Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time.

Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.

Rapid increase in southern elephant seal genetic diversity after a founder event.

Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal (Mirounga leonina) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population.

Adélie penguins and temperature changes in Antarctica: a long-term view.

During the summer months, Adélie penguins represent the dominant biomass of terrestrial Antarctica. Literally millions of individuals nest in ice-free areas around the coast of the continent. Hence, these modern populations of Adélie penguins have often been championed as an ideal biological indicator of ecological and environmental changes that we currently face. In addition, Adélie penguins show an extraordinary record of sub-fossil remains, dating back to the late Pleistocene. At this time, temperatures were much lower than now. Hence, this species offers unique long-term information, at both the genomic and ecological levels, about how a species has responded to climate change over more than 40 000 years.

Stable isotopes reveal Holocene changes in the diet of Adélie penguins in Northern Victoria Land (Ross Sea, Antarctica).

Adélie penguin (Pygoscelis adeliae) modern and fossil eggshells and guano samples collected from ornithogenic soils in Terra Nova Bay (Victoria Land, Ross Sea) were processed for carbon and nitrogen isotopic ratios with the aim of detecting past penguin dietary changes. A detailed and greatly expanded Adélie penguin dietary record dated back to 7,200 years BP has been reconstructed for the investigated area. Our data indicate a significant dietary shift between fish and krill, with a gradual decrease from past to present time in the proportion of fish compared to krill in Adélie penguin diet. From 7,200 to 2,000 years BP, δ(13)C and δ(15)N values indicate fish as the most eaten prey. The dietary contribution of lower-trophic prey in penguin diet started becoming evident not earlier than 2,000 years BP, when the δ(13)C values reveal a change in the penguin feeding behavior. Modern eggshell and guano samples reveal a major dietary contribution of krill but not a krill-dominated diet, since δ(13)C values remain much too high if krill prevail in the diet. According to the Holocene environmental background attested for Victoria Land, Adélie penguin dietary shifts between fish and krill seem to reflect penguin paleoecological responses to different paleoenvironmental settings with different conditions of sea-ice extension and persistence. Furthermore, Adélie penguin diet appears to be particularly affected by environmental changes in a very specific period within the breeding season, namely the egg-laying period when penguin dietary and feeding habit shifts are clearly documented by the δ(13)C of eggshell carbonate.

High mitogenomic evolutionary rates and time dependency.

Using entire modern and ancient mitochondrial genomes of Adélie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of evolution at constrained sites, including nonsynonymous positions and RNAs, varies more than twofold with time (between shallow and deep nodes), the rate of evolution at synonymous sites remains the same. The time-independent neutral evolutionary rates reported here would be useful for the study of recent evolutionary events.

Rapid response of a marine mammal species to holocene climate and habitat change.

Environmental change drives demographic and evolutionary processes that determine diversity within and among species. Tracking these processes during periods of change reveals mechanisms for the establishment of populations and provides predictive data on response to potential future impacts, including those caused by anthropogenic climate change. Here we show how a highly mobile marine species responded to the gain and loss of new breeding habitat. Southern elephant seal, Mirounga leonina, remains were found along the Victoria Land Coast (VLC) in the Ross Sea, Antarctica, 2,500 km from the nearest extant breeding site on Macquarie Island (MQ). This habitat was released after retreat of the grounded ice sheet in the Ross Sea Embayment 7,500-8,000 cal YBP, and is within the range of modern foraging excursions from the MQ colony. Using ancient mtDNA and coalescent models, we tracked the population dynamics of the now extinct VLC colony and the connectivity between this and extant breeding sites. We found a clear expansion signal in the VLC population approximately 8,000 YBP, followed by directional migration away from VLC and the loss of diversity at approximately 1,000 YBP, when sea ice is thought to have expanded. Our data suggest that VLC seals came initially from MQ and that some returned there once the VLC habitat was lost, approximately 7,000 years later. We track the founder-extinction dynamics of a population from inception to extinction in the context of Holocene climate change and present evidence that an unexpectedly diverse, differentiated breeding population was founded from a distant source population soon after habitat became available.

Mutation and evolutionary rates in adélie penguins from the antarctic.

Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (micro) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29-0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.

A single vaccination with attenuated SIVmac 239 via the tonsillar route confers partial protection against challenge with SIVmac 251 at a distant mucosal site, the rectum.

Elucidating the mechanisms that protect monkeys previously immunized with attenuated SIV (SIVDeltanef) against challenge infection with pathogenic virus may reveal new strategies for the development of an effective HIV vaccine. Here we show that a single atraumatic application of SIVDeltanef to the tonsils of four rhesus macaques conferred protection against SIVmac251 applied intrarectally 26 weeks later. While this protection was not complete, i.e., challenge virus could be isolated from all immunized animals, it was reflected by significantly lower viral loads in the blood (weeks 2-16 after challenge, p < 0.01) and considerably lower loads in lymphoid organs, and more stable peripheral CD4 counts in a proportion of the immunized animals as compared to four non-immunized, SIVmac251-infected control monkeys. SIV-specific humoral as well as systemic and mucosal T cell responses were detected in the immunized animals, but there was no correlation between their magnitude of expression and the level of protection. Analyses of leukocyte subsets in these animals at necropsy (24 weeks after challenge) did not reveal a significantly enhanced proportion of gamma/delta T cells in the tissues of protected monkeys. Therefore, tonsillar application of attenuated SIV induces protection in some animals against a superinfection with wild-type SIV distant at a distant mucosal site.

Laminin alpha2 chain-positive vessels and epidermal growth factor in lung neuroendocrine carcinoma: a model of a novel cooperative role of laminin-2 and epidermal growth factor in vessel neoplastic invasion and metastasis.

Capillaries expressing the laminin alpha2 chain in basement membranes may be considered early developing vessels in normal and neoplastic human tissues. Therefore, we investigated whether up-regulation of this extracellular matrix protein favors transendothelial migration of neoplastic cells and then metastasis. In lung small and large cell neuroendocrine carcinomas, which exhibit a stronger metastatic tendency among carcinomas, laminin alpha2 chain-positive vessels were more numerous than in carcinoid tumors and supraglottis, breast, and lung non-small cell carcinomas, suggesting a direct relationship between these vessels and metastasis. In vitro studies showed that epidermal growth factor (EGF) induced a more efficient migration of the AE-2 lung neuroendocrine carcinoma cell line through the purified laminin alpha2 chain rather than through the laminin beta1 chain and fibronectin. AE-2 cells constitutively expressed all EGF receptors and the alpha6beta1 integrin, which is one of the laminin alpha2 chain receptors. EGF up-regulated alpha6beta1 expression in several tumors. In this regard, we show that EGF increased the chemo-kinetic migration of AE-2 cells through EAHY endothelial monolayers, which was inhibited by the anti-alpha6 integrin chain monoclonal antibody. These data indicate that laminin alpha2 chain and alpha6beta1 may be mutually involved in EGF-dependent migration of AE-2 cells and that laminin alpha2 chain-positive vessels may favor metastasis of EGF-dependent tumors.

Ancient DNA enables timing of the pleistocene origin and holocene expansion of two adélie penguin lineages in antarctica.

The timing of divergent events in history is one of the central goals of contemporary evolutionary biology. Such studies are however dependent on accurate evolutionary rates. Recent developments in ancient DNA analysis enable the estimation of more accurate evolutionary rates and therefore more accurate timing of divergence events. Consequently, this leads to a better understanding of changes in populations through time. We use an evolutionary rate calculated from ancient DNA of Adélie penguins (Pygoscelis adeliae) to time divergent events in their history. We report the presence of two distinct and highly variable mitochondrial DNA lineages and track changes in these lineages through space and time. When the ancient DNA and the phylogenetic rates are used to estimate the time of origin of the lineages, two very different estimates resulted. In addition, these same rates provide very different estimates of the time of expansion of these lineages. We suggest that the rate calculated from ancient DNA is more consistent with the glacial history of Antarctica and requires fewer assumptions than does a narrative based on the phylogenetic rate. Finally, we suggest that our study indicates an important new role for ancient DNA studies in the timing of divergent events in history.