impounded at the margin at 30-km increments during deglaciation. Palaeogeographic reconstructions match well with previous independent estimates of lake coverage inferred from field evidence, and results suggest that the development of a deep lake in the Thelon drainage basin may have been influential in initiating the ice stream by inducing calving, drawing down ice and triggering fast ice flow. This is the only location alongside this sector of the ice sheet where large (>3000 km(2)), deep lakes (similar to120 m) are impounded for a significant length of time and exactly matches the location of the ice stream. It is speculated that the commencement of calving at the ice sheet margin may have taken the system beyond a threshold and was sufficient to trigger rapid motion but that once initiated, calving processes and losses were insignificant to the functioning of the ice stream. It is thus concluded that proglacial lakes are likely to have been an important control on ice sheet dynamics during deglaciation of the Laurentide Ice Sheet. (C) 2004 Elsevier B.V. All rights reserved.

A singular vector perspective of 4DVAR: The spatial structure and evolution of baroclinic weather systems

The extent to which the four-dimensional variational data assimilation (4DVAR) is able to use information about the time evolution of the atmosphere to infer the vertical spatial structure of baroclinic weather systems is investigated. The singular value decomposition (SVD) of the 4DVAR observability matrix is introduced as a novel technique to examine the spatial structure of analysis increments. Specific results are illustrated using 4DVAR analyses and SVD within an idealized 2D Eady model setting. Three different aspects are investigated. The first aspect considers correcting errors that result in normal-mode growth or decay. The results show that 4DVAR performs well at correcting growing errors but not decaying errors. Although it is possible for 4DVAR to correct decaying errors, the assimilation of observations can be detrimental to a forecast because 4DVAR is likely to add growing errors instead of correcting decaying errors. The second aspect shows that the singular values of the observability matrix are a useful tool to identify the optimal spatial and temporal locations for the observations. The results show that the ability to extract the time-evolution information can be maximized by placing the observations far apart in time. The third aspect considers correcting errors that result in nonmodal rapid growth. 4DVAR is able to use the model dynamics to infer some of the vertical structure. However, the specification of the case-dependent background error variances plays a crucial role.

Phylogeny, function, and evolution of the cupins, a structurally conserved, functionally diverse superfamily of proteins

The cupin superfamily is a group of functionally diverse proteins that are found in all three kingdoms of life, Archaea, Eubacteria, and Eukaryota. These proteins have a characteristic signature domain comprising two histidine- containing motifs separated by an intermotif region of variable length. This domain consists of six beta strands within a conserved beta barrel structure. Most cupins, such as microbial phosphomannose isomerases (PMIs), AraC- type transcriptional regulators, and cereal oxalate oxidases (OXOs), contain only a single domain, whereas others, such as seed storage proteins and oxalate decarboxylases (OXDCs), are bi-cupins with two pairs of motifs. Although some cupins have known functions and have been characterized at the biochemical level, the majority are known only from gene cloning or sequencing projects. In this study, phylogenetic analyses were conducted on the conserved domain to investigate the evolution and structure/function relationships of cupins, with an emphasis on single- domain plant germin-like proteins (GLPs). An unrooted phylogeny of cupins from a wide spectrum of evolutionary lineages identified three main clusters, microbial PMIs, OXDCs, and plant GLPs. The sister group to the plant GLPs in the global analysis was then used to root a phylogeny of all available plant GLPs. The resulting phylogeny contained three main clades, classifying the GLPs into distinct subfamilies. It is suggested that these subfamilies correlate with functional categories, one of which contains the bifunctional barley germin that has both OXO and superoxide dismutase (SOD) activity. It is proposed that GLPs function primarily as SODs, enzymes that protect plants from the effects of oxidative stress. Closer inspection of the DNA sequence encoding the intermotif region in plant GLPs showed global conservation of thymine in the second codon position, a character associated with hydrophobic residues. Since many of these proteins are multimeric and enzymatically inactive in their monomeric state, this conservation of hydrophobicity is thought to be associated with the need to maintain the various monomer- monomer interactions. The type of structure-based predictive analysis presented in this paper is an important approach for understanding gene function and evolution in an era when genomes from a wide range of organisms are being sequenced at a rapid rate.

Speciation as an active force in promoting genetic evolution

There is a growing appreciation among evolutionary biologists that the rate and tempo of molecular evolution might often be altered at or near the time of speciation, i.e. that speciation is in some way a special time for genes. Molecular phylogenies frequently reveal increased rates of genetic evolution associated with speciation and other lines of investigation suggest that various types of abrupt genomic disruption can play an important role in promoting speciation via reproductive isolation. These phenomena are in conflict with the gradual view of molecular evolution that is implicit in much of our thinking about speciation and in the tools of modern biology. This raises the prospect of studying the molecular evolutionary consequences of speciation per se and studying the footprint of speciation as an active force in promoting genetic divergence. Here we discuss the reasons to believe that speciation can play such a role and elaborate on possible mechanisms for accelerated rates of evolution following speciation. We provide an example of how it is possible detect whether accelerated bursts of evolution occur in neutral and/or adaptive regions of genes and discuss the implications of rapid episodes of change for conventional models of molecular evolution. Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche.

Antarctic Peninsula ice sheet evolution during the Cenozoic Era

The Antarctic Peninsula region is currently undergoing rapid environmental change, resulting in the thinning, acceleration and recession of glaciers and the sequential collapse of ice shelves. It is important to view these changes in the context of long-term palaeoenvironmental complexity and to understand the key processes controlling ice sheet growth and recession. In addition, numerical ice sheet models require detailed geological data for tuning and testing. Therefore, this paper systematically and holistically reviews published geological evidence for Antarctic Peninsula Ice Sheet variability for each key locality throughout the Cenozoic, and brings together the prevailing consensus of the extent, character and behaviour of the glaciations of the Antarctic Peninsula region. Major contributions include a downloadable database of 186 terrestrial and marine calibrated dates; an original reconstruction of the LGM ice sheet; and a new series of isochrones detailing ice sheet retreat following the LGM. Glaciation of Antarctica was initiated around the Eocene/Oligocene transition in East Antarctica. Palaeogene records of Antarctic Peninsula glaciation are primarily restricted to King George Island, where glacigenic sediments provide a record of early East Antarctic glaciations, but with modification of far-travelled erratics by local South Shetland Island ice caps. Evidence for Neogene glaciation is derived primarily from King George Island and James Ross Island, where glaciovolcanic strata indicate that ice thicknesses reached 500–850 m during glacials. This suggests that the Antarctic Peninsula Ice Sheet draped, rather than drowned, the topography. Marine geophysical investigations indicate multiple ice sheet advances during this time. Seismic profiling of continental shelf-slope deposits indicates up to ten large advances of the Antarctic Peninsula Ice Sheet during the Early Pleistocene, when the ice sheet was dominated by 40 kyr cycles. Glacials became more pronounced, reaching the continental shelf edge, and of longer duration during the Middle Pleistocene. During the Late Pleistocene, repeated glacials reached the shelf edge, but ice shelves inhibited iceberg rafting. The Last Glacial Maximum (LGM) occurred at 18 ka BP, after which transitional glaciomarine sediments on the continental shelf indicate ice-sheet retreat. The continental shelf contains large bathymetric troughs, which were repeatedly occupied by large ice streams during Pleistocene glaciations. Retreat after the LGM was episodic in the Weddell Sea, with multiple readvances and changes in ice-flow direction, but rapid in the Bellingshausen Sea. The late Holocene Epoch was characterised by repeated fluctuations in palaeoenvironmental conditions, with associated glacial readvances. However, this has been subsumed by rapid warming and ice-shelf collapse during the twentieth century.

Rapid changes in the redox conditions of the western Tethys Ocean during the early Aptian oceanic anoxic event

The early Aptian (125 to 121 Ma) records an episode of severe environmental change including a major perturbation of the carbon cycle, an oceanic anoxic event (OAE 1a, 122.5 Ma), a platform drowning episode and a biocalcification crisis. We propose to trace changes in the oxygenation state of the ocean during the early Aptian anoxic event using the redox-sensitive trace-element (RSTE) distribution, phosphorus accumulation rates (PARs) and organic-matter characterization in three different basins of the western Tethys. The following sections have been investigated: Gorgo a Cerbara (central Italy) in the Umbria Marche basin, Glaise (SE France) in the Vocontian basin and Cassis/La Bédoule (SE France) located in the Provencal basin. In the Gorgo a Cerbara section, RSTE distributions show a low background level along the main part of the section, contrasted by different maxima in concentrations within the Selli level. In the Glaise section, the Goguel level displays a weak increase in RSTE contents coeval with moderate TOC values. At Cassis/La Bédoule, no significant RSTE enrichments have been observed in sediments equivalent to the Selli level. These differences in the records of the geochemical proxies of the Selli level or its equivalent indicate the deposition under different redox conditions, probably related to the paleogeography. Our data indicate the development of anoxic–euxinic conditions in the deeper part of the Tethys during OAE 1a, whereas in the shallower environments, conditions were less reducing. Moreover, at Gorgo a Cerbara, the Selli level is characterized by rapid changes in the intensity of reducing conditions in the water column. Ocean eutrophication seems to be a major factor in the development and the persistence of anoxia as suggested by the PAR evolution. Higher PAR values at the onset of OAE 1a suggest an increase in nutrient input, whereas the return to lower values through the first part of the OAE 1a interval may be related to the weakened capacity to retain P in the sedimentary reservoir due to bottom-water oxygen depletion. This general pattern is contrasted by the data of Gorgo a Cerbara, where the sediments deposited during the OAE 1a interval show P-enrichments (mainly authigenic P). This is associated with maxima in TOC values and Corg:Ptot ratios, suggesting that a part of the remobilized P was trapped in the sediments and as such prevented from returning to the water column.

Adaptive evolution toward larger size in mammals

The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope’s rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both.