Mitochondrial sequence divergence among Antarctic killer whale ecotypes is consistent with multiple species

Recently, three visually distinct forms of killer whales (Orcinus orca) were described from Antarctic waters and designated as types A, B and C. Based on consistent differences in prey selection and habitat preferences, morphological divergence and apparent lack of interbreeding among these broadly sympatric forms, it was suggested that they may represent separate species. To evaluate this hypothesis, we compared complete sequences of the mitochondrial control region from 81 Antarctic killer whale samples, including 9 type A, 18 type B, 47 type C and 7 type-undetermined individuals. We found three fixed differences that separated type A from B and C, and a single fixed difference that separated type C from A and B. These results are consistent with reproductive isolation among the different forms, although caution is needed in drawing further conclusions. Despite dramatic differences in morphology and ecology, the relatively low levels of sequence divergence in Antarctic killer whales indicate that these evolutionary changes occurred relatively rapidly and recently.     

Linking killer whale survival and prey abundance: food limitation in the oceans' apex predator?

Killer whales (Orcinus orca) are large predators that occupy the top trophic position in the world''s oceans and as such may have important roles in marine ecosystem dynamics. Although the possible top-down effects of killer whale predation on populations of their prey have received much recent attention, little is known of how the abundance of these predators may be limited by bottom-up processes. Here we show, using 25 years of demographic data from two populations of fish-eating killer whales in the northeastern Pacific Ocean, that population trends are driven largely by changes in survival, and that survival rates are strongly correlated with the availability of their principal prey species, Chinook salmon (Oncorhynchus tshawytscha). Our results suggest that, although these killer whales may consume a variety of fish species, they are highly specialized and dependent on this single salmonid species to an extent that it is a limiting factor in their population dynamics. Other ecologically specialized killer whale populations may be similarly constrained to a narrow range of prey species by culturally inherited foraging strategies, and thus are limited in their ability to adapt rapidly to changing prey availability.     

Rugged adaptive landscapes shape a complex,sympatric radiation

Strong disruptive ecological selection can initiate speciation, even in the absence of physical isolation of diverging populations. Species evolving under disruptive ecological selection are expected to be ecologically distinct but, at least initially, genetically weakly differentiated. Strong selection and the associated fitness advantages of narrowly adapted individuals, coupled with assortative mating, are predicted to overcome the homogenizing effects of gene flow. Theoretical plausibility is, however, contrasted by limited evidence for the existence of rugged adaptive landscapes in nature. We found evidence for multiple, disruptive ecological selection regimes that have promoted divergence in the sympatric, incipient radiation of ‘sharpfin’ sailfin silverside fishes in ancient Lake Matano (Sulawesi, Indonesia). Various modes of ecological specialization have led to adaptive morphological differences between the species, and differently adapted morphs display significant but incomplete reproductive isolation. Individual fitness and variation in morphological key characters show that disruptive selection shapes a rugged adaptive landscape in this small but complex incipient lake fish radiation.     

Modelling the multidimensional niche by linking functional traits to competitive performance

Linking competitive outcomes to environmental conditions is necessary for understanding species'' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified, and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts.     

Spatial niche partitioning in dinosaurs from the latest cretaceous (Maastrichtian) of North America

We examine patterns of occurrence of associated dinosaur specimens (n = 343) from the North American Upper Cretaceous Hell Creek Formation and equivalent beds, by comparing their relative abundance in sandstone and mudstone. Ceratopsians preferentially occur in mudstone, whereas hadrosaurs and the small ornithopod Thescelosaurus show a strong association with sandstone. By contrast, the giant carnivore Tyrannosaurus rex shows no preferred association with either lithology. These lithologies are used as an indicator of environment of deposition, with sandstone generally representing river environments, and finer grained sediments typically representing floodplain environments. Given these patterns of occurrence, we argue that spatial niche partitioning helped reduce competition for resources between the herbivorous dinosaurs. Within coastal lowlands ceratopsians preferred habitats farther away from rivers, whereas hadrosaurs and Thescelosaurus preferred habitats in close proximity to rivers, and T. rex, the ecosystem's sole large carnivore, inhabited both palaeoenvironments. Spatial partitioning of the environment helps explain how several species of large herbivorous dinosaurs coexisted. This study emphasizes that different lithologies can preserve dramatically dissimilar vertebrate assemblages, even when deposited in close proximity and within a narrow window of time. The lithology in which fossils are preserved should be recorded as these data can provide unique insights into the palaeoecology of the animals they preserve.     

Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane

Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher ¹⁵N-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS.     

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria

Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O₂ concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO₂ fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO₂ seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.     

Adaptation and niche construction in human prehistory: a case study from the southern Scandinavian Late Glacial

The niche construction model postulates that human bio-social evolution is composed of three inheritance domains, genetic, cultural and ecological, linked by feedback selection. This paper argues that many kinds of archaeological data can serve as proxies for human niche construction processes, and presents a method for investigating specific niche construction hypotheses. To illustrate this method, the repeated emergence of specialized reindeer (Rangifer tarandus) hunting/herding economies during the Late Palaeolithic (ca 14.7-11.5 kyr BP) in southern Scandinavia is analysed from a niche construction/triple-inheritance perspective. This economic relationship resulted in the eventual domestication of Rangifer. The hypothesis of whether domestication was achieved as early as the Late Palaeolithic, and whether this required the use of domesticated dogs (Canis familiaris) as hunting, herding or transport aids, is tested via a comparative analysis using material culture-based phylogenies and ecological datasets in relation to demographic/genetic proxies. Only weak evidence for sustained niche construction behaviours by prehistoric hunter-gatherer in southern Scandinavia is found, but this study nonetheless provides interesting insights into the likely processes of dog and reindeer domestication, and into processes of adaptation in Late Glacial foragers.     

The shape of things to come: woodland herb niche contraction begins during recruitment in mesic forest microhabitat

Natural abundance is shaped by the abiotic requirements and biotic interactions that shape a species' niche, yet these influences are rarely decoupled. Moreover, most plant mortality occurs during early life stages, making seed recruitment critical in structuring plant populations. We find that natural abundance of two woodland herbs, Hexastylis arifolia and Hepatica nobilis, peaks at intermediate resource levels, a pattern probably formed by concurrent abiotic and biotic interactions. To determine how this abundance patterning reflects intrinsic physiological optima and extrinsic biotic interactions, we translocate adults and seeds to novel locations across experimentally extended abiotic gradients. These experiments indicate that the plant distributions probably reflect biotic interactions as much as physiological requirements, and that adult abundance provides a poor indication of the underlying niche requirements. The positive response exhibited by adult transplants in the wettest conditions is offset by increased fungal attack on buried seeds consistent with peak natural abundance where soil moisture is intermediate. This contraction of niche space is best described by Connell's model--species are limited by physiological tolerances where resources are low and biotic interactions where resources are high.     

The function of multi-pod aggregations of fish-eating killer whales (<Emphasis Type="Italic">Orcinus orca</Emphasis>) in Kamchatka,Far East Russia

In fish-eating North Pacific killer whales, large multi-pod aggregations of up to 100 animals often occur. These aggregations are thought to be reproductive gatherings where mating between members of different pods takes place. However, killer whales are social animals, and the role of these aggregations might also be establishing and maintaining social bonds between pods. Alternatively, it is also possible that multi-pod aggregations are in some way connected with foraging or searching for fish. In this study of killer whales in the western North Pacific, we describe multi-pod aggregations quantitatively and suggest their functional role in the life of fish-eating killer whales. We show that foraging is rare in multi-pod aggregations, whether inter-clan or intra-clan, and thus they are unlikely to play an important role in cooperative foraging. Socialising occurs more frequently in inter-clan rather than in intra-clan aggregations, which suggests the higher arousal level and possible mating during inter-clan aggregations. In summary, multi-pod aggregations of Kamchatka killer whales might be both reproductive assemblages and “clubs” of some kind in which whales gather to establish and maintain social bonds.     

Evidence of social niche construction: persistent and repeated social interactions generate stronger personalities in a social spider

While there are now a number of theoretical models predicting how consistent individual differences in behaviour may be generated and maintained, so far, there are few empirical tests. The social niche specialization hypothesis predicts that repeated social interactions among individuals may generate among-individual differences and reinforce within-individual consistency through positive feedback mechanisms. Here, we test this hypothesis using groups of the social spider Stegodyphus mimosarum that differ in their level of familiarity. In support of the social niche specialization hypothesis, individuals in groups of spiders that were more familiar with each other showed greater repeatable among-individual variation in behaviour. Additionally, individuals that were more familiar with each other exhibited lower within-individual variation in behaviour, providing one of the first examples of how the social environment can influence behavioural consistency. Our study demonstrates the potential for the social environment to generate and reinforce consistent individual differences in behaviour and provides a potentially general mechanism to explain this type of behavioural variation in animals with stable social groups.     

A test of the sympatric host race formation hypothesis in Neodiprion (Hymenoptera: Diprionidae)

Theory suggests that sympatric speciation is possible; however, its prevalence in nature remains unknown. Because Neodiprion sawflies are host specialists and mate on their hosts, sympatric speciation via host shifts may be common in this genus. Here, we test this hypothesis using near-complete taxonomic sampling of a species group, comprehensive geographical and ecological data, and multiple comparative methods. Host-use data suggest that host shifts contributed to the evolution of reproductive isolation in Neodiprion and previous work has shown that gene flow accompanied divergence. However, geographical data provide surprisingly little support for the hypothesis that host shifts occurred in sympatry. While these data do not rule out sympatric host race formation in Neodiprion, they suggest that this speciation mode is uncommon in the genus and possibly in nature.     

Chimpanzee fauna isotopes provide new interpretations of fossil ape and hominin ecologies

Carbon and oxygen stable isotopes within modern and fossil tooth enamel record the aspects of an animal''s diet and habitat use. This investigation reports the first isotopic analyses of enamel from a large chimpanzee community and associated fauna, thus providing a means of comparing fossil ape and early hominin palaeoecologies with those of a modern ape. Within Kibale National Park forest, oxygen isotopes differentiate primate niches, allowing for the first isotopic reconstructions of degree of frugivory versus folivory as well as use of arboreal versus terrestrial resources. In a comparison of modern and fossil community isotopic profiles, results indicate that Sivapithecus, a Miocene ape from Pakistan, fed in the forest canopy, as do chimpanzees, but inhabited a forest with less continuous canopy or fed more on leaves. Ardipithecus, an early hominin from Ethiopia, fed both arboreally and terrestrially in a more open habitat than inhabited by chimpanzees.     

Evidence of photosymbiosis in Palaeozoic tabulate corals

Coral reefs form the most diverse of all marine ecosystems on the Earth. Corals are among their main components and owe their bioconstructing abilities to a symbiosis with algae (Symbiodinium). The coral–algae symbiosis had been traced back to the Triassic (ca 240 Ma). Modern reef-building corals (Scleractinia) appeared after the Permian–Triassic crisis; in the Palaeozoic, some of the main reef constructors were extinct tabulate corals. The calcium carbonate secreted by extant photosymbiotic corals bears characteristic isotope (C and O) signatures. The analysis of tabulate corals belonging to four orders (Favositida, Heliolitida, Syringoporida and Auloporida) from Silurian to Permian strata of Europe and Africa shows these characteristic carbon and oxygen stable isotope signatures. The δ¹⁸O to δ¹³C ratios in recent photosymbiotic scleractinians are very similar to those of Palaeozoic tabulates, thus providing strong evidence of such symbioses as early as the Middle Silurian (ca 430 Ma). Corals in Palaeozoic reefs used the same cellular mechanisms for carbonate secretion as recent reefs, and thus contributed to reef formation.     

Development of the male germline stem cell niche in Drosophila

Stem cells are found in specialized microenvironments, or "niches", which regulate stem cell identity and behavior. The adult testis and ovary in Drosophila contain germline stem cells (GSCs) with well-defined niches, and are excellent models for studying niche development. Here, we investigate the formation of the testis GSC niche, or "hub", during the late stages of embryogenesis. By morphological and molecular criteria, we identify and follow the development of an embryonic hub that forms from a subset of anterior somatic gonadal precursors (SGPs) in the male gonad. Embryonic hub cells form a discrete cluster apart from other SGPs, express several molecular markers in common with the adult hub and organize anterior-most germ cells in a rosette pattern characteristic of GSCs in the adult. The sex determination genes transformer and doublesex ensure that hub formation occurs only in males. Interestingly, hub formation occurs in both XX and XY gonads mutant for doublesex, indicating that doublesex is required to repress hub formation in females. This work establishes the Drosophila male GSC niche as a model for understanding the mechanisms controlling niche formation and initial stem cell recruitment, as well as the development of sexual dimorphism in the gonad.     

Live image profiling of neural crest lineages in zebrafish transgenic lines

Zebrafish transgenic lines are important experimental tools for lineage tracing and imaging studies. It is crucial to precisely characterize the cell lineages labeled in transgenic lines to understand their limitations and thus properly interpret the data obtained from their use; only then can we confidently select a line appropriate for our particular research objectives. Here we profiled the cell lineages labeled in the closely related neural crest transgenic lines Tg(foxd3:GFP), Tg(sox10:eGFP) and Tg(sox10:mRFP). These fish were crossed to generate embryos, in which foxd3 and sox10 transgenic neural crest labeling could be directly compared at the cellular level using live confocal imaging. We have identified key differences in the cell lineages labeled in each line during early neural crest development and demonstrated that the most anterior cranial neural crest cells initially migrating out of neural tube at the level of forebrain and anterior midbrain express sox10:eGFP and sox10:mRFP, but not foxd3:GFP. This differential profile was robustly maintained in the different-tiating progeny of the neural crest lineages until 3.5dpf. Our data will enable researchers to make an informed choice in selecting transgenic lines for future neural crest research.     

Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background

Despite the existence of formal models to explain how chromosomal rearrangements can be fixed in a population in the presence of gene flow, few empirical data are available regarding the mechanisms by which genome shuffling contributes to speciation, especially in mammals. In order to shed light on this intriguing evolutionary process, here we present a detailed empirical study that shows how Robertsonian (Rb) fusions alter the chromosomal distribution of recombination events during the formation of the germline in a Rb system of the western house mouse (Mus musculus domesticus). Our results indicate that both the total number of meiotic crossovers and the chromosomal distribution of recombination events are reduced in mice with Rb fusions and that this can be related to alterations in epigenetic signatures for heterochromatinization. Furthermore, we detected novel house mouse Prdm9 allelic variants in the Rb system. Remarkably, mean recombination rates were positively correlated with a decrease in the number of ZnF domains in the Prdm9 gene. The suggestion that recombination can be modulated by both chromosomal reorganizations and genetic determinants that control the formation of double-stranded breaks during meiosis opens new avenues for understanding the role of recombination in chromosomal speciation.