Evolutionary biogeography of the terrestrial biota of the Marquesas Islands,one of the world's remotest archipelagos

Aim

Here I review phylogenetic studies concerning the biogeography of the Marquesas Islands, an oceanic hotspot archipelago in the Pacific Ocean formed <5.5 Ma, and compare patterns (particularly pertaining to colonization and diversification) within the archipelago to those reported from the Hawaiian and Society Islands.

Location

Marquesas Islands, French Polynesia (Pacific Ocean).

Methods

I reviewed 37 phylogenetic studies incorporating Marquesas‐endemic taxa. I asked the following questions: (a) where are the sister‐groups of Marquesas lineages distributed? (b) are Marquesas‐endemic “radiations” monophyletic or polyphyletic? (c) what major between‐island phylogeographic barriers are seen in the Marquesas? (d) what evidence exists for diversification within islands? (e) how old is the Marquesas biota compared to the archipelago's age? Finally, these patterns are compared with those seen in the Society Islands and Hawaii.

Results

Most Marquesan lineages have their closest known relatives on other Pacific plate archipelagos (particularly the Society, Hawaiian, and Austral islands). Most Marquesas‐endemic radiations are found to be monophyletic, and among‐island diversification appears to be common. There is limited evidence for within‐island diversification. Some radiations may be consistent with a weak progression rule in which younger lineages are on younger islands. Crown ages of no Marquesas radiations appear to be older than the age of the archipelago (with one exception).

Main conclusions

Diversification of the Marquesas biota resembles that of the Hawaiian Islands more than that of the Society Islands. Many radiations are monophyletic and some appear to diversify in parallel with the formation of the archipelago.

     

Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein

With the development of de novo binders for protein targets from non‐related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single‐chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking “disembodied” amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein‐antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen‐based detection agents for typhoid diagnostics.     

Systematic characterization of pan‐cancer mutation clusters

Cancer genome sequencing has shown that driver genes can often be distinguished not only by the elevated mutation frequency but also by specific nucleotide positions that accumulate changes at a high rate. However, properties associated with a residue's potential to drive tumorigenesis when mutated have not yet been systematically investigated. Here, using a novel methodological approach, we identify and characterize a compendium of 180 hotspot residues within 160 human proteins which occur with a significant frequency and are likely to have functionally relevant impact. We find that such mutations (i) are more prominent in proteins that can exist in the on and off state, (ii) reflect the identity of a tumor of origin, and (iii) often localize within interfaces which mediate interactions with other proteins or ligands. Following, we further examine structural data for human protein complexes and identify a number of additional protein interfaces that accumulate cancer mutations at a high rate. Jointly, these analyses suggest that disruption and dysregulation of protein interactions can be instrumental in switching functions of cancer proteins and activating downstream changes.     

Contrasting intraspecific foliar trait responses to stressful conditions of two rhizomatous granite outcrop species at different scales in southwestern Australia

Plants respond to changing environmental conditions, and their ability to adjust intra‐specifically to such shifts represents an ecological and evolutionary advantage. We studied seven plant traits for two common, rhizomatous granite outcrop species (the fern Cheilanthes austrotenuifolia, and the herb Stypandra glauca) with seasonal foliage during the cooler, wetter winter months at seven sites across an aridity gradient in southwestern Australia. We investigated trait patterns at regional and habitat scale, by investigating changes in trait values along the aridity gradient, and by comparing two different habitats types (sun‐exposed and sheltered). We expected plants occurring in more arid sites and highly irradiated, shallow‐soil (sun‐exposed) habitats, to exhibit traits indicative of more conservative resource acquisition, retention and use strategies. At the habitat scale, we found support for our prediction, with plants in more stressful, sun‐exposed habitats showing traits’ values associated with more conservative strategies (especially for water), such as smaller plants, denser leaves, higher foliar δ¹³C and C/N. However, at the regional scale many traits displayed the opposite pattern, suggesting less conservative resource acquisition in more arid sites. This evidence was particularly pronounced for specific leaf area (SLA), which exhibited a significant, positive relationship with increasing aridity. We suggest that the unexpected regional trends in foliar traits relate to shorter lived, faster growing leaves linked to highly efficient resource acquisition and use strategies during the shorter growing season in the more arid regions. These highly exploitative strategies may enable plants to avoid climate extremes, that is, hot and dry periods in the more arid sites. Our findings of contrasting foliar traits responses at different scales support the importance of multi‐scale approaches to quantify the role of intraspecific trait variability.     

Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes

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Predicting the influence of wolf-provided carrion on scavenger community dynamics under climate change scenarios

Climate change poses an immediate threat to the persistence and distribution of many species, yet our ability to forecast changes in species composition is hindered by poor understanding of the extent to which higher trophic‐level interactions may buffer or exacerbate the adverse effects of warming. We incorporated species‐specific consumption data from 240 wolf‐killed elk carcasses from Yellowstone National Park into stochastic simulation models to link trends in the El Niño Southern Oscillation (ENSO) to food procurement by a guild of scavengers as a function of gray wolf reintroduction. We find that a shift in ENSO towards the El Niño (warming) phase of the cycle coincident with increasing global temperatures reduces carrion for scavengers, particularly those with strong seasonal patterns in resource use such as grizzly bears. Wolves alleviate these warming‐induced food shortages by rendering control over this crucial resource to biotic rather than abiotic factors. Ecosystems with intact top predators are likely to exhibit stronger biotic regulation and should be more resistant to climate change than ecosystems lacking them.     

Herbivore influence on soil microbial biomass and nitrogen mineralization in a northern grassland ecosystem: Yellowstone National Park

Microorganisms are largely responsible for soil nutrient cycling and energy flow in terrestrial ecosystems. Although soil microorganisms are affected by topography and grazing, little is known about how these two variables may interact to influence microbial processes. Even less is known about how these variables influence microorganisms in systems that contain large populations of free-roaming ungulates. In this study, we compared microbial biomass size and activity, as measured by in situ net N mineralization, inside and outside 35- to 40-year exclosures across a topographic gradient in northern Yellowstone National Park. The objective was to determine the relative effect of topography and large grazers on microbial biomass and nitrogen mineralization. Microbial C and N varied by almost an order of magnitude across sites. Topographic depressions that contained high plant biomass and fine-textured soils supported the greatest microbial biomass. We found that plant biomass accurately predicted microbial biomass across our sites suggesting that carbon inputs from plants constrained microbial biomass. Chronic grazing neither depleted soil C nor reduced microbial biomass. We hypothesize that microbial populations in grazed grasslands are sustained mainly by inputs of labile C from dung deposition and increased root turnover or root exudation beneath grazed plants. Mineral N fluxes were affected more by grazing than topography. Net N mineralization rates were highest in grazed grassland and increased from dry, unproductive to mesic, highly productive communities. Overall, our results indicate that topography mainly influences microbial biomass size, while mineral N fluxes (microbial activity) are affected more by grazing in this grassland ecosystem. Received: 4 June 1997 / Accepted: 16 December 1997     

Patterns in the diversity and endemism of extant Eocene age lineages across southern Africa

Southern Africa boasts a wealth of endemic fauna and flora, comprising both massive recent radiations such as those characteristic of the Cape flora, and solitary ancient species such as the peculiar desert gymnosperm Welwitschia. This study was undertaken to identify ancient biological lineages (tetrapod and vascular plant lineages of Eocene age or older) endemic to southern Africa, and to map their distribution across the region. Twenty‐seven (17 plant and ten animal) lineages were identified, and distribution maps were generated for each of them across 74 operational geographic units, which were then combined into total endemism and corrected weighted endemism per unit area. Total endemism peaked along South Africa's coast and Great Escarpment, but in the case of weighted endemism high values were also recorded along other portions of the Great Escarpment further north. A review of the lineages sister to southern African ancient endemic lineages showed that these are often globally widespread, and many of them differ substantially from the southern African ancient lineages in terms of morphology and ecology. The mechanisms of ancient lineage survival in the region are discussed, and their importance for conservation in southern Africa is emphasised.