hp‐rare 1.0: a computer program for performing rarefaction on measures of allelic richness

The number of alleles in a sample (allelic richness) is a fundamental measure of genetic diversity. However, this diversity measure has been difficult to use because large samples are expected to contain more alleles than small samples. The statistical technique of rarefaction compensates for this sampling disparity. Here I introduce a computer program that performs rarefaction on private alleles and hierarchical sampling designs.     

The biogeography of Miniopterus bats (Chiroptera: Miniopteridae) from the Comoro Archipelago inferred from mitochondrial DNA

The endemic fauna of the Comoro Archipelago is composed of a mixture of taxa originating from Africa and Madagascar. Bats are the only native land dwelling mammals on this archipelago, but the biogeographical origins for the vast majority of species within this group are ambiguous. We report here genetic analyses based on two mitochondrial DNA markers to infer the origin of Comorian bats belonging to a reputed species complex of Miniopterus that is further distributed across Africa and Madagascar. Phylogenetic reconstructions show that east African M. minor are not closely related to the insular Miniopterus of Madagascar and the Comoros (Grande Comore and Anjouan). The latter cluster into two distinct, monophyletic clades (Clade 1 and Clade 2). Representatives of these clades occur sympatrically both on the Comoros and on Madagascar, and are distinguished by a large genetic distance (K2P: 9.9% for cytochrome b). No haplotypes are shared between any islands, suggesting the absence of contemporary gene flow. Populations of the widespread Clade 1 are furthermore characterized by a significant inter‐island structure (Φ_CT = 0.249), and by high haplotype and nucleotide diversities (h = 0.90–0.98, π = 0.04–0.06). Demographic analyses of Clade 1 suggest secondary contact between two distinct phylogroups (Subclade 1 A and 1B) that reached Grande Comore and Anjouan, and a large, stable population with a long evolutionary history on Madagascar. These results and the current distribution of related lineages suggest that the Comoros were colonized independently at least two or three times by ancestors from Madagascar.     

Systematic assessment of terrestrial biogeochemistry in coupled climate–carbon models

With representation of the global carbon cycle becoming increasingly complex in climate models, it is important to develop ways to quantitatively evaluate model performance against in situ and remote sensing observations. Here we present a systematic framework, the Carbon‐LAnd Model Intercomparison Project (C‐LAMP), for assessing terrestrial biogeochemistry models coupled to climate models using observations that span a wide range of temporal and spatial scales. As an example of the value of such comparisons, we used this framework to evaluate two biogeochemistry models that are integrated within the Community Climate System Model (CCSM) – Carnegie‐Ames‐Stanford Approach′ (CASA′) and carbon–nitrogen (CN). Both models underestimated the magnitude of net carbon uptake during the growing season in temperate and boreal forest ecosystems, based on comparison with atmospheric CO₂ measurements and eddy covariance measurements of net ecosystem exchange. Comparison with MODerate Resolution Imaging Spectroradiometer (MODIS) measurements show that this low bias in model fluxes was caused, at least in part, by 1–3 month delays in the timing of maximum leaf area. In the tropics, the models overestimated carbon storage in woody biomass based on comparison with datasets from the Amazon. Reducing this model bias will probably weaken the sensitivity of terrestrial carbon fluxes to both atmospheric CO₂ and climate. Global carbon sinks during the 1990s differed by a factor of two (2.4 Pg C yr^?1 for CASA′ vs. 1.2 Pg C yr^?1 for CN), with fluxes from both models compatible with the atmospheric budget given uncertainties in other terms. The models captured some of the timing of interannual global terrestrial carbon exchange during 1988–2004 based on comparison with atmospheric inversion results from TRANSCOM (r=0.66 for CASA′ and r=0.73 for CN). Adding (CASA′) or improving (CN) the representation of deforestation fires may further increase agreement with the atmospheric record. Information from C‐LAMP has enhanced model performance within CCSM and serves as a benchmark for future development. We propose that an open source, community‐wide platform for model‐data intercomparison is needed to speed model development and to strengthen ties between modeling and measurement communities. Important next steps include the design and analysis of land use change simulations (in both uncoupled and coupled modes), and the entrainment of additional ecological and earth system observations. Model results from C‐LAMP are publicly available on the Earth System Grid.     

A test for Allee effects in the self‐incompatible wasp‐pollinated milkweed Gomphocarpus physocarpus

It has been suggested that plants that are good colonizers will generally have either an ability to self‐fertilize or a generalist pollination system. This prediction is based on the idea that these reproductive traits should confer resistance to Allee effects in founder populations and was tested using Gomphocarpus physocarpus (Asclepiadoideae: Apocynaceae), a species native to South Africa that is invasive in other parts of the world. We found no significant relationships between the size of G. physocarpus populations and various measures of pollination success (pollen deposition, pollen removal and pollen transfer efficiency) and fruit set. A breeding system experiment showed that plants in a South African population are genetically self‐incompatible and thus obligate outcrossers. Outcrossing is further enhanced by mechanical reconfiguration of removed pollinaria before the pollinia can be deposited. Self‐pollination is reduced when such reconfiguration exceeds the average duration of pollinator visits to a plant. Observations suggest that a wide variety of wasp species in the genera Belonogaster and Polistes (Vespidae) are the primary pollinators. We conclude that efficient pollination of plants in small founding populations, resulting from their generalist wasp‐pollination system, contributes in part to the colonizing success of G. physocarpus. The presence of similar wasps in other parts of the world has evidently facilitated the expansion of the range of this milkweed.     

Lolium multiflorum density responses under ozone and herbicide stress

Adaptations to overcrowding of individual plants result in density dependant control of growth and development. There is little information on how anthropogenic stresses modify these responses. We investigated whether combinations of diclofop‐methyl herbicide and tropospheric ozone alter the pattern of expected growth compensation with density changes resulting from intraspecific competition in Lolium multiforum Lam (Poacea) plants. Individual plant vegetative parameters and total seed production were assessed for plants growing under various densities and different herbicide rates and ozone treatments. The stressors differently changed the frequency distribution for average individual plant weight resulting from increasing densities. Only herbicide affected seedling mortality. Plants were able to compensate during grain filling maintaining similar seed production – density relationships in all treatments. Our findings contribute to the understanding of the impact of stress factors on the demographic changes in plant populations. Important ecological implications arise: (i) contrasting responses to ozone and herbicide, alone and in combination of individual plants resulted in different biomass – density relationships; (ii) stress effects on plant populations could not be predicted from individual responses; and (iii) changes in competitive outcome by single or combined stress factors may alter the expected genotype frequency in a crowded population with few dominant individuals.     

Evaluation of Factors Restricting Distribution of the Endangered Key Largo Woodrat

ABSTRACT We examined a suite of models in an information theoretic framework to identify factors restricting presence of the endangered Key Largo woodrat (Neotoma floridana smalli) throughout its remaining habitat. Models containing variables related to availability of nest sites and mammalian predator abundances were supported by our data. Abundance of natural (large overstory trees) and artificial (rock and debris piles) nest substrate were the most important predictor variables, followed by indices of feral cat and raccoon (Procyon lotor) abundance. We recommend increasing abundance of nest substrate in the short term through addition of artificial nest substrate and in the long term through continued protection of remaining forest habitat.     

Assessment of Predictive Habitat Models for Bighorn Sheep in California's Peninsular Ranges

ABSTRACT We developed predictive habitat models for a bighorn sheep (Ovis Canadensis) population in the Peninsular Ranges of southern California, USA, using 2 Geographic Information System modeling techniques, Ecological Niche Factor Analysis (ENFA) and Genetic Algorithm for Rule-set Production (GARP). We used >16,000 Global Positioning System locations from 34 animals in 5 subpopulations to develop and test ENFA and GARP models, and we then compared these models to each other and to the expert-based model presented in the United States Fish and Wildlife Service's Recovery Plan for this population. Based on a suite of evaluation methods, we found both ENFA and GARP to provide useful predictions of habitat; however, models developed with GARP appeared to have higher predictive power. Habitat delineations resulting from GARP models were similar to the expert-based model, affirming that the expert-based model provided a useful delineation of bighorn sheep habitat in the Peninsular Ranges. In addition, all 3 models identified continuous bighorn sheep habitat from the northern to southern extent of our study area, indicating that the Recovery Plan's recommendation of maintaining habitat connectivity throughout the range is an appropriate goal.     

Perspectives from early career researchers on the publication process in ecology – a response to Statzner & Resh (2010)

1. Two senior ecologists summarised their experience of the scientific publication process ( Statzner & Resh, Freshwater Biology, 2010 ; 55 , 2639) to generate discussion, particularly among early career researchers (ECRs). As a group of eight ECRs, we comment on the six trends they described. 2. We generally agree with most of the trends identified by Statzner & Resh (2010) , but also highlight a number of divergent perspectives and provide recommendations for change. Trends of particular concern are the use of inappropriate metrics to evaluate research quality (e.g. impact factor) and the salami slicing of papers to increase paper count. We advocate a transparent and comprehensive system for evaluating the research. 3. We stress the importance of impartiality and independence in the peer review process. We therefore suggest implementation of double‐blind review and quality control measures for reviewers and possibly editors. Besides such structural changes, editors should be confident to overrule biased reviewer recommendations, while reviewers should provide helpful reviews but be explicit if a submission does not meet quality standards. Authors should always conduct a thorough literature search and acknowledge historical scientific ideas and methods. Additionally, authors should report low‐quality copy editing and reviews to the editors. 4. Both early and late career researchers should jointly implement these recommendations to reverse the negative trends identified by Statzner & Resh (2010) . However, more senior scientists will always have to take the lead with respect to structural changes in the publication system given that they occupy the majority of decision‐making positions.     

More than meets the eye: a morphological and phylogenetic comparison of long‐spurred,white‐flowered Satyrium species (Orchidaceae) in South Africa

Superficial similarities among unrelated species are often a result of convergent evolution and can cause considerable taxonomic confusion. A case in point is Satyrium eurycalcaratum , described here as a new species, which has been confused with several other Satyrium spp. with similar long‐spurred, white flowers. A phylogenetic analysis, based on molecular data, indicated that S. eurycalcaratum is not closely related to any of the species with which it has been previously confused. A comparative analysis of morphological characters in the seven South African Satyrium spp. with long‐spurred, white flowers showed that each of these, including S. eurycalcaratum , is characterized by a unique combination of traits. Despite the similarity in pollination syndrome characters, such as spur length and flower colour, variation in rostellum structure was particularly pronounced and four distinctive forms were present. There was no phylogenetic signal in patterns of interspecific rostellum variation, as some closely related species had different rostella, whereas some distantly related species shared similar rostellum structures. We therefore conclude that the use of rostellum traits in conjunction with phylogenetic evidence can resolve species delimitations among orchid species that share the same pollination syndrome. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166 , 417–430.     

Morphological profiling using machine learning reveals emergent subpopulations of interferon-γ–stimulated mesenchymal stromal cells that predict immunosuppression

Background

Although a preponderance of pre-clinical data demonstrates the immunosuppressive potential of mesenchymal stromal cells (MSCs), significant heterogeneity and lack of critical quality attributes (CQAs) based on immunosuppressive capacity likely have contributed to inconsistent clinical outcomes. This heterogeneity exists not only between MSC lots derived from different donors, tissues and manufacturing conditions, but also within a given MSC lot in the form of functional subpopulations. We therefore explored the potential of functionally relevant morphological profiling (FRMP) to identify morphological subpopulations predictive of the immunosuppressive capacity of MSCs derived from multiple donors, manufacturers and passages.