Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

PubMed

Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

2017-04-21

Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA 2 s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA 2 s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not

Patterns of Limnohabitans Microdiversity across a Large Set of Freshwater Habitats as Revealed by Reverse Line Blot Hybridization

PubMed Central

Jezbera, Jan; Jezberová, Jitka; Kasalický, Vojtěch; Šimek, Karel; Hahn, Martin W.

2013-01-01

Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization) probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S–23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus) patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of these bacteria

A global analysis of bird plumage patterns reveals no association between habitat and camouflage

PubMed Central

Marshall, Kate L.A.; Gluckman, Thanh-Lan

2016-01-01

Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types—mottled (irregular), scales, bars and spots (regular)—and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species’ geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world’s birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world’s eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis. PMID:27867762

A global analysis of bird plumage patterns reveals no association between habitat and camouflage.

PubMed

Somveille, Marius; Marshall, Kate L A; Gluckman, Thanh-Lan

2016-01-01

Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types-mottled (irregular), scales, bars and spots (regular)-and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species' geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world's birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world's eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

NASA Astrophysics Data System (ADS)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-04-01

Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P < .01); (2) The ATR-Ft/VMS molecular technique was able to detect the processing induced CHO molecular structure changes; (3) Induced CHO molecular structure spectral features are significantly correlated (P < .05) to CHO subfractions, CHO biodegradation and biodigestion and could be applied to potentially predict CHO biodegradation (R2 = 0.87, RSD = 0.74, P < .01) and intestinal digestible undegraded CHO (R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

Single Turnover at Molecular Polymerization Catalysts Reveals Spatiotemporally Resolved Reactions.

PubMed

Easter, Quinn T; Blum, Suzanne A

2017-10-23

Multiple active individual molecular ruthenium catalysts have been pinpointed within growing polynorbornene, thereby revealing information on the reaction dynamics and location that is unavailable through traditional ensemble experiments. This is the first single-turnover imaging of a molecular catalyst by fluorescence microscopy and allows detection of individual monomer reactions at an industrially important molecular ruthenium ring-opening metathesis polymerization (ROMP) catalyst under synthetically relevant conditions (e.g. unmodified industrial catalyst, ambient pressure, condensed phase, ca. 0.03 m monomer). These results further establish the key fundamentals of this imaging technique for characterizing the reactivity and location of active molecular catalysts even when they are the minor components. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group (Teleostei: Adrianichthyidae).

PubMed

Mokodongan, Daniel F; Montenegro, Javier; Mochida, Koji; Fujimoto, Shingo; Ishikawa, Asano; Kakioka, Ryo; Yong, Lengxob; Mulis; Hadiaty, Renny K; Mandagi, Ixchel F; Masengi, Kawilarang W A; Wachi, Nakatada; Hashiguchi, Yasuyuki; Kitano, Jun; Yamahira, Kazunori

2018-01-01

The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations. Second, their phylogenetic relationships did not support the presence of three species; phylogenies using mitochondrial DNA and genomic data obtained from RNA-Seq revealed that the eight populations could not be sorted into three different clades representing three described species. Third, phylogenetic corrections of body shape variations and ancestral state reconstruction of body shapes demonstrated that body shape divergence between riverine and lacustrine populations persisted even if the phylogenies were considered and that body shape evolved rapidly irrespective of phylogeny. Sexual dimorphism in body shape was also evident, but the degree of dimorphism did not significantly differ between riverine and lacustrine populations after phylogenetic corrections, suggesting that sexual selection may not substantially contribute to geographical variations in body shape. Overall, these results indicate that the deep-elongated body shape divergence of the O. woworae species group evolved locally in response to habitat environments, such as water currents, and that a thorough taxonomic reexamination of the O. woworae species group may be necessary. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular data and ecological niche modelling reveal the phylogeographic pattern of Cotinus coggygria (Anacardiaceae) in China's warm-temperate zone.

PubMed

Wang, W; Tian, C Y; Li, Y H; Li, Y

2014-11-01

The phylogeography of common and widespread species helps to elucidate the history of local flora and vegetation. In this study, we selected Cotinus coggygria, a species widely distributed in China's warm-temperate zone. One chloroplast DNA (cpDNA) region and ecological niche modelling were used to examine the phylogeographic pattern of C. coggygria. The cpDNA data revealed two phylogeographic groups (Southern and Northern) corresponding to the geographic regions. Divergence time analyses revealed that divergence of the two groups occurred at approximately 147,000 years before the present (BP), which coincided with the formation of the downstream area of the Yellow River, indicating that the Yellow River was a weak phylogeographic divide for C. coggygria. The molecular data and ecological niche modelling also indicated that C. coggyria did not experience population expansion after glaciations. This study thus supports the fact that Pleistocene glacial cycles only slightly affected C. coggygria, which survived in situ and occupied multiple localised glacial refugia during glaciations. This finding is contrary to the hypothesis of large-scale range habitat contraction and retreat into a few main refugia. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis.

PubMed

Davies, Kalina T J; Bennett, Nigel C; Tsagkogeorga, Georgia; Rossiter, Stephen J; Faulkes, Christopher G

2015-12-01

During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein-protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Application of network methods for understanding evolutionary dynamics in discrete habitats.

PubMed

Greenbaum, Gili; Fefferman, Nina H

2017-06-01

In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene-flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population-genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene-flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. © 2017 John Wiley & Sons Ltd.

Habitat Use and Selection by Giant Pandas.

PubMed

Hull, Vanessa; Zhang, Jindong; Huang, Jinyan; Zhou, Shiqiang; Viña, Andrés; Shortridge, Ashton; Li, Rengui; Liu, Dian; Xu, Weihua; Ouyang, Zhiyun; Zhang, Hemin; Liu, Jianguo

2016-01-01

Animals make choices about where to spend their time in complex and dynamic landscapes, choices that reveal information about their biology that in turn can be used to guide their conservation. Using GPS collars, we conducted a novel individual-based analysis of habitat use and selection by the elusive and endangered giant pandas (Ailuropoda melanoleuca). We constructed spatial autoregressive resource utilization functions (RUF) to model the relationship between the pandas' utilization distributions and various habitat characteristics over a continuous space across seasons. Results reveal several new insights, including use of a broader range of habitat characteristics than previously understood for the species, particularly steep slopes and non-forest areas. We also used compositional analysis to analyze habitat selection (use with respect to availability of habitat types) at two selection levels. Pandas selected against low terrain position and against the highest clumped forest at the at-home range level, but no significant factors were identified at the within-home range level. Our results have implications for modeling and managing the habitat of this endangered species by illustrating how individual pandas relate to habitat and make choices that differ from assumptions made in broad scale models. Our study also highlights the value of using a spatial autoregressive RUF approach on animal species for which a complete picture of individual-level habitat use and selection across space is otherwise lacking.

Habitat Use and Selection by Giant Pandas

PubMed Central

Hull, Vanessa; Zhang, Jindong; Huang, Jinyan; Zhou, Shiqiang; Viña, Andrés; Shortridge, Ashton; Li, Rengui; Liu, Dian; Xu, Weihua; Ouyang, Zhiyun; Zhang, Hemin; Liu, Jianguo

2016-01-01

Animals make choices about where to spend their time in complex and dynamic landscapes, choices that reveal information about their biology that in turn can be used to guide their conservation. Using GPS collars, we conducted a novel individual-based analysis of habitat use and selection by the elusive and endangered giant pandas (Ailuropoda melanoleuca). We constructed spatial autoregressive resource utilization functions (RUF) to model the relationship between the pandas' utilization distributions and various habitat characteristics over a continuous space across seasons. Results reveal several new insights, including use of a broader range of habitat characteristics than previously understood for the species, particularly steep slopes and non-forest areas. We also used compositional analysis to analyze habitat selection (use with respect to availability of habitat types) at two selection levels. Pandas selected against low terrain position and against the highest clumped forest at the at-home range level, but no significant factors were identified at the within-home range level. Our results have implications for modeling and managing the habitat of this endangered species by illustrating how individual pandas relate to habitat and make choices that differ from assumptions made in broad scale models. Our study also highlights the value of using a spatial autoregressive RUF approach on animal species for which a complete picture of individual-level habitat use and selection across space is otherwise lacking. PMID:27627805

Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

PubMed Central

Hudson, Nathan E.; Ding, Feng; Bucay, Igal; O’Brien, E. Timothy; Gorkun, Oleg V.; Superfine, Richard; Lord, Susan T.; Dokholyan, Nikolay V.; Falvo, Michael R.

2013-01-01

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin’s elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin’s mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. PMID:23790375

Habitat use by fishes in coral reefs, seagrass beds and mangrove habitats in the Philippines.

PubMed

Honda, Kentaro; Nakamura, Yohei; Nakaoka, Masahiro; Uy, Wilfredo H; Fortes, Miguel D

2013-01-01

Understanding the interconnectivity of organisms among different habitats is a key requirement for generating effective management plans in coastal ecosystems, particularly when determining component habitat structures in marine protected areas. To elucidate the patterns of habitat use by fishes among coral, seagrass, and mangrove habitats, and between natural and transplanted mangroves, visual censuses were conducted semiannually at two sites in the Philippines during September and March 2010-2012. In total, 265 species and 15,930 individuals were recorded. Species richness and abundance of fishes were significantly higher in coral reefs (234 species, 12,306 individuals) than in seagrass (38 species, 1,198 individuals) and mangrove (47 species, 2,426 individuals) habitats. Similarity tests revealed a highly significant difference among the three habitats. Fishes exhibited two different strategies for habitat use, inhabiting either a single (85.6% of recorded species) or several habitats (14.4%). Some fish that utilized multiple habitats, such as Lutjanus monostigma and Parupeneus barberinus, showed possible ontogenetic habitat shifts from mangroves and/or seagrass habitats to coral reefs. Moreover, over 20% of commercial fish species used multiple habitats, highlighting the importance of including different habitat types within marine protected areas to achieve efficient and effective resource management. Neither species richness nor abundance of fishes significantly differed between natural and transplanted mangroves. In addition, 14 fish species were recorded in a 20-year-old transplanted mangrove area, and over 90% of these species used multiple habitats, further demonstrating the key role of transplanted mangroves as a reef fish habitat in this region.

Habitat Use by Fishes in Coral Reefs, Seagrass Beds and Mangrove Habitats in the Philippines

PubMed Central

Honda, Kentaro; Nakamura, Yohei; Nakaoka, Masahiro; Uy, Wilfredo H.; Fortes, Miguel D.

2013-01-01

Understanding the interconnectivity of organisms among different habitats is a key requirement for generating effective management plans in coastal ecosystems, particularly when determining component habitat structures in marine protected areas. To elucidate the patterns of habitat use by fishes among coral, seagrass, and mangrove habitats, and between natural and transplanted mangroves, visual censuses were conducted semiannually at two sites in the Philippines during September and March 2010–2012. In total, 265 species and 15,930 individuals were recorded. Species richness and abundance of fishes were significantly higher in coral reefs (234 species, 12,306 individuals) than in seagrass (38 species, 1,198 individuals) and mangrove (47 species, 2,426 individuals) habitats. Similarity tests revealed a highly significant difference among the three habitats. Fishes exhibited two different strategies for habitat use, inhabiting either a single (85.6% of recorded species) or several habitats (14.4%). Some fish that utilized multiple habitats, such as Lutjanus monostigma and Parupeneus barberinus, showed possible ontogenetic habitat shifts from mangroves and/or seagrass habitats to coral reefs. Moreover, over 20% of commercial fish species used multiple habitats, highlighting the importance of including different habitat types within marine protected areas to achieve efficient and effective resource management. Neither species richness nor abundance of fishes significantly differed between natural and transplanted mangroves. In addition, 14 fish species were recorded in a 20-year-old transplanted mangrove area, and over 90% of these species used multiple habitats, further demonstrating the key role of transplanted mangroves as a reef fish habitat in this region. PMID:23976940

US-Canada Monitoring Network Reveals Biodiversity Patterns in Data-poor Marine Cobble-Boulder Habitats of the Coastal Northwest Atlantic

NASA Astrophysics Data System (ADS)

Wahle, R.; Hunt, H.; Tremblay, J.; Comeau, M.; Silva, A.; Rochette, R.

2016-02-01

In the Northeast US and Atlantic Canada a regional collaborative of marine resource agencies, academics, and fishing industry participants monitor more than 100 coastal sites with subtidal cobble-boulder habitat, a prime nursery of commercially important lobsters and crabs. The survey's prime motivation is to quantify annual recruitment of early juvenile stages of these crustaceans. Quantifying faunal abundance in subtidal cobble-boulder habitats is logistically challenging, defying trawl, core and camera. Until recently surveys of cobble habitats were solely conducted by divers using airlift suction samplers in natural cobble beds. In 2005 we developed standardized cobble-filled collectors that considerably expand the survey's reach to greater depths and offshore areas. In addition to their value in monitoring commercial crustaceans, these vessel-deployed collectors have proven to be especially useful in biodiversity studies. Here we describe patterns of species richness and abundance of decapod crustaceans and small demersal fishes colonizing 800 cobble-filled collectors deployed yearly in 2008 and 2009 at near-shore sites across the steep thermal and biogeographic gradient from Rhode Island, USA to Newfoundland, Canada to 76 m depth. At least 17 decapod and 24 fish genera were represented, including cryptic fish taxa not readily detected with other sampling gear. Species richness at shallow sites (5-10 m) was greatest in the south, but did not follow a simple latitudinal cline; rather, it correlated strongly with the complex geography of summer bottom temperature, thereby setting a baseline for climate change studies. Given the world-wide prevalence of this coastal habitat, broader monitoring will reveal new insights on biodiversity patterns and ecosystem services it provides. We seek wider collaboration with the scientific community and stakeholders toward a broader understanding of this poorly studied marine habitat.

Revealing the distinct habitat ranges and hybrid zone of genetic sub-populations within Pseudo-nitzschia pungens (Bacillariophyceae) in the West Pacific area.

PubMed

Kim, Jin Ho; Wang, Pengbin; Park, Bum Soo; Kim, Joo-Hwan; Patidar, Shailesh Kumar; Han, Myung-Soo

2018-03-01

Genetic sub-populations (clades) of cosmopolitan marine diatom Pseudo-nitzschia pungens might have distinct habitats, and their hybrid zone is suspected in higher latitude area of the West Pacific area, however, it is still unrevealed because of technical difficulties and lack of evidences in natural environments. The aim of this study is to investigate the habitat characteristics of each clade of P. pungens on geographical distribution with the habitat temperature ranges of each clade and to reveal their hybrid zone in the West Pacific area. We employed the 137 number of nucleotide sequences of P. pungens and its sampling data (spatial and temporal scale) originated from the West Pacific area, and used field application of qPCR assay for intra-specific level of P. pungens. Only two genotypes, clade I and III, were identified in the West Pacific area. Clade I was distributed from 39 to 32.3°N, and clade III were from 1.4 to 34.4°N. The estimated habitat temperature for the clade I and clade III ranges were 8.1-26.9 °C and 24.2-31.2 °C, respectively. The latitudinal distributions and temperature ranges of each clade were significantly different. The qPCR assay employed, and results suggested that the hybrid zone for clade I and III has been observed in the southern Korean coasts, and clade III might be introduced from the Southern Pacific area. The cell abundances of clade III were strongly related with the higher seawater temperature and warm current force. This study has defined distinct habitat characteristics of genetically different sub-populations of P. pungens, and revealed its hybrid zone in natural environment for the first time. We also provided strong evidences about dispersion of the population of clade III to higher latitude in the West Pacific area. Copyright © 2018. Published by Elsevier B.V.

Challenges in rendering Coral Triangle habitat richness in remotely sensed habitat maps: The case of Bunaken Island (Indonesia).

PubMed

Ampou, Eghbert Elvan; Ouillon, Sylvain; Andréfouët, Serge

2018-06-01

The Coral Triangle is the epicenter of marine biodiversity, yet the numbers of habitats that can be found on coral reefs remain poorly described. First surveys for habitat mapping in Indonesia revealed a high number of habitats (>150) even for structurally simple reefs. To be able to represent all these habitats, typical habitat mapping procedures and performances are poorly effective even using very high resolution satellite images. Using Bunaken Island (North Sulawesi, Indonesia) as a case study, we devised a way to maintain all the in situ habitat information in remote sensing habitat map products without loss and with mapping procedures based on photo-interpretation. The result is a product which is consistent with a per-polygon fuzzy classification. As such, it is a complex product that meets our habitat representation goal, but its complexity can also limit its immediate use by managers and conservation planners when analyses per habitat are needed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics.

PubMed

Hudson, Nathan E; Ding, Feng; Bucay, Igal; O'Brien, E Timothy; Gorkun, Oleg V; Superfine, Richard; Lord, Susan T; Dokholyan, Nikolay V; Falvo, Michael R

2013-06-18

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin's elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin's mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Tracing multi-habitat support of coastal fishes

EPA Science Inventory

Hydrologic linkages among coastal wetland and nearshore areas allow coastal fish to move among the habitats, which has led to a variety of habitat use patterns. In the Great Lakes, fine-scale microchemical analyses of yellow perch otoliths have revealed life-history categories th...

DNA metabarcoding of nestling feces reveals provisioning of aquatic prey and resource partitioning among Neotropical migratory songbirds in a riparian habitat.

PubMed

Trevelline, Brian K; Nuttle, Tim; Hoenig, Brandon D; Brouwer, Nathan L; Porter, Brady A; Latta, Steven C

2018-05-01

Riparian habitats are characterized by substantial flows of emergent aquatic insects that cross the stream-forest interface and provide an important source of prey for insectivorous birds. The increased availability of prey arising from aquatic subsidies attracts high densities of Neotropical migratory songbirds that are thought to exploit emergent aquatic insects as a nestling food resource; however, the prey preferences and diets of birds in these communities are only broadly understood. In this study, we utilized DNA metabarcoding to investigate the extent to which three syntopic species of migratory songbirds-Acadian Flycatcher, Louisiana Waterthrush, and Wood Thrush-breeding in Appalachian riparian habitats (Pennsylvania, USA) exploit and partition aquatic prey subsidies as a nestling food resource. Despite substantial differences in adult foraging strategies, nearly every nestling in this study consumed aquatic taxa, suggesting that aquatic subsidies are an important prey resource for Neotropical migrants nesting in riparian habitats. While our results revealed significant interspecific dietary niche divergence, the diets of Acadian Flycatcher and Wood Thrush nestlings were strikingly similar and exhibited significantly more overlap than expected. These results suggest that the dietary niches of Neotropical migrants with divergent foraging strategies may converge due to the opportunistic provisioning of non-limiting prey resources in riparian habitats. In addition to providing the first application of DNA metabarcoding to investigate diet in a community of Neotropical migrants, this study emphasizes the importance of aquatic subsidies in supporting breeding songbirds and improves our understanding of how anthropogenic disturbances to riparian habitats may negatively impact long-term avian conservation.

The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

PubMed

Woo, Patrick C Y; Lau, Susanna K P; Tse, Herman; Teng, Jade L L; Curreem, Shirly O T; Tsang, Alan K L; Fan, Rachel Y Y; Wong, Gilman K M; Huang, Yi; Loman, Nicholas J; Snyder, Lori A S; Cai, James J; Huang, Jian-Dong; Mak, William; Pallen, Mark J; Lok, Si; Yuen, Kwok-Yung

2009-03-01

Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors-such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-are present. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and 20 degrees C (freshwater habitat temperature) showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37 degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be employed by other

Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities.

PubMed

Quattrini, Andrea M; Nizinski, Martha S; Chaytor, Jason D; Demopoulos, Amanda W J; Roark, E Brendan; France, Scott C; Moore, Jon A; Heyl, Taylor; Auster, Peter J; Kinlan, Brian; Ruppel, Carolyn; Elliott, Kelley P; Kennedy, Brian R C; Lobecker, Elizabeth; Skarke, Adam; Shank, Timothy M

2015-01-01

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration

Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities

PubMed Central

Quattrini, Andrea M.; Nizinski, Martha S.; Chaytor, Jason D.; Demopoulos, Amanda W. J.; Roark, E. Brendan; France, Scott C.; Moore, Jon A.; Heyl, Taylor; Auster, Peter J.; Kinlan, Brian; Ruppel, Carolyn; Elliott, Kelley P.; Kennedy, Brian R.C.; Lobecker, Elizabeth; Skarke, Adam; Shank, Timothy M.

2015-01-01

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration

Hemimetabolous genomes reveal molecular basis of termite eusociality.

PubMed

Harrison, Mark C; Jongepier, Evelien; Robertson, Hugh M; Arning, Nicolas; Bitard-Feildel, Tristan; Chao, Hsu; Childers, Christopher P; Dinh, Huyen; Doddapaneni, Harshavardhan; Dugan, Shannon; Gowin, Johannes; Greiner, Carolin; Han, Yi; Hu, Haofu; Hughes, Daniel S T; Huylmans, Ann-Kathrin; Kemena, Carsten; Kremer, Lukas P M; Lee, Sandra L; Lopez-Ezquerra, Alberto; Mallet, Ludovic; Monroy-Kuhn, Jose M; Moser, Annabell; Murali, Shwetha C; Muzny, Donna M; Otani, Saria; Piulachs, Maria-Dolors; Poelchau, Monica; Qu, Jiaxin; Schaub, Florentine; Wada-Katsumata, Ayako; Worley, Kim C; Xie, Qiaolin; Ylla, Guillem; Poulsen, Michael; Gibbs, Richard A; Schal, Coby; Richards, Stephen; Belles, Xavier; Korb, Judith; Bornberg-Bauer, Erich

2018-03-01

Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.

Intrapopulation variability in the timing of ontogenetic habitat shifts in sea turtles revealed using δ15N values from bone growth rings

PubMed Central

Turner Tomaszewicz, Calandra N.; Seminoff, Jeffrey A.; Peckham, S. Hoyt; Avens, Larisa; Kurle, Carolyn M.

2016-01-01

alternative ontogenetic shifts and habitat use patterns for juveniles foraging in the eastern NPO.We combine two techniques, skeletochronology and stable isotope analysis, to reconstruct multi-year habitat use patterns of a remote migratory species, linked to estimated ages and body sizes of individuals, to reveal variable ontogeny during the juvenile life stage that could drive alternate life histories and that has the potential to illuminate the migration patterns for other species with accretionary tissues. PMID:28075017

Molecular evidence of Rickettsia spp. in ixodid ticks and rodents in suburban, natural and rural habitats in Slovakia.

PubMed

Minichová, Lenka; Hamšíková, Zuzana; Mahríková, Lenka; Slovák, Mirko; Kocianová, Elena; Kazimírová, Mária; Škultéty, Ľudovít; Štefanidesová, Katarína; Špitalská, Eva

2017-03-24

Natural foci of tick-borne spotted fever group (SFG) rickettsiae of public health concern have been found in Slovakia, but the role of rodents in their circulation is unclear. Ticks (Ixodes ricinus, Ixodes trianguliceps, Dermacentor marginatus, Dermacentor reticulatus, Haemaphysalis concinna and Haemaphysalis inermis) and tissues of rodents (Apodemus flavicollis, Apodemus sylvaticus, Myodes glareolus, Microtus arvalis, Microtus subterraneus and Micromys minutus) were examined for the presence of SFG rickettsiae and Coxiella burnetii by molecular methods. Suburban, natural and rural habitats were monitored to acquire information on the role of ticks and rodents in the agents' maintenance in various habitat types of Slovakia. The overall prevalence of rickettsial infection in questing I. ricinus and D. marginatus was 6.6% and 21.4%, respectively. Rickettsia helvetica, R. monacensis and non-identified rickettsial species were detected in I. ricinus, whereas R. slovaca and R. raoultii were identified in D. marginatus. Rickettsia spp.-infected I. ricinus occurred during the whole tick questing period. Rickettsia helvetica dominated (80.5%) followed by R. monacensis (6.5%). The species were present in all studied habitats. Rickettsia slovaca (66.7%) and R. raoultii (33.3%) were identified in D. marginatus from the rural habitat. Apodemus flavicollis was the most infested rodent species with I. ricinus, but My. glareolus carried the highest proportion of Rickettsia-positive I. ricinus larvae. Only 0.5% of rodents (A. flavicollis) and 5.2% of engorged I. ricinus removed from My. glareolus, A. flavicollis and M. arvalis were R. helvetica- and R. monacensis-positive. Coxiella burnetii was not detected in any of the tested samples. We hypothesize that rodents could play a role as carriers of infected ticks and contribute to the maintenance of rickettsial pathogens in natural foci. Long-term presence of SFG Rickettsia spp. was confirmed in questing ticks from different habitat

Experimental food supplementation reveals habitat-dependent male reproductive investment in a migratory bird

PubMed Central

Kaiser, Sara A.; Sillett, T. Scott; Risk, Benjamin B.; Webster, Michael S.

2015-01-01

Environmental factors can shape reproductive investment strategies and influence the variance in male mating success. Environmental effects on extrapair paternity have traditionally been ascribed to aspects of the social environment, such as breeding density and synchrony. However, social factors are often confounded with habitat quality and are challenging to disentangle. We used both natural variation in habitat quality and a food supplementation experiment to separate the effects of food availability—one key aspect of habitat quality—on extrapair paternity (EPP) and reproductive success in the black-throated blue warbler, Setophaga caerulescens. High natural food availability was associated with higher within-pair paternity (WPP) and fledging two broods late in the breeding season, but lower EPP. Food-supplemented males had higher WPP leading to higher reproductive success relative to controls, and when in low-quality habitat, food-supplemented males were more likely to fledge two broods but less likely to gain EPP. Our results demonstrate that food availability affects trade-offs in reproductive activities. When food constraints are reduced, males invest in WPP at the expense of EPP. These findings imply that environmental change could alter how individuals allocate their resources and affect the selective environment that drives variation in male mating success. PMID:25673677

Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.

PubMed

Alcaide, María; Stogios, Peter J; Lafraya, Álvaro; Tchigvintsev, Anatoli; Flick, Robert; Bargiela, Rafael; Chernikova, Tatyana N; Reva, Oleg N; Hai, Tran; Leggewie, Christian C; Katzke, Nadine; La Cono, Violetta; Matesanz, Ruth; Jebbar, Mohamed; Jaeger, Karl-Erich; Yakimov, Michail M; Yakunin, Alexander F; Golyshin, Peter N; Golyshina, Olga V; Savchenko, Alexei; Ferrer, Manuel

2015-02-01

The present study provides a deeper view of protein functionality as a function of temperature, salt and pressure in deep-sea habitats. A set of eight different enzymes from five distinct deep-sea (3040-4908 m depth), moderately warm (14.0-16.5°C) biotopes, characterized by a wide range of salinities (39-348 practical salinity units), were investigated for this purpose. An enzyme from a 'superficial' marine hydrothermal habitat (65°C) was isolated and characterized for comparative purposes. We report here the first experimental evidence suggesting that in salt-saturated deep-sea habitats, the adaptation to high pressure is linked to high thermal resistance (P value = 0.0036). Salinity might therefore increase the temperature window for enzyme activity, and possibly microbial growth, in deep-sea habitats. As an example, Lake Medee, the largest hypersaline deep-sea anoxic lake of the Eastern Mediterranean Sea, where the water temperature is never higher than 16°C, was shown to contain halopiezophilic-like enzymes that are most active at 70°C and with denaturing temperatures of 71.4°C. The determination of the crystal structures of five proteins revealed unknown molecular mechanisms involved in protein adaptation to poly-extremes as well as distinct active site architectures and substrate preferences relative to other structurally characterized enzymes. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Quantifying multi-habitat support of Great Lakes fishes

EPA Science Inventory

Recent advances in trophic ecology have revealed the interconnectedness of diverse habitats in support of aquatic food webs. Understanding the degree to which different habitats support fish can be valuable for fisheries management and ecosystem protection. For example, stable is...

Population genetic dynamics of three-spined sticklebacks (Gasterosteus aculeatus) in anthropogenic altered habitats

PubMed Central

Scharsack, Joern P; Schweyen, Hannah; Schmidt, Alexander M; Dittmar, Janine; Reusch, Thorsten BH; Kurtz, Joachim

2012-01-01

In industrialized and/or agriculturally used landscapes, inhabiting species are exposed to a variety of anthropogenic changes in their environments. Genetic diversity may be reduced if populations encounter founder events, bottlenecks, or isolation. Conversely, genetic diversity may increase if populations adapt to changes in selective regimes in newly created habitats. With the present study, genetic variability of 918 sticklebacks from 43 samplings (21.3 ± 3.8 per sample) at 36 locations from cultivated landscapes in Northwest Germany was analyzed at nine neutral microsatellite loci. To test if differentiation is influenced by habitat alterations, sticklebacks were collected from ancient running waters and adjacent artificial stagnant waters, from brooks with salt water inflow of anthropogenic and natural origin and adjacent freshwater sites. Overall population structure was dominated by isolation by distance (IBD), which was significant across all populations, and analysis of molecular variance (AMOVA) revealed that 10.6% of the variation was explained by river catchment area. Populations in anthropogenic modified habitats deviated from the general IBD structure and in the AMOVA, grouping by habitat type running/stagnant water explained 4.9% of variation and 1.4% of the variation was explained by salt-/freshwater habitat. Sticklebacks in salt-polluted water systems seem to exhibit elevated migratory activity between fresh- and saltwater habitats, reducing IBD. In other situations, populations showed distinct signs of genetic isolation, which in some locations was attributed to mechanical migration barriers, but in others to potential anthropogenic induced bottleneck or founder effects. The present study shows that anthropogenic habitat alterations may have diverse effects on the population genetic structure of inhabiting species. Depending on the type of habitat change, increased genetic differentiation, diversification, or isolation are possible consequences

Population genetic dynamics of three-spined sticklebacks (Gasterosteus aculeatus) in anthropogenic altered habitats.

PubMed

Scharsack, Joern P; Schweyen, Hannah; Schmidt, Alexander M; Dittmar, Janine; Reusch, Thorsten Bh; Kurtz, Joachim

2012-06-01

In industrialized and/or agriculturally used landscapes, inhabiting species are exposed to a variety of anthropogenic changes in their environments. Genetic diversity may be reduced if populations encounter founder events, bottlenecks, or isolation. Conversely, genetic diversity may increase if populations adapt to changes in selective regimes in newly created habitats. With the present study, genetic variability of 918 sticklebacks from 43 samplings (21.3 ± 3.8 per sample) at 36 locations from cultivated landscapes in Northwest Germany was analyzed at nine neutral microsatellite loci. To test if differentiation is influenced by habitat alterations, sticklebacks were collected from ancient running waters and adjacent artificial stagnant waters, from brooks with salt water inflow of anthropogenic and natural origin and adjacent freshwater sites. Overall population structure was dominated by isolation by distance (IBD), which was significant across all populations, and analysis of molecular variance (AMOVA) revealed that 10.6% of the variation was explained by river catchment area. Populations in anthropogenic modified habitats deviated from the general IBD structure and in the AMOVA, grouping by habitat type running/stagnant water explained 4.9% of variation and 1.4% of the variation was explained by salt-/freshwater habitat. Sticklebacks in salt-polluted water systems seem to exhibit elevated migratory activity between fresh- and saltwater habitats, reducing IBD. In other situations, populations showed distinct signs of genetic isolation, which in some locations was attributed to mechanical migration barriers, but in others to potential anthropogenic induced bottleneck or founder effects. The present study shows that anthropogenic habitat alterations may have diverse effects on the population genetic structure of inhabiting species. Depending on the type of habitat change, increased genetic differentiation, diversification, or isolation are possible consequences.

Inference from habitat-selection analysis depends on foraging strategies.

PubMed

Bastille-Rousseau, Guillaume; Fortin, Daniel; Dussault, Christian

2010-11-01

1. Several methods have been developed to assess habitat selection, most of which are based on a comparison between habitat attributes in used vs. unused or random locations, such as the popular resource selection functions (RSFs). Spatial evaluation of residency time has been recently proposed as a promising avenue for studying habitat selection. Residency-time analyses assume a positive relationship between residency time within habitat patches and selection. We demonstrate that RSF and residency-time analyses provide different information about the process of habitat selection. Further, we show how the consideration of switching rate between habitat patches (interpatch movements) together with residency-time analysis can reveal habitat-selection strategies. 2. Spatially explicit, individual-based modelling was used to simulate foragers displaying one of six foraging strategies in a heterogeneous environment. The strategies combined one of three patch-departure rules (fixed-quitting-harvest-rate, fixed-time and fixed-amount strategy), together with one of two interpatch-movement rules (random or biased). Habitat selection of simulated foragers was then assessed using RSF, residency-time and interpatch-movement analyses. 3. Our simulations showed that RSFs and residency times are not always equivalent. When foragers move in a non-random manner and do not increase residency time in richer patches, residency-time analysis can provide misleading assessments of habitat selection. This is because the overall time spent in the various patch types not only depends on residency times, but also on interpatch-movement decisions. 4. We suggest that RSFs provide the outcome of the entire selection process, whereas residency-time and interpatch-movement analyses can be used in combination to reveal the mechanisms behind the selection process. 5. We showed that there is a risk in using residency-time analysis alone to infer habitat selection. Residency-time analyses, however

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China.

PubMed

Zhang, Mingwang; Rao, Dingqi; Yang, Junxing; Yu, Guohua; Wilkinson, Jeffery A

2010-01-01

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000-2600m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L. ailaonicum may represent more than one distinct species and should at least be separated into four management units

Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis

PubMed Central

Davies, Kalina T.J.; Bennett, Nigel C.; Tsagkogeorga, Georgia; Rossiter, Stephen J.; Faulkes, Christopher G.

2015-01-01

During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein–protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group. PMID:26318402

Submillimeter Array reveals molecular complexity of dying stars

NASA Astrophysics Data System (ADS)

Tomasz

2018-01-01

The unique capabilities of the Submillimeter Array (SMA) have allowed unprecedented studies of cool evolved stars at submillimeter wavelengths. In particular, the SMA now offers the possibility to image multiple molecular transitions at once, owing to the 32-GHz wide instantaneous bandwidth of SWARM, the SMA’s new correlator. Molecular gas located far and very close to the photosphere of an asymptotic-giant branch (AGB) star, a red supergiant, or a pre-planetary nebula can now be examined in transitions observed simultaneously from a wide range of energy levels. This allows a very detailed quantitative investigation of physical and chemical conditions around these variable objects. Several imaging line surveys have been obtained with the SMA to reveal the beautiful complexity of these evolved systems. The surveys resulted in first submillimeter-wave identifications of molecules of prime astrophysical interest, e.g. of TiO, TiO2, and of rotational transitions at excited vibrational states of CO. An overview of recent SMA observations of cool evolved stars will be given with an emphasize on the interferometric line surveys. We will demonstrate their importance in unraveling the mass-loss phenomena, propagation of shocks in the circumstellar medium, and production of dust at elevated temperatures. The SMA studies of these molecular factories have a direct impact on our understanding of the chemical evolution of the Galaxy and stellar evolution at low and high masses.

Fish habitat selection in a large hydropeaking river: Strong individual and temporal variations revealed by telemetry.

PubMed

Capra, Hervé; Plichard, Laura; Bergé, Julien; Pella, Hervé; Ovidio, Michaël; McNeil, Eric; Lamouroux, Nicolas

2017-02-01

Modeling individual fish habitat selection in highly variable environments such as hydropeaking rivers is required for guiding efficient management decisions. We analyzed fish microhabitat selection in the heterogeneous hydraulic and thermal conditions (modeled in two-dimensions) of a reach of the large hydropeaking Rhône River locally warmed by the cooling system of a nuclear power plant. We used modern fixed acoustic telemetry techniques to survey 18 fish individuals (five barbels, six catfishes, seven chubs) signaling their position every 3s over a three-month period. Fish habitat selection depended on combinations of current microhabitat hydraulics (e.g. velocity, depth), past microhabitat hydraulics (e.g. dewatering risk or maximum velocities during the past 15days) and to a lesser extent substrate and temperature. Mixed-effects habitat selection models indicated that individual effects were often stronger than specific effects. In the Rhône, fish individuals appear to memorize spatial and temporal environmental changes and to adopt a "least constraining" habitat selection. Avoiding fast-flowing midstream habitats, fish generally live along the banks in areas where the dewatering risk is high. When discharge decreases, however, they select higher velocities but avoid both dewatering areas and very fast-flowing midstream habitats. Although consistent with the available knowledge on static fish habitat selection, our quantitative results demonstrate temporal variations in habitat selection, depending on individual behavior and environmental history. Their generality could be further tested using comparative experiments in different environmental configurations. Copyright © 2016 Elsevier B.V. All rights reserved.

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.

PubMed

Petras, Daniel; Nothias, Louis-Félix; Quinn, Robert A; Alexandrov, Theodore; Bandeira, Nuno; Bouslimani, Amina; Castro-Falcón, Gabriel; Chen, Liangyu; Dang, Tam; Floros, Dimitrios J; Hook, Vivian; Garg, Neha; Hoffner, Nicole; Jiang, Yike; Kapono, Clifford A; Koester, Irina; Knight, Rob; Leber, Christopher A; Ling, Tie-Jun; Luzzatto-Knaan, Tal; McCall, Laura-Isobel; McGrath, Aaron P; Meehan, Michael J; Merritt, Jonathan K; Mills, Robert H; Morton, Jamie; Podvin, Sonia; Protsyuk, Ivan; Purdy, Trevor; Satterfield, Kendall; Searles, Stephen; Shah, Sahil; Shires, Sarah; Steffen, Dana; White, Margot; Todoric, Jelena; Tuttle, Robert; Wojnicz, Aneta; Sapp, Valerie; Vargas, Fernando; Yang, Jin; Zhang, Chao; Dorrestein, Pieter C

2016-11-15

The cars we drive, the homes we live in, the restaurants we visit, and the laboratories and offices we work in are all a part of the modern human habitat. Remarkably, little is known about the diversity of chemicals present in these environments and to what degree molecules from our bodies influence the built environment that surrounds us and vice versa. We therefore set out to visualize the chemical diversity of five built human habitats together with their occupants, to provide a snapshot of the various molecules to which humans are exposed on a daily basis. The molecular inventory was obtained through untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of samples from each human habitat and from the people that occupy those habitats. Mapping MS-derived data onto 3D models of the environments showed that frequently touched surfaces, such as handles (e.g., door, bicycle), resemble the molecular fingerprint of the human skin more closely than other surfaces that are less frequently in direct contact with humans (e.g., wall, bicycle frame). Approximately 50% of the MS/MS spectra detected were shared between people and the environment. Personal care products, plasticizers, cleaning supplies, food, food additives, and even medications that were found to be a part of the human habitat. The annotations indicate that significant transfer of chemicals takes place between us and our built environment. The workflows applied here will lay the foundation for future studies of molecular distributions in medical, forensic, architectural, space exploration, and environmental applications.

Intrapopulation variability in the timing of ontogenetic habitat shifts in sea turtles revealed using δ15 N values from bone growth rings.

PubMed

Turner Tomaszewicz, Calandra N; Seminoff, Jeffrey A; Peckham, S Hoyt; Avens, Larisa; Kurle, Carolyn M

2017-05-01

evidence of alternative ontogenetic shifts and habitat-use patterns for juveniles foraging in the eastern NPO. We combine two techniques, skeletochronology and stable isotope analysis, to reconstruct multi-year habitat-use patterns of a remote migratory species, linked to estimated ages and body sizes of individuals, to reveal variable ontogeny during the juvenile life stage that could drive alternate life histories and that has the potential to illuminate the migration patterns for other species with accretionary tissues. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Grizzly bear habitat research in Glacier National Park, Montana

USGS Publications Warehouse

Martinka, C.J.; Kendall, K.C.

1986-01-01

Grizzly bear habitat research began in 1967 and is continuing in Glacier National Park, MT. Direct observations and fecal analysis revealed a relatively definable pattern of habitat use by the bears. Habitat data were subsequently used to develop management models and explore the relationships between grizzlies and park visitors. Current research strategy is based on the concept that humans are an integral components of grizzly bear habitat. A geographic information system is being developed to assist in the application of habitat data. In addition, the behavioral response of grizzlies to annual changes in food production is being studied. Management that addresses bears, humans, and their habitat as a system is proposed.

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

PubMed Central

Simon, Meinhard; Scheuner, Carmen; Meier-Kolthoff, Jan P; Brinkhoff, Thorsten; Wagner-Döbler, Irene; Ulbrich, Marcus; Klenk, Hans-Peter; Schomburg, Dietmar; Petersen, Jörn; Göker, Markus

2017-01-01

Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As ‘Roseobacter clade', these ‘roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term ‘Roseobacter group' for the marine Rhodobacteraceae strains. PMID:28106881

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats.

PubMed

Simon, Meinhard; Scheuner, Carmen; Meier-Kolthoff, Jan P; Brinkhoff, Thorsten; Wagner-Döbler, Irene; Ulbrich, Marcus; Klenk, Hans-Peter; Schomburg, Dietmar; Petersen, Jörn; Göker, Markus

2017-06-01

Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.

Variation of mucin adhesion, cell surface characteristics, and molecular mechanisms among Lactobacillus plantarum isolated from different habitats.

PubMed

Buntin, Nirunya; de Vos, Willem M; Hongpattarakere, Tipparat

2017-10-01

The adhesion ability to mucin varied greatly among 18 Lactobacillus plantarum isolates depending on their isolation habitats. Such ability remained at high level even though they were sequentially exposed to the gastrointestinal (GI) stresses. The majority of L. plantarum isolated from shrimp intestine and about half of food isolates exhibited adhesion ability (51.06-55.04%) about the same as the well-known adhesive L. plantarum 299v. Interestingly, five infant isolates of CIF17A2, CIF17A4, CIF17A5, CIF17AN2, and CIF17AN8 exhibited extremely high adhesion ranging from 62.69 to 72.06%. Such highly adhesive property correlating to distinctively high cell surface hydrophobicity was significantly weaken after pretreatment with LiCl and guanidine-HCl confirming the entailment of protein moiety. Regarding the draft genome information, all molecular structures of major cell wall-anchored proteins involved in the adhesion based on L. plantarum WCSF1, including lp_0964, lp_1643, lp_3114, lp_2486, lp_3127, and lp_3059 orthologues were detected in all isolates. Exceptionally, the gene-trait matching between yeast agglutination assay and the relevant mannose-specific adhesin (lp_1229) encoding gene confirmed the Msa absence in five infant isolates expressed distinctively high adhesion. Interestingly, the predicted flagellin encoding genes (fliC) firstly revealed in lp_1643, lp_2486, and lp_3114 orthologues may potentially contribute to such highly adhesive property of these isolates.

Roosting behaviour and habitat selection of Pteropus giganteus reveals potential links to Nipah virus epidemiology

PubMed Central

Hahn, Micah B.; Epstein, Jonathan H.; Gurley, Emily S.; Islam, Mohammad S.; Luby, Stephen P.; Daszak, Peter; Patz, Jonathan A.

2014-01-01

Summary 1. Flying foxes Pteropus spp. play a key role in forest regeneration as seed dispersers and are also the reservoir of many viruses, including Nipah virus in Bangladesh. Little is known about their habitat requirements, particularly in South Asia. Identifying Pteropus habitat preferences could assist in understanding the risk of zoonotic disease transmission broadly, and in Bangladesh, could help explain the spatial distribution of human Nipah virus cases. 2. We analysed characteristics of Pteropus giganteus roosts and constructed an ecological niche model to identify suitable habitat in Bangladesh. We also assessed the distribution of suitable habitat in relation to the location of human Nipah virus cases. 3. Compared to non-roost trees, P. giganteus roost trees are taller with larger diameters, and are more frequently canopy trees. Colony size was larger in densely forested regions and smaller in flood-affected areas. Roosts were located in areas with lower annual precipitation and higher human population density than non-roost sites. 4. We predicted that 2–17% of Bangladesh's land area is suitable roosting habitat. Nipah virus outbreak villages were 2.6 times more likely to be located in areas predicted as highly suitable habitat for P. giganteus compared to non-outbreak villages. 5. Synthesis and applications. Habitat suitability modelling may help identify previously undocumented Nipah outbreak locations and improve our understanding of Nipah virus ecology by highlighting regions where there is suitable bat habitat but no reported human Nipah virus. Conservation and public health education is a key component of P. giganteus management in Bangladesh due to the general misunderstanding and fear of bats that are a reservoir of Nipah virus. Affiliation between Old World fruit bats (Pteropodidae) and people is common throughout their range, and in order to conserve these keystone bat species and prevent emergence of zoonotic viruses, it is imperative that

Roosting behaviour and habitat selection of Pteropus giganteus reveals potential links to Nipah virus epidemiology.

PubMed

Hahn, Micah B; Epstein, Jonathan H; Gurley, Emily S; Islam, Mohammad S; Luby, Stephen P; Daszak, Peter; Patz, Jonathan A

2014-04-01

1. Flying foxes Pteropus spp. play a key role in forest regeneration as seed dispersers and are also the reservoir of many viruses, including Nipah virus in Bangladesh. Little is known about their habitat requirements, particularly in South Asia. Identifying Pteropus habitat preferences could assist in understanding the risk of zoonotic disease transmission broadly, and in Bangladesh, could help explain the spatial distribution of human Nipah virus cases. 2. We analysed characteristics of Pteropus giganteus roosts and constructed an ecological niche model to identify suitable habitat in Bangladesh. We also assessed the distribution of suitable habitat in relation to the location of human Nipah virus cases. 3. Compared to non-roost trees, P. giganteus roost trees are taller with larger diameters, and are more frequently canopy trees. Colony size was larger in densely forested regions and smaller in flood-affected areas. Roosts were located in areas with lower annual precipitation and higher human population density than non-roost sites. 4. We predicted that 2-17% of Bangladesh's land area is suitable roosting habitat. Nipah virus outbreak villages were 2.6 times more likely to be located in areas predicted as highly suitable habitat for P. giganteus compared to non-outbreak villages. 5. Synthesis and applications . Habitat suitability modelling may help identify previously undocumented Nipah outbreak locations and improve our understanding of Nipah virus ecology by highlighting regions where there is suitable bat habitat but no reported human Nipah virus. Conservation and public health education is a key component of P. giganteus management in Bangladesh due to the general misunderstanding and fear of bats that are a reservoir of Nipah virus. Affiliation between Old World fruit bats ( Pteropodidae ) and people is common throughout their range, and in order to conserve these keystone bat species and prevent emergence of zoonotic viruses, it is imperative that we

Exploration of the canyon-incised continental margin of the northeastern United States reveals dynamic habitats and diverse communities

USGS Publications Warehouse

Quattrini, Andrea; Nizinski, Martha S.; Chaytor, Jason; Demopoulos, Amanda W.J.; Roark, E. Brendan; France, Scott; Moore, Jon A.; Heyl, Taylor P.; Auster, Peter J.; Ruppel, Carolyn D.; Elliott, Kelley P.; Kennedy, Brian R.C.; Lobecker, Elizabeth A.; Skarke, Adam; Shank, Timothy M.

2015-01-01

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichosand the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

PubMed Central

Knief, Claudia

2015-01-01

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities. PMID:26696968

Habitat and food resources of otters (Mustelidae) in Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Abdul-Patah, P.; Nur-Syuhada, N.; Md-Nor, S.; Sasaki, H.; Md-Zain, B. M.

2014-09-01

Habitat and food resources of otters were studied in several locations in Peninsular Malaysia. A total of 210 fecal samples were collected from April 2010 to March 2011 believed to be of otter's were analyzed for their diet composition and their habitat preferences. The DNA testing conducted revealed that only 126 samples were identified as Lultrogale perspicillata and Aonyx cinereus with 105 and 21 samples, respectively. Habitat analyses revealed that these two species preferred paddy fields and mangroves as their main habitats but L. perspicillata preferred to hunt near habitat with large water bodies, such as mangroves, rivers, ponds, and lakes. A. cinereus on the other hand, were mainly found near land-based habitat, such as paddy fields, casuarinas forest and oil palms near mangroves. Habitats chosen were influenced by their food preferences where L. perspicillata consumed a variety of fish species with a supplementary diet of prawns, small mammals, and amphibians, compared to A. cinereus which consumed less fish and more non-fish food items, such as insects, crabs, and snails. Since, the most of the otter habitats in this study are not located within the protected areas, conservation effort involving administrations, landowners, private organizations and public are necessary.

Intraspecific ecomorphological variation: linear and geometric morphometrics reveal habitat-related patterns within Podarcis bocagei wall lizards.

PubMed

Kaliontzopoulou, Antigoni; Carretero, M A; Llorente, G A

2010-06-01

Morphological variation in relation to habitat is known to occur in several lizard groups. Comparative studies have linked morphology and habitat use, showing that locomotion is the principal mediator of this evolutionary relationship. Here, we investigate intraspecific ecomorphological variation in Podarcis bocagei by examining three habitat types, representing a variety between saxicolous and ground-dwelling habits. Our results indicate variation in absolute and relative limb length, but patterns are only partially concordant to biomechanical predictions. Whereas the femur and hind foot are longer in ground-dwelling lizards, confirming previous observations, the tibia and hind limb are relatively shorter, contradicting expectations. Additionally, head shape varies substantially between habitats, in line with a hypothesis of mechanical restrictions related to microhabitat and refuge use. Finally, we detect male-specific variation between habitats in total body size and head size, providing evidence for interactions between natural and sexual selection. Although performance and behaviour studies are necessary to definitely confirm the functional and evolutionary significance of the observed patterns, our study indicates that ecomorphological adaptations can arise in a very short evolutionary time in this group of lizards.

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation.

PubMed

Mayer, Teresa; Blachowicz, Adriana; Probst, Alexander J; Vaishampayan, Parag; Checinska, Aleksandra; Swarmer, Tiffany; de Leon, Pablo; Venkateswaran, Kasthuri

2016-06-02

For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contamination of closed habitats presents a risk for crewmembers due to reduced human immune response during long-term confinement. To make future habitat designs safer for crewmembers, lessons learned from characterizing analogous habitats is very critical. One of the key issues is that how human presence influences the accumulation of microorganisms in the closed habitat. Molecular technologies, along with traditional microbiological methods, were utilized to catalog microbial succession during a 30-day human occupation of a simulated inflatable lunar/Mars habitat. Surface samples were collected at different time points to capture the complete spectrum of viable and potential opportunistic pathogenic bacterial population. Traditional cultivation, propidium monoazide (PMA)-quantitative polymerase chain reaction (qPCR), and adenosine triphosphate (ATP) assays were employed to estimate the cultivable, viable, and metabolically active microbial population, respectively. Next-generation sequencing was used to elucidate the microbial dynamics and community profiles at different locations of the habitat during varying time points. Statistical analyses confirm that occupation time has a strong influence on bacterial community profiles. The Day 0 samples (before human occupation) have a very different microbial diversity compared to the later three time points. Members of Proteobacteria (esp. Oxalobacteraceae and Caulobacteraceae) and Firmicutes (esp. Bacillaceae) were most abundant before human occupation (Day 0), while other members of Firmicutes (Clostridiales) and Actinobacteria (esp. Corynebacteriaceae) were abundant during the 30-day occupation. Treatment of samples with PMA (a DNA-intercalating dye for selective detection of viable microbial population) had a

Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes

PubMed Central

2008-01-01

Background Little is known about the role ecological shifts play in the evolution of Neotropical radiations that have colonized a variety of environments. We here examine habitat shifts in the evolutionary history of Elaenia flycatchers, a Neotropical bird lineage that lives in a range of forest and open habitats. We evaluate phylogenetic relationships within the genus based on mitochondrial and nuclear DNA sequence data, and then employ parsimony-based and Bayesian methods to reconstruct preferences for a number of habitat types and migratory behaviour throughout the evolutionary history of the genus. Using a molecular clock approach, we date the most important habitat shifts. Results Our analyses resolve phylogenetic relationships among Elaenia species and confirm several species associations predicted by morphology while furnishing support for other taxon placements that are in conflict with traditional classification, such as the elevation of various Elaenia taxa to species level. While savannah specialism is restricted to one basal clade within the genus, montane forest was invaded from open habitat only on a limited number of occasions. Riparian growth may have been favoured early on in the evolution of the main Elaenia clade and subsequently been deserted on several occasions. Austral long-distance migratory behaviour evolved on several occasions. Conclusion Ancestral reconstructions of habitat preferences reveal pronounced differences not only in the timing of the emergence of certain habitat preferences, but also in the frequency of habitat shifts. The early origin of savannah specialism in Elaenia highlights the importance of this habitat in Neotropical Pliocene and late Miocene biogeography. While forest in old mountain ranges such as the Tepuis and the Brazilian Shield was colonized early on, the most important colonization event of montane forest was in conjunction with Pliocene Andean uplift. Riparian habitats may have played an important role in

Whole-lake invasive crayfish removal and qualitative modeling reveal habitat-specific food web topology

DOE PAGES

Hansen, Gretchen J. A.; Tunney, Tyler D.; Winslow, Luke A.; ...

2017-02-10

Patterning of the presence/absence of food web linkages (hereafter topology) is a fundamental characteristic of ecosystems that can influence species responses to perturbations. However, the insight from food web topology into dynamic effects of perturbations on species is potentially hindered because most described topologies represent data integrated across spatial and temporal scales. We conducted a 10-year, whole-lake experiment in which we removed invasive rusty crayfish ( Orconectes rusticus) from a 64-ha north-temperate lake and monitored responses of multiple trophic levels. We compared species responses observed in two sub-habitats to the responses predicted from all topologies of an integrated, literature-informed basemore » food web model of 32 potential links. Out of 4.3 billion possible topologies, only 308,833 (0.0072%) predicted responses that qualitatively matched observed species responses in cobble habitat, and only 12,673 (0.0003%) matched observed responses in sand habitat. Furthermore, when constrained to predictions that both matched observed responses and were highly reliable (i.e., predictions were robust to link strength values), only 5040 (0.0001%) and 140 (0.000003%) topologies were identified for cobble and sand habitats, respectively. A small number of linkages were nearly always present in these valid, reliable networks in sand, while a greater variety of possible network configurations were possible in cobble. Direct links involving invasive rusty crayfish were more important in cobble, while indirect effects involving Lepomis spp. were more important in sand. Importantly, the importance of individual species linkages differed dramatically among cobble and sand sub-habitats within a single lake, even though species composition was identical. Furthermore the true topology of food webs is difficult to determine, constraining topologies to include spatial resolution that matches observed experimental outcomes may reduce possibilities

Whole-lake invasive crayfish removal and qualitative modeling reveal habitat-specific food web topology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansen, Gretchen J. A.; Tunney, Tyler D.; Winslow, Luke A.

Patterning of the presence/absence of food web linkages (hereafter topology) is a fundamental characteristic of ecosystems that can influence species responses to perturbations. However, the insight from food web topology into dynamic effects of perturbations on species is potentially hindered because most described topologies represent data integrated across spatial and temporal scales. We conducted a 10-year, whole-lake experiment in which we removed invasive rusty crayfish ( Orconectes rusticus) from a 64-ha north-temperate lake and monitored responses of multiple trophic levels. We compared species responses observed in two sub-habitats to the responses predicted from all topologies of an integrated, literature-informed basemore » food web model of 32 potential links. Out of 4.3 billion possible topologies, only 308,833 (0.0072%) predicted responses that qualitatively matched observed species responses in cobble habitat, and only 12,673 (0.0003%) matched observed responses in sand habitat. Furthermore, when constrained to predictions that both matched observed responses and were highly reliable (i.e., predictions were robust to link strength values), only 5040 (0.0001%) and 140 (0.000003%) topologies were identified for cobble and sand habitats, respectively. A small number of linkages were nearly always present in these valid, reliable networks in sand, while a greater variety of possible network configurations were possible in cobble. Direct links involving invasive rusty crayfish were more important in cobble, while indirect effects involving Lepomis spp. were more important in sand. Importantly, the importance of individual species linkages differed dramatically among cobble and sand sub-habitats within a single lake, even though species composition was identical. Furthermore the true topology of food webs is difficult to determine, constraining topologies to include spatial resolution that matches observed experimental outcomes may reduce possibilities

Feral Cats Are Better Killers in Open Habitats, Revealed by Animal-Borne Video.

PubMed

McGregor, Hugh; Legge, Sarah; Jones, Menna E; Johnson, Christopher N

2015-01-01

One of the key gaps in understanding the impacts of predation by small mammalian predators on prey is how habitat structure affects the hunting success of small predators, such as feral cats. These effects are poorly understood due to the difficulty of observing actual hunting behaviours. We attached collar-mounted video cameras to feral cats living in a tropical savanna environment in northern Australia, and measured variation in hunting success among different microhabitats (open areas, dense grass and complex rocks). From 89 hours of footage, we recorded 101 hunting events, of which 32 were successful. Of these kills, 28% were not eaten. Hunting success was highly dependent on microhabitat structure surrounding prey, increasing from 17% in habitats with dense grass or complex rocks to 70% in open areas. This research shows that habitat structure has a profound influence on the impacts of small predators on their prey. This has broad implications for management of vegetation and disturbance processes (like fire and grazing) in areas where feral cats threaten native fauna. Maintaining complex vegetation cover can reduce predation rates of small prey species from feral cat predation.

Feral Cats Are Better Killers in Open Habitats, Revealed by Animal-Borne Video

PubMed Central

McGregor, Hugh; Legge, Sarah; Jones, Menna E.; Johnson, Christopher N.

2015-01-01

One of the key gaps in understanding the impacts of predation by small mammalian predators on prey is how habitat structure affects the hunting success of small predators, such as feral cats. These effects are poorly understood due to the difficulty of observing actual hunting behaviours. We attached collar-mounted video cameras to feral cats living in a tropical savanna environment in northern Australia, and measured variation in hunting success among different microhabitats (open areas, dense grass and complex rocks). From 89 hours of footage, we recorded 101 hunting events, of which 32 were successful. Of these kills, 28% were not eaten. Hunting success was highly dependent on microhabitat structure surrounding prey, increasing from 17% in habitats with dense grass or complex rocks to 70% in open areas. This research shows that habitat structure has a profound influence on the impacts of small predators on their prey. This has broad implications for management of vegetation and disturbance processes (like fire and grazing) in areas where feral cats threaten native fauna. Maintaining complex vegetation cover can reduce predation rates of small prey species from feral cat predation. PMID:26288224

A submarine volcanic eruption leads to a novel microbial habitat.

PubMed

Danovaro, Roberto; Canals, Miquel; Tangherlini, Michael; Dell'Anno, Antonio; Gambi, Cristina; Lastras, Galderic; Amblas, David; Sanchez-Vidal, Anna; Frigola, Jaime; Calafat, Antoni M; Pedrosa-Pàmies, Rut; Rivera, Jesus; Rayo, Xavier; Corinaldesi, Cinzia

2017-04-24

Submarine volcanic eruptions are major catastrophic events that allow investigation of the colonization mechanisms of newly formed seabed. We explored the seafloor after the eruption of the Tagoro submarine volcano off El Hierro Island, Canary Archipelago. Near the summit of the volcanic cone, at about 130 m depth, we found massive mats of long, white filaments that we named Venus's hair. Microscopic and molecular analyses revealed that these filaments are made of bacterial trichomes enveloped within a sheath and colonized by epibiotic bacteria. Metagenomic analyses of the filaments identified a new genus and species of the order Thiotrichales, Thiolava veneris. Venus's hair shows an unprecedented array of metabolic pathways, spanning from the exploitation of organic and inorganic carbon released by volcanic degassing to the uptake of sulfur and nitrogen compounds. This unique metabolic plasticity provides key competitive advantages for the colonization of the new habitat created by the submarine eruption. A specialized and highly diverse food web thrives on the complex three-dimensional habitat formed by these microorganisms, providing evidence that Venus's hair can drive the restart of biological systems after submarine volcanic eruptions.

Molecular Characterization and Phylogenetic Analysis of Pseudomonas aeruginosa Isolates Recovered from Greek Aquatic Habitats Implementing the Double-Locus Sequence Typing Scheme.

PubMed

Pappa, Olga; Beloukas, Apostolos; Vantarakis, Apostolos; Mavridou, Athena; Kefala, Anastasia-Maria; Galanis, Alex

2017-07-01

The recently described double-locus sequence typing (DLST) scheme implemented to deeply characterize the genetic profiles of 52 resistant environmental Pseudomonas aeruginosa isolates deriving from aquatic habitats of Greece. DLST scheme was able not only to assign an already known allelic profile to the majority of the isolates but also to recognize two new ones (ms217-190, ms217-191) with high discriminatory power. A third locus (oprD) was also used for the molecular typing, which has been found to be fundamental for the phylogenetic analysis of environmental isolates given the resulted increased discrimination between the isolates. Additionally, the circulation of acquired resistant mechanisms in the aquatic habitats according to their genetic profiles was proved to be more extent. Hereby, we suggest that the combination of the DLST to oprD typing can discriminate phenotypically and genetically related environmental P. aeruginosa isolates providing reliable phylogenetic analysis at a local level.

Anopheline larval habitats seasonality and species distribution: a prerequisite for effective targeted larval habitats control programmes.

PubMed

Kweka, Eliningaya J; Zhou, Guofa; Munga, Stephen; Lee, Ming-Chieh; Atieli, Harrysone E; Nyindo, Mramba; Githeko, Andrew K; Yan, Guiyun

2012-01-01

Larval control is of paramount importance in the reduction of malaria vector abundance and subsequent disease transmission reduction. Understanding larval habitat succession and its ecology in different land use managements and cropping systems can give an insight for effective larval source management practices. This study investigated larval habitat succession and ecological parameters which influence larval abundance in malaria epidemic prone areas of western Kenya. A total of 51 aquatic habitats positive for anopheline larvae were surveyed and visited once a week for a period of 85 weeks in succession. Habitats were selected and identified. Mosquito larval species, physico-chemical parameters, habitat size, grass cover, crop cycle and distance to nearest house were recorded. Polymerase chain reaction revealed that An. gambiae s.l was the most dominant vector species comprised of An.gambiae s.s (77.60%) and An.arabiensis (18.34%), the remaining 4.06% had no amplification by polymerase chain reaction. Physico-chemical parameters and habitat size significantly influenced abundance of An. gambiae s.s (P = 0.024) and An. arabiensis (P = 0.002) larvae. Further, larval species abundance was influenced by crop cycle (P≤0.001), grass cover (P≤0.001), while distance to nearest houses significantly influenced the abundance of mosquito species larvae (r = 0.920;P≤0.001). The number of predator species influenced mosquito larval abundance in different habitat types. Crop weeding significantly influenced with the abundance of An.gambiae s.l (P≤0.001) when preceded with fertilizer application. Significantly higher anopheline larval abundance was recorded in habitats in pasture compared to farmland (P = 0.002). When habitat stability and habitat types were considered, hoof print were the most productive followed by disused goldmines. These findings suggest that implementation of effective larval control programme should be targeted with larval habitats

Local sparse bump hunting reveals molecular heterogeneity of colon tumors‡

PubMed Central

Dazard, Jean-Eudes; Rao, J. Sunil; Markowitz, Sanford

2013-01-01

The question of molecular heterogeneity and of tumoral phenotype in cancer remains unresolved. To understand the underlying molecular basis of this phenomenon, we analyzed genome-wide expression data of colon cancer metastasis samples, as these tumors are the most advanced and hence would be anticipated to be the most likely heterogeneous group of tumors, potentially exhibiting the maximum amount of genetic heterogeneity. Casting a statistical net around such a complex problem proves difficult because of the high dimensionality and multi-collinearity of the gene expression space, combined with the fact that genes act in concert with one another and that not all genes surveyed might be involved. We devise a strategy to identify distinct subgroups of samples and determine the genetic/molecular signature that defines them. This involves use of the local sparse bump hunting algorithm, which provides a much more optimal and biologically faithful transformed space within which to search for bumps. In addition, thanks to the variable selection feature of the algorithm, we derived a novel sparse gene expression signature, which appears to divide all colon cancer patients into two populations: a population whose expression pattern can be molecularly encompassed within the bump and an outlier population that cannot be. Although all patients within any given stage of the disease, including the metastatic group, appear clinically homogeneous, our procedure revealed two subgroups in each stage with distinct genetic/molecular profiles. We also discuss implications of such a finding in terms of early detection, diagnosis and prognosis. PMID:22052459

Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences.

PubMed

Söllinger, Andrea; Schwab, Clarissa; Weinmaier, Thomas; Loy, Alexander; Tveit, Alexander T; Schleper, Christa; Urich, Tim

2016-01-01

Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Specializing on vulnerable habitat: Acropora selectivity among damselfish recruits and the risk of bleaching-induced habitat loss

NASA Astrophysics Data System (ADS)

Bonin, M. C.

2012-03-01

Coral reef habitats are increasingly being degraded and destroyed by a range of disturbances, most notably climate-induced coral bleaching. Habitat specialists, particularly those associated with susceptible coral species, are clearly among the most vulnerable to population decline or extinction. However, the degree of specialization on coral microhabitats is still unclear for one of the most ubiquitous, abundant and well studied of coral reef fish families—the damselfishes (Pomacentridae). Using high taxonomic resolution surveys of microhabitat use and availability, this study provides the first species-level description of patterns of Acropora selectivity among recruits of 10 damselfish species in order to determine their vulnerability to habitat degradation. In addition, surveys of the bleaching susceptibility of 16 branching coral species revealed which preferred recruitment microhabitats are at highest risk of decline as a result of chronic coral bleaching. Four species (i.e., Chrysiptera parasema, Pomacentrus moluccensis, Dascyllus melanurus and Chromis retrofasciata) were identified as highly vulnerable because they used only branching hard corals as recruitment habitat and primarily associated with only 2-4 coral species. The bleaching surveys revealed that five species of Acropora were highly susceptible to bleaching, with more than 50% of colonies either severely bleached or already dead. These highly susceptible corals included two of the preferred microhabitats of the specialist C. parasema and represented a significant proportion of its total recruitment microhabitat. In contrast, highly susceptible corals were rarely used by another specialist, P. moluccensis, suggesting that this species faces a lower risk of bleaching-induced habitat loss compared to C. parasema. As degradation to coral reef habitats continues, specialists will increasingly be forced to use alternative recruitment microhabitats, and this is likely to reduce population

Mangrove Habitat Use by Juvenile Reef Fish: Meta-Analysis Reveals that Tidal Regime Matters More than Biogeographic Region

PubMed Central

Igulu, Mathias M.; Nagelkerken, Ivan; Dorenbosch, Martijn; Grol, Monique G. G.; Harborne, Alastair R.; Kimirei, Ismael A.; Mumby, Peter J.; Olds, Andrew D.; Mgaya, Yunus D.

2014-01-01

Identification of critical life-stage habitats is key to successful conservation efforts. Juveniles of some species show great flexibility in habitat use while other species rely heavily on a restricted number of juvenile habitats for protection and food. Considering the rapid degradation of coastal marine habitats worldwide, it is important to evaluate which species are more susceptible to loss of juvenile nursery habitats and how this differs across large biogeographic regions. Here we used a meta-analysis approach to investigate habitat use by juvenile reef fish species in tropical coastal ecosystems across the globe. Densities of juvenile fish species were compared among mangrove, seagrass and coral reef habitats. In the Caribbean, the majority of species showed significantly higher juvenile densities in mangroves as compared to seagrass beds and coral reefs, while for the Indo-Pacific region seagrass beds harbored the highest overall densities. Further analysis indicated that differences in tidal amplitude, irrespective of biogeographic region, appeared to be the major driver for this phenomenon. In addition, juvenile reef fish use of mangroves increased with increasing water salinity. In the Caribbean, species of specific families (e.g. Lutjanidae, Haemulidae) showed a higher reliance on mangroves or seagrass beds as juvenile habitats than other species, whereas in the Indo-Pacific family-specific trends of juvenile habitat utilization were less apparent. The findings of this study highlight the importance of incorporating region-specific tidal inundation regimes into marine spatial conservation planning and ecosystem based management. Furthermore, the significant role of water salinity and tidal access as drivers of mangrove fish habitat use implies that changes in seawater level and rainfall due to climate change may have important effects on how juvenile reef fish use nearshore seascapes in the future. PMID:25551761

Mangrove habitat use by juvenile reef fish: meta-analysis reveals that tidal regime matters more than biogeographic region.

PubMed

Igulu, Mathias M; Nagelkerken, Ivan; Dorenbosch, Martijn; Grol, Monique G G; Harborne, Alastair R; Kimirei, Ismael A; Mumby, Peter J; Olds, Andrew D; Mgaya, Yunus D

2014-01-01

Identification of critical life-stage habitats is key to successful conservation efforts. Juveniles of some species show great flexibility in habitat use while other species rely heavily on a restricted number of juvenile habitats for protection and food. Considering the rapid degradation of coastal marine habitats worldwide, it is important to evaluate which species are more susceptible to loss of juvenile nursery habitats and how this differs across large biogeographic regions. Here we used a meta-analysis approach to investigate habitat use by juvenile reef fish species in tropical coastal ecosystems across the globe. Densities of juvenile fish species were compared among mangrove, seagrass and coral reef habitats. In the Caribbean, the majority of species showed significantly higher juvenile densities in mangroves as compared to seagrass beds and coral reefs, while for the Indo-Pacific region seagrass beds harbored the highest overall densities. Further analysis indicated that differences in tidal amplitude, irrespective of biogeographic region, appeared to be the major driver for this phenomenon. In addition, juvenile reef fish use of mangroves increased with increasing water salinity. In the Caribbean, species of specific families (e.g. Lutjanidae, Haemulidae) showed a higher reliance on mangroves or seagrass beds as juvenile habitats than other species, whereas in the Indo-Pacific family-specific trends of juvenile habitat utilization were less apparent. The findings of this study highlight the importance of incorporating region-specific tidal inundation regimes into marine spatial conservation planning and ecosystem based management. Furthermore, the significant role of water salinity and tidal access as drivers of mangrove fish habitat use implies that changes in seawater level and rainfall due to climate change may have important effects on how juvenile reef fish use nearshore seascapes in the future.

Support of Coastal Fishes by Nearshore and Coastal Wetland Habitats

EPA Science Inventory

Hydrologic linkages among Great Lakes nearshore and coastal wetlands free coastal fish to move among the habitats, which has led to a variety of habitat use patterns. Fine-scale microchemical analyses of yellow perch otoliths have revealed life-history categories that include per...

Recent research on inherent molecular structure, physiochemical properties, and bio-functions of food and feed-type Avena sativa oats and processing-induced changes revealed with molecular microspectroscopic techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prates, Luciana Louzada; Yu, Peiqiang

Avena sativa oat is a cereal widely used as human food and livestock feed. However, the low metabolized energy and the rapid rumen degradations of protein and starch have limited the use of A. sativa oat grains. To overcome this disadvantage, new A. sativa oat varieties have been developed. Additionally, heat-related processing has been performed to decrease the degradation rate and improve the absorption of amino acids in the small intestine. The nutritive value is reflected by both chemical composition and inherent molecular structure conformation. However, the traditional wet chemical analysis is not able to detect the inherent molecular structuresmore » within an intact tissue. The advanced synchrotron-radiation and globar-based molecular microspectroscopy have been developed recently and applied to study internal molecular structures and the processing induced structure changes in A. sativa oats and reveal how molecular structure changes in relation to nutrient availability. This review aimed to obtain the recent information regarding physiochemical properties, molecular structures, metabolic characteristics of protein, and the heat-induced changes in new A. sativa oat varieties. The use of the advanced vibrational molecular spectroscopy was emphasized, synchrotron- and globar-based (micro)spectroscopy, to reveal the inherent structure of A. sativa oats at cellular and molecular levels and to reveal the heat processing effect on the degradation characteristics and the protein molecular structure in A. sativa oats. The relationship between nutrient availability and protein molecular inherent structure was also presented. Information described in this review gives better insight in the physiochemical properties, molecular structure, and the heat-induced changes in A. sativa oat detected with advanced molecular spectroscopic techniques in combinination with conventional nutrition study techniques.« less

Living at the edge: biogeographic patterns of habitat segregation conform to speciation by niche expansion in Anopheles gambiae

PubMed Central

Costantini, Carlo; Ayala, Diego; Guelbeogo, Wamdaogo M; Pombi, Marco; Some, Corentin Y; Bassole, Imael HN; Ose, Kenji; Fotsing, Jean-Marie; Sagnon, N'Falé; Fontenille, Didier; Besansky, Nora J; Simard, Frédéric

2009-01-01

Background Ongoing lineage splitting within the African malaria mosquito Anopheles gambiae is compatible with ecological speciation, the evolution of reproductive isolation by divergent natural selection acting on two populations exploiting alternative resources. Divergence between two molecular forms (M and S) identified by fixed differences in rDNA, and characterized by marked, although incomplete, reproductive isolation is occurring in West and Central Africa. To elucidate the role that ecology and geography play in speciation, we carried out a countrywide analysis of An. gambiae M and S habitat requirements, and that of their chromosomal variants, across Burkina Faso. Results Maps of relative abundance by geostatistical interpolators produced a distinct pattern of distribution: the M-form dominated in the northernmost arid zones, the S-form in the more humid southern regions. Maps of habitat suitability, quantified by Ecological Niche Factor Analysis based on 15 eco-geographical variables revealed less contrast among forms. M was peculiar as it occurred proportionally more in habitat of marginal quality. Measures of ecological niche breadth and overlap confirmed the mismatch between the fundamental and realized patterns of habitat occupation: forms segregated more than expected from the extent of divergence of their environmental envelope – a signature of niche expansion. Classification of chromosomal arm 2R karyotypes by multilocus genetic clustering identified two clusters loosely corresponding to molecular forms, with 'mismatches' representing admixed individuals due to shared ancestral polymorphism and/or residual hybridization. In multivariate ordination space, these karyotypes plotted in habitat of more marginal quality compared to non-admixed, 'typical', karyotypes. The distribution of 'typical' karyotypes along the main eco-climatic gradient followed a consistent pattern within and between forms, indicating an adaptive role of inversions at this

Molecular characterization of an influenza A virus (H4N2) isolated from waterfowl habitats in the State of Mexico.

PubMed

Ornelas-Eusebio, Erika; Obregón-Ascencio, Alejandro; Chávez-Maya, Fernando; García-Espinosa, Gary

2015-03-01

Wild waterfowl and their habitats are the main reservoirs of influenza A virus (IAV) mainly during the breeding season and prior to migration. This study describes the molecular characterization of an IAV isolated from 240 water samples of a small wetland during non-breeding season of migratory wild ducks in the State of Mexico, Mexico. The results showed that the virus belongs to the H4N2 subtype and each of its eight segments of the viral genome has similarity to IAV isolated from ducks in North America. This study suggests that IAV can be isolated from small wetland during non-breeding season of migrating waterfowl.

Pupal productivity & nutrient reserves of Aedes mosquitoes breeding in sewage drains & other habitats of Kolkata, India: Implications for habitat expansion & vector management.

PubMed

Banerjee, Soumyajit; Mohan, Sushree; Saha, Nabaneeta; Mohanty, Siba Prasad; Saha, Goutam K; Aditya, Gautam

2015-12-01

The quality of breeding sites is reflected through the pupal productivity and the life history traits of Aedes mosquitoes. Using nutrient reserves and pupal productivity of Aedes as indicators, the larval habitats including sewage drains were characterized to highlight the habitat expansion and vector management. The pupae and adults collected from the containers and sewage drains were characterized in terms of biomass and nutrient reserves and the data were subjected to three way factorial ANOVA. Discriminant function analyses were performed to highlight the differences among the habitats for sustenance of Aedes mosquitoes. Survey of larval habitats from the study area revealed significant differences (P<0.05) in the pupal productivity of Aedes among the habitats and months. Despite sewage drains being comparatively less utilized for breeding, the pupae were of higher biomass with corresponding adults having longer wings in contrast to other habitats. The nutrient reserve of the adults emerging from pupae of sewage drains was significantly higher (P<0.05), compared to other habitats, as reflected through the discriminant function analysis. The present results showed that for both Ae. aegypti and Ae. albopictus, sewage drains were equally congenial habitat as were plastic, porcelain and earthen habitats. Availability of Aedes immature in sewage drains poses increased risk of dengue, and thus vector control programme should consider inclusion of sewage drains as breeding habitat of dengue vector mosquitoes.

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

PubMed

Hertig, Samuel; Latorraca, Naomi R; Dror, Ron O

2016-06-01

Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

Avian habitat relationships in pinyon-juniper woodland

USGS Publications Warehouse

Sedgwick, James A.

1987-01-01

Habitat relationships of breeding birds were examined in northwestern Colorado in pinyon-juniper (Pinus edulis-Juniperus osteosperma) woodland and in openings where most overstory trees had been knocked down by anchor chaining. Vegetation characteristics and physical habitat features were measured in 233 0.04-ha circular plots around singing males of 13 species of birds from 15 May to 15 July 1980. Thirteen-group discriminant function analysis ordinated bird species along three habitat dimensions described by (1) canopy height; (2) slope, shrub size, and shrub species diversity; and (3) percentage canopy cover, large tree density, distance from a habitat edge, litter cover, and green cover. Woodland, open-area, and intermediate edge species were clearly segregated along the first discriminant axis, and species' associations with shrubs, inclination, ground cover, and edges were revealed by the ordinations along the second and third discriminant axes. Two-group discriminant analyses comparing occupied and available plots identified additional and more specific habitat associations. For example, Hermit Thrushes (Catharus guttatus) were associated with mature forested habitats and forest interiors, Virginia's Warblers (Vermivora virginiae) favored steep, oak-covered draws, Rock Wrens (Salpinctes obsoletus) selected areas where percentage log cover and small tree density were high, and Dusky Flycatchers (Empidonax oberholseri) preferred shrubby slopes with scattered large trees near woodland edges.

Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome

PubMed Central

2013-01-01

Background Down syndrome (DS), caused by an extra copy of chromosome 21, affects 1 in 750 live births and is characterized by cognitive impairment and a constellation of congenital defects. Currently, little is known about the molecular pathogenesis and no direct genotype-phenotype relationship has yet been confirmed. Since DS amniocytes are expected to have a distinct biological behaviour compared to normal amniocytes, we hypothesize that relative quantification of proteins produced from trisomy and euploid (chromosomally normal) amniocytes will reveal dysregulated molecular pathways. Results Chromosomally normal- and Trisomy 21-amniocytes were quantitatively analyzed by using Stable Isotope Labeling of Amino acids in Cell culture and tandem mass spectrometry. A total of 4919 unique proteins were identified from the supernatant and cell lysate proteome. More specifically, 4548 unique proteins were identified from the lysate, and 91% of these proteins were quantified based on MS/MS spectra ratios of peptides containing isotope-labeled amino acids. A total of 904 proteins showed significant differential expression and were involved in 25 molecular pathways, each containing a minimum of 16 proteins. Sixty of these proteins consistently showed aberrant expression from trisomy 21 affected amniocytes, indicating their potential role in DS pathogenesis. Nine proteins were analyzed with a multiplex selected reaction monitoring assay in an independent set of Trisomy 21-amniocyte samples and two of them (SOD1 and NES) showed a consistent differential expression. Conclusions The most extensive proteome of amniocytes and amniotic fluid has been generated and differentially expressed proteins from amniocytes with Trisomy 21 revealed molecular pathways that seem to be most significantly affected by the presence of an extra copy of chromosome 21. PMID:23394617

Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

PubMed

Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

2012-01-01

Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

Habitat segregation and cryptic adaptation of species of Periophthalmus (Gobioidei: Gobiidae).

PubMed

Polgar, G; Zaccara, S; Babbucci, M; Fonzi, F; Antognazza, C M; Ishak, N; Sulaiman, Z; Crosa, G

2017-05-01

A study was conducted on the habitat distribution of four sympatric species of Periophthalmus (the silver-lined mudskipper Periophthalmus argentilineatus, the slender mudskipper Periophthalmus gracilis, the kalolo mudskipper Periophthalmus kalolo and the Malacca mudskipper Periophthalmus malaccensis) from northern Sulawesi. Molecular phylogenetic reconstructions based on one mtDNA marker (16S) were used to validate the morphological taxa, identifying five molecular clades. Periophthalmus argentilineatus includes two molecular species, which are named Periophthalmus argentilineatus clades F and K. Multivariate direct gradient analysis show that these species form three distinct ecological guilds, with the two molecular species occurring in different guilds. Periophthalmus clade F is ecologically eurytypic; Periophthalmus clade K and P. kalolo are prevalent in ecosystems isolated by strong oceanic currents and at shorter distances from the sea; P. gracilis plus P. malaccensis are prevalent in ecosystems connected by shallow coastal waters, in vegetated habitats at larger distances from the sea. This indicates for the first time that mudskipper species exhibit a range of adaptations to semiterrestrialism not only within genera, but even within morphospecies, delineating a much more complex adaptive scenario than previously assumed. © 2017 The Fisheries Society of the British Isles.

Habitat modeling and genetic signatures of postglacial recolonization for tidal estuaries

NASA Astrophysics Data System (ADS)

Dolby, G. A.; Jacobs, D. K.

2014-12-01

Pleistocene glacial cycles are a foremost influence on the genetic diversity and species distribution patterns observed today. Though much work has centered on biotic response to such climatic forcing, little of it has regarded estuarine or other aquatic coastal taxa whose habitat formation is a function of sea level, hydrography, and coastal geomorphology. These physical parameters required for habitat formation suggest that glacial cycles impart a significant effect on such taxa through glacially driven eustatic changes. Additionally, the steepened coastline and rainfall-limited Mediterranean climate suggest limited glacial habitat for estuarine species in southern and Baja California. Here we present GIS modeled habitat for tidal estuaries for three co-distributed estuarine fishes (Gillichthys mirabilis, Quietula y-cauda, Fundulus parvipinnis) since the last glacial maximum. Parameterization of sea level and slope enables biologically relevant temporal resolution of near-millennial scale. At lowstand our approach reveals two refuges along the coast at 1000km distance from each other, with habitat rapidly increasing 15 - 12 ka during meltwater pulse 1A. Habitat area peaked in the early Holocene and began decreasing with the current stillstand roughly 7 ka, probably as a result of coastal maturation towards less tidal systems. To target the postglacial recolonization process we applied discriminant function analysis to highly polymorphic microsatellite data to partition out the alleles associated with refuges identified a priori by habitat modeling. The frequencies of these alleles were calculated for all individuals at intervening populations and regressed against geographic distance. This analysis revealed nonlinear mixing curves, suggesting uneven allelic mixing efficiency along the coastline, perhaps as a result of differential habitat origination times as indicated by the habitat models. These results highlight the dynamism of estuarine habitat in recent

STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp

We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by highermore » BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.« less

Estuarine intertidal habitat use by birds in a Pacific Northwest coastal estuary

EPA Science Inventory

Results of a year long study of the distribution of birds across five intertidal estuarine habitats reveal that tide level largely controls use of the habitats by birds. A total census of all birds observed from shoreline observation locations was made at five tide levels over s...

The Molecular Architecture of Cell Adhesion: Dynamic Remodeling Revealed by Videonanoscopy.

PubMed

Sergé, Arnauld

2016-01-01

The plasma membrane delimits the cell, which is the basic unit of living organisms, and is also a privileged site for cell communication with the environment. Cell adhesion can occur through cell-cell and cell-matrix contacts. Adhesion proteins such as integrins and cadherins also constitute receptors for inside-out and outside-in signaling within proteolipidic platforms. Adhesion molecule targeting and stabilization relies on specific features such as preferential segregation by the sub-membrane cytoskeleton meshwork and within membrane proteolipidic microdomains. This review presents an overview of the recent insights brought by the latest developments in microscopy, to unravel the molecular remodeling occurring at cell contacts. The dynamic aspect of cell adhesion was recently highlighted by super-resolution videomicroscopy, also named videonanoscopy. By circumventing the diffraction limit of light, nanoscopy has allowed the monitoring of molecular localization and behavior at the single-molecule level, on fixed and living cells. Accessing molecular-resolution details such as quantitatively monitoring components entering and leaving cell contacts by lateral diffusion and reversible association has revealed an unexpected plasticity. Adhesion structures can be highly specialized, such as focal adhesion in motile cells, as well as immune and neuronal synapses. Spatiotemporal reorganization of adhesion molecules, receptors, and adaptors directly relates to structure/function modulation. Assembly of these supramolecular complexes is continuously balanced by dynamic events, remodeling adhesions on various timescales, notably by molecular conformation switches, lateral diffusion within the membrane and endo/exocytosis. Pathological alterations in cell adhesion are involved in cancer evolution, through cancer stem cell interaction with stromal niches, growth, extravasation, and metastasis.

Intertidal estuarine habitat utilization by birds in a Pacific Northwest coastal estuary

EPA Science Inventory

Results of a year long study of the distribution of birds across five intertidal estuarine habitats reveal that tide level largely controls use of the habitats by birds. A total census of all birds observed from shoreline locations was made at five tide levels over six, 2-month ...

Opportunistically collected data reveal habitat selection by migrating Whooping Cranes in the U.S. Northern Plains

USGS Publications Warehouse

Niemuth, Neil D.; Ryba, Adam J.; Pearse, Aaron T.; Kvas, Susan M.; Brandt, David; Wangler, Brian; Austin, Jane; Carlisle, Martha J.

2018-01-01

The Whooping Crane (Grus americana) is a federally endangered species in the United States and Canada that relies on wetland, grassland, and cropland habitat during its long migration between wintering grounds in coastal Texas, USA, and breeding sites in Alberta and Northwest Territories, Canada. We combined opportunistic Whooping Crane sightings with landscape data to identify correlates of Whooping Crane occurrence along the migration corridor in North Dakota and South Dakota, USA. Whooping Cranes selected landscapes characterized by diverse wetland communities and upland foraging opportunities. Model performance substantially improved when variables related to detection were included, emphasizing the importance of accounting for biases associated with detection and reporting of birds in opportunistic datasets. We created a predictive map showing relative probability of occurrence across the study region by applying our model to GIS data layers; validation using independent, unbiased locations from birds equipped with platform transmitting terminals indicated that our final model adequately predicted habitat use by migrant Whooping Cranes. The probability map demonstrated that existing conservation efforts have protected much top-tier Whooping Crane habitat, especially in the portions of North Dakota and South Dakota that lie east of the Missouri River. Our results can support species recovery by informing prioritization for acquisition and restoration of landscapes that provide safe roosting and foraging habitats. Our results can also guide the siting of structures such as wind towers and electrical transmission and distribution lines, which pose a strike and mortality risk to migrating Whooping Cranes.

Contrasting patterns of survival and dispersal in multiple habitats reveal an ecological trap in a food-caching bird.

PubMed

Norris, D Ryan; Flockhart, D T Tyler; Strickland, Dan

2013-11-01

A comprehensive understanding of how natural and anthropogenic variation in habitat influences populations requires long-term information on how such variation affects survival and dispersal throughout the annual cycle. Gray jays Perisoreus canadensis are widespread boreal resident passerines that use cached food to survive over the winter and to begin breeding during the late winter. Using multistate capture-recapture analysis, we examined apparent survival and dispersal in relation to habitat quality in a gray jay population over 34 years (1977-2010). Prior evidence suggests that natural variation in habitat quality is driven by the proportion of conifers on territories because of their superior ability to preserve cached food. Although neither adults (>1 year) nor juveniles (<1 year) had higher survival rates on high-conifer territories, both age classes were less likely to leave high-conifer territories and, when they did move, were more likely to disperse to high-conifer territories. In contrast, survival rates were lower on territories that were adjacent to a major highway compared to territories that did not border the highway but there was no evidence for directional dispersal towards or away from highway territories. Our results support the notion that natural variation in habitat quality is driven by the proportion of coniferous trees on territories and provide the first evidence that high-mortality highway habitats can act as an equal-preference ecological trap for birds. Reproductive success, as shown in a previous study, but not survival, is sensitive to natural variation in habitat quality, suggesting that gray jays, despite living in harsh winter conditions, likely favor the allocation of limited resources towards self-maintenance over reproduction.

Seasonally biased or single-habitat sampling is not informative on the real prevalence of Dermacentor reticulatus-borne rickettsiae - A pilot study.

PubMed

Hornok, Sándor; Meli, Marina L; Gönczi, Enikő; Hofmann-Lehmann, Regina

2017-03-01

Dermacentor reticulatus is a tick species of high medical and veterinary importance, emerging in several parts of Europe. Up to now most studies focusing on zoonotic rickettsiae in D. reticulatus were based on ticks collected in a limited part of the questing period, and did not take into account the potential seasonal variations in the rate of infection with tick-borne rickettsiae. The aim of the present study was to investigate the latter phenomenon, i.e. to screen D. reticulatus adults, collected monthly in two urban habitats of Budapest, for the presence of three zoonotic Rickettsia spp. Altogether 852 D. reticulatus adults were collected, which showed significantly similar seasonal activity in the two evaluated habitats. Among the 413 molecularly analysed ticks, R. helvetica-infected D. reticulatus were only collected during autumn in habitat-1, in contrast to habitat-2. The overall prevalence of R. raoultii in D. reticulatus adults was significantly higher in habitat-1 than in habitat-2. In addition, the seasonal distribution of R. raoultii-infected ticks was different between the two habitats (in habitat-2 significantly more R. raoultii-infected ticks were collected in the autumn, in comparison with winter and spring). Rickettsia slovaca was not detected in any of the molecularly analysed ticks. The results clearly indicate that a single-time or seasonally biased collection of D. reticulatus adults and their subsequent molecular analysis may not be informative on the real prevalence of rickettsiae. This is because the availability/ activity of infected ticks shows significant seasonal fluctuations, both within and between habitats. Instead, for screening D. reticulatus-borne rickettsiae, it is important to collect monthly samples and then to assess seasonal prevalence and actual habitat-associated eco-epidemiological risks.

Stratification of habitats for identifying habitat selection by Merriam's turkeys

Treesearch

Mark A. Rumble; Stanley H. Anderson

1992-01-01

Habitat selection patterns of Merriam’s Turkeys were compared in hierarchical analyses of three levels of habitat stratification. Habitat descriptions in first-level analyses were based on dominant species of vegetation. Habitat descriptions in second-level analyses were based on dominant species of vegetation and overstory canopy cover. Habitat descriptions in third-...

Identification of Lygus hesperus by DNA barcoding reveals insignificant levels of genetic structure among distant and habitat diverse populations.

PubMed

Zhou, Changqing; Kandemir, Irfan; Walsh, Douglas B; Zalom, Frank G; Lavine, Laura Corley

2012-01-01

The western tarnished plant bug Lygus hesperus is an economically important pest that belongs to a complex of morphologically similar species that makes identification problematic. The present study provides evidence for the use of DNA barcodes from populations of L. hesperus from the western United States of America for accurate identification. This study reports DNA barcodes for 134 individuals of the western tarnished plant bug from alfalfa and strawberry agricultural fields in the western United States of America. Sequence divergence estimates of <3% reveal that morphologically variable individuals presumed to be L. hesperus were accurately identified. Paired estimates of F(st) and subsequent estimates of gene flow show that geographically distinct populations of L. hesperus are genetically similar. Therefore, our results support and reinforce the relatively recent (<100 years) migration of the western tarnished plant bug into agricultural habitats across the western United States. This study reveals that despite wide host plant usage and phenotypically plastic morphological traits, the commonly recognized western tarnished plant bug belongs to a single species, Lygus hesperus. In addition, no significant genetic structure was found for the geographically diverse populations of western tarnished plant bug used in this study.

Subsurface microbial habitats on Mars

NASA Technical Reports Server (NTRS)

Boston, P. J.; Mckay, C. P.

1991-01-01

We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

Development and validation of a habitat suitability model for ...

EPA Pesticide Factsheets

We developed a spatially-explicit, flexible 3-parameter habitat suitability model that can be used to identify and predict areas at higher risk for non-native dwarf eelgrass (Zostera japonica) invasion. The model uses simple environmental parameters (depth, nearshore slope, and salinity) to quantitatively describe habitat suitable for Z. japonica invasion based on ecology and physiology from the primary literature. Habitat suitability is defined with values ranging from zero to one, where one denotes areas most conducive to Z. japonica and zero denotes areas not likely to support Z. japonica growth. The model was applied to Yaquina Bay, Oregon, USA, an area that has well documented Z. japonica expansion over the last two decades. The highest suitability values for Z. japonica occurred in the mid to upper portions of the intertidal zone, with larger expanses occurring in the lower estuary. While the upper estuary did contain suitable habitat, most areas were not as large as in the lower estuary, due to inappropriate depth, a steeply sloping intertidal zone, and lower salinity. The lowest suitability values occurred below the lower intertidal zone, within the Yaquina River channel. The model was validated by comparison to a multi-year time series of Z. japonica maps, revealing a strong predictive capacity. Sensitivity analysis performed to evaluate the contribution of each parameter to the model prediction revealed that depth was the most important factor. Sh

Home range and movements of American alligators (Alligator mississippiensis) in an estuary habitat

USGS Publications Warehouse

Fujisaki, Ikuko; Hart, Kristen M.; Mazzotti, Frank J.; Cherkiss, Michael S.; Sartain-Iverson, Autumn R.; Jeffery, Brian M.; Beauchamp, Jeffrey S.; Denton, Mathew J.

2014-01-01

This study reveals consistent use of estuary habitat by American alligators. The alligators showed variations in their movement pattern and seasonal habitat, with movement attributable to environmental factors. Although satellite-derived locations were more dispersed compared to locations collected using VHF radio-tags, data collected from VHF tracking omitted some habitat used for a short period of time, indicating the effectiveness of satellite telemetry to continuously track animals for ecosystem-scale studies.

Earth is a Marine Habitat. Habitat Conservation Program.

ERIC Educational Resources Information Center

National Oceanic and Atmospheric Administration (DOC), Rockville, MD.

This brochure is intended to educate the public about the need to conserve and preserve the earth's environment (man's habitat). It contains an introduction to the ocean world and threats to coastal habitat. Photos and narrative revolve around the theme "Earth is a Marine Habitat." Sections include: "The Web of…

Macrofaunal communities associated with chemosynthetic habitats from the U.S. Atlantic margin: A comparison among depth and habitat types

USGS Publications Warehouse

Bourque, Jill R.; Robertson, Craig M.; Brooke, Sandra; Demopoulos, Amanda W.J.

2016-01-01

Hydrocarbon seeps support distinct benthic communities capable of tolerating extreme environmental conditions and utilizing reduced chemical compounds for nutrition. In recent years, several locations of methane seepage have been mapped along the U.S. Atlantic continental slope. In 2012 and 2013, two newly discovered seeps were investigated in this region: a shallow site near Baltimore Canyon (BCS, 366–412 m) and a deep site near Norfolk Canyon (NCS, 1467–1602 m), with both sites containing extensive chemosynthetic mussel bed and microbial mat habitats. Sediment push cores, suction samples, and Ekman box cores were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 μm) in mussel beds, mats, and slope habitats at both sites. Community data from the deep site were also assessed in relation to the associated sediment environment (organic carbon and nitrogen, stable carbon and nitrogen isotopes, grain size, and depth). Infaunal assemblages and densities differed both between depths and among habitat types. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments and were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in BCS microbial mat habitats, but higher in mussel and slope sediments compared to NCS habitats. Multivariate statistical analysis revealed specific sediment properties as important for distinguishing the macrofaunal communities, including larger grain sizes present within NCS microbial mat habitats and depleted stable carbon isotopes (δ13C) in sediments present at mussel beds. These results suggest that habitat differences in the quality and source of organic matter are driving the observed patterns in the infaunal assemblages, including high β diversity and high variability in the macrofaunal community composition. This

Macrofaunal communities associated with chemosynthetic habitats from the U.S. Atlantic margin: A comparison among depth and habitat types

NASA Astrophysics Data System (ADS)

Bourque, Jill R.; Robertson, Craig M.; Brooke, Sandra; Demopoulos, Amanda W. J.

2017-03-01

Hydrocarbon seeps support distinct benthic communities capable of tolerating extreme environmental conditions and utilizing reduced chemical compounds for nutrition. In recent years, several locations of methane seepage have been mapped along the U.S. Atlantic continental slope. In 2012 and 2013, two newly discovered seeps were investigated in this region: a shallow site near Baltimore Canyon (BCS, 366-412 m) and a deep site near Norfolk Canyon (NCS, 1467-1602 m), with both sites containing extensive chemosynthetic mussel bed and microbial mat habitats. Sediment push cores, suction samples, and Ekman box cores were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 μm) in mussel beds, mats, and slope habitats at both sites. Community data from the deep site were also assessed in relation to the associated sediment environment (organic carbon and nitrogen, stable carbon and nitrogen isotopes, grain size, and depth). Infaunal assemblages and densities differed both between depths and among habitat types. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments and were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in BCS microbial mat habitats, but higher in mussel and slope sediments compared to NCS habitats. Multivariate statistical analysis revealed specific sediment properties as important for distinguishing the macrofaunal communities, including larger grain sizes present within NCS microbial mat habitats and depleted stable carbon isotopes (δ13C) in sediments present at mussel beds. These results suggest that habitat differences in the quality and source of organic matter are driving the observed patterns in the infaunal assemblages, including high β diversity and high variability in the macrofaunal community composition. This study is

Surface Habitat Systems

NASA Technical Reports Server (NTRS)

Kennedy, Kriss J.

2009-01-01

The Surface Habitat Systems (SHS) Focused Investment Group (FIG) is part of the National Aeronautics and Space Administration (NASA) Johnson Space Center (JSC) effort to provide a focused direction and funding to the various projects that are working on human surface habitat designs and technologies for the planetary exploration missions. The overall SHS-FIG effort focuses on directing and guiding those projects that: 1) develop and demonstrate new surface habitat system concepts, innovations, and technologies to support human exploration missions, 2) improve environmental systems that interact with human habitats, 3) handle and emplace human surface habitats, and 4) focus on supporting humans living and working in habitats on planetary surfaces. The activity areas of the SHS FIG described herein are focused on the surface habitat project near-term objectives as described in this document. The SHS-FIG effort focuses on mitigating surface habitat risks (as identified by the Lunar Surface Systems Project Office (LSSPO) Surface Habitat Element Team; and concentrates on developing surface habitat technologies as identified in the FY08 gap analysis. The surface habitat gap assessment will be updated annually as the surface architecture and surface habitat definition continues to mature. These technologies are mapped to the SHS-FIG Strategic Development Roadmap. The Roadmap will bring to light the areas where additional innovative efforts are needed to support the development of habitat concepts and designs and the development of new technologies to support of the LSSPO Habitation Element development plan. Three specific areas of development that address Lunar Architecture Team (LAT)-2 and Constellation Architecture Team (CxAT) Lunar habitat design issues or risks will be focused on by the SHS-FIG. The SHS-FIG will establish four areas of development that will help the projects prepare in their planning for surface habitat systems development. Those development areas are

Riverine habitat dynamics

USGS Publications Warehouse

Jacobson, R.B.

2013-01-01

The physical habitat template is a fundamental influence on riverine ecosystem structure and function. Habitat dynamics refers to the variation in habitat through space and time as the result of varying discharge and varying geomorphology. Habitat dynamics can be assessed at spatial scales ranging from the grain (the smallest resolution at which an organism relates to its environment) to the extent (the broadest resolution inclusive of all space occupied during its life cycle). In addition to a potentially broad range of spatial scales, assessments of habitat dynamics may include dynamics of both occupied and nonoccupied habitat patches because of process interactions among patches. Temporal aspects of riverine habitat dynamics can be categorized into hydrodynamics and morphodynamics. Hydrodynamics refers to habitat variation that results from changes in discharge in the absence of significant change of channel morphology and at generally low sediment-transport rates. Hydrodynamic assessments are useful in cases of relatively high flow exceedance (percent of time a flow is equaled or exceeded) or high critical shear stress, conditions that are applicable in many studies of instream flows. Morphodynamics refers to habitat variation resulting from changes to substrate conditions or channel/floodplain morphology. Morphodynamic assessments are necessary when channel and floodplain boundary conditions have been significantly changed, generally by relatively rare flood events or in rivers with low critical shear stress. Morphodynamic habitat variation can be particularly important as disturbance mechanisms that mediate population growth or for providing conditions needed for reproduction, such as channel-migration events that erode cutbanks and provide new pointbar surfaces for germination of riparian trees. Understanding of habitat dynamics is increasing in importance as societal goals shift toward restoration of riverine ecosystems. Effective investment in restoration

Molecular Ecological Basis of Grasshopper (Oedaleus asiaticus) Phenotypic Plasticity under Environmental Selection

PubMed Central

Qin, Xinghu; Hao, Kun; Ma, Jingchuan; Huang, Xunbing; Tu, Xiongbing; Ali, Md. Panna; Pittendrigh, Barry R.; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Whitman, Douglas W.; Zhang, Zehua

2017-01-01

While ecological adaptation in insects can be reflected by plasticity of phenotype, determining the causes and molecular mechanisms for phenotypic plasticity (PP) remains a crucial and still difficult question in ecology, especially where control of insect pests is involved. Oedaleus asiaticus is one of the most dominant pests in the Inner Mongolia steppe and represents an excellent system to study phenotypic plasticity. To better understand ecological factors affecting grasshopper phenotypic plasticity and its molecular control, we conducted a full transcriptional screening of O. asiaticus grasshoppers reared in four different grassland patches in Inner Mongolia. Grasshoppers showed different degrees of PP associated with unique gene expressions and different habitat plant community compositions. Grasshopper performance variables were susceptible to habitat environment conditions and closely associated with plant architectures. Intriguingly, eco-transcriptome analysis revealed five potential candidate genes playing important roles in grasshopper performance, with gene expression closely relating to PP and plant community factors. By linking the grasshopper performances to gene profiles and ecological factors using canonical regression, we first demonstrated the eco-transcriptomic architecture (ETA) of grasshopper phenotypic traits (ETAGPTs). ETAGPTs revealed plant food type, plant density, coverage, and height were the main ecological factors influencing PP, while insect cuticle protein (ICP), negative elongation factor A (NELFA), and lactase-phlorizin hydrolase (LCT) were the key genes associated with PP. Our study gives a clear picture of gene-environment interaction in the formation and maintenance of PP and enriches our understanding of the transcriptional events underlying molecular control of rapid phenotypic plasticity associated with environmental variability. The findings of this study may also provide new targets for pest control and highlight the

Multi scale habitat relationships of Martes americana in northern Idaho, U.S.A.

Treesearch

Tzeidle N. Wasserman; Samuel A. Cushman; David O. Wallin; Jim Hayden

2012-01-01

We used bivariate scaling and logistic regression to investigate multiple-scale habitat selection by American marten (Martes americana). Bivariate scaling reveals dramatic differences in the apparent nature and strength of relationships between marten occupancy and a number of habitat variables across a range of spatial scales. These differences include reversals in...

Insects colonising carcasses in open and forest habitats of Central Europe: search for indicators of corpse relocation.

PubMed

Matuszewski, Szymon; Szafałowicz, Michał; Jarmusz, Mateusz

2013-09-10

Several traces may reveal the post-mortem relocation of a corpse. Insects are particularly useful for that purpose. The use of insects for inferring the transfer of a corpse rests on a premise that particular species colonise corpses in different habitats. However, only some insects reveal a strong preference for a given type of habitat. In order to find those insects which colonise corpses exclusively in open habitats, as opposed to forest habitats, a pig carrion study was made in rural open and rural forest habitats of Central Europe. Lucilia sericata (Diptera: Calliphoridae), Dermestes frischi, Dermestes laniarius (Coleoptera: Dermestidae), Omosita colon, some species of Nitidula (Coleoptera: Nitidulidae) and Necrobia rufipes (Coleoptera: Cleridae) were found to breed exclusively in open habitats. Only Oiceoptoma thoracicum (Coleoptera: Silphidae) avoided definitely breeding in open habitats. Sarcophaga caerulescens (Diptera: Sarcophagidae) regularly bred in open habitats but rarely bred in forests. Accordingly, L. sericata, D. frischi, O. colon, species of Nitidula and supposedly N. rufipes may be classified as indicators of corpse relocation from rural open to rural forest habitats of Central Europe. Only O. thoracicum may be classified as an indicator of the relocation in an opposite direction. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Identifying regions vulnerable to habitat degradation under future irrigation scenarios

NASA Astrophysics Data System (ADS)

Terrado, Marta; Sabater, Sergi; Acuña, Vicenç

2016-11-01

The loss and degradation of natural habitats is a primary cause of biodiversity decline. The increasing impacts of climate and land use change affect water availability, ultimately decreasing agricultural production. Areas devoted to irrigation have been increased to compensate this reduction, causing habitat and biodiversity losses, especially in regions undergoing severe water stress. These effects might intensify under global change, probably contributing to a decrease in habitat quality. We selected four European river basins across a gradient of water scarcity and irrigation agriculture. The habitat quality in the basins was assessed as a function of habitat suitability and threats under current and future global change scenarios of irrigation. Results revealed that the most threatened regions under future scenarios of global change were among those suffering of water scarcity and with bigger areas devoted to irrigation. Loss of habitat quality reached 10% in terrestrial and 25% in aquatic ecosystems under climate change scenarios involving drier conditions. The aquatic habitats were the most degraded in all scenarios, since they were affected by threats from both the terrestrial and the aquatic parts of the basin. By identifying in advance the regions most vulnerable to habitat and biodiversity loss, our approach can assist decision makers in deciding the conservation actions to be prioritized for mitigation and adaptation to the effects of climate change, particularly front the development of irrigation plans.

Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat.

PubMed

Mao, Donghai; Yu, Li; Chen, Dazhou; Li, Lanying; Zhu, Yuxing; Xiao, Yeqing; Zhang, Dechun; Chen, Caiyan

2015-07-01

Dongxiang wild rice is phylogenetically close to temperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat. Understanding the nature of adaptation in wild populations will benefit crop breeding in the development of climate-resilient crop varieties. Dongxiang wild rice (DXWR), the northernmost common wild rice known, possesses a high degree of cold tolerance and can survive overwintering in its native habitat. However, to date, it is still unclear how DXWR evolved to cope with low-temperature environment, resulting in limited application of DXWR in rice breeding programs. In this study, we carried out both QTL mapping and phylogenetic analysis to discern the genetic mechanism underlying the strong cold resistance. Through a combination of interval mapping and single locus analysis in two genetic populations, at least 13 QTLs for seedling cold tolerance were identified in DXWR. A phylogenetic study using both genome-wide InDel markers and markers associated with cold tolerance loci reveals that DXWR belongs to the Or-III group, which is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows. Our study paves the way toward an understanding of the nature of adaptation to a northern habitat in O. rufipogon. The QTLs identified in DXWR in this study will be useful for molecular breeding of cold-tolerant rice.

Multi-scale habitat selection of the endangered Hawaiian Goose

USGS Publications Warehouse

Leopold, Christina R.; Hess, Steven C.

2013-01-01

After a severe population reduction during the mid-20th century, the endangered Hawaiian Goose (Branta sandvicensis), or Nēnē, has only recently re-established its seasonal movement patterns on Hawai‘i Island. Little is currently understood about its movements and habitat use during the nonbreeding season. The objectives of this research were to identify habitats preferred by two subpopulations of the Nēnē and how preferences shift seasonally at both meso-and fine scales. From 2009 to 2011, ten Nēnē ganders were outfitted with 40-to 45-g satellite transmitters with GPS capability. We used binary logistic regression to compare habitat use versus availability and an information-theoretic approach for model selection. Meso-scale habitat modeling revealed that Nēnē preferred exotic grass and human-modified landscapes during the breeding and molting seasons and native subalpine shrubland during the nonbreeding season. Fine-scale habitat modeling further indicated preference for exotic grass, bunch grass, and absence of trees. Proximity to water was important during molt, suggesting that the presence of water may provide escape from introduced mammalian predators while Nēnē are flightless. Finescale species-composition data added relatively little to understanding of Nēnē habitat preferences modeled at the meso scale, suggesting that the meso-scale is appropriate for management planning. Habitat selection during our study was consistent with historical records, although dissimilar from more recent studies of other subpopulations. Nēnē make pronounced seasonal movements between existing reserves and use distinct habitat types; understanding annual patterns has implications for the protection and restoration of important seasonal habitats.

Molecular basis of structural make-up of feeds in relation to nutrient absorption in ruminants, revealed with advanced molecular spectroscopy: A review on techniques and models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahman, Md. Mostafizar; Yu, Peiqiang

Progress in ruminant feed research is no more feasible only based on wet chemical analysis, which is merely able to provide information on chemical composition of feeds regardless of their digestive features and nutritive value in ruminants. Studying internal structural make-up of functional groups/feed nutrients is often vital for understanding the digestive behaviors and nutritive values of feeds in ruminant because the intrinsic structure of feed nutrients is more related to its overall absorption. In this article, the detail information on the recent developments in molecular spectroscopic techniques to reveal microstructural information of feed nutrients and the use of nutritionmore » models in regards to ruminant feed research was reviewed. The emphasis of this review was on (1) the technological progress in the use of molecular spectroscopic techniques in ruminant feed research; (2) revealing spectral analysis of functional groups of biomolecules/feed nutrients; (3) the use of advanced nutrition models for better prediction of nutrient availability in ruminant systems; and (4) the application of these molecular techniques and combination of nutrient models in cereals, co-products and pulse crop research. The information described in this article will promote better insight in the progress of research on molecular structural make-up of feed nutrients in ruminants.« less

Single molecule spectroscopy reveals heterogeneous transport mechanisms for molecular ions in a polyelectrolyte polymer brush.

PubMed

Reznik, Carmen; Estillore, Nicel; Advincula, Rigoberto C; Landes, Christy F

2009-11-05

Single molecule polarization and fluorescence correlation spectroscopy were used to evaluate heterogeneous transport mechanisms of molecular ions within supported polyelectrolyte brushes. Modes of diffusive transport include periods of significantly restricted rotational motion, often maintained over tens of milliseconds; periods of fast molecular rotation; and occasional adsorption of fluorescent probe molecules in the brush. The studies reveal rapid switching between orientational states during each observed mode of motion. Through quantitative analysis of state occupation times, the rate constants for transitions from weakly associated to strongly associated states were extracted. Additionally, the pH dependence of the ion transport rates in the brush exhibits an abrupt, rather than continuous, trend. These single molecule studies demonstrate the presence of dynamic anisotropic interactions between the charged molecular probe and the polymer brush and provide experimental evidence of stimuli responsive switchable transport functionality in the polyelectrolyte brush.

Habitat-related specialization of lateral-line system morphology in a habitat-generalist and a habitat-specialist New Zealand eleotrid.

PubMed

Vanderpham, J P; Nakagawa, S; Senior, A M; Closs, G P

2016-04-01

An investigation of intraspecific habitat-related patterns of variation in oculoscapular lateral-line superficial neuromasts (SN) identified a decrease in the ratio of total SNs to pores, and a trend towards decreased asymmetry in SNs in the habitat-generalist common bully Gobiomorphus cotidianus from fluvial habitats compared to lacustrine habitats, suggesting habitat-related phenotypic variability. A greater ratio of pores to SNs, as well as less variation in the total number and asymmetry of SNs observed in the fluvial habitat-specialist redfin bully Gobiomorphus huttoni may provide further evidence of variations in the oculoscapular lateral-line morphology of fluvial habitat G. cotidianus individuals serving as adaptations to more turbulent environments. © 2016 The Fisheries Society of the British Isles.

Macroalgal Composition Determines the Structure of Benthic Assemblages Colonizing Fragmented Habitats.

PubMed

Matias, Miguel G; Arenas, Francisco; Rubal, Marcos; Pinto, Isabel S

2015-01-01

Understanding the consequences of fragmentation of coastal habitats is an important topic of discussion in marine ecology. Research on the effects of fragmentation has revealed complex and context-dependent biotic responses, which prevent generalizations across different habitats or study organisms. The effects of fragmentation in marine environments have been rarely investigated across heterogeneous habitats, since most studies have focused on a single type of habitat or patch. In this study, we assessed the effects of different levels of fragmentation (i.e. decreasing size of patches without overall habitat loss). We measured these effects using assemblages of macro-invertebrates colonizing representative morphological groups of intertidal macroalgae (e.g. encrusting, turf and canopy-forming algae). For this purpose, we constructed artificial assemblages with different combinations of morphological groups and increasing levels of fragmentation by manipulating the amount of bare rock or the spatial arrangement of different species in mixed assemblages. In general, our results showed that 1) fragmentation did not significantly affect the assemblages of macroinvertebrates; 2) at greater levels of fragmentation, there were greater numbers of species in mixed algal assemblages, suggesting that higher habitat complexity promotes species colonization. Our results suggest that predicting the consequences of fragmentation in heterogeneous habitats is dependent on the type and diversity of morphological groups making up those habitats.

Habitat use of bats in relation to wind turbines revealed by GPS tracking

PubMed Central

Roeleke, Manuel; Blohm, Torsten; Kramer-Schadt, Stephanie; Yovel, Yossi; Voigt, Christian C.

2016-01-01

Worldwide, many countries aim at countering global climate change by promoting renewable energy. Yet, recent studies highlight that so-called green energy, such as wind energy, may come at environmental costs, for example when wind turbines kill birds and bats. Using miniaturized GPS loggers, we studied how an open-space foraging bat with high collision risk with wind turbines, the common noctule Nyctalus noctula (Schreber, 1774), interacts with wind turbines. We compared actual flight trajectories to correlated random walks to identify habitat variables explaining the movements of bats. Both sexes preferred wetlands but used conventionally managed cropland less than expected based on availability. During midsummer, females traversed the land on relatively long flight paths and repeatedly came close to wind turbines. Their flight heights above ground suggested a high risk of colliding with wind turbines. In contrast, males recorded in early summer commuted straight between roosts and foraging areas and overall flew lower than the operating range of most turbine blades, suggesting a lower collision risk. Flight heights of bats suggest that during summer the risk of collision with wind turbines was high for most studied bats at the majority of currently installed wind turbines. For siting of wind parks, preferred bat habitats and commuting routes should be identified and avoided. PMID:27373219

Habitat use of bats in relation to wind turbines revealed by GPS tracking

NASA Astrophysics Data System (ADS)

Roeleke, Manuel; Blohm, Torsten; Kramer-Schadt, Stephanie; Yovel, Yossi; Voigt, Christian C.

2016-07-01

Worldwide, many countries aim at countering global climate change by promoting renewable energy. Yet, recent studies highlight that so-called green energy, such as wind energy, may come at environmental costs, for example when wind turbines kill birds and bats. Using miniaturized GPS loggers, we studied how an open-space foraging bat with high collision risk with wind turbines, the common noctule Nyctalus noctula (Schreber, 1774), interacts with wind turbines. We compared actual flight trajectories to correlated random walks to identify habitat variables explaining the movements of bats. Both sexes preferred wetlands but used conventionally managed cropland less than expected based on availability. During midsummer, females traversed the land on relatively long flight paths and repeatedly came close to wind turbines. Their flight heights above ground suggested a high risk of colliding with wind turbines. In contrast, males recorded in early summer commuted straight between roosts and foraging areas and overall flew lower than the operating range of most turbine blades, suggesting a lower collision risk. Flight heights of bats suggest that during summer the risk of collision with wind turbines was high for most studied bats at the majority of currently installed wind turbines. For siting of wind parks, preferred bat habitats and commuting routes should be identified and avoided.

Habitat use of bats in relation to wind turbines revealed by GPS tracking.

PubMed

Roeleke, Manuel; Blohm, Torsten; Kramer-Schadt, Stephanie; Yovel, Yossi; Voigt, Christian C

2016-07-04

Worldwide, many countries aim at countering global climate change by promoting renewable energy. Yet, recent studies highlight that so-called green energy, such as wind energy, may come at environmental costs, for example when wind turbines kill birds and bats. Using miniaturized GPS loggers, we studied how an open-space foraging bat with high collision risk with wind turbines, the common noctule Nyctalus noctula (Schreber, 1774), interacts with wind turbines. We compared actual flight trajectories to correlated random walks to identify habitat variables explaining the movements of bats. Both sexes preferred wetlands but used conventionally managed cropland less than expected based on availability. During midsummer, females traversed the land on relatively long flight paths and repeatedly came close to wind turbines. Their flight heights above ground suggested a high risk of colliding with wind turbines. In contrast, males recorded in early summer commuted straight between roosts and foraging areas and overall flew lower than the operating range of most turbine blades, suggesting a lower collision risk. Flight heights of bats suggest that during summer the risk of collision with wind turbines was high for most studied bats at the majority of currently installed wind turbines. For siting of wind parks, preferred bat habitats and commuting routes should be identified and avoided.

Ubiquity of Polynucleobacter necessarius subsp. asymbioticus in lentic freshwater habitats of a heterogenous 2000 km2 area

PubMed Central

Jezberová, Jitka; Jezbera, Jan; Brandt, Ulrike; Lindström, Eva S.; Langenheder, Silke; Hahn, Martin W.

2010-01-01

Summary We present a survey on the distribution and habitat range of P. necessarius subspecies asymbioticus (PnecC), an important taxon in the water column of freshwater systems. We systematically sampled stagnant freshwater habitats in a heterogeneous 2000 km2 area, together with ecologically different habitats outside this area. In total, 137 lakes, ponds and puddles were investigated, which represent an enormous diversity of habitats differing, i.e., in depth (<10 cm – 171 m) and pH (3.9 – 8.5). PnecC was detected by cultivation-independent methods in all investigated habitats, and its presence was confirmed by cultivation of strains from selected habitats including the most extreme ones. The determined relative abundance of the subspecies ranged from slightly above 0% to 67% (average 14.5% ± 14.3%), and the highest observed absolute abundance was 5.3×106 cells mL−1. Statistical analyses revealed that the abundance of PnecC is partially controlled by factors linked to concentrations of humic substances, which might support the hypothesis that these bacteria utilize photodegradation products of humic substances. . Statistical analyses revealed that the abundance of PnecC is partially controlled by low conductivity and pH and factors linked to concentrations of humic substances. Based on the revealed statistical relationships, an average relative abundance of this subspecies of 20% in global freshwater habitats was extrapolated. Our study provides important implications for the current debate on ubiquity and biogeography in microorganisms. PMID:20041938

RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug

PubMed Central

2012-01-01

Background Bed bugs (Cimex lectularius) are hematophagous nocturnal parasites of humans that have attained high impact status due to their worldwide resurgence. The sudden and rampant resurgence of C. lectularius has been attributed to numerous factors including frequent international travel, narrower pest management practices, and insecticide resistance. Results We performed a next-generation RNA sequencing (RNA-Seq) experiment to find differentially expressed genes between pesticide-resistant (PR) and pesticide-susceptible (PS) strains of C. lectularius. A reference transcriptome database of 51,492 expressed sequence tags (ESTs) was created by combining the databases derived from de novo assembled mRNA-Seq tags (30,404 ESTs) and our previous 454 pyrosequenced database (21,088 ESTs). The two-way GLMseq analysis revealed ~15,000 highly significant differentially expressed ESTs between the PR and PS strains. Among the top 5,000 differentially expressed ESTs, 109 putative defense genes (cuticular proteins, cytochrome P450s, antioxidant genes, ABC transporters, glutathione S-transferases, carboxylesterases and acetyl cholinesterase) involved in penetration resistance and metabolic resistance were identified. Tissue and development-specific expression of P450 CYP3 clan members showed high mRNA levels in the cuticle, Malpighian tubules, and midgut; and in early instar nymphs, respectively. Lastly, molecular modeling and docking of a candidate cytochrome P450 (CYP397A1V2) revealed the flexibility of the deduced protein to metabolize a broad range of insecticide substrates including DDT, deltamethrin, permethrin, and imidacloprid. Conclusions We developed significant molecular resources for C. lectularius putatively involved in metabolic resistance as well as those participating in other modes of insecticide resistance. RNA-Seq profiles of PR strains combined with tissue-specific profiles and molecular docking revealed multi-level insecticide resistance in C. lectularius

Northern bobwhite response to habitat restoration in eastern oklahoma

USGS Publications Warehouse

Crosby, Andrew D.; Elmore, R.D.; Leslie,, David M.

2013-01-01

In response to the decline of northern bobwhite (Colinus virginianus; hereafter, bobwhite) in eastern Oklahoma, USA, a cost-share incentive program for private landowners was initiated to restore early successional habitat. Our objectives were to determine whether the program had an effect on bobwhite occupancy in the restoration areas and evaluate how local-and landscape-level habitat characteristics affect occupancy in both restoration and control areas. We surveyed 14 sample units that received treatment between 2009 and 2011, and 17 sample units that were controls. We used single-season occupancy models, with year as a dummy variable, to test for an effect of restoration treatment and habitat variables on occupancy. We found no significant treatment effect. Model selection showed that occupancy was best explained by the combination of overstory canopy cover and habitat area at both the local and landscape scales. Moran's I revealed positive spatial autocorrelation in the 1,000-3,000-m distance band, indicating that the likelihood of bobwhite occupancy increased with proximity to other populations. We show that creating ≥ 20 ha of habitat within 1-3 km of existing bobwhite populations increases the chance of restoration being successful.

Habitat use by giant panda in relation to man-made forest in Wanglang Nature Reserve of China.

PubMed

Kang, Dongwei; Wang, Xiaorong; Yang, Hongwei; Duan, Lijuan; Li, Junqing

2014-12-01

To evaluate the effectiveness of human restoration in species conservation, in this study, we undertook a field survey of giant panda (Ailuropoda melanoleuca) habitat and man-made forest habitat in Wanglang Nature Reserve of China. Our results revealed that giant panda did not use the man-made forest in this area so far, and that there were significant differences between the giant panda habitat and the man-made forest habitat. Compared with giant panda habitat, the man-made forest habitat was characterized by lower shrub coverage, thinner trees and lower bamboo density. To improve the effectiveness of human restoration, the habitat requirement of giant panda should be fully consider in the whole process of habitat restoration.

Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

PubMed

Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

2015-01-01

Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

Vulnerable Habitats Alter African Meliponine Bee’s (Hymenoptera: Apidae) Assemblages in an Eastern Afromontane Biodiversity Hotspot

PubMed Central

Bobadoye, Bridget O; Ndegwa, Paul N; Irungu, Lucy; Fombong, Ayuka T

2017-01-01

Habitat degradation has over time formed synergy with other factors to contribute to dwindling populations of both fauna and flora by altering their habitats. The disturbance of natural habitats affects the diversity of both vertebrates and invertebrates by altering both feeding and nesting sites for which organisms are known to depend on for survival. Little is known of the extent to which vulnerable habitats could shape the diversity of most indigent pollinators such as African meliponine bee species in tropical ecosystems. This study was conducted to determine how disturbance could shape the natural occurrence of African meliponine bee species in different ecological habitats of Taita Hills, leading to changes in their diversity. A total of four species depicted by the Renyi diversity profile was recorded in five of the six main habitat types surveyed, and a further extrapolation with Shannon index (EH) also predicted the highest species richness of 4.24 in a deciduous habitat type. These meliponine bee species (Hypotrigona gribodoi, Hypotrigona ruspolii, Meliponula ferruginea (black), and Plebeina hildebrandti) were observed to be unevenly distributed across all habitats, further indicating that mixed deciduous habitat was more diverse than acacia-dominated bush lands, grasslands, and exotic forest patches. Geometric morphometrics categorized all four meliponine bee species into two major clusters—cluster 1 (H gribodoi, H ruspolii, M ferruginea (black)) and cluster 2 (P hildebrandti)—and further discriminated populations against the 4 potential habitats they are likely to persist or survive in. Each habitat appeared to consist of a cluster of subpopulations and may possibly reveal ecotypes within the four meliponine populations. This has revealed that unprecedented conversions of natural habitats to agroecosystems are a key driving factor causing increased habitat isolation and vulnerability in this Afromontane region which may potentially distort local

Triatoma maculata, the Vector of Trypanosoma cruzi, in Venezuela. Phenotypic and Genotypic Variability as Potential Indicator of Vector Displacement into the Domestic Habitat

PubMed Central

García-Alzate, Roberto; Lozano-Arias, Daisy; Reyes-Lugo, Rafael Matías; Morocoima, Antonio; Herrera, Leidi; Mendoza-León, Alexis

2014-01-01

Triatoma maculata is a wild vector of Trypanosoma cruzi, the causative agent of Chagas disease; its incursion in the domestic habitat is scant. In order to establish the possible domestic habitat of T. maculata, we evaluated wing variability and polymorphism of genotypic markers in subpopulations of T. maculata that live in different habitats in Venezuela. As markers, we used the mtCyt b gene, previously apply to evaluate population genetic structure in triatomine species, and the β-tubulin gene region, a marker employed to study genetic variability in Leishmania subgenera. Adults of T. maculata were captured in the period 2012–2013 at domestic, peridomestic (PD), and wild areas of towns in the Venezuelan states of Anzoátegui, Bolívar, Portuguesa, Monagas, Nueva Esparta, and Sucre. The phenotypic analysis was conducted through the determination of the isometric size and conformation of the left wing of each insect (492 individuals), using the MorphoJ program. Results reveal that insects of the domestic habitat showed significant reductions in wing size and variations in anatomical characteristics associated with flying, in relation to the PD and wild habitats. The largest variability was found in Anzoátegui and Monagas. The genotypic variability was assessed by in silico sequence comparison of the molecular markers and PCR-RFLP assays, demonstrating a marked polymorphism for the markers in insects of the domestic habitat in comparison with the other habitats. The highest polymorphism was found for the β-tubulin marker with enzymes BamHI and KpnI. Additionally, the infection rate by T. cruzi was higher in Monagas and Sucre (26.8 and 37.0%, respectively), while in domestic habitats the infestation rate was highest in Anzoátegui (22.3%). Results suggest domestic habitat colonization by T. maculata that in epidemiological terms, coupled with the presence in this habitat of nymphs of the vector, represents a high risk of transmission of Chagas disease. PMID

A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae).

PubMed

Holstein, Norbert; Renner, Susanne S

2011-01-26

Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological gradients in East Africa and

Estuarine intertidal sediment temperature variability in Zoster marina and Z. japonica habitats in Yaquina Bay, Oregon

EPA Science Inventory

Physical characterization of intertidal estuarine plant habitats over time may reveal distribution-limiting thresholds. Temperature data from loggers embedded in sediment in transects crossing Zostera marina and Z. japonica habitats in lower Yaquina Bay, Oregon display signific...

MMP-13 In-Vivo Molecular Imaging Reveals Early Expression in Lung Adenocarcinoma

PubMed Central

Salaün, Mathieu; Peng, Jing; Hensley, Harvey H.; Roder, Navid; Flieder, Douglas B.; Houlle-Crépin, Solène; Abramovici-Roels, Olivia; Sabourin, Jean-Christophe; Thiberville, Luc; Clapper, Margie L.

2015-01-01

Introduction Several matrix metalloproteinases (MMPs) are overexpressed in lung cancer and may serve as potential targets for the development of bioactivable probes for molecular imaging. Objective To characterize and monitor the activity of MMPs during the progression of lung adenocarcinoma. Methods K-rasLSL-G12D mice were imaged serially during the development of adenocarcinomas using fluorescence molecular tomography (FMT) and a probe specific for MMP-2, -3, -9 and -13. Lung tumors were identified using FMT and MRI co-registration, and the probe concentration in each tumor was assessed at each time-point. The expression of Mmp2, -3, -9, -13 was quantified by qRT-PCR using RNA isolated from microdissected tumor cells. Immunohistochemical staining of overexpressed MMPs in animals was assessed on human lung tumors. Results In mice, 7 adenomas and 5 adenocarcinomas showed an increase in fluorescent signal on successive FMT scans, starting between weeks 4 and 8. qRT-PCR assays revealed significant overexpression of only Mmp-13 in mice lung tumors. In human tumors, a high MMP-13 immunostaining index was found in tumor cells from invasive lesions (24/27), but in none of the non-invasive (0/4) (p=0.001). Conclusion MMP-13 is detected in early pulmonary invasive adenocarcinomas and may be a potential target for molecular imaging of lung cancer. PMID:26193700

Diet of diamondback terrapins (Malaclemys terrapin) in subtropical mangrove habitats in South Florida

USGS Publications Warehouse

Denton, Mathew J.; Hart, Kristen M.; Demopoulos, Amanda W.J.; Oleinik, Anton; Baldwin, John N.

2016-01-01

Unique among turtles as the only exclusively estuarine species, the diamondback terrapin’s (Malaclemys terrapin) life history predisposes it to impacts from humans both on land and in the near-shore environment. Terrapins are found in salt marshes and mangroves along the Atlantic and Gulf coasts from Massachusetts to Texas. Whereas previous dietary studies have elucidated terrapins’ role in temperate salt marsh food webs, food resources for terrapins inhabiting subtropical mangrove habitats have not been studied. We examined dietary resource use for diamondback terrapins in subtropical mangrove creek and island habitats within Everglades National Park, Florida, to determine foraging strategies of terrapins inhabiting south Florida (SF) mangrove systems. Fecal analysis revealed 6 categories of food items, with gastropods, crabs, and bivalves being the dominant food items. Multivariate analysis revealed differences in food sources based on habitat more so than by terrapin size class. Our results revealed that like their counterparts in temperate salt marshes, SF terrapins consume similar prey categories but with different species and abundances comprising each category.

Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers.

PubMed

Ibanez, Sébastien; Manneville, Olivier; Miquel, Christian; Taberlet, Pierre; Valentini, Alice; Aubert, Serge; Coissac, Eric; Colace, Marie-Pascale; Duparc, Quentin; Lavorel, Sandra; Moretti, Marco

2013-12-01

Food preferences and food availability are two major determinants of the diet of generalist herbivores and of their spatial distribution. How do these factors interact and eventually lead to diet differentiation in co-occurring herbivores? We quantified the diet of four grasshopper species co-occurring in subalpine grasslands using DNA barcoding of the plants contained in the faeces of individuals sampled in the field. The food preferences of each grasshopper species were assessed by a choice (cafeteria) experiment from among 24 plant species common in five grassland plots, in which the four grasshoppers were collected, while the habitat was described by the relative abundance of plant species in the grassland plots. Plant species were characterised by their leaf economics spectrum (LES), quantifying their nutrient vs. structural tissue content. The grasshoppers' diet, described by the mean LES of the plants eaten, could be explained by their plant preferences but not by the available plants in their habitat. The diet differed significantly across four grasshopper species pairs out of six, which validates food preferences assessed in standardised conditions as indicators for diet partitioning in nature. In contrast, variation of the functional diversity (FD) for LES in the diet was mostly correlated to the FD of the available plants in the habitat, suggesting that diet mixing depends on the environment and is not an intrinsic property of the grasshopper species. This study sheds light on the mechanisms determining the feeding niche of herbivores, showing that food preferences influence niche position whereas habitat diversity affects niche breadth.

Modeling effects of climate change on Yakima River salmonid habitats

USGS Publications Warehouse

Hatten, James R.; Batt, Thomas R.; Connolly, Patrick J.; Maule, Alec G.

2014-01-01

We evaluated the potential effects of two climate change scenarios on salmonid habitats in the Yakima River by linking the outputs from a watershed model, a river operations model, a two-dimensional (2D) hydrodynamic model, and a geographic information system (GIS). The watershed model produced a discharge time series (hydrograph) in two study reaches under three climate scenarios: a baseline (1981–2005), a 1-°C increase in mean air temperature (plus one scenario), and a 2-°C increase (plus two scenario). A river operations model modified the discharge time series with Yakima River operational rules, a 2D model provided spatially explicit depth and velocity grids for two floodplain reaches, while an expert panel provided habitat criteria for four life stages of coho and fall Chinook salmon. We generated discharge-habitat functions for each salmonid life stage (e.g., spawning, rearing) in main stem and side channels, and habitat time series for baseline, plus one (P1) and plus two (P2) scenarios. The spatial and temporal patterns in salmonid habitats differed by reach, life stage, and climate scenario. Seventy-five percent of the 28 discharge-habitat responses exhibited a decrease in habitat quantity, with the P2 scenario producing the largest changes, followed by P1. Fry and spring/summer rearing habitats were the most sensitive to warming and flow modification for both species. Side channels generally produced more habitat than main stem and were more responsive to flow changes, demonstrating the importance of lateral connectivity in the floodplain. A discharge-habitat sensitivity analysis revealed that proactive management of regulated surface waters (i.e., increasing or decreasing flows) might lessen the impacts of climate change on salmonid habitats.

Hydrologic habitat preferences of select southeastern USA fishes resilient to river ecosystem fragmentation

Treesearch

Andrew L. Rypel; David R. Bayne

2009-01-01

Large-scale habitat preferences of riverine taxa are not always revealed by examining community data. Here, we show how lipid and growth can be used to evaluate hydrologic habitat preferences of fishes resilient to river fragmentation (i.e. species that can tolerate river fragmentation by dams, but not collapse). Lipid content was examined for seven fishes in a major...

Isolation of Cryptococcus gattii molecular type VGIII, from Corymbia ficifolia detritus in Colombia.

PubMed

Escandón, P; Sánchez, A; Firacative, C; Castañeda, E

2010-06-01

An environmental sampling survey was carried out in different areas of Bogotá, Colombia, to obtain isolates of members of the Cryptococcus neoformans/C. gattii species complex from Corymbia ficifolia trees. During a 6-month period in 2007, 128 samples consisting of bark, soil around trunk bases, detritus, seeds and flowers were collected from 91 trees and processed according to standard procedures. The molecular type was determined using URA5 restriction fragment length polymorphism (RFLP) analysis and the mating type was established by PCR using specific primers for Mfalpha and Mfa C. gattii was isolated from 15 of the 128 (11.7%) samples, of which three (20%) were recovered from the red flower extract and the remaining 12 from C. ficifolia detritus. URA5 RFLP analysis revealed that all 15 isolates belonged to the molecular type VGIII and mating type specific PCR revealed that all were mating type a. The isolation of C. gattii from C. ficifolia represents an important finding since this is the first report revealing C. ficifolia as a habitat for C. gattii and adds additional information to the ever growing spectrum of tree species from which C. gattii can be recovered.

Estimates of connectivity reveal non-equilibrium epiphyte occurrence patterns almost 180 years after habitat decline.

PubMed

Johansson, Victor; Snäll, Tord; Ranius, Thomas

2013-06-01

Habitat loss is a major cause of species decline and extinction. Immediately after habitat loss, species occurrences are not in equilibrium with the new landscape and more closely reflect the previous landscape structure. Species with slow colonisation-extinction dynamics may display long time-lags before reaching a new equilibrium. We investigated the importance of connectivity to current and historical dispersal sources with the aim of explaining the occurrence pattern of epiphytic lichens with different traits among 104 old oaks. We used oak survey data collected from 1830 and 2009 for a Swedish landscape where oak densities declined drastically shortly after 1830. We fitted a commonly used connectivity measure and estimated the confidence interval for the spatial scale parameter. Small differences in the spatial scale parameter resulted in large differences in model fit. Connectivity to trees in 1830 better explained the occurrence of three of the four species compared to the connectivity in 2009. The explanatory power of the historical landscape structure was highest for the species with traits that may result in a low colonisation rate--both a narrow niche (here few suitable trees) and large dispersal propagules. The results suggest that oak-dependent epiphytic lichens have not reached equilibrium with the spatial landscape structure 180 years after the drastic decline in habitat. For the long-term persistence of epiphytes associated with old trees, conservation efforts should focus on (1) protecting and restoring stands where specialised species with large dispersal propagules (i.e. with low colonisation rates) occur today and (2) promoting tree regeneration in their near vicinity.

Rates and patterns of molecular evolution in freshwater versus terrestrial insects.

PubMed

Mitterboeck, T Fatima; Fu, Jinzhong; Adamowicz, Sarah J

2016-11-01

Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group. While ratios of nonsynonymous-to-synonymous substitutions across available loci were higher in terrestrial than freshwater-associated taxa in 26 of 42 lineage pairs, a stronger trend was observed (20 of 31, p binomial = 0.15, p Wilcoxon = 0.017) when examining only terrestrial-aquatic pairs including fully aquatic taxa. We did not observe any widespread changes at particular amino acid sites in COI associated with habitat shifts, although there may be general differences in selection regime linked to habitat.

A multiscale investigation of habitat use and within-river distribution of sympatric sand darter species

USGS Publications Warehouse

Thompson, Patricia A.; Welsh, Stuart A.; Strager, Michael P.; Rizzo, Austin A.

2018-01-01

The western sand darter Ammocrypta clara, and eastern sand darter Ammocrypta pellucida, are sand-dwelling fishes of conservation concern. Past research has emphasized the importance of studying individual populations of conservation concern, while recent research has revealed the importance of incorporating landscape scale processes that structure habitat mosaics and local populations. We examined habitat use and distributions of western and eastern sand darters in the lower Elk River of West Virginia. At the sandbar habitat use scale, western sand darters were detected in sandbars with greater area, higher proportions of coarse grain sand and faster bottom current velocity, while the eastern sand darter used a wider range of sandbar habitats. The landscape scale analysis revealed that contributing drainage area was an important predictor for both species, while sinuosity, which presumably represents valley type, also contributed to the western sand darter’s habitat suitability. Sandbar quality (area, grain size, and velocity) and fluvial geomorphic variables (drainage area and valley type) are likely key driving factors structuring sand darter distributions in the Elk River. This multiscale study of within-river species distribution and habitat use is unique, given that only a few sympatric populations are known of western and eastern sand darters.

Life on the rocks: habitat use drives morphological and performance evolution in lizards.

PubMed

Goodman, Brett A; Miles, Donald B; Schwarzkopf, Lin

2008-12-01

As a group, lizards occupy a vast array of habitats worldwide, yet there remain relatively few cases where habitat use (ecology), morphology, and thus, performance, are clearly related. The best known examples include: increased limb length in response to increased arboreal perch diameter in anoles and increased limb length in response to increased habitat openness for some skinks. Rocky habitats impose strong natural selection on specific morphological characteristics, which differs from that imposed on terrestrial species, because moving about on inclined substrates of irregular sizes and shapes constrains locomotor performance in predictable ways. We quantified habitat use, morphology, and performance of 19 species of lizards (family Scincidae, subfamily Lygosominae) from 23 populations in tropical Australia. These species use habitats with considerable variation in rock availability. Comparative phylogenetic analyses revealed that occupation of rock-dominated habitats correlated with the evolution of increased limb length, compared to species from forest habitats that predominantly occupied leaf litter. Moreover, increased limb length directly affected performance, with species from rocky habitats having greater sprinting, climbing, and clinging ability than their relatives from less rocky habitats. Thus, we found that the degree of rock use is correlated with both morphological and performance evolution in this group of tropical lizards.

Macroalgal Composition Determines the Structure of Benthic Assemblages Colonizing Fragmented Habitats

PubMed Central

Matias, Miguel G.; Arenas, Francisco; Rubal, Marcos; Pinto, Isabel S.

2015-01-01

Understanding the consequences of fragmentation of coastal habitats is an important topic of discussion in marine ecology. Research on the effects of fragmentation has revealed complex and context-dependent biotic responses, which prevent generalizations across different habitats or study organisms. The effects of fragmentation in marine environments have been rarely investigated across heterogeneous habitats, since most studies have focused on a single type of habitat or patch. In this study, we assessed the effects of different levels of fragmentation (i.e. decreasing size of patches without overall habitat loss). We measured these effects using assemblages of macro-invertebrates colonizing representative morphological groups of intertidal macroalgae (e.g. encrusting, turf and canopy-forming algae). For this purpose, we constructed artificial assemblages with different combinations of morphological groups and increasing levels of fragmentation by manipulating the amount of bare rock or the spatial arrangement of different species in mixed assemblages. In general, our results showed that 1) fragmentation did not significantly affect the assemblages of macroinvertebrates; 2) at greater levels of fragmentation, there were greater numbers of species in mixed algal assemblages, suggesting that higher habitat complexity promotes species colonization. Our results suggest that predicting the consequences of fragmentation in heterogeneous habitats is dependent on the type and diversity of morphological groups making up those habitats. PMID:26554924

Human presence impacts fungal diversity of inflated lunar/Mars analog habitat.

PubMed

Blachowicz, A; Mayer, T; Bashir, M; Pieber, T R; De León, P; Venkateswaran, K

2017-07-11

An inflatable lunar/Mars analog habitat (ILMAH), simulated closed system isolated by HEPA filtration, mimics International Space Station (ISS) conditions and future human habitation on other planets except for the exchange of air between outdoor and indoor environments. The ILMAH was primarily commissioned to measure physiological, psychological, and immunological characteristics of human inhabiting in isolation, but it was also available for other studies such as examining its microbiological aspects. Characterizing and understanding possible changes and succession of fungal species is of high importance since fungi are not only hazardous to inhabitants but also deteriorate the habitats. Observing the mycobiome changes in the presence of human will enable developing appropriate countermeasures with reference to crew health in a future closed habitat. Succession of fungi was characterized utilizing both traditional and state-of-the-art molecular techniques during the 30-day human occupation of the ILMAH. Surface samples were collected at various time points and locations to observe both the total and viable fungal populations of common environmental and opportunistic pathogenic species. To estimate the cultivable fungal population, potato dextrose agar plate counts method was utilized. The internal transcribed spacer region-based iTag Illumina sequencing was employed to measure the community structure and fluctuation of the mycobiome over time in various locations. Treatment of samples with propidium monoazide (PMA; a DNA intercalating dye for selective detection of viable microbial populations) had a significant effect on the microbial diversity compared to non-PMA-treated samples. Statistical analysis confirmed that viable fungal community structure changed (increase in diversity and decrease in fungal burden) over the occupation time. Samples collected at day 20 showed distinct fungal profiles from samples collected at any other time point (before or after

Epigenetic Differentiation of Natural Populations of Lilium bosniacum Associated with Contrasting Habitat Conditions.

PubMed

Zoldoš, Vlatka; Biruš, Ivan; Muratovic, Edina; Šatovic, Zlatko; Vojta, Aleksandar; Robin, Odile; Pustahija, Fatima; Bogunic, Faruk; Vicic Bockor, Vedrana; Siljak-Yakovlev, Sonja

2018-01-01

Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses revealed that the three populations did not differentiate genetically, but were clearly separated in three distinct clusters according to DNA methylation profiles. Principal coordinate analysis showed that overall epigenetic variation was closely related to habitat conditions. A new methylation-sensitive amplification polymorphism scoring approach allowed identification of mainly unmethylated (φST = 0.190) and fully CpG methylated (φST = 0.118) subepiloci playing a role in overall population differentiation, in comparison with hemimethylated sites (φST = 0.073). In addition, unusual rDNA repatterning and the presence of B chromosomes bearing 5S rDNA loci were recorded in the population growing on serpentine soil, suggesting dynamic chromosome rearrangements probably linked to global genome demethylation, which might have reactivated some mobile elements. We discuss our results considering our earlier data on morphology and leaf anatomy of several L. bosniacum populations, and suggest a possible role of epigenetics as a key element in population differentiation associated with environmental stress in these particular lily populations. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae).

PubMed

Donkpegan, Armel S L; Doucet, Jean-Louis; Migliore, Jérémy; Duminil, Jérôme; Dainou, Kasso; Piñeiro, Rosalía; Wieringa, Jan J; Champluvier, Dominique; Hardy, Olivier J

2017-02-01

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20Ma while extant tetraploid species started diverging c. 7.0 or 9.4Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics. Copyright © 2016 Elsevier Inc. All rights reserved.

Crystal structure of P58(IPK) TPR fragment reveals the mechanism for its molecular chaperone activity in UPR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Jiahui; Petrova, Kseniya; Ron, David

2010-05-25

P58(IPK) might function as an endoplasmic reticulum molecular chaperone to maintain protein folding homeostasis during unfolded protein responses. P58(IPK) contains nine tetratricopeptide repeat (TPR) motifs and a C-terminal J-domain within its primary sequence. To investigate the mechanism by which P58(IPK) functions to promote protein folding within the endoplasmic reticulum, we have determined the crystal structure of P58(IPK) TPR fragment to 2.5 {angstrom} resolution by the SAD method. The crystal structure of P58(IPK) revealed three domains (I-III) with similar folds and each domain contains three TPR motifs. An ELISA assay indicated that P58(IPK) acts as a molecular chaperone by interacting withmore » misfolded proteins such as luciferase and rhodanese. The P58(IPK) structure reveals a conserved hydrophobic patch located in domain I that might be involved in binding the misfolded polypeptides. Structure-based mutagenesis for the conserved hydrophobic residues located in domain I significantly reduced the molecular chaperone activity of P58(IPK).« less

Quantitative analysis of American woodcock nest and brood habitat

USGS Publications Warehouse

Bourgeois, A.; Keppie, Daniel M.; Owen, Ray B.

1977-01-01

Sixteen nest and 19 brood sites of American woodcock (Philohela minoI) were examined in northern lower Michigan between 15 April and 15 June 1974 to determine habitat structure associated with these sites. Woodcock hens utilized young, second-growth forest stands which were similar in species composition for both nesting and brood rearing. A multi-varIate discriminant function analysis revealed a significant (P< 0.05) difference, however, in habitat structure. Nest habitat was characterized by lower tree density (2176 trees/ha) and basal area (8.6 m2/ha), by being close to forest openings (7 m) and by being situated on dry, relatively well drained sites. In contrast, woodcock broods were located in sites that had nearly twice the tree density (3934 trees/hal and basal area (16.5 m2/ha), was located over twice as far from forest openings (18 m) and generally occurred on damp sites, near (8 m) standing water. Importance of the habitat features to the species and possible management implications are discussed.

Ciliates in chalk-stream habitats congregate in biodiversity hot spots.

PubMed

Bradley, Mark W; Esteban, Genoveva F; Finlay, Bland J

2010-09-01

Free-living ciliates are a diverse group of microbial eukaryotes that inhabit aquatic environments. They have a vital role within the 'microbial loop', being consumers of microscopic prey such as bacteria, micro-algae, and flagellates, and representing a link between the microscopic and macroscopic components of aquatic food webs. This investigation describes the ciliate communities of four habitats located in the catchment of the River Frome, the major chalk-stream in southern Britain. The ciliate communities were characterised in terms of community assemblage, species abundance and size classes. The ciliate communities investigated proved to be highly diverse, yielding a total of 114 active species. An additional 15 'cryptic' ciliate species were also uncovered. Heterogeneity in the ciliate communities was evident at multiple spatial scales, revealing hot spots of species richness, both within and between habitats. The ciliate communities of habitats with flowing water were composed of smaller ciliates compared to the still-water habitats examined. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Molecular interaction of 2-mercaptobenzimidazole with catalase reveals a potentially toxic mechanism of the inhibitor.

PubMed

Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong

2014-12-01

2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT. Copyright © 2014 Elsevier B.V. All rights reserved.

Assessing habitat connectivity for ground-dwelling animals in an urban environment.

PubMed

Braaker, S; Moretti, M; Boesch, R; Ghazoul, J; Obrist, M K; Bontadina, F

To ensure viable species populations in fragmented landscapes, individuals must be able to move between suitable habitat patches. Despite the increased interest in biodiversity assessment in urban environments, the ecological relevance of habitat connectivity in highly fragmented landscapes remains largely unknown. The first step to understanding the role of habitat connectivity in urban ecology is the challenging task of assessing connectivity in the complex patchwork of contrasting habitats that is found in cities. We developed a data-based framework, minimizing the use of subjective assumptions, to assess habitat connectivity that consists of the following sequential steps: (1) identification of habitat preference based on empirical habitat-use data; (2) derivation of habitat resistance surfaces evaluating various transformation functions; (3) modeling of different connectivity maps with electrical circuit theory (Circuitscape), a method considering all possible pathways across the landscape simultaneously; and (4) identification of the best connectivity map with information-theoretic model selection. We applied this analytical framework to assess habitat connectivity for the European hedgehog Erinaceus europaeus, a model species for ground-dwelling animals, in the city of Zurich, Switzerland, using GPS track points from 40 individuals. The best model revealed spatially explicit connectivity “pinch points,” as well as multiple habitat connections. Cross-validation indicated the general validity of the selected connectivity model. The results show that both habitat connectivity and habitat quality affect the movement of urban hedgehogs (relative importance of the two variables was 19.2% and 80.8%, respectively), and are thus both relevant for predicting urban animal movements. Our study demonstrates that even in the complex habitat patchwork of cities, habitat connectivity plays a major role for ground-dwelling animal movement. Data-based habitat connectivity

Endogenous molecular network reveals two mechanisms of heterogeneity within gastric cancer.

PubMed

Li, Site; Zhu, Xiaomei; Liu, Bingya; Wang, Gaowei; Ao, Ping

2015-05-30

Intratumor heterogeneity is a common phenomenon and impedes cancer therapy and research. Gastric cancer (GC) cells have generally been classified into two heterogeneous cellular phenotypes, the gastric and intestinal types, yet the mechanisms of maintaining two phenotypes and controlling phenotypic transition are largely unknown. A qualitative systematic framework, the endogenous molecular network hypothesis, has recently been proposed to understand cancer genesis and progression. Here, a minimal network corresponding to such framework was found for GC and was quantified via a stochastic nonlinear dynamical system. We then further extended the framework to address the important question of intratumor heterogeneity quantitatively. The working network characterized main known features of normal gastric epithelial and GC cell phenotypes. Our results demonstrated that four positive feedback loops in the network are critical for GC cell phenotypes. Moreover, two mechanisms that contribute to GC cell heterogeneity were identified: particular positive feedback loops are responsible for the maintenance of intestinal and gastric phenotypes; GC cell progression routes that were revealed by the dynamical behaviors of individual key components are heterogeneous. In this work, we constructed an endogenous molecular network of GC that can be expanded in the future and would broaden the known mechanisms of intratumor heterogeneity.

Endogenous molecular network reveals two mechanisms of heterogeneity within gastric cancer

PubMed Central

Li, Site; Zhu, Xiaomei; Liu, Bingya; Wang, Gaowei; Ao, Ping

2015-01-01

Intratumor heterogeneity is a common phenomenon and impedes cancer therapy and research. Gastric cancer (GC) cells have generally been classified into two heterogeneous cellular phenotypes, the gastric and intestinal types, yet the mechanisms of maintaining two phenotypes and controlling phenotypic transition are largely unknown. A qualitative systematic framework, the endogenous molecular network hypothesis, has recently been proposed to understand cancer genesis and progression. Here, a minimal network corresponding to such framework was found for GC and was quantified via a stochastic nonlinear dynamical system. We then further extended the framework to address the important question of intratumor heterogeneity quantitatively. The working network characterized main known features of normal gastric epithelial and GC cell phenotypes. Our results demonstrated that four positive feedback loops in the network are critical for GC cell phenotypes. Moreover, two mechanisms that contribute to GC cell heterogeneity were identified: particular positive feedback loops are responsible for the maintenance of intestinal and gastric phenotypes; GC cell progression routes that were revealed by the dynamical behaviors of individual key components are heterogeneous. In this work, we constructed an endogenous molecular network of GC that can be expanded in the future and would broaden the known mechanisms of intratumor heterogeneity. PMID:25962957

Tundra swan habitat preferences during migration in North Dakota

USGS Publications Warehouse

Earnst, Susan L.

1994-01-01

I studied tundra swan (Cygnus columbianus columbianus) habitat preference in North Dakota during autumn migration, 1988-89. Many thousand tundra swans stop in the Prairie Pothole region during autumn migration, but swan resource use has not been quantified. I examined habitat preference in relation to an index of sago pondweed (Potamogeton pectinatus) presence, extent of open water, and wetland size. I compared habitat preference derived from counts of all swans to those derived from foraging swans only and cygnets only. Foraging swans preferred wetlands with sago pondweed (P = 0.03); the number of foraging swans per wetland was >4 times higher on wetlands with sago pondweed than on wetlands without sago. In contrast, nonforaging swans did not prefer wetlands with sago pondweed (P = 0.85) but preferred large wetlands (P = 0.02) and those with a high proportion of contiguous open water (P < 0.01). Thus, conclusions about habitat preference derived from counts of all swans, most of which were nonforaging, would not have revealed the importance of sago pondweed. Cygnets were more likely to be feeding than adults (P = 0.03) and occurred proportionately more often in smaller flocks (P = 0.04), but cygnets and adults had similar habitat preferences.

Endangered winter-run Chinook salmon rely on diverse rearing habitats in a highly altered landscape

DOE PAGES

Phillis, Corey C.; Sturrock, Anna M.; Johnson, Rachel C.; ...

2017-11-24

Protecting habitats for imperiled species is central to conservation efforts. However, for migratory species, identifying juvenile habitats that confer success requires tracking individuals to reproduction. Here in this paper, we used otolith strontium isotope ratios ( 87Sr/ 86Sr) to reconstruct juvenile habitat use by endangered Sacramento River winter-run Chinook salmon that survived to adulthood. The isotope data revealed that 44–65% of surviving adults reared in non-natal habitats, most of which is not designated as critical habitat under the Endangered Species Act. Juveniles entered these non-natal habitats at small sizes, yet left freshwater at a similar size to those that rearedmore » in the mainstem Sacramento River, suggesting these alternate rearing habitats provide suitable growth conditions. These findings indicate Sacramento River winter-run Chinook salmon rely on rearing habitats across a broader geographic region than previously known, potentially opening up greater restoration and conservation opportunities for species recovery.« less

Endangered winter-run Chinook salmon rely on diverse rearing habitats in a highly altered landscape

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phillis, Corey C.; Sturrock, Anna M.; Johnson, Rachel C.

Protecting habitats for imperiled species is central to conservation efforts. However, for migratory species, identifying juvenile habitats that confer success requires tracking individuals to reproduction. Here in this paper, we used otolith strontium isotope ratios ( 87Sr/ 86Sr) to reconstruct juvenile habitat use by endangered Sacramento River winter-run Chinook salmon that survived to adulthood. The isotope data revealed that 44–65% of surviving adults reared in non-natal habitats, most of which is not designated as critical habitat under the Endangered Species Act. Juveniles entered these non-natal habitats at small sizes, yet left freshwater at a similar size to those that rearedmore » in the mainstem Sacramento River, suggesting these alternate rearing habitats provide suitable growth conditions. These findings indicate Sacramento River winter-run Chinook salmon rely on rearing habitats across a broader geographic region than previously known, potentially opening up greater restoration and conservation opportunities for species recovery.« less

Indicators: Shallow Water Habitat/In-stream Fish Habitat

EPA Pesticide Factsheets

Shallow water habitat, also referred to as in-stream fish habitat, refers to areas that fish and other aquatic organisms need for concealment, breeding and feeding. This includes large woody snags, boulders, rock ledges, and undercut banks.

The Habitat Connection.

ERIC Educational Resources Information Center

Naturescope, 1987

1987-01-01

Consists of activities which address the causes of habitat destruction and the effects of habitat loss on animals and plants. Identifies habitat loss as the major reason for the endangerment and extinction of plant and animal species. (ML)

Parallel Evolution of Larval Feeding Behavior, Morphology, and Habitat in the Snail-Kiling fly Genus Tetanocera

NASA Astrophysics Data System (ADS)

Chapman, E. G.; Foote, B. A.; Malukiewicz, J.; Hoeh, W. R.

2005-05-01

Sciomyzid larvae (Diptera: Acalyptratae) display a wide range of feeding behaviors, typically preying on a wide variety of gastropods. The genus Tetanocera is particularly interesting because its species occupy five larval feeding groups with each species' larvae living in one of two habitat types (aquatic or terrestrial). We constructed a molecular phylogeny for Tetanocera, estimated evolutionary transitions in larval feeding behaviors and habitats that occurred during Tetanocera phylogenesis, and investigated potential correlations among larval habitat and morphological characteristics. Approximately 3800 base pairs (both mitochondrial and nuclear) of sequence data were used to build the phylogeny. Larval feeding groups and habitat type were mapped onto the phylogeny and pair-wise comparisons were used to evaluate potential associations between habitat and morphology. Feeding and habitat groups within Tetanocera were usually not monophyletic and it was estimated that Tetanocera lineages made at least three independent aquatic to terrestrial transitions. These parallel habitat shifts were typically accompanied by parallel character state changes in four morphological characteristics (larval color and three posterior spiracular disc characters). These larval habitat-morphology associations were statistically significant and consistent with the action of natural selection in facilitating the morphological changes that occurred during aquatic to terrestrial habitat transitions in Tetanocera.

NASA Habitat Demonstration Unit (HDU) Deep Space Habitat Analog

NASA Technical Reports Server (NTRS)

Howe, A. Scott; Kennedy, Kriss J.; Gill, Tracy

2013-01-01

The NASA Habitat Demonstration Unit (HDU) vertical cylinder habitat was established as a exploration habitat testbed platform for integration and testing of a variety of technologies and subsystems that will be required in a human-occupied planetary surface outpost or Deep Space Habitat (DSH). The HDU functioned as a medium-fidelity habitat prototype from 2010-2012 and allowed teams from all over NASA to collaborate on field analog missions, mission operations tests, and system integration tests to help shake out equipment and provide feedback for technology development cycles and crew training. This paper documents the final 2012 configuration of the HDU, and discusses some of the testing that took place. Though much of the higher-fidelity functionality has 'graduated' into other NASA programs, as of this writing the HDU, renamed Human Exploration Research Analog (HERA), will continue to be available as a volumetric and operational mockup for NASA Human Research Program (HRP) research from 2013 onward.

Plant epiphytism in semiarid conditions revealed the influence of habitat and climate variables on AM fungi communities distribution

NASA Astrophysics Data System (ADS)

Torrecillas, Emma; Torres, Pilar; Díaz, Gisela; del Mar Alguacil, Maria; Querejeta, Jose Ignacio; García, Fuensanta; Roldán, Antonio

2014-05-01

In semiarid Mediterranean ecosystems epiphytic plant species are practically absent and only some species of palm-trees can support epiphytes growing in their lower crown area, such as Phoenix dactylifera L. (date palm). In this study we focused in Sonchus tenerrimus L. plants growing as facultative epiphytes in P. dactylifera and its terrestrial forms growing in adjacent soils, Our aim was to determine the possible presence of AMF in these peculiar habitats and to relate AMF communities with climatic variations. We investigated the AMF community composition of epiphytic and terrestrial S. tenerrimus plants along a temperature and precipitation gradient across 12 localities. Epiphytic roots were colonized by AM fungi as determined by microscopic observation, all epiphytic and terrestrial samples analysed showed AMF sequences from taxa belonging to the phylum Glomeromycota, which were grouped in 30 AMF OTUs. The AMF community composition was clearly different between epiphytic and terrestrial root samples and this could be attributable to dispersal constraints and/or the contrasting environmental and ecophysiological conditions prevailing in each habitat. Across sites, the richness and diversity of terrestrial AMF communities was positively correlated with rainfall amount during the most recent growing season. In contrast, there was no significant correlation between climate variables and AMF richness and diversity for epiphytic AMF communities, which suggests that the composition of AMF communities in epiphytic habitats appears to be largely determined by the availability and dispersion of fungal propagules from adjacent terrestrial habitats.

Chapter 5. Using Habitat Models for Habitat Mapping and Monitoring

Treesearch

Samuel A. Cushman; Timothy J. Mersmann; Gretchen G. Moisen; Kevin S. McKelvey; Christina D. Vojta

2013-01-01

This chapter provides guidance for applying existing habitat models to map and monitor wildlife habitat. Chapter 2 addresses the use of conceptual models to create a solid foundation for selecting habitat attributes to monitor and to translate these attributes into quantifiable and reportable monitoring measures. Most wildlife species, however, require a complex suite...

Habitat classification modeling with incomplete data: Pushing the habitat envelope

USGS Publications Warehouse

Zarnetske, P.L.; Edwards, T.C.; Moisen, Gretchen G.

2007-01-01

Habitat classification models (HCMs) are invaluable tools for species conservation, land-use planning, reserve design, and metapopulation assessments, particularly at broad spatial scales. However, species occurrence data are often lacking and typically limited to presence points at broad scales. This lack of absence data precludes the use of many statistical techniques for HCMs. One option is to generate pseudo-absence points so that the many available statistical modeling tools can be used. Traditional techniques generate pseudoabsence points at random across broadly defined species ranges, often failing to include biological knowledge concerning the species-habitat relationship. We incorporated biological knowledge of the species-habitat relationship into pseudo-absence points by creating habitat envelopes that constrain the region from which points were randomly selected. We define a habitat envelope as an ecological representation of a species, or species feature's (e.g., nest) observed distribution (i.e., realized niche) based on a single attribute, or the spatial intersection of multiple attributes. We created HCMs for Northern Goshawk (Accipiter gentilis atricapillus) nest habitat during the breeding season across Utah forests with extant nest presence points and ecologically based pseudo-absence points using logistic regression. Predictor variables were derived from 30-m USDA Landfire and 250-m Forest Inventory and Analysis (FIA) map products. These habitat-envelope-based models were then compared to null envelope models which use traditional practices for generating pseudo-absences. Models were assessed for fit and predictive capability using metrics such as kappa, thresholdindependent receiver operating characteristic (ROC) plots, adjusted deviance (Dadj2), and cross-validation, and were also assessed for ecological relevance. For all cases, habitat envelope-based models outperformed null envelope models and were more ecologically relevant, suggesting

An assessment of bird habitat quality using population growth rates

USGS Publications Warehouse

Knutson, M.G.; Powell, L.A.; Hines, R.K.; Friberg, M.A.; Niemi, G.J.

2006-01-01

Survival and reproduction directly affect population growth rate (lambda) making lambda a fundamental parameter for assessing habitat quality. We used field data, literature review, and a computer simulation to predict annual productivity and lambda for several species of landbirds breeding in floodplain and upland forests in the Midwestern United States. We monitored 1735 nests of 27 species; 760 nests were in the uplands and 975 were in the floodplain. Each type of forest habitat (upland and floodplain) was a source habitat for some species. Despite a relatively low proportion of regional forest cover, the majority of species had stable or increasing populations in all or some habitats, including six species of conservation concern. In our search for a simple analog for lambda, we found that only adult apparent survival, juvenile survival, and annual productivity were correlated with lambda; daily nest survival and relative abundance estimated from point counts were not. Survival and annual productivity are among the most costly demographic parameters to measure and there does not seem to be a low-cost alternative. In addition, our literature search revealed that the demographic parameters needed to model annual productivity and lambda were unavailable for several species. More collective effort across North America is needed to fill the gaps in our knowledge of demographic parameters necessary to model both annual productivity and lambda. Managers can use habitat-specific predictions of annual productivity to compare habitat quality among species and habitats for purposes of evaluating management plans.

Habitat collapse due to overgrazing threatens turtle conservation in marine protected areas.

PubMed

Christianen, Marjolijn J A; Herman, Peter M J; Bouma, Tjeerd J; Lamers, Leon P M; van Katwijk, Marieke M; van der Heide, Tjisse; Mumby, Peter J; Silliman, Brian R; Engelhard, Sarah L; van de Kerk, Madelon; Kiswara, Wawan; van de Koppel, Johan

2014-02-22

Marine protected areas (MPAs) are key tools for combatting the global overexploitation of endangered species. The prevailing paradigm is that MPAs are beneficial in helping to restore ecosystems to more 'natural' conditions. However, MPAs may have unintended negative effects when increasing densities of protected species exert destructive effects on their habitat. Here, we report on severe seagrass degradation in a decade-old MPA where hyper-abundant green turtles adopted a previously undescribed below-ground foraging strategy. By digging for and consuming rhizomes and roots, turtles create abundant bare gaps, thereby enhancing erosion and reducing seagrass regrowth. A fully parametrized model reveals that the ecosystem is approaching a tipping point, where consumption overwhelms regrowth, which could potentially lead to complete collapse of the seagrass habitat. Seagrass recovery will not ensue unless turtle density is reduced to nearly zero, eliminating the MPA's value as a turtle reserve. Our results reveal an unrecognized, yet imminent threat to MPAs, as sea turtle densities are increasing at major nesting sites and the decline of seagrass habitat forces turtles to concentrate on the remaining meadows inside reserves. This emphasizes the need for policy and management approaches that consider the interactions of protected species with their habitat.

Habitat collapse due to overgrazing threatens turtle conservation in marine protected areas

PubMed Central

Christianen, Marjolijn J. A.; Herman, Peter M. J.; Bouma, Tjeerd J.; Lamers, Leon P. M.; van Katwijk, Marieke M.; van der Heide, Tjisse; Mumby, Peter J.; Silliman, Brian R.; Engelhard, Sarah L.; van de Kerk, Madelon; Kiswara, Wawan; van de Koppel, Johan

2014-01-01

Marine protected areas (MPAs) are key tools for combatting the global overexploitation of endangered species. The prevailing paradigm is that MPAs are beneficial in helping to restore ecosystems to more ‘natural’ conditions. However, MPAs may have unintended negative effects when increasing densities of protected species exert destructive effects on their habitat. Here, we report on severe seagrass degradation in a decade-old MPA where hyper-abundant green turtles adopted a previously undescribed below-ground foraging strategy. By digging for and consuming rhizomes and roots, turtles create abundant bare gaps, thereby enhancing erosion and reducing seagrass regrowth. A fully parametrized model reveals that the ecosystem is approaching a tipping point, where consumption overwhelms regrowth, which could potentially lead to complete collapse of the seagrass habitat. Seagrass recovery will not ensue unless turtle density is reduced to nearly zero, eliminating the MPA's value as a turtle reserve. Our results reveal an unrecognized, yet imminent threat to MPAs, as sea turtle densities are increasing at major nesting sites and the decline of seagrass habitat forces turtles to concentrate on the remaining meadows inside reserves. This emphasizes the need for policy and management approaches that consider the interactions of protected species with their habitat. PMID:24403341

Biodiversity: Habitat Suitability

EPA Science Inventory

Habitat suitability quantifies the relationship between species and habitat, and is evaluated according to the species’ fitness (i.e. proportion of birth rate to death rate). Even though it might maximize evolutionary success, species are not always in habitat that optimizes fit...

Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

PubMed Central

Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

2014-01-01

The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

Habitat use and habitat overlap of riparian birds in three elevational zones

Treesearch

Deborah M. Finch

1989-01-01

I examined patterns of variance in habitat use and habitat overlap in 20 breeding bird species found along a riparian vegetational gradient in southeastern Wyoming to test whether habitat use in species differed (1) from availability of random habitat resources, (2) among elevational zones, and (3) between species that inhabited only one zone and species that occupied...

HABITAT ASSESSMENT METHODS

EPA Science Inventory

This chapter summarizes and evaluated the habitat assessment protocols of five agencies, USEPA/EMAP/SW, USGS/NAWQA, USEPA/RBP, Ohio EPA, and MDNR/MBSS. It begins with a description of the origin of the habitat indices most widely used by these agencies. Then the habitat assessmen...

Overlooked habitat of a vulnerable gorgonian revealed in the Mediterranean and Eastern Atlantic by ecological niche modelling

PubMed Central

Boavida, Joana; Assis, Jorge; Silva, Inga; Serrão, Ester A.

2016-01-01

Factors shaping the distribution of mesophotic octocorals (30–200 m depth) remain poorly understood, potentially leaving overlooked coral areas, particularly near their bathymetric and geographic distributional limits. Yet, detailed knowledge about habitat requirements is crucial for conservation of sensitive gorgonians. Here we use Ecological Niche Modelling (ENM) relating thirteen environmental predictors and a highly comprehensive presence dataset, enhanced by SCUBA diving surveys, to investigate the suitable habitat of an important structuring species, Paramuricea clavata, throughout its distribution (Mediterranean and adjacent Atlantic). Models showed that temperature (11.5–25.5 °C) and slope are the most important predictors carving the niche of P. clavata. Prediction throughout the full distribution (TSS 0.9) included known locations of P. clavata alongside with previously unknown or unreported sites along the coast of Portugal and Africa, including seamounts. These predictions increase the understanding of the potential distribution for the northern Mediterranean and indicate suitable hard bottom areas down to >150 m depth. Poorly sampled habitats with predicted presence along Algeria, Alboran Sea and adjacent Atlantic coasts encourage further investigation. We propose that surveys of target areas from the predicted distribution map, together with local expert knowledge, may lead to discoveries of new P. clavata sites and identify priority conservation areas. PMID:27841263

Molecular Cytogenetic Analysis of One African and Five Asian Macaque Species Reveals Identical Karyotypes as in Mandrill.

PubMed

Sangpakdee, Wiwat; Tanomtong, Alongkoad; Chaveerach, Arunrat; Pinthong, Krit; Trifonov, Vladimir; Loth, Kristina; Hensel, Christiana; Liehr, Thomas; Weise, Anja; Fan, Xiaobo

2018-04-01

The question how evolution and speciation work is one of the major interests of biology. Especially, genetic including karyotypic evolution within primates is of special interest due to the close phylogenetic position of Macaca and Homo sapiens and the role as in vivo models in medical research, neuroscience, behavior, pharmacology, reproduction and Acquired Immune Deficiency Syndrome (AIDS). Karyotypes of five macaque species from South East Asia and of one macaque species as well as mandrill from Africa were analyzed by high resolution molecular cytogenetics to obtain new insights into karyotypic evolution of old world monkeys. Molecular cytogenetics applying human probes and probe sets was applied in chromosomes of Macaca arctoides, M. fascicularis, M. nemestrina, M. assamensis, M. sylvanus, M. mulatta and Mandrillus sphinx. Established two- to multicolor-fluorescence in situ hybridization (FISH) approaches were applied. Locus-specific probes, whole and partial chromosome paint probes were hybridized. Especially the FISH-banding approach multicolor-banding (MCB) as well as probes oriented towards heterochromatin turned out to be highly efficient for interspecies comparison. Karyotypes of all seven studied species could be characterized in detail. Surprisingly, no evolutionary conserved differences were found among macaques, including mandrill. Between the seven here studied and phenotypically so different species we expected several via FISH detectable karyoypic and submicroscopic changes and were surprised to find none of them on a molecular cytogenetic level. Spatial separation, may explain the speciation and different evolution for some of them, like African M. sylvanus, Mandrillus sphinx and the South Asian macaques. However, for the partially or completely overlapping habitats of the five studied South Asian macaques the species separation process can also not be deduced to karyotypic separation.

Habitat selection and productivity of least terns on the lower Platte River, Nebraska

USGS Publications Warehouse

Kirsch, Eileen M.

1996-01-01

. Proportion of terns using each habitat was similar to proportion of available sand on each habitat. The distribution of nest initiation dates and rates of colony-site turnover also were similar on both habitats. Productivity did not differ between habitats but varied significantly among sites. Nest success, fledging success, and fledglings per pair averaged 0.54, 0.28, and 0.47, respectively. Key factor analysis revealed that chick survival had a greater influence on production of fledglings (on both sandbars and sandpits) than did failure to produce a maximum clutch size or egg mortality. Most egg mortality was caused by predation on sandpits and by flooding on sandbars. Predation was suspected as the major cause of loss for chicks on both habitats. Path analysis revealed no strong or consistent correlations among mortality, numbers of nests and chicks, track trails of intruders into colonies, and habitat variables at colonies on either habitat. Theoretically, terns should not prefer a habitat when habitats are equally suitable if terns have had time to respond to habitat changes. Although sandbars and sandpits appeared equally suitable and terns did not prefer either habitat, local productivity will not support this population unless annual postfledging survival is higher than current estimates for the species. Population trend estimated with fledglings per pair = 0.50 was negative for all but the highest (ca 0.90) rates of annual postfledging survival. Furthermore, deterministic models like the one used in this study overstimate trend. Productivity insufficient to support the local population, in spite of habitat use that reflects habitat suitability, could be due to increased predation caused by habitat alteration adjacent to the river that may have changed the predator community. Alternatively, terns in this area could persist in spite of prevailing low productivity because they are relatively long-lived birds, if highly productive years occasionally occur or if this

Habitat-specific foraging of prothonotary warblers: Deducing habitat quality

USGS Publications Warehouse

Lyons, J.E.

2005-01-01

Foraging behavior often reflects food availability in predictable ways. For example, in habitats where food availability is high, predators should attack prey more often and move more slowly than in habitats where food availability is low. To assess relative food availability and habitat quality, I studied the foraging behavior of breeding Prothonotary Warblers (Protonotaria citrea) in two forest habitat types, cypress-gum swamp forest and coastal-plain levee forest. I quantified foraging behavior with focal animal sampling and continuous recording during foraging bouts. I measured two aspects of foraging behavior: 1) prey attack rate (attacks per minute), using four attack maneuvers (glean, sally, hover, strike), and 2) foraging speed (movements per minute), using three types of movement (hop, short flight [???1 m], long flight [>1 m]). Warblers attacked prey more often in cypress-gum swamp forest than in coastal-plain levee forest. Foraging speed, however, was not different between habitats. I also measured foraging effort (% time spent foraging) and relative frequency of attack maneuvers employed in each habitat; neither of these variables was influenced by forest type. I conclude that Prothonotary Warblers encounter more prey when foraging in cypress-gum swamps than in coastal-plain levee forest, and that greater food availability results in higher density and greater reproductive success for birds breeding in cypress-gum swamp.

Ecological values of shallow-water habitats: Implications for the restoration of disturbed ecosystems

USGS Publications Warehouse

Lopez, C.B.; Cloern, J.E.; Schraga, T.S.; Little, A.J.; Lucas, L.V.; Thompson, J.K.; Burau, J.R.

2006-01-01

A presumed value of shallow-habitat enhanced pelagic productivity derives from the principle that in nutrient-rich aquatic systems phytoplankton growth rate is controlled by light availability, which varies inversely with habitat depth. We measured a set of biological indicators across the gradient of habitat depth within the Sacramento-San Joaquin River Delta (California) to test the hypothesis that plankton biomass, production, and pelagic energy flow also vary systematically with habitat depth. Results showed that phytoplankton biomass and production were only weakly related to phytoplankton growth rates whereas other processes (transport, consumption) were important controls. Distribution of the invasive clam Corbicula fluminea was patchy, and heavily colonized habitats all supported low phytoplankton biomass and production and functioned as food sinks. Surplus primary production in shallow, uncolonized habitats provided potential subsidies to neighboring recipient habitats. Zooplankton in deeper habitats, where grazing exceeded phytoplankton production, were likely supported by significant fluxes of phytoplankton biomass from connected donor habitats. Our results provide three important lessons for ecosystem science: (a) in the absence of process measurements, derived indices provide valuable information to improve our mechanistic understanding of ecosystem function and to benefit adaptive management strategies; (b) the benefits of some ecosystem functions are displaced by water movements, so the value of individual habitat types can only be revealed through a regional perspective that includes connectedness among habitats; and (c) invasive species can act as overriding controls of habitat function, adding to the uncertainty of management outcomes. ?? 2006 Springer Science+Business Media, Inc.

Do ampharetids take sedimented steps between vents and seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems.

PubMed

Eilertsen, Mari H; Kongsrud, Jon A; Alvestad, Tom; Stiller, Josefin; Rouse, Greg W; Rapp, Hans T

2017-10-31

A range of higher animal taxa are shared across various chemosynthesis-based ecosystems (CBEs), which demonstrates the evolutionary link between these habitats, but on a global scale the number of species inhabiting multiple CBEs is low. The factors shaping the distributions and habitat specificity of animals within CBEs are poorly understood, but geographic proximity of habitats, depth and substratum have been suggested as important. Biogeographic studies have indicated that intermediate habitats such as sedimented vents play an important part in the diversification of taxa within CBEs, but this has not been assessed in a phylogenetic framework. Ampharetid annelids are one of the most commonly encountered animal groups in CBEs, making them a good model taxon to study the evolution of habitat use in heterotrophic animals. Here we present a review of the habitat use of ampharetid species in CBEs, and a multi-gene phylogeny of Ampharetidae, with increased taxon sampling compared to previous studies. The review of microhabitats showed that many ampharetid species have a wide niche in terms of temperature and substratum. Depth may be limiting some species to a certain habitat, and trophic ecology and/or competition are identified as other potentially relevant factors. The phylogeny revealed that ampharetids have adapted into CBEs at least four times independently, with subsequent diversification, and shifts between ecosystems have happened in each of these clades. Evolutionary transitions are found to occur both from seep to vent and vent to seep, and the results indicate a role of sedimented vents in the transition between bare-rock vents and seeps. The high number of ampharetid species recently described from CBEs, and the putative new species included in the present phylogeny, indicates that there is considerable diversity still to be discovered. This study provides a molecular framework for future studies to build upon and identifies some ecological and

Bacterial community variation in human body habitats across space and time.

PubMed

Costello, Elizabeth K; Lauber, Christian L; Hamady, Micah; Fierer, Noah; Gordon, Jeffrey I; Knight, Rob

2009-12-18

Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.

Environment degeneration affects habitat diversity of Tamarix spp. in arid zone

NASA Astrophysics Data System (ADS)

Li, Tiejun; Yang, Weikang

2003-07-01

There are 18 species of Tamarix spp. in China and 16 of them in Xinjiang. As a group of bushes which widespread in salty and sandy land in arid zone, Tamarix spp. had gotten more and more attention by ecologists because of their unique bio-ecological characteristics, ecological and social economy functions. Wide Distribution of Tamarix spp. affects ecological environment stabilization of arid zone in western China. The modern distribution and habitat of Tamarix spp. diversity in Xinjiang were studied in this paper. Result revealed that water (surface water and high groundwater ) is the critical environment factor which determines the modern distribution of Tamarix spp.. Depend on analyzing groundwater lever and salt content of soil(two environment factors), author divided the habitat of Tamarix spp. into six type groups (low salt type with high groundwater, middle salt type with high groundwater, high salt type with high groundwater, low salt type with low groundwater and middle salt type with low groundwater etc.) which consisting of ten habitat types. Habitat of Tamarix spp. in Xinjiang never exists in isolation, but associate with each other. The groundwater lever and salt content of soil varies with the lapse of time, then habitats transform from one type into another and species of Tamarix spp. in habitats transforms accordingly.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments.

PubMed

Rocha, Lidianne L; Colares, Geórgia B; Nogueira, Vanessa L R; Paes, Fernanda A; Melo, Vânia M M

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

PubMed Central

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

Electronic Tagging of Atlantic Bluefin Tuna (Thunnus thynnus, L.) Reveals Habitat Use and Behaviors in the Mediterranean Sea

PubMed Central

Cermeño, Pablo; Quílez-Badia, Gemma; Ospina-Alvarez, Andrés; Sainz-Trápaga, Susana; Boustany, Andre M.; Seitz, Andy C.; Tudela, Sergi; Block, Barbara A.

2015-01-01

We analyzed the movements of Atlantic tuna (Thunnus thynnus L.) in the Mediterranean Sea using data from 2 archival tags and 37 pop-up satellite archival tags (PAT). Bluefin tuna ranging in size from 12 to 248 kg were tagged on board recreational boats in the western Mediterranean and the Adriatic Sea between May and September during two different periods (2000 to 2001 and 2008 to 2012). Although tuna migrations between the Mediterranean Sea and the Atlantic Ocean have been well reported, our results indicate that part of the bluefin tuna population remains in the Mediterranean basin for much of the year, revealing a more complex population structure. In this study we demonstrate links between the western Mediterranean, the Adriatic and the Gulf of Sidra (Libya) using over 4336 recorded days of location and behavior data from tagged bluefin tuna with a maximum track length of 394 days. We described the oceanographic preferences and horizontal behaviors during the spawning season for 4 adult bluefin tuna. We also analyzed the time series data that reveals the vertical behavior of one pop-up satellite tag recovered, which was attached to a 43.9 kg tuna. This fish displayed a unique diving pattern within 16 days of the spawning season, suggesting a use of the thermocline as a thermoregulatory mechanism compatible with spawning. The results obtained hereby confirm that the Mediterranean is clearly an important habitat for this species, not only as spawning ground, but also as an overwintering foraging ground. PMID:25671316

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

PubMed Central

Tan, Cheng; Takada, Shoji

2017-01-01

While nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements. PMID:29194442

An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach.

PubMed

Parmar, Krupa; Dafale, Nishant; Pal, Rajesh; Tikariha, Hitesh; Purohit, Hemant

2018-02-01

Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses. Differential relative abundance of phage families-Siphoviridae (34%) and Myoviridae (26%) in WWTP, Myoviridae (30%) and Podoviridae (23%) in fresh water, and Myoviridae (41%) and Podoviridae (8%) in marine-was found to be a discriminating factor among four habitats while Rudiviridae (9%), Globuloviridae (8%), and Lipothrixviridae (1%) were exclusively observed in hot water spring. Subsequently, at genera level, Bpp-1-like virus, Chlorovirus, and T4-like virus were found abundant in WWTP, fresh, and marine habitat, respectively. PCA analysis revealed completely disparate composition of phage in hot water spring from other three ecosystems. Similar analysis of relative abundance of functional features corroborated observations from taxa analysis. Functional features corresponding to phage packaging machinery, replication, integration and excision, and gene transfer discriminated among four habitats. The comparative metagenomics approach exhibited genetically distinct phage communities among four habitats. Results revealed that selective distribution of phage communities would help in understanding the role of phages in food chains, nutrient cycling, and microbial ecology. Study of specific phages would also help in controlling environmental pathogens including MDR bacterial populations using phage therapy approach by selective mining and

Ontogenetic loops in habitat use highlight the importance of littoral habitats for early life-stages of oceanic fishes in temperate waters

NASA Astrophysics Data System (ADS)

Polte, Patrick; Kotterba, Paul; Moll, Dorothee; von Nordheim, Lena

2017-02-01

General concepts of larval fish ecology in temperate oceans predominantly associate dispersal and survival to exogenous mechanisms such as passive drift along ocean currents. However, for tropical reef fish larvae and species in inland freshwater systems behavioural aspects of habitat selection are evidently important components of dispersal. This study is focused on larval Atlantic herring (Clupea harengus) distribution in a Baltic Sea retention area, free of lunar tides and directed current regimes, considered as a natural mesocosm. A Lorenz curve originally applied in socio-economics to describe demographic income distribution was adapted to a 20 year time-series of weekly larval herring distribution, revealing size-dependent spatial homogeneity. Additional quantitative sampling of distinct larval development stages across pelagic and littoral areas uncovered a loop in habitat use during larval ontogeny, revealing a key role of shallow littoral waters. With increasing rates of coastal change, our findings emphasize the importance of the littoral zone when considering reproduction of pelagic, ocean-going fish species; highlighting a need for more sensitive management of regional coastal zones.

Ontogenetic loops in habitat use highlight the importance of littoral habitats for early life-stages of oceanic fishes in temperate waters

PubMed Central

Polte, Patrick; Kotterba, Paul; Moll, Dorothee; von Nordheim, Lena

2017-01-01

General concepts of larval fish ecology in temperate oceans predominantly associate dispersal and survival to exogenous mechanisms such as passive drift along ocean currents. However, for tropical reef fish larvae and species in inland freshwater systems behavioural aspects of habitat selection are evidently important components of dispersal. This study is focused on larval Atlantic herring (Clupea harengus) distribution in a Baltic Sea retention area, free of lunar tides and directed current regimes, considered as a natural mesocosm. A Lorenz curve originally applied in socio-economics to describe demographic income distribution was adapted to a 20 year time-series of weekly larval herring distribution, revealing size-dependent spatial homogeneity. Additional quantitative sampling of distinct larval development stages across pelagic and littoral areas uncovered a loop in habitat use during larval ontogeny, revealing a key role of shallow littoral waters. With increasing rates of coastal change, our findings emphasize the importance of the littoral zone when considering reproduction of pelagic, ocean-going fish species; highlighting a need for more sensitive management of regional coastal zones. PMID:28205543

Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

USGS Publications Warehouse

Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

2017-01-01

To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

Ghosts of habitats past: Contribution of landscape change to current habitats used by shrubland birds

USGS Publications Warehouse

Knick, Steven T.; Rotenberry, J.T.

2000-01-01

Models of habitat associations for species often are developed with an implicit assumption that habitats are static, even though recent disturbance may have altered the landscape. We tested our hypothesis that trajectory and magnitude of habitat change influenced observed distribution and abundance of passerine birds breeding in shrubsteppe habitats of southwestern Idaho. Birds in this region live in dynamic landscapes undergoing predominantly large-scale, radical, and unidirectional habitat change because wildfires are converting shrublands into expanses of exotic annual grasslands. We used data from field surveys and satellite image analyses in a series of redundancy analyses to partition variances and to determine the relative contribution of habitat change and current landscapes. Although current habitats explained a greater proportion of total variation, changes in habitat and measures of habitat richness and texture also contributed to variation in abundance of Horned Larks (Eremophila alpestris), Brewera??s Sparrows (Spizella breweri), and Sage Sparrows (Amphispiza belli). Abundance of birds was insensitive to scale for nonspatial habitat variables. In contrast, spatial measures of habitat richness and texture in the landscape were significant only at large spatial scales. Abundance of Horned Larks, Western Meadowlarks (Sturnella neglecta), and Brewera??s Sparrows, but not Sage Thrashers (Oreoscoptes montanus) or Sage Sparrows, was positively correlated with changes toward stable habitats. Because dominant habitat changes were toward less stable conditions, regional declines of those birds in shrubsteppe habitats reflect current landscapes as well as the history, magnitude, and trajectory of habitat change.

Mapping anuran habitat suitability to estimate effects of grassland and wetland conservation programs

USGS Publications Warehouse

Mushet, David M.; Euliss, Ned H.; Stockwell, Craig A.

2012-01-01

The conversion of the Northern Great Plains of North America to a landscape favoring agricultural commodity production has negatively impacted wildlife habitats. To offset impacts, conservation programs have been implemented by the U.S. Department of Agriculture and other agencies to restore grassland and wetland habitat components. To evaluate effects of these efforts on anuran habitats, we used call survey data and environmental data in ecological niche factor analyses implemented through the program Biomapper to quantify habitat suitability for five anuran species within a 196 km2 study area. Our amphibian call surveys identified Northern Leopard Frogs (Lithobates pipiens), Wood Frogs (Lithobates sylvaticus), Boreal Chorus Frogs (Pseudacris maculata), Great Plains Toads (Anaxyrus cognatus), and Woodhouse’s Toads (Anaxyrus woodhousii) occurring within the study area. Habitat suitability maps developed for each species revealed differing patterns of suitable habitat among species. The most significant findings of our mapping effort were 1) the influence of deep-water overwintering wetlands on suitable habitat for all species encountered except the Boreal Chorus Frog; 2) the lack of overlap between areas of core habitat for both the Northern Leopard Frog and Wood Frog compared to the core habitat for both toad species; and 3) the importance of conservation programs in providing grassland components of Northern Leopard Frog and Wood Frog habitat. The differences in habitats suitable for the five species we studied in the Northern Great Plains, i.e., their ecological niches, highlight the importance of utilizing an ecosystem based approach that considers the varying needs of multiple species in the development of amphibian conservation and management plans.

Spatial Dynamics and Expanded Vertical Niche of Blue Sharks in Oceanographic Fronts Reveal Habitat Targets for Conservation

PubMed Central

Queiroz, Nuno; Humphries, Nicolas E.; Noble, Leslie R.; Santos, António M.; Sims, David W.

2012-01-01

Dramatic population declines among species of pelagic shark as a result of overfishing have been reported, with some species now at a fraction of their historical biomass. Advanced telemetry techniques enable tracking of spatial dynamics and behaviour, providing fundamental information on habitat preferences of threatened species to aid conservation. We tracked movements of the highest pelagic fisheries by-catch species, the blue shark Prionace glauca, in the North-east Atlantic using pop-off satellite-linked archival tags to determine the degree of space use linked to habitat and to examine vertical niche. Overall, blue sharks moved south-west of tagging sites (English Channel; southern Portugal), exhibiting pronounced site fidelity correlated with localized productive frontal areas, with estimated space-use patterns being significantly different from that of random walks. Tracked female sharks displayed behavioural variability in diel depth preferences, both within and between individuals. Diel depth use ranged from normal DVM (nDVM; dawn descent, dusk ascent), to reverse DVM (rDVM; dawn ascent, dusk descent), to behavioural patterns where no diel differences were apparent. Results showed that blue sharks occupy some of the most productive marine zones for extended periods and structure diel activity patterns across multiple spatio-temporal scales in response to particular habitat types. In so doing, sharks occupied an extraordinarily broad vertical depth range for their size (1.0–2.0 m fork length), from the surface into the bathypelagic realm (max. dive depth, 1160 m). The space-use patterns of blue sharks indicated they spend much of the time in areas where pelagic longlining activities are often highest, and in depth zones where these fisheries particularly target other species, which could account for the rapid declines recently reported for blue sharks in many parts of the world's oceans. Our results provide habitat targets for blue shark conservation

Homology modelling, molecular docking, and molecular dynamics simulations reveal the inhibition of Leishmania donovani dihydrofolate reductase-thymidylate synthase enzyme by Withaferin-A.

PubMed

Vadloori, Bharadwaja; Sharath, A K; Prabhu, N Prakash; Maurya, Radheshyam

2018-04-16

Present in silico study was carried out to explore the mode of inhibition of Leishmania donovani dihydrofolate reductase-thymidylate synthase (Ld DHFR-TS) enzyme by Withaferin-A, a withanolide isolated from Withania somnifera. Withaferin-A (WA) is known for its profound multifaceted properties, but its antileishmanial activity is not well understood. The parasite's DHFR-TS enzyme is diverse from its mammalian host and could be a potential drug target in parasites. A 3D model of Ld DHFR-TS enzyme was built and verified using Ramachandran plot and SAVES tools. The protein was docked with WA-the ligand, methotrexate (MTX)-competitive inhibitor of DHFR, and dihydrofolic acid (DHFA)-substrate for DHFR-TS. Molecular docking studies reveal that WA competes for active sites of both Hu DHFR and TS enzymes whereas it binds to a site other than active site in Ld DHFR-TS. Moreover, Lys 173 residue of DHFR-TS forms a H-bond with WA and has higher binding affinity to Ld DHFR-TS than Hu DHFR and Hu TS. The MD simulations confirmed the H-bonding interactions were stable. The binding energies of WA with Ld DHFR-TS were calculated using MM-PBSA. Homology modelling, molecular docking and MD simulations of Ld DHFR-TS revealed that WA could be a potential anti-leishmanial drug.

Trust Species and Habitat Branch: using the innovative approaches of today to conserve biodiversity for tomorrow

USGS Publications Warehouse

Stevens, Patricia; Walters, Katie D.

2015-01-01

The Trust Species and Habitats Branch of the Fort Collins Science Center includes a diverse group of scientists encompassing both traditional and specialized expertise in wildlife biology, ecosystem ecology, quantitative ecology, disease ecology, molecular genetics, and stable isotope geochemistry. Using our expertise and collaborating with others around the world, our goal is to provide the information, tools, and technologies that our partners need to support conservation, management, and restoration of terrestrial vertebrate populations, habitats, and ecosystem function in a changing world.

Selection of nest-site habitat by interior least terns in relation to sandbar construction

USGS Publications Warehouse

Sherfy, M.H.; Stucker, J.H.; Buhl, D.A.

2012-01-01

Federally endangered interior least terns (Sternula antillarum) nest on bare or sparsely vegetated sandbars on midcontinent river systems. Loss of nesting habitat has been implicated as a cause of population declines, and managing these habitats is a major initiative in population recovery. One such initiative involves construction of mid-channel sandbars on the Missouri River, where natural sandbar habitat has declined in quantity and quality since the late 1990s. We evaluated nest-site habitat selection by least terns on constructed and natural sandbars by comparing vegetation, substrate, and debris variables at nest sites (na =a 798) and random points (na =a 1,113) in bare or sparsely vegetated habitats. Our logistic regression models revealed that a broader suite of habitat features was important in nest-site selection on constructed than on natural sandbars. Odds ratios for habitat variables indicated that avoidance of habitat features was the dominant nest-site selection process on both sandbar types, with nesting terns being attracted to nest-site habitat features (gravel and debris) and avoiding vegetation only on constructed sandbars, and avoiding silt and leaf litter on both sandbar types. Despite the seemingly uniform nature of these habitats, our results suggest that a complex suite of habitat features influences nest-site choice by least terns. However, nest-site selection in this social, colonially nesting species may be influenced by other factors, including spatial arrangement of bare sand habitat, proximity to other least terns, and prior habitat occupancy by piping plovers (Charadrius melodus). We found that nest-site selection was sensitive to subtle variation in habitat features, suggesting that rigor in maintaining habitat condition will be necessary in managing sandbars for the benefit of least terns. Further, management strategies that reduce habitat features that are avoided by least terns may be the most beneficial to nesting least terns

Selection of nest-site habitat by interior least terns in relation to sandbar construction

USGS Publications Warehouse

Sherfy, Mark H.; Stucker, Jennifer H.; Buhl, Deborah A.

2012-01-01

Federally endangered interior least terns (Sternula antillarum) nest on bare or sparsely vegetated sandbars on midcontinent river systems. Loss of nesting habitat has been implicated as a cause of population declines, and managing these habitats is a major initiative in population recovery. One such initiative involves construction of mid-channel sandbars on the Missouri River, where natural sandbar habitat has declined in quantity and quality since the late 1990s. We evaluated nest-site habitat selection by least terns on constructed and natural sandbars by comparing vegetation, substrate, and debris variables at nest sites (n = 798) and random points (n = 1,113) in bare or sparsely vegetated habitats. Our logistic regression models revealed that a broader suite of habitat features was important in nest-site selection on constructed than on natural sandbars. Odds ratios for habitat variables indicated that avoidance of habitat features was the dominant nest-site selection process on both sandbar types, with nesting terns being attracted to nest-site habitat features (gravel and debris) and avoiding vegetation only on constructed sandbars, and avoiding silt and leaf litter on both sandbar types. Despite the seemingly uniform nature of these habitats, our results suggest that a complex suite of habitat features influences nest-site choice by least terns. However, nest-site selection in this social, colonially nesting species may be influenced by other factors, including spatial arrangement of bare sand habitat, proximity to other least terns, and prior habitat occupancy by piping plovers (Charadrius melodus). We found that nest-site selection was sensitive to subtle variation in habitat features, suggesting that rigor in maintaining habitat condition will be necessary in managing sandbars for the benefit of least terns. Further, management strategies that reduce habitat features that are avoided by least terns may be the most beneficial to nesting least terns.

Data Collection and Simulation of Ecological Habitat and Recreational Habitat in the Shenandoah River, Virginia

USGS Publications Warehouse

Krstolic, Jennifer L.

2015-01-01

Time-series analyses were used to investigate changes in habitat availability with increased water withdrawals of 10, 20, and almost 50 percent (48.6 percent) up to the 2040 amounts projected by local water supply plans. Adult and sub-adult smallmouth bass frequently had habitat availability outside the normal range for habitat conditions during drought years, yet 10- or 20-percent increases in withdrawals did not contribute to a large reduction in habitat. When withdrawals were increased by 50 percent, there was an additional decrease in habitat. During 2002 drought scenarios, reduced habitat availability for sub-adult redbreast sunfish or river chub was only slightly evident with 50-percent increased withdrawal scenarios. Recreational habitat represented by canoeing decreased lower than normal during the 2002 drought. For a recent normal year, like 2012, increased water-withdrawal scenarios did not affect habitat availability for fish such as adult and sub-adult smallmouth bass, sub-adult redbreast sunfish, or river chub. Canoeing habitat availability was within the normal range most of 2012, and increased water-withdrawal scenarios showed almost no affect. For both ecological fish habitat and recreational canoeing habitat, the antecedent conditions (habitat within normal range of habitat or below normal) appear to govern whether additional water withdrawals will affect habitat availability. As human populations and water demands increase, many of the ecological or recreational stresses may be lessened by managing the timing of water withdrawals from the system.

Bacterial Community Variation in Human Body Habitats Across Space and Time

PubMed Central

Costello, Elizabeth K.; Lauber, Christian L.; Hamady, Micah; Fierer, Noah; Gordon, Jeffrey I.; Knight, Rob

2010-01-01

Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in 7–9 healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, while individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time: such trends may ultimately reveal how microbiome changes cause or prevent disease. PMID:19892944

Wildlife Habitat Restoration: Chapter 12

USGS Publications Warehouse

Conway, Courtney J.; Borgmann, Kathi L.; Morrison, Michael L.; Mathewson, Heather A.

2015-01-01

As the preceding chapters point out, many wildlife species and the habitat they depend on are in peril. However, opportunities exist to restore habitat for many imperiled wildlife species. But what is wildlife habitat restoration? We begin this chapter by defining habitat restoration and then provide recommendations on how to maximize success of future habitat restoration efforts for wildlife. Finally, we evaluate whether we have been successful in restoring wildlife habitat and supply recommendations to advance habitat restoration. Successful restoration requires clear and explicit goals that are based on our best understanding of what the habitat was like prior to the disturbing event. Ideally, a restoration project would include: (1) a summary of prerestoration conditions that define the existing status of wildlife populations and their habitat; (2) a description of habitat features required by the focal or indicator species for persistence; (3) an a priori description of measurable, quantitative metrics that define restoration goals and measures of success; (4) a monitoring plan; (5) postrestoration comparisons of habitat features and wildlife populations with adjacent unmodified areas that are similar to the restoration site; and (6) expert review of the entire restoration plan (i.e., the five aforementioned components).

Microbial existence in controlled habitats and their resistance to space conditions.

PubMed

Venkateswaran, Kasthuri; La Duc, Myron T; Horneck, Gerda

2014-09-17

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC's call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat.

PubMed

Perazzolli, Michele; Herrero, Noemí; Sterck, Lieven; Lenzi, Luisa; Pellegrini, Alberto; Puopolo, Gerardo; Van de Peer, Yves; Pertot, Ilaria

2016-10-27

Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms. A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea. This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol

Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

2010-06-01

Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

Ord's kangaroo rats living in floodplain habitats: Factors contributing to habitat attraction

USGS Publications Warehouse

Miller, M.S.; Wilson, K.R.; Andersen, D.C.

2003-01-01

High densities of an aridland granivore, Ord's kangaroo rat (Dipodomys ordii), have been documented in floodplain habitats along the Yampa River in northwestern Colorado. Despite a high probability of inundation and attendant high mortality during the spring flood period, the habitat is consistently recolonized. To understand factors that potentially make riparian habitats attractive to D. ordii, we compared density and spatial pattern of seeds, density of a competitor (western harvester ant, Pogonomyrmex occidentalis), and digging energetics within floodplain habitats and between floodplain and adjacent upland habitats. Seed density within the floodplain was greatest in the topographically high (rarely flooded) floodplain and lowest immediately after a spring flood in the topographically low (frequently flooded) floodplain. Seed densities in adjacent upland habitat that never floods were higher than the lowest floodplain habitat. In the low floodplain prior to flooding, seeds had a clumped spatial pattern, which D. ordii is adept at exploiting; after spring flooding, a more random pattern resulted. Populations of the western harvester ant were low in the floodplain relative to the upland. Digging by D. ordii was energetically less expensive in floodplain areas than in upland areas. Despite the potential for mortality due to annual spring flooding, the combination of less competition from harvester ants and lower energetic costs of digging might promote the use of floodplain habitat by D. ordii.

Habitat quality and geometry affect patch occupancy of two Orthopteran species.

PubMed

Pasinelli, Gilberto; Meichtry-Stier, Kim; Birrer, Simon; Baur, Bruno; Duss, Martin

2013-01-01

Impacts of habitat loss and fragmentation on distribution and population size of many taxa are well established. In contrast, less is known about the role of within-patch habitat quality for the spatial dynamics of species, even though within-patch habitat quality may substantially influence the dynamics of population networks. We studied occurrence patterns of two Orthopteran species in relation to size, isolation and quality of habitat patches in an intensively managed agricultural landscape (16.65 km(2)) in the Swiss lowland. Occurrence of field crickets (Gryllus campestris) was positively related to patch size and negatively to the distance to the nearest occupied patch, two measures of patch geometry. Moreover, field crickets were more likely to occur in extensively managed meadows, meadows used at low intensity and meadows dominated by Poa pratensis, three measures of patch quality. Occurrence of the large gold grasshopper (Chrysochraon dispar) was negatively related to two measures of patch geometry, distance to the nearest occupied patch and perimeter index (ratio of perimeter length to patch area). Further, large gold grasshoppers were more likely to occupy patches close to water and patches with vegetation left uncut over winter, two measures of patch quality. Finally, examination of patch occupancy dynamics of field crickets revealed that patches colonized in 2009 and patches occupied in both 2005 and 2009 were larger, better connected and of other quality than patches remaining unoccupied and patches from which the species disappeared. The strong relationships between Orthopteran occurrence and aspects of patch geometry found in this study support the "area-and-isolation paradigm". Additionally, our study reveals the importance of patch quality for occurrence patterns of both species, and for patch occupancy dynamics in the field cricket. An increased understanding of patch occupancy patterns may be gained if inference is based on variables related to

Source-Sink Colonization as a Possible Strategy of Insects Living in Temporary Habitats.

PubMed

Frouz, Jan; Kindlmann, Pavel

2015-01-01

Continuous colonization and re-colonization is critical for survival of insect species living in temporary habitats. When insect populations in temporary habitats are depleted, some species may escape extinction by surviving in permanent, but less suitable habitats, in which long-term population survival can be maintained only by immigration from other populations. Such situation has been repeatedly described in nature, but conditions when and how this occurs and how important this phenomenon is for insect metapopulation survival are still poorly known, mainly because it is difficult to study experimentally. Therefore, we used a simulation model to investigate, how environmental stochasticity, growth rate and the incidence of dispersal affect the positive effect of permanent but poor ("sink") habitats on the likelihood of metapopulation persistence in a network of high quality but temporary ("source") habitats. This model revealed that permanent habitats substantially increase the probability of metapopulation persistence of insect species with poor dispersal ability if the availability of temporary habitats is spatio-temporally synchronized. Addition of permanent habitats to a system sometimes enabled metapopulation persistence even in cases in which the metapopulation would otherwise go extinct, especially for species with high growth rates. For insect species with low growth rates the probability of a metapopulation persistence strongly depended on the proportions of "source" to "source" and "sink" to "source" dispersal rates.

Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages.

PubMed

Colin, Nicole; Villéger, Sébastien; Wilkes, Martin; de Sostoa, Adolfo; Maceda-Veiga, Alberto

2018-06-01

Trait-based ecology has been developed for decades to infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive dataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N=389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have ≤3 species (specialization, FSpe; originality, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native:total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive datasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is

On the salty side of life: molecular, physiological and anatomical adaptation and acclimation of trees to extreme habitats.

PubMed

Polle, Andrea; Chen, Shaoliang

2015-09-01

Saline and sodic soils that cannot be used for agriculture occur worldwide. Cultivating stress-tolerant trees to obtain biomass from salinized areas has been suggested. Various tree species of economic importance for fruit, fibre and timber production exhibit high salinity tolerance. Little is known about the mechanisms enabling tree crops to cope with high salinity for extended periods. Here, the molecular, physiological and anatomical adjustments underlying salt tolerance in glycophytic and halophytic model tree species, such as Populus euphratica in terrestrial habitats, and mangrove species along coastlines are reviewed. Key mechanisms that have been identified as mediating salt tolerance are discussed at scales from the genetic to the morphological level, including leaf succulence and structural adjustments of wood anatomy. The genetic and transcriptomic bases for physiological salt acclimation are salt sensing and signalling networks that activate target genes; the target genes keep reactive oxygen species under control, maintain the ion balance and restore water status. Evolutionary adaptation includes gene duplication in these pathways. Strategies for and limitations to tree improvement, particularly transgenic approaches for increasing salt tolerance by transforming trees with single and multiple candidate genes, are discussed. © 2014 John Wiley & Sons Ltd.

Surveillance for Toxoplasma gondii in California mussels (Mytilus californianus) reveals transmission of atypical genotypes from land to sea.

PubMed

Shapiro, Karen; VanWormer, Elizabeth; Aguilar, Beatriz; Conrad, Patricia A

2015-11-01

Coastal habitat contamination with Toxoplasma gondii is a health risk to humans and marine wildlife, with infections documented in both nearshore and pelagic marine mammals. Due to lack of sensitive methods for detection of T. gondii in water, this study utilized an alternative surveillance approach for evaluating marine habitat contamination using wild mussels. The objectives of this study were to (i) validate sensitive molecular tools for T. gondii detection in mussels and (ii) apply optimized methods in a surveillance study to determine the prevalence and genotype(s) of T. gondii in mussels. Simplex polymerase chain reaction screening and multiplex genotyping assays were validated and then applied on 959 wild-caught mussels collected from central California. Thirteen mussels (1.4%) had detectable T. gondii DNA and the presence of T. gondii in mussels was significantly associated with proximity to freshwater run-off and collection during the wet season. Molecular characterization revealed alleles from T. gondii types I, II/III, X at the B1 locus, and a novel atypical B1 allele that was recently documented in T. gondii-infected carnivores from California. Findings demonstrate higher than previously reported T. gondii contamination of California coastlines, and describe novel strains of the parasite that further link terrestrial sources with marine contamination. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Lunar base habitat designs: Characterizing the environment, and selecting habitat designs for future trade-offs

NASA Technical Reports Server (NTRS)

Ganapathi, Gani B.; Ferrall, Joseph; Seshan, P. K.

1993-01-01

A survey of distinct conceptual lunar habitat designs covering the pre- and post-Apollo era is presented. The impact of the significant lunar environmental challenges such as temperature, atmosphere, radiation, soil properties, meteorites, and seismic activity on the habitat design parameters are outlined. Over twenty habitat designs were identified and classified according to mission type, crew size; total duration of stay, modularity, environmental protection measures, and emplacement. Simple selection criteria of (1) post-Apollo design, (2) uniqueness of the habitat design, (3) level of thoroughness in design layout, (4) habitat dimensions are provided, and (5) materials of construction for the habitat shell are specified, are used to select five habitats for future trade studies. Habitat emplacement scenarios are created to examine the possible impact of emplacement of the habitat in different locations, such as lunar poles vs. equatorial, above ground vs. below ground, etc.

The airspace is habitat

USGS Publications Warehouse

Diehl, Robert H.

2013-01-01

A preconception concerning habitat persists and has gone unrecognized since use of the term first entered the lexicon of ecological and evolutionary biology many decades ago. Specifically, land and water are considered habitats, while the airspace is not. This might at first seem a reasonable, if unintended, demarcation, since years of education and personal experience as well as limits to perception predispose a traditional view of habitat. Nevertheless, the airspace satisfies the definition and functional role of a habitat, and its recognition as habitat may have implications for policy where expanding anthropogenic development of airspace could impact the conservation of species and subject parts of the airspace to formalized legal protection.

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

PubMed

Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P; Rai, Vandna; Singh, Ashok K; Singh, Nagendra K

2018-01-01

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon , and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho - taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

PubMed Central

Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P.; Rai, Vandna; Singh, Ashok K.; Singh, Nagendra K.

2018-01-01

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones

Adaptation and survival of plants in high stress habitats via fungal endophyte conferred stress tolerance

USGS Publications Warehouse

Rodriguez, Rusty J.; Woodward, Claire; Redman, Regina S.

2010-01-01

From the Arctic to the Antarctic, plants thrive in diverse habitats that impose different levels of adaptive pressures depending on the type and degree of biotic and abiotic stresses inherent to each habitat (Stevens, 1989). At any particular location, the abundance and distribution of individual plant species vary tremendously and is theorized to be based on the ability to tolerate a wide range of edaphic conditions and habitat-specific stresses (Pianka, 1966). The ability of individual plant species to thrive in diverse habitats is commonly referred to as phenotypic plasticity and is thought to involve adaptations based on changes in the plant genome (Givnish, 2002; Pan et al., 2006; Robe and Griffiths, 2000; Schurr et al., 2006). Habitats that impose high levels of abiotic stress are typically colonized with fewer plant species compared to habitats imposing low levels of stress. Moreover, high stress habitats have decreased levels of plant abundance compared to low stress habitats even though these habitats may occur in close proximity to one another (Perelman et al., 2007). This is particularly interesting because all plants are known to perceive, transmit signals, and respond to abiotic stresses such as drought, heat, and salinity (Bartels and Sunkar, 2005; Bohnert et al., 1995). Although there has been extensive research performed to determine the genetic, molecular, and physiological bases of how plants respond to and tolerate stress, the nature of plant adaptation to high stress habitats remains unresolved (Leone et al., 2003; Maggio et al., 2003; Tuberosa et al., 2003). However, recent evidence indicates that a ubiquitous aspect of plant biology (fungal symbiosis) is involved in the adaptation and survival of at least some plants in high stress habitats (Rodriguez et al., 2008).

Indirect effects of species interactions on habitat provisioning.

PubMed

Holbrook, Sally J; Schmitt, Russell J; Brooks, Andrew J

2011-07-01

Species that shelter in a biogenic habitat can influence their refugia and, in turn, play an essential role in shaping local patterns of biodiversity. Here we explore a positive feedback loop between the provisioning rate of habitat-forming branching corals and their associated fishes and show how interactions between two groups of fish--the planktivorous damselfish and predatory hawkfish--altered the feedback. A field experiment confirmed that skeletal growth of branching coral (genus Pocillopora) increased substantially with increasing numbers (biomass) of resident fishes, likely because they greatly increased the interstitial concentrations of nutrients. Because there is a positive relationship between colony size and number (biomass) of associated fishes (primarily damselfishes in the Family Pomacentridae), a structure-function feedback loop exists in which increasing numbers of damselfish enhance coral growth and larger corals host greater abundances (and species richness) of fish. However, interactions between damselfishes and arc-eye hawkfish, Paracirrhites arcatus, a largely solitary resident, can disrupt this positive feedback loop. Field surveys revealed a marked pattern of fish occupancy related to coral size: Pocillopora colonies of sufficient size to host fish (>40 cm circumference) had either groups of damselfish or an arc-eye hawkfish; only larger colonies (>75 cm) were occupied by both the damselfish and hawkfish. Subsequent short- and long-term experiments revealed that on intermediate-sized Pocillopora colonies, arc-eye hawkfish prevented the establishment of damselfish by suppressing their recruitment. The demographic consequences to the host coral were substantial; in a 1-year-long experiment, intermediate-size Pocillopora occupied by hawkfish grew at half the rate of corals that hosted groups of damselfish. These findings indicate that: (1) species which occupy a biogenic habitat can enhance the provisioning rate of their habitat; (2) such

Pandora's mycological box: molecular sequences vs. morphology in understanding fungal relationships and biodiversity.

PubMed

Hawksworth, David L

2006-09-01

Fundamental reappraisals of diverse traditional ideas in mycology have become necessary as a result of molecular insights. These different insights are discussed in relation to: the positions of microsporidia, slime moulds and oomycetes; the basal position of lichen fungi in the evolution of ascomycetes forming fruit bodies; remodelling of orders and families; changed generic concepts; the issue of whether permitting a dual nomenclature for the different states of pleomorphic fungi should be continued; and the recognition of additional cryptic species within a "species". The molecular data has necessitated a reassessment of the systematic importance of many types of characters. Also, the techniques open exciting horizons and undreamed of abilities through being able to identify non-sporing fungi in ecological samples and plant material, and revealing unexpected levels of diversity in hitherto little-explored habitats. Major advances in understanding how fungi operate through total genomic approaches can be anticipated as more are completely sequenced. The Pandora's box of molecular surprises is to be seen as one of blessings and not one of miseries and evils.

Habitat Suitability Index Models: Beaver

USGS Publications Warehouse

Allen, Arthur W.

1982-01-01

Habitat preferences of the beaver (Castor canadensis) are described in this publication, which is one of a series of Habitat Suitability Index (HSI) models. Habitat use information is presented in a synthesis of the literature on the species-habitat requirements of the beaver, followed by the development of the HSI model. The model is designed to provide information for use in impact assessment and habitat management activities, and should be used in conjunction with habitat evaluation procedures previously developed by the Fish and Wildlife Service. This revised model updates the original publication dated September 1982.

[Genetic relationship analysis of Ephedra intermedia from different habitat in Gansu by ISSR analysis].

PubMed

Zhu, Tian-Tian; Jin, Ling; Du, Tao; Cui, Zhi-Jia; Zhang, Xian-Fei; Wu, Di

2013-09-01

To investigate the genetic relationship of Ephedra intermedia from different habitats in Gansu. The genetic diversity and genetic relationship of E. intermedia from different habitats in Gansu were studied by ISSR molecular marker technique. Twelve ISSR primers were selected from 70 ISSR primers and used for ISSR amplification. Total 112 loci were amplified, in which 81 were polymorphic loci, the average percentage of polymorphie bands (PPB) was 72.32%. Clustering results indicated that the wild species and cultivating species were clustered into different group. The wild species, which had closer distance, were clustered into a group. E. intermedia of different habitats in Gansu have rich genetic diversities among species, it is the reason that E. intermedia has strong adaptability and wide distribution. Further, the genetic distance of E. intermedia is associated with geographical distance, the further distance can hinder the gene flow.

Assessment of chevron dikes for the enhancement of physical-aquatic habitat within the Middle Mississippi River, USA

NASA Astrophysics Data System (ADS)

Remo, J. W.; Pinter, N.

2012-12-01

Along the Middle Mississippi River (MMR), rehabilitation of aquatic habitat is being undertaken using river-training structures such as the blunt-nose chevron dike. Chevron dikes were initially designed to concentrate flow and thus facilitate river navigation, but this new river-training structure is now justified, in part, as a tool for creating aquatic habitat and promoting habitat heterogeneity. The ability of chevrons to create and diversify physical-aquatic habitat has not been verified. In this study, we used 2-D hydrodynamic modeling and reach-scale habitat metrics to assess changes in physical habitat and habitat heterogeneity for pre-chevron and post-chevron along a 2- km reach of the Mississippi River at St. Louis, MO. A historic reference condition (circa 1890) was also modeled to compare physical habitat in a less engineered river channel versus the new physical-habitat patches created by chevron-dike enhancement. This modeling approach quantified changes in habitat availability and diversity among selected reference conditions for a wide range of in-channel flows. Depth-velocity habitat classes were used for assessment of change in physical-habitat patches, and spatial statistical tools were employed to evaluate the reach-scale habitat patch diversity. Modeling of post-chevron channel conditions revealed increases in deep to very deep (>3.0 m) areas of slow moving (<0.6 m/s) water downstream of these structures under emergent flow conditions (≤ 1.5 x mean annual flow[MAF]) relative to pre-construction conditions. Chevron construction increased potential over-wintering habitat (deep [>3.0 m], low velocity [<0.6 m/s]) by up to 7.6 ha. The addition of the chevrons to the river channel also created some (0.8-3.8 ha) shallow-water habitat (0-1.5 m depth with a 0-0.6 m/s velocity) for flows ≤2.0 x MAF and contributed to an 8-35% increase in physical-habitat diversity compared to pre-chevron channel conditions. Comparison of the historic reference

Substrate channel in nitrogenase revealed by a molecular dynamics approach.

PubMed

Smith, Dayle; Danyal, Karamatullah; Raugei, Simone; Seefeldt, Lance C

2014-04-15

Mo-dependent nitrogenase catalyzes the biological reduction of N2 to two NH3 molecules at FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized submicrosecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel. The viability of this observed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, resulting in the discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment and that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations.

PubMed

Druliner, Brooke R; Wang, Panwen; Bae, Taejeong; Baheti, Saurabh; Slettedahl, Seth; Mahoney, Douglas; Vasmatzis, Nikolaos; Xu, Hang; Kim, Minsoo; Bockol, Matthew; O'Brien, Daniel; Grill, Diane; Warner, Nathaniel; Munoz-Gomez, Miguel; Kossick, Kimberlee; Johnson, Ruth; Mouchli, Mohamad; Felmlee-Devine, Donna; Washechek-Aletto, Jill; Smyrk, Thomas; Oberg, Ann; Wang, Junwen; Chia, Nicholas; Abyzov, Alexej; Ahlquist, David; Boardman, Lisa A

2018-02-16

The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients. CAPs had significantly more mutations, altered expression and hypermethylation compared to CFPs. APC was significantly mutated in both polyp groups, but mutations in TP53, FBXW7, PIK3CA, KIAA1804 and SMAD2 were exclusive to CAPs. We found significant expression changes between CAPs and CFPs in GREM1, IGF2, CTGF, and PLAU, and both expression and methylation alterations in FES and HES1. Integrative analyses revealed 124 genes with alterations in at least two platforms, and ERBB3 and E2F8 showed aberrations specific to CAPs across all platforms. These findings provide a resource of molecular distinctions between polyps with and without cancer, which have the potential to enhance the diagnosis, risk assessment and management of polyps.

Habitat preferences of baleen whales in a mid-latitude habitat

NASA Astrophysics Data System (ADS)

Prieto, Rui; Tobeña, Marta; Silva, Mónica A.

2017-07-01

Understanding the dynamics of baleen whale distribution is essential to predict how environmental changes can affect their ecology and, in turn, ecosystem functioning. Recent work showed that mid-latitude habitats along migratory routes may play an important role on the feeding ecology of baleen whales. This study aimed to investigate the function of a mid-latitude habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei (Balaenoptera borealis) whales occurring in sympatry during spring and summer months and to what extent their environmental niches overlap. We addressed those questions by developing environmental niche models (ENM) for each species and then making pairwise comparisons of niche overlap and relative habitat patch importance among the three species. ENMs were created using sightings from the Azorean Fisheries Observer Program from May to November, between 2004 and 2009, and a set of 18 predictor environmental variables. We then assessed monthly (April-July) overlap among ENMs using a modified Hellinger's distance metric (I). Results show that the habitat niches of blue and fin whales are strongly influenced by primary productivity and sea surface temperature and are highly dynamic both spatially and temporally due to the oceanography of the region. Niche overlap analyses show that blue and fin whale environmental niches are similar and that the suitable habitats for the two species have high degree of spatial coincidence. These results in combination suggest that this habitat may function as a mid-latitude feeding ground to both species while conditions are adequate. The sei whale model, on the other hand, did not include variables considered to be proxies for prey distribution and little environmental niche overlap was found between this species and the other two. We argue that these results suggest that the region holds little importance as a foraging habitat for the sei whale.

Wildlife habitats in managed rangelands—the Great Basin of southeastern Oregon: manmade habitats.

Treesearch

Chris Maser; Jack Ward Thomas; Ira David Luman; Ralph. Anderson

1979-01-01

Manmade structures on rangelands provide specialized habitats for some species. These habitats and how they function as specialized habitat features are examined in this publication. The relationships of the wildlife of the Great Basin to such structures are detailed.

Hydrologic and water-quality rehabilitation of environments for suitable fish habitat

NASA Astrophysics Data System (ADS)

Zhao, C. S.; Yang, S. T.; Xiang, H.; Liu, C. M.; Zhang, H. T.; Yang, Z. L.; Zhang, Y.; Sun, Y.; Mitrovic, S. M.; Yu, Q.; Lim, R. P.

2015-11-01

estimated and graded, and the priority of habitat factors for rehabilitation was determined. Application of the model to Jinan City, a pilot city for the construction of a civilized and ecological city in China, proved effective, revealing that carbonate is the poorest habitat factor and has the highest priority for ecological rehabilitation. This was tested using two methods: alternative priority models and a dataset of all habitat factors in place of only the principal habitat factors. We also found that hydrological factors have higher priority than the water quality factors at the levels of both the whole city and its subordinate eco-regions and therefore that hydrological factors deserve special attention in the future ecosystem rehabilitation. Further, the current habitat state makes nearly half of the habitats in Jinan City undesirable for fish communities, largely due to long-term agricultural practices. Spatially, rivers in the mountainous region south of Jinan city and adjacent to the urban area and rivers in the agricultural region north of the city should be emphasized in future habitat rehabilitation. All of these findings have substantial ramifications for the rehabilitation of aquatic ecosystems in Jinan City as a reference for river ecological remediation in rivers with scarce ecological data worldwide.

Propagule Limitation, Disparate Habitat Quality, and Variation in Phenotypic Selection at a Local Species Range Boundary

PubMed Central

Moore, Kara A.; Stanton, Maureen L.

2014-01-01

Adaptation to novel conditions beyond current range boundaries requires the presence of suitable sites within dispersal range, but may be impeded when emigrants encounter poor habitat and sharply different selection pressures. We investigated fine-scale spatial heterogeneity in ecological dynamics and selection at a local population boundary of the annual plant Gilia tricolor. In two years, we planted G. tricolor seeds in core habitat, margin habitat at the edge of the local range, and exterior habitat in order to measure spatial and temporal variation in habitat quality, opportunity for selection, and selection on phenotypic traits. We found a striking decline in average habitat quality with distance from the population core, yet some migrant seeds were successful in suitable, unoccupied microsites at and beyond the range boundary. Total and direct selection on four out of five measured phenotypic traits varied across habitat zones, as well as between years. Moreover, the margin habitat often exerted unique selection pressures that were not intermediate between core and exterior habitats. This study reveals that a combination of ecological and evolutionary forces, including propagule limitation, variation in habitat quality and spatial heterogeneity in phenotypic selection may reduce opportunities for adaptive range expansion, even across a very local population boundary. PMID:24717472

Detroit River habitat inventory

USGS Publications Warehouse

Manny, Bruce A.

2003-01-01

This inventory complements a previous survey of habitat in Ontario waters of the Detroit River (OMNR,1993). It is a starting point for balanced and sustained use of the river for natural resource conservation and economic development. The objectives of the inventory were to: (1) locate candidate sites for protection and restoration of fish and wildlife habitat in Michigan waters of the Detroit River; (2) describe the ownership and size of each site, as well as its potential for habitat protection and restoration; and (3) subjectively assess the extent to which existing habitat along the river is productive of fish and wildlife and protected from land uses that have degraded or destroyed such habitat.

The Importance of Biologically Relevant Microclimates in Habitat Suitability Assessments

PubMed Central

Varner, Johanna; Dearing, M. Denise

2014-01-01

Predicting habitat suitability under climate change is vital to conserving biodiversity. However, current species distribution models rely on coarse scale climate data, whereas fine scale microclimate data may be necessary to assess habitat suitability and generate predictive models. Here, we evaluate disparities between temperature data at the coarse scale from weather stations versus fine-scale data measured in microhabitats required for a climate-sensitive mammal, the American pika (Ochotona princeps). We collected two years of temperature data in occupied talus habitats predicted to be suitable (high elevation) and unsuitable (low elevation) by the bioclimatic envelope approach. At low elevations, talus surface and interstitial microclimates drastically differed from ambient temperatures measured on-site and at a nearby weather station. Interstitial talus temperatures were frequently decoupled from high ambient temperatures, resulting in instantaneous disparities of over 30°C between these two measurements. Microhabitat temperatures were also highly heterogeneous, such that temperature measurements within the same patch of talus were not more correlated than measurements at distant patches. An experimental manipulation revealed that vegetation cover may cool the talus surface by up to 10°C during the summer, which may contribute to this spatial heterogeneity. Finally, low elevation microclimates were milder and less variable than typical alpine habitat, suggesting that, counter to species distribution model predictions, these seemingly unsuitable habitats may actually be better refugia for this species under climate change. These results highlight the importance of fine-scale microhabitat data in habitat assessments and underscore the notion that some critical refugia may be counterintuitive. PMID:25115894

The importance of biologically relevant microclimates in habitat suitability assessments.

PubMed

Varner, Johanna; Dearing, M Denise

2014-01-01

Predicting habitat suitability under climate change is vital to conserving biodiversity. However, current species distribution models rely on coarse scale climate data, whereas fine scale microclimate data may be necessary to assess habitat suitability and generate predictive models. Here, we evaluate disparities between temperature data at the coarse scale from weather stations versus fine-scale data measured in microhabitats required for a climate-sensitive mammal, the American pika (Ochotona princeps). We collected two years of temperature data in occupied talus habitats predicted to be suitable (high elevation) and unsuitable (low elevation) by the bioclimatic envelope approach. At low elevations, talus surface and interstitial microclimates drastically differed from ambient temperatures measured on-site and at a nearby weather station. Interstitial talus temperatures were frequently decoupled from high ambient temperatures, resulting in instantaneous disparities of over 30 °C between these two measurements. Microhabitat temperatures were also highly heterogeneous, such that temperature measurements within the same patch of talus were not more correlated than measurements at distant patches. An experimental manipulation revealed that vegetation cover may cool the talus surface by up to 10 °C during the summer, which may contribute to this spatial heterogeneity. Finally, low elevation microclimates were milder and less variable than typical alpine habitat, suggesting that, counter to species distribution model predictions, these seemingly unsuitable habitats may actually be better refugia for this species under climate change. These results highlight the importance of fine-scale microhabitat data in habitat assessments and underscore the notion that some critical refugia may be counterintuitive.

Habitat Suitability Index Models: Veery

USGS Publications Warehouse

Sousa, Patrick J.

1982-01-01

Habitat preferences and species characteristics of the veery (Catharus fuscesens) are described in this publication. It is one of a series of Habitat Suitability Index (HSI) models and was developed through an analysis of available scientific data on the habitat requirements of the veery. Habitat use information is presented in a review of the literature, followed by the development of an HSI model. The model is presented in three formats: graphic; word; and mathematical. Suitability index graphs quantify the species-habitat relationship. These data are synthesized into a model designed to provide information for use in impact assessment and habitat management.

Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.

PubMed

Pachov, Dimitar V; van den Bedem, Henry

2015-07-01

Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs) is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key structural

Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs

PubMed Central

Pachov, Dimitar V.; van den Bedem, Henry

2015-01-01

Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs) is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key structural

Habitat Suitability Index Models: Pronghorn

USGS Publications Warehouse

Allen, Arthur W.; Cook, John G.; Armbruster, Michael J.

1984-01-01

This is one of a series of publications that provide information on the habitat requirements of selected fish and wildlife species. Literature describing the relationship between habitat variables related to life requisites and habitat suitability for the pronghorn (Antilocapra americana) are synthesized. These data are subsequently used to develop Habitat Suitability Index (HSI) models. The HSI models are designed to provide information that can be used in impact assessment and habitat management.

Habitat Suitability Index Models: Muskellunge

USGS Publications Warehouse

Cook, Mark F.; Solomon, R. Charles

1987-01-01

A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the muskellunge (Esox masquinongy Mitchell). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

Habitat selection by postbreeding female diving ducks: Influence of habitat attributes and conspecifics

USGS Publications Warehouse

Austin, Jane E.; O'Neil, Shawn T.; Warren, Jeffrey M.

2017-01-01

Habitat selection studies of postbreeding waterfowl have rarely focused on within-wetland attributes such as water depth, escape cover, and food availability. Flightless waterfowl must balance habitat selection between avoiding predation risks and feeding. Reproductively successful female ducks face the greatest challenges because they begin the definitive prebasic molt at or near the end of brood rearing, when their body condition is at a low point. We assessed the relative importance of habitat attributes and group effects in habitat selection by postbreeding female lesser scaup Aythya affinis on a 2332-ha montane wetland complex during the peak flightless period (August) over seven years. Hypothesis-based habitat attributes included percent open water, open water:emergent edge density, water depth, percent flooded bare substrate, fetch (distance wind can travel unobstructed), group size, and several interactions representing functional responses to interannual variation in water levels. Surveys of uniquely marked females were conducted within randomly ordered survey blocks. We fitted two-part generalized linear mixed-effects models to counts of marked females within survey blocks, which allowed us to relate habitat attributes to relative probability of occurrence and, given the presence of a marked female, abundance of marked individuals. Postbreeding female scaup selected areas with water depths > 40 cm, large open areas, and intermediate edge densities but showed no relation to flooded bare substrate, suggesting their habitat preferences were more influenced by avoiding predation risks and disturbances than in meeting foraging needs. Grouping behavior by postbreeding scaup suggests habitat selection is influenced in part by behavioral components and/or social information, conferring energetic and survival benefits (predation and disturbance risks) but potentially also contributing to competition for food resources. This study demonstrates the importance of

Varying congruence among spatial patterns of vascular plants and vertebrates based on habitat groups.

PubMed

Xu, Haigen; Cao, Yun; Cao, Mingchang; Wu, Jun; Wu, Yi; Le, Zhifang; Cui, Peng; Li, Jiaqi; Ma, Fangzhou; Liu, Li; Hu, Feilong; Chen, Mengmeng; Tong, Wenjun

2017-11-01

Proxies are adopted to represent biodiversity patterns due to inadequate information for all taxa. Despite the wide use of proxies, their efficacy remains unclear. Previous analyses focused on overall species richness for fewer groups, affecting the generality and depth of inference. Biological taxa often exhibit very different habitat preferences. Habitat groupings may be an appropriate approach to advancing the study of richness patterns. Diverse geographical patterns of species richness and their potential mechanisms were then examined for habitat groups. We used a database of the spatial distribution of 32,824 species of mammals, birds, reptiles, amphibians and plants from 2,376 counties across China, divided the five taxa into 30 habitat groups, calculated Spearman correlations of species richness among taxa and habitat groups, and tested five hypotheses about richness patterns using multivariate models. We identified one major group [i.e., forest- and shrub-dependent (FS) groups], and some minor groups such as grassland-dependent vertebrates and desert-dependent vertebrates. There were mostly high or moderate correlations among FS groups, but mostly low or moderate correlations among other habitat groups. The prominent variables differed among habitat groups of the same taxon, such as birds and reptiles. The sets of predictors were also different within the same habitat, such as forests, grasslands, and deserts. Average correlations among the same habitat groups of vertebrates and among habitat groups of a single taxon were low or moderate, except correlations among FS groups. The sets of prominent variables of species richness differed strongly among habitat groups, although elevation range was the most important variable for most FS groups. The ecological and evolutionary processes that underpin richness patterns might be disparate among different habitat groups. Appropriate groupings based on habitats could reveal important patterns of richness gradients

Fine-scale planktonic habitat partitioning at a shelf-slope front revealed by a high-resolution imaging system

NASA Astrophysics Data System (ADS)

Greer, Adam T.; Cowen, Robert K.; Guigand, Cedric M.; Hare, Jonathan A.

2015-02-01

Ocean fronts represent productive regions of the ocean, but predator-prey interactions within these features are poorly understood partially due to the coarse-scale and biases of net-based sampling methods. We used the In Situ Ichthyoplankton Imaging System (ISIIS) to sample across a front near the Georges Bank shelf edge on two separate sampling days in August 2010. Salinity characterized the transition from shelf to slope water, with isopycnals sloping vertically, seaward, and shoaling at the thermocline. A frontal feature defined by the convergence of isopycnals and a surface temperature gradient was sampled inshore of the shallowest zone of the shelf-slope front. Zooplankton and larval fishes were abundant on the shelf side of the front and displayed taxon-dependent depth distributions but were rare in the slope waters. Supervised automated particle counting showed small particles with high solidity, verified to be zooplankton (copepods and appendicularians), aggregating near surface above the front. Salps were most abundant in zones of intermediate chlorophyll-a fluorescence, distinctly separate from high abundances of other grazers and found almost exclusively in colonial form (97.5%). Distributions of gelatinous zooplankton differed among taxa but tended to follow isopycnals. Fine-scale sampling revealed distinct habitat partitioning of various planktonic taxa, resulting from a balance of physical and biological drivers in relation to the front.

Tumor invasion unit in gastric cancer revealed by QDs-based in situ molecular imaging and multispectral analysis.

PubMed

Hu, Wen-Qing; Fang, Min; Zhao, Hao-Liang; Yan, Shu-Guang; Yuan, Jing-Ping; Peng, Chun-Wei; Yang, Gui-Fang; Li, Yan; Li, Jian-Ding

2014-04-01

In tumor tissues, cancer cells, tumor infiltrating macrophages and tumor neo-vessels in close spatial vicinity with one another form tumor invasion unit, which is a biologically important tumor microenvironment of metastasis to facilitate cancer invasion and metastasis. Establishing an in situ molecular imaging technology to simultaneously reveal these three components is essential for the in-depth investigation of tumor invasion unit. In this report, we have developed a computer-aided algorithm by quantum dots (QDs)-based multiplexed molecular imaging technique for such purpose. A series of studies on gastric cancer tumor tissues demonstrated that the tumor invasion unit was correlated with major unfavorable pathological features and worse clinical outcomes, which illustrated the significantly negative impacts and predictive power of tumor invasion unit on patient overall survival. This study confirmed the technical advantages of QDs-based in situ and simultaneous molecular imaging of key cancer molecules to gain deeper insights into the biology of cancer invasion. Copyright © 2014 Elsevier Ltd. All rights reserved.

Plausible Martian Habitats

NASA Image and Video Library

2009-10-13

Unfrozen brine in cryopegs and fracture networks provides habitats for the survival and growth of organisms both within and under frozen rocky materials on Earth and, by analogy, could provide habitats on Mars.

Glacial Refugia and Future Habitat Coverage of Selected Dactylorhiza Representatives (Orchidaceae)

PubMed Central

2015-01-01

The intensively discussed taxonomic complexity of the Dactylorhiza genus is probably correlated with its migration history during glaciations and interglacial periods. Previous studies on past processes affecting the current distribution of Dactylorhiza species as well as the history of the polyploid complex formation were based only on molecular data. In the present study the ecological niche modeling (ENM) technique was applied in order to describe the distribution of potential refugia for the selected Dactylorhiza representatives during the Last Glacial Maximum. Additionally, future changes in their potential habitat coverage were measured with regard to three various climatic change scenarios. The maximum entropy method was used to create models of suitable niche distribution. A database of Dactylorhiza localities was prepared on the grounds of information collected from literature and data gathered during field works. Our research indicated that the habitats of majority of the studied taxa will decrease by 2080, except for D. incarnata var. incarnata, for which suitable habitats will increase almost two-fold in the global scale. Moreover, the potential habitats of some taxa are located outside their currently known geographical ranges, e.g. the Aleutian Islands, the western slopes of the Rocky Mountains, Newfoundland, southern Greenland and Iceland. ENM analysis did not confirm that the Balkans, central Europe or central Russia served as the most important refugia for individual representatives of the Dactylorhiza incarnata/maculata complex. Our study rather indicated that the Black Sea coast, southern Apennines and Corsica were the main areas characterized by habitats suitable for most of the taxa. PMID:26599630

Habitat Suitability Index Models: Marten

USGS Publications Warehouse

Allen, Arthur W.

1982-01-01

Habitat preferences and species characteristics of the pine marten (Martes americana) are described in this publication. It is one of a series of Habitat Suitability Index (HSI) models and was developed through an analysis of available scientific data on the species-habitat requirements of the pine marten. Habitat use information is presented in a review of the literature, followed by the development of a HSI model. The model is presented in three formats: graphic, word and mathematical. Suitability index graphs quantify the species-habitat relationship. These data are then synthesized into a model which is designed to provide information for use in impact assessment and habitat management activities.

Assessment of chevron dikes for the enhancement of physical-aquatic habitat within the Middle Mississippi River, USA

NASA Astrophysics Data System (ADS)

Remo, Jonathan W. F.; Khanal, Anish; Pinter, Nicholas

2013-09-01

Blunt-nosed chevron dikes, a new invention now being widely constructed on the Middle Mississippi River (MMR), have been justified as a tool for enhancing physical-aquatic habitat. Chevron dikes were initially designed to concentrate flow, induce channel scour, and thus facilitate river navigation. More recently, these structures have been justified, in part, for promoting habitat heterogeneity. The ability of chevrons to create and diversify physical-aquatic habitat, however, has not been empirically evaluated. To assess the ability of chevrons to create and diversify physical-aquatic habitat, we compiled hydrologic and geospatial data for three channel reference conditions along a 2.0 km (∼140 ha) reach of the MMR where three chevrons were constructed in late 2007. We used the hydrologic and hydraulic data to construct detailed 2-D hydrodynamic models for three reference condition: historic (circa 1890), pre-chevron, and post-chevron channel conditions. These models documented changes in depths and flow dynamics for a wide range of in-channel discharges. Depth-velocity habitat classes were used to assess change in physical-aquatic habitat patches and spatial statistical tools in order to evaluate the reach-scale habitat patch diversity. Comparisons of pre- and post-chevron conditions revealed increases in deep to very deep (>3.0 m) areas of slow moving (<0.6 m/s) water downstream of these structures under emergent flow conditions (⩽1.5 × mean annual flow [MAF]). Chevron construction added up to 7.6 ha of potential over-wintering habitat (deep [>3.0 m], low velocity [<0.6 m/s]). Chevron construction also created some (0.8-3.8 ha) shallow-water habitat (0-1.5 m depth with a 0-0.6 m/s velocity) for flows ⩽2.0 × MAF and contributed to an 8-35% increase in physical-aquatic-habitat diversity compared to pre-chevron channel conditions. However, modeling of the historic reference condition (less engineered channel, circa 1890) revealed that the historical

Landscape habitat suitability index software

Treesearch

William D. Dijak; Chadwick D. Rittenhouse; Michael A. Larson; Frank R. III Thompson; Joshua J. Millspaugh

2007-01-01

Habitat suitability index (HSI) models are traditionally used to evaluate habitat quality for wildlife at a local scale. Rarely have such models incorporated spatial relationships of habitat components. We introduce Landscape HSImodels, a new Microsoft Windowst (Microsoft, Redmond, WA)-based program that incorporates local habitat as well as landscape-scale attributes...

Ecological opportunities, habitat, and past climatic fluctuations influenced the diversification of modern turtles.

PubMed

Rodrigues, João Fabrício Mota; Diniz-Filho, José Alexandre Felizola

2016-08-01

Habitat may be viewed as an important life history component potentially related to diversification patterns. However, differences in diversification rates between aquatic and terrestrial realms are still poorly explored. Testudines is a group distributed worldwide that lives in aquatic and terrestrial environments, but until now no-one has evaluated the diversification history of the group as a whole. We aim here to investigate the diversification history of turtles and to test if habitat influenced speciation rate in these animals. We reconstructed the phylogeny of the modern species of chelonians and estimated node divergence dates using molecular markers and a Bayesian approach. Then, we used Bayesian Analyses of Macroevolutionary Mixtures to evaluate the diversification history of turtles and evaluate the effect of habitat on this pattern. Our reconstructed phylogeny covered 300 species (87% of the total diversity of the group). We found that the emydid subfamily Deirochelyinae, which forms the turtle hotspot in south-eastern United States, had an increase in its speciation rate, and that Galapagos tortoises had similar increases. Current speciation rates are lower in terrestrial turtles, contradicting studies supporting the idea terrestrial animals diversify more than aquatic species. Our results suggest that habitat, ecological opportunities, island invasions, and climatic factors are important drivers of diversification in modern turtles and reinforce the importance of habitat as a diversification driver. Copyright © 2016 Elsevier Inc. All rights reserved.

Effects of regulated river flows on habitat suitability for the robust redhorse

USGS Publications Warehouse

Fisk, J. M.; Kwak, Thomas J.; Heise, R. J.

2015-01-01

The Robust Redhorse Moxostoma robustum is a rare and imperiled fish, with wild populations occurring in three drainages from North Carolina to Georgia. Hydroelectric dams have altered the species’ habitat and restricted its range. An augmented minimum-flow regime that will affect Robust Redhorse habitat was recently prescribed for Blewett Falls Dam, a hydroelectric facility on the Pee Dee River, North Carolina. Our objective was to quantify suitable spawning and nonspawning habitat under current and proposed minimum-flow regimes. We implanted radio transmitters into 27 adult Robust Redhorses and relocated the fish from spring 2008 to summer 2009, and we described habitat at 15 spawning capture locations. Nonspawning habitat consisted of deep, slow-moving pools (mean depth D 2.3 m; mean velocity D 0.23 m/s), bedrock and sand substrates, and boulders or coarse woody debris as cover. Spawning habitat was characterized as shallower, faster-moving water (mean depth D 0.84 m; mean velocity D 0.61 m/s) with gravel and cobble as substrates and boulders as cover associated with shoals. Telemetry relocations revealed two behavioral subgroups: a resident subgroup (linear range [mean § SE] D 7.9 § 3.7 river kilometers [rkm]) that remained near spawning areas in the Piedmont region throughout the year; and a migratory subgroup (linear range D 64.3 § 8.4 rkm) that migrated extensively downstream into the Coastal Plain region. Spawning and nonspawning habitat suitability indices were developed based on field microhabitat measurements and were applied to model suitable available habitat (weighted usable area) for current and proposed augmented minimum flows. Suitable habitat (both spawning and nonspawning) increased for each proposed seasonal minimum flow relative to former minimum flows, with substantial increases for spawning sites. Our results contribute to an understanding of how regulated flows affect available habitats for imperiled species. Flow managers can use these

Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

PubMed

Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

2016-05-01

Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

Classification of pasture habitats by Hungarian herders in a steppe landscape (Hungary)

PubMed Central

2012-01-01

). Conclusions Despite all the difficulties of studying habitat classifications (more implicit, more variable knowledge than knowledge on species), conducting landscape ethnoecological research will inevitably reveal a deeper human understanding of biological organization at a supraspecific level, where natural discontinuities are less sharp than at the species or population level. PMID:22853549

Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions

PubMed Central

Venkateswaran, Kasthuri; La Duc, Myron T.; Horneck, Gerda

2014-01-01

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC’s call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space. PMID:25130881

Tradeoffs between homing and habitat quality for spawning site selection by hatchery-origin Chinook salmon

USGS Publications Warehouse

Cram, Jeremy M.; Torgersen, Christian E.; Klett, Ryan S.; Pess, George R.; May, Darran; Pearsons, Todd N.; Dittman, Andrew H.

2013-01-01

Spawning site selection by female salmon is based on complex and poorly understood tradeoffs between the homing instinct and the availability of appropriate habitat for successful reproduction. Previous studies have shown that hatchery-origin Chinook salmon (Oncorhynchus tshawytscha) released from different acclimation sites return with varying degrees of fidelity to these areas. To investigate the possibility that homing fidelity is associated with aquatic habitat conditions, we quantified physical habitat throughout 165 km in the upper Yakima River basin (Washington, USA) and mapped redd and carcass locations from 2004 to 2008. Principal components analysis identified differences in substrate, cover, stream width, and gradient among reaches surrounding acclimation sites, and canonical correspondence analysis revealed that these differences in habitat characteristics were associated with spatial patterns of spawning (p < 0.01). These analyses indicated that female salmon may forego spawning near their acclimation area if the surrounding habitat is unsuitable. Evaluating the spatial context of acclimation areas in relation to surrounding habitat may provide essential information for effectively managing supplementation programs and prioritizing restoration actions.

The impacts of Cenozoic climate and habitat changes on small mammal diversity of North America

NASA Astrophysics Data System (ADS)

Samuels, Joshua X.; Hopkins, Samantha S. B.

2017-02-01

Through the Cenozoic, paleoclimate records show general trends of global cooling and increased aridity, and environments in North America shifted from predominantly forests to more open habitats. Paleobotanical records indicate grasses were present on the continent in the Eocene; however, paleosol and phytolith studies indicate that open habitats did not arise until the late Eocene or even later in the Oligocene. Studies of large mammalian herbivores have documented changes in ecomorphology and community structure through time, revealing that shifts in mammalian morphology occurred millions of years after the environmental changes thought to have triggered them. Smaller mammals, like rodents and lagomorphs, should more closely track climate and habitat changes due to their shorter generation times and smaller ranges, but these animals have received much less study. To examine changes in smaller mammals through time, we have assembled and analyzed an ecomorphological database of all North American rodent and lagomorph species. Analyses of these data found that rodent and lagomorph community structure changed dramatically through the Cenozoic, and shifts in diversity and ecology correspond closely with the timing of habitat changes. Cenozoic rodent and lagomorph species diversity is strongly biased by sampling of localities, but sampling-corrected diversity reveals diversity dynamics that, after an initial density-dependent diversification in the Eocene, track habitat changes and the appearance of new ecological adaptations. As habitats became more open and arid through time, rodent and lagomorph crown heights increased while burrowing, jumping, and cursorial adaptations became more prevalent. Through time, open-habitat specialists were added during periods of diversification, while closed-habitat taxa were disproportionately lost in subsequent diversity declines. While shifts among rodents and lagomorphs parallel changes in ungulate communities, they started

Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants

NASA Astrophysics Data System (ADS)

Olafsdottir, Thorunn A.; Lindqvist, Madelene; Nookaew, Intawat; Andersen, Peter; Maertzdorf, Jeroen; Persson, Josefine; Christensen, Dennis; Zhang, Yuan; Anderson, Jenna; Khoomrung, Sakda; Sen, Partho; Agger, Else Marie; Coler, Rhea; Carter, Darrick; Meinke, Andreas; Rappuoli, Rino; Kaufmann, Stefan H. E.; Reed, Steven G.; Harandi, Ali M.

2016-12-01

A better understanding of the mechanisms of action of human adjuvants could inform a rational development of next generation vaccines for human use. Here, we exploited a genome wide transcriptomics analysis combined with a systems biology approach to determine the molecular signatures induced by four clinically tested vaccine adjuvants, namely CAF01, IC31, GLA-SE and Alum in mice. We report signature molecules, pathways, gene modules and networks, which are shared by or otherwise exclusive to these clinical-grade adjuvants in whole blood and draining lymph nodes of mice. Intriguingly, co-expression analysis revealed blood gene modules highly enriched for molecules with documented roles in T follicular helper (TFH) and germinal center (GC) responses. We could show that all adjuvants enhanced, although with different magnitude and kinetics, TFH and GC B cell responses in draining lymph nodes. These results represent, to our knowledge, the first comparative systems analysis of clinically tested vaccine adjuvants that may provide new insights into the mechanisms of action of human adjuvants.

Habitat Suitability Index Models: Yellow perch

USGS Publications Warehouse

Krieger, Douglas A.; Terrell, James W.; Nelson, Patrick C.

1983-01-01

A review and synthesis of existing information were used to develop riverine and lacustrine habitat models for yellow perch (Perca flavescens). The models are scaled to produce an index of habitat suitability between 0 (unsuitable habitat) to 1 (optimally suitable habitat) for riverine, lacustrine, and palustrine habitat in the 48 contiguous United States. Habitat Suitability Indexes (HSI's) are designed for use with the Habitat Evaluation Procedures developed by the U.S. Fish and Wildlife Service. Also included are discussions of Suitability Index (SI) curves as used in the Instream Flow Incremental Methodology (IFIM) and SI curves available for an IFIM analysis of yellow perch habitat.

Microbial community pattern detection in human body habitats via ensemble clustering framework.

PubMed

Yang, Peng; Su, Xiaoquan; Ou-Yang, Le; Chua, Hon-Nian; Li, Xiao-Li; Ning, Kang

2014-01-01

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body

Microbial community pattern detection in human body habitats via ensemble clustering framework

PubMed Central

2014-01-01

Background The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. Results To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. Conclusions In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is

Habitat suitability index models: Black crappie

USGS Publications Warehouse

Edwards, Elizabeth A.; Krieger, Douglas A.; Bacteller, Mary; Maughan, O. Eugene

1982-01-01

Characteristics and habitat requirements of the black crappie (Pomoxis nigromaculatus) are described in a review of Habitat Suitability Index models. This is one in a series of publications to provide information on the habitat requirements of selected fish and wildlife species. Numerous literature sources have been consulted in an effort to consolidate scientific data on species-habitat relationships. These data have subsequently been synthesized into explicit Habitat Suitability Index (HSI) models. The models are based on suitability indices indicating habitat preferences. Indices have been formulated for variables found to affect the life cycle and survival of each species. Habitat Suitability Index (HSI) models are designed to provide information for use in impact assessment and habitat management activities. The HSI technique is a corollary to the U.S. Fish and Wildlife Service's Habitat Evaluation Procedures.

Psychosocial Accommodation to Group Confinement in the Advanced Base Habitat

DTIC Science & Technology

1988-06-01

16 Recommendations................................................ 22 Conflict Management ....................................... 22... Conflict Management . Even these brief tests revealed significant potential for interpersonal conflict. Further, crew members stated that the brevity of the...that specific attention be given to conflict management in the Advanced Base Habitat. This may take the form of selection of crew members who have highly

The grass was greener: Repeated evolution of specialized morphologies and habitat shifts in ghost spiders following grassland expansion in South America.

PubMed

Ceccarelli, F Sara; Mongiardino Koch, Nicolás; Soto, Eduardo M; Barone, Mariana L; Arnedo, Miquel A; Ramírez, Martín J

2018-04-14

While grasslands, one of Earth's major biomes, are known for their close evolutionary ties with ungulate grazers, these habitats are also paramount to the origins and diversification of other animals. Within the primarily South American spider subfamily Amaurobioidinae (Anyphaenidae), several species are found living in the continent's grasslands, with some displaying putative morphological adaptations to dwelling unnoticed in the grass blades. Here, a dated molecular phylogeny provides the backbone for analyses revealing the ecological and morphological processes behind these spiders' grassland adaptations. The multiple switches from Patagonian forests to open habitats coincide with the expansion of South America's grasslands during the Miocene, while the specialized morphology of several grass-dwelling spiders originated at least three independent times and is best described as the result of different selective regimes operating on macroevolutionary timescales. Although grass-adapted lineages evolved towards different peaks in adaptive landscape, they all share one characteristic: an anterior narrowing of the prosoma allowing spiders to extend the first two pairs of legs, thus maintaining a slender resting posture in the grass blade. By combining phylogenetic, morphological, and biogeographic perspectives we disentangle multiple factors determining the evolution of a clade of terrestrial invertebrate predators alongside their biomes.

Winter habitat predictions of a key Southern Ocean predator, the Antarctic fur seal (Arctocephalus gazella)

NASA Astrophysics Data System (ADS)

Arthur, Benjamin; Hindell, Mark; Bester, Marthan; De Bruyn, P. J. Nico; Trathan, Phil; Goebel, Michael; Lea, Mary-Anne

2017-06-01

Quantification of the physical and biological environmental factors that influence the spatial distribution of higher trophic species is central to inform management and develop ecosystem models, particularly in light of ocean changes. We used tracking data from 184 female Antarctic fur seals (Arctocephalus gazella) to develop habitat models for three breeding colonies for the poorly studied Southern Ocean winter period. Models were used to identify and predict the broadly important winter foraging habitat and to elucidate the environmental factors influencing these areas. Model predictions closely matched observations and several core areas of foraging habitat were identified for each colony, with notable areas of inter-colony overlap suggesting shared productive foraging grounds. Seals displayed clear choice of foraging habitat, travelling through areas of presumably poorer quality to access habitats that likely offer an energetic advantage in terms of prey intake. The relationships between environmental predictors and foraging habitat varied between colonies, with the principal predictors being wind speed, sea surface temperature, chlorophyll a concentration, bathymetry and distance to the colony. The availability of core foraging areas was not consistent throughout the winter period. The habitat models developed in this study not only reveal the core foraging habitats of Antarctic fur seals from multiple colonies, but can facilitate the hindcasting of historical foraging habitats as well as novel predictions of important habitat for other major colonies currently lacking information of the at-sea distribution of this major Southern Ocean consumer.

Use of non-alpine anthropogenic habitats by American pikas (Ochotona princeps) in western Oregon, USA

USGS Publications Warehouse

Manning, Tom; Hagar, Joan C.

2011-01-01

The American pika (Ochotona princeps Richardson) has long been characterized in field guides and popular literature as an obligate inhabitant of alpine talus and as having relatively low dispersal capability. However, recent work reveals pikas to have broader habitat associations than previously reported. Over a large portion of the western slope of the Cascade Range in Oregon, pikas inhabit relatively low-elevation sites far from alpine areas and frequently occur in rocky man-made habitats such as roadcuts or rock quarries. We present observations of pikas in these previously overlooked habitats and discuss implications for (1) the proposed listing of the American pika as an endangered or threatened species; (2) furthering our understanding of pika population dynamics, habitat associations, and dispersal capabilites; and (3) management of federal, state, and private forest lands.

Spawning distribution of sockeye salmon in a glacially influenced watershed: The importance of glacial habitats

USGS Publications Warehouse

Young, Daniel B.; Woody, C.A.

2007-01-01

The spawning distribution of sockeye salmon Oncorhynchus nerka was compared between clear and glacially turbid habitats in Lake Clark, Alaska, with the use of radiotelemetry. Tracking of 241 adult sockeye salmon to 27 spawning locations revealed both essential habitats and the relationship between spawn timing and seasonal turbidity cycles. Sixty-six percent of radio-tagged sockeye salmon spawned in turbid waters (???5 nephelometric turbidity units) where visual observation was difficult. Spawning in turbid habitats coincided with seasonal temperature declines and associated declines in turbidity and suspended sediment concentration. Because spawn timing is heritable and influenced by temperature, the observed behavior suggests an adaptive response to glacier-fed habitats, as it would reduce embryonic exposure to the adverse effects of fine sediments. ?? Copyright by the American Fisheries Society 2007.

Effects of tide cycles on habitat selection and habitat partitioning by migrating shorebirds

USGS Publications Warehouse

Burger, J.; Howe, M.A.; Hahn, D.C.; Chase, J.

1977-01-01

We studied assemblages of feeding shorebirds in three intertidal habitats on the coast of New Jersey during August to document how species segregate spatially both among and within habitats and to determine the effects of tidal cycles on these patterns. The habitats were a sandy beach facing the ocean proper (outer beach), a sandy beach on the mainland side of a barrier island (inner beach), and a small mudflat adjacent to a Spartina alterniflora salt marsh. We were able to identify several microhabitats on the outer beach and mudflat. Most species fed in more than one habitat, but only two, Charadrius semipalmatus and Calidris canutus, used all three habitats regularly. Within habitats, most species exhibited strong preferences for the wettest areas, but we found differences among species in degrees of preference. The least amount of partitioning occurred on the inner beach, where birds crowded into a small zone near the water's edge and had frequent agonistic encounters suggesting intense competition. Shorebird feeding activity was partly a function of tide time: each habitat had a characteristic temporal pattern of use by shorebirds related to tide time rather than diel time; within habitats, we found species-characteristic feeding activity rhythms that were also a function of tide time. Feeding by most species peaked during the first 2 hours after low tide on the outer beach and mudflat. The results are discussed in terms of feeding strategies and interspecific competition.

Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis.

PubMed

Gao, Yingning; Roberts, Christopher C; Toop, Aaron; Chang, Chia-En A; Wheeldon, Ian

2016-08-03

Understanding and controlling the molecular interactions between enzyme substrates and DNA nanostructures has important implications in the advancement of enzyme-DNA technologies as solutions in biocatalysis. Such hybrid nanostructures can be used to create enzyme systems with enhanced catalysis by controlling the local chemical and physical environments and the spatial organization of enzymes. Here we have used molecular simulations with corresponding experiments to describe a mechanism of enhanced catalysis due to locally increased substrate concentrations. With a series of DNA nanostructures conjugated to horseradish peroxidase, we show that binding interactions between substrates and the DNA structures can increase local substrate concentrations. Increased local substrate concentrations in HRP(DNA) nanostructures resulted in 2.9- and 2.4-fold decreases in the apparent Michaelis constants of tetramethylbenzidine and 4-aminophenol, substrates of HRP with tunable binding interactions to DNA nanostructures with dissociation constants in the micromolar range. Molecular simulations and kinetic analysis also revealed that increased local substrate concentrations enhanced the rates of substrate association. Identification of the mechanism of increased local concentration of substrates in close proximity to enzymes and their active sites adds to our understanding of nanostructured biocatalysis from which we can develop guidelines for enhancing catalysis in rationally designed systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Urban Areas. Habitat Pac.

ERIC Educational Resources Information Center

Fish and Wildlife Service (Dept. of Interior), Washington, DC.

The materials in this educational packet are designed for use with students in grades 4 through 7. They consist of an overview, teaching guides and student data sheets for three activities, and a poster. The overview discusses the city as an ecosystem, changing urban habitats, urban wildlife habitats, values of wildlife, habitat management, and…

Principles of wildlife habitat management

Treesearch

Ernie P. Wiggers

1989-01-01

Simply stated, habitat is where an animal lives and must include all the resources an animal needs to survive and reproduce. An animal's habitat has to provide five essential factors: food, cover, water, space, and interspersion. Habitat management is identifying which factors are scarce enough to limit populations, and then improving the habitat to remove the...

Expandable Lunar Habitat (X-Hab)

NASA Image and Video Library

2010-09-23

Expandable Lunar Habitat (X-Hab).ILC Dover, under contract by NASA Langley Research Center, and in cooperation with NASA Johnson Space Center has designed and manufactured an expandable lunar habitat. This cylindrical habitat, or Expandable Lunar Habitat (X-Hab) is a hybrid system with two hard end caps and a deployable softgoods section in the center.

Geographic, Anthropogenic and Habitat Influences on Great Lakes Coastal Wetland Fish Assemblages

EPA Science Inventory

We analyzed data from coastal wetlands across all five Laurentian Great Lakes to identify patterns in fish assemblages and relationships to local habitat, watershed condition, and regional setting. NMDS ordination of electrofishing catch-per-effort data revealed an overriding ge...

ESTUARINE HABITAT RESTORATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thom, Ronald M.; Borde, Amy B.

2015-09-01

Restoring estuarine habitats generally means repairing damages caused by humans and natural forces. Because of the extensive human occupation, development, and use of coastal areas for centuries, the extensive estuarine habitats have been either destroyed or significantly impaired.

Self-recognition in corals facilitates deep-sea habitat engineering

USGS Publications Warehouse

Hennige, Sebastian J; Morrison, Cheryl L.; Form, Armin U.; Buscher, Janina; Kamenos, Nicholas A.; Roberts, J. Murray

2014-01-01

The ability of coral reefs to engineer complex three-dimensional habitats is central to their success and the rich biodiversity they support. In tropical reefs, encrusting coralline algae bind together substrates and dead coral framework to make continuous reef structures, but beyond the photic zone, the cold-water coral Lophelia pertusa also forms large biogenic reefs, facilitated by skeletal fusion. Skeletal fusion in tropical corals can occur in closely related or juvenile individuals as a result of non-aggressive skeletal overgrowth or allogeneic tissue fusion, but contact reactions in many species result in mortality if there is no ‘self-recognition’ on a broad species level. This study reveals areas of ‘flawless’ skeletal fusion in Lophelia pertusa, potentially facilitated by allogeneic tissue fusion, are identified as having small aragonitic crystals or low levels of crystal organisation, and strong molecular bonding. Regardless of the mechanism, the recognition of ‘self’ between adjacent L. pertusa colonies leads to no observable mortality, facilitates ecosystem engineering and reduces aggression-related energetic expenditure in an environment where energy conservation is crucial. The potential for self-recognition at a species level, and subsequent skeletal fusion in framework-forming cold-water corals is an important first step in understanding their significance as ecological engineers in deep-seas worldwide.

Long-term habitat changes in a protected area: Implications for herpetofauna habitat management and restoration.

PubMed

Markle, Chantel E; Chow-Fraser, Gillian; Chow-Fraser, Patricia

2018-01-01

Point Pelee National Park, located at the southern-most tip of Canada's mainland, historically supported a large number of herpetofauna species; however, despite nearly a century of protection, six snake and five amphibian species have disappeared, and remaining species-at-risk populations are thought to be in decline. We hypothesized that long-term changes in availability and distribution of critical habitat types may have contributed to the disappearance of herpetofauna. To track habitat changes we used aerial image data spanning 85 years (1931-2015) and manually digitized and classified image data using a standardized framework. Change-detection analyses were used to evaluate the relative importance of proportionate loss and fragmentation of 17 habitat types. Marsh habitat diversity and aquatic connectivity has declined since 1931. The marsh matrix transitioned from a graminoid and forb shallow marsh interspersed with water to a cattail dominated marsh, altering critical breeding, foraging, and overwintering habitat. Reduced diversity of marsh habitats appears to be linked to the expansion of invasive Phragmites australis, which invaded prior to 2000. Loss of open habitats such as savanna and meadow has reduced availability of high quality thermoregulation habitat for reptiles. Restoration of the northwestern region and tip of Point Pelee National Park to a mixed landscape of shallow wetlands (cattail, graminoid, forb, open water) and eradication of dense Phragmites stands should improve habitat diversity. Our results suggest that long-term landscape changes resulting from habitat succession and invasive species can negatively affect habitat suitability for herpetofauna and protection of land alone does not necessarily equate to protection of sensitive herpetofauna.

Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C

PubMed Central

Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Guerra-Peraza, Orlene; Breton, Michèle Claire; Arena, Gabriella Dias; Nunes, Maria Andreia; Kitajima, Elliot Watanabe; Machado, Marcos Antonio; Freitas-Astúa, Juliana

2016-01-01

Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2–IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5′-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies. PMID:27275832

Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis.

PubMed

Wijnrocx, K; François, L; Stinckens, A; Janssens, S; Buys, N

2016-10-01

The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity. © 2016 Blackwell Verlag GmbH.

Benefits and shortcomings of non-destructive benthic imagery for monitoring hard-bottom habitats.

PubMed

Beisiegel, Kolja; Darr, Alexander; Gogina, Mayya; Zettler, Michael L

2017-08-15

Hard-bottom habitats with complex topography and fragile epibenthic communities are still not adequately considered in benthic monitoring programs, despite their potential ecological importance. While indicators of ecosystem health are defined by major EU directives, methods commonly used to measure them are deficient in quantification of biota on hard surfaces. We address the suitability of seafloor imaging for monitoring activities. We compared the ability of high-resolution imagery and physical sampling methods (grab, dredge, SCUBA-diving) to detect taxonomic and functional components of epibenthos. Results reveal that (1) with minimal habitat disturbance on large spatial scales, imagery provides valuable, cost-effective assessment of rocky reef habitat features and community structure, (2) despite poor taxonomic resolution, image-derived data for habitat-forming taxa might be sufficient to infer richness of small sessile and mobile fauna, (3) physical collections are necessary to develop a robust record of species richness, including species-level taxonomic identifications, and to establish a baseline. Copyright © 2017. Published by Elsevier Ltd.

Habitat selection by two beluga whale populations in the Chukchi and Beaufort seas.

PubMed

Hauser, Donna D W; Laidre, Kristin L; Stern, Harry L; Moore, Sue E; Suydam, Robert S; Richard, Pierre R

2017-01-01

There has been extensive sea ice loss in the Chukchi and Beaufort seas where two beluga whale (Delphinapterus leucas) populations occur between July-November. Our goal was to develop population-specific beluga habitat selection models that quantify relative use of sea ice and bathymetric features related to oceanographic processes, which can provide context to the importance of changing sea ice conditions. We established habitat selection models that incorporated daily sea ice measures (sea ice concentration, proximity to ice edge and dense ice) and bathymetric features (slope, depth, proximity to the continental slope, Barrow Canyon, and shore) to establish quantitative estimates of habitat use for the Eastern Chukchi Sea ('Chukchi') and Eastern Beaufort Sea ('Beaufort') populations. We applied 'used v. available' resource selection functions to locations of 65 whales tagged from 1993-2012, revealing large variations in seasonal habitat selection that were distinct between sex and population groups. Chukchi whales of both sexes were predicted to use areas in close proximity to Barrow Canyon (typically <200 km) as well as the continental slope in summer, although deeper water and denser ice were stronger predictors for males than females. Habitat selection differed more between sexes for Beaufort belugas. Beaufort males selected higher ice concentrations (≥40%) than females (0-40%) in July-August. Proximity to shore (<200 km) strongly predicted summer habitat of Beaufort females, while distance to the ice edge was important for male habitat selection, especially during westward migration in September. Overall, our results indicate that sea ice variables were rarely the primary drivers of beluga summer-fall habitat selection. While diminished sea ice may indirectly affect belugas through changes in the ecosystem, associations with bathymetric features that affect prey availability seemed key to habitat selection during summer and fall. These results provide a

75 FR 34975 - Notice of Estuary Habitat Restoration Council's Intent to Revise its Estuary Habitat Restoration...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-21

... Estuary Habitat Restoration Council's Intent to Revise its Estuary Habitat Restoration Strategy; Request... interagency Estuary Habitat Restoration Council, is providing notice of the Council's intent to revise the ''Estuary Habitat Restoration Strategy'' and requesting public comments to guide its revision. DATES...

Vacant habitats in the Universe.

PubMed

Cockell, Charles S

2011-02-01

The search for life on other planets usually makes the assumption that where there is a habitat, it will contain life. On the present-day Earth, uninhabited habitats (or vacant habitats) are rare, but might occur, for example, in subsurface oils or impact craters that have been thermally sterilized in the past. Beyond Earth, vacant habitats might similarly exist on inhabited planets or on uninhabited planets, for example on a habitable planet where life never originated. The hypothesis that vacant habitats are abundant in the Universe is testable by studying other planets. In this review, I discuss how the study of vacant habitats might ultimately inform an understanding of how life has influenced geochemical conditions on Earth. Copyright © 2010 Elsevier Ltd. All rights reserved.

Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations

PubMed Central

Grouleff, Julie; Schiøtt, Birgit

2013-01-01

The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432

No net loss of fish habitat: a review and analysis of habitat compensation in Canada.

PubMed

Harper, D J; Quigley, J T

2005-09-01

The achievement of No Net Loss (NNL) through habitat compensation has rarely been assessed in Canada. Files relating to 124 Fisheries Act Section 35(2) authorizations issued by Fisheries and Oceans Canada for the harmful alteration, disruption, and destruction of fish habitat (HADD) were collected and reviewed. Data extracted from these files were pooled and analyzed to provide an indication of the types of HADDs that have been authorized in Canada, what habitats have been affected, and what habitat management approaches have been used when compensating for HADDs and monitoring and ensuring the success of the compensation. Determinations regarding the effectiveness of habitat compensation in achieving NNL were made. Impacts to 419,562 m2 of fish habitat from the 124 authorized HADDs were offset by 1,020,388 m2 of compensatory habitat. Eighty percent of the authorizations had compensation ratios (compensation area:HADD area) of 2:1 or less, and 25% of the authorizations had a compensation ratio that was less than 1:1. In-channel and riparian habitat were the most frequently impacted habitats. Urban development and roads and highways resulted in the greatest areal loss of habitat. The compensation option that was most often selected was the creation of in-kind habitat. The mean duration of post-construction monitoring programs was 3.7 years. Determinations of NNL could only be made for 17 authorizations as a result of poor proponent compliance with monitoring requirements and the qualitative assessment procedures used by the monitoring programs. Adequate resources, proper training, and standardized approaches to data management and monitoring programs are required to ensure that the conservation goal of NNL can be achieved in Canada.

Long-term habitat changes in a protected area: Implications for herpetofauna habitat management and restoration

PubMed Central

Chow-Fraser, Gillian; Chow-Fraser, Patricia

2018-01-01

Point Pelee National Park, located at the southern-most tip of Canada’s mainland, historically supported a large number of herpetofauna species; however, despite nearly a century of protection, six snake and five amphibian species have disappeared, and remaining species-at-risk populations are thought to be in decline. We hypothesized that long-term changes in availability and distribution of critical habitat types may have contributed to the disappearance of herpetofauna. To track habitat changes we used aerial image data spanning 85 years (1931–2015) and manually digitized and classified image data using a standardized framework. Change-detection analyses were used to evaluate the relative importance of proportionate loss and fragmentation of 17 habitat types. Marsh habitat diversity and aquatic connectivity has declined since 1931. The marsh matrix transitioned from a graminoid and forb shallow marsh interspersed with water to a cattail dominated marsh, altering critical breeding, foraging, and overwintering habitat. Reduced diversity of marsh habitats appears to be linked to the expansion of invasive Phragmites australis, which invaded prior to 2000. Loss of open habitats such as savanna and meadow has reduced availability of high quality thermoregulation habitat for reptiles. Restoration of the northwestern region and tip of Point Pelee National Park to a mixed landscape of shallow wetlands (cattail, graminoid, forb, open water) and eradication of dense Phragmites stands should improve habitat diversity. Our results suggest that long-term landscape changes resulting from habitat succession and invasive species can negatively affect habitat suitability for herpetofauna and protection of land alone does not necessarily equate to protection of sensitive herpetofauna. PMID:29444129

Quantifying home range habitat requirements for bobcats (Lynx rufus) in Vermont, USA

USGS Publications Warehouse

Donovan, T.M.; Freeman, M.; Abouelezz, H.; Royar, Kim; Howard, A.; Mickey, R.

2011-01-01

We demonstrate how home range and habitat use analysis can inform landscape-scale conservation planning for the bobcat, Lynx rufus, in Vermont USA. From 2005 to 2008, we outfitted fourteen bobcats with GPS collars that collected spatially explicit locations from individuals every 4. h for 3-4. months. Kernel home range techniques were used to estimate home range size and boundaries, and to quantify the utilization distribution (UD), which is a spatially explicit, topographic mapping of how different areas within the home range are used. We then used GIS methods to quantify both biotic (e.g. habitat types, stream density) and abiotic (e.g. slope) resources within each bobcat's home range. Across bobcats, upper 20th UD percentiles (core areas) had 18% less agriculture, 42% less development, 26% more bobcat habitat (shrub, deciduous, coniferous forest, and wetland cover types), and 33% lower road density than lower UD percentiles (UD valleys). For each bobcat, we used Akaike's Information Criterion (AIC) to evaluate and compare 24 alternative Resource Utilization Functions (hypotheses) that could explain the topology of the individual's UD. A model-averaged population-level Resource Utilization Function suggested positive responses to shrub, deciduous, coniferous forest, and wetland cover types within 1. km of a location, and negative responses to roads and mixed forest cover types within 1. km of a location. Applying this model-averaged function to each pixel in the study area revealed habitat suitability for bobcats across the entire study area, with suitability scores ranging between -1.69 and 1.44, where higher values were assumed to represent higher quality habitat. The southern Champlain Valley, which contained ample wetland and shrub habitat, was a concentrated area of highly suitable habitat, while areas at higher elevation areas were less suitable. Female bobcat home ranges, on average, had an average habitat suitability score of near 0, indicating that home

Desired future condition: Fish habitat in southwestern riparian-stream habitats

Treesearch

John N. Rinne

1996-01-01

Riparian ecosystems in the southwestern United States provide valuable habitats for many living organisms including native fishes. An analysis of habitat components important to native fishes was made based on the literature, case histories, and unpublished and observational data. Results suggest a natural, surface water hydrograph and lack of introduced species of...

Assessing critical habitat: Evaluating the relative contribution of habitats to population

EPA Science Inventory

A principal challenge of species conservation is to identify the specific habitats that are essential for long-term persistence or recovery of imperiled species. However, many approaches to identifying important habitats do not provide direct insight into the contribution of hab...

Migratory bird habitat in relation to tile drainage and poorly drained hydrologic soil groups

USGS Publications Warehouse

Kastner, Brandi; Christensen, Victoria G.; Williamson, Tanja N.; Sanocki, Chris A.

2016-01-01

The Prairie Pothole Region (PPR) is home to more than 50% of the migratory waterfowl in North America. Although the PPR provides an abundance of temporary and permanent wetlands for nesting and feeding, increases in commodity prices and agricultural drainage practices have led to a trend of wetland drainage. The Northern Shoveler is a migratory dabbling duck species that uses wetland habitats and cultivated croplands in the PPR. Richland County in North Dakota and Roberts County in South Dakota have an abundance of wetlands and croplands and were chosen as the study areas for this research to assess the wetland size and cultivated cropland in relation to hydrologic soil groups for the Northern Shoveler habitat. This study used geographic information system data to analyze Northern Shoveler habitats in association with Natural Resource Conservation Service soil data. Habitats, which are spatially associated with certain hydrologic soil groups, may be at risk of artificial drainage installations because of their proximity to cultivated croplands and soil lacking in natural drainage that may become wet or inundated. Findings indicate that most wetlands that are part of Northern Shoveler habitats were within or adjacent to cultivated croplands. The results also revealed soil hydrologic groups with high runoff potential and low water transmission rates account for most of the soil within the Northern Shoveler‘s wetland and cropland habitats. Habitats near agriculture with high runoff potential are likely to be drained and this has the potential of reducing Northern Shoveler habitat.

The Habitat Project

ERIC Educational Resources Information Center

Hein, Annamae J.

2011-01-01

The Habitat Project is a multiday, differentiated, interdisciplinary environmental science lesson that incorporates skill-building and motivational strategies to internalize ecosystem vocabulary. Middle school students research an animal, display its physical characteristics on a poster, build a three-dimensional habitat and present their work…

Changing land use and its impact on the habitat suitability for wintering Anseriformes in China's Poyang Lake region.

PubMed

Tang, Xuguang; Li, Hengpeng; Xu, Xibao; Yang, Guishan; Liu, Guihua; Li, Xinyan; Chen, Dongqiang

2016-07-01

As an internationally important wetland for migratory waterbirds, China's Poyang Lake region has experienced substantial changes in land use during the past two decades owing to climate change and anthropogenic disturbances. Recent dam constructions on the Yangtze River and its tributaries for agriculture and hydroelectric power exert strong effects on the hydrological regimes of this lake. However, few studies have investigated how the land-use changes through time affect the habitat suitability for wintering Anseriformes-the largest community in this region. Thus, it is necessary to timely monitor changes in the habitat quality and understand the potential factors that alter it. In this study, three periods (1995, 2005 and 2014) of typical environmental indicators that have direct impacts on foraging and resting for the Anserformes, including proximity to water (density of lakes, rivers and ponds), human disturbances (density of residences and various road networks), preferred land cover types and food availability (NDVI), are integrated to develop a habitat suitability index model for habitat mapping. The results indicate that long-term lake shrinkage in low-water periods led to greatly expanded wetlands in these years, which provided more suitable habitat for migratory waterfowl. The amount of highly suitable habitat in 2014 was nearly twice as much as in 1995. Recent survey data from 1997 to 2013 also revealed an increase in the population size, and confirmed the improvement of habitat suitability in the Poyang Lake region. Spatial analysis revealed that land use changes contributed most to the improved habitat coverage between 1995 and 2014. However, the relative significances of these transformations for highly suitable and moderately suitable habitats are strikingly different. Increases in wetland and paddy field area are the main reasons for explaining these improvements, respectively. The framework model proposed in this study will help governments to

Habitat Suitability Index Models: Laughing gull

USGS Publications Warehouse

Zale, Alexander V.; Mulholland, Rosemarie

1985-01-01

A review and synthesis of existing information were used to develop a habitat model for laughing gull (Larus atricilla). The model is scaled to produce an index of habitat suitability between 0 (unsuitable habitat) and 1.0 (optimally suitable habitat) for areas along the Gulf of Mexico coast. Habitat suitability indices are designed for use with the Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service. Guidelines for application of the model and techniques for measuring model variables are described.

Inferring Evolution of Habitat Usage and Body Size in Endangered, Seasonal Cynopoeciline Killifishes from the South American Atlantic Forest through an Integrative Approach (Cyprinodontiformes: Rivulidae)

PubMed Central

Costa, Wilson J. E. M.

2016-01-01

Cynopoecilines comprise a diversified clade of small killifishes occurring in the Atlantic Forest, one of the most endangered biodiversity hotspots in the world. They are found in temporary pools of savannah-like and dense forest habitats, and most of them are highly threatened with extinction if not already extinct. The greatest gap in our knowledge of cynopoecilines stems from the absence of an integrative approach incorporating molecular phylogenetic data of species still found in their habitats with phylogenetic data taken from the rare and possibly extinct species without accessible molecular information. An integrative analysis combining 115 morphological characters with a multigene dataset of 2,108 bp comprising three nuclear loci (GLYT1, ENC1, Rho), provided a robust phylogeny of cynopoeciline killifishes, which was herein used to attain an accurate phylogenetic placement of nearly extinct species. The analysis indicates that the most recent common ancestor of the Cynopoecilini lived in open vegetation habitats of the Atlantic Forest of eastern Brazil and was a miniature species, reaching between 25 and 28 mm of standard length. The rare cases of cynopoecilines specialized in inhabiting pools within dense forests are interpreted as derived from four independent evolutionary events. Shifts in habitat usage and biogeographic patterns are tentatively associated to Cenozoic paleogeographic events, but the evolutionary history of cynopoecilines may be partially lost by a combination of poor past sampling and recent habitat decline. A sharp evolutionary shift directed to increased body size in a clade encompassing the genera Campellolebias and Cynopoecilus may be related to a parallel acquisition of an internally-fertilizing reproductive strategy, unique among aplocheiloid killifishes. This study reinforces the importance of adding morphological information to molecular databases as a tool to understand the biological complexity of organisms under intense

Inferring Evolution of Habitat Usage and Body Size in Endangered, Seasonal Cynopoeciline Killifishes from the South American Atlantic Forest through an Integrative Approach (Cyprinodontiformes: Rivulidae).

PubMed

Costa, Wilson J E M

2016-01-01

Cynopoecilines comprise a diversified clade of small killifishes occurring in the Atlantic Forest, one of the most endangered biodiversity hotspots in the world. They are found in temporary pools of savannah-like and dense forest habitats, and most of them are highly threatened with extinction if not already extinct. The greatest gap in our knowledge of cynopoecilines stems from the absence of an integrative approach incorporating molecular phylogenetic data of species still found in their habitats with phylogenetic data taken from the rare and possibly extinct species without accessible molecular information. An integrative analysis combining 115 morphological characters with a multigene dataset of 2,108 bp comprising three nuclear loci (GLYT1, ENC1, Rho), provided a robust phylogeny of cynopoeciline killifishes, which was herein used to attain an accurate phylogenetic placement of nearly extinct species. The analysis indicates that the most recent common ancestor of the Cynopoecilini lived in open vegetation habitats of the Atlantic Forest of eastern Brazil and was a miniature species, reaching between 25 and 28 mm of standard length. The rare cases of cynopoecilines specialized in inhabiting pools within dense forests are interpreted as derived from four independent evolutionary events. Shifts in habitat usage and biogeographic patterns are tentatively associated to Cenozoic paleogeographic events, but the evolutionary history of cynopoecilines may be partially lost by a combination of poor past sampling and recent habitat decline. A sharp evolutionary shift directed to increased body size in a clade encompassing the genera Campellolebias and Cynopoecilus may be related to a parallel acquisition of an internally-fertilizing reproductive strategy, unique among aplocheiloid killifishes. This study reinforces the importance of adding morphological information to molecular databases as a tool to understand the biological complexity of organisms under intense

Determining habitat quality for species that demonstrate dynamic habitat selection

USGS Publications Warehouse

Beerens, James M.; Frederick, Peter C; Noonburg, Erik G; Gawlik, Dale E.

2015-01-01

Determining habitat quality for wildlife populations requires relating a species' habitat to its survival and reproduction. Within a season, species occurrence and density can be disconnected from measures of habitat quality when resources are highly seasonal, unpredictable over time, and patchy. Here we establish an explicit link among dynamic selection of changing resources, spatio-temporal species distributions, and fitness for predictive abundance and occurrence models that are used for short-term water management and long-term restoration planning. We used the wading bird distribution and evaluation models (WADEM) that estimate (1) daily changes in selection across resource gradients, (2) landscape abundance of flocks and individuals, (3) conspecific foraging aggregation, and (4) resource unit occurrence (at fixed 400 m cells) to quantify habitat quality and its consequences on reproduction for wetland indicator species. We linked maximum annual numbers of nests detected across the study area and nesting success of Great Egrets (Ardea alba), White Ibises (Eudocimus albus), and Wood Storks (Mycteria americana) over a 20-year period to estimated daily dynamics of food resources produced by WADEM over a 7490 km2 area. For all species, increases in predicted species abundance in March and high abundance in April were strongly linked to breeding responses. Great Egret nesting effort and success were higher when birds also showed greater conspecific foraging aggregation. Synthesis and applications: This study provides the first empirical evidence that dynamic habitat selection processes and distributions of wading birds over environmental gradients are linked with reproductive measures over periods of decades. Further, predictor variables at a variety of temporal (daily-multiannual) resolutions and spatial (400 m to regional) scales effectively explained variation in ecological processes that change habitat quality. The process used here allows managers to develop

Naturally acidified habitat selects for ocean acidification–tolerant mussels

PubMed Central

Thomsen, Jörn; Stapp, Laura S.; Haynert, Kristin; Schade, Hanna; Danelli, Maria; Lannig, Gisela; Wegner, K. Mathias; Melzner, Frank

2017-01-01

Ocean acidification severely affects bivalves, especially their larval stages. Consequently, the fate of this ecologically and economically important group depends on the capacity and rate of evolutionary adaptation to altered ocean carbonate chemistry. We document successful settlement of wild mussel larvae (Mytilus edulis) in a periodically CO2-enriched habitat. The larval fitness of the population originating from the CO2-enriched habitat was compared to the response of a population from a nonenriched habitat in a common garden experiment. The high CO2–adapted population showed higher fitness under elevated Pco2 (partial pressure of CO2) than the non-adapted cohort, demonstrating, for the first time, an evolutionary response of a natural mussel population to ocean acidification. To assess the rate of adaptation, we performed a selection experiment over three generations. CO2 tolerance differed substantially between the families within the F1 generation, and survival was drastically decreased in the highest, yet realistic, Pco2 treatment. Selection of CO2-tolerant F1 animals resulted in higher calcification performance of F2 larvae during early shell formation but did not improve overall survival. Our results thus reveal significant short-term selective responses of traits directly affected by ocean acidification and long-term adaptation potential in a key bivalve species. Because immediate response to selection did not directly translate into increased fitness, multigenerational studies need to take into consideration the multivariate nature of selection acting in natural habitats. Combinations of short-term selection with long-term adaptation in populations from CO2-enriched versus nonenriched natural habitats represent promising approaches for estimating adaptive potential of organisms facing global change. PMID:28508039

Naturally acidified habitat selects for ocean acidification-tolerant mussels.

PubMed

Thomsen, Jörn; Stapp, Laura S; Haynert, Kristin; Schade, Hanna; Danelli, Maria; Lannig, Gisela; Wegner, K Mathias; Melzner, Frank

2017-04-01

Ocean acidification severely affects bivalves, especially their larval stages. Consequently, the fate of this ecologically and economically important group depends on the capacity and rate of evolutionary adaptation to altered ocean carbonate chemistry. We document successful settlement of wild mussel larvae ( Mytilus edulis ) in a periodically CO 2 -enriched habitat. The larval fitness of the population originating from the CO 2 -enriched habitat was compared to the response of a population from a nonenriched habitat in a common garden experiment. The high CO 2 -adapted population showed higher fitness under elevated P co 2 (partial pressure of CO 2 ) than the non-adapted cohort, demonstrating, for the first time, an evolutionary response of a natural mussel population to ocean acidification. To assess the rate of adaptation, we performed a selection experiment over three generations. CO 2 tolerance differed substantially between the families within the F 1 generation, and survival was drastically decreased in the highest, yet realistic, P co 2 treatment. Selection of CO 2 -tolerant F 1 animals resulted in higher calcification performance of F 2 larvae during early shell formation but did not improve overall survival. Our results thus reveal significant short-term selective responses of traits directly affected by ocean acidification and long-term adaptation potential in a key bivalve species. Because immediate response to selection did not directly translate into increased fitness, multigenerational studies need to take into consideration the multivariate nature of selection acting in natural habitats. Combinations of short-term selection with long-term adaptation in populations from CO 2 -enriched versus nonenriched natural habitats represent promising approaches for estimating adaptive potential of organisms facing global change.

Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy

PubMed Central

Gibbons, Don L.; Pricl, Sabrina; Posocco, Paola; Laurini, Erik; Fermeglia, Maurizio; Sun, Hanshi; Talpaz, Moshe; Donato, Nicholas; Quintás-Cardama, Alfonso

2014-01-01

The acquisition of mutations within the BCR-ABL1 kinase domain is frequently associated with tyrosine kinase inhibitor (TKI) failure in chronic myeloid leukemia. Sensitive sequencing techniques have revealed a high prevalence of compound BCR-ABL1 mutations (polymutants) in patients failing TKI therapy. To investigate the molecular consequences of such complex mutant proteins with regards to TKI resistance, we determined by cloning techniques the presence of polymutants in a cohort of chronic-phase patients receiving imatinib followed by dasatinib therapy. The analysis revealed a high frequency of polymutant BCR-ABL1 alleles even after failure of frontline imatinib, and also the progressive exhaustion of the pool of unmutated BCR-ABL1 alleles over the course of sequential TKI therapy. Molecular dynamics analyses of the most frequent polymutants in complex with TKIs revealed the basis of TKI resistance. Modeling of BCR-ABL1 in complex with the potent pan-BCR-ABL1 TKI ponatinib highlighted potentially effective therapeutic strategies for patients carrying these recalcitrant and complex BCR-ABL1 mutant proteins while unveiling unique mechanisms of escape to ponatinib therapy. PMID:24550512

Habitat quality influences population distribution, individual space use and functional responses in habitat selection by a large herbivore.

PubMed

Bjørneraas, Kari; Herfindal, Ivar; Solberg, Erling Johan; Sæther, Bernt-Erik; van Moorter, Bram; Rolandsen, Christer Moe

2012-01-01

Identifying factors shaping variation in resource selection is central for our understanding of the behaviour and distribution of animals. We examined summer habitat selection and space use by 108 Global Positioning System (GPS)-collared moose in Norway in relation to sex, reproductive status, habitat quality, and availability. Moose selected habitat types based on a combination of forage quality and availability of suitable habitat types. Selection of protective cover was strongest for reproducing females, likely reflecting the need to protect young. Males showed strong selection for habitat types with high quality forage, possibly due to higher energy requirements. Selection for preferred habitat types providing food and cover was a positive function of their availability within home ranges (i.e. not proportional use) indicating functional response in habitat selection. This relationship was not found for unproductive habitat types. Moreover, home ranges with high cover of unproductive habitat types were larger, and smaller home ranges contained higher proportions of the most preferred habitat type. The distribution of moose within the study area was partly related to the distribution of different habitat types. Our study shows how distribution and availability of habitat types providing cover and high-quality food shape ungulate habitat selection and space use.

Satellite tracking reveals habitat use by juvenile green sea turtles Chelonia mydas in the Everglades, Florida, USA

USGS Publications Warehouse

Hart, Kristen M.; Fujisaki, Ikuko

2010-01-01

We tracked the movements of 6 juvenile green sea turtles captured in coastal areas of southwest Florida within Everglades National Park (ENP) using satellite transmitters for periods of 27 to 62 d in 2007 and 2008 (mean ± SD: 47.7 ± 12.9 d). Turtles ranged in size from 33.4 to 67.5 cm straight carapace length (45.7 ± 12.9 cm) and 4.4 to 40.8 kg in mass (16.0 ± 13.8 kg). These data represent the first satellite tracking data gathered on juveniles of this endangered species at this remote study site, which may represent an important developmental habitat and foraging ground. Satellite tracking results suggested that these immature turtles were resident for several months very close to capture and release sites, in waters from 0 to 10 m in depth. Mean home range for this springtime tracking period as represented by minimum convex polygon (MCP) was 1004.9 ± 618.8 km2 (range 374.1 to 2060.1 km2), with 4 of 6 individuals spending a significant proportion of time within the ENP boundaries in 2008 in areas with dense patches of marine algae. Core use areas determined by 50% kernel density estimates (KDE) ranged from 5.0 to 54.4 km2, with a mean of 22.5 ± 22.1 km2. Overlap of 50% KDE plots for 6 turtles confirmed use of shallow-water nearshore habitats =0.6 m deep within the park boundary. Delineating specific habitats used by juvenile green turtles in this and other remote coastal areas with protected status will help conservation managers to prioritize their efforts and increase efficacy in protecting endangered species.

Ammonite habitat revealed via isotopic composition and comparisons with co-occurring benthic and planktonic organisms

NASA Astrophysics Data System (ADS)

Sessa, Jocelyn Anne; Larina, Ekaterina; Knoll, Katja; Garb, Matthew; Cochran, J. Kirk; Huber, Brian T.; MacLeod, Kenneth G.; Landman, Neil H.

2015-12-01

Ammonites are among the best-known fossils of the Phanerozoic, yet their habitat is poorly understood. Three common ammonite families (Baculitidae, Scaphitidae, and Sphenodiscidae) co-occur with well-preserved planktonic and benthic organisms at the type locality of the upper Maastrichtian Owl Creek Formation, offering an excellent opportunity to constrain their depth habitats through isotopic comparisons among taxa. Based on sedimentary evidence and the micro- and macrofauna at this site, we infer that the 9-m-thick sequence was deposited at a paleodepth of 70-150 m. Taxa present throughout the sequence include a diverse assemblage of ammonites, bivalves, and gastropods, abundant benthic foraminifera, and rare planktonic foraminifera. No stratigraphic trends are observed in the isotopic data of any taxon, and thus all of the data from each taxon are considered as replicates. Oxygen isotope-based temperature estimates from the baculites and scaphites overlap with those of the benthos and are distinct from those of the plankton. In contrast, sphenodiscid temperature estimates span a range that includes estimates of the planktonic foraminifera and of the warmer half of the benthic values. These results suggest baculites and scaphites lived close to the seafloor, whereas sphenodiscids sometimes inhabited the upper water column and/or lived closer to shore. In fact, the rarity and poorer preservation of the sphenodiscids relative to the baculites and scaphites suggests that the sphenodiscid shells may have only reached the Owl Creek locality by drifting seaward after death.

Omics approaches on fresh-cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment.

PubMed

Daddiego, Loretta; Bianco, Linda; Capodicasa, Cristina; Carbone, Fabrizio; Dalmastri, Claudia; Daroda, Lorenza; Del Fiore, Antonella; De Rossi, Patrizia; Di Carli, Mariasole; Donini, Marcello; Lopez, Loredana; Mengoni, Alessio; Paganin, Patrizia; Perrotta, Gaetano; Bevivino, Annamaria

2018-01-01

Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Molecular evolution and diversification of snake toxin genes, revealed by analysis of intron sequences.

PubMed

Fujimi, T J; Nakajyo, T; Nishimura, E; Ogura, E; Tsuchiya, T; Tamiya, T

2003-08-14

The genes encoding erabutoxin (short chain neurotoxin) isoforms (Ea, Eb, and Ec), LsIII (long chain neurotoxin) and a novel long chain neurotoxin pseudogene were cloned from a Laticauda semifasciata genomic library. Short and long chain neurotoxin genes were also cloned from the genome of Laticauda laticaudata, a closely related species of L. semifasciata, by PCR. A putative matrix attached region (MAR) sequence was found in the intron I of the LsIII gene. Comparative analysis of 11 structurally relevant snake toxin genes (three-finger-structure toxins) revealed the molecular evolution of these toxins. Three-finger-structure toxin genes diverged from a common ancestor through two types of evolutionary pathways (long and short types), early in the course of evolution. At a later stage of evolution in each gene, the accumulation of mutations in the exons, especially exon II, by accelerated evolution may have caused the increased diversification in their functions. It was also revealed that the putative MAR sequence found in the LsIII gene was integrated into the gene after the species-level divergence.

Habitat loss and gain: Influence on habitat attractiveness for estuarine fish communities

NASA Astrophysics Data System (ADS)

Amorim, Eva; Ramos, Sandra; Elliott, Michael; Franco, Anita; Bordalo, Adriano A.

2017-10-01

Habitat structure and complexity influence the structuring and functioning of fish communities. Habitat changes are one of the main pressures affecting estuarine systems worldwide, yet the degree and rate of change and its impact on fish communities is still poorly understood. In order to quantify historical modifications in habitat structure, an ecohydrological classification system using physiotopes, i.e. units with homogenous abiotic characteristics, was developed for the lower Lima estuary (NW Portugal). Field data, aerial imagery, historical maps and interpolation methods were used to map input variables, including bathymetry, substratum (hard/soft), sediment composition, hydrodynamics (current velocity) and vegetation coverage. Physiotopes were then mapped for the years of 1933 and 2013 and the areas lost and gained over the 80 years were quantified. The implications of changes for the benthic and demersal fish communities using the lower estuary were estimated using the attractiveness to those communities of each physiotope, while considering the main estuarine habitat functions for fish, namely spawning, nursery, feeding and refuge areas and migratory routes. The lower estuary was highly affected due to urbanisation and development and, following a port/harbour expansion, its boundary moved seaward causing an increase in total area. Modifications led to the loss of most of its sandy and saltmarsh intertidal physiotopes, which were replaced by deeper subtidal physiotopes. The most attractive physiotopes for fish (defined as the way in which they supported the fish ecological features) decreased in area while less attractive ones increased, producing an overall lower attractiveness of the studied area in 2013 compared to 1933. The implications of habitat alterations for the fish using the estuary include potential changes in the nursery carrying capacity and the functioning of the fish community. The study also highlighted the poor knowledge of the impacts of

Ocean acidification alters fish populations indirectly through habitat modification

NASA Astrophysics Data System (ADS)

Nagelkerken, Ivan; Russell, Bayden D.; Gillanders, Bronwyn M.; Connell, Sean D.

2016-01-01

Ocean ecosystems are predicted to lose biodiversity and productivity from increasing ocean acidification. Although laboratory experiments reveal negative effects of acidification on the behaviour and performance of species, more comprehensive predictions have been hampered by a lack of in situ studies that incorporate the complexity of interactions between species and their environment. We studied CO2 vents from both Northern and Southern hemispheres, using such natural laboratories to investigate the effect of ocean acidification on plant-animal associations embedded within all their natural complexity. Although we substantiate simple direct effects of reduced predator-avoidance behaviour by fishes, as observed in laboratory experiments, we here show that this negative effect is naturally dampened when fish reside in shelter-rich habitats. Importantly, elevated CO2 drove strong increases in the abundance of some fish species through major habitat shifts, associated increases in resources such as habitat and prey availability, and reduced predator abundances. The indirect effects of acidification via resource and predator alterations may have far-reaching consequences for population abundances, and its study provides a framework for a more comprehensive understanding of increasing CO2 emissions as a driver of ecological change.

Molecular modifiers reveal a mechanism of pathological crystal growth inhibition

NASA Astrophysics Data System (ADS)

Chung, Jihae; Granja, Ignacio; Taylor, Michael G.; Mpourmpakis, Giannis; Asplin, John R.; Rimer, Jeffrey D.

2016-08-01

Crystalline materials are crucial to the function of living organisms, in the shells of molluscs, the matrix of bone, the teeth of sea urchins, and the exoskeletons of coccoliths. However, pathological biomineralization can be an undesirable crystallization process associated with human diseases. The crystal growth of biogenic, natural and synthetic materials may be regulated by the action of modifiers, most commonly inhibitors, which range from small ions and molecules to large macromolecules. Inhibitors adsorb on crystal surfaces and impede the addition of solute, thereby reducing the rate of growth. Complex inhibitor-crystal interactions in biomineralization are often not well elucidated. Here we show that two molecular inhibitors of calcium oxalate monohydrate crystallization—citrate and hydroxycitrate—exhibit a mechanism that differs from classical theory in that inhibitor adsorption on crystal surfaces induces dissolution of the crystal under specific conditions rather than a reduced rate of crystal growth. This phenomenon occurs even in supersaturated solutions where inhibitor concentration is three orders of magnitude less than that of the solute. The results of bulk crystallization, in situ atomic force microscopy, and density functional theory studies are qualitatively consistent with a hypothesis that inhibitor-crystal interactions impart localized strain to the crystal lattice and that oxalate and calcium ions are released into solution to alleviate this strain. Calcium oxalate monohydrate is the principal component of human kidney stones and citrate is an often-used therapy, but hydroxycitrate is not. For hydroxycitrate to function as a kidney stone treatment, it must be excreted in urine. We report that hydroxycitrate ingested by non-stone-forming humans at an often-recommended dose leads to substantial urinary excretion. In vitro assays using human urine reveal that the molecular modifier hydroxycitrate is as effective an inhibitor of nucleation

Hydroacoustic habitat mapping in Potter Cove (King George Island, Antarctica)

NASA Astrophysics Data System (ADS)

Hass, H. Christian; Wölfl, Anne-Cathrin; Kuhn, Gerhard; Jerosch, Kerstin; Scharf, Frauke; Abele, Doris

2016-04-01

Climate change increasingly affects the coastal areas off Antarctica. Strongest environmental response occurs in the transition zones that mediate between the polar and subpolar latitudes. Potter Cove, a minor fjord at the northern tip of the Antarctic Peninsula is significantly affected by rising temperatures and retreating ice sheets. Large amounts of turbid meltwaters affect both, the seafloor and the water column and cause stress for many biota. There is an increasing demand to monitor the ongoing change and to work out means for comparison with similar coastal ecosystems under pressure. Marine habitat maps provide information on the seafloor characteristics that allow to describe and evaluate the status of the recent coastal ecosystem and to predict its future development. We used a RoxAnn acoustic ground discrimination system, a sidescan sonar, grab samples (grain size and TOC) and underwater video footage to gain habitat information. Supervised and unsupervised classification routines (including fuzzy k-means clustering and LDA) were employed to calculate models ranging from two classes (soft bottom habitat, stone habitat) to 7 classes (including classes of rocks with and without macroalgae as well as classes of gravels, sands and silts). Including organic carbon in the database allowed to identify a carbon-depleted class proximal to the glacier front. Potter Cove reveals features that are related to the climate-controlled environmental change: very rough seafloor topography in a small basin close to the fjord head which was cleared by the retreating tidewater glacier through the past two decades. The increasing distance to the glacier down-fjord causes existing habitats to smooth and mature and new habitats to form. This process will change the terrestrial and marine face of Potter Cove until the ongoing climatic change stops or even reverses. It becomes apparent that the final interpretation of the results benefits significantly from the different

Satellite-based remote sensing of running water habitats at large riverscape scales: Tools to analyze habitat heterogeneity for river ecosystem management

NASA Astrophysics Data System (ADS)

Hugue, F.; Lapointe, M.; Eaton, B. C.; Lepoutre, A.

2016-01-01

(V) over the 17-km Kiamika reach. The joint distribution of D and V variables over wetted zones then is used to reveal structural patterns in hydraulic habitat availability at patch, reach, and segment scales. Here we analyze 156 bivariate (D, V) density function plots estimated over moving reach windows along the satellite scene extent to extract 14 physical habitat metrics (such as river width, mean and modal depths and velocity, variances and covariance in D and V over 1-m pixels, HMID, entropy). A principal component analysis on the set of metrics is then used to cluster river reaches in regard to similarity in their hydraulic habitat composition and heterogeneity. Applications of this approach can include (i) specific fish habitat detection at riverscape scales (e.g., large areas of riffle spawning beds, deeper pools) for regional management, (ii) studying how river habitat heterogeneity is correlated to fish distribution and (iii) guidance for site location for restoration of key habitats or for post regulation monitoring of representative reaches of various types.

Stable isotopes reveal habitat-related diet shifts in facultative deposit-feeders

NASA Astrophysics Data System (ADS)

Rossi, Francesca; Baeta, Alexandra; Marques, João C.

2015-01-01

Seagrass patches interspersed in a sediment matrix may vary environmental conditions and affect feeding habits of consumers and food-web structure. This paper investigates diet shifts between bare sediments and a Zostera noltei (Hornemann, 1832) meadow for three facultative deposit-feeding macrofaunal consumers, notably the bivalve Scrobicularia plana (da Costa, 1778), the polychaete Hediste diversicolor (O.T. Müller, 1776), and the gastropod Hydrobia ulvae (Pennant, 1778). In July 2008, one eelgrass meadow and two bare sediment locations were chosen in the Mondego estuary (40° 08″ N, 8° 50‧ W, Portugal) and sampled for stable isotope signatures (δ13C and δ15N) of macrofauna consumers and some of their potential basal food sources, such as sedimentary organic matter (SOM), microphytobenthos (MPB), seagrass shoots, leaves and seaweeds laying on the surface sediment. The δ15N of H. diversicolor was 3‰ higher in the eelgrass meadow than in bare sediment, indicating a change of trophic position, whereas the Bayesian stable-isotope mixing model showed that S. plana assimilated more macroalgal detritus than microphytobenthos in the eelgrass bed. Such habitat-related diet shifts have the potential to change structure and spatial dynamics of benthic food webs.

Predation of stink bugs (Hemiptera: Pentatomidae) by a complex of predators and adjoining soybean habitats in Georgia, USA

USDA-ARS?s Scientific Manuscript database

Molecular gut-content analysis was used to examine predation on stink bugs (Hemiptera: Pentatomidae) by arthropod predators in habitats of soybean with and without buckwheat and adjoining cotton. Nezara viridula (L.), Euschistus servus (Say), Chinavia hilaris (Say), and Euschistus quadrator Rolston,...

Evolutionary history of genus Macrobrachium inferred from mitochondrial markers: a molecular clock approach.

PubMed

Jose, Deepak; Harikrishnan, Mahadevan

2018-04-17

Caridea, an infraorder of shrimps coming under Pleocyemata was first reported from the oceans before 417 million years followed by their radiation recorded during the Permian period. Hitherto, about 3877 extant caridean species were accounted within which one quarter constitute freshwater species. Freshwater prawns of genus Macrobrachium (Infraorder Caridea; Family Palaemonidae), with more than 240 species are inhabitants of diverse aquatic habitats like coastal lagoons, lakes, tropical streams, ponds and rivers. Previous studies on Macrobrachium relied on the highly variable morphological characters which were insufficient for accurate diagnosis of natural species groups. Present study focuses on the utility of molecular markers (viz. COI and 16S rRNA) for resolving the evolutionary history of genus Macrobrachium using a combination of phylogeny and timescale components. It is for the first time a molecular clock approach had been carried out towards genus Macrobrachium in a broad aspect with the incorporation of congeners inhabiting diverse geographical realms including endemic species M. striatum from South West coast of India. Molecular results obtained revealed the phylogenetic relationships between congeners of genus Macrobrachium at intra/inter-continental level along with the corresponding evolutionary time estimates.

Optimization of Martian regolith and ultra-high molecular weight polyethylene composites for radiation shielding and habitat structures

NASA Astrophysics Data System (ADS)

Wilkins, Richard; Gersey, Brad; Baburaj, Abhijit; Barnett, Milan; Zhou, Xianren

2012-07-01

In preparation for long duration missions to the moon, Mars or, even near earth asteroids, one challenge, amongst many others, that the space program faces is shielding against space radiation. It is difficult to effectively shield all sources of space radiation because of the broad range of types and high energies found in space, so the most important goal is to minimize the damaging effects that may occur to humans and electronics during long duration space flight. For a long duration planetary habitat, a shielding option is to use in situ resources such as the native regolith. A possible way to utilize regolith on a planet is to combine it with a binder to form a structural material that also exhibits desirable shielding properties. In our studies, we explore Martian regolith and ultra-high molecular weight polyethylene (UHMWPE) composites. We selected UHMWPE as the binder in our composites due to its high hydrogen content; a desirable characteristic for shielding materials in a space environment. Our initial work has focused on the process of developing the right ratio of simulated Martian regolith and UHMWPE to yield the best results in material endurance and strength, while retaining good shielding characteristics. Another factor in our optimization process is to determine the composite ratio that minimizes the amount of ex situ UHMWPE while retaining desirable structural and shielding properties. This consideration seeks to minimize mission weight and costs. Mechanical properties such as tensile strength of the Martian regolith/UHMWPE composite as a function of its grain size, processing parameters, and different temperature variations used are discussed. The radiation shielding effectiveness of loose mixtures of Martian regolith/ UHMWPE is evaluated using a 200 MeV proton beam and a tissue equivalent proportional counter. Preliminary results show that composites with an 80/20 ratio percent weight of regolith to UHMWPE can be fabricated with potentially

Measuring habitat heterogeneity reveals new insights into bird community composition.

PubMed

Stirnemann, Ingrid A; Ikin, Karen; Gibbons, Philip; Blanchard, Wade; Lindenmayer, David B

2015-03-01

Fine-scale vegetation cover is a common variable used to explain animal occurrence, but we know less about the effects of fine-scale vegetation heterogeneity. Theoretically, fine-scale vegetation heterogeneity is an important driver of biodiversity because it captures the range of resources available in a given area. In this study we investigated how bird species richness and birds grouped by various ecological traits responded to vegetation cover and heterogeneity. We found that both fine-scale vegetation cover (of tall trees, medium-sized trees and shrubs) and heterogeneity (of tall trees, and shrubs) were important predictors of bird richness, but the direction of the response of bird richness to shrub heterogeneity differed between sites with different proportions of tall tree cover. For example, bird richness increased with shrub heterogeneity in sites with high levels of tall tree cover, but declined in sites with low levels of tall tree cover. Our findings indicated that an increase in vegetation heterogeneity will not always result in an increase in resources and niches, and associated higher species richness. We also found birds grouped by traits responded in a predictable way to vegetation heterogeneity. For example, we found small birds benefited from increased shrub heterogeneity supporting the textual discontinuity hypothesis and non-arboreal (ground or shrub) nesting species were associated with high vegetation cover (low heterogeneity). Our results indicated that focusing solely on increasing vegetation cover (e.g. through restoration) may be detrimental to particular animal groups. Findings from this investigation can help guide habitat management for different functional groups of birds.

Stable Isotopes of C and N Reveal Habitat Dependent Dietary Overlap between Native and Introduced Turtles Pseudemys rubriventris and Trachemys scripta

PubMed Central

Pearson, Steven H.; Avery, Harold W.; Kilham, Susan S.; Velinsky, David J.; Spotila, James R.

2013-01-01

Habitat degradation and species introductions are two of the leading causes of species declines on a global scale. Invasive species negatively impact native species through predation and competition for limited resources. The impacts of invasive species may be increased in habitats where habitat degradation is higher due to reductions of prey abundance and distribution. Using stable isotope analyses and extensive measurements of resource availability we determined how resource availability impacts the long term carbon and nitrogen assimilation of the invasive red-eared slider turtle (Trachemys scripta elegans) and a native, threatened species, the red-bellied turtle (Pseudemys rubriventris) at two different freshwater wetland complexes in Pennsylvania, USA. At a larger wetland complex with greater vegetative species richness and diversity, our stable isotope analyses showed dietary niche partitioning between species, whereas analyses from a smaller wetland complex with lower vegetative species richness and diversity showed significant dietary niche overlap. Determining the potential for competition between these two turtle species is important to understanding the ecological impacts of red-eared slider turtles in wetland habitats. In smaller wetlands with increased potential for competition between native turtles and invasive red-eared slider turtles we expect that when shared resources become limited, red-eared slider turtles will negatively impact native turtle species leading to long term population declines. Protection of intact wetland complexes and the reduction of introduced species populations are paramount to preserving populations of native species. PMID:23675437

Stable isotopes of C and N reveal habitat dependent dietary overlap between native and introduced turtles Pseudemys rubriventris and Trachemys scripta.

PubMed

Pearson, Steven H; Avery, Harold W; Kilham, Susan S; Velinsky, David J; Spotila, James R

2013-01-01

Habitat degradation and species introductions are two of the leading causes of species declines on a global scale. Invasive species negatively impact native species through predation and competition for limited resources. The impacts of invasive species may be increased in habitats where habitat degradation is higher due to reductions of prey abundance and distribution. Using stable isotope analyses and extensive measurements of resource availability we determined how resource availability impacts the long term carbon and nitrogen assimilation of the invasive red-eared slider turtle (Trachemys scripta elegans) and a native, threatened species, the red-bellied turtle (Pseudemys rubriventris) at two different freshwater wetland complexes in Pennsylvania, USA. At a larger wetland complex with greater vegetative species richness and diversity, our stable isotope analyses showed dietary niche partitioning between species, whereas analyses from a smaller wetland complex with lower vegetative species richness and diversity showed significant dietary niche overlap. Determining the potential for competition between these two turtle species is important to understanding the ecological impacts of red-eared slider turtles in wetland habitats. In smaller wetlands with increased potential for competition between native turtles and invasive red-eared slider turtles we expect that when shared resources become limited, red-eared slider turtles will negatively impact native turtle species leading to long term population declines. Protection of intact wetland complexes and the reduction of introduced species populations are paramount to preserving populations of native species.

Integrated systems analysis reveals a molecular network underlying autism spectrum disorders

PubMed Central

Li, Jingjing; Shi, Minyi; Ma, Zhihai; Zhao, Shuchun; Euskirchen, Ghia; Ziskin, Jennifer; Urban, Alexander; Hallmayer, Joachim; Snyder, Michael

2014-01-01

Autism is a complex disease whose etiology remains elusive. We integrated previously and newly generated data and developed a systems framework involving the interactome, gene expression and genome sequencing to identify a protein interaction module with members strongly enriched for autism candidate genes. Sequencing of 25 patients confirmed the involvement of this module in autism, which was subsequently validated using an independent cohort of over 500 patients. Expression of this module was dichotomized with a ubiquitously expressed subcomponent and another subcomponent preferentially expressed in the corpus callosum, which was significantly affected by our identified mutations in the network center. RNA-sequencing of the corpus callosum from patients with autism exhibited extensive gene mis-expression in this module, and our immunochemical analysis showed that the human corpus callosum is predominantly populated by oligodendrocyte cells. Analysis of functional genomic data further revealed a significant involvement of this module in the development of oligodendrocyte cells in mouse brain. Our analysis delineates a natural network involved in autism, helps uncover novel candidate genes for this disease and improves our understanding of its molecular pathology. PMID:25549968

Habitat Suitability Index Models: Hairy woodpecker

USGS Publications Warehouse

Sousa, Patrick J.

1987-01-01

A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the hairy woodpecker (Picoides villosus). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

Habitat Suitability Index Models: Snapping turtle

USGS Publications Warehouse

Graves, Brent M.; Anderson, Stanley H.

1987-01-01

A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the snapping turtle (Chelydra serpentina). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) and 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

Habitat Suitability Index Models: Spotted owl

USGS Publications Warehouse

Laymon, Stephen A.; Salwasser, Hal; Barrett, Reginald H.

1985-01-01

A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the spotted owl (Strix occidentalis). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation.

PubMed

Silveira, Rodrigo L; Stoyanov, Stanislav R; Gusarov, Sergey; Skaf, Munir S; Kovalenko, Andriy

2015-01-02

Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance.

Clear Creek Watershed Flood Risk Management Habitat Assessments Using Habitat Evaluation Procedures (HEP): Analyses, Results and Documentation

DTIC Science & Technology

2013-07-01

endangered species and their associated habitats as an important goal of ecosystem restoration and management. There is no doubt the determination of...accounting process developed to appraise habitat suitability for fish and wildlife species in response to potential change (USFWS 1980a-c). HEP is an... habitat to a species is likely to exhibit strong thresholds below which the habitat is usually unsuitable and above which further changes in habitat

Distribution of millipedes (Myriapoda, Diplopoda) along a forest interior - forest edge - grassland habitat complex.

PubMed

Bogyó, Dávid; Magura, Tibor; Nagy, Dávid D; Tóthmérész, Béla

2015-01-01

We studied the distribution of millipedes in a forest interior-forest edge-grassland habitat complex in the Hajdúság Landscape Protection Area (NE Hungary). The habitat types were as follows: (1) lowland oak forest, (2) forest edge with increased ground vegetation and shrub cover, and (3) mesophilous grassland. We collected millipedes by litter and soil sifting. There were overall 30 sifted litter and soil samples: 3 habitat types × 2 replicates × 5 soil and litter samples per habitats. We collected 9 millipede species; the most abundant species was Glomeristetrasticha, which was the most abundant species in the forest edge as well. The most abundant species in the forest interior was Kryphioiulusoccultus, while the most abundant species in the grassland was Megaphyllumunilineatum. Our result showed that the number of millipede species was significantly lower in the grassland than in the forest or in the edge, however there were no significant difference in the number of species between the forest interior and the forest edge. We found significantly the highest number of millipede individuals in the forest edge. There were differences in the composition of the millipede assemblages of the three habitats. The results of the DCCA showed that forest edge and forest interior habitats were clearly separated from the grassland habitats. The forest edge habitat was characterized by high air temperature, high soil moisture, high soil pH, high soil enzyme activity, high shrub cover and low canopy cover. The IndVal and the DCCA methods revealed the following character species of the forest edge habitats: Glomeristetrasticha and Leptoiuluscibdellus. Changes in millipede abundance and composition were highly correlated with the vegetation structure.

Habitat Demonstration Unit (HDU) Vertical Cylinder Habitat

NASA Technical Reports Server (NTRS)

Howe, Alan; Kennedy, Kriss J.; Gill, Tracy R.; Tri, Terry O.; Toups, Larry; Howard, Robert I.; Spexarth, Gary R.; Cavanaugh, Stephen; Langford, William M.; Dorsey, John T.

2014-01-01

NASA's Constellation Architecture Team defined an outpost scenario optimized for intensive mobility that uses small, highly mobile pressurized rovers supported by portable habitat modules that can be carried between locations of interest on the lunar surface. A compact vertical cylinder characterizes the habitat concept, where the large diameter maximizes usable flat floor area optimized for a gravity environment and allows for efficient internal layout. The module was sized to fit into payload fairings for the Constellation Ares V launch vehicle, and optimized for surface transport carried by the All-Terrain Hex-Limbed Extra-Terrestrial Explorer (ATHLETE) mobility system. Launch and other loads are carried through the barrel to a top and bottom truss that interfaces with a structural support unit (SSU). The SSU contains self-leveling feet and docking interfaces for Tri-ATHLETE grasping and heavy lift. A pressurized module needed to be created that was appropriate for the lunar environment, could be easily relocated to new locations, and could be docked together in multiples for expanding pressurized volume in a lunar outpost. It was determined that horizontally oriented pressure vessels did not optimize floor area, which takes advantage of the gravity vector for full use. Hybrid hard-inflatable habitats added an unproven degree of complexity that may eventually be worked out. Other versions of vertically oriented pressure vessels were either too big, bulky, or did not optimize floor area. The purpose of the HDU vertical habitat module is to provide pressurized units that can be docked together in a modular way for lunar outpost pressurized volume expansion, and allow for other vehicles, rovers, and modules to be attached to the outpost to allow for IVA (intra-vehicular activity) transfer between them. The module is a vertically oriented cylinder with a large radius to allow for maximal floor area and use of volume. The modular, 5- m-diameter HDU vertical habitat

Habitat specialization through germination cueing: a comparative study of herbs from forests and open habitats.

PubMed

Ten Brink, Dirk-Jan; Hendriksma, Harmen Pieter; Bruun, Hans Henrik

2013-02-01

This study examined the adaptive association between seed germination ecology and specialization to either forest or open habitats across a range of evolutionary lineages of seed plants, in order to test the hypotheses that (1) species' specialization to open vs. shaded habitats is consistently accompanied by specialization in their regeneration niche; and (2) species are thereby adapted to utilize different windows of opportunity in time (season) and space (habitat). Seed germination response to temperature, light and stratification was tested for 17 congeneric pairs, each consisting of one forest species and one open-habitat species. A factorial design was used with temperature levels and diurnal temperature variation (10 °C constant, 15-5 °C fluctuating, 20 °C constant, 25-15 °C fluctuating), and two light levels (light and darkness) and a cold stratification treatment. The congeneric species pair design took phylogenetic dependence into account. Species from open habitats germinated better at high temperatures, whereas forest species performed equally well at low and high temperatures. Forest species tended to germinate only after a period of cold stratification that could break dormancy, while species from open habitats generally germinated without cold stratification. The empirically derived germination strategies correspond quite well with establishment opportunities for forest and open-habitat plant species in nature. Annual changes in temperature and light regime in temperate forest delimit windows of opportunity for germination and establishment. Germination strategies of forest plants are adaptations to utilize such narrow windows in time. Conversely, lack of fit between germination ecology and environment may explain why species of open habitats generally fail to establish in forests. Germination strategy should be considered an important mechanism for habitat specialization in temperate herbs to forest habitats. The findings strongly suggest that

MEGAEPIFAUNA-HABITAT RELATIONSHIPS IN YAQUINA BAY, OR

EPA Science Inventory

Habitat-based ecological risk assessments rely, in part, on estimates of the ecological value of the habitats at risk. As part of a larger programmatic effort to estimate estuarine habitat values, we determined megaepifauna-habitat relationships for four major intertidal habitat...

A spatial model of white sturgeon rearing habitat in the lower Columbia River, USA

USGS Publications Warehouse

Hatten, J.R.; Parsley, M.J.

2009-01-01

Concerns over the potential effects of in-water placement of dredged materials prompted us to develop a GIS-based model that characterizes in a spatially explicit manner white sturgeon Acipenser transmontanus rearing habitat in the lower Columbia River, USA. The spatial model was developed using water depth, riverbed slope and roughness, fish positions collected in 2002, and Mahalanobis distance (D2). We created a habitat suitability map by identifying a Mahalanobis distance under which >50% of white sturgeon locations occurred in 2002 (i.e., high-probability habitat). White sturgeon preferred relatively moderate to high water depths, and low to moderate riverbed slope and roughness values. The eigenvectors indicated that riverbed slope and roughness were slightly more important than water depth, but all three variables were important. We estimated the impacts that fill might have on sturgeon habitat by simulating the addition of fill to the thalweg, in 3-m increments, and recomputing Mahalanobis distances. Channel filling simulations revealed that up to 9 m of fill would have little impact on high-probability habitat, but 12 and 15 m of fill resulted in habitat declines of ???12% and ???45%, respectively. This is the first spatially explicit predictive model of white sturgeon rearing habitat in the lower Columbia River, and the first to quantitatively predict the impacts of dredging operations on sturgeon habitat. Future research should consider whether water velocity improves the accuracy and specificity of the model, and to assess its applicability to other areas in the Columbia River.

Expansion of oxygen minimum zones may reduce available habitat for tropical pelagic fishes

NASA Astrophysics Data System (ADS)

Stramma, Lothar; Prince, Eric D.; Schmidtko, Sunke; Luo, Jiangang; Hoolihan, John P.; Visbeck, Martin; Wallace, Douglas W. R.; Brandt, Peter; Körtzinger, Arne

2012-01-01

Climate model predictions and observations reveal regional declines in oceanic dissolved oxygen, which are probably influenced by global warming. Studies indicate ongoing dissolved oxygen depletion and vertical expansion of the oxygen minimum zone (OMZ) in the tropical northeast Atlantic Ocean. OMZ shoaling may restrict the usable habitat of billfishes and tunas to a narrow surface layer. We report a decrease in the upper ocean layer exceeding 3.5mll-1 dissolved oxygen at a rate of <=1myr-1 in the tropical northeast Atlantic (0-25°N, 12-30°W), amounting to an annual habitat loss of ~5.95×1013m3, or 15% for the period 1960-2010. Habitat compression and associated potential habitat loss was validated using electronic tagging data from 47 blue marlin. This phenomenon increases vulnerability to surface fishing gear for billfishes and tunas, and may be associated with a 10-50% worldwide decline of pelagic predator diversity. Further expansion of the Atlantic OMZ along with overfishing may threaten the sustainability of these valuable pelagic fisheries and marine ecosystems.

Headwater Stream Management Dichotomies: Local Amphibian Habitat vs. Downstream Fish Habitat

NASA Astrophysics Data System (ADS)

Jackson, C. R.

2002-12-01

Small headwater streams in mountainous areas of the Pacific Northwest often do not harbor fish populations because of low water depth and high gradients. Rather, these streams provide habitat for dense assemblages of stream-dwelling amphibians. A variety of management goals have been suggested for such streams such as encouraging large woody debris recruitment to assist in sediment trapping and valley floor formation, encouraging large woody debris recruitment to provide downstream wood when debris flows occur, providing continuous linear stream buffers within forest harvest areas to provide shade and bank stability, etc. A basic problem with analying the geomorphic or biotic benefits of any of these strategies is the lack of explicit management goals for such streams. Should managers strive to optimize downstream fish habitat, local amphibian habitat, or both? Through observational data and theoretical considerations, it will be shown that these biotic goals will lead to very different geomorphic management recommendations. For instance, woody debris greater than 60 cm diameter may assist in valley floor development, but it is likely to create subsurface channel flow of unknown value to amphibians. Trapping and retention of fine sediments within headwater streams may improve downstream spawning gravels, but degrades stream-dwelling amphibian habitat. In response to the need for descriptive information on habitat and channel morphology specific to small, non-fish-bearing streams in the Pacific Northwest, morphologies and wood frequencies in forty-two first- and second-order forested streams less than four meters wide were surveyed. Frequencies and size distributions of woody debris were compared between small streams and larger fish-bearing streams as well as between second-growth and virgin timber streams. Statistical models were developed to explore dominant factors affecting channel morphology and habitat. Findings suggest geomorphological relationships

Habitat Suitability Index Models: Eastern meadowlark

USGS Publications Warehouse

Schroeder, Richard L.; Sousa, Patrick J.

1982-01-01

Habitat preferences of the eastern meadowlark (Sturnella magna) are described in this publication, which is one of a series of Habitat Suitability Index (HSI) models. Habitat use information is presented in a synthesis of the literature on the species-habitat requirements of the eastern meadowlark, followed by the development of the HSI model. The model is presented in three formats: graphic, word, and mathematical, and is designed to provide information for use in impact assessment and habitat management activities.

Habitat Suitability Index Models: Pine warbler

USGS Publications Warehouse

Schroeder, Richard L.

1982-01-01

Habitat preferences of the pine warbler (Dendroica pinus) are described in this publication, which is one of a series of Habitat Suitability Index (HSI) models. Habitat use information is presented in a synthesis of the literature on the species-habitat requirements of the pine warbler, followed by the development of the HSI model. The model is presented in three formats: graphic, word, and mathematical, and is designed to provide information for use in impact assessment and habitat management activities.

Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

PubMed

Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

2010-03-01

Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy.

PubMed

Kong, Bo; Bruns, Philipp; Behler, Nora A; Chang, Ligong; Schlitter, Anna Melissa; Cao, Jing; Gewies, Andreas; Ruland, Jürgen; Fritzsche, Sina; Valkovskaya, Nataliya; Jian, Ziying; Regel, Ivonne; Raulefs, Susanne; Irmler, Martin; Beckers, Johannes; Friess, Helmut; Erkan, Mert; Mueller, Nikola S; Roth, Susanne; Hackert, Thilo; Esposito, Irene; Theis, Fabian J; Kleeff, Jörg; Michalski, Christoph W

2018-01-01

The initial steps of pancreatic regeneration versus carcinogenesis are insufficiently understood. Although a combination of oncogenic Kras and inflammation has been shown to induce malignancy, molecular networks of early carcinogenesis remain poorly defined. We compared early events during inflammation, regeneration and carcinogenesis on histological and transcriptional levels with a high temporal resolution using a well-established mouse model of pancreatitis and of inflammation-accelerated Kras G12D -driven pancreatic ductal adenocarcinoma. Quantitative expression data were analysed and extensively modelled in silico. We defined three distinctive phases-termed inflammation, regeneration and refinement-following induction of moderate acute pancreatitis in wild-type mice. These corresponded to different waves of proliferation of mesenchymal, progenitor-like and acinar cells. Pancreas regeneration required a coordinated transition of proliferation between progenitor-like and acinar cells. In mice harbouring an oncogenic Kras mutation and challenged with pancreatitis, there was an extended inflammatory phase and a parallel, continuous proliferation of mesenchymal, progenitor-like and acinar cells. Analysis of high-resolution transcriptional data from wild-type animals revealed that organ regeneration relied on a complex interaction of a gene network that normally governs acinar cell homeostasis, exocrine specification and intercellular signalling. In mice with oncogenic Kras, a specific carcinogenic signature was found, which was preserved in full-blown mouse pancreas cancer. These data define a transcriptional signature of early pancreatic carcinogenesis and a molecular network driving formation of preneoplastic lesions, which allows for more targeted biomarker development in order to detect cancer earlier in patients with pancreatitis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Interclonal proteomic responses to predator exposure in Daphnia magna may depend on predator composition of habitats.

PubMed

Otte, Kathrin A; Schrank, Isabella; Fröhlich, Thomas; Arnold, Georg J; Laforsch, Christian

2015-08-01

Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterizing the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the water flea, is a textbook example for predator-induced phenotypic plastic defences; however, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages. We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. To get a more comprehensive idea of this phenomenon, we studied four genotypes with five biological replicates each, originating from habitats characterized by different predator composition, ranging from predator-free habitats to habitats containing T. cancriformis. We analysed the morphologies as well as proteomes of predator-exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high-throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype-dependent manner. Proteins connected to genotype-dependent responses were related to the cuticle, protein synthesis and calcium binding, whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype-dependent responses at the proteome level were most distinct for the only genotype that shares its habitat with Triops. Altogether, our study provides new insights concerning genotype-dependent and general molecular processes involved in predator-induced phenotypic plasticity in D. magna. © 2015 John Wiley & Sons Ltd.

Seasonal and habitat-related distribution pattern of Synechococcus genotypes in Lake Constance.

PubMed

Becker, Sven; Richl, Petra; Ernst, Anneliese

2007-10-01

The abundance and distribution of Synechococcus spp. in the autotrophic picoplankton of Lake Constance, were followed in the pelagic and littoral habitat by qPCR over 2 years. One genotype, represented by isolated phycoerythrin-rich strain BO 8807, showed a seasonal distribution pattern in both habitats. Before a stable thermal stratification, the maximum of both the Synechococcus population and genotype BO 8807 occurred at 15 or 20 m water depth in the pelagic habitat. During the summer stratification, when the absolute abundance of all Synechococcus spp. was highest above 15 m, the absolute and relative abundance of genotype BO 8807 was maximal at 20 m. These results indicate that Synechococcus spp. or single genotypes are present in deep maxima in Lake Constance. The in situ dynamics of genotype BO 8807 is consistent with the observation that isolated strain BO 8807 requires higher phosphate concentrations for maximum growth rates than a strain from the same phylogenetic cluster that dominates the pelagic summer population. In contrast to these findings, low genome numbers of phycocyanin-rich genotype BO 8805 were found temporarily only in both the littoral and pelagic plankton. Microscopy revealed that PC-rich cells in general occurred preferentially in the littoral habitat. We discuss our results with respect to the versatility of picocyanobacteria of the evolutionary lineage VI of cyanobacteria, and a habitat-related distribution pattern of Synechococcus genotypes.

Habitat selection by two beluga whale populations in the Chukchi and Beaufort seas

PubMed Central

Laidre, Kristin L.; Stern, Harry L.; Moore, Sue E.; Suydam, Robert S.; Richard, Pierre R.

2017-01-01

There has been extensive sea ice loss in the Chukchi and Beaufort seas where two beluga whale (Delphinapterus leucas) populations occur between July-November. Our goal was to develop population-specific beluga habitat selection models that quantify relative use of sea ice and bathymetric features related to oceanographic processes, which can provide context to the importance of changing sea ice conditions. We established habitat selection models that incorporated daily sea ice measures (sea ice concentration, proximity to ice edge and dense ice) and bathymetric features (slope, depth, proximity to the continental slope, Barrow Canyon, and shore) to establish quantitative estimates of habitat use for the Eastern Chukchi Sea (‘Chukchi’) and Eastern Beaufort Sea (‘Beaufort’) populations. We applied ‘used v. available’ resource selection functions to locations of 65 whales tagged from 1993–2012, revealing large variations in seasonal habitat selection that were distinct between sex and population groups. Chukchi whales of both sexes were predicted to use areas in close proximity to Barrow Canyon (typically <200 km) as well as the continental slope in summer, although deeper water and denser ice were stronger predictors for males than females. Habitat selection differed more between sexes for Beaufort belugas. Beaufort males selected higher ice concentrations (≥40%) than females (0–40%) in July-August. Proximity to shore (<200 km) strongly predicted summer habitat of Beaufort females, while distance to the ice edge was important for male habitat selection, especially during westward migration in September. Overall, our results indicate that sea ice variables were rarely the primary drivers of beluga summer-fall habitat selection. While diminished sea ice may indirectly affect belugas through changes in the ecosystem, associations with bathymetric features that affect prey availability seemed key to habitat selection during summer and fall. These

Range expansion and habitat shift triggered elevated diversification of the rice genus (Oryza, Poaceae) during the Pleistocene.

PubMed

Lin, Li; Tang, Liang; Bai, Yun-Jun; Tang, Zhi-Yao; Wang, Wei; Chen, Zhi-Duan

2015-09-03

The rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans. However, little is known about the process by which the genus diversified or the factors that drove its speciation. Here, we integrated the phylogenetic, molecular dating and biogeographic methods to investigate the spatial-temporal patterns of Oryza diversification, and used a series of model tests to examine whether intercontinental migrations and/or key innovations were associated with significant changes in diversification rates in the genus. Oryza became differentiated in tropical Asia in the Miocene. There were two migrations from the ancestral area into Africa and Australia during the Miocene. We inferred at least 10 migration events out of tropical Asia since the Pleistocene, mainly involving the species adapting open habitat. A rapid increase in diversification rates of the whole Oryza occurred during the Pleistocene. Intercontinental migrations from tropical Asia to other tropical regions were positively correlated with shift in habitat, but not with changes in life history. A habitat preference shift from shade tolerant to open habitat predated the burst in diversification rates. Rice species may have been pre-adapted to invade open habitat. Significant increase in diversification rates occurred during the Pleistocene and is associated with range expansion and habitat shift, but not with life history. The rice genus provides an excellent case supporting the idea that range expansion and invasion of novel habitats can drive the diversification of a group.

New England wildlife: management forested habitats

Treesearch

Richard M. DeGraaf; Mariko Yamasaki; William B. Leak; John W. Lanier

1992-01-01

Presents silvicultural treatments for six major cover-type groups in New England to produce stand conditions that provide habitat opportunities for a wide range of wildlife species. Includes matrices for species occurrence and utilization by forested and nonforested habitats, habitat breadth and size class, and structural habitat features for the 338 wildlife species...

Transport Infrastructure Shapes Foraging Habitat in a Raptor Community

PubMed Central

Planillo, Aimara; Kramer-Schadt, Stephanie; Malo, Juan E.

2015-01-01

Transport infrastructure elements are widespread and increasing in size and length in many countries, with the subsequent alteration of landscapes and wildlife communities. Nonetheless, their effects on habitat selection by raptors are still poorly understood. In this paper, we analyzed raptors’ foraging habitat selection in response to conventional roads and high capacity motorways at the landscape scale, and compared their effects with those of other variables, such as habitat structure, food availability, and presence of potential interspecific competitors. We also analyzed whether the raptors’ response towards infrastructure depends on the spatial scale of observation, comparing the attraction or avoidance behavior of the species at the landscape scale with the response of individuals observed in the proximity of the infrastructure. Based on ecological hypotheses for foraging habitat selection, we built generalized linear mixed models, selected the best models according to Akaike Information Criterion and assessed variable importance by Akaike weights. At the community level, the traffic volume was the most relevant variable in the landscape for foraging habitat selection. Abundance, richness, and diversity values reached their maximum at medium traffic volumes and decreased at highest traffic volumes. Individual species showed different degrees of tolerance toward traffic, from higher abundance in areas with high traffic values to avoidance of it. Medium-sized opportunistic raptors increased their abundance near the traffic infrastructures, large scavenger raptors avoided areas with higher traffic values, and other species showed no direct response to traffic but to the presence of prey. Finally, our cross-scale analysis revealed that the effect of transport infrastructures on the behavior of some species might be detectable only at a broad scale. Also, food availability may attract raptor species to risky areas such as motorways. PMID:25786218

Transport infrastructure shapes foraging habitat in a raptor community.

PubMed

Planillo, Aimara; Kramer-Schadt, Stephanie; Malo, Juan E

2015-01-01

Transport infrastructure elements are widespread and increasing in size and length in many countries, with the subsequent alteration of landscapes and wildlife communities. Nonetheless, their effects on habitat selection by raptors are still poorly understood. In this paper, we analyzed raptors' foraging habitat selection in response to conventional roads and high capacity motorways at the landscape scale, and compared their effects with those of other variables, such as habitat structure, food availability, and presence of potential interspecific competitors. We also analyzed whether the raptors' response towards infrastructure depends on the spatial scale of observation, comparing the attraction or avoidance behavior of the species at the landscape scale with the response of individuals observed in the proximity of the infrastructure. Based on ecological hypotheses for foraging habitat selection, we built generalized linear mixed models, selected the best models according to Akaike Information Criterion and assessed variable importance by Akaike weights. At the community level, the traffic volume was the most relevant variable in the landscape for foraging habitat selection. Abundance, richness, and diversity values reached their maximum at medium traffic volumes and decreased at highest traffic volumes. Individual species showed different degrees of tolerance toward traffic, from higher abundance in areas with high traffic values to avoidance of it. Medium-sized opportunistic raptors increased their abundance near the traffic infrastructures, large scavenger raptors avoided areas with higher traffic values, and other species showed no direct response to traffic but to the presence of prey. Finally, our cross-scale analysis revealed that the effect of transport infrastructures on the behavior of some species might be detectable only at a broad scale. Also, food availability may attract raptor species to risky areas such as motorways.

Bacterial diversity in three distinct sub-habitats within the pitchers of the northern pitcher plant, Sarracenia purpurea.

PubMed

Krieger, Joseph R; Kourtev, Peter S

2012-03-01

Pitcher plants have been widely used in ecological studies of food webs; however, their bacterial communities are poorly characterized. Pitchers of Sarracenia purpurea contain several distinct sub-habitats, namely the bottom sediment, the liquid, and the internal pitcher wall. We hypothesized that those three sub-habitats within pitcher plants are inhabited by distinct bacterial populations. We used denaturing gradient gel electrophoresis and 16S rRNA gene sequencing to characterize bacterial populations in pitchers from three bogs. DGGE and sequencing revealed that in any given pitcher, the three sub-habitats contain significantly different bacterial populations. However, there was significant variability between bacterial populations inhabiting the same type of habitat in different pitchers, even at the same site. Therefore, no consistent set of bacterial populations was enriched in any of the three sub-habitats. All sub-habitats appeared to be dominated by alpha- and betaproteobacteria in differing proportions. In addition, sequences from the Bacteroidetes and Firmicutes were obtained from all three sub-habitats. We conclude that container aquatic habitats such as the pitchers of S. purpurea possess a very high bacterial diversity, with many unique bacterial populations enriched in individual pitchers. Within an individual pitcher, populations of certain bacterial families may be enriched in one of the three studied sub-habitats. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Habitats of North American sea ducks.

USGS Publications Warehouse

Derksen, Dirk V.; Petersen, Margaret R.; Savard, Jean-Pierre L.

2015-01-01

Breeding, molting, fall and spring staging, and wintering habitats of the sea duck tribe Mergini are described based on geographic locations and distribution in North America, geomorphology, vegetation and soil types, and fresh water and marine characteristics. The dynamics of habitats are discussed in light of natural and anthropogenic events that shape areas important to sea ducks. Strategies for sea duck habitat management are outlined and recommendations for international collaboration to preserve key terrestrial and aquatic habitats are advanced. We follow the definition of habitat advanced by Odum (1971), which is the place or space where an organism lives. Weller (1999) emphasized that habitats for waterbirds required presence of sufficient resources (i.e., food, water, cover, space) for maintenance during a portion of their annual cycle. Habitats exploited by North American sea ducks are diverse, widespread across the continent and adjacent marine waters and until recently, most were only superficially known. A 15-year-long effort funded research on sea duck habitats through the Sea Duck Joint Venture and the Endangered or Threatened Species programs of the United States and Canada. Nevertheless, important gaps remain in our understanding of key elements required by some species during various life stages. Many significant habitats, especially staging and wintering sites, have been and continue to be destroyed or altered by anthropogenic activities. The goal of this chapter is to develop a comprehensive summary of marine, freshwater, and terrestrial habitats and their characteristics by considering sea duck species with similar needs as groups within the tribe Mergini. Additionally, we examine threats and changes to sea duck habitats from human-caused and natural events. Last, we evaluate conservation and management programs underway or available for maintenance and enhancement of habitats critical for sea ducks.

Wildlife habitat considerations

Treesearch

Helen Y. Smith

2000-01-01

Fire, insects, disease, harvesting, and precommercial thinning all create mosaics on Northern Rocky Mountain landscapes. These mosaics are important for faunal habitat. Consequently, changes such as created openings or an increase in heavily stocked areas affect the water, cover, and food of forest habitats. The “no action” alternative in ecosystem management of low...

Vision in the dimmest habitats on earth.

PubMed

Warrant, Eric

2004-10-01

A very large proportion of the world's animal species are active in dim light, either under the cover of night or in the depths of the sea. The worlds they see can be dim and extended, with light reaching the eyes from all directions at once, or they can be composed of bright point sources, like the multitudes of stars seen in a clear night sky or the rare sparks of bioluminescence that are visible in the deep sea. The eye designs of nocturnal and deep-sea animals have evolved in response to these two very different types of habitats, being optimised for maximum sensitivity to extended scenes, or to point sources, or to both. After describing the many visual adaptations that have evolved across the animal kingdom for maximising sensitivity to extended and point-source scenes, I then use case studies from the recent literature to show how these adaptations have endowed nocturnal animals with excellent vision. Nocturnal animals can see colour and negotiate dimly illuminated obstacles during flight. They can also navigate using learned terrestrial landmarks, the constellations of stars or the dim pattern of polarised light formed around the moon. The conclusion from these studies is clear: nocturnal habitats are just as rich in visual details as diurnal habitats are, and nocturnal animals have evolved visual systems capable of exploiting them. The same is certainly true of deep-sea animals, as future research will no doubt reveal.

Quantifying home range habitat requirements for bobcats (Lynx rufus) in Vermont, USA

USGS Publications Warehouse

Donovan, Therese; Freeman, Mark; Abouelezz, Hanem; Royar, Kim; Howard, Alan D.; Mickey, R.

2011-01-01

We demonstrate how home range and habitat use analysis can inform landscape-scale conservation planning for the bobcat, Lynx rufus, in Vermont USA. From 2005 to 2008, we outfitted fourteen bobcats with GPS collars that collected spatially explicit locations from individuals every 4 h for 3–4 months. Kernel home range techniques were used to estimate home range size and boundaries, and to quantify the utilization distribution (UD), which is a spatially explicit, topographic mapping of how different areas within the home range are used. We then used GIS methods to quantify both biotic (e.g. habitat types, stream density) and abiotic (e.g. slope) resources within each bobcat’s home range. Across bobcats, upper 20th UD percentiles (core areas) had 18% less agriculture, 42% less development, 26% more bobcat habitat (shrub, deciduous, coniferous forest, and wetland cover types), and 33% lower road density than lower UD percentiles (UD valleys). For each bobcat, we used Akaike’s Information Criterion (AIC) to evaluate and compare 24 alternative Resource Utilization Functions (hypotheses) that could explain the topology of the individual’s UD. A model-averaged population-level Resource Utilization Function suggested positive responses to shrub, deciduous, coniferous forest, and wetland cover types within 1 km of a location, and negative responses to roads and mixed forest cover types within 1 km of a location. Applying this model-averaged function to each pixel in the study area revealed habitat suitability for bobcats across the entire study area, with suitability scores ranging between −1.69 and 1.44, where higher values were assumed to represent higher quality habitat. The southern Champlain Valley, which contained ample wetland and shrub habitat, was a concentrated area of highly suitable habitat, while areas at higher elevation areas were less suitable. Female bobcat home ranges, on average, had an average habitat suitability score of near 0, indicating

Molecular architecture of botulinum neurotoxin E revealed by single particle electron microscopy.

PubMed

Fischer, Audrey; Garcia-Rodriguez, Consuelo; Geren, Isin; Lou, Jianlong; Marks, James D; Nakagawa, Terunaga; Montal, Mauricio

2008-02-15

Clostridial botulinum neurotoxin (BoNT) causes a neuroparalytic condition recognized as botulism by arresting synaptic vesicle exocytosis. Although the crystal structures of full-length BoNT/A and BoNT/B holotoxins are known, the molecular architecture of the five other serotypes remains elusive. Here, we present the structures of BoNT/A and BoNT/E using single particle electron microscopy. Labeling of the particles with three different monoclonal antibodies raised against BoNT/E revealed the positions of their epitopes in the electron microscopy structure, thereby identifying the three hallmark domains of BoNT (protease, translocation, and receptor binding). Correspondingly, these antibodies selectively inhibit BoNT translocation activity as detected using a single molecule assay. The global structure of BoNT/E is strikingly different from that of BoNT/A despite strong sequence similarity. We postulate that the unique architecture of functionally conserved modules underlies the distinguishing attributes of BoNT/E and contributes to differences with BoNT/A.

Assessing critical habitat: Evaluating the relative contribution of habitats to population persistence

EPA Science Inventory

1. A principal challenge of species conservation is to identify the specific habitats that are essential for long-term persistence or recovery of species at risk. However, many commonly used approaches to identifying important habitats do not provide direct insight into the contr...

Sound solutions for habitat monitoring

Treesearch

Mary M. Rowland; Lowell H. Suring; Christina D. Vojta

2015-01-01

For agencies and organizations to effectively manage wildlife, knowledge about the status and trend of wildlife habitat is critical. Traditional wildlife monitoring, however, has focused on populations rather than habitat, because ultimately population status drives long-term species viability. Still, habitat loss has contributed to the decline of nearly all at-risk...

MALDI-TOF mass spectrometry imaging reveals molecular level changes in ultrahigh molecular weight polyethylene joint implants in correlation with lipid adsorption.

PubMed

Fröhlich, Sophie M; Archodoulaki, Vasiliki-Maria; Allmaier, Günter; Marchetti-Deschmann, Martina

2014-10-07

Ultrahigh molecular weight polyethylene (PE-UHMW), a material with high biocompatibility and excellent mechanical properties, is among the most commonly used materials for acetabular cup replacement in artificial joint systems. It is assumed that the interaction with synovial fluid in the biocompartment leads to significant changes relevant to material failure. In addition to hyaluronic acid, lipids are particularly relevant for lubrication in an articulating process. This study investigates synovial lipid adsorption on two different PE-UHMW materials (GUR-1050 and vitamin E-doped) in an in vitro model system by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry imaging (MSI). Lipids were identified by high performance thin layer chromatography (HP-TLC) and tandem mass spectrometry (MS/MS) analysis, with an analytical focus on phospholipids and cholesterol, both being species of high importance for lubrication. Scanning electron microscopy (SEM) analysis was applied in the study to correlate molecular information with PE-UHMW material qualities. It is demonstrated that lipid adsorption preferentially occurs in rough or oxidized polymer regions. Polymer modifications were colocalized with adsorbed lipids and found with high density in regions identified by SEM. Explanted, the in vivo polymer material showed comparable and even more obvious polymer damage and lipid adsorption when compared with the static in vitro model. A three-dimensional reconstruction of MSI data from consecutive PE-UHMW slices reveals detailed information about the diffusion process of lipids in the acetabular cup and provides, for the first time, a promising starting point for future studies correlating molecular information with commonly used techniques for material analysis (e.g., Fourier-transform infrared spectroscopy, nanoindentation).

Habitat use by fishes of Lake Superior. II. Consequences of diel habitat use for habitat linkages and habitat coupling in nearshore and offshore waters

USGS Publications Warehouse

Gorman, Owen T.; Yule, Daniel L.; Stockwell, Jason D.

2012-01-01

Diel migration patterns of fishes in nearshore (15–80 m depth) and offshore (>80 m) waters of Lake Superior were examined to assess the potential for diel migration to link benthic and pelagic, and nearshore and offshore habitats. In our companion article, we described three types of diel migration: diel vertical migration (DVM), diel bank migration (DBM), and no diel migration. DVM was expressed by fishes migrating from benthopelagic to pelagic positions and DBM was expressed by fishes migrating horizontally from deep to shallow waters at night. Fishes not exhibiting diel migration typically showed increased activity by moving from benthic to benthopelagic positions within demersal habitat. The distribution and biomass of fishes in Lake Superior was characterized by examining 704 bottom trawl samples collected between 2001 and 2008 from four depth zones: ≤40, 41–80, 81–160, and >160 m. Diel migration behaviors of fishes described in our companion article were applied to estimates of areal biomass (kg ha−1) for each species by depth zone. The relative strength of diel migrations were assessed by applying lake area to areal biomass estimates for each species by depth zone to yield estimates of lake-wide biomass (metric tonnes). Overall, species expressing DVM accounted for 83%, DBM 6%, and non-migration 11% of the total lake-wide community biomass. In nearshore waters, species expressing DVM represented 74% of the biomass, DBM 25%, and non-migration 1%. In offshore waters, species expressing DVM represented 85%, DBM 1%, and non-migration 14% of the biomass. Of species expressing DVM, 83% of total biomass occurred in offshore waters. Similarly, 97% of biomass of non-migrators occurred in offshore waters while 83% of biomass of species expressing DBM occurred in nearshore waters. A high correlation (R2 = 0.996) between lake area and community biomass by depth zone resulted in 81% of the lake-wide biomass occurring in offshore waters. Accentuating this

Is the microplastic selective according to the habitat? Records in amphioxus sands, Mäerl bed habitats and Cymodocea nodosa habitats.

PubMed

Renzi, Monia; Blašković, Andrea; Fastelli, Paolo; Marcelli, Massimiliano; Guerranti, Cristiana; Cannas, Susanna; Barone, Lorenzo; Massara, Francesca

2018-05-01

This study estimated for the first time the total loads of plastic litter (macro- meso- and micro-plastics) in sediments of different habitat types from the Northern Adriatic Sea. Samples were collected in March 2016. The sampling sites were settled in shoreline, on the C. nodosa bottoms, Amphioxus sands, and Mäerl bed habitats. Microplastics items were present in all sampling site and ranging within 137-703 items/kg d.w. from Mäerl bed habitat to the shoreline. In C. nodosa bottoms 170 items/kg d.w. were found, while in Amphioxus sands were recorded on average 194 items/kg d.w. Due to the absence of statistical associations among litter levels and abundance of B. lanceolatum in the study area, this research present the needs to develop a new method and more research to for the evaluation of how much the interrelation between sensible habitats and microplastic exist. Copyright © 2018 Elsevier Ltd. All rights reserved.

Habitat Heterogeneity Variably Influences Habitat Selection by Wild Herbivores in a Semi-Arid Tropical Savanna Ecosystem

PubMed Central

Muposhi, Victor K.; Gandiwa, Edson; Chemura, Abel; Bartels, Paul; Makuza, Stanley M.; Madiri, Tinaapi H.

2016-01-01

An understanding of the habitat selection patterns by wild herbivores is critical for adaptive management, particularly towards ecosystem management and wildlife conservation in semi arid savanna ecosystems. We tested the following predictions: (i) surface water availability, habitat quality and human presence have a strong influence on the spatial distribution of wild herbivores in the dry season, (ii) habitat suitability for large herbivores would be higher compared to medium-sized herbivores in the dry season, and (iii) spatial extent of suitable habitats for wild herbivores will be different between years, i.e., 2006 and 2010, in Matetsi Safari Area, Zimbabwe. MaxEnt modeling was done to determine the habitat suitability of large herbivores and medium-sized herbivores. MaxEnt modeling of habitat suitability for large herbivores using the environmental variables was successful for the selected species in 2006 and 2010, except for elephant (Loxodonta africana) for the year 2010. Overall, large herbivores probability of occurrence was mostly influenced by distance from rivers. Distance from roads influenced much of the variability in the probability of occurrence of medium-sized herbivores. The overall predicted area for large and medium-sized herbivores was not different. Large herbivores may not necessarily utilize larger habitat patches over medium-sized herbivores due to the habitat homogenizing effect of water provisioning. Effect of surface water availability, proximity to riverine ecosystems and roads on habitat suitability of large and medium-sized herbivores in the dry season was highly variable thus could change from one year to another. We recommend adaptive management initiatives aimed at ensuring dynamic water supply in protected areas through temporal closure and or opening of water points to promote heterogeneity of wildlife habitats. PMID:27680673

Incubation success and habitat selection of shore-spawning kokanee Onchorhynchus nerka: effects of water level regulation and habitat characteristics.

USGS Publications Warehouse

Whitlock, Steven L.; Quist, Michael C.; Dux, Andrew M.

2014-01-01

Changes to water-level regimes have been known to restructure fish assemblages and interfere with the population dynamics of both littoral and pelagic species. The effect of altered water-level regimes on shore-spawning kokanee Oncorhynchus nerka incubation success was evaluated using a comprehensive in situ study in Lake Pend Oreille, ID, USA. Survival was not related to substrate size composition or depth, indicating that shore-spawning kokanee do not currently receive a substrate-mediated survival benefit from higher winter water levels. Substrate composition also did not differ among isobaths in the nearshore area. On average, the odds of an egg surviving to the preemergent stage were more than three times greater for sites in downwelling areas than those lacking downwelling. This study revealed that shoreline spawning habitat is not as limited as previously thought. Downwelling areas appear to contribute substantially to shore-spawning kokanee recruitment. This research illustrates the value of rigorous in situ studies both for testing potential mechanisms underlying population trends and providing insight into spawning habitat selection.

Spatiotemporal patterns and habitat associations of smallmouth bass (Micropterus dolomieu) invading salmon-rearing habitat

USGS Publications Warehouse

Lawrence, David J.; Olden, Julian D.; Torgersen, Christian E.

2012-01-01

1. Smallmouth bass (Micropterus dolomieu) have been widely introduced to fresh waters throughout the world to promote recreational fishing opportunities. In the Pacific Northwest (U.S.A.), upstream range expansions of predatory bass, especially into subyearling salmon-rearing grounds, are of increasing conservation concern, yet have received little scientific inquiry. Understanding the habitat characteristics that influence bass distribution and the timing and extent of bass and salmon overlap will facilitate the development of management strategies that mitigate potential ecological impacts of bass.2. We employed a spatially continuous sampling design to determine the extent of bass and subyearling Chinook salmon (Oncorhynchus tshawytscha) sympatry in the North Fork John Day River (NFJDR), a free-flowing river system in the Columbia River Basin that contains an upstream expanding population of non-native bass. Extensive (i.e. 53 km) surveys were conducted over 2 years and during an early and late summer period of each year, because these seasons provide a strong contrast in the river’s water temperature and flow condition. Classification and regression trees were applied to determine the primary habitat correlates of bass abundance at reach and channel-unit scales.3. Our study revealed that bass seasonally occupy up to 22% of the length of the mainstem NFJDR where subyearling Chinook salmon occur, and the primary period of sympatry between these species was in the early summer and not during peak water temperatures in late summer. Where these species co-occurred, bass occupied 60–76% of channel units used by subyearling Chinook salmon in the early summer and 28–46% of the channel units they occupied in the late summer. Because these rearing salmon were well below the gape limitation of bass, this overlap could result in either direct predation or sublethal effects of bass on subyearling Chinook salmon. The upstream extent of bass increased 10–23�

Coral reef habitats as surrogates of species, ecological functions, and ecosystem services.

PubMed

Mumby, Peter J; Broad, Kenneth; Brumbaugh, Daniel R; Dahlgren, Craig P; Harborne, Alastair R; Hastings, Alan; Holmes, Katherine E; Kappel, Carrie V; Micheli, Fiorenza; Sanchirico, James N

2008-08-01

Habitat maps are often the core spatially consistent data set on which marine reserve networks are designed, but their efficacy as surrogates for species richness and applicability to other conservation measures is poorly understood. Combining an analysis of field survey data, literature review, and expert assessment by a multidisciplinary working group, we examined the degree to which Caribbean coastal habitats provide useful planning information on 4 conservation measures: species richness, the ecological functions of fish species, ecosystem processes, and ecosystem services. Approximately one-quarter to one-third of benthic invertebrate species and fish species (disaggregated by life phase; hereafter fish species) occurred in a single habitat, and Montastraea-dominated forereefs consistently had the highest richness of all species, processes, and services. All 11 habitats were needed to represent all 277 fish species in the seascape, although reducing the conservation target to 95% of species approximately halved the number of habitats required to ensure representation. Species accumulation indices (SAIs) were used to compare the efficacy of surrogates and revealed that fish species were a more appropriate surrogate of benthic species (SAI = 71%) than benthic species were for fishes (SAI = 42%). Species of reef fishes were also distributed more widely across the seascape than invertebrates and therefore their use as a surrogate simultaneously included mangroves, sea grass, and coral reef habitats. Functional classes of fishes served as effective surrogates of fish and benthic species which, given their ease to survey, makes them a particularly useful measure for conservation planning. Ecosystem processes and services exhibited great redundancy among habitats and were ineffective as surrogates of species. Therefore, processes and services in this case were generally unsuitable for a complementarity-based approach to reserve design. In contrast, the representation

Pervasive Local-Scale Tree-Soil Habitat Association in a Tropical Forest Community.

PubMed

Allié, Elodie; Pélissier, Raphaël; Engel, Julien; Petronelli, Pascal; Freycon, Vincent; Deblauwe, Vincent; Soucémarianadin, Laure; Weigel, Jean; Baraloto, Christopher

2015-01-01

We examined tree-soil habitat associations in lowland forest communities at Paracou, French Guiana. We analyzed a large dataset assembling six permanent plots totaling 37.5 ha, in which extensive LIDAR-derived topographical data and soil chemical and physical data have been integrated with precise botanical determinations. Map of relative elevation from the nearest stream summarized both soil fertility and hydromorphic characteristics, with seasonally inundated bottomlands having higher soil phosphate content and base saturation, and plateaus having higher soil carbon, nitrogen and aluminum contents. We employed a statistical test of correlations between tree species density and environmental maps, by generating Monte Carlo simulations of random raster images that preserve autocorrelation of the original maps. Nearly three fourths of the 94 taxa with at least one stem per ha showed a significant correlation between tree density and relative elevation, revealing contrasted species-habitat associations in term of abundance, with seasonally inundated bottomlands (24.5% of species) and well-drained plateaus (48.9% of species). We also observed species preferences for environments with or without steep slopes (13.8% and 10.6%, respectively). We observed that closely-related species were frequently associated with different soil habitats in this region (70% of the 14 genera with congeneric species that have a significant association test) suggesting species-habitat associations have arisen multiple times in this tree community. We also tested if species with similar habitat preferences shared functional strategies. We found that seasonally inundated forest specialists tended to have smaller stature (maximum diameter) than species found on plateaus. Our results underline the importance of tree-soil habitat associations in structuring diverse communities at fine spatial scales and suggest that additional studies are needed to disentangle community assembly mechanisms

Pervasive Local-Scale Tree-Soil Habitat Association in a Tropical Forest Community

PubMed Central

Allié, Elodie; Pélissier, Raphaël; Engel, Julien; Petronelli, Pascal; Freycon, Vincent; Deblauwe, Vincent; Soucémarianadin, Laure; Weigel, Jean; Baraloto, Christopher

2015-01-01

We examined tree-soil habitat associations in lowland forest communities at Paracou, French Guiana. We analyzed a large dataset assembling six permanent plots totaling 37.5 ha, in which extensive LIDAR-derived topographical data and soil chemical and physical data have been integrated with precise botanical determinations. Map of relative elevation from the nearest stream summarized both soil fertility and hydromorphic characteristics, with seasonally inundated bottomlands having higher soil phosphate content and base saturation, and plateaus having higher soil carbon, nitrogen and aluminum contents. We employed a statistical test of correlations between tree species density and environmental maps, by generating Monte Carlo simulations of random raster images that preserve autocorrelation of the original maps. Nearly three fourths of the 94 taxa with at least one stem per ha showed a significant correlation between tree density and relative elevation, revealing contrasted species-habitat associations in term of abundance, with seasonally inundated bottomlands (24.5% of species) and well-drained plateaus (48.9% of species). We also observed species preferences for environments with or without steep slopes (13.8% and 10.6%, respectively). We observed that closely-related species were frequently associated with different soil habitats in this region (70% of the 14 genera with congeneric species that have a significant association test) suggesting species-habitat associations have arisen multiple times in this tree community. We also tested if species with similar habitat preferences shared functional strategies. We found that seasonally inundated forest specialists tended to have smaller stature (maximum diameter) than species found on plateaus. Our results underline the importance of tree-soil habitat associations in structuring diverse communities at fine spatial scales and suggest that additional studies are needed to disentangle community assembly mechanisms

MODELING PHYSICAL HABITAT PARAMETERS

EPA Science Inventory

Salmonid populations can be affected by alterations in stream physical habitat. Fish productivity is determined by the stream's physical habitat structure ( channel form, substrate distribution, riparian vegetation), water quality, flow regime and inputs from the watershed (sedim...

Indicators: Physical Habitat Complexity

EPA Pesticide Factsheets

Physical habitat complexity measures the amount and variety of all types of cove at the water’s edge in lakes. In general, dense and varied shoreline habitat is able to support more diverse communities of aquatic life.

Microscopic properties of ionic liquid/organic semiconductor interfaces revealed by molecular dynamics simulations.

PubMed

Yokota, Yasuyuki; Miyamoto, Hiroo; Imanishi, Akihito; Takeya, Jun; Inagaki, Kouji; Morikawa, Yoshitada; Fukui, Ken-Ichi

2018-05-09

Electric double-layer transistors based on ionic liquid/organic semiconductor interfaces have been extensively studied during the past decade because of their high carrier densities at low operation voltages. Microscopic structures and the dynamics of ionic liquids likely determine the device performance; however, knowledge of these is limited by a lack of appropriate experimental tools. In this study, we investigated ionic liquid/organic semiconductor interfaces using molecular dynamics to reveal the microscopic properties of ionic liquids. The organic semiconductors include pentacene, rubrene, fullerene, and 7,7,8,8-tetracyanoquinodimethane (TCNQ). While ionic liquids close to the substrate always form the specific layered structures, the surface properties of organic semiconductors drastically alter the ionic dynamics. Ionic liquids at the fullerene interface behave as a two-dimensional ionic crystal because of the energy gain derived from the favorable electrostatic interaction on the corrugated periodic substrate.

DHA-fluorescent probe is sensitive to membrane order and reveals molecular adaptation of DHA in ordered lipid microdomains☆

PubMed Central

Teague, Heather; Ross, Ron; Harris, Mitchel; Mitchell, Drake C.; Shaikh, Saame Raza

2012-01-01

Docosahexaenoic acid (DHA) disrupts the size and order of plasma membrane lipid microdomains in vitro and in vivo. However, it is unknown how the highly disordered structure of DHA mechanistically adapts to increase the order of tightly packed lipid microdomains. Therefore, we studied a novel DHA-Bodipy fluorescent probe to address this issue. We first determined if the DHA-Bodipy probe localized to the plasma membrane of primary B and immortal EL4 cells. Image analysis revealed that DHA-Bodipy localized into the plasma membrane of primary B cells more efficiently than EL4 cells. We then determined if the probe detected changes in plasma membrane order. Quantitative analysis of time-lapse movies established that DHA-Bodipy was sensitive to membrane molecular order. This allowed us to investigate how DHA-Bodipy physically adapted to ordered lipid microdomains. To accomplish this, we employed steady-state and time-resolved fluorescence anisotropy measurements in lipid vesicles of varying composition. Similar to cell culture studies, the probe was highly sensitive to membrane order in lipid vesicles. Moreover, these experiments revealed, relative to controls, that upon incorporation into highly ordered microdomains, DHA-Bodipy underwent an increase in its fluorescence lifetime and molecular order. In addition, the probe displayed a significant reduction in its rotational diffusion compared to controls. Altogether, DHA-Bodipy was highly sensitive to membrane order and revealed for the first time that DHA, despite its flexibility, could become ordered with less rotational motion inside ordered lipid microdomains. Mechanistically, this explains how DHA acyl chains can increase order upon formation of lipid microdomains in vivo. PMID:22841541

Predictive Seagrass Habitat Model

EPA Science Inventory

Restoration of ecosystem services provided by seagrass habitats in estuaries requires a firm understanding of the modes of action of multiple interacting stressors including nutrients, climate change, coastal land-use change, and habitat modification. We explored the application...

Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2.

PubMed

Spellmon, Nicholas; Sun, Xiaonan; Sirinupong, Nualpun; Edwards, Brian; Li, Chunying; Yang, Zhe

2015-01-01

SMYD proteins are an exciting field of study as they are linked to many types of cancer-related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open-closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative correlated inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to by a twisting motion of the C-lobe with respect to the N-lobe and a clamshell-like motion between the lobes. Dynamical network analysis defines possible allosteric paths for the correlated dynamics. There are nine communities in the dynamical network with six in the N-lobe and three in the C-lobe, and the communication between the lobes is mediated by a lobe-bridging β hairpin. This study provides insight into the dynamical nature of SMYD2 and could facilitate better understanding of SMYD2 substrate specificity.

Invertebrate population genetics across Earth's largest habitat: The deep-sea floor.

PubMed

Taylor, M L; Roterman, C N

2017-10-01

Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Can Sgr A* flares reveal the molecular gas density PDF?

NASA Astrophysics Data System (ADS)

Churazov, E.; Khabibullin, I.; Sunyaev, R.; Ponti, G.

2017-11-01

Illumination of dense gas in the Central Molecular Zone by powerful X-ray flares from Sgr A* leads to prominent structures in the reflected emission that can be observed long after the end of the flare. By studying this emission, we learn about past activity of the supermassive black hole in our Galactic Center and, at the same time, we obtain unique information on the structure of molecular clouds that is essentially impossible to get by other means. Here we discuss how X-ray data can improve our knowledge of both sides of the problem. Existing data already provide (I) an estimate of the flare age, (II) a model-independent lower limit on the luminosity of Sgr A* during the flare and (III) an estimate of the total emitted energy during Sgr A* flare. On the molecular clouds side, the data clearly show a voids-and-walls structure of the clouds and can provide an almost unbiased probe of the mass/density distribution of the molecular gas with the hydrogen column densities lower than few 1023 cm-2. For instance, the probability distribution function of the gas density PDF(ρ) can be measured this way. Future high energy resolution X-ray missions will provide the information on the gas velocities, allowing, for example, a reconstruction of the velocity field structure functions and cross-matching the X-ray and molecular data based on positions and velocities.

Effects of spatial habitat heterogeneity on habitat selection and annual fecundity for a migratory forest songbird

USGS Publications Warehouse

Cornell, K.L.; Donovan, T.M.

2010-01-01

Understanding how spatial habitat patterns influence abundance and dynamics of animal populations is a primary goal in landscape ecology. We used an information-theoretic approach to investigate the association between habitat patterns at multiple spatial scales and demographic patterns for black-throated blue warblers (Dendroica caerulescens) at 20 study sites in west-central Vermont, USA from 2002 to 2005. Sites were characterized by: (1) territory-scale shrub density, (2) patch-scale shrub density occurring within 25 ha of territories, and (3) landscape-scale habitat patterns occurring within 5 km radius extents of territories. We considered multiple population parameters including abundance, age ratios, and annual fecundity. Territory-scale shrub density was most important for determining abundance and age ratios, but landscape-scale habitat structure strongly influenced reproductive output. Sites with higher territory-scale shrub density had higher abundance, and were more likely to be occupied by older, more experienced individuals compared to sites with lower shrub density. However, annual fecundity was higher on sites located in contiguously forested landscapes where shrub density was lower than the fragmented sites. Further, effects of habitat pattern at one spatial scale depended on habitat conditions at different scales. For example, abundance increased with increasing territory-scale shrub density, but this effect was much stronger in fragmented landscapes than in contiguously forested landscapes. These results suggest that habitat pattern at different spatial scales affect demographic parameters in different ways, and that effects of habitat patterns at one spatial scale depends on habitat conditions at other scales. ?? Springer Science+Business Media B.V. 2009.

Selecting compact habitat reserves for species with differential habitat size needs

Treesearch

Vladimir Marianov; Charles ReVelle; Stephanie Snyder

2008-01-01

We propose a model for the design of protected habitat reserves, which maximizes the number of species represented at least once in a limited set of reserved sites or parcels. Most models for reserve design do not differentiate eligible habitat sites by their size. Also, they assume that protection is guaranteed through the selection of one site for any species, not...

Molecular imaging reveals elevated VEGFR-2 expression in retinal capillaries in diabetes: a novel biomarker for early diagnosis

PubMed Central

Sun, Dawei; Nakao, Shintaro; Xie, Fang; Zandi, Souska; Bagheri, Abouzar; Kanavi, Mozhgan Rezaei; Samiei, Shahram; Soheili, Zahra-Soheila; Frimmel, Sonja; Zhang, Zhongyu; Ablonczy, Zsolt; Ahmadieh, Hamid; Hafezi-Moghadam, Ali

2014-01-01

Diabetic retinopathy (DR) is a microvascular complication of diabetes and a leading cause of vision loss. Biomarkers and methods for early diagnosis of DR are urgently needed. Using a new molecular imaging approach, we show up to 94% higher accumulation of custom designed imaging probes against vascular endothelial growth factor receptor 2 (VEGFR-2) in retinal and choroidal vessels of diabetic animals (P<0.01), compared to normal controls. More than 80% of the VEGFR-2 in the diabetic retina was in the capillaries, compared to 47% in normal controls (P<0.01). Angiography in rabbit retinas revealed microvascular capillaries to be the location for VEGF-A-induced leakage, as expressed by significantly higher rate of fluorophore spreading with VEGF-A injection when compared to vehicle control (26±2 vs. 3±1 μm/s, P<0.05). Immunohistochemistry showed VEGFR-2 expression in capillaries of diabetic animals but not in normal controls. Macular vessels from diabetic patients (n=7) showed significantly more VEGFR-2 compared to nondiabetic controls (n=5) or peripheral retinal regions of the same retinas (P<0.01 in both cases). Here we introduce a new approach for early diagnosis of DR and VEGFR-2 as a molecular marker. VEGFR-2 could become a key diagnostic target, one that might help to prevent retinal vascular leakage and proliferation in diabetic patients.—Sun, D., Nakao, S., Xie, F., Zandi, S., Bagheri, A., Kanavi, M. R., Samiei, S., Soheili, Z.-S., Frimmel, S., Zhang, Z., Ablonczy, Z., Ahmadieh, H., Hafezi-Moghadam, A. Molecular imaging reveals elevated VEGFR-2 expression in retinal capillaries in diabetes: a novel biomarker for early diagnosis. PMID:24903276

Salinity Is an Agent of Divergent Selection Driving Local Adaptation of Arabidopsis to Coastal Habitats1[OPEN

PubMed Central

Teres, Joana; Bomblies, Kirsten; Douglas, Alex; Salt, David E.

2015-01-01

Understanding the molecular mechanism of adaptive evolution in plants provides insights into the selective forces driving adaptation and the genetic basis of adaptive traits with agricultural value. The genomic resources available for Arabidopsis (Arabidopsis thaliana) make it well suited to the rapid molecular dissection of adaptive processes. Although numerous potentially adaptive loci have been identified in Arabidopsis, the consequences of divergent selection and migration (both important aspects of the process of local adaptation) for Arabidopsis are not well understood. Here, we use a multiyear field-based reciprocal transplant experiment to detect local populations of Arabidopsis composed of multiple small stands of plants (demes) that are locally adapted to the coast and adjacent inland habitats in northeastern Spain. We identify fitness tradeoffs between plants from these different habitats when grown together in inland and coastal common gardens and also, under controlled conditions in soil excavated from coastal and inland sites. Plants from the coastal habitat also outperform those from inland when grown under high salinity, indicating local adaptation to soil salinity. Sodium can be toxic to plants, and we find its concentration to be elevated in soil and plants sampled at the coast. We conclude that the local adaptation that we observe between adjacent coastal and inland populations is caused by ongoing divergent selection driven by the differential salinity between coastal and inland soils. PMID:26034264

Prioritizing Urban Habitats for Connectivity Conservation: Integrating Centrality and Ecological Metrics.

PubMed

Poodat, Fatemeh; Arrowsmith, Colin; Fraser, David; Gordon, Ascelin

2015-09-01

Connectivity among fragmented areas of habitat has long been acknowledged as important for the viability of biological conservation, especially within highly modified landscapes. Identifying important habitat patches in ecological connectivity is a priority for many conservation strategies, and the application of 'graph theory' has been shown to provide useful information on connectivity. Despite the large number of metrics for connectivity derived from graph theory, only a small number have been compared in terms of the importance they assign to nodes in a network. This paper presents a study that aims to define a new set of metrics and compares these with traditional graph-based metrics, used in the prioritization of habitat patches for ecological connectivity. The metrics measured consist of "topological" metrics, "ecological metrics," and "integrated metrics," Integrated metrics are a combination of topological and ecological metrics. Eight metrics were applied to the habitat network for the fat-tailed dunnart within Greater Melbourne, Australia. A non-directional network was developed in which nodes were linked to adjacent nodes. These links were then weighted by the effective distance between patches. By applying each of the eight metrics for the study network, nodes were ranked according to their contribution to the overall network connectivity. The structured comparison revealed the similarity and differences in the way the habitat for the fat-tailed dunnart was ranked based on different classes of metrics. Due to the differences in the way the metrics operate, a suitable metric should be chosen that best meets the objectives established by the decision maker.

Sedimentary facies, geomorphic features and habitat distribution at the Hudson Canyon head from AUV multibeam data

NASA Astrophysics Data System (ADS)

Pierdomenico, Martina; Guida, Vincent G.; Macelloni, Leonardo; Chiocci, Francesco L.; Rona, Peter A.; Scranton, Mary I.; Asper, Vernon; Diercks, Arne

2015-11-01

Mapping of physical benthic habitats at the head of Hudson Canyon was performed by means of integrated analysis of acoustic data, video surveys and seafloor sampling. Acoustic mapping, performed using AUV-mounted multibeam sonar, provided ultra-high resolution bathymetric and backscatter imagery for the identification of geomorphological features and the characterization of surficial sediments. Habitat characterization in terms of seafloor texture and identification of benthic and demersal communities was accomplished by visual analysis of still photographs from underwater vehicles. Habitat classes were defined on the basis of the seafloor texture observed on photos and then compared with the geophysical data in order to associate habitats to acoustic classes and/or geomorphological features. This enabled us to infer habitat distribution on the basis of morpho-acoustic classes and extrapolate results over larger areas. Results from bottom trawling were used to determine the overall biodiversity within the identified habitats. Our analysis revealed a variety of topographic and sedimentological structures that provide a wide range of physical habitats. A variety of sandy and muddy substrates, gravel patches and mudstone outcrops host rich and varied faunal assemblages, including cold-water corals and sponge communities. Pockmark fields below 300 m depth suggest that methane-based chemosynthetic carbonate deposition may contributes to creation of specific benthic habitats. Hummocky terrain has been delineated along the canyon rims and associated with extensive, long-term burrowing activity by golden tilefish (Lopholatilus chamaeleonticeps). These results show the relationships of physical features to benthic habitat variation, support the notion of the area as a biodiversity hotspot and define essential habitats for planning of sustainable regional fisheries.

Gene flow connects coastal populations of a habitat specialist, the Clapper Rail Rallus crepitans

USGS Publications Warehouse

Coster, Stephanie S.; Welsh, Amy B.; Costanzo, Gary R.; Harding, Sergio R.; Anderson, James T.; Katzner, Todd

2018-01-01

Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographic range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of North America, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks, and a weak pattern of genetic differentiation that increased with geographic distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the North American Atlantic coast, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioral factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.

Breeding habitat associations and predicted distribution of an obligate tundra-breeding bird, Smith's Longspur

USGS Publications Warehouse

Wild, Teri C.; Kendall, Steven J.; Guldager, Nikki; Powell, Abby N.

2015-01-01

Smith's Longspur (Calcarius pictus) is a species of conservation concern which breeds in Arctic habitats that are expected to be especially vulnerable to climate change. We used bird presence and habitat data from point-transect surveys conducted at 12 sites across the Brooks Range, Alaska, 2003–2009, to identify breeding areas, describe local habitat associations, and identify suitable habitat using a predictive model of Smith's Longspur distribution. Smith's Longspurs were observed at seven sites, where they were associated with a variety of sedge–shrub habitats composed primarily of mosses, sedges, tussocks, and dwarf shrubs; erect shrubs were common but sparse. Nonmetric multidimensional scaling ordination of ground cover revealed positive associations of Smith's Longspur presence with sedges and mosses and a negative association with high cover of shrubs. To model predicted distribution, we used boosted regression trees to relate landscape variables to occurrence. Our model predicted that Smith's Longspurs may occur in valleys and foothills of the northeastern and southeastern mountains and in upland plateaus of the western mountains, and farther west than currently documented, over a predicted area no larger than 15% of the Brooks Range. With climate change, shrubs are expected to grow larger and denser, while soil moisture and moss cover are predicted to decrease. These changes may reduce Smith's Longspur habitat quality and limit distribution in the Brooks Range to poorly drained lowlands and alpine plateaus where sedge–shrub tundra is likely to persist. Conversely, northward advance of shrubs into sedge tundra may create suitable habitat, thus supporting a northward longspur distribution shift.

Alteration of biomacromolecule in corn by steam flaking in relation to biodegradation kinetics in ruminant, revealed with vibrational molecular spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-02-01

Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (P < 0.01) rumen degradable DM (RDDM) and starch (RDSt), but decreased (P < 0.01) rumen degradable protein (RDP). (3) Molecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (P < 0.01), but protein amides associated molecular spectral intensities were lower (P < 0.01) in SFC. (4). The molecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (P < 0.10) associated with RDDM and RDSt and protein amide spectral intensities were positively (P < 0.10) associated with RDP. This results indicated that the steam flaking induced molecular structure changes had an interactive relationship with rumen degradation kinetics.

Habitat Suitability Index Models: Black-shouldered kite

USGS Publications Warehouse

Faanes, Craig A.; Howard, Rebecca J.

1987-01-01

A review and synthesis of existing information were used to develop a model for evaluating black-shouldered kite habitat quality. The model is scaled to produce an index between 0 (unsuitable habitat) to 1.0 (optimal habitat). Habitat suitability index models are designed for use with the Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service. Guidelines for model application are provided.

Anthropogenic areas as incidental substitutes for original habitat.

PubMed

Martínez-Abraín, Alejandro; Jiménez, Juan

2016-06-01

One speaks of ecological substitutes when an introduced species performs, to some extent, the ecosystem function of an extirpated native species. We suggest that a similar case exists for habitats. Species evolve within ecosystems, but habitats can be destroyed or modified by natural and human-made causes. Sometimes habitat alteration forces animals to move to or remain in a suboptimal habitat type. In that case, the habitat is considered a refuge, and the species is called a refugee. Typically refugee species have lower population growth rates than in their original habitats. Human action may lead to the unintended generation of artificial or semiartificial habitat types that functionally resemble the essential features of the original habitat and thus allow a population growth rate of the same magnitude or higher than in the original habitat. We call such areas substitution habitats and define them as human-made habitats within the focal species range that by chance are partial substitutes for the species' original habitat. We call species occupying a substitution habitat adopted species. These are 2 new terms in conservation biology. Examples of substitution habitats are dams for European otters, wheat and rice fields for many steppeland and aquatic birds, and urban areas for storks, falcons, and swifts. Although substitution habitats can bring about increased resilience against the agents of global change, the conservation of original habitat types remains a conservation priority. © 2016 Society for Conservation Biology.

Habitat Design Optimization and Analysis

NASA Technical Reports Server (NTRS)

SanSoucie, Michael P.; Hull, Patrick V.; Tinker, Michael L.

2006-01-01

Long-duration surface missions to the Moon and Mars will require habitats for the astronauts. The materials chosen for the habitat walls play a direct role in the protection against the harsh environments found on the surface. Choosing the best materials, their configuration, and the amount required is extremely difficult due to the immense size of the design region. Advanced optimization techniques are necessary for habitat wall design. Standard optimization techniques are not suitable for problems with such large search spaces; therefore, a habitat design optimization tool utilizing genetic algorithms has been developed. Genetic algorithms use a "survival of the fittest" philosophy, where the most fit individuals are more likely to survive and reproduce. This habitat design optimization tool is a multi-objective formulation of structural analysis, heat loss, radiation protection, and meteoroid protection. This paper presents the research and development of this tool.

Drought survival is a threshold function of habitat size and population density in a fish metapopulation.

PubMed

White, Richard S A; McHugh, Peter A; McIntosh, Angus R

2016-10-01

Because smaller habitats dry more frequently and severely during droughts, habitat size is likely a key driver of survival in populations during climate change and associated increased extreme drought frequency. Here, we show that survival in populations during droughts is a threshold function of habitat size driven by an interaction with population density in metapopulations of the forest pool dwelling fish, Neochanna apoda. A mark-recapture study involving 830 N. apoda individuals during a one-in-seventy-year extreme drought revealed that survival during droughts was high for populations occupying pools deeper than 139 mm, but declined steeply in shallower pools. This threshold was caused by an interaction between increasing population density and drought magnitude associated with decreasing habitat size, which acted synergistically to increase physiological stress and mortality. This confirmed two long-held hypotheses, firstly concerning the interactive role of population density and physiological stress, herein driven by habitat size, and secondly, the occurrence of drought survival thresholds. Our results demonstrate how survival in populations during droughts will depend strongly on habitat size and highlight that minimum habitat size thresholds will likely be required to maximize survival as the frequency and intensity of droughts are projected to increase as a result of global climate change. © 2016 John Wiley & Sons Ltd.

Retention of Habitat Complexity Minimizes Disassembly of Reef Fish Communities following Disturbance: A Large-Scale Natural Experiment

PubMed Central

Emslie, Michael J.; Cheal, Alistair J.; Johns, Kerryn A.

2014-01-01

High biodiversity ecosystems are commonly associated with complex habitats. Coral reefs are highly diverse ecosystems, but are under increasing pressure from numerous stressors, many of which reduce live coral cover and habitat complexity with concomitant effects on other organisms such as reef fishes. While previous studies have highlighted the importance of habitat complexity in structuring reef fish communities, they employed gradient or meta-analyses which lacked a controlled experimental design over broad spatial scales to explicitly separate the influence of live coral cover from overall habitat complexity. Here a natural experiment using a long term (20 year), spatially extensive (∼115,000 kms2) dataset from the Great Barrier Reef revealed the fundamental importance of overall habitat complexity for reef fishes. Reductions of both live coral cover and habitat complexity had substantial impacts on fish communities compared to relatively minor impacts after major reductions in coral cover but not habitat complexity. Where habitat complexity was substantially reduced, species abundances broadly declined and a far greater number of fish species were locally extirpated, including economically important fishes. This resulted in decreased species richness and a loss of diversity within functional groups. Our results suggest that the retention of habitat complexity following disturbances can ameliorate the impacts of coral declines on reef fishes, so preserving their capacity to perform important functional roles essential to reef resilience. These results add to a growing body of evidence about the importance of habitat complexity for reef fishes, and represent the first large-scale examination of this question on the Great Barrier Reef. PMID:25140801

Retention of habitat complexity minimizes disassembly of reef fish communities following disturbance: a large-scale natural experiment.

PubMed

Emslie, Michael J; Cheal, Alistair J; Johns, Kerryn A

2014-01-01

High biodiversity ecosystems are commonly associated with complex habitats. Coral reefs are highly diverse ecosystems, but are under increasing pressure from numerous stressors, many of which reduce live coral cover and habitat complexity with concomitant effects on other organisms such as reef fishes. While previous studies have highlighted the importance of habitat complexity in structuring reef fish communities, they employed gradient or meta-analyses which lacked a controlled experimental design over broad spatial scales to explicitly separate the influence of live coral cover from overall habitat complexity. Here a natural experiment using a long term (20 year), spatially extensive (∼ 115,000 kms(2)) dataset from the Great Barrier Reef revealed the fundamental importance of overall habitat complexity for reef fishes. Reductions of both live coral cover and habitat complexity had substantial impacts on fish communities compared to relatively minor impacts after major reductions in coral cover but not habitat complexity. Where habitat complexity was substantially reduced, species abundances broadly declined and a far greater number of fish species were locally extirpated, including economically important fishes. This resulted in decreased species richness and a loss of diversity within functional groups. Our results suggest that the retention of habitat complexity following disturbances can ameliorate the impacts of coral declines on reef fishes, so preserving their capacity to perform important functional roles essential to reef resilience. These results add to a growing body of evidence about the importance of habitat complexity for reef fishes, and represent the first large-scale examination of this question on the Great Barrier Reef.

Range and Primary Habitats of Hawaiian Insular False Killer Whales: Informing Determination of Critical Habitat

DTIC Science & Technology

2012-07-20

whales Eubalaena glacialis (in 1994), ‘ southern resident ’ killer whales (in 2006), North Pacific right whales E...reviewed evaluation of specific and essential habitat features. For example, for southern resident killer whales , a population that uses both US and...critical habitat for southern resident killer whale . Federal Register 71: 69054−69070 Federal Register (2008) Designation of critical habitat for

Accounting for groundwater in stream fish thermal habitat responses to climate change

USGS Publications Warehouse

Snyder, Craig D.; Hitt, Nathaniel P.; Young, John A.

2015-01-01

Forecasting climate change effects on aquatic fauna and their habitat requires an understanding of how water temperature responds to changing air temperature (i.e., thermal sensitivity). Previous efforts to forecast climate effects on brook trout habitat have generally assumed uniform air-water temperature relationships over large areas that cannot account for groundwater inputs and other processes that operate at finer spatial scales. We developed regression models that accounted for groundwater influences on thermal sensitivity from measured air-water temperature relationships within forested watersheds in eastern North America (Shenandoah National Park, USA, 78 sites in 9 watersheds). We used these reach-scale models to forecast climate change effects on stream temperature and brook trout thermal habitat, and compared our results to previous forecasts based upon large-scale models. Observed stream temperatures were generally less sensitive to air temperature than previously assumed, and we attribute this to the moderating effect of shallow groundwater inputs. Predicted groundwater temperatures from air-water regression models corresponded well to observed groundwater temperatures elsewhere in the study area. Predictions of brook trout future habitat loss derived from our fine-grained models were far less pessimistic than those from prior models developed at coarser spatial resolutions. However, our models also revealed spatial variation in thermal sensitivity within and among catchments resulting in a patchy distribution of thermally suitable habitat. Habitat fragmentation due to thermal barriers therefore may have an increasingly important role for trout population viability in headwater streams. Our results demonstrate that simple adjustments to air-water temperature regression models can provide a powerful and cost-effective approach for predicting future stream temperatures while accounting for effects of groundwater.

Prevalence and molecular characterization of Cryptosporidium in giant panda (Ailuropoda melanoleuca) in Sichuan province, China.

PubMed

Wang, Tao; Chen, Zuqin; Xie, Yue; Hou, Rong; Wu, Qidun; Gu, Xiaobing; Lai, Weiming; Peng, Xuerong; Yang, Guangyou

2015-06-25

Cryptosporidium spp. have been extensively reported to cause significant diarrheal disease in humans and domestic animals. On the contrary, little information is available on the prevalence and characterization of Cryptosporidium in wild animals in China, especially in giant pandas. The aim of the present study was to detect Cryptosporidium infections and identify Cryptosporidium species at the molecular level in both captive and wild giant pandas in Sichuan province, China. Using a PCR approach, we amplified and sequenced the 18S rRNA gene from 322 giant pandas fecal samples (122 from 122 captive individuals and 200 collected from four habitats) in Sichuan province, China. The Cryptosporidium species/genotypes were identified via a BLAST comparison against published Cryptosporidium sequences available in GenBank followed by phylogenetic analysis. The results revealed that both captive and wild giant pandas were infected with a single Cryptosporidium species, C. andersoni, at a prevalence of 15.6% (19/122) and 0.5% (1/200) in captive and wild giant pandas, respectively. The present study revealed the existence of C. andersoni in both captive and wild giant panda fecal samples for the first time, and also provided useful fundamental data for further research on the molecular epidemiology and control of Cryptosporidium infection in giant pandas.

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

PubMed

Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

2013-09-01

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

Molecular mechanism for the effects of trehalose on beta-hairpin folding revealed by molecular dynamics simulation.

PubMed

Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

2008-11-01

Recent work has shown that trehalose can facilitate and inhibit protein folding, but little is known about the molecular basis of these effects. Molecular-level insights into how the osmolyte affects protein folding are of significance for the rational design of small molecular additives for enhancing or hindering the folding of proteins. To investigate the molecular mechanisms of the facilitation and inhibition effects of trehalose on protein folding, molecular dynamics (MD) simulation of a beta-hairpin peptide (Trp-Arg-Tyr-Tyr-Glu-Ser-Ser-Leu-Glu-Pro-Glu-Pro-Asp) in different trehalose concentrations (0-0.26 mol/L) is performed using an all-atom model. It is found that at a proper trehalose concentration (0.065 mol/L), the peptide folds faster than that in water, but it cannot fold to the beta-hairpin at higher trehalose concentrations. Free energy landscape analysis indicates the presence of three intermediate states in both pure water and in 0.065 mol/L trehalose, but the potential energy barriers in the folding pathway decrease greatly in 0.065 mol/L trehalose, so the peptide folding is facilitated. Moreover, at this trehalose concentration, there is a favorable balance between the peptide backbone hydrogen bonds (H-bonds) and the peptide-trehalose H-bonds, leading to the stabilization of the folded peptide. At higher trehalose concentrations, however, trehalose molecules cluster in the peptide region and interact with the peptide via many H-bonds that prevent the peptide from folding to its native structure. The energy landscape analysis indicates that the potential energy barriers increase so greatly that the peptide cannot overcome it, getting trapped in a local free energy basin. The work reported herein has elucidated the molecular mechanism of the peptide folding in the presence of trehalose.

NEKTON-HABITAT ASSOCIATIONS IN YAQUINA BAY, OREGON

EPA Science Inventory

Habitat-based ecological risk assessments rely, in part, on estimates of the ecological value of the habitats at risk. To estimate estuarine habitat values with respect to the nekton (small fish, crabs and other invertebrates), we determined nekton-habitat associations in four i...

Genetic and epigenetic diversity and structure of Phragmites australis from local habitats of the Songnen Prairie using amplified fragment length polymorphism markers.

PubMed

Qiu, T; Jiang, L L; Yang, Y F

2016-08-19

The genetic and epigenetic diversity and structure of naturally occurring Phragmites australis populations occupying two different habitats on a small spatial scale in the Songnen Prairie in northeastern China were investigated by assessing amplified fragment length polymorphisms (AFLPs) and methylation-sensitive amplified polymorphisms (MSAPs) through fluorescent capillary detection. The two groups of P. australis were located in a seasonal waterlogged low-lying and alkalized meadow with a pH of 8-8.5 and in an alkaline patch without accumulated rainwater and with a pH greater than 10. These groups showed high levels of genetic diversity at the habitat level based on the percentage of polymorphic bands (90.32, 82.56%), Nei's gene diversity index (0.262, 0.248), and the Shannon diversity index (0.407, 0.383). Although little is known about the between-habitat genetic differentiation of P. australis on a small spatial scale, our results implied significant genetic differentiation between habitats. Extensive epigenetic diversity within habitats, along with clear differentiation, was found. Specifically, the former habitat (Habitat 1, designated H1) harbored higher levels of genetic and epigenetic diversity than the latter (Habitat 2, designated H2), and population-level diversity was also high. This study represents one of few attempts to predict habitat-based genetic differentiation of reeds on a small scale. These assessments of genetic and epigenetic variation are integral aspects of molecular ecological studies on P. australis. Possible causes for within- and between-habitat genetic and epigenetic variations are discussed.

Exploring deep sea habitats for baseline characterization using NOAA Ship Okeanos Explorer

NASA Astrophysics Data System (ADS)

McKenna, L.; Cantwell, K. L.; Kennedy, B. R.; Lobecker, E.; Sowers, D.; Elliott, K.

2015-12-01

In 2015, NOAA Ship Okeanos Explorer, the only US federal ship dedicated to ocean exploration, systematically explored previously unknown deep sea ecosystems in the Caribbean and remote regions in the vicinity of the Hawaiian Islands. Initial characterization of these areas is essential in order to establish a baseline against which to assess potential future changes due to climate and anthropogenic change. In the Caribbean, over 37,500 sq km of previously unmapped seafloor were mapped with a high resolution multibeam revealing rugged canyons along shelf breaks, intricate incised channels, and complex tectonic features. 12 ROV dives, in the 300-6,000 m depth range, visually explored seamounts, escarpments, submarine canyons, and the water column revealing diverse ecosystems and habitats. Discoveries include large assemblages of deep sea corals, range extensions, and observations of several rare and potentially new organisms - including a seastar that had not been documented since its holotype specimen. In the Pacific, over 50,000 sq km of seafloor were mapped in high-resolution, revealing long linear ridge and tectonic fracture zone features, both peaked and flat-topped seamounts, and numerous features that appear to be volcanic in origin. To better understand ecosystem dynamics in depths greater than 2,000 m, the deepest ever ROV surveys and sampling were conducted in remote Pacific island marine sanctuaries and monuments. Novel observations include range extensions and exploration of dense deep sea coral and sponge habitat. Baseline habitat characterization was also conducted on seamounts within the Prime Crust Zone (PCZ), an area with the highest expected concentration of deep-sea minerals in the Pacific. The Hawaiian operations marked the first ever ROV sampling effort conducted onboard Okeanos, and several geological and biological samples are now available at museums and sample repositories in addition to all digital data available through the National

Coastal habitat mapping in the Aegean Sea using high resolution orthophoto maps

NASA Astrophysics Data System (ADS)

Topouzelis, Konstantinos; Papakonstantinou, Apostolos; Doukari, Michaela; Stamatis, Panagiotis; Makri, Despina; Katsanevakis, Stelios

2017-09-01

The significance of coastal habitat mapping lies in the need to prevent from anthropogenic interventions and other factors. Until 2015, Landsat-8 (30m) imagery were used as medium spatial resolution satellite imagery. So far, Sentinel-2 satellite imagery is very useful for more detailed regional scale mapping. However, the use of high resolution orthophoto maps, which are determined from UAV data, is expected to improve the mapping accuracy. This is due to small spatial resolution of the orthophoto maps (30 cm). This paper outlines the integration of UAS for data acquisition and Structure from Motion (SfM) pipeline for the visualization of selected coastal areas in the Aegean Sea. Additionally, the produced orthophoto maps analyzed through an object-based image analysis (OBIA) and nearest-neighbor classification for mapping the coastal habitats. Classification classes included the main general habitat types, i.e. seagrass, soft bottom, and hard bottom The developed methodology applied at the Koumbara beach (Ios Island - Greece). Results showed that UAS's data revealed the sub-bottom complexity in large shallow areas since they provide such information in the spatial resolution that permits the mapping of seagrass meadows with extreme detail. The produced habitat vectors are ideal as reference data for studies with satellite data of lower spatial resolution.

Molecular Analysis of Sarcoidosis Granulomas Reveals Antimicrobial Targets

PubMed Central

Celada, Lindsay J.; Polosukhin, Vasiliy V.; Atkinson, James B.; Drake, Wonder P.

2016-01-01

Sarcoidosis is a granulomatous disease of unknown cause. Prior molecular and immunologic studies have confirmed the presence of mycobacterial virulence factors, such as catalase peroxidase and superoxide dismutase A, within sarcoidosis granulomas. Molecular analysis of granulomas can identify targets of known antibiotics classes. Currently, major antibiotics are directed against DNA synthesis, protein synthesis, and cell wall formation. We conducted molecular analysis of 40 sarcoidosis diagnostic specimens and compared them with 33 disease control specimens for the presence of mycobacterial genes that encode antibiotic targets. We assessed for genes involved in DNA synthesis (DNA gyrase A [gyrA] and DNA gyrase B), protein synthesis (RNA polymerase subunit β), cell wall synthesis (embCAB operon and enoyl reductase), and catalase peroxidase. Immunohistochemical analysis was conducted to investigate the locale of mycobacterial genes such as gyrA within 12 sarcoidosis specimens and 12 disease controls. Mycobacterial DNA was detected in 33 of 39 sarcoidosis specimens by quantitative real-time polymerase chain reaction compared with 2 of 30 disease control specimens (P < 0.001, two-tailed Fisher’s test). Twenty of 39 were positive for three or more mycobacterial genes, compared with 1 of 30 control specimens (P < 0.001, two-tailed Fisher’s test). Immunohistochemistry analysis localized mycobacterial gyrA nucleic acids to sites of granuloma formation in 9 of 12 sarcoidosis specimens compared with 1 of 12 disease controls (P < 0.01). Microbial genes encoding enzymes that can be targeted by currently available antimycobacterial antibiotics are present in sarcoidosis specimens and localize to sites of granulomatous inflammation. Use of antimicrobials directed against target enzymes may be an innovative treatment alternative. PMID:26807608

Links between plant and fungal diversity in habitat fragments of coastal shrubland

DOE PAGES

Maltz, Mia R.; Treseder, Kathleen K.; McGuire, Krista L.

2017-09-19

Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant littermore » diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation's constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of

Links between plant and fungal diversity in habitat fragments of coastal shrubland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maltz, Mia R.; Treseder, Kathleen K.; McGuire, Krista L.

Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant littermore » diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation's constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of

Habitat Suitability Index Models: Red king crab

USGS Publications Warehouse

Jewett, Stephen C.; Onuf, Christopher P.

1988-01-01

A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for evaluating habitat of different life stages of red king crab (Paralithodes camtschatica). A model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) and 1.0 (optimum habitat) in Alaskan coastal waters, especially in the Gulf of Alaska and the southeastern Bering Sea. HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

A mistletoe tale: postglacial invasion of Psittacanthus schiedeanus (Loranthaceae) to Mesoamerican cloud forests revealed by molecular data and species distribution modeling.

PubMed

Ornelas, Juan Francisco; Gándara, Etelvina; Vásquez-Aguilar, Antonio Acini; Ramírez-Barahona, Santiago; Ortiz-Rodriguez, Andrés Ernesto; González, Clementina; Mejía Saules, María Teresa; Ruiz-Sanchez, Eduardo

2016-04-12

Ecological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities. Our analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate

Anthropogenic habitat disturbance and ecological divergence between incipient species of the malaria mosquito Anopheles gambiae.

PubMed

Kamdem, Colince; Tene Fossog, Billy; Simard, Frédéric; Etouna, Joachim; Ndo, Cyrille; Kengne, Pierre; Boussès, Philippe; Etoa, François-Xavier; Awono-Ambene, Parfait; Fontenille, Didier; Antonio-Nkondjio, Christophe; Besansky, Nora J; Costantini, Carlo

2012-01-01

Anthropogenic habitat disturbance is a prime cause in the current trend of the Earth's reduction in biodiversity. Here we show that the human footprint on the Central African rainforest, which is resulting in deforestation and growth of densely populated urban agglomerates, is associated to ecological divergence and cryptic speciation leading to adaptive radiation within the major malaria mosquito Anopheles gambiae. In southern Cameroon, the frequency of two molecular forms--M and S--among which reproductive isolation is strong but still incomplete, was correlated to an index of urbanisation extracted from remotely sensed data, expressed as the proportion of built-up surface in each sampling unit. The two forms markedly segregated along an urbanisation gradient forming a bimodal cline of ∼6-km width: the S form was exclusive to the rural habitat, whereas only the M form was present in the core of densely urbanised settings, co-occurring at times in the same polluted larval habitats of the southern house mosquito Culex quinquefasciatus--a species association that was not historically recorded before. Our results indicate that when humans create novel habitats and ecological heterogeneities, they can provide evolutionary opportunities for rapid adaptive niche shifts associated with lineage divergence, whose consequences upon malaria transmission might be significant.

Urban expansion dynamics and natural habitat loss in China: a multiscale landscape perspective.

PubMed

He, Chunyang; Liu, Zhifeng; Tian, Jie; Ma, Qun

2014-09-01

China's extensive urbanization has resulted in a massive loss of natural habitat, which is threatening the nation's biodiversity and socioeconomic sustainability. A timely and accurate understanding of natural habitat loss caused by urban expansion will allow more informed and effective measures to be taken for the conservation of biodiversity. However, the impact of urban expansion on natural habitats is not well-understood, primarily due to the lack of accurate spatial information regarding urban expansion across China. In this study, we proposed an approach that can be used to accurately summarize the dynamics of urban expansion in China over two recent decades (1992-2012), by integrating data on nighttime light levels, a vegetation index, and land surface temperature. The natural habitat loss during the time period was evaluated at the national, ecoregional, and local scales. The results revealed that China had experienced extremely rapid urban growth from 1992 to 2012 with an average annual growth rate of 8.74%, in contrast with the global average of 3.20%. The massive urban expansion has resulted in significant natural habitat loss in some areas in China. Special attention needs to be paid to the Pearl River Delta, where 25.79% or 1518 km(2) of the natural habitat and 41.99% or 760 km(2) of the local wetlands were lost during 1992-2012. This raises serious concerns about species viability and biodiversity. Effective policies and regulations must be implemented and enforced to sustain regional and national development in the context of rapid urbanization. © 2014 John Wiley & Sons Ltd.

Habitat Selectivity and Reliance on Live Corals for Indo-Pacific Hawkfishes (Family: Cirrhitidae).

PubMed

Coker, Darren J; Hoey, Andrew S; Wilson, Shaun K; Depczynski, Martial; Graham, Nicholas A J; Hobbs, Jean-Paul A; Holmes, Thomas H; Pratchett, Morgan S

2015-01-01

Hawkfishes (family: Cirrhitidae) are small conspicuous reef predators that commonly perch on, or shelter within, the branches of coral colonies. This study examined habitat associations of hawkfishes, and explicitly tested whether hawkfishes associate with specific types of live coral. Live coral use and habitat selectivity of hawkfishes was explored at six locations from Chagos in the central Indian Ocean extending east to Fiji in the Pacific Ocean. A total of 529 hawkfishes from seven species were recorded across all locations with 63% of individuals observed perching on, or sheltering within, live coral colonies. Five species (all except Cirrhitus pinnulatus and Cirrhitichthys oxycephalus) associated with live coral habitats. Cirrhitichthys falco selected for species of Pocillopora while Paracirrhites arcatus and P. forsteri selected for both Pocillopora and Acropora, revealing that these habitats are used disproportionately more than expected based on the local cover of these coral genera. Habitat selection was consistent across geographic locations, and species of Pocillopora were the most frequently used and most consistently selected even though this coral genus never comprised more than 6% of the total coral cover at any of the locations. Across locations, Paracirrhites arcatus and P. forsteri were the most abundant species and variation in their abundance corresponded with local patterns of live coral cover and abundance of Pocilloporid corals, respectively. These findings demonstrate the link between small predatory fishes and live coral habitats adding to the growing body of literature highlighting that live corals (especially erect branching corals) are critically important for sustaining high abundance and diversity of fishes on coral reefs.

Habitat Suitability Index Models: Yellow-headed blackbird

USGS Publications Warehouse

Schroeder, Richard L.

1982-01-01

Habitat preferences of the yellow-headed blackbird (Xanthocephalus xanthocephalus) are described in this publication. It is one of a series of Habitat Suitability Index (HSI) models and was developed through an analysis of available infomration on the species-habitat requirements of the species. Habitat use information is presented in a review of the literature, followed by the development of an HSI model, designed for use in impact assessment and habitat management activities.

Brief notes on habitat geology and clay pipe habitat on Stellwagen Bank

USGS Publications Warehouse

Valentine, Page C.; Dorsey, Eleanor M.; Pederson, Judith

1998-01-01

In our studies of sea floor habitats, my colleagues and I use both biological and geological approaches. We call our studies “habitat geology,” a term coined by a biologist friend of mine. We view it as the study of sea floor materials and biological and geological processes that influence where species live. Some of the factors that we consider are the following:composition of the sea bed, which ranges from mud to sand, gravel, bedrock, and shell beds;shape and steepness of the bottom;roughness of the bottom, which is enhanced by the presence of cobbles, boulders, sand waves and ripples, burrows into the bottom, and species that extend above the bottom;bottom currents generated by storm waves and tides, which can move sediment and expose or cover habitats; andthe way in which the sea bed is utilized by species.In addition, we take into account the impact of sea bed disturbance by bottom fishing trawls and dredges. Habitats characterized by attached and burrowing species that protrude above the sea bed appear to be most vulnerable to disturbance.

Telemetry-Determined Habitat Use Informs Multi-Species Habitat Management in an Urban Harbour.

PubMed

Rous, Andrew M; Midwood, Jonathon D; Gutowsky, Lee F G; Lapointe, Nicolas W R; Portiss, Rick; Sciscione, Thomas; Wells, Mathew G; Doka, Susan E; Cooke, Steven J

2017-01-01

Widespread human development has led to impairment of freshwater coastal wetlands and embayments, which provide critical and unique habitat for many freshwater fish species. This is particularly evident in the Laurentian Great Lakes, where such habitats have been severely altered over the last century as a result of industrial activities, urbanization, dredging and infilling. In Toronto Harbour, extensive restoration efforts have been directed towards improving the amount and quality of aquatic habitat, especially for fishes. To evaluate the effectiveness of this restoration work, use of the restored area by both target species and the fish community as a whole must be assessed. Individuals from four species (Common Carp, Largemouth Bass, Northern Pike and Yellow Perch) were tagged and tracked continuously for 1 year using an acoustic telemetry array in Toronto Harbour area of Lake Ontario. Daily site fidelity was estimated using a mixed-effects logistic regression model. Daily site fidelity was influenced by habitat restoration and its interactions with species and body size, as well as season and its interactions with species and body size. Daily site fidelity was higher in restored sites compared to non-restored sites for Yellow Perch and Northern Pike, but lower for Largemouth Bass and Common Carp. For all species, daily site fidelity estimates were highest during the summer and lowest during autumn. The approach used here has merit for evaluating restoration success and informing future habitat management activities. Creating diverse habitats that serve multiple functions and species are more desirable than single-function-oriented or single-species-oriented designs.

Telemetry-Determined Habitat Use Informs Multi-Species Habitat Management in an Urban Harbour

NASA Astrophysics Data System (ADS)

Rous, Andrew M.; Midwood, Jonathon D.; Gutowsky, Lee F. G.; Lapointe, Nicolas W. R.; Portiss, Rick; Sciscione, Thomas; Wells, Mathew G.; Doka, Susan E.; Cooke, Steven J.

2017-01-01

Widespread human development has led to impairment of freshwater coastal wetlands and embayments, which provide critical and unique habitat for many freshwater fish species. This is particularly evident in the Laurentian Great Lakes, where such habitats have been severely altered over the last century as a result of industrial activities, urbanization, dredging and infilling. In Toronto Harbour, extensive restoration efforts have been directed towards improving the amount and quality of aquatic habitat, especially for fishes. To evaluate the effectiveness of this restoration work, use of the restored area by both target species and the fish community as a whole must be assessed. Individuals from four species (Common Carp, Largemouth Bass, Northern Pike and Yellow Perch) were tagged and tracked continuously for 1 year using an acoustic telemetry array in Toronto Harbour area of Lake Ontario. Daily site fidelity was estimated using a mixed-effects logistic regression model. Daily site fidelity was influenced by habitat restoration and its interactions with species and body size, as well as season and its interactions with species and body size. Daily site fidelity was higher in restored sites compared to non-restored sites for Yellow Perch and Northern Pike, but lower for Largemouth Bass and Common Carp. For all species, daily site fidelity estimates were highest during the summer and lowest during autumn. The approach used here has merit for evaluating restoration success and informing future habitat management activities. Creating diverse habitats that serve multiple functions and species are more desirable than single-function-oriented or single-species-oriented designs.

Lyme borreliosis habitat assessment.

PubMed

Gray, J S; Kahl, O; Robertson, J N; Daniel, M; Estrada-Peña, A; Gettinby, G; Jaenson, T G; Jensen, P; Jongejan, F; Korenberg, E; Kurtenbach, K; Zeman, P

1998-03-01

Tick ecologists throughout Europe provided descriptions of Lyme borreliosis habitats according to a standardised format and data for 105 habitats in 16 countries were received. The data showed that high risk situations, as defined by the presence of large numbers of B. burgdorferi sensu lato-infected nymphal I. ricinus, occur in heterogeneous deciduous woodland, usually with a recreational function and with a diverse fauna, usually including deer. Large numbers of ticks occurred in some other habitats, but infection prevalence was usually low. The situation for adult I. ricinus was similar but less clearly defined. Tick infection rates were found to be lower in western Europe than in the east, and the infection rate in I. persulcatus, the most easterly vector species, was markedly higher than in I. ricinus. In the vast majority of habitats the infection rate in adult I. ricinus was greater than in nymphs. Larvae were rarely found to be infected.

Molecular interaction of triclosan with superoxide dismutase (SOD) reveals a potentially toxic mechanism of the antimicrobial agent.

PubMed

Mi, Chenyu; Teng, Yue; Wang, Xiaofang; Yu, Hongyan; Huang, Zhenxing; Zong, Wansong; Zou, Luyi

2018-05-30

In this article, the interaction mechanism between the superoxide dismutase (SOD) and the triclosan (TCS), a kind of antimicrobial agent which is of widely application with potential effects both on environment and human health, was explored through a series of spectroscopic methods, animal experiment and the molecular docking simulation. The negative free energy change ∆G, enthalpy change (∆H = 162.21 kJmol -1 ) and entropy change (∆S = 615 Jmol -1 K -1 ) demonstrated that TCS could combine with SOD spontaneously through hydrophobic interaction to form a complex. The binding constants of K a293 and K a313 were 1.706 × 10 3 and 1.2 × 10 5 Lmol -1 , respectively. Furthermore, the interaction could also influence the skeleton structure and secondary contents of SOD. The molecular docking analysis revealed the TCS located between two subunits of SOD, and there was a hydrogen bond between TCS and the residue Asn51 of SOD, which influenced the structure of protein and resulted in a decrease of enzyme activity. This work could help understand the interaction mechanism between SOD and TCS. Moreover, it could also be used to consult for toxicity assessment of TCS at molecular level. Copyright © 2018 Elsevier Inc. All rights reserved.

Habitat Selection and Risk of Predation: Re-colonization by Lynx had Limited Impact on Habitat Selection by Roe Deer

PubMed Central

Samelius, Gustaf; Andrén, Henrik; Kjellander, Petter; Liberg, Olof

2013-01-01

Risk of predation is an evolutionary force that affects behaviors of virtually all animals. In this study, we examined how habitat selection by roe deer was affected by risk of predation by Eurasian lynx – the main predator of roe deer in Scandinavia. Specifically, we compared how habitat selection by roe deer varied (1) before and after lynx re-established in the study area and (2) in relation to habitat-specific risk of predation by lynx. All analyses were conducted at the spatial and temporal scales of home ranges and seasons. We did not find any evidence that roe deer avoided habitats in which the risk of predation by lynx was greatest and information-theoretic model selection showed that re-colonization by lynx had limited impact on habitat selection by roe deer despite lynx predation causing 65% of known mortalities after lynx re-colonized the area. Instead we found that habitat selection decreased when habitat availability increased for 2 of 5 habitat types (a pattern referred to as functional response in habitat selection). Limited impact of re-colonization by lynx on habitat selection by roe deer in this study differs from elk in North America altering both daily and seasonal patterns in habitat selection at the spatial scales of habitat patches and home ranges when wolves were reintroduced to Yellowstone National Park. Our study thus provides further evidence of the complexity by which animals respond to risk of predation and suggest that it may vary between ecosystems and predator-prey constellations. PMID:24069419

Habitat selection and risk of predation: re-colonization by lynx had limited impact on habitat selection by roe deer.

PubMed

Samelius, Gustaf; Andrén, Henrik; Kjellander, Petter; Liberg, Olof

2013-01-01

Risk of predation is an evolutionary force that affects behaviors of virtually all animals. In this study, we examined how habitat selection by roe deer was affected by risk of predation by Eurasian lynx - the main predator of roe deer in Scandinavia. Specifically, we compared how habitat selection by roe deer varied (1) before and after lynx re-established in the study area and (2) in relation to habitat-specific risk of predation by lynx. All analyses were conducted at the spatial and temporal scales of home ranges and seasons. We did not find any evidence that roe deer avoided habitats in which the risk of predation by lynx was greatest and information-theoretic model selection showed that re-colonization by lynx had limited impact on habitat selection by roe deer despite lynx predation causing 65% of known mortalities after lynx re-colonized the area. Instead we found that habitat selection decreased when habitat availability increased for 2 of 5 habitat types (a pattern referred to as functional response in habitat selection). Limited impact of re-colonization by lynx on habitat selection by roe deer in this study differs from elk in North America altering both daily and seasonal patterns in habitat selection at the spatial scales of habitat patches and home ranges when wolves were reintroduced to Yellowstone National Park. Our study thus provides further evidence of the complexity by which animals respond to risk of predation and suggest that it may vary between ecosystems and predator-prey constellations.

Molecular markers reveal no genetic differentiation between Myrica rivas-martinezii and M. faya (Myricaceae)

PubMed Central

González-Pérez, Miguel A.; Sosa, Pedro A.; Rivero, Elisabeth; González-González, Edna A.; Naranjo, Agustín

2009-01-01

Background and Aims Myrica rivas-martinezii is a critically endangered endemic of the laurel forest of the Canary Islands and co-occurs very close to M. faya. Some authors suggest that M. rivas-martinezii and M. faya are two morphs of the same species, so molecular markers were used to estimate the levels and structuring of genetic variation within and among natural populations in order to evaluate genetic relationships between these two congeners. Methods Six polymorphic microsatellite (simple sequence repeat, SSR) markers were used to determine the genetic diversity and the genetic relationship between both Myrica species. Key Results Most of the natural populations analysed were in Hardy–Weinberg equilibrium for both taxa. Analysis of molecular variance (AMOVA) for both species revealed that most of the genetic variability detected was contained within populations (92·48 and 85·91 % for M. faya and M. rivas-martinezii, respectively), which it is consistent with outcrossing and dioecious plants. Estimates of interpopulation genetic variation, calculated from FST and G′ST, were quite low in the two taxa, and these values did not increase substantially when M. rivas-martinezii and M. faya populations were compared. The UPGMA dendrogram based on Nei's genetic distance clustered the populations by their island origin, independently of taxon. In fact, the mixture of individuals of both taxa did not appreciably disrupt the intrapopulational genetic cohesion, and only 3·76 % variation existed between species. Conclusions All the results obtained using molecular markers indicate clearly that both taxa share the same genetic pool, and they are probably the same taxa. Considering that M. rivas-martinezii is classified as at risk of extinction, there should be a change of focus of the current management actions for the conservation of this putatively endangered Canarian endemic. PMID:19008254

Deep-sea dives reveal an unexpected hexactinellid sponge garden on the Rio Grande Rise (SW Atlantic). A mimicking habitat?

NASA Astrophysics Data System (ADS)

Hajdu, Eduardo; Castello-Branco, Cristiana; Lopes, Daniela A.; Sumida, Paulo Yukio Gomes; Perez, Jose Angel Alvarez

2017-12-01

Long overlooked, sponge grounds are now recognised as important habitats which support high biodiversity. Some of these deep-sea sponge aggregations are formed by hexactinellids, in varying densities, which can occur on both soft and hard substrates. Despite their ecological importance as habitat framework building taxa, hexactinellids have been little studied and only 33 species in this Class were reported from the entire South Atlantic until now. Most of this knowledge was gained from studies conducted on the eastern South America continental slope. Here we report a new hexactinellid sponge garden found by the Shinkai 6500 manned submersible on the Rio Grande Rise, a prominent topographic feature of the deep SW Atlantic. This is the first sponge garden worldwide found to be dominated by the stiff, often dichotomously branching, Sarostegia oculata which may occur in densities of over 5 individuals per square meter. This sponge, of uncertain familial allocation, seems to always carry epibiotic zoanthids, thus mimicking the 3D skeletal framework of actual coral gardens

Predicting occurrence of juvenile shark habitat to improve conservation planning.

PubMed

Oh, Beverly Z L; Sequeira, Ana M M; Meekan, Mark G; Ruppert, Jonathan L W; Meeuwig, Jessica J

2017-06-01

Fishing and habitat degradation have increased the extinction risk of sharks, and conservation strategies recognize that survival of juveniles is critical for the effective management of shark populations. Despite the rapid expansion of marine protected areas (MPAs) globally, the paucity of shark-monitoring data on large scales (100s-1000s km) means that the effectiveness of MPAs in halting shark declines remains unclear. Using data collected by baited remote underwater video systems (BRUVS) in northwestern Australia, we developed generalized linear models to elucidate the ecological drivers of habitat suitability for juvenile sharks. We assessed occurrence patterns at the order and species levels. We included all juvenile sharks sampled and the 3 most abundant species sampled separately (grey reef [Carcharhinus amblyrhynchos], sandbar [Carcharhinus plumbeus], and whitetip reef sharks [Triaenodon obesus]). We predicted the occurrence of juvenile sharks across 490,515 km 2 of coastal waters and quantified the representation of highly suitable habitats within MPAs. Our species-level models had higher accuracy (ĸ ≥ 0.69) and deviance explained (≥48%) than our order-level model (ĸ = 0.36 and deviance explained of 10%). Maps of predicted occurrence revealed different species-specific patterns of highly suitable habitat. These differences likely reflect different physiological or resource requirements between individual species and validate concerns over the utility of conservation targets based on aggregate species groups as opposed to a species-focused approach. Highly suitable habitats were poorly represented in MPAs with the most restrictions on extractive activities. This spatial mismatch possibly indicates a lack of explicit conservation targets and information on species distribution during the planning process. Non-extractive BRUVS provided a useful platform for building the suitability models across large scales to assist conservation planning across

Seasonal variation in coastal marine habitat use by the European shag: Insights from fine scale habitat selection modeling and diet

NASA Astrophysics Data System (ADS)

Michelot, Candice; Pinaud, David; Fortin, Matthieu; Maes, Philippe; Callard, Benjamin; Leicher, Marine; Barbraud, Christophe

2017-07-01

Studies of habitat selection by higher trophic level species are necessary for using top predator species as indicators of ecosystem functioning. However, contrary to terrestrial ecosystems, few habitat selection studies have been conducted at a fine scale for coastal marine top predator species, and fewer have coupled diet data with habitat selection modeling to highlight a link between prey selection and habitat use. The aim of this study was to characterize spatially and oceanographically, at a fine scale, the habitats used by the European Shag Phalacrocorax aristotelis in the Special Protection Area (SPA) of Houat-Hœdic in the Mor Braz Bay during its foraging activity. Habitat selection models were built using in situ observation data of foraging shags (transect sampling) and spatially explicit environmental data to characterize marine benthic habitats. Observations were first adjusted for detectability biases and shag abundance was subsequently spatialized. The influence of habitat variables on shag abundance was tested using Generalized Linear Models (GLMs). Diet data were finally confronted to habitat selection models. Results showed that European shags breeding in the Mor Braz Bay changed foraging habitats according to the season and to the different environmental and energetic constraints. The proportion of the main preys also varied seasonally. Rocky and coarse sand habitats were clearly preferred compared to fine or muddy sand habitats. Shags appeared to be more selective in their foraging habitats during the breeding period and the rearing of chicks, using essentially rocky areas close to the colony and consuming preferentially fish from the Labridae family and three other fish families in lower proportions. During the post-breeding period shags used a broader range of habitats and mainly consumed Gadidae. Thus, European shags seem to adjust their feeding strategy to minimize energetic costs, to avoid intra-specific competition and to maximize access

The ecological and evolutionary consequences of noise-induced acoustic habitat loss

NASA Astrophysics Data System (ADS)

Tennessen, Jennifer Beissinger

Anthropogenic threats are facilitating rapid environmental change and exerting novel pressures on the integrity of ecological patterns and processes. Currently, habitat loss is the leading factor contributing to global biodiversity loss. Noise created by human activities is nearly ubiquitous in terrestrial and marine systems, and causes acoustic habitat loss by interfering with species' abilities to freely send and receive critical acoustic biological information. My dissertation investigates how novel sounds from human activities affect ecological and evolutionary processes in space and time in marine and terrestrial systems, and how species may cope with this emerging novel pressure. Using species from both marine and terrestrial systems, I present results from a theoretical investigation, and four acoustic playback experiments combining laboratory studies and field trials, that reveal a range of eco-evolutionary consequences of noiseinduced acoustic habitat loss. First, I use sound propagation modeling to assess how marine shipping noise reduces communication space between mother-calf pairs of North Atlantic right whales (Eubalaena glacialis ), an important unit of an endangered species. I show that shipping noise poses significant challenges for mother-calf pairs, but that vocal compensation strategies can substantially improve communication space. Next, in a series of acoustic playback experiments I show that road traffic noise impairs breeding migration behavior and physiology of wood frogs (Lithobates sylvaticus ). This work reveals the first evidence that traffic noise elicits a physiological stress response and suppresses production of antimicrobial peptides (a component of the innate immune response) in anurans. Further, wood frogs from populations with a history of inhabiting noisy sites mounted reduced physiological stress responses to continuous traffic noise exposure. This research using wood frogs suggests that chronic traffic noise exposure has

Habitat Suitability Index Models: Red-winged blackbird

USGS Publications Warehouse

Short, Henry L.

1985-01-01

A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the red-winged blackbird (Agelaius phoeniceus L.). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

Following a Foraging Fish-Finder: Diel Habitat Use of Blainville's Beaked Whales Revealed by Echolocation

PubMed Central

Arranz, Patricia; de Soto, Natacha Aguilar; Madsen, Peter T.; Brito, Alberto; Bordes, Fernando; Johnson, Mark P.

2011-01-01

Simultaneous high resolution sampling of predator behavior and habitat characteristics is often difficult to achieve despite its importance in understanding the foraging decisions and habitat use of predators. Here we tap into the biosonar system of Blainville's beaked whales, Mesoplodon densirostris, using sound and orientation recording tags to uncover prey-finding cues available to echolocating predators in the deep-sea. Echolocation sounds indicate where whales search and encounter prey, as well as the altitude of whales above the sea-floor and the density of organisms around them, providing a link between foraging activity and the bio-physical environment. Tagged whales (n = 9) hunted exclusively at depth, investing most of their search time either in the lower part of the deep scattering layer (DSL) or near the sea-floor with little diel change. At least 43% (420/974) of recorded prey-capture attempts were performed within the benthic boundary layer despite a wide range of dive depths, and many dives included both meso- and bentho-pelagic foraging. Blainville's beaked whales only initiate searching when already deep in the descent and encounter prey suitable for capture within 2 min of the start of echolocation, suggesting that these whales are accessing prey in reliable vertical strata. Moreover, these prey resources are sufficiently dense to feed the animals in what is effectively four hours of hunting per day enabling a strategy in which long dives to exploit numerous deep-prey with low nutritional value require protracted recovery periods (average 1.5 h) between dives. This apparent searching efficiency maybe aided by inhabiting steep undersea slopes with access to both the DSL and the sea-floor over small spatial scales. Aggregations of prey in these biotopes are located using biosonar-derived landmarks and represent stable and abundant resources for Blainville's beaked whales in the otherwise food-limited deep-ocean. PMID:22163295

Testing projected wild bee distributions in agricultural habitats: predictive power depends on species traits and habitat type.

PubMed

Marshall, Leon; Carvalheiro, Luísa G; Aguirre-Gutiérrez, Jesús; Bos, Merijn; de Groot, G Arjen; Kleijn, David; Potts, Simon G; Reemer, Menno; Roberts, Stuart; Scheper, Jeroen; Biesmeijer, Jacobus C

2015-10-01

Species distribution models (SDM) are increasingly used to understand the factors that regulate variation in biodiversity patterns and to help plan conservation strategies. However, these models are rarely validated with independently collected data and it is unclear whether SDM performance is maintained across distinct habitats and for species with different functional traits. Highly mobile species, such as bees, can be particularly challenging to model. Here, we use independent sets of occurrence data collected systematically in several agricultural habitats to test how the predictive performance of SDMs for wild bee species depends on species traits, habitat type, and sampling technique. We used a species distribution modeling approach parametrized for the Netherlands, with presence records from 1990 to 2010 for 193 Dutch wild bees. For each species, we built a Maxent model based on 13 climate and landscape variables. We tested the predictive performance of the SDMs with independent datasets collected from orchards and arable fields across the Netherlands from 2010 to 2013, using transect surveys or pan traps. Model predictive performance depended on species traits and habitat type. Occurrence of bee species specialized in habitat and diet was better predicted than generalist bees. Predictions of habitat suitability were also more precise for habitats that are temporally more stable (orchards) than for habitats that suffer regular alterations (arable), particularly for small, solitary bees. As a conservation tool, SDMs are best suited to modeling rarer, specialist species than more generalist and will work best in long-term stable habitats. The variability of complex, short-term habitats is difficult to capture in such models and historical land use generally has low thematic resolution. To improve SDMs' usefulness, models require explanatory variables and collection data that include detailed landscape characteristics, for example, variability of crops and

[ISSR analysis for genetic polymorphism of Aconitum leucostomum from different habitats].

PubMed

Gao, Fu-chun; Sun, Yun; Zhang, Jing; Zhang, Fan

2014-01-01

To investigate the genetic diversities and variations of Aconitum leucostomum,and to supply essential characteristics for identifying Aconitum crude drugs. Plant genome extraction kit was applied to extract DNA,and ultraviolet spectrophotometer was used to detect the concentrations and purity of DNA. 60 ISSR primers were screened to analyze the DNA of Aconitum leucostomum from 10 habitats. Biosoftwares including POPGEN32 and NTSYS-PC were used to analyze the polymorphic bands obtained, and hence to yield the genetic similarity coefficient of the 10 habitats and map the related graphics, and cluster analysis were performed by UPGMA method. 11 primers selected from 60 ISSR primers were used for amplification and a total of 101 DNA bands were obtained, including 89 polymorphic bands,the average percentage of polymorphic bands (PPB) was 88.1%. Shannon information index (I) was 0.5298, the genetic similarity coefficient (H) was 0.3648, observed number of alleles was 1.8911, and effective number of alleles was 1.6555. The genetic identity was from 0.4950 to 0.6931, and the genetic distances were from 0.3666 to 0.7031. According to cluster analysis result of ISSR, the 10 habitats of Aconitum leucostomum were classified into five groups. Germplasm resources of Aconitum leucostomum show abundant polymorphism and higher genetic variation, which might supply molecular level basis, and provide basis for building DNA fingerprint.

Cryptic species revealed by molecular phylogenetic analysis of sequences obtained from basidiomata of Tulasnella.

PubMed

Cruz, Darío; Suárez, Juan Pablo; Kottke, Ingrid; Piepenbring, Meike

2014-01-01

Delimitation of species and the search for a proper threshold for defining phylogenetic species in fungi are under discussion. In this study, morphological and molecular data are correlated to delimit species of Tulasnella, the most important mycobionts of Orchidaceae, which suffer from poor taxonomy. Resupinate basidiomata of Tulasnella species were collected in Ecuador and Germany, and 11 specimens (seven from Ecuador, four from Germany) were assigned to traditional species concepts by use of morphological keys. The specimens were compared by micro-anatomical examination with 75 specimens of Tulasnella borrowed from fungaria to obtain better insights on variation of characters. Sequences of the ITS region (127) were obtained after cloning from the fresh basidiomata and from pure cultures. Proportional variability of ITS sequences was analyzed within and among the cultures and the specimens designated to different morphospecies. Results suggested an intragenomic variation of less than 2%, an intraspecific variation of up to 4% and an interspecific divergence of more than 9% in Tulasnella. Cryptic species in Tulasnella, mostly from Ecuador, were revealed by phylogenetic analyses with 4% intraspecific divergence as a minimum threshold for delimiting species. Conventional diagnostic morphological characters appeared insufficient for species characterization. Arguments are presented for molecular delimitation of the established species Tulasnella albida, T. asymmetrica, T. eichleriana, T. cf. pinicola, T. tomaculum and T. violea. © 2014 by The Mycological Society of America.

50 CFR 17.94 - Critical habitats.

Code of Federal Regulations, 2010 CFR

2010-10-01

... the listed species within these defined Critical Habitats. (See part 402 for rules concerning this prohibition; see also part 424 for rules concerning the determination of Critical Habitat). (b) The map... of a Critical Habitat. Such maps are provided for reference purposes to guide Federal agencies and...

Molecular phylogeny of the bivalve superfamily Galeommatoidea (Heterodonta, Veneroida) reveals dynamic evolution of symbiotic lifestyle and interphylum host switching

PubMed Central

2012-01-01

-feeding habits even in symbiotic habitats. The results of the molecular phylogenetic analysis did not correspond with the current taxonomic circumscription. Galeommatidae and Lasaeidae were polyphyletic, and Basterotia, which is traditionally assigned to Cyamioidea, formed a monophyletic clade within Galeommatoidea. PMID:22954375

A meta-analysis of lesser prairie-chicken nesting and brood-rearing habitats: implications for habitat management

USGS Publications Warehouse

Hagen, Christian A.; Grisham, Blake A.; Boal, Clint W.; Haukos, David A.

2013-01-01

The distribution and range of lesser prairie-chicken (Tympanuchus pallidicinctus) has been reduced by >90% since European settlement of the Great Plains of North America. Currently, lesser prairie-chickens occupy 3 general vegetation communities: sand sagebrush (Artemisia filifolia), sand shinnery oak (Quercus havardii), and mixed-grass prairies juxtaposed with Conservation Reserve Program grasslands. As a candidate for protection under the Endangered Species Act, there is a need for a synthesis that characterizes habitat structure rangewide. Thus, we conducted a meta-analysis of vegetation characteristics at nest sites and brood habitats to determine whether there was an overall effect (Hedges' d) of habitat selection and to estimate average (95% CI) habitat characteristics at use sites. We estimated effect sizes (di) from the difference between use (nests and brood sites) and random sampling sites for each study (n = 14), and derived an overall effect size (d++). There was a general effect for habitat selection as evidenced by low levels of variation in effect sizes across studies and regions. There was a small to medium effect (d++) = 0.20-0.82) of selection for greater vertical structure (visual obstruction) by nesting females in both vegetation communities, and selection against bare ground (d++ = 0.20-0.58). Females with broods exhibited less selectivity for habitat components except for vertical structure. The variation of d++ was greater during nesting than brooding periods, signifying a seasonal shift in habitat use, and perhaps a greater range of tolerance for brood-rearing habitat. The overall estimates of vegetation cover were consistent with those provided in management guidelines for the species.

Wildlife Habitat Evaluation Handbook.

ERIC Educational Resources Information Center

Neilson, Edward L., Jr.; Benson, Delwin E.

The National 4-H Wildlife Invitational is a competitive event to teach youth about the fundamentals of wildlife management. Youth learn that management for wildlife means management of wildlife habitat and providing for the needs of wildlife. This handbook provides information about wildlife habitat management concepts in both urban and rural…

Molecular analyses on host-seeking black flies (Diptera: Simuliidae) reveal a diverse assemblage of Leucocytozoon (Apicomplexa: Haemospororida) parasites in an alpine ecosystem.

PubMed

Murdock, Courtney C; Adler, Peter H; Frank, Jared; Perkins, Susan L

2015-06-25

Molecular studies have suggested that the true diversity of Leucocytozoon (Apicomplexa: Haemospororida) species well exceeds the approximately 35 currently described taxa. Further, the degree of host-specificity may vary substantially among lineages. Parasite distribution can be influenced by the ability of the parasite to infect a host, vector preferences for certain avian hosts, or other factors such as microhabitat requirements that increase the probability that vertebrate hosts and vectors are in frequent contact with each other. Whereas most studies of haemosporidians have focused on passerine hosts, sampling vectors in the same habitats may allow the detection of other lineages affecting other hosts. We sampled abundant, ornithophilic black flies (Simuliidae) across a variety of sites and habitats in the Colorado Rocky Mountains throughout the summer of 2007. Black flies were screened with PCR using Leucocytozoon-specific primers that amplify a portion of the cytochrome b gene, and the sequences were compared to the haplotypes in the MalAvi database. Infections of Leucocytozoon from birds sampled in the same area were also included. We recovered 33 unique haplotypes from the black flies in this study area, which represented a large phylogenetic diversity of Leucocytozoon parasites. However, there were no clear patterns of avian host species or geography for the distribution of Leucocytozoon haplotypes in the phylogeny. Sampling host-seeking vectors is a useful way to obtain a wide variety of avian haemosporidian haplotypes from a given area and may prove useful for understanding the global patterns of host, parasite, and vector associations of these ubiquitous and diverse parasites.

X-Ray Structure of the Human Calreticulin Globular Domain Reveals a Peptide-Binding Area and Suggests a Multi-Molecular Mechanism

PubMed Central

Chouquet, Anne; Païdassi, Helena; Ling, Wai Li; Frachet, Philippe; Houen, Gunnar; Arlaud, Gérard J.; Gaboriaud, Christine

2011-01-01

In the endoplasmic reticulum, calreticulin acts as a chaperone and a Ca2+-signalling protein. At the cell surface, it mediates numerous important biological effects. The crystal structure of the human calreticulin globular domain was solved at 1.55 Å resolution. Interactions of the flexible N-terminal extension with the edge of the lectin site are consistently observed, revealing a hitherto unidentified peptide-binding site. A calreticulin molecular zipper, observed in all crystal lattices, could further extend this site by creating a binding cavity lined by hydrophobic residues. These data thus provide a first structural insight into the lectin-independent binding properties of calreticulin and suggest new working hypotheses, including that of a multi-molecular mechanism. PMID:21423620

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem.

PubMed

Amaral, Katrina E; Palace, Michael; O'Brien, Kathleen M; Fenderson, Lindsey E; Kovach, Adrienne I

2016-01-01

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem

PubMed Central

Amaral, Katrina E.; Palace, Michael; O’Brien, Kathleen M.; Fenderson, Lindsey E.; Kovach, Adrienne I.

2016-01-01

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists. PMID:26954014

Identifying Pelagic Habitat Hotspots of Neon Flying Squid in the Temperate Waters of the Central North Pacific.

PubMed

Alabia, Irene D; Saitoh, Sei-Ichi; Mugo, Robinson; Igarashi, Hiromichi; Ishikawa, Yoichi; Usui, Norihisa; Kamachi, Masafumi; Awaji, Toshiyuki; Seito, Masaki

2015-01-01

We identified the pelagic habitat hotspots of the neon flying squid (Ommastrephes bartramii) in the central North Pacific from May to July and characterized the spatial patterns of squid aggregations in relation to oceanographic features such as mesoscale oceanic eddies and the Transition Zone Chlorophyll-a Front (TZCF). The data used for the habitat model construction and analyses were squid fishery information, remotely-sensed and numerical model-derived environmental data from May to July 1999-2010. Squid habitat hotspots were deduced from the monthly Maximum Entropy (MaxEnt) models and were identified as regions of persistent high suitable habitat across the 12-year period. The distribution of predicted squid habitat hotspots in central North Pacific revealed interesting spatial and temporal patterns likely linked with the presence and dynamics of oceanographic features in squid's putative foraging grounds from late spring to summer. From May to June, the inferred patches of squid habitat hotspots developed within the Kuroshio-Oyashio transition zone (KOTZ; 37-40°N) and further expanded north towards the subarctic frontal zone (SAFZ; 40-44°N) in July. The squid habitat hotspots within the KOTZ and areas west of the dateline (160°W-180°) were likely influenced and associated with the highly dynamic and transient oceanic eddies and could possibly account for lower squid suitable habitat persistence obtained from these regions. However, predicted squid habitat hotspots located in regions east of the dateline (180°-160°W) from June to July, showed predominantly higher squid habitat persistence presumably due to their proximity to the mean position of the seasonally-shifting TZCF and consequent utilization of the highly productive waters of the SAFZ.

Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat.

PubMed

Teng, Huajing; Zhang, Yaohua; Shi, Chengmin; Mao, Fengbiao; Hou, Lingling; Guo, Hongling; Sun, Zhongsheng; Zhang, Jianxu

2016-07-07

Whole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches. Copyright © 2016 Teng et al.

'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

PubMed

Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

2018-01-01

A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

The Hidden Diversity of Zanclea Associated with Scleractinians Revealed by Molecular Data

PubMed Central

Montano, Simone; Maggioni, Davide; Arrigoni, Roberto; Seveso, Davide; Puce, Stefania; Galli, Paolo

2015-01-01

Scleractinian reef corals have recently been acknowledged as the most numerous host group found in association with hydroids belonging to the Zanclea genus. However, knowledge of the molecular phylogenetic relationships among Zanclea species associated with scleractinians is just beginning. This study, using the nuclear 28S rDNA region and the fast-evolving mitochondrial 16S rRNA and COI genes, provides the most comprehensive phylogenetic reconstruction of the genus Zanclea with a particular focus on the genetic diversity among Zanclea specimens associated with 13 scleractinian genera. The monophyly of Zanclea associated with scleractinians was strongly supported in all nuclear and mitochondrial phylogenetic reconstructions. Furthermore, a combined mitochondrial 16S and COI phylogenetic tree revealed a multitude of hidden molecular lineages within this group (Clades I, II, III, V, VI, VII, and VIII), suggesting the existence of both host-generalist and genus-specific lineages of Zanclea associated with scleractinians. In addition to Z. gallii living in association with the genus Acropora, we discovered four well-supported lineages (Clades I, II, III, and VII), each one forming a strict association with a single scleractinian genus, including sequences of Zanclea associated with Montipora from two geographically separated areas (Maldives and Taiwan). Two host-generalist Zanclea lineages were also observed, and one of them was formed by Zanclea specimens symbiotic with seven scleractinian genera (Clade VIII). We also found that the COI gene allows the recognition of separated hidden lineages in agreement with the commonly recommended mitochondrial 16S as a DNA barcoding gene for Hydrozoa and shows reasonable potential for phylogenetic and evolutionary analyses in the genus Zanclea. Finally, as no DNA sequences are available for the majority of the nominal Zanclea species known, we note that they will be necessary to elucidate the diversity of the Zanclea

Molecular Epidemiology Reveals Genetic Diversity amongst Isolates of the Cryptococcus neoformans/C. gattii Species Complex in Thailand

PubMed Central

Kaocharoen, Sirada; Ngamskulrungroj, Popchai; Firacative, Carolina; Trilles, Luciana; Piyabongkarn, Dumrongdej; Banlunara, Wijit; Poonwan, Natteewan; Chaiprasert, Angkana; Meyer, Wieland; Chindamporn, Ariya

2013-01-01

To gain a more detailed picture of cryptococcosis in Thailand, a retrospective study of 498 C. neoformans and C. gattii isolates has been conducted. Among these, 386, 83 and 29 strains were from clinical, environmental and veterinary sources, respectively. A total of 485 C. neoformans and 13 C. gattii strains were studied. The majority of the strains (68.9%) were isolated from males (mean age of 37.97 years), 88.5% of C. neoformans and only 37.5% of C. gattii strains were from HIV patients. URA5-RFLP and/or M13 PCR-fingerprinting analysis revealed that the majority of the isolates were C. neoformans molecular type VNI regardless of their sources (94.8%; 94.6% of the clinical, 98.8% of the environmental and 86.2% of the veterinary isolates). In addition, the molecular types VNII (2.4%; 66.7% of the clinical and 33.3% of the veterinary isolates), VNIV (0.2%; 100% environmental isolate), VGI (0.2%; 100% clinical isolate) and VGII (2.4%; 100% clinical isolates) were found less frequently. Multilocus Sequence Type (MLST) analysis using the ISHAM consensus MLST scheme for the C. neoformans/C. gattii species complex identified a total of 20 sequence types (ST) in Thailand combining current and previous data. The Thai isolates are an integrated part of the global cryptococcal population genetic structure, with ST30 for C. gattii and ST82, ST83, ST137, ST141, ST172 and ST173 for C. neoformans being unique to Thailand. Most of the C. gattii isolates were ST7 = VGIIb, which is identical to the less virulent minor Vancouver island outbreak genotype, indicating Thailand as a stepping stone in the global spread of this outbreak strain. The current study revealed a greater genetic diversity and a wider range of major molecular types being present amongst Thai cryptococcal isolates than previously reported. PMID:23861989

Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

PubMed

Förster, Yvonne; Schmidt, Johannes R; Wissenbach, Dirk K; Pfeiffer, Susanne E M; Baumann, Sven; Hofbauer, Lorenz C; von Bergen, Martin; Kalkhof, Stefan; Rammelt, Stefan

2016-01-01

Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles

PubMed Central

Wissenbach, Dirk K.; Pfeiffer, Susanne E. M.; Baumann, Sven; Hofbauer, Lorenz C.; von Bergen, Martin; Kalkhof, Stefan; Rammelt, Stefan

2016-01-01

Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis. PMID:27441377

Habitat mapping and interpretation in New England

Treesearch

William B. Leak

1982-01-01

Recommendations are given on the classification of forest land in New England on the basis of physiographic region, climate (elevation, latitude), mineralogy, and habitat. A habitat map for the Bartlett Experimental Forest in New Hampshire is presented based on land form, vegetation, and soil materials. For each habitat or group of habitats, data are presented on stand...

Habitat stability, predation risk and 'memory syndromes'.

PubMed

Dalesman, S; Rendle, A; Dall, S R X

2015-05-27

Habitat stability and predation pressure are thought to be major drivers in the evolutionary maintenance of behavioural syndromes, with trait covariance only occurring within specific habitats. However, animals also exhibit behavioural plasticity, often through memory formation. Memory formation across traits may be linked, with covariance in memory traits (memory syndromes) selected under particular environmental conditions. This study tests whether the pond snail, Lymnaea stagnalis, demonstrates consistency among memory traits ('memory syndrome') related to threat avoidance and foraging. We used eight populations originating from three different habitat types: i) laboratory populations (stable habitat, predator-free); ii) river populations (fairly stable habitat, fish predation); and iii) ditch populations (unstable habitat, invertebrate predation). At a population level, there was a negative relationship between memories related to threat avoidance and food selectivity, but no consistency within habitat type. At an individual level, covariance between memory traits was dependent on habitat. Laboratory populations showed no covariance among memory traits, whereas river populations showed a positive correlation between food memories, and ditch populations demonstrated a negative relationship between threat memory and food memories. Therefore, selection pressures among habitats appear to act independently on memory trait covariation at an individual level and the average response within a population.

Persistence in a Two-Dimensional Moving-Habitat Model.

PubMed

Phillips, Austin; Kot, Mark

2015-11-01

Environmental changes are forcing many species to track suitable conditions or face extinction. In this study, we use a two-dimensional integrodifference equation to analyze whether a population can track a habitat that is moving due to climate change. We model habitat as a simple rectangle. Our model quickly leads to an eigenvalue problem that determines whether the population persists or declines. After surveying techniques to solve the eigenvalue problem, we highlight three findings that impact conservation efforts such as reserve design and species risk assessment. First, while other models focus on habitat length (parallel to the direction of habitat movement), we show that ignoring habitat width (perpendicular to habitat movement) can lead to overestimates of persistence. Dispersal barriers and hostile landscapes that constrain habitat width greatly decrease the population's ability to track its habitat. Second, for some long-distance dispersal kernels, increasing habitat length improves persistence without limit; for other kernels, increasing length is of limited help and has diminishing returns. Third, it is not always best to orient the long side of the habitat in the direction of climate change. Evidence suggests that the kurtosis of the dispersal kernel determines whether it is best to have a long, wide, or square habitat. In particular, populations with platykurtic dispersal benefit more from a wide habitat, while those with leptokurtic dispersal benefit more from a long habitat. We apply our model to the Rocky Mountain Apollo butterfly (Parnassius smintheus).

Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta,Y.; Nair, D.; Wharton, R.

2008-01-01

Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycBreverse and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, inmore » effect, acting as a 'spacer.' The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo.« less

Generalisation of physical habitat-discharge relationships

NASA Astrophysics Data System (ADS)

Booker, D. J.; Acreman, M. C.

2007-01-01

Physical habitat is increasingly used worldwide as a measure of river ecosystem health when assessing changes to river flows, such as those caused by abstraction. The major drawback with this approach is that defining precisely the relationships between physical habitat and flow for a given river reach requires considerable data collection and analysis. Consequently, widely used models such as the Physical Habitat Simulation (PHABSIM) system are expensive to apply. There is, thus, a demand for rapid methods for defining habitat-discharge relationships from simple field measurements. This paper reports the analysis of data from 63 sites in the UK where PHABSIM has been applied. The results demonstrate that there are strong relationships between single measurements of channel form and river hydraulics and the habitat available for target species. The results can form the basis of a method to estimate sensitivity of physical habitat to flow change by visiting a site at only one flow. Furthermore, the uncertainty in estimates reduces as more information is collected. This allows the user to select the level of investment in data collection appropriate for the desired confidence in the estimates. The method is demonstrated using habitat indicators for different life stages of Atlantic salmon, brown trout, roach and dace.

Fine-scale habitat preference of green sturgeon (Acipenser medirostris) within three spawning locations in the Sacramento River, California

USGS Publications Warehouse

Wyman, Megan T.; Thomas, Michael J.; McDonald, Richard R.; Hearn, Alexander R.; Battleson, Ryan D.; Chapman, Eric D.; Kinzel, Paul J.; Minear, J. Tobey; Mora, Ethan A.; Nelson, Jonathan M.; Pagel, Matthew D.; Klimley, A. Peter

2018-01-01

Vast sections of the Sacramento River have been listed as critical habitat by the National Marine Fisheries Service for green sturgeon spawning (Acipenser medirostris), yet spawning is known to occur at only a few specific locations. This study reveals the range of physical habitat variables selected by adult green sturgeon during their spawning period. We integrated fine-scale fish positions, physical habitat characteristics, discharge, bathymetry, and simulated velocity and depth using a 2-dimensional hydraulic model (FaSTMECH). The objective was to create habitat suitability curves for depth, velocity, and substrate type within three known spawning locations over two years. An overall cumulative habitat suitability score was calculated that averaged the depth, velocity, and substrate scores over all fish, sites, and years. A weighted usable area (WUA) index was calculated throughout the sampling periods for each of the three sites. Cumulative results indicate that the microhabitat characteristics most preferred by green sturgeon in these three spawning locations were velocities between 1.0-1.1 m/s, depths of 8-9 m, and gravel and sand substrate. This study provides guidance for those who may in the future want to increase spawning habitat for green sturgeon within the Sacramento River.

High gene flow in epiphytic ferns despite habitat loss and fragmentation.

PubMed

Winkler, Manuela; Koch, Marcus; Hietz, Peter

2011-01-01

Tropical montane forests suffer from increasing fragmentation and replacement by other types of land-use such as coffee plantations. These processes are known to affect gene flow and genetic structure of plant populations. Epiphytes are particularly vulnerable because they depend on their supporting trees for their entire life-cycle. We compared population genetic structure and genetic diversity derived from AFLP markers of two epiphytic fern species differing in their ability to colonize secondary habitats. One species, Pleopeltis crassinervata , is a successful colonizer of shade trees and isolated trees whereas the other species, Polypodium rhodopleuron , is restricted to forests with anthropogenic separation leading to significant isolation between populations. By far most genetic variation was distributed within rather than among populations in both species, and a genetic admixture analysis did not reveal any clustering. Gene flow exceeded by far the benchmark of one migrant per generation to prevent genetic divergence between populations in both species. Though populations are threatened by habitat loss, long-distance dispersal is likely to support gene flow even between distant populations, which efficiently delays genetic isolation. Consequently, populations may rather be threatened by ecological consequences of habitat loss and fragmentation.

Global ecological success of Thalassoma fishes in extreme coral reef habitats.

PubMed

Fulton, Christopher J; Wainwright, Peter C; Hoey, Andrew S; Bellwood, David R

2017-01-01

Phenotypic adaptations can allow organisms to relax abiotic selection and facilitate their ecological success in challenging habitats, yet we have relatively little data for the prevalence of this phenomenon at macroecological scales. Using data on the relative abundance of coral reef wrasses and parrotfishes (f. Labridae) spread across three ocean basins and the Red Sea, we reveal the consistent global dominance of extreme wave-swept habitats by fishes in the genus Thalassoma , with abundances up to 15 times higher than any other labrid. A key locomotor modification-a winged pectoral fin that facilitates efficient underwater flight in high-flow environments-is likely to have underpinned this global success, as numerical dominance by Thalassoma was contingent upon the presence of high-intensity wave energy. The ecological success of the most abundant species also varied with species richness and the presence of congeneric competitors. While several fish taxa have independently evolved winged pectoral fins, Thalassoma appears to have combined efficient high-speed swimming (to relax abiotic selection) with trophic versatility (to maximize exploitation of rich resources) to exploit and dominate extreme coral reef habitats around the world.

Advanced Plant Habitat (APH)

NASA Technical Reports Server (NTRS)

Richards, Stephanie E. (Compiler); Levine, Howard G.; Reed, David W.

2016-01-01

The Advanced Plant Habitat (APH) hardware will be a large growth volume plant habitat, capable of hosting multigenerational studies, in which environmental variables (e.g., temperature, relative humidity, carbon dioxide level light intensity and spectral quality) can be tracked and controlled in support of whole plant physiological testing and Bio-regenerative Life Support System investigations.

Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea.

PubMed

Lauria, V; Gristina, M; Attrill, M J; Fiorentino, F; Garofalo, G

2015-08-14

Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world's sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea.

Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea

NASA Astrophysics Data System (ADS)

Lauria, V.; Gristina, M.; Attrill, M. J.; Fiorentino, F.; Garofalo, G.

2015-08-01

Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world’s sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea.

Does habitat disturbance affect stress, body condition and parasitism in two sympatric lemurs?

PubMed Central

Rakotoniaina, Josué H; Kappeler, Peter M; Ravoniarimbinina, Pascaline; Pechouskova, Eva; Hämäläinen, Anni M; Grass, Juliane; Kirschbaum, Clemens; Kraus, Cornelia

2016-01-01