Responses Of Taxa Research Articles

From individual to joint species distribution models: A comparison of model complexity and predictive performance

AbstractAimSpecies distribution models (SDMs) are widely used to study geographic distributions of taxa in response to natural and anthropogenic environmental conditions. For a community, common approaches include fitting individual SDMs (iSDMs) to all taxa or directly modelling community properties such as richness. However, the parameters of iSDMs are difficult to identify for rare taxa, and community properties do not reveal taxon‐specific responses. Individual models can be combined into a hierarchical multispecies distribution model (mSDM) that constrains taxon‐specific parameters according to overarching community parameters, or a joint model (jSDM) in which interdependencies between taxa are jointly inferred. We compare how individual, hierarchical multispecies and joint SDMs differ in quality of fit, explanatory power and predictive performance, and analyse how these properties depend on the prevalence of taxa.TaxaPresence–absence observations of 245 benthic macroinvertebrate taxa identified at a mixed taxonomic resolution.LocationFour hundred and ninety‐two sites in rivers throughout Switzerland.MethodsIndividual, hierarchical and joint hierarchical generalized linear models (GLM) were developed for all taxa. Parameters were estimated using maximum likelihood estimation or Bayesian inference with Hamiltonian Markov chain Monte Carlo simulations. Predictive performance was assessed with cross‐validation. In addition, the predicted family and species richness of the models was compared with a GLM for richness.ResultsIndividual models show a slightly higher quality of fit largely due to overfitting for rare taxa. The mSDM achieves a similar quality of fit and explanatory power, mitigates overfitting for rare taxa and considerably improves predictive performance over the whole community. The joint models further improve the quality of fit, but decrease predictive performance and increase predictive uncertainty.Main conclusionsWe show that even a relatively simple mSDM combines many of the analytical capabilities of iSDMs and improves predictive performance. Increasingly complex mSDMs and jSDMs provide additional analytical possibilities, but depending on the data and research questions, different levels of complexity may be appropriate.

Transcriptomic responses to predator kairomones in embryos of the aquatic snail Radix balthica.

The ability of organisms to respond to predation threat by exhibiting induced defenses is well documented, but studies on the potential mechanistic basis for such responses are scarce. Here, we examine the transcriptomic response to predator kairomones of two functionally distinct developmental stages in embryos of the aquatic snail Radix balthica: E8—the stage at which a range‐finding trial indicated that kairomone‐induced accelerated growth and development first occurred; and E9—the stage at which embryos switched from ciliary‐ to crawling‐driven locomotion. We tested whether expression profiles were influenced by kairomones and whether this influence varied between stages. We also identified potential candidate genes for investigating mechanisms underpinning induced responses. There were 6,741 differentially expressed transcripts between developmental stages, compared to just five in response to predator kairomones. However, on examination of functional enrichment in the transcripts responding to predator kairomones and adopting a less stringent significance threshold, 206 transcripts were identified relating to muscle function, growth, and development, with this response being greater at the later E9 stage. Furthermore, these transcripts included putative annotations for genes identified as responding to predator kairomones in other taxa, including C1q, lectin, and actin domains. Globally, transcript expression appeared reduced in response to predator kairomones and we hypothesize that this might be a result of metabolic suppression, as has been reported in other taxa in response to predation threat.

Long‐Term Monitoring of Macroinvertebrate Communities Over 2,300 km of the Murray River Reveals Ecological Signs of Salinity Mitigation Against a Backdrop of Climate Variability

AbstractWe investigated the ecological effects of salinity mitigation strategies in the Murray‐Darling Basin (MDB) using macroinvertebrate data collected over 2,300 km of the Murray River between 1980 and 2012. The MDB covers 1 × 106km2 and includes both temperate and semiarid climate zones. It was extensively developed to support irrigated agriculture in the early to mid‐1900s, and the secondary salinization that followed has become a major concern. During 1975–1985 daily salinity levels, measured as electrical conductivity above the Murray River off‐take points for South Australia's major urban water supplies, were above 800 μS/cm for 40% of the time, necessitating mitigation strategies that have reduced the average salinity by about 150 μS/cm since monitoring began. The MDB has also experienced several major floods and droughts during this time, and surface temperatures in the MDB have increased by 0.8 °C since 1910, mostly in the last 50 years. We hypothesized that (1) taxa richness would increase in response to floods; (2) community structure would shift toward tolerant, opportunistic taxa in response to warming; and (3) geographical ranges of species would change in response to shifting stream isotherms and reducing salinity. Our hypotheses were supported, although increases in water temperature appeared to be due principally to the 1997–2009 Millennium drought. Importantly, against a backdrop of significant climate variability, we believe we have distinguished a change in community structure along a salinity gradient and that changes over the 33 years can in part be attributed to mitigation strategies.

Changes in the Geographic Distribution of the Diana Fritillary (Speyeria diana: Nymphalidae) under Forecasted Predictions of Climate Change.

Climate change is predicted to alter the geographic distribution of a wide variety of taxa, including butterfly species. Research has focused primarily on high latitude species in North America, with no known studies examining responses of taxa in the southeastern United States. The Diana fritillary (Speyeria diana) has experienced a recent range retraction in that region, disappearing from lowland sites and now persisting in two phylogenetically distinct high elevation populations. These findings are consistent with the predicted effects of a warming climate on numerous taxa, including other butterfly species in North America and Europe. We used ecological niche modeling to predict future changes to the distribution of S. diana under several climate models. To evaluate how climate change might influence the geographic distribution of this butterfly, we developed ecological niche models using Maxent. We used two global circulation models, the community climate system model (CCSM) and the model for interdisciplinary research on climate (MIROC), under low and high emissions scenarios to predict the future distribution of S. diana. Models were evaluated using the receiver operating characteristics area under curve (AUC) test and the true skill statistics (TSS) (mean AUC = 0.91 ± 0.0028 SE, TSS = 0.87 ± 0.0032 SE for representative concentration pathway (RCP) = 4.5; and mean AUC = 0.87 ± 0.0031 SE, TSS = 0.84 ± 0.0032 SE for RCP = 8.5), which both indicate that the models we produced were significantly better than random (0.5). The four modeled climate scenarios resulted in an average loss of 91% of suitable habitat for S. diana by 2050. Populations in the southern Appalachian Mountains were predicted to suffer the most severe fragmentation and reduction in suitable habitat, threatening an important source of genetic diversity for the species. The geographic and genetic isolation of populations in the west suggest that those populations are equally as vulnerable to decline in the future, warranting ongoing conservation of those populations as well. Our results suggest that the Diana fritillary is under threat of decline by 2050 across its entire distribution from climate change, and is likely to be negatively affected by other human-induced factors as well.

Divergent gene expression among phytoplankton taxa in response to upwelling.

Frequent blooms of phytoplankton occur in coastal upwelling zones creating hotspots of biological productivity in the ocean. As cold, nutrient-rich water is brought up to sunlit layers from depth, phytoplankton are also transported upwards to seed surface blooms that are often dominated by diatoms. The physiological response of phytoplankton to this process, commonly referred to as shift-up, is characterized by increases in nitrate assimilation and rapid growth rates. To examine the molecular underpinnings behind this phenomenon, metatranscriptomics was applied to a simulated upwelling experiment using natural phytoplankton communities from the California Upwelling Zone. An increase in diatom growth following 5 days of incubation was attributed to the genera Chaetoceros and Pseudo-nitzschia. Here, we show that certain bloom-forming diatoms exhibit a distinct transcriptional response that coordinates shift-up where diatoms exhibited the greatest transcriptional change following upwelling; however, comparison of co-expressed genes exposed overrepresentation of distinct sets within each of the dominant phytoplankton groups. The analysis revealed that diatoms frontload genes involved in nitrogen assimilation likely in order to outcompete other groups for available nitrogen during upwelling events. We speculate that the evolutionary success of diatoms may be due, in part, to this proactive response to frequently encountered changes in their environment.

Trophic structure of an African savanna river and organic matter inputs by large terrestrial herbivores: A stable isotope approach

Abstract Knowledge of trophic structure is important to understand sources and pathways of energy resources in community ecology and to identify determinants of ecosystem changes. Yet, little is known from rivers of African savanna receiving large inputs of terrestrial organic matter and nutrients by large mammalian herbivores. We used Stable Isotope (δ13C and δ15N) Bayesian Ellipses in R (SIBER) and Layman's community‐wide metrics to describe seasonal variation in trophic niches and trophic structures in midorder river reaches in the Mara River (Kenya) that differed in environmental conditions (agricultural vs. forested) and amounts of organic matter and nutrients (low vs. high inputs by livestock and hippopotami, Hippopotamus amphibius). These analyses were supplemented with data on the trophic diversity of macroinvertebrate functional feeding groups (FFGs) and fish trophic guilds. The δ13C and δ15N of basal resources and consumers differed between sites and changed with seasons. Sites in agricultural areas that were utilised by livestock and a site with hippopotami had higher δ13C than the forested site due to the presence of C4 carbon from egestion and excretion by the grazers. The forested site recorded the most taxon‐rich and trophic‐diverse invertebrate community, suggesting both autochthonous and allochthonous sources of energy were available. Agricultural sites and the site with hippopotami recorded high abundances of collector taxa in response to large inputs of organic matter. Fish trophic guilds were less diverse and were dominated by insectivores. The food web at the forested site had the widest trophic niche size and highest isotopic trophic diversity compared to sites in areas with large mammalian herbivores. Invertebrate and fish trophic niche sizes changed according to food resources varying with space and time. Invertebrates had higher δ13C values during the dry season. In contrast, fish showed higher δ13C values during the wet season, and trophic niche sizes were constricted and considerably overlapping, suggesting feeding on a narrow range of food sources with high trophic redundancy. This study showed that increased terrestrial organic matter by large mammalian herbivores affected trophic diversity and niche sizes for aquatic consumers in rivers draining the African savanna. Linking the density of terrestrial large mammalian herbivores to aquatic ecosystem structure and function could help manage their populations sustainably.

Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter.

In the Southern Ocean, natural iron fertilization in the wake of islands leads to annually occurring spring phytoplankton blooms associated with enhanced heterotrophic activity through the release of labile dissolved organic matter (DOM). The aim of this study was to investigate experimentally how diatom-derived DOM affects the composition of Southern Ocean winter water bacterial communities and to identify the most responsive taxa. A bacterial community collected in the naturally iron-fertilized region off Kerguelen Island (KEOPS2 October-November 2011) was grown onboard in continuous cultures, on winter water alone or amended with diatom-derived DOM supplied at identical DOC concentrations. 454 sequencing of 16S amplicons revealed that the two DOM sources sustained strikingly different bacterial communities, with higher relative abundances of Sulfitobacter, Colwellia and Methylophaga operational taxonomic units (OTUs) and lower relative abundances of Polaribacter, Marinobacter, NAC11-7 and SAR11 OTUs in diatom-DOM compared to winter water conditions. Using a modeling approach, we obtained growth rates for phylogenetically diverse taxa varying between 0.12 and 0.49 d-1 under carbon-limited conditions. Our results identify diatom DOM as a key factor shaping Southern Ocean winter water bacterial communities and suggest a role for niche partitioning and microbial interactions in organic matter utilization.

Divergent gene expression among phytoplankton taxa in response to upwelling

Divergent gene expression among phytoplankton taxa in response to upwelling

Arab-Madagascan brachiopod dispersal along the North-Gondwana paleomargin towards the Western Tethys Ocean during the Early Toarcian (Jurassic)

Multiple approaches, mainly focused on assessing the depositional environments, paleotemperature, chronostratigraphical and paleobiogeographical data, morphometrical analyses and the study of the internal structure of spiriferinide brachiopods assigned to the genus Calyptoria, have revealed that this brachiopod fauna migrated from their Arab-Madagascan homeland along the North-Gondwana paleomargin into the peri-Iberian epicontinental platform system, in the same well-known spreading episode suffered by the Arab-Madagascan Bouleiceras ammonite fauna over the worldwide-distributed early Toarcian platforms. This brachiopod fauna has been so far overlooked as potential Arab-Madagascan immigrant fauna, as it was integrated together with diverse assemblages well-established in the peri-Iberian basins. Dispersal of Calyptoria stock was conditioned by the interplay of several factors, such as the tectonic framework, the development of epicontinental seas on both Tethyan margins, the early Toarcian transgression, the prevailing ocean current pattern, and their limited ability for dispersal. The revised chronostratigraphical framework of this dispersal episode reveals the coincidence with the thermal maximum recorded prior to the Early Toarcian Mass Extinction Event (ETMEE) in the westernmost Tethys Ocean. The concurrence of these factors played a significant role in the Calyptoria spreading, showing an inter-tropical distribution between 0° and 30° in both hemispheres. The taxonomical updating performed in the light of the current systematic trends support this adaptive strategy carried out by Calyptoria species, consisting of a sudden and practically synchronous dispersal without outstanding morphological changes instead of the diverse evolution of different brachiopod taxa in response to the environmental changes related to the ETMEE. Updating and rearranging of the species attributed to the genus Calyptoria suggest a new systematic scheme for several former attributions, supporting that lower Toarcian occurrences of L. undulata from westernmost Tethyan areas belong to Calyptoria, thus pointing towards the dispersal from the Northern peri-Gondwana seas to the westernmost Tethyan epicontinental platforms. Similar adaptive strategies were linked to other extinction events, supporting a possible pattern in the response of certain brachiopod populations to such biotic crises.

Forest bees are replaced in agricultural and urban landscapes by native species with different phenologies and life-history traits.

Anthropogenic landscapes are associated with biodiversity loss and large shifts in species composition and traits. These changes predict the identities of winners and losers of future global change, and also reveal which environmental variables drive a taxon's response to land use change. We explored how the biodiversity of native bee species changes across forested, agricultural, and urban landscapes. We collected bee community data from 36 sites across a 75,000km2 region, and analyzed bee abundance, species richness, composition, and life-history traits. Season-long bee abundance and richness were not detectably different between natural and anthropogenic landscapes, but community phenologies differed strongly, with an early spring peak followed by decline in forests, and a more extended summer season in agricultural and urban habitats. Bee community composition differed significantly between all three land use types, as did phylogenetic composition. Anthropogenic land use had negative effects on the persistence of several life-history strategies, including early spring flight season and brood parasitism, which may indicate adaptation to conditions in forest habitat. Overall, anthropogenic communities are not diminished subsets of contemporary natural communities. Rather, forest species do not persist in anthropogenic habitats, but are replaced by different native species and phylogenetic lineages preadapted to open habitats. Characterizing compositional and functional differences is crucial for understanding land use as a global change driver across large regional scales.

Impact of pyrene and cadmium co-contamination on prokaryotic community in coastal sediment microcosms

Acute ecological impacts of co-contamination of polycyclic aromatic hydrocarbons (PAHs) and heavy metals on diversity and composition of coastal benthic prokaryotes were unclear. We took pyrene (Pyr) and cadmium (Cd) as the representatives and mimicked an eight-week exposure of moderate and high levels of Pyr, Cd and their mixtures. 16S rRNA amplicon sequencing was used to investigate interaction of the contaminants in temporal succession of prokaryotes. Generally, concentrations of Pyr and HCl-extractable Cd in the sediments were stable over time. Effects and interaction of Pyr and Cd on prokaryotic α-diversity were temporally- and dose-dependent with a decreasing trend in richness and Shannon index under various contamination regimes, particularly in the single-Cd contaminated groups at the early stage. Temporal variability and Pyr-induced pattern in prokaryotic composition were observed. However, Pyr and Cd showed a persistent interaction in prokaryotic composition after 7 days, altering successional trajectories of communities. The communities under Pyr contamination regardless of Cd could be at a developing stage for an active PAH-degrading community with appearance of a pioneer Cycloclasticus phylotype, persistently showing a strong correlation with Pyr level. The associations of phylotypes and Cd level were short-lived and weak, corresponding to the overall resistance of prokaryotic composition to Cd. In the high-throughput sequencing era, using microcosm experiment, we renewed the knowledge about how prokaryotes vary in terms of α-diversity, composition and specific taxa in response to co-contamination of model contaminants at a temporal scale.

Small noncoding RNA expression during extreme anoxia tolerance of annual killifish (Austrofundulus limnaeus) embryos.

Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance. Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrates known, surviving over 100 days at their peak tolerance at 25°C. Their anoxia tolerance and physiology vary over development, such that both anoxia-tolerant and anoxia-sensitive phenotypes comprise the species. This allows for a robust comparison to identify sncRNAs essential to anoxia-tolerance. For this study, RNA sequencing was used to identify and quantify expression of sncRNAs in four embryonic stages of A. limnaeus in response to an exposure to anoxia and subsequent aerobic recovery. Unique stage-specific patterns of expression were identified that correlate with anoxia tolerance. In addition, embryos of A. limnaeus appear to constitutively express stress-responsive miRNAs. Most differentially expressed sncRNAs were expressed at higher levels during recovery. Many novel groups of sncRNAs with expression profiles suggesting a key role in anoxia tolerance were identified, including sncRNAs derived from mitochondrial tRNAs. This global analysis has revealed groups of candidate sncRNAs that we hypothesize support anoxia tolerance.

Fertilization decreases compositional variation of paddy bacterial community across geographical gradient

Fertilization is one of the most common agricultural practices to meet an increasing global demand for food products. Few investigations have been reported on spatial variation of microbial community composition in response to fertilizations in agroecosystems at a large scale. To improve the related understandings, we have evaluated the taxonomic and phylogenetic diversities of bacterial taxa in response to three fertilization strategies in six paddy experiment sites spanning across subtropical China. We found the large-scale compositional variation of paddy bacterial community is shaped by both geographic location and environmental selection, and the former is the dominant factor. The slopes of distance-decay relationships (DDR) are flattened by fertilizations, NPK (mineral NPK fertilizers) and OM (mineral NPK fertilizers plus organic amendments) when compared to Control. A flattened DDR implies that bacterial community composition is greatly homogenized by fertilizations in paddies. It is also inferred that fertilization decreases sensitivity of bacterial community to geographic and environmental factors, which is speculated to be beneficial for agroecosystem stability and yield sustainability. Results from this investigation correlate microscopic agroecosystem with macroscopic agricultural practices.

Modern diatoms from a temperate river in South America: the Colorado River (North Patagonia, Argentina)

Diatom assemblage composition and distribution from surface sediment samples of the Colorado River, Patagonia were analysed in relation to environmental variables using multivariate techniques. The aim of this study was to determine the ecological preferences of the taxa and provide analogues for paleoenvironmental reconstructions in estuarine and fluvial environments of southern South America. Cluster analysis identified two main diatom assemblages, one grouping sites with a marine influence, and another group influenced by typical riverine conditions. Canonical correspondence analysis indicated that major ion concentrations contribute significantly to explain the variation in the composition of diatom assemblages. A total of 208 taxa belonging to 56 genera were recorded. In estuarine sites, the assemblages were characterized by marine-brackish tychoplankton, such as Cymatosira belgica, Rhaphoneis amphiceros, Delphineis minutissima, Paralia sulcata and Paralia sulcata var. coronota. Diatom communities in riverine sites were dominated by freshwater taxa such as Staurosira venter, Pseudostaurosira brevistriata, Punctastriata glubokoensis and Punctastriata lancettula. Two Punctastriata species that were difficult to distinguish with LM were examined in detail with SEM, and the value of detailed LM and SEM analysis for distinguishing Punctastriata spp. and other small fragilarioids is discussed. Based on their autoecological affinities, it is likely that the dominance of small fragilarioids is related to the increase in ionic concentration in the basin, as a consequence of both precipitation decrease, and an increase in urban, industrial and agricultural activities. The construction of a flood-control structure in the northern branch of the delta modified the diatom community so that marine taxa were replaced by brackish-freshwater taxa in response to changes in salinity, substrata and water depth.

Birds as surrogates for mammals and reptiles: Are patterns of cross-taxonomic associations stable over time in a human-modified landscape?

Cross-taxonomic surrogates can be feasible alternatives to direct measurements of biodiversity in conservation if validated with robust data and used with explicit goals. However, few studies of cross-taxonomic surrogates have examined how temporal changes in composition or richness in one taxon can drive variation in concordant patterns of diversity in another taxon, particularly in a dynamic and heavily modified landscape. We examined this problem by assessing changes in cross-taxonomic associations over time between the surrogate (birds) and target vertebrate taxa (mammals, reptiles) that demand high sampling effort, in a heterogeneous mosaic landscape comprising pine monoculture, eucalypt woodland remnants and agricultural land. Focussing on four study years (1999, 2001, 2011, 2013) from a dataset spanning 15 years, we: (1) investigated temporal changes in cross-taxonomic congruency among three animal taxa, (2) explored how temporal variation in composition and species richness of each taxon might account for variation in cross-taxonomic congruency, and (3) identified habitat structural variables that are strongly correlated with species composition of each taxon. We found the strength of cross-taxonomic congruency varied between taxa in response to both landscape context and over time. Among the three taxa, overall correlations were weak but were consistently positive and strongest between birds and mammals, while correlations involving reptiles were usually weak and negative. We also found that stronger species richness and composition correlations between birds and mammals were not only more prevalent in woodland remnants in the agricultural matrix, but they also increased in strength over time. Temporal shifts in species composition differed in rate and extent among the taxa even though these changes were significant over time, while important habitat structural correlates were seldom shared across taxa. Our study highlights the role of the landscape matrix and time in shaping animal communities and the resulting cross-taxonomic associations in the woodland remnants, especially after a major perturbation event (i.e. plantation establishment). In such dynamic landscapes, differing and taxon-specific shifts in diversity over time can influence the strength, direction and consistency of cross-taxonomic correlations, therefore posing a ‘temporal’ problem for the use of surrogates like birds in monitoring and assessments of biodiversity, and conservation management practices.

Distribution pattern of black fly (Diptera: Simuliidae) assemblages along an altitudinal gradient in Peninsular Malaysia.

BackgroundPreimaginal black flies (Diptera: Simuliidae) are important components of the stream ecosystem. However, there has been limited research undertaken on the vertical distribution of preimaginal black flies and their associated ecological factors. Stream conditions are generally variable along the altitudinal gradient. Therefore, we conducted an in-depth entomological survey to investigate the simuliid distribution pattern along an altitudinal gradient in Peninsular Malaysia.MethodsA total of 432 collections were performed in this study (24 samplings at each of 18 fixed-streams at monthly intervals) from February 2012 to January 2014. Larvae and pupae attached on aquatic substrates such as grasses, leaves and stems, twigs, plant roots and rocks were collected by hand using fine forceps. Stream depth (m), width (m), velocity (m/s), water temperature (°C), acidity (pH), conductivity (mS/cm) and dissolved oxygen (mg/L) were measured at the time of each collection.ResultsA total of 35 black fly species were recorded in the present study. The most frequently collected species were Simulium tani (31.7 %) and S. whartoni (21.5 %), while the relatively common species were Simulium sp. (nr. feuerborni) (16.2 %), S. decuplum (15.5 %), S. angulistylum (14.8 %), S. bishopi (13.2 %) and S. izuae (11.8 %). Total estimated species richness ranged between 39.8 and 41.3, which yielded more than 80 % of sampling efficiency. Six simuliid species were distributed below 500 m, whereas eight species were distributed above 1400 m. Simulium sp. (nr. feuerborni) and S. asakoae were found from middle to high altitudes (711–1813 m). Simulium whartoni, S. brevipar and S. bishopi were distributed widely from low to high altitudes (159–1813 m). Regression analysis between species richness and PCs revealed that the species richness was significantly associated with wider, deeper and faster streams at low altitude, normal water temperature (23–25 °C), low conductivity, higher discharge, more canopy cover and riparian vegetation and with larger streambed particles (F = 20.8, df = 1, 422, P < 0.001). Forward logistic regression indicated four species were significantly related to the stream variables (S. whartoni, Simulium sp. (nr. feuerborni), S. tani and S. angulistylum). Canonical correspondence analysis indicated that the temperature, stream size and discharge were the most important factors contributing to the separation of the stream sites from different altitude and hence are the predictors for the distribution of black fly species assemblages.ConclusionsThis study has provided insight into the distribution pattern of preimaginal black fly assemblages along an altitudinal gradient in Peninsular Malaysia. This study could deepen our knowledge on the ecology and biology of the specialised taxa in response to environmental changes.

Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander.

Ecological models predict that, in the face of climate change, taxa occupying steep altitudinal gradients will shift their distributions, leading to the contraction or extinction of the high-elevation (cold-adapted) taxa. However, hybridization between ecomorphologically divergent taxa commonly occurs in nature and may lead to alternative evolutionary outcomes, such as genetic merger or gene flow at specific genes. We evaluate this hypothesis by studying patterns of divergence and gene flow across three replicate contact zones between high- and low-elevation ecomorphs of the fire salamander (Salamandra salamandra) that have experienced altitudinal range shifts over the current postglacial period. Strong population structure with high genetic divergence in mitochondrial DNA suggests that vicariant evolution has occurred over several glacial-interglacial cycles and that it has led to cryptic differentiation within ecomorphs. In current parapatric boundaries, we do not find evidence for local extinction and replacement upon postglacial expansion. Instead, parapatric taxa recurrently show discordance between mitochondrial and nuclear markers, suggesting nuclear-mediated gene flow across contact zones. Isolation with migration models support this hypothesis by showing significant gene flow across all five parapatric boundaries. Together, our results suggest that, while some genomic regions, such as the mitochondria, may follow morphologic species traits and retreat to isolated mountain tops, other genomic regions, such as nuclear markers, may flow across parapatric boundaries, sometimes leading to a complete genetic merger. We show that despite high ecologic and morphologic divergence over prolonged periods of time, hybridization allows for evolutionary outcomes alternative to extinction and replacement of taxa in response to climate change.

Acoustic behavior of melon-headed whales varies on a diel cycle.

Many terrestrial and marine species have a diel activity pattern, and their acoustic signaling follows their current behavioral state. Whistles and echolocation clicks on long-term recordings produced by melon-headed whales (Peponocephala electra) at Palmyra Atoll indicated that these signals were used selectively during different phases of the day, strengthening the idea of nighttime foraging and daytime resting with afternoon socializing for this species. Spectral features of their echolocation clicks changed from day to night, shifting the median center frequency up. Additionally, click received levels increased with increasing ambient noise during both day and night. Ambient noise over a wide frequency band was on average higher at night. The diel adjustment of click features might be a reaction to acoustic masking caused by these nighttime sounds. Similar adaptations have been documented for numerous taxa in response to noise. Or it could be, unrelated, an increase in biosonar source levels and with it a shift in center frequency to enhance detection distances during foraging at night. Call modifications in intensity, directionality, frequency, and duration according to echolocation task are well established for bats. This finding indicates that melon-headed whales have flexibility in their acoustic behavior, and they collectively and repeatedly adapt their signals from day- to nighttime circumstances.Electronic supplementary materialThe online version of this article (doi:10.1007/s00265-015-1967-0) contains supplementary material, which is available to authorized users.

Simulated Macro-Algal Outbreak Triggers a Large-Scale Response on Coral Reefs.

Ecosystem degradation has become common throughout the world. On coral reefs, macroalgal outbreaks are one of the most widely documented signs of degradation. This study simulated local-scale degradation on a healthy coral reef to determine how resident taxa, with the potential to reverse algal outbreaks, respond. We utilized a combination of acoustic and video monitoring to quantify changes in the movements and densities, respectively, of coral reef herbivores following a simulated algal outbreak. We found an unprecedented accumulation of functionally important herbivorous taxa in response to algal increases. Herbivore densities increased by 267% where algae were present. The increase in herbivore densities was driven primarily by an accumulation of the browsing taxa Naso unicornis and Kyphosus vaigiensis, two species which are known to be important in removing macroalgae and which may be capable of reversing algal outbreaks. However, resident individuals at the site of algal increase exhibited no change in their movements. Instead, analysis of the size classes of the responding individuals indicates that large functionally-important non-resident individuals changed their movement patterns to move in and feed on the algae. This suggests that local-scale reef processes may not be sufficient to mitigate the effects of local degradation and highlights the importance of mobile links and cross-scale interactions.

Rapid changes in key ruminal microbial populations during the induction of and recovery from diet-induced milk fat depression in dairy cows.

The ruminant provides a powerful model for understanding the temporal dynamics of gastrointestinal microbial communities. Diet-induced milk fat depression (MFD) in the dairy cow is caused by rumen-derived bioactive fatty acids, and is commonly attributed to the changes in the microbial population. The aim of the present study was to determine the changes occurring in nine ruminal bacterial taxa with well-characterised functions, and abundance of total fungi, ciliate protozoa and bacteria during the induction of and recovery from MFD. Interactions between treatment and time were observed for ten of the twelve populations. The total number of both fungi and ciliate protozoa decreased rapidly (days 4 and 8, respectively) by more than 90% during the induction period and increased during the recovery period. The abundance of Streptococcus bovis (amylolytic) peaked at 350% of control levels on day 4 of induction and rapidly decreased during the recovery period. The abundance of Prevotella bryantii (amylolytic) decreased by 66% from day 8 to 20 of the induction period and increased to the control levels on day 12 of the recovery period. The abundance of Megasphaera elsdenii and Selenomonas ruminantium (lactate-utilising bacteria) increased progressively until day 12 of induction (>170%) and decreased during the recovery period. The abundance of Fibrobacter succinogenes (fibrolytic) decreased by 97% on day 4 of induction and increased progressively to an equal extent during the recovery period, although smaller changes were observed for other fibrolytic bacteria. The abundance of the Butyrivibrio fibrisolvens/Pseudobutyrivibrio group decreased progressively during the induction period and increased during the recovery period, whereas the abundance of Butyrivibrio hungatei was not affected by treatment. Responsive taxa were modified rapidly, with the majority of changes occurring within 8 d and their time course was similar to the time course of the induction of MFD, demonstrating a strong correlation between changes in ruminal microbial populations and MFD.