Terrestrial or marine species distribution model: Why not both? A case study with seabirds

Species reliant on both the terrestrial and marine realms present a challenge for conventional species distribution models (SDMs). For such species, standard single‐realm SDMs may omit key information that could result in decreased model accuracy and performance. Existing approaches to habitat suitability modeling typically do not effectively combine information from multiple realms; this methodological gap can ultimately hamper management efforts for groups such as seabirds, seals, and turtles. This study, for the first time, jointly incorporates both terrestrial information and marine information into a single species distribution model framework. We do this by sampling nearby marine conditions for a given terrestrial point and vice versa using parameters set by each species’ mean maximum foraging distance and then use standard SDM methods to generate habitat suitability predictions; therefore, our method does not rely on post hoc combination of several different models. Using three seabird species with very different ecologies, we investigate whether this new multi‐realm approach can improve our ability to identify suitable habitats for these species. Results show that incorporating terrestrial information into marine SDMs, or vice versa, generally improves model performance, sometimes drastically. However, there is considerable variability between species in the level of improvement as well as in the particular method that produces the most improvement. Our approach provides a repeatable and transparent method to combine information from multiple ecological realms in a single SDM framework. Important advantages over existing solutions include the opportunity to, firstly, easily combine terrestrial and marine information for species that forage large distances inland or out to sea and, secondly, consider interactions between terrestrial and marine variables.     

The lantibiotic nisin, a special case or not?

Nisin is a 34-residue-long peptide belonging to the group A lantibiotics with antimicrobial activity against Gram-positive bacteria. The presence of dehydrated residues and lanthionine rings (thioether bonds) in nisin, imposing structural restrains on the peptide, make it an interesting case for studying the mode of action. In addition, the relatively high activity (nM range) of nisin against Gram-positive bacteria indicates that nisin may be a special case in the large family of pore-forming peptides antibiotics. In this review, we attempted to dissect the mode of action of nisin concentrating on studies that used model membranes or biological membranes. The picture that emerges suggests that in model membrane systems, composed of only phospholipids, nisin behaves similar to the antimicrobial peptide magainin, albeit with an activity that is much lower as compared to its activity towards biological membranes. This difference can be contributed to a missing factor which nisin needs for its high activity. Novel results have identified the factor as Lipid II, a precursor in the bacterial cell wall synthesis. The special high affinity interaction of nisin with Lipid II resulting in high activity and the active role of Lipid II in the pore-formation process make nisin a special case.     

Ecological variation within Sellaphora species complexes (Bacillariophyceae): specialists or generalists?

The genus Sellaphora has become a model system for studies of the species concept, speciation and automated identification in diatoms. Three species, S. pupula, S. bacillum and S. laevissima, have proved to be complexes containing several or many species, which are difficult to distinguish morphologically but which are genetically differentiated and (where tested) reproductively isolated. Until now, however, there has been little information about the ecology of the species within this complex, except in relation to parasite sensitivity. In order to test whether semi- and pseudo-cryptic Sellaphora species are ecologically differentiated with respect to trophic status, we used tools recently developed in the UK in response to the EU Water Framework Directive (WFD). Diatom samples from three substrata (plants, rocks, sediment) were taken from 22 lakes in Scotland and England, covering a gradient from oligotrophic mountain lakes to eutrophic lowland ponds. The epilithic and epiphytic diatom assemblages were used to evaluate lake trophic status according to the UK WFD assessment system and showed that there was a strong environmental gradient in the dataset. Sellaphora species occurred in the sediment-derived epipelon and their distributions were analysed in relation to the trophic gradient. A total of 28 Sellaphora phenodemes (putative species) were found, and some of them differed in their environmental demands. Two groups were distinguished: (1) a group indicating rather oligotrophic conditions and containing several demes with linear valves and subcapitate or capitate poles (referred to here as S. [pupula] cap-A, cap-B and cap-C and (2) a group occurring in eutrophic lakes and containing the recently described species S. blackfordensis, S. capitata and S. obesa, as well as S. [pupula] Φ ‘small lanceolate’. The data obtained are also discussed with respect to Finlay’s hypothesis on microalgal cosmopolitanism. Handling editor: J. Padisak     

Yeast as a model to study apoptosis?

Programmed cell death (PCD) serves as a major mechanism for the precise regulation of cell numbers, and as a defense mechanism to remove unwanted and potentially dangerous cells. Despite the striking heterogeneity of cell death induction pathways, the execution of the death program is often associated with characteristic morphological and biochemical changes termed apoptosis. Although for a long time the absence of mitochondrial changes was considered as a hallmark of apoptosis, mitochondria appear today as the central executioner of programmed cell death. This crucial position of mitochondria in programmed cell death control is not due to a simple loss of function (deficit in energy supplying), but rather to an active process in the regulation of effector mechanisms.The large diversity of regulators of apoptosis in mammals and their numerous interactions complicate the analysis of their individual functions. Yeast, eukaryotic but unicellular organism, lack the main regulators of apoptosis (caspases, Bcl-2 family members, . . .) found in mammals. This absence render them a powerful tool for heterologous expression, functional studies, and even cloning of new regulators of apoptosis.Great advances have thus been made in our understanding of the molecular mechanisms of Bcl-2 family members interactions with themselves and other cellular proteins, specially thanks to the two hybrid system and the easy manipulation of yeast (molecular biology and genetics).This review will focus on the use of yeast as a tool to identify new regulators and study function of mammalian apoptosis regulators.     

What happens to the sown species if a biodiversity experiment is not weeded?

Studies in experimental grasslands have extensively documented the effects of sown plant diversity on the colonization of new species, but the responses of the sown plant combinations themselves have rarely been investigated. We established experimental grasslands differing in species richness (1, 2, 4, 8, and 16) and functional group number and composition (1–4; legumes, grasses, small herbs, tall herbs), and we studied the changes in the abundance of sown species (residents) in both weeded and non-weeded subplots over a period of five years after sowing. The accumulation of new species through spontaneous colonization in the non-weeded treatment did not affect the number of resident species, but had increasingly negative effects over time on the cover of resident species and their aboveground biomass production at community level. Temporal stability of resident populations was lower and year-to-year changes in resident species composition were larger in non-weeded than in weeded subplots. Compositional dissimilarity between weeded and non-weeded treatments increased through time. These negative effects of the colonization of new species on the abundances and stability of resident populations depended on resident species identity and not on additional variation between different functional groups. The colonization of new species did not change the number of resident species emerging from seeds, but reduced seedling densities of residents. Colonization did not affect the structure of resident communities as measured by species evenness, functional trait diversity and mean trait values suggesting that colonization can destabilize the species composition of residents in terms of abundance while leaving them unchanged in terms of functional characteristics. Generally, negative impacts of colonizing species on residents which accelerated through time decreased with an increasing number of sown species. Sowing more diverse grassland mixtures increases their predictability in terms of ecosystem characteristics, which is important for ecological restoration and sustainable agriculture.     

Abundance–suitability relationships for invasive species: Epiphyas postvittana as a case study

Biological Invasions - Prediction of the geographic distribution of an exotic species in a new environment is an important element of risk assessment as it provides an assessment of the spatial...     

Cryptic speciation in the Acari: a function of species lifestyles or our ability to separate species?

There are approximately 55,000 described Acari species, accounting for almost half of all known Arachnida species, but total estimated Acari diversity is reckoned to be far greater. One important source of currently hidden Acari diversity is cryptic speciation, which poses challenges to taxonomists documenting biodiversity assessment as well as to researchers in medicine and agriculture. In this review, we revisit the subject of biodiversity in the Acari and investigate what is currently known about cryptic species within this group. Based on a thorough literature search, we show that the probability of occurrence of cryptic species is mainly related to the number of attempts made to detect them. The use of, both, DNA tools and bioassays significantly increased the probability of cryptic species detection. We did not confirm the generally-accepted idea that species lifestyle (i.e. free-living vs. symbiotic) affects the number of cryptic species. To increase detection of cryptic lineages and to understand the processes leading to cryptic speciation in Acari, integrative approaches including multivariate morphometrics, molecular tools, crossing, ecological assays, intensive sampling, and experimental evolution are recommended. We conclude that there is a demonstrable need for future investigations focusing on potentially hidden mite and tick species and addressing evolutionary mechanisms behind cryptic speciation within Acari.     

Why does the unimodal species richness–productivity relationship not apply to woody species: a lack of clonality or a legacy of tropical evolutionary history?

Aim  To study how differences in species richness patterns of woody and herbaceous plants may be influenced by ecological and evolutionary factors. Unimodal species richness–productivity relationships (SRPRs) have been of interest to ecologists since they were first described three decades ago for British herbaceous vegetation by J. P. Grime. The decrease in richness at high productivity may be due to competitive exclusion of subordinate species, or diverse factors related to evolution and dispersal. Unimodal SRPRs are most often reported for plants, but there are exceptions. For example, unimodal SRPRs are common in the temperate zone but not in the tropics. Similarly, woody species and forest communities in the Northern Hemisphere do not tend to show unimodal SRPRs.
Location  Global.
Methods  We used data from the literature to test whether a unimodal SRPR applies to woody species and forest communities on a global scale. We explored whether the shape of SRPRs may be related to the lack of clonality in woody species (which may prevent their being competitively superior), or the legacy of evolutionary history (most temperate woody species originate from tropical lineages, and due to niche conservatism they may still demonstrate 'tropical patterns'). We used case studies that reported the names of the dominant or most abundant species for productive sites.
Results  Woody species were indeed less clonal than herbaceous species. Both clonality and the temperate evolutionary background of dominating species were associated with unimodality in SRPRs, with woodiness modifying the clonality effect.
Main conclusions  The unimodal SRPR has been common in the ecological literature because most such studies originate from temperate herbaceous communities with many clonal species. Consequently, both evolutionary and ecological factors may influence species richness patterns.     

Diaporthe amygdali,a species complex or a complex species?

Delimitation of species boundaries within the fungal genus Diaporthe has been challenging, but the analyses of combined multilocus DNA sequences has become an important tool to infer phylogenetic relationships and to circumscribe species. However, analyses of congruence between individual gene genealogies and the application of the genealogical concordance principle have been somehow overlooked. We noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, commonly known as D. amygdali complex, occupy a monophyletic clade in Diaporthe phylogenies but the limits of all species within the complex are not entirely clear. To assess the boundaries of species within this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and coalescence-based models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). The incongruence detected between individual gene phylogenies, as well as the results of coalescent methods do not support the recognition of lineages within the complex as distinct species. Moreover, results support the absence of reproductive isolation and barriers to gene flow in this complex, thus providing further evidence that the D. amygdali species complex constitutes a single species. This study highlights the relevance of the application of the GCPSR principle, showing that concatenation analysis of multilocus DNA sequences, although being a powerful tool, might lead to an erroneous definition of species limits. Additionally, it further shows that coalescent methods are useful tools to assist in a more robust delimitation of species boundaries in the genus Diaporthe.     

Can indicator species predict restoration outcomes early in the monitoring process? a case study with peatlands

Success in ecological restoration is rarely assessed rigorously due to insufficient planning for post-restoration monitoring programs, limited funding and, especially, lack of scientifically validated evaluation criteria and protocols. In this article, we propose the use of the Indicator Value Index technique (IndVal), which statistically determines the association of species to one or several particular site types, to obtain indicators of success at the early stages of the recovery process in restoration projects. Peat bogs extracted by the vacuum method, subsequently restored by a moss-transfer technique and regularly monitored for ~10 years were used as a model system to test this approach. We first identified 34 restored sectors of ~10 ha from 4 to 11 years old in twelve eastern-Canadian bogs. These sectors were then classified according to their degree of success in recovering a typical sphagnum moss carpet (restoration goal). Then, we retrospectively reviewed vegetation communities recorded at the third year after restoration to identify indicator species of different categories of restoration success, using the IndVal methodology. By identifying early indicator species, our method provides a tool that guides intervention soon after restoration if a site is not on a desired successional trajectory. Typical bog species, namely the bryophytes S. rubellum and Mylia anomala and the tree Picea mariana, were indicative of successful restoration; while bare peat, lichens and one species of ericaceous shrubs (Empetrum nigrum), which cope better under drier conditions, indicated sites where restoration failed. A surprising finding was that the moss Polytrichum strictum, which is known to facilitate the colonization of sphagnum in disturbed peatlands, is an early indicator of unsuccessful restoration. This finding made us question the nursing role of P. strictum at a cover threshold above ca. 30%, when P. strictum could be outcompeting sphagnum and become dominant. We conclude that the IndVal method is an effective tool to identify early indicators of restoration success when combined with a thoughtful examination of species frequency and cover within each site type.     

To be or not to be a good social partner?

Cooperation based in mutual benefit provides a perfect scenario to start selfish behaviors aimed to obtain greater benefit at the expense of the partner. Here we investigate if mutual benefit cooperation can be stable between individuals that cooperate with kindness (good partners) or if they will be displaced by other individuals that try to obtain more benefit with less cost (bad partners). Our model assumes an asymmetry between partners in such a way that one of them (actor) proposes the cooperation whereas the other (receiver) always accepts the offer. It also assumes that actors can choose the partner on the basis of their past experiences with the potential partners. With the help of a simple two-locus mathematical model we show that not only the gene that conditions the actor preference to choose good partners can increase in frequency but also the gene responsible of the good partner behavior.     

How to remain nonfolded and pliable: the linkers in modular α-amylases as a case study

The primary structure of linkers in a new class of modular α-amylases constitutes a paradigm of the structural basis that allows a polypeptide to remain nonfolded, extended and pliable. Unfolding is mediated through a depletion of hydrophobic residues and an enrichment of hydrophilic residues, amongst which Ser and Thr are over-represented. An extended and flexible conformation is promoted by the sequential arrangement of Pro and Gly, which are the most abundant residues in these linkers. This is complemented by charge repulsion, charge clustering and disulfide-bridged loops. Molecular dynamics simulations suggest the existence of conformational transitions resulting from a transient and localized hydrophobic collapse, arising from the peculiar composition of the linkers. Accordingly, these linkers should not be regarded as fully disordered, but rather as possessing various discrete structural patterns allowing them to fulfill their biological function as a free energy reservoir for concerted motions between structured domains.     

Testing Allsop and West’s size at sex change invariant within a fish species: a spurious ratio or a useful group descriptor?

Recently, it has been suggested that sequential hermaphrodites, from a variety of taxa and a wide range of sizes, change sex at the same relative size. It is said that there exists an invariant (a constant ratio) for such a life trait. However, recent criticisms point out that these results could be a statistical artefact. It has been argued that the wider the range of x-axis values (from 2 mm to 1.5 m in the case of sex change), the higher the probability of identifying an invariant by chance. Here, the invariance of the size at sex change ratio is analysed within a single fish species for which the size of sex change varies within a range of only 6.5 cm. Our results support the invariant rule that fishes change sex when reaching 79% of their maximum size.     

Enhancing lipophilicity as a strategy to overcome resistance against platinum complexes?

Decreased influx represents one of the major resistance mechanisms of platinum complexes. In order to address the question if this mechanism of resistance can be overcome by enhancing the lipophilicity of platinum complexes, we investigated the influence of lipophilicity on cellular accumulation and cytotoxicity in a panel of oxaliplatin analogues with different carrier ligands. Cellular accumulation, DNA platination and cytotoxicity were measured in a cisplatin-sensitive and -resistant ovarian carcinoma (A2780/A2780cis) and in an oxaliplatin-sensitive and -resistant ileocecal colorectal adenocarcinoma (HCT-8/HCT-8ox) cell line pair. Platinum concentrations were determined by flameless atomic absorption spectrometry or adsorptive stripping voltammetry. Passive diffusion represented the main influx mechanism of oxaliplatin analogues during the first minutes of incubation as indicated by a correlation between lipophilicity and early influx rate. Afterwards, the predominant influx mechanism was lipophilicity-independent. More lipophilic complexes showed a reduced cytotoxic activity, although the early influx rate was increased. The resistance profiles of the two cell line pairs were found to be different: HCT-8ox cells were less resistant against more lipophilic complexes, whereas A2780cis cells exhibited a comparable degree of resistance against all investigated compounds. However, the reduction in resistance factor of HCT-8ox cells cannot be explained by increased influx suggesting that other resistance mechanisms are circumvented upon exposure to more lipophilic compounds. Though resistance against more lipophilic platinum complexes analogues is lower we conclude that enhancing lipophilicity is not a successful strategy to overcome platinum resistance as higher lipophilicity is also associated with lower cytotoxic activity.