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Sample records for mammals increased taxon

  1. Increased taxon sampling greatly reduces phylogenetic error.

    PubMed

    Zwickl, Derrick J; Hillis, David M

    2002-08-01

    Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall

  2. Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage.

    PubMed

    Feijoo, M; Parada, A

    2017-08-01

    In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughput sequencing data (RNA or DNA) generated for other biological studies and available in public databases. Following this procedure we addressed pending or controversial issues concerning the phylogenetic position of Dermoptera, Pholidota and Chiroptera, considering multiple and independent loci. Also for Chiroptera and Arctoidea we evaluated the relationships of the lineages that compose it. Although the maximum number of genes used is moderate (95), in some cases taxon coverage doubles that of previous related studies. Globally, all coalescent-based (STAR, MP-EST and ASTRAL) and concatenated (IQ-TREE and BEAST2) methods used for species tree reconstruction were consistent to each other and most of interrogated nodes received high statistical support. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals.

    PubMed

    Janowski, Andrew B; Krishnamurthy, Siddharth R; Lim, Efrem S; Zhao, Guoyan; Brenchley, Jason M; Barouch, Dan H; Thakwalakwa, Chrissie; Manary, Mark J; Holtz, Lori R; Wang, David

    2017-04-01

    Next-generation sequencing has expanded our understanding of the viral populations that constitute the mammalian virome. We describe a novel taxon of viruses named Statoviruses, for Stool associated Tombus-like viruses, present in multiple metagenomic datasets. These viruses define a novel clade that is phylogenetically related to the RNA virus families Tombusviridae and Flaviviridae. Five distinct statovirus types were identified in human, macaque, mouse, and cow gastrointestinal tract samples. The prototype genome, statovirus A, was frequently identified in macaque stool samples from multiple geographically distinct cohorts. Another genome, statovirus C1, was discovered in a stool sample from a human child with fever, cough, and rash. Further experimental data will clarify whether these viruses are infectious to mammals or if they originate from another source present in the mammalian gastrointestinal tract.

  4. Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals

    PubMed Central

    Janowski, Andrew B.; Krishnamurthy, Siddharth R.; Lim, Efrem S.; Zhao, Guoyan; Brenchley, Jason M.; Barouch, Dan H.; Thakwalakwa, Chrissie; Manary, Mark J.; Holtz, Lori R.; Wang, David

    2017-01-01

    Next-generation sequencing has expanded our understanding of the viral populations that constitute the mammalian virome. We describe a novel taxon of viruses named Statoviruses, for Stool associated Tombus-like viruses, present in multiple metagenomic datasets. These viruses define a novel clade that is phylogenetically related to the RNA virus families Tombusviridae and Flaviviridae. Five distinct statovirus types were identified in human, macaque, mouse, and cow gastrointestinal tract samples. The prototype genome, statovirus A, was frequently identified in macaque stool samples from multiple geographically distinct cohorts. Another genome, statovirus C1, was discovered in a stool sample from a human child with fever, cough, and rash. Further experimental data will clarify whether these viruses are infectious to mammals or if they originate from another source present in the mammalian gastrointestinal tract. PMID:28152382

  5. Assessing the Value of DNA Barcodes for Molecular Phylogenetics: Effect of Increased Taxon Sampling in Lepidoptera

    PubMed Central

    Wilson, John James

    2011-01-01

    Background A common perception is that DNA barcode datamatrices have limited phylogenetic signal due to the small number of characters available per taxon. However, another school of thought suggests that the massively increased taxon sampling afforded through the use of DNA barcodes may considerably increase the phylogenetic signal present in a datamatrix. Here I test this hypothesis using a large dataset of macrolepidopteran DNA barcodes. Methodology/Principal Findings Taxon sampling was systematically increased in datamatrices containing macrolepidopteran DNA barcodes. Sixteen family groups were designated as concordance groups and two quantitative measures; the taxon consistency index and the taxon retention index, were used to assess any changes in phylogenetic signal as a result of the increase in taxon sampling. DNA barcodes alone, even with maximal taxon sampling (500 species per family), were not sufficient to reconstruct monophyly of families and increased taxon sampling generally increased the number of clades formed per family. However, the scores indicated a similar level of taxon retention (species from a family clustering together) in the cladograms as the number of species included in the datamatrix was increased, suggesting substantial phylogenetic signal below the ‘family’ branch. Conclusions/Significance The development of supermatrix, supertree or constrained tree approaches could enable the exploitation of the massive taxon sampling afforded through DNA barcodes for phylogenetics, connecting the twigs resolved by barcodes to the deep branches resolved through phylogenomics. PMID:21931848

  6. Increased taxon sampling reveals thousands of hidden orthologs in flatworms.

    PubMed

    Martín-Durán, José M; Ryan, Joseph F; Vellutini, Bruno C; Pang, Kevin; Hejnol, Andreas

    2017-07-01

    Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages-mistakenly considered new genes-but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3427 putative hidden orthologs, some unidentified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its "average" evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g., planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution. © 2017 Martín-Durán et al.; Published by Cold Spring Harbor Laboratory Press.

  7. Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition.

    PubMed

    Pollock, D D; Bruno, W J

    2000-12-01

    Assessment of the evolutionary process is crucial for understanding the effect of protein structure and function on sequence evolution and for many other analyses in molecular evolution. Here, we used simulations to study how taxon sampling affects accuracy of parameter estimation and topological inference in the absence of branch length asymmetry. With maximum-likelihood analysis, we find that adding taxa dramatically improves both support for the evolutionary model and accurate assessment of its parameters when compared with increasing the sequence length. Using a method we call "doppelgänger trees," we distinguish the contributions of two sources of improved topological inference: greater knowledge about internal nodes and greater knowledge of site-specific rate parameters. Surprisingly, highly significant support for the correct general model does not lead directly to improved topological inference. Instead, substantial improvement occurs only with accurate assessment of the evolutionary process at individual sites. Although these results are based on a simplified model of the evolutionary process, they indicate that in general, assuming processes are not independent and identically distributed among sites, more extensive sampling of taxonomic biodiversity will greatly improve analytical results in many current sequence data sets with moderate sequence lengths.

  8. Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling

    PubMed Central

    Crête-Lafrenière, Alexis; Weir, Laura K.; Bernatchez, Louis

    2012-01-01

    Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63) to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY) old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ∼0.31%/MY (CI: 0.27–0.36%/MY). Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our findings

  9. Intensive removal of signal crayfish (Pacifastacus leniusculus) from rivers increases numbers and taxon richness of macroinvertebrate species.

    PubMed

    Moorhouse, Tom P; Poole, Alison E; Evans, Laura C; Bradley, David C; Macdonald, David W

    2014-02-01

    Invasive species are a major cause of species extinction in freshwater ecosystems, and crayfish species are particularly pervasive. The invasive American signal crayfish Pacifastacus leniusculus has impacts over a range of trophic levels, but particularly on benthic aquatic macroinvertebrates. Our study examined the effect on the macroinvertebrate community of removal trapping of signal crayfish from UK rivers. Crayfish were intensively trapped and removed from two tributaries of the River Thames to test the hypothesis that lowering signal crayfish densities would result in increases in macroinvertebrate numbers and taxon richness. We removed 6181 crayfish over four sessions, resulting in crayfish densities that decreased toward the center of the removal sections. Conversely in control sections (where crayfish were trapped and returned), crayfish density increased toward the center of the section. Macroinvertebrate numbers and taxon richness were inversely correlated with crayfish densities. Multivariate analysis of the abundance of each taxon yielded similar results and indicated that crayfish removals had positive impacts on macroinvertebrate numbers and taxon richness but did not alter the composition of the wider macroinvertebrate community. Synthesis and applications: Our results demonstrate that non-eradication-oriented crayfish removal programmes may lead to increases in the total number of macroinvertebrates living in the benthos. This represents the first evidence that removing signal crayfish from riparian systems, at intensities feasible during control attempts or commercial crayfishing, may be beneficial for a range of sympatric aquatic macroinvertebrates.

  10. Intensive removal of signal crayfish (Pacifastacus leniusculus) from rivers increases numbers and taxon richness of macroinvertebrate species

    PubMed Central

    Moorhouse, Tom P; Poole, Alison E; Evans, Laura C; Bradley, David C; Macdonald, David W

    2014-01-01

    Invasive species are a major cause of species extinction in freshwater ecosystems, and crayfish species are particularly pervasive. The invasive American signal crayfish Pacifastacus leniusculus has impacts over a range of trophic levels, but particularly on benthic aquatic macroinvertebrates. Our study examined the effect on the macroinvertebrate community of removal trapping of signal crayfish from UK rivers. Crayfish were intensively trapped and removed from two tributaries of the River Thames to test the hypothesis that lowering signal crayfish densities would result in increases in macroinvertebrate numbers and taxon richness. We removed 6181 crayfish over four sessions, resulting in crayfish densities that decreased toward the center of the removal sections. Conversely in control sections (where crayfish were trapped and returned), crayfish density increased toward the center of the section. Macroinvertebrate numbers and taxon richness were inversely correlated with crayfish densities. Multivariate analysis of the abundance of each taxon yielded similar results and indicated that crayfish removals had positive impacts on macroinvertebrate numbers and taxon richness but did not alter the composition of the wider macroinvertebrate community. Synthesis and applications: Our results demonstrate that non-eradication-oriented crayfish removal programmes may lead to increases in the total number of macroinvertebrates living in the benthos. This represents the first evidence that removing signal crayfish from riparian systems, at intensities feasible during control attempts or commercial crayfishing, may be beneficial for a range of sympatric aquatic macroinvertebrates. PMID:24634733

  11. Increased homeothermy during reproduction in a basal placental mammal.

    PubMed

    Levesque, Danielle L; Lovegrove, Barry G

    2014-05-01

    Homeothermic endothermy, the maintenance of a high and stable body temperature (Tb) using heat produced by elevated metabolism, is energetically expensive. There is increasing evidence that the earliest endotherms were heterotherms that, rather than maintaining strict homeothermy, allowed Tb to fluctuate with large variations between active and rest-phase Tb. The high level of homeothermy observed in modern mammals is therefore likely to have evolved from an ancestral heterothermic state. One of the hypotheses for the evolution of endothermy is that homeothermy allows for greater energetic output during reproduction (parental care model). We tested this hypothesis by measuring metabolic rates over a range of ambient temperatures in both reproductive and non-reproductive greater hedgehog tenrecs (Setifer setosus), a physiologically primitive mammal from Madagascar. Tenrecs have some of the lowest metabolic rates and highest levels of Tb variability of any mammal and are therefore good models of the ancestral eutherian state. During pregnancy and lactation, there was an increase in metabolism and Tb below the thermoneutral zone, accompanied by a decrease in Tb variability. The lower critical limit of the thermoneutral zone was estimated at ~25°C. However, whereas increases in resting metabolism were substantial below 20°C (up to 150% higher during reproduction), daytime rest-phase ambient temperatures at the study site rarely reached equivalent low levels. Thus, S. setosus provide an example for how relatively low-cost increases in homeothermy could have led to substantial increases in fitness by allowing for the faster production of young. The mechanisms necessary for increases in thermogenesis during reproduction would have further benefited the development of homeothermy in mammals.

  12. The taxon concept: is it taxonic?

    PubMed

    Grove, William M

    2008-06-01

    The question of whether the concept of a "taxon" (a nonarbitrary latent category) is itself categorical, or is a matter of degree, has lain dormant within taxometrics. I analyze the problem conceptually. Part of the meaning of "taxon," I hold, goes beyond the manifest statistical properties of admixed probability distributions; any of certain forms of causal nexus leading to admixed distributions are involved as well. I defend the thesis that the threshold question, "Is there a taxon?" has a yes-or-no answer, establishing that "taxonicity" is categorical (taxonic), but also that as some taxa are much more readily distinguished from their complement classes than are others, the taxon question is also quantitative. It is on this basis that Meehl and others held the view that taxonicity is a matter of degree; however, they were wrong to hold that it is only a matter of degree.

  13. Larger brain size indirectly increases vulnerability to extinction in mammals.

    PubMed

    Gonzalez-Voyer, Alejandro; González-Suárez, Manuela; Vilà, Carles; Revilla, Eloy

    2016-06-01

    Although previous studies have addressed the question of why large brains evolved, we have limited understanding of potential beneficial or detrimental effects of enlarged brain size in the face of current threats. Using novel phylogenetic path analysis, we evaluated how brain size directly and indirectly, via its effects on life history and ecology, influences vulnerability to extinction across 474 mammalian species. We found that larger brains, controlling for body size, indirectly increase vulnerability to extinction by extending the gestation period, increasing weaning age, and limiting litter sizes. However, we found no evidence of direct, beneficial, or detrimental effects of brain size on vulnerability to extinction, even when we explicitly considered the different types of threats that lead to vulnerability. Order-specific analyses revealed qualitatively similar patterns for Carnivora and Artiodactyla. Interestingly, for Primates, we found that larger brain size was directly (and indirectly) associated with increased vulnerability to extinction. Our results indicate that under current conditions, the constraints on life history imposed by large brains outweigh the potential benefits, undermining the resilience of the studied mammals. Contrary to the selective forces that have favored increased brain size throughout evolutionary history, at present, larger brains have become a burden for mammals. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  14. Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution

    PubMed Central

    Spaulding, Michelle; O'Leary, Maureen A.; Gatesy, John

    2009-01-01

    Background Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. Methodology/Principal Findings We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, †Creodonta, Lipotyphla, and the †raoellid artiodactylan †Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to †Indohyus, with †Mesonychia outside of Artiodactyla. The relationships of †Mesonychia and †Indohyus are highly unstable, however - in trees only two steps longer than minimum length, †Mesonychia falls inside Artiodactyla and displaces †Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. Conclusions/Significance Integration of new fossil material of †Indohyus impacts placement of another extinct clade †Mesonychia, pushing it much farther down the tree. The phylogenetic position of †Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales + hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup. PMID:19774069

  15. Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution.

    PubMed

    Spaulding, Michelle; O'Leary, Maureen A; Gatesy, John

    2009-09-23

    Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, Creodonta, Lipotyphla, and the raoellid artiodactylan Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to Indohyus, with Mesonychia outside of Artiodactyla. The relationships of Mesonychia and Indohyus are highly unstable, however--in trees only two steps longer than minimum length, Mesonychia falls inside Artiodactyla and displaces Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. Integration of new fossil material of Indohyus impacts placement of another extinct clade Mesonychia, pushing it much farther down the tree. The phylogenetic position of Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales+hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.

  16. Cross-taxon congruence and environmental conditions.

    PubMed

    Toranza, Carolina; Arim, Matías

    2010-07-16

    Diversity patterns of different taxa typically covary in space, a phenomenon called cross-taxon congruence. This pattern has been explained by the effect of one taxon diversity on taxon diversity, shared biogeographic histories of different taxa, and/or common responses to environmental conditions. A meta-analysis of the association between environment and diversity patterns found that in 83 out of 85 studies, more than 60% of the spatial variability in species richness was related to variables representing energy, water or their interaction. The role of the environment determining taxa diversity patterns leads us to hypothesize that this would explain the observed cross-taxon congruence. However, recent analyses reported the persistence of cross-taxon congruence when environmental effect was statistically removed. Here we evaluate this hypothesis, analyzing the cross-taxon congruence between birds and mammals in the Brazilian Cerrado, and assess the environmental role on the spatial covariation in diversity patterns. We found a positive association between avian and mammal richness and a positive latitudinal trend for both groups in the Brazilian Cerrado. Regression analyses indicated an effect of latitude, PET, and mean temperature over both biological groups. In addition, we show that NDVI was only associated with avian diversity; while the annual relative humidity, was only correlated with mammal diversity. We determined the environmental effects on diversity in a path analysis that accounted for 73% and 76% of the spatial variation in avian and mammal richness. However, an association between avian and mammal diversity remains significant. Indeed, the importance of this link between bird and mammal diversity was also supported by a significant association between birds and mammal spatial autoregressive model residuals. Our study corroborates the main role of environmental conditions on diversity patterns, but suggests that other important mechanisms, which

  17. Cross-taxon congruence and environmental conditions

    PubMed Central

    2010-01-01

    Background Diversity patterns of different taxa typically covary in space, a phenomenon called cross-taxon congruence. This pattern has been explained by the effect of one taxon diversity on taxon diversity, shared biogeographic histories of different taxa, and/or common responses to environmental conditions. A meta-analysis of the association between environment and diversity patterns found that in 83 out of 85 studies, more than 60% of the spatial variability in species richness was related to variables representing energy, water or their interaction. The role of the environment determining taxa diversity patterns leads us to hypothesize that this would explain the observed cross-taxon congruence. However, recent analyses reported the persistence of cross-taxon congruence when environmental effect was statistically removed. Here we evaluate this hypothesis, analyzing the cross-taxon congruence between birds and mammals in the Brazilian Cerrado, and assess the environmental role on the spatial covariation in diversity patterns. Results We found a positive association between avian and mammal richness and a positive latitudinal trend for both groups in the Brazilian Cerrado. Regression analyses indicated an effect of latitude, PET, and mean temperature over both biological groups. In addition, we show that NDVI was only associated with avian diversity; while the annual relative humidity, was only correlated with mammal diversity. We determined the environmental effects on diversity in a path analysis that accounted for 73% and 76% of the spatial variation in avian and mammal richness. However, an association between avian and mammal diversity remains significant. Indeed, the importance of this link between bird and mammal diversity was also supported by a significant association between birds and mammal spatial autoregressive model residuals. Conclusion Our study corroborates the main role of environmental conditions on diversity patterns, but suggests that other

  18. Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA.

    PubMed

    Dohrmann, Martin; Voigt, Oliver; Erpenbeck, Dirk; Wörheide, Gert

    2006-09-01

    Calcareous sponges (Porifera, Calcarea) play an important role for our understanding of early metazoan evolution, since several molecular studies suggested their closer relationship to Eumetazoa than to the other two sponge 'classes,' Demospongiae and Hexactinellida. The division of Calcarea into the subtaxa Calcinea and Calcaronea is well established by now, but their internal relationships remain largely unresolved. Here, we estimate phylogenetic relationships within Calcarea in a Bayesian framework, using full-length 18S and partial 28S ribosomal DNA sequences. Both genes were analyzed separately and in combination and were further partitioned by stem and loop regions, the former being modelled to take non-independence of paired sites into account. By substantially increasing taxon sampling, we show that most of the traditionally recognized supraspecific taxa within Calcinea and Calcaronea are not monophyletic, challenging the existing classification system, while monophyly of Calcinea and Calcaronea is again highly supported.

  19. Seed predation by Neotropical rain forest mammals increases diversity in seedling recruitment.

    PubMed

    Paine, C E Timothy; Beck, Harald

    2007-12-01

    Seed dispersal and seedling recruitment (the transition of seeds to seedlings) set the spatiotemporal distribution of new individuals in plant communities. Many terrestrial rain forest mammals consume post-dispersal seeds and seedlings, often inflicting density-dependent mortality. In part because of density-dependent mortality, diversity often increases during seedling recruitment, making it a critical stage for species coexistence. We determined how mammalian predators, adult tree abundance, and seed mass interact to affect seedling recruitment in a western Amazonian rain forest. We used exclosures that were selectively permeable to three size classes of mammals: mice and spiny rats (weighing <1 kg), medium-sized rodents (1-12 kg), and large mammals (20-200 kg). Into each exclosure, we placed seeds of 13 tree species and one canopy liana, which varied by an order of magnitude in adult abundance and seed mass. We followed the fates of the seeds and resulting seedlings for at least 17 months. We assessed the effect of each mammalian size class on seed survival, seedling survival and growth, and the density and diversity of the seedlings that survived to the end of the experiment. Surprisingly, large mammals had no detectable effect at any stage of seedling recruitment. In contrast, small- and medium-sized mammals significantly reduced seed survival, seedling survival, and seedling density. Furthermore, predation by small mammals increased species richness on a per-stem basis. This increase in diversity resulted from their disproportionately intense predation on common species and large-seeded species. Small mammals thereby generated a rare-species advantage in seedling recruitment, the critical ingredient for frequency dependence. Predation by small (and to a lesser extent, medium-sized) mammals on seeds and seedlings significantly increases tree species diversity in tropical forests. This is the first long-term study to dissect the effects of various mammalian

  20. Arboreality has allowed for the evolution of increased longevity in mammals.

    PubMed

    Shattuck, Milena R; Williams, Scott A

    2010-03-09

    The evolutionary theory of aging predicts that species will experience delayed senescence and increased longevity when rates of extrinsic mortality are reduced. It has long been recognized that birds and bats are characterized by lower rates of extrinsic mortality and greater longevities than nonvolant endotherms, presumably because flight reduces exposure to terrestrial predators, disease, and environmental hazards. Like flight, arboreality may act to reduce extrinsic mortality, delay senescence, and increase longevity and has been suggested as an explanation for the long lifespans of primates. However, this hypothesis has yet to be tested in mammals in general. We analyze a large dataset of mammalian longevity records to test whether arboreal mammals are characterized by greater longevities than terrestrial mammals. Here, we show that arboreal mammals are longer lived than terrestrial mammals at common body sizes, independent of phylogeny. Subclade analyses demonstrate that this trend holds true in nearly every mammalian subgroup, with two notable exceptions-metatherians (marsupials) and euarchontans (primates and their close relatives). These subgroups are unique in that each has experienced a long and persistent arboreal evolutionary history, with subsequent transitions to terrestriality occurring multiple times within each group. In all other clades examined, terrestriality appears to be the primitive condition, and species that become arboreal tend to experience increased longevity, often independently in multiple lineages within each clade. Adoption of an arboreal lifestyle may have allowed for increased longevity in these lineages and in primates in general. Overall, these results confirm the fundamental predictions of the evolutionary theory of aging.

  1. Arboreality has allowed for the evolution of increased longevity in mammals

    PubMed Central

    Shattuck, Milena R.; Williams, Scott A.

    2010-01-01

    The evolutionary theory of aging predicts that species will experience delayed senescence and increased longevity when rates of extrinsic mortality are reduced. It has long been recognized that birds and bats are characterized by lower rates of extrinsic mortality and greater longevities than nonvolant endotherms, presumably because flight reduces exposure to terrestrial predators, disease, and environmental hazards. Like flight, arboreality may act to reduce extrinsic mortality, delay senescence, and increase longevity and has been suggested as an explanation for the long lifespans of primates. However, this hypothesis has yet to be tested in mammals in general. We analyze a large dataset of mammalian longevity records to test whether arboreal mammals are characterized by greater longevities than terrestrial mammals. Here, we show that arboreal mammals are longer lived than terrestrial mammals at common body sizes, independent of phylogeny. Subclade analyses demonstrate that this trend holds true in nearly every mammalian subgroup, with two notable exceptions—metatherians (marsupials) and euarchontans (primates and their close relatives). These subgroups are unique in that each has experienced a long and persistent arboreal evolutionary history, with subsequent transitions to terrestriality occurring multiple times within each group. In all other clades examined, terrestriality appears to be the primitive condition, and species that become arboreal tend to experience increased longevity, often independently in multiple lineages within each clade. Adoption of an arboreal lifestyle may have allowed for increased longevity in these lineages and in primates in general. Overall, these results confirm the fundamental predictions of the evolutionary theory of aging. PMID:20176952

  2. Hibernation is associated with increased survival and the evolution of slow life histories among mammals.

    PubMed

    Turbill, Christopher; Bieber, Claudia; Ruf, Thomas

    2011-11-22

    Survival probability is predicted to underlie the evolution of life histories along a slow-fast continuum. Hibernation allows a diverse range of small mammals to exhibit seasonal dormancy, which might increase survival and consequently be associated with relatively slow life histories. We used phylogenetically informed GLS models to test for an effect of hibernation on seasonal and annual survival, and on key attributes of life histories among mammals. Monthly survival was in most cases higher during hibernation compared with the active season, probably because inactivity minimizes predation. Hibernators also have approximately 15 per cent higher annual survival than similar sized non-hibernating species. As predicted, we found an effect of hibernation on the relationships between life history attributes and body mass: small hibernating mammals generally have longer maximum life spans (50% greater for a 50 g species), reproduce at slower rates, mature at older ages and have longer generation times compared with similar-sized non-hibernators. In accordance with evolutionary theories, however, hibernating species do not have longer life spans than non-hibernators with similar survival rates, nor do they have lower reproductive rates than non-hibernators with similar maximum life spans. Thus, our combined results suggest that (i) hibernation is associated with high rates of overwinter and annual survival, and (ii) an increase in survival in hibernating species is linked with the coevolution of traits indicative of relatively slow life histories.

  3. Hibernation is associated with increased survival and the evolution of slow life histories among mammals

    PubMed Central

    Turbill, Christopher; Bieber, Claudia; Ruf, Thomas

    2011-01-01

    Survival probability is predicted to underlie the evolution of life histories along a slow–fast continuum. Hibernation allows a diverse range of small mammals to exhibit seasonal dormancy, which might increase survival and consequently be associated with relatively slow life histories. We used phylogenetically informed GLS models to test for an effect of hibernation on seasonal and annual survival, and on key attributes of life histories among mammals. Monthly survival was in most cases higher during hibernation compared with the active season, probably because inactivity minimizes predation. Hibernators also have approximately 15 per cent higher annual survival than similar sized non-hibernating species. As predicted, we found an effect of hibernation on the relationships between life history attributes and body mass: small hibernating mammals generally have longer maximum life spans (50% greater for a 50 g species), reproduce at slower rates, mature at older ages and have longer generation times compared with similar-sized non-hibernators. In accordance with evolutionary theories, however, hibernating species do not have longer life spans than non-hibernators with similar survival rates, nor do they have lower reproductive rates than non-hibernators with similar maximum life spans. Thus, our combined results suggest that (i) hibernation is associated with high rates of overwinter and annual survival, and (ii) an increase in survival in hibernating species is linked with the coevolution of traits indicative of relatively slow life histories. PMID:21450735

  4. Modeling effectiveness of gradual increases in source level to mitigate effects of sonar on marine mammals.

    PubMed

    Von Benda-Beckmann, Alexander M; Wensveen, Paul J; Kvadsheim, Petter H; Lam, Frans-Peter A; Miller, Patrick J O; Tyack, Peter L; Ainslie, Michael A

    2014-02-01

    Ramp-up or soft-start procedures (i.e., gradual increase in the source level) are used to mitigate the effect of sonar sound on marine mammals, although no one to date has tested whether ramp-up procedures are effective at reducing the effect of sound on marine mammals. We investigated the effectiveness of ramp-up procedures in reducing the area within which changes in hearing thresholds can occur. We modeled the level of sound killer whales (Orcinus orca) were exposed to from a generic sonar operation preceded by different ramp-up schemes. In our model, ramp-up procedures reduced the risk of killer whales receiving sounds of sufficient intensity to affect their hearing. The effectiveness of the ramp-up procedure depended strongly on the assumed response threshold and differed with ramp-up duration, although extending the duration of the ramp up beyond 5 min did not add much to its predicted mitigating effect. The main factors that limited effectiveness of ramp up in a typical antisubmarine warfare scenario were high source level, rapid moving sonar source, and long silences between consecutive sonar transmissions. Our exposure modeling approach can be used to evaluate and optimize mitigation procedures.

  5. Strong Artificial Selection in Domestic Mammals Did Not Result in an Increased Recombination Rate

    PubMed Central

    Muñoz-Fuentes, Violeta; Marcet-Ortega, Marina; Alkorta-Aranburu, Gorka; Linde Forsberg, Catharina; Morrell, Jane M.; Manzano-Piedras, Esperanza; Söderberg, Arne; Daniel, Katrin; Villalba, Adrian; Toth, Attila; Di Rienzo, Anna; Roig, Ignasi; Vilà, Carles

    2015-01-01

    Recombination rates vary in intensity and location at the species, individual, sex and chromosome levels. Despite the fundamental biological importance of this process, the selective forces that operate to shape recombination rate and patterns are unclear. Domestication offers a unique opportunity to study the interplay between recombination and selection. In domesticates, intense selection for particular traits is imposed on small populations over many generations, resulting in organisms that differ, sometimes dramatically, in morphology and physiology from their wild ancestor. Although earlier studies suggested increased recombination rate in domesticates, a formal comparison of recombination rates between domestic mammals and their wild congeners was missing. In order to determine broad-scale recombination rate, we used immunolabeling detection of MLH1 foci as crossover markers in spermatocytes in three pairs of closely related wild and domestic species (dog and wolf, goat and ibex, and sheep and mouflon). In the three pairs, and contrary to previous suggestions, our data show that contemporary recombination rate is higher in the wild species. Subsequently, we inferred recombination breakpoints in sequence data for 16 genomic regions in dogs and wolves, each containing a locus associated with a dog phenotype potentially under selection during domestication. No difference in the number and distribution of recombination breakpoints was found between dogs and wolves. We conclude that our data indicate that strong directional selection did not result in changes in recombination in domestic mammals, and that both upper and lower bounds for crossover rates may be tightly regulated. PMID:25414125

  6. The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages.

    PubMed

    Soares, André E R; Schrago, Carlos G

    2015-01-07

    Although taxon sampling is commonly considered an important issue in phylogenetic inference, it is rarely considered in the Bayesian estimation of divergence times. In fact, the studies conducted to date have presented ambiguous results, and the relevance of taxon sampling for molecular dating remains unclear. In this study, we developed a series of simulations that, after six hundred Bayesian molecular dating analyses, allowed us to evaluate the impact of taxon sampling on chronological estimates under three scenarios of among-lineage rate heterogeneity. The first scenario allowed us to examine the influence of the number of terminals on the age estimates based on a strict molecular clock. The second scenario imposed an extreme example of lineage specific rate variation, and the third scenario permitted extensive rate variation distributed along the branches. We also analyzed empirical data on selected mitochondrial genomes of mammals. Our results showed that in the strict molecular-clock scenario (Case I), taxon sampling had a minor impact on the accuracy of the time estimates, although the precision of the estimates was greater with an increased number of terminals. The effect was similar in the scenario (Case III) based on rate variation distributed among the branches. Only under intensive rate variation among lineages (Case II) taxon sampling did result in biased estimates. The results of an empirical analysis corroborated the simulation findings. We demonstrate that taxonomic sampling affected divergence time inference but that its impact was significant if the rates deviated from those derived for the strict molecular clock. Increased taxon sampling improved the precision and accuracy of the divergence time estimates, but the impact on precision is more relevant. On average, biased estimates were obtained only if lineage rate variation was pronounced. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Relationship among body mass, metabolic rate and the intrinsic rate of natural increase in mammals.

    PubMed

    Hennemann, Willard W

    1983-01-01

    The intrinsic rate of natural increase, rm, was calculated for 44 mammalian species using the Cole (1954) equation and life history data from the literature. Values of r m so calculated were plotted as log10 r m versus log10 body mass revealing a linear relationship with a slope of-0.2622. The equation of the regression line fitting these data was then used to correct r m for body mass so that interspecific comparisons with respect to r m and basal metabolic rate could be made to determine if a positive relationship exists between these two parameters. Basal metabolic rate correlates positively with r m, and apparently is one of many factors operating in the evolution of r m. Implications of these conclusions with respect to food habits, resource limitations, and the possible existence of a trade-off between maintenance and reproduction in certain environments is discussed.If one assumes that all mammals face environmental limits on the amount of energy available for maintenance, growth, and reproduction, it follows that any reduction in maintenance costs should provide more energy for growth and/or reproduction. The proposed existence of such a trade-off between maintenance and reproduction was a major premise upon which MacArthur and Wilson (1967) based their concept of "r- and K-selection". Recently, however, McNab (1980) has suggested that for mammals that reproduce when food is not limiting, an increase in one maintenace cost, i.e. basal metabolic rate, may not detract from but may actually increase the intrinsic rate of natural increase, r m. Although this idea may seem counterintuitive, if one assumes an unlimited amount of energy, the factor limiting growth and reproduction will be the rate at which the energy can be used; a higher metabolic rate will mean a higher rate of biosynthesis, a faster growth rate, s shorter generation time, and hence a higher r m. Since some animal species appear not to be food-limited during their reproductive seasons (Armitage

  8. Increased food availability raises eviction rate in a cooperative breeding mammal.

    PubMed

    Dubuc, C; English, S; Thavarajah, N; Dantzer, B; Sharp, S P; Spence-Jones, H C; Gaynor, D; Clutton-Brock, T H

    2017-04-01

    In group-living mammals, the eviction of subordinate females from breeding groups by dominants may serve to reduce feeding competition or to reduce breeding competition. Here, we combined both correlational and experimental approaches to investigate whether increases in food intake by dominant females reduces their tendency to evict subordinate females in wild meerkats (Suricata suricatta). We used 20 years of long-term data to examine the association between foraging success and eviction rate, and provisioned dominant females during the second half of their pregnancy, when they most commonly evict subordinates. We show that rather than reducing the tendency for dominants to evict subordinates, foraging success of dominant females is positively associated with the probability that pregnant dominant females will evict subordinate females and that experimental feeding increased their rates of eviction. Our results suggest that it is unlikely that the eviction of subordinate females serves to reduce feeding competition and that its principal function may be to reduce reproductive competition. The increase in eviction rates following experimental feeding also suggests that rather than feeding competition, energetic constraints may normally constrain eviction rates. © 2017 The Author(s).

  9. Increased food availability raises eviction rate in a cooperative breeding mammal

    PubMed Central

    Thavarajah, N.; Sharp, S. P.; Spence-Jones, H. C.; Gaynor, D.

    2017-01-01

    In group-living mammals, the eviction of subordinate females from breeding groups by dominants may serve to reduce feeding competition or to reduce breeding competition. Here, we combined both correlational and experimental approaches to investigate whether increases in food intake by dominant females reduces their tendency to evict subordinate females in wild meerkats (Suricata suricatta). We used 20 years of long-term data to examine the association between foraging success and eviction rate, and provisioned dominant females during the second half of their pregnancy, when they most commonly evict subordinates. We show that rather than reducing the tendency for dominants to evict subordinates, foraging success of dominant females is positively associated with the probability that pregnant dominant females will evict subordinate females and that experimental feeding increased their rates of eviction. Our results suggest that it is unlikely that the eviction of subordinate females serves to reduce feeding competition and that its principal function may be to reduce reproductive competition. The increase in eviction rates following experimental feeding also suggests that rather than feeding competition, energetic constraints may normally constrain eviction rates. PMID:28404820

  10. Contrasting coloration in terrestrial mammals

    PubMed Central

    Caro, Tim

    2008-01-01

    Here I survey, collate and synthesize contrasting coloration in 5000 species of terrestrial mammals focusing on black and white pelage. After briefly reviewing alternative functional hypotheses for coloration in mammals, I examine nine colour patterns and combinations on different areas of the body and for each mammalian taxon to try to identify the most likely evolutionary drivers of contrasting coloration. Aposematism and perhaps conspecific signalling are the most consistent explanations for black and white pelage in mammals; background matching may explain white pelage. Evidence for contrasting coloration is being involved in crypsis through pattern blending, disruptive coloration or serving other functions, such as signalling dominance, lures, reducing eye glare or in temperature regulation has barely moved beyond anecdotal stages of investigation. Sexual dichromatism is limited in this taxon and its basis is unclear. Astonishingly, the functional significance of pelage coloration in most large charismatic black and white mammals that were new to science 150 years ago still remains a mystery. PMID:18990666

  11. A new phylogeny for basal Trechnotheria and Cladotheria and affinities of South American endemic Late Cretaceous mammals.

    PubMed

    Averianov, Alexander O; Martin, Thomas; Lopatin, Alexey V

    2013-04-01

    The endemic South American mammals Meridiolestida, considered previously as dryolestoid cladotherians, are found to be non-cladotherian trechnotherians related to spalacotheriid symmetrodontans based on a parsimony analysis of 137 morphological characters among 44 taxa. Spalacotheriidae is the sister taxon to Meridiolestida, and the latter clade is derived from a primitive spalacolestine that migrated to South America from North America at the beginning of the Late Cretaceous. Meridiolestida survived until the early Paleocene (Peligrotherium) and early Miocene (Necrolestes) in South America, and their extinction is probably linked to the increasing competition with metatherian and eutherian tribosphenic mammals. The clade Meridiolestida plus Spalacotheriidae is the sister taxon to Cladotheria and forms a new clade Alethinotheria. Alethinotheria and its sister taxon Zhangheotheria, new clade (Zhangheotheriidae plus basal taxa), comprise Trechnotheria. Cladotheria is divided into Zatheria (plus stem taxa, including Amphitherium) and Dryolestida, including Dryolestidae and a paraphyletic array of basal dryolestidans (formerly classified as "Paurodontidae"). The South American Vincelestes and Groebertherium are basal dryolestidans.

  12. A new phylogeny for basal Trechnotheria and Cladotheria and affinities of South American endemic Late Cretaceous mammals

    NASA Astrophysics Data System (ADS)

    Averianov, Alexander O.; Martin, Thomas; Lopatin, Alexey V.

    2013-04-01

    The endemic South American mammals Meridiolestida, considered previously as dryolestoid cladotherians, are found to be non-cladotherian trechnotherians related to spalacotheriid symmetrodontans based on a parsimony analysis of 137 morphological characters among 44 taxa. Spalacotheriidae is the sister taxon to Meridiolestida, and the latter clade is derived from a primitive spalacolestine that migrated to South America from North America at the beginning of the Late Cretaceous. Meridiolestida survived until the early Paleocene ( Peligrotherium) and early Miocene ( Necrolestes) in South America, and their extinction is probably linked to the increasing competition with metatherian and eutherian tribosphenic mammals. The clade Meridiolestida plus Spalacotheriidae is the sister taxon to Cladotheria and forms a new clade Alethinotheria. Alethinotheria and its sister taxon Zhangheotheria, new clade (Zhangheotheriidae plus basal taxa), comprise Trechnotheria. Cladotheria is divided into Zatheria (plus stem taxa, including Amphitherium) and Dryolestida, including Dryolestidae and a paraphyletic array of basal dryolestidans (formerly classified as "Paurodontidae"). The South American Vincelestes and Groebertherium are basal dryolestidans.

  13. Does moonlight increase predation risk? Meta-analysis reveals divergent responses of nocturnal mammals to lunar cycles.

    PubMed

    Prugh, Laura R; Golden, Christopher D

    2014-03-01

    The risk of predation strongly affects mammalian population dynamics and community interactions. Bright moonlight is widely believed to increase predation risk for nocturnal mammals by increasing the ability of predators to detect prey, but the potential for moonlight to increase detection of predators and the foraging efficiency of prey has largely been ignored. Studies have reported highly variable responses to moonlight among species, calling into question the assumption that moonlight increases risk. Here, we conducted a quantitative meta-analysis examining the effects of moonlight on the activity of 59 nocturnal mammal species to test the assumption that moonlight increases predation risk. We examined patterns of lunarphilia and lunarphobia across species in relation to factors such as trophic level, habitat cover preference and visual acuity. Across all species included in the meta-analysis, moonlight suppressed activity. The magnitude of suppression was similar to the presence of a predator in experimental studies of foraging rodents (13.6% and 18.7% suppression, respectively). Contrary to the expectation that moonlight increases predation risk for all prey species, however, moonlight effects were not clearly related to trophic level and were better explained by phylogenetic relatedness, visual acuity and habitat cover. Moonlight increased the activity of prey species that use vision as their primary sensory system and suppressed the activity of species that primarily use other senses (e.g. olfaction, echolocation), and suppression was strongest in open habitat types. Strong taxonomic patterns underlay these relationships: moonlight tended to increase primate activity, whereas it tended to suppress the activity of rodents, lagomorphs, bats and carnivores. These results indicate that visual acuity and habitat cover jointly moderate the effect of moonlight on predation risk, whereas trophic position has little effect. While the net effect of moonlight appears

  14. A Century of Change in Kenya's Mammal Communities: Increased Richness and Decreased Uniqueness in Six Protected Areas

    PubMed Central

    Tóth, Anikó B.; Lyons, S. Kathleen; Behrensmeyer, Anna K.

    2014-01-01

    The potential for large-scale biodiversity losses as a result of climate change and human impact presents major challenges for ecology and conservation science. Governments around the world have established national parks and wildlife reserves to help protect biodiversity, but there are few studies on the long-term consequences of this strategy. We use Kenya as a case study to investigate species richness and other attributes of mammal communities in 6 protected areas over the past century. Museum records from African expeditions that comprehensively sampled mammals from these same areas in the early 1900's provide a baseline for evaluating changes in species richness and community structure over time. We compare species lists assembled from archived specimens (1896–1950) to those of corresponding modern protected areas (1950–2013). Species richness in Kenya was stable or increased at 5 out of 6 sites from historical to modern times. Beta-diversity, in contrast, decreased across all sites. Potential biases such as variable historical vs. modern collection effort and detection of small-bodied, rare, and low-visibility species do not account for the observed results. We attribute the pattern of decreased beta diversity primarily to increased site occupancy by common species across all body size classes. Despite a decrease in land area available to wildlife, our data do not show the extinctions predicted by species-area relationships. Moreover, the results indicate that species-area curves based solely on protected areas could underestimate diversity because they do not account for mammal species whose ranges extend beyond protected area boundaries. We conclude that the 6 protected areas have been effective in preserving species richness in spite of continuing conversion of wild grasslands to cropland, but the overall decrease in beta diversity indicates a decline in the uniqueness of mammal communities that historically characterized Kenya's varied landscape

  15. A century of change in Kenya's mammal communities: increased richness and decreased uniqueness in six protected areas.

    PubMed

    Tóth, Anikó B; Lyons, S Kathleen; Behrensmeyer, Anna K

    2014-01-01

    The potential for large-scale biodiversity losses as a result of climate change and human impact presents major challenges for ecology and conservation science. Governments around the world have established national parks and wildlife reserves to help protect biodiversity, but there are few studies on the long-term consequences of this strategy. We use Kenya as a case study to investigate species richness and other attributes of mammal communities in 6 protected areas over the past century. Museum records from African expeditions that comprehensively sampled mammals from these same areas in the early 1900's provide a baseline for evaluating changes in species richness and community structure over time. We compare species lists assembled from archived specimens (1896-1950) to those of corresponding modern protected areas (1950-2013). Species richness in Kenya was stable or increased at 5 out of 6 sites from historical to modern times. Beta-diversity, in contrast, decreased across all sites. Potential biases such as variable historical vs. modern collection effort and detection of small-bodied, rare, and low-visibility species do not account for the observed results. We attribute the pattern of decreased beta diversity primarily to increased site occupancy by common species across all body size classes. Despite a decrease in land area available to wildlife, our data do not show the extinctions predicted by species-area relationships. Moreover, the results indicate that species-area curves based solely on protected areas could underestimate diversity because they do not account for mammal species whose ranges extend beyond protected area boundaries. We conclude that the 6 protected areas have been effective in preserving species richness in spite of continuing conversion of wild grasslands to cropland, but the overall decrease in beta diversity indicates a decline in the uniqueness of mammal communities that historically characterized Kenya's varied landscape.

  16. Testing for Depéret's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data

    PubMed Central

    Bokma, Folmer; Godinot, Marc; Maridet, Olivier; Ladevèze, Sandrine; Costeur, Loïc; Solé, Floréal; Gheerbrant, Emmanuel; Peigné, Stéphane; Jacques, Florian; Laurin, Michel

    2016-01-01

    Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed “Cope's rule” but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Depéret's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes. PMID:26508768

  17. Testing for Depéret's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data.

    PubMed

    Bokma, Folmer; Godinot, Marc; Maridet, Olivier; Ladevèze, Sandrine; Costeur, Loïc; Solé, Floréal; Gheerbrant, Emmanuel; Peigné, Stéphane; Jacques, Florian; Laurin, Michel

    2016-01-01

    Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed "Cope's rule" but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Depéret's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  18. Can diving-induced tissue nitrogen supersaturation increase the chance of acoustically driven bubble growth in marine mammals?

    PubMed

    Houser, D S; Howard, R; Ridgway, S

    2001-11-21

    The potential for acoustically mediated causes of stranding in cetaceans (whales and dolphins) is of increasing concern given recent stranding events associated with anthropogenic acoustic activity. We examine a potentially debilitating non-auditory mechanism called rectified diffusion. Rectified diffusion causes gas bubble growth, which in an insonified animal may produce emboli, tissue separation and high, localized pressure in nervous tissue. Using the results of a dolphin dive study and a model of rectified diffusion for low-frequency exposure, we demonstrate that the diving behavior of cetaceans prior to an intense acoustic exposure may increase the chance of rectified diffusion. Specifically, deep diving and slow ascent/descent speed contributes to increased gas-tissue saturation, a condition that amplifies the likelihood of rectified diffusion. The depth of lung collapse limits nitrogen uptake per dive and the surface interval duration influences the amount of nitrogen washout from tissues between dives. Model results suggest that low-frequency rectified diffusion models need to be advanced, that the diving behavior of marine mammals of concern needs to be investigated to identify at-risk animals, and that more intensive studies of gas dynamics within diving marine mammals should be undertaken.

  19. Small mammals and high elevation vegetation in Yosemite National Park could be responding to smaller temperature increases than previously reported

    NASA Astrophysics Data System (ADS)

    Conklin, D. R.; Daly, C.

    2009-12-01

    Recent research related the dynamics of Sierra Nevada subalpine conifers to 20th century warming, and used temperature records from Yosemite National Park headquarters and two other locations outside the Park to estimate a 3.7°C rise in average minimum temperature. More recently, observed elevational shifts of small mammals in Yosemite National Park were linked to the same upward trend in minimum monthly temperatures. However, our analysis of spatially explicit, monthly time series of temperatures, derived using the PRISM model, suggests that the large increase in minimum monthly temperatures may be limited to Yosemite Valley, where the Park headquarters itself is located. PRISM bases its interpolations on observations from 195 temperature recording stations within and near Yosemite National Park. Minimum monthly temperatures over most of the Park do not show a centennial-scale trend, but for the final quarter of the century they do trend upwards by 1°C. Our new estimate of the spatial and temporal pattern of 20th century changes in minimum temperatures in the Park could affect conclusions about the relative importance for subalpine conifers of the centennial trend compared to interdecadal variability of temperature. It also raises a question of whether the elevational shifts of the mammals took place only in the latter part of the century, and in response to smaller temperature increases. It challenges us to accept that these plants and animals are responding to smaller changes in minimum temperatures than previously estimated or else to find reasons other than an increase in minimum temperatures for the changes that have been documented, by these and other studies, over the last century in Yosemite.

  20. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships.

    PubMed

    Pick, K S; Philippe, H; Schreiber, F; Erpenbeck, D; Jackson, D J; Wrede, P; Wiens, M; Alié, A; Morgenstern, B; Manuel, M; Wörheide, G

    2010-09-01

    Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.

  1. Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

    PubMed Central

    Pick, K.S.; Philippe, H.; Schreiber, F.; Erpenbeck, D.; Jackson, D.J.; Wrede, P.; Wiens, M.; Alié, A.; Morgenstern, B.; Manuel, M.; Wörheide, G.

    2010-01-01

    Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745–749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes. PMID:20378579

  2. Density triggers maternal hormones that increase adaptive offspring growth in a wild mammal.

    PubMed

    Dantzer, Ben; Newman, Amy E M; Boonstra, Rudy; Palme, Rupert; Boutin, Stan; Humphries, Murray M; McAdam, Andrew G

    2013-06-07

    In fluctuating environments, mothers may enhance the fitness of their offspring by adjusting offspring phenotypes to match the environment they will experience at independence. In free-ranging red squirrels, natural selection on offspring postnatal growth rates varies according to population density, with selection favoring faster-growing offspring under high-density conditions. We show that exposing mothers to high-density cues, accomplished via playbacks of territorial vocalizations, led to increased offspring growth rates in the absence of additional food resources. Experimental elevation of actual and perceived density induced higher maternal glucocorticoid levels, and females with naturally or experimentally increased glucocorticoids produced offspring that grew faster than controls. Therefore, social cues reflecting population density were sufficient to elicit increased offspring growth through an adaptive hormone-mediated maternal effect.

  3. Increasing longevity through caloric restriction or rapamycin feeding in mammals: common mechanisms for common outcomes?

    PubMed

    Cox, Lynne S; Mattison, Julie A

    2009-09-01

    Significant extension of lifespan in important mammalian species is bound to attract the attention not only of the aging research community, but also the media and the wider public. Two recent papers published by Harrison et al. (2009) in Nature and by Colman et al. (2009) in Science report increased longevity of mice fed with rapamycin and of rhesus monkeys undergoing caloric restriction, respectively. These papers have generated considerable debate in the aging community. Here we assess what is new about these findings, how they fit with our knowledge of lifespan extension from other studies and what prospects this new work holds out for improvements in human longevity and human health span.

  4. Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses

    PubMed Central

    2008-01-01

    Background Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae:Geogale). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed. Results Within Afrotheria the vast majority of the nodes received a high support, including the grouping of hyrax with sea cow and the monophyly of both Afroinsectivora (Macroscelidea + Afrosoricida) and Afroinsectiphillia (Tubulidentata + Afroinsectivora). Strongly supported relationships were also recovered among all tenrec genera, allowing us to firmly establish the grouping of Geogale with Oryzorictinae, and to confirm the previously hypothesized nesting of Limnogale within the genus Microgale. The timeline of Malagasy tenrec diversification does not reflect a fast adaptive radiation after the arrival on Madagascar, indicating that morphological specializations have appeared over the whole evolutionary history of the family, and not just in a short period after colonization. In our analysis, age estimates at the root of a clade became older with increased taxon sampling of that clade. Moreover an augmentation of data partitions resulted in older age estimates as well, whereas standard deviations increased when more extreme partition schemes were used. Conclusion Our results provide as yet the best resolved gene tree comprising all Malagasy tenrec genera, and may lead to a revision of tenrec

  5. Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analyses.

    PubMed

    Poux, Céline; Madsen, Ole; Glos, Julian; de Jong, Wilfried W; Vences, Miguel

    2008-03-31

    Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae:Geogale). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed. Within Afrotheria the vast majority of the nodes received a high support, including the grouping of hyrax with sea cow and the monophyly of both Afroinsectivora (Macroscelidea + Afrosoricida) and Afroinsectiphillia (Tubulidentata + Afroinsectivora). Strongly supported relationships were also recovered among all tenrec genera, allowing us to firmly establish the grouping of Geogale with Oryzorictinae, and to confirm the previously hypothesized nesting of Limnogale within the genus Microgale. The timeline of Malagasy tenrec diversification does not reflect a fast adaptive radiation after the arrival on Madagascar, indicating that morphological specializations have appeared over the whole evolutionary history of the family, and not just in a short period after colonization. In our analysis, age estimates at the root of a clade became older with increased taxon sampling of that clade. Moreover an augmentation of data partitions resulted in older age estimates as well, whereas standard deviations increased when more extreme partition schemes were used. Our results provide as yet the best resolved gene tree comprising all Malagasy tenrec genera, and may lead to a revision of tenrec taxonomy. A timeframe of tenrec

  6. Placental mammal diversification and the Cretaceous-Tertiary boundary.

    PubMed

    Springer, Mark S; Murphy, William J; Eizirik, Eduardo; O'Brien, Stephen J

    2003-02-04

    Competing hypotheses for the timing of the placental mammal radiation focus on whether extant placental orders originated and diversified before or after the Cretaceous-Tertiary (KT) boundary. Molecular studies that have addressed this issue suffer from single calibration points, unwarranted assumptions about the molecular clock, andor taxon sampling that lacks representatives of all placental orders. We investigated this problem using the largest available molecular data set for placental mammals, which includes segments of 19 nuclear and three mitochondrial genes for representatives of all extant placental orders. We used the ThorneKishino method, which permits simultaneous constraints from the fossil record and allows rates of molecular evolution to vary on different branches of a phylogenetic tree. Analyses that used different sets of fossil constraints, different priors for the base of Placentalia, and different data partitions all support interordinal divergences in the Cretaceous followed by intraordinal diversification mostly after the KT boundary. Four placental orders show intraordinal diversification that predates the KT boundary, but only by an average of 10 million years. In contrast to some molecular studies that date the rat-mouse split as old as 46 million years, our results show improved agreement with the fossil record and place this split at 16-23 million years. To test the hypothesis that molecular estimates of Cretaceous divergence times are an artifact of increased body size subsequent to the KT boundary, we also performed analyses with a "KT body size" taxon set. In these analyses, interordinal splits remained in the Cretaceous.

  7. Nongame mammals

    Treesearch

    Susan C. Loeb; Lynn D. Wike; John J. Mayer; Brent J. Danielson

    2005-01-01

    Fifty-four species of mammals inhabit (or have recently inhabited) the Savannah River Site (SRS; Cothran et al. 1991; table 4.24). Although far fewer in number than other taxa (see the previous five sections of this chapter), the mammals of SRS represent a wide diversity of body sizez, life histories, habitat affinities, and food habits. They range in body size from...

  8. [Jaws of herbivorous mammals].

    PubMed

    Konishi, Shogo

    2005-08-01

    The jaws of herbivorous mammals are characterized by their large occlusal surface of the molar; high crown of the molar; long snout; etc. However, elephants, the biggest herbivorous mammal, have other characteristics. In the evolutionary trends of proboscidean skulls, concomitant with the increase in tusk size comes on the enlargement, antero-posterior shortening, dorso-ventral elongation of the cranium with increasing cheek teeth size. Naturally, the jaw follows the same evolutionary trends as the cranium.

  9. Mean Annual Precipitation Explains Spatiotemporal Patterns of Cenozoic Mammal Beta Diversity and Latitudinal Diversity Gradients in North America

    PubMed Central

    Fraser, Danielle; Hassall, Christopher; Gorelick, Root; Rybczynski, Natalia

    2014-01-01

    Spatial diversity patterns are thought to be driven by climate-mediated processes. However, temporal patterns of community composition remain poorly studied. We provide two complementary analyses of North American mammal diversity, using (i) a paleontological dataset (2077 localities with 2493 taxon occurrences) spanning 21 discrete subdivisions of the Cenozoic based on North American Land Mammal Ages (36 Ma – present), and (ii) climate space model predictions for 744 extant mammals under eight scenarios of future climate change. Spatial variation in fossil mammal community structure (β diversity) is highest at intermediate values of continental mean annual precipitation (MAP) estimated from paleosols (∼450 mm/year) and declines under both wetter and drier conditions, reflecting diversity patterns of modern mammals. Latitudinal gradients in community change (latitudinal turnover gradients, aka LTGs) increase in strength through the Cenozoic, but also show a cyclical pattern that is significantly explained by MAP. In general, LTGs are weakest when continental MAP is highest, similar to modern tropical ecosystems in which latitudinal diversity gradients are weak or undetectable. Projections under modeled climate change show no substantial change in β diversity or LTG strength for North American mammals. Our results suggest that similar climate-mediated mechanisms might drive spatial and temporal patterns of community composition in both fossil and extant mammals. We also provide empirical evidence that the ecological processes on which climate space models are based are insufficient for accurately forecasting long-term mammalian response to anthropogenic climate change and inclusion of historical parameters may be essential. PMID:25203658

  10. Mean annual precipitation explains spatiotemporal patterns of Cenozoic mammal beta diversity and latitudinal diversity gradients in North America.

    PubMed

    Fraser, Danielle; Hassall, Christopher; Gorelick, Root; Rybczynski, Natalia

    2014-01-01

    Spatial diversity patterns are thought to be driven by climate-mediated processes. However, temporal patterns of community composition remain poorly studied. We provide two complementary analyses of North American mammal diversity, using (i) a paleontological dataset (2077 localities with 2493 taxon occurrences) spanning 21 discrete subdivisions of the Cenozoic based on North American Land Mammal Ages (36 Ma--present), and (ii) climate space model predictions for 744 extant mammals under eight scenarios of future climate change. Spatial variation in fossil mammal community structure (β diversity) is highest at intermediate values of continental mean annual precipitation (MAP) estimated from paleosols (∼ 450 mm/year) and declines under both wetter and drier conditions, reflecting diversity patterns of modern mammals. Latitudinal gradients in community change (latitudinal turnover gradients, aka LTGs) increase in strength through the Cenozoic, but also show a cyclical pattern that is significantly explained by MAP. In general, LTGs are weakest when continental MAP is highest, similar to modern tropical ecosystems in which latitudinal diversity gradients are weak or undetectable. Projections under modeled climate change show no substantial change in β diversity or LTG strength for North American mammals. Our results suggest that similar climate-mediated mechanisms might drive spatial and temporal patterns of community composition in both fossil and extant mammals. We also provide empirical evidence that the ecological processes on which climate space models are based are insufficient for accurately forecasting long-term mammalian response to anthropogenic climate change and inclusion of historical parameters may be essential.

  11. Foundational issues concerning taxa and taxon names.

    PubMed

    Ereshefsky, Marc

    2007-04-01

    In a series of articles, Rieppel (2005, Biol. Philos. 20:465-487; 2006a, Cladistics 22:186-197; 2006b, Systematist 26:5-9), Keller et al. (2003, Bot. Rev. 69:93-110), and Nixon and Carpenter (2000, Cladistics 16:298-318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render taxonomy untestable. These charges are unsound. Such charges turn on confusions over rigid designator theory and the distinction between kinds and individuals. In addition, Rieppel's, Keller et al.'s, and Nixon and Carpenter's proposed alternatives are no better and have their own problems. The individuality thesis and rigid designator theory should not be quickly abandoned.

  12. Prolonged food deprivation increases mRNA expression of deiodinase 1 and 2, and thyroid hormone receptor β-1 in a fasting-adapted mammal.

    PubMed

    Martinez, Bridget; Soñanez-Organis, José G; Vázquez-Medina, José Pablo; Viscarra, Jose A; MacKenzie, Duncan S; Crocker, Daniel E; Ortiz, Rudy M

    2013-12-15

    Food deprivation in mammals is typically associated with reduced thyroid hormone (TH) concentrations and deiodinase content and activity to suppress metabolism. However, in prolonged-fasted, metabolically active elephant seal pups, TH levels are maintained, if not elevated. The functional relevance of this apparent paradox is unknown and demonstrates variability in the regulation of TH levels, metabolism and function in food-deprived mammals. To address our hypothesis that cellular TH-mediated activity is upregulated with fasting duration, we quantified the mRNA expression and protein content of adipose and muscle deiodinase type I (DI1) and type II (DI2), and TH receptor beta-1 (THrβ-1) after 1, 3 and 7 weeks of fasting in northern elephant seal pups (N=5-7 per week). Fasting did not decrease the concentrations of plasma thyroid stimulating hormone, total triiodothyronine (tT3), free T3, total thyroxine (tT4) or free T4, suggesting that the hypothalamic-pituitary-thyroid axis is not suppressed, but rather maintained during fasting. Mean mRNA expression of adipose DI1 and DI2 increased threefold and fourfold, respectively, and 20- and 30-fold, respectively, in muscle. With the exception of adipose DI1, protein expression of adipose DI2 and muscle DI1 and DI2 increased twofold to fourfold. Fasting also increased adipose (fivefold) and muscle (fourfold) THrβ-1 mRNA expression, suggesting that the mechanisms mediating cellular TH activity are upregulated with prolonged fasting. The data demonstrate a unique, atypical mechanism of TH activity and regulation in mammals adapted to prolonged food deprivation in which the potential responsiveness of peripheral tissues and cellular TH activity are increased, which may contribute to their lipid-based metabolism.

  13. Exotic Mammal Laparoscopy.

    PubMed

    Sladakovic, Izidora; Divers, Stephen J

    2016-01-01

    Laparoscopy is an evolving field in veterinary medicine, and there is an increased interest in using laparoscopic techniques in nondomestic mammals, including zoo animals, wildlife, and exotic pets. The aim of this article is to summarize the approach to laparoscopic procedures, including instrumentation, patient selection and preparation, and surgical approaches, and to review the current literature on laparoscopy in exotic mammals. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Molecular phylogenetics and the origins of placental mammals.

    PubMed

    Murphy, W J; Eizirik, E; Johnson, W E; Zhang, Y P; Ryder, O A; O'Brien, S J

    2001-02-01

    The precise hierarchy of ancient divergence events that led to the present assemblage of modern placental mammals has been an area of controversy among morphologists, palaeontologists and molecular evolutionists. Here we address the potential weaknesses of limited character and taxon sampling in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals. We examined sequence variation in 18 homologous gene segments (including nearly 10,000 base pairs) that were selected for maximal phylogenetic informativeness in resolving the hierarchy of early mammalian divergence. Phylogenetic analyses identify four primary superordinal clades: (I) Afrotheria (elephants, manatees, hyraxes, tenrecs, aardvark and elephant shrews); (II) Xenarthra (sloths, anteaters and armadillos); (III) Glires (rodents and lagomorphs), as a sister taxon to primates, flying lemurs and tree shrews; and (IV) the remaining orders of placental mammals (cetaceans, artiodactyls, perissodactyls, carnivores, pangolins, bats and core insectivores). Our results provide new insight into the pattern of the early placental mammal radiation.

  15. Increased brain size in mammals is associated with size variations in gene families with cell signalling, chemotaxis and immune-related functions.

    PubMed

    Castillo-Morales, Atahualpa; Monzón-Sandoval, Jimena; Urrutia, Araxi O; Gutiérrez, Humberto

    2014-01-22

    Genomic determinants underlying increased encephalization across mammalian lineages are unknown. Whole genome comparisons have revealed large and frequent changes in the size of gene families, and it has been proposed that these variations could play a major role in shaping morphological and physiological differences among species. Using a genome-wide comparative approach, we examined changes in gene family size (GFS) and degree of encephalization in 39 fully sequenced mammalian species and found a significant over-representation of GFS variations in line with increased encephalization in mammals. We found that this relationship is not accounted for by known correlates of brain size such as maximum lifespan or body size and is not explained by phylogenetic relatedness. Genes involved in chemotaxis, immune regulation and cell signalling-related functions are significantly over-represented among those gene families most highly correlated with encephalization. Genes within these families are prominently expressed in the human brain, particularly the cortex, and organized in co-expression modules that display distinct temporal patterns of expression in the developing cortex. Our results suggest that changes in GFS associated with encephalization represent an evolutionary response to the specific functional requirements underlying increased brain size in mammals.

  16. Interaction between Locale and Taxon Strategies in Human Spatial Learning

    ERIC Educational Resources Information Center

    Redhead, Edward S.; Hamilton, Derek A.

    2007-01-01

    Three computer-based experiments which tested human participants in a non-immersive virtual watermaze task sought to determine factors which dictate whether the presence of a visual platform disrupts locale learning and taxon learning. In Experiment 1, the visible platform disrupted locale but not taxon learning based on viewpoint-independent and…

  17. Novel symptomatology and changing epidemiology of domoic acid toxicosis in California sea lions (Zalophus californianus): an increasing risk to marine mammal health

    PubMed Central

    Goldstein, T; Mazet, J.A.K; Zabka, T.S; Langlois, G; Colegrove, K.M; Silver, M; Bargu, S; Van Dolah, F; Leighfield, T; Conrad, P.A; Barakos, J; Williams, D.C; Dennison, S; Haulena, M; Gulland, F.M.D

    2007-01-01

    Harmful algal blooms are increasing worldwide, including those of Pseudo-nitzschia spp. producing domoic acid off the California coast. This neurotoxin was first shown to cause mortality of marine mammals in 1998. A decade of monitoring California sea lion (Zalophus californianus) health since then has indicated that changes in the symptomatology and epidemiology of domoic acid toxicosis in this species are associated with the increase in toxigenic blooms. Two separate clinical syndromes now exist: acute domoic acid toxicosis as has been previously documented, and a second novel neurological syndrome characterized by epilepsy described here associated with chronic consequences of previous sub-lethal exposure to the toxin. This study indicates that domoic acid causes chronic damage to California sea lions and that these health effects are increasing. PMID:18006409

  18. Novel symptomatology and changing epidemiology of domoic acid toxicosis in California sea lions (Zalophus californianus): an increasing risk to marine mammal health.

    PubMed

    Goldstein, T; Mazet, J A K; Zabka, T S; Langlois, G; Colegrove, K M; Silver, M; Bargu, S; Van Dolah, F; Leighfield, T; Conrad, P A; Barakos, J; Williams, D C; Dennison, S; Haulena, M; Gulland, F M D

    2008-02-07

    Harmful algal blooms are increasing worldwide, including those of Pseudo-nitzschia spp. producing domoic acid off the California coast. This neurotoxin was first shown to cause mortality of marine mammals in 1998. A decade of monitoring California sea lion (Zalophus californianus) health since then has indicated that changes in the symptomatology and epidemiology of domoic acid toxicosis in this species are associated with the increase in toxigenic blooms. Two separate clinical syndromes now exist: acute domoic acid toxicosis as has been previously documented, and a second novel neurological syndrome characterized by epilepsy described here associated with chronic consequences of previous sub-lethal exposure to the toxin. This study indicates that domoic acid causes chronic damage to California sea lions and that these health effects are increasing.

  19. Marine Mammals.

    ERIC Educational Resources Information Center

    Meith, Nikki

    Marine mammals have not only fascinated and inspired human beings for thousands of years, but they also support a big business by providing flesh for sea-borne factories, sustaining Arctic lifestyles and traditions, and attracting tourists to ocean aquaria. While they are being harpooned, bludgeoned, shot, netted, and trained to jump through…

  20. Marine Mammals.

    ERIC Educational Resources Information Center

    Meith, Nikki

    Marine mammals have not only fascinated and inspired human beings for thousands of years, but they also support a big business by providing flesh for sea-borne factories, sustaining Arctic lifestyles and traditions, and attracting tourists to ocean aquaria. While they are being harpooned, bludgeoned, shot, netted, and trained to jump through…

  1. Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

    PubMed

    Höhna, Sebastian

    2014-01-01

    Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be

  2. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling

    PubMed Central

    Höhna, Sebastian

    2014-01-01

    Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models – ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models – on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be

  3. Increased expression of X-linked genes in mammals is associated with a higher stability of transcripts and an increased ribosome density.

    PubMed

    Faucillion, Marie-Line; Larsson, Jan

    2015-03-18

    Mammalian sex chromosomes evolved from the degeneration of one homolog of a pair of ancestral autosomes, the proto-Y. This resulted in a gene dose imbalance that is believed to be restored (partially or fully) through upregulation of gene expression from the single active X-chromosome in both sexes by a dosage compensatory mechanism. We analyzed multiple genome-wide RNA stability data sets and found significantly longer average half-lives for X-chromosome transcripts than for autosomal transcripts in various human cell lines, both male and female, and in mice. Analysis of ribosome profiling data shows that ribosome density is higher on X-chromosome transcripts than on autosomal transcripts in both humans and mice, suggesting that the higher stability is causally linked to a higher translation rate. Our results and observations are in accordance with a dosage compensatory upregulation of expressed X-linked genes. We therefore propose that differential mRNA stability and translation rates of the autosomes and sex chromosomes contribute to an evolutionarily conserved dosage compensation mechanism in mammals. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. Audubon Mammal Study Program.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    Included are an illustrated student reader, "The Story of Mammals," a leaders' guide, a large wall chart picturing 39 North American mammals, and a separate booklet describing the mammals on the wall chart. The student reader presents these main topics: What Is a Mammal?; How Mammals Differ From Each Other; Where, When, and How To Find Mammals;…

  5. Audubon Mammal Study Program.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    Included are an illustrated student reader, "The Story of Mammals," a leaders' guide, a large wall chart picturing 39 North American mammals, and a separate booklet describing the mammals on the wall chart. The student reader presents these main topics: What Is a Mammal?; How Mammals Differ From Each Other; Where, When, and How To Find Mammals;…

  6. Demographic consequences of increased winter births in a large aseasonally breeding mammal (Bos taurus) in response to climate change.

    PubMed

    Burthe, Sarah; Butler, Adam; Searle, Kate R; Hall, Stephen J G; Thackeray, Stephen J; Wanless, Sarah

    2011-11-01

    1. Studies examining changes in the scheduling of breeding in response to climate change have focused on species with well-defined breeding seasons. Species exhibiting year-round breeding have received little attention and the magnitudes of any responses are unknown. 2. We investigated phenological data for an enclosed feral population of cattle (Bos taurus L.) in northern England exhibiting year-round breeding. This population is relatively free of human interference. 3. We assessed whether the timing of births had changed over the last 60 years, in response to increasing winter and spring temperatures, changes in herd density, and a regime of lime fertilisation. 4. Median birth date became earlier by 1·0 days per year. Analyses of the seasonal distribution of calving dates showed that significantly fewer calves were born in summer (decline from 44% of total births to 20%) and significantly more in winter (increase from 12% to 30%) over the study period. The most pronounced changes occurred in winter, with significant increases in both the proportion and number of births. Winter births arise from conceptions in the previous spring, and we considered models that investigated climate and weather variables associated with the winter preceding and the spring of conceptions. 5. The proportion of winter births was higher when the onset of the plant growing season was earlier during the spring of conceptions. This relationship was much weaker during years when the site had been fertilised with lime, suggesting that increased forage biomass was over-riding the impacts of changing plant phenology. When the onset of the growing season was late, winter births increased with female density. 6. Recruitment estimates from a stage-structured state-space population model were significantly negatively correlated with the proportion of births in the preceding winter, suggesting that calves born in winter are less likely to survive than those born in other seasons. 7.

  7. Increasing levels of long-chain perfluorocarboxylic acids (PFCAs) in Arctic and North Atlantic marine mammals, 1984-2009.

    PubMed

    Rotander, Anna; Kärrman, Anna; van Bavel, Bert; Polder, Anuschka; Rigét, Frank; Auðunsson, Guðjón Atli; Víkingsson, Gísli; Gabrielsen, Geir Wing; Bloch, Dorete; Dam, Maria

    2012-01-01

    Temporal variations in concentrations of perfluorinated carboxylic acids (PFCAs) and sulfonic acids (PFSAs), including perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) structural isomers, were examined in livers of pilot whale (Globicephala melas), ringed seal (Phoca hisida), minke whale (Balaenoptera acutorostrata), harbor porpoise (Phocoena phocoena), hooded seal (Cystophora cristata), Atlantic white-sided dolphin (Lagenorhynchus acutus) and in muscle tissue of fin whales (Balaenoptera physalus). The sampling spanned over 20 years (1984-2009) and covered a large geographical area of the North Atlantic and West Greenland. Liver and muscle samples were homogenized, extracted with acetonitrile, cleaned up using hexane and solid phase extraction (SPE), and analyzed by liquid chromatography with negative electrospray tandem mass spectrometry (LC-MS/MS). In general, the levels of the long-chained PFCAs (C9-C12) increased whereas the levels of PFOS remained steady over the studied period. The PFOS isomer pattern in pilot whale liver was relatively constant over the sampling years. However, in ringed seals there seemed to be a decrease in linear PFOS (L-PFOS) with time, going from 91% in 1984 to 83% in 2006.

  8. Temporal, spatial and ecological dynamics of speciation among amphi-Beringian small mammals

    USGS Publications Warehouse

    Hope, Andrew G.; Takebayashi, Naoki; Galbreath, Kurt E.; Talbot, Sandra L.; Cook, Joseph A.

    2013-01-01

    Quaternary climate cycles played an important role in promoting diversification across the Northern Hemisphere, although details of the mechanisms driving evolutionary change are still poorly resolved. In a comparative phylogeographical framework, we investigate temporal, spatial and ecological components of evolution within a suite of Holarctic small mammals. We test a hypothesis of simultaneous divergence among multiple taxon pairs, investigating time to coalescence and demographic change for each taxon in response to a combination of climate and geography.

  9. PB2 substitutions V598T/I increase the virulence of H7N9 influenza A virus in mammals.

    PubMed

    Hu, Meng; Yuan, Shuofeng; Zhang, Ke; Singh, Kailash; Ma, Qiang; Zhou, Jie; Chu, Hin; Zheng, Bo-Jian

    2017-01-15

    PB2 is one of the subunits of the influenza A virus (IAV) polymerase complex. By bioinformatics analysis we identified PB2 substitutions at positions 389 and 598 among IAV isolates from humans, which might associate with viral pathogenicity. To evaluate the biological significance of these substitutions, PB2-K389R and -V598T/I mutant viruses of avian H7N9 IAVs were generated by reverse genetics. Compared to the wild type, the mutant viruses displayed an enhanced growth capacity in human and mammalian cells. Meanwhile, they presented increased transcription and replication by producing higher levels of viral mRNA, cRNA and vRNA. Minireplicon assays indicated that the polymerase activity was elevated by these substitutions. Notably, the PB2-V598T/I substitutions substantially increased virus replication and virulence in mice. Together, we demonstrated that the substitutions PB2-V598T/I contributed to higher IAV replication and virulence in mammals, which added to the knowledge of IAV virulence determinants and benefited the surveillance of IAVs.

  10. Mammals of the Sea.

    ERIC Educational Resources Information Center

    Naturescope, 1986

    1986-01-01

    Presents information on sea mammals, including definitions and characteristics of cetaceans, pinnipeds, and sirenians. Contains descriptions of the teaching activities "Whale Music,""Draw A Whale to Scale,""Adopt a Sea Mammal," and "Sea Mammal Sleuths." (TW)

  11. Mammals of the Sea.

    ERIC Educational Resources Information Center

    Naturescope, 1986

    1986-01-01

    Presents information on sea mammals, including definitions and characteristics of cetaceans, pinnipeds, and sirenians. Contains descriptions of the teaching activities "Whale Music,""Draw A Whale to Scale,""Adopt a Sea Mammal," and "Sea Mammal Sleuths." (TW)

  12. Mitochondrial data are not suitable for resolving placental mammal phylogeny.

    PubMed

    Morgan, Claire C; Creevey, Christopher J; O'Connell, Mary J

    2014-12-01

    Mitochondrial data have traditionally been used in reconstructing a variety of species phylogenies. The low rates of recombination and thorough characterization of mitochondrial data across vertebrate species make it a particularly attractive phylogenetic marker. The relatively low number of fully sequenced mammal genomes and the lack of extensive sampling within Superorders have posed a serious problem for reaching agreement on the placement mammal species. The use of mitochondrial data sequences from large numbers of mammals could serve to circumvent the taxon-sampling deficit. Here we assess the suitability of mitochondrial data as a phylogenetic marker in mammal phylogenetics. MtDNA datasets of mammal origin have been filtered as follows: (i) we have sampled sparsely across the phylogenetic tree, (ii) we have constrained our sampling to genes with high taxon coverage, (iii) we have categorised rates across sites in a phylogeny independent manner and have removed fast evolving sites, and (iv), we have sampled from very shallow divergence times to reduce phylogenetic conflict. However, topologies obtained using these filters are not consistent with previous studies and are discordant across different genes. Individual mitochondrial genes, and indeed all mitochondrial genes analysed as a supermatrix, resulted in poor resolution of the species phylogeny. Overall, our study highlights the limitations of mitochondrial data, not only for resolving deep divergences and but also for shallow divergences in the mammal phylogeny.

  13. Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Sackett, O.; Armand, L.; Beardall, J.; Hill, R.; Doblin, M.; Connelly, C.; Howes, J.; Stuart, B.; Ralph, P.; Heraud, P.

    2014-05-01

    Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value, furthermore data on taxon-specific responses is almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate and carbohydrates. In contrast to some previous studies, silicate levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community measurements, highlighting the

  14. Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Sackett, O.; Armand, L.; Beardall, J.; Hill, R.; Doblin, M.; Connelly, C.; Howes, J.; Stuart, B.; Ralph, P.; Heraud, P.

    2014-10-01

    Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value - furthermore, data on taxon-specific responses are almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate/silicic acid and carbohydrates. In contrast to some previous studies, silicate/silicic acid levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community

  15. What Makes a Mammal a Mammal?

    ERIC Educational Resources Information Center

    Naturescope, 1986

    1986-01-01

    Describes the distinctive characteristics of mammals and compares modern mammals with their prehistoric relatives as well as with other animal groups. Includes activities and ready-to-copy games, illustrations, and diagrams of wolves, vertebrates, and past and present mammals. (ML)

  16. What Makes a Mammal a Mammal?

    ERIC Educational Resources Information Center

    Naturescope, 1986

    1986-01-01

    Describes the distinctive characteristics of mammals and compares modern mammals with their prehistoric relatives as well as with other animal groups. Includes activities and ready-to-copy games, illustrations, and diagrams of wolves, vertebrates, and past and present mammals. (ML)

  17. 7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 5 2013-01-01 2013-01-01 false Petitions to add a taxon to the noxious weed list. 360... to add a taxon to the noxious weed list. A person may petition the Administrator to have a taxon added to the noxious weeds lists in § 360.200. Details of the petitioning process for adding a taxon...

  18. Increasing density leads to generalization in both coarse-grained habitat selection and fine-grained resource selection in a large mammal.

    PubMed

    van Beest, Floris M; Uzal, Antonio; Vander Wal, Eric; Laforge, Michel P; Contasti, Adrienne L; Colville, David; McLoughlin, Philip D

    2014-01-01

    Density is a fundamental driver of many ecological processes including habitat selection. Theory on density-dependent habitat selection predicts that animals should be distributed relative to profitability of habitat, resulting in reduced specialization in selection (i.e. generalization) as density increases and competition intensifies. Despite mounting empirical support for density-dependent habitat selection using isodars to describe coarse-grained (interhabitat) animal movements, we know little of how density affects fine-grained resource selection of animals within habitats [e.g. using resource selection functions (RSFs)]. Using isodars and RSFs, we tested whether density simultaneously modified habitat selection and within-habitat resource selection in a rapidly growing population of feral horses (Equus ferus caballus Linnaeus; Sable Island, Nova Scotia, Canada; 42% increase in population size from 2008 to 2012). Among three heterogeneous habitat zones on Sable Island describing population clusters distributed along a west-east resource gradient (west-central-east), isodars revealed that horses used available habitat in a density-dependent manner. Intercepts and slopes of isodars demonstrated a pattern of habitat selection that first favoured the west, which generalized to include central and east habitats with increasing population size consistent with our understanding of habitat quality on Sable Island. Resource selection functions revealed that horses selected for vegetation associations similarly at two scales of extent (total island and within-habitat zone). When densities were locally low, horses were able to select for sites of the most productive forage (grasslands) relative to those of poorer quality. However, as local carrying capacity was approached, selection for the best of available forage types weakened while selection for lower-quality vegetation increased (and eventually exceeded that of grasslands). Isodars can effectively describe coarse

  19. Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms.

    PubMed

    Burleigh, J Gordon; Hilu, Khidir W; Soltis, Douglas E

    2009-03-17

    Phylogenetic analyses of angiosperm relationships have used only a small percentage of available sequence data, but phylogenetic data matrices often can be augmented with existing data, especially if one allows missing characters. We explore the effects on phylogenetic analyses of adding 378 matK sequences and 240 26S rDNA sequences to the complete 3-gene, 567-taxon angiosperm phylogenetic matrix of Soltis et al. We performed maximum likelihood bootstrap analyses of the complete, 3-gene 567-taxon data matrix and the incomplete, 5-gene 567-taxon data matrix. Although the 5-gene matrix has more missing data (27.5%) than the 3-gene data matrix (2.9%), the 5-gene analysis resulted in higher levels of bootstrap support. Within the 567-taxon tree, the increase in support is most evident for relationships among the 170 taxa for which both matK and 26S rDNA sequences were added, and there is little gain in support for relationships among the 119 taxa having neither matK nor 26S rDNA sequences. The 5-gene analysis also places the enigmatic Hydrostachys in Lamiales (BS = 97%) rather than in Cornales (BS = 100% in 3-gene analysis). The placement of Hydrostachys in Lamiales is unprecedented in molecular analyses, but it is consistent with embryological and morphological data. Adding available, and often incomplete, sets of sequences to existing data sets can be a fast and inexpensive way to increase support for phylogenetic relationships and produce novel and credible new phylogenetic hypotheses.

  20. Phylogenomics with incomplete taxon coverage: the limits to inference

    PubMed Central

    2010-01-01

    Background Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa. The impact of missing data has been widely studied in phylogenetics, but it has proven difficult to distinguish effects due to error in tree reconstruction from effects due to missing data per se. We approach this problem using a explicitly phylogenomic criterion of success, decisiveness, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa. Results We establish theoretical bounds on the impact of missing data on decisiveness. Results are derived for two contexts: a fixed taxon coverage pattern, such as that observed from an already assembled data set, and a randomly generated pattern derived from a process of sampling new data, such as might be observed in an ongoing comparative genomics sequencing project. Lower bounds on how many loci are needed for decisiveness are derived for the former case, and both lower and upper bounds for the latter. When data are not decisive for all trees, we estimate the probability of decisiveness and the chances that a given edge in the tree will be distinguishable. Theoretical results are illustrated using several empirical examples constructed by mining sequence databases, genomic libraries such as ESTs and BACs, and complete genome sequences. Conclusion Partial taxon coverage among loci can limit phylogenomic inference by making it impossible to distinguish among multiple alternative trees. However, even though lack of decisiveness is typical of many sparse phylogenomic data sets, it is often still possible to distinguish a large fraction of edges in the tree. PMID:20500873

  1. The dissociative experiences taxon is related to fantasy proneness.

    PubMed

    Giesbrecht, Timo; Merckelbach, Harald; Geraerts, Elke

    2007-09-01

    Some authors have argued that nonpathological dissociation should be distinguished from a taxon form of pathological dissociation, which is indexed by the Dissociative Experiences Scale Taxon (DES-T). We tested to what extent DES-T scores are independent from fantasy immersion and whether DES-T scores are uniquely related to trauma self-reports. To this end, subsamples of undergraduate students (n = 930), healthy adults (n = 20), schizophrenic patients (n = 22), borderline personality disordered patients (n = 20), patients with mood disorder without psychosis (n = 19), and women with a history of childhood sexual abuse (n = 55) completed the Dissociative Experiences Scale and a measure of fantasy immersion. DES-T scores were related to absorption and fantasy immersion to a lesser extent than the original DES. However, the fact that nontrivial percentages within all groups, except for the healthy adults, were classified as taxon members casts doubts on the assumption that DES-T is a reliable index of pathological dissociation. Also, we found that the DES-T was not exclusively related to reports of childhood sexual abuse.

  2. [Jaws of primitive mammals].

    PubMed

    Tsubamoto, Takehisa

    2005-06-01

    Some of main osteological differences between mammals and reptiles are seen in the number of bones that constitute lower jaw and in jaw articulation. A lower jaw of mammals consists of only one bone, while in reptiles it consists of several bones (e.g., four to six in lizards and five in crocodiles). The jaw articulation in mammals is performed by squamosal of the skull and the mandible ( = dentary), while in reptiles it is done by quadrate of the skull and articular of the lower jaw. When mammals first appeared about 200 million years ago in the Mesozoic Era, the jaws of primitive mammals were morphologically intermediate between those of reptiles and typical mammals. Here, I briefly introduce the evolution of lower jaw morphology from the reptilian one to the mammalian one, showing lower jaw features of some mammal-like reptiles and primitive mammals.

  3. Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships.

    PubMed

    Townsend, Jeffrey P; Lopez-Giraldez, Francesc

    2010-07-01

    A controversial topic that underlies much of phylogenetic experimental design is the relative utility of increased taxonomic versus character sampling. Conclusions about the relative utility of adding characters or taxa to a current phylogenetic study have subtly hinged upon the appropriateness of the rate of evolution of the characters added for resolution of the phylogeny in question. Clearly, the addition of characters evolving at optimal rates will have much greater impact upon accurate phylogenetic analysis than will the addition of characters with an inappropriate rate of evolution. Development of practical analytical predictions of the asymptotic impact of adding additional taxa would complement computational investigations of the relative utility of these two methods of expanding acquired data. Accordingly, we here formulate a measure of the phylogenetic informativeness of the additional sampling of character states from a new taxon added to the canonical phylogenetic quartet. We derive the optimal rate of evolution for characters assessed in taxa to be sampled and a metric of informativeness based on the rate of evolution of the characters assessed in the new taxon and the distance of the new taxon from the internode of interest. Calculation of the informativeness per base pair of additional character sampling for included taxa versus additional character sampling for novel taxa can be used to estimate cost-effectiveness and optimal efficiency of phylogenetic experimental design. The approach requires estimation of rates of evolution of individual sites based on an alignment of genes orthologous to those to be sequenced, which may be identified in a well-established clade of sister taxa or of related taxa diverging at a deeper phylogenetic scale. Some approximate idea of the potential phylogenetic relationships of taxa to be sequenced is also desirable, such as may be obtained from ribosomal RNA sequence alone. Application to the solution of recalcitrant

  4. Anterior commissure versus corpus callosum: A quantitative comparison across mammals.

    PubMed

    Ashwell, Ken W S

    2016-04-01

    Mammals rely on two major pathways to transfer information between the two hemispheres of the brain: the anterior commissure and the corpus callosum. Metatheria and monotremes rely exclusively on the anterior commissure for interhemispheric transfer between the isocortices and olfactory allocortices of each side, whereas Eutheria use a combination of the anterior commissure and an additional pathway exclusive to Eutheria, the corpus callosum. Midline cross-sectional area of the anterior commissure and corpus callosum were measured in a range of mammals from all three infraclasses and plotted against brain volume to determine how midline anterior commissure area and its size relative to the corpus callosum vary with brain size and taxon. In Metatheria, the square root of anterior commissure area rises in almost direct proportion with the cube root of brain volume (i.e. the ratio of the two is relatively constant), whereas among Eutheria the ratio of the square root of anterior commissure area to the cube root of brain volume declines slightly with increasing brain size. The total of isocortical and olfactory allocortical commissure area rises more rapidly with increasing brain volume among Eutheria than among Metatheria. This means that the midline isocortical and olfactory allocortical commissural area of metatherians with large brains (about 70 ml) is only about 50% of that among eutherians with similarly sized brains. On the other hand, isocortical and olfactory allocortical commissural area is similar in Metatheria and Eutheria at brain volumes around 1 ml. Among the Eutheria, some groups make less use of the anterior commissure pathway than do others: soricomorphs, rodents and cetaceans have smaller anterior commissures for their brain size than do afrosoricids, erinaceomorphs and proboscideans. The findings suggest that use of the anterior commissural route for isocortical commissural connections may have placed limitations on interhemispheric transfer of

  5. Blood lead concentrations in marine mammals validate estimates of 10{sup 2}- to 10{sup 3}-fold increase in human blood lead concentrations

    SciTech Connect

    Owen, B.D.; Flegal, A.R.

    1998-08-01

    Measurements of ultra-low ambient blood lead (PbB) concentrations (mean {+-} SD = 0.13 {+-} 0.06 {micro}g/dL) in Northern elephant seals (Mirounga angustirostris) validate previous estimates of ultra-low PbB levels in preindustrial humans. These estimates had been unsubstituted, since PbB levels in this range had never been measured in any organisms prior to this study. Similarities in PbB levels among these contemporary and preindustrial mammals are consistent with similarities in their measured and estimated lead exposures, respectively. The marginally higher PbB levels and rates of lead exposure in contemporary marine mammals are, also, consistent with lead isotopic composition analyses that indicate their PbB levels have been elevated from exposure to industrial lead. Consequently, these analyses substantiate concerns that current baseline PbB levels in humans, which are estimated to be two to three orders of magnitude above natural levels, may still constitute public health risks.

  6. Protection of Marine Mammals.

    PubMed

    Knoll, Michaela; Ciaccia, Ettore; Dekeling, René; Kvadsheim, Petter; Liddell, Kate; Gunnarsson, Stig-Lennart; Ludwig, Stefan; Nissen, Ivor; Lorenzen, Dirk; Kreimeyer, Roman; Pavan, Gianni; Meneghetti, Nello; Nordlund, Nina; Benders, Frank; van der Zwan, Timo; van Zon, Tim; Fraser, Leanne; Johansson, Torbjörn; Garmelius, Martin

    2016-01-01

    Within the European Defense Agency (EDA), the Protection of Marine Mammals (PoMM) project, a comprehensive common marine mammal database essential for risk mitigation tools, was established. The database, built on an extensive dataset collection with the focus on areas of operational interest for European navies, consists of annual and seasonal distribution and density maps, random and systematic sightings, an encyclopedia providing knowledge on the characteristics of 126 marine mammal species, data on marine mammal protection areas, and audio information including numerous examples of various vocalizations. Special investigations on marine mammal acoustics were carried out to improve the detection and classification capabilities.

  7. Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling.

    PubMed

    Reddy, Sushma; Kimball, Rebecca T; Pandey, Akanksha; Hosner, Peter A; Braun, Michael J; Hackett, Shannon J; Han, Kin-Lan; Harshman, John; Huddleston, Christopher J; Kingston, Sarah; Marks, Ben D; Miglia, Kathleen J; Moore, William S; Sheldon, Frederick H; Witt, Christopher C; Yuri, Tamaki; Braun, Edward L

    2017-03-27

    Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic datasets can also result in conflicting estimates of phylogeny. Here we use the early divergences in Neoaves, the largest clade of extant birds, as a 'model system' to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [∼42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters (∼0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be

  8. Developing terrestrial, multi-taxon indices of biological integrity: An example from coastal sage scrub

    USGS Publications Warehouse

    Diffendorfer, J.E.; Fleming, G.M.; Duggan, J.M.; Chapman, R.E.; Rahn, M.E.; Mitrovich, M.J.; Fisher, R.N.

    2007-01-01

    We screened 351 species or genera for their response to disturbance in coastal sage scrub (CSS) to develop a 15-metric, 5-taxon Index of Biological Integrity (IBI). We collected data on ants, birds, herpetofauna, small mammals, and plants for two years on 46 sites established across a gradient of disturbance in three reserves. The gradient spanned relatively intact CSS with thick stands of shrubs, to former CSS stands type-converted to exotic grasses. ANOVAs and clustering analyses indicated the IBI could distinguish four levels of disturbance in CSS. General measures of community structure, such as richness, did not show changes across the gradient for most taxa, and responses of taxa across the gradient were varied and rarely correlated. However, turnover in species or genera across the gradient was common across all taxa as shrub-obligate life forms were replaced by those favoring grassy or disturbed habitats. Our data indicate index-based approaches based on data collected across disturbance gradients may outperform more traditional community level metrics when responses to anthropogenic influences are complex and vary across species. ?? 2007 Elsevier Ltd. All rights reserved.

  9. Lagenidium giganteum pathogenicity in mammals.

    PubMed

    Vilela, Raquel; Taylor, John W; Walker, Edward D; Mendoza, Leonel

    2015-02-01

    Infections of mammals by species in the phylum Oomycota taxonomically and molecularly similar to known Lagenidium giganteum strains have increased. During 2013-2014, we conducted a phylogenetic study of 21 mammalian Lagenidium isolates; we found that 11 cannot be differentiated from L. giganteum strains that the US Environmental Protection Agency approved for biological control of mosquitoes; these strains were later unregistered and are no longer available. L. giganteum strains pathogenic to mammals formed a strongly supported clade with the biological control isolates, and both types experimentally infected mosquito larvae. However, the strains from mammals grew well at 25°C and 37°C, whereas the biological control strains developed normally at 25°C but poorly at higher temperatures. The emergence of heat-tolerant strains of L. giganteum pathogenic to lower animals and humans is of environmental and public health concern.

  10. Lagenidium giganteum Pathogenicity in Mammals

    PubMed Central

    Vilela, Raquel; Taylor, John W.; Walker, Edward D.

    2015-01-01

    Infections of mammals by species in the phylum Oomycota taxonomically and molecularly similar to known Lagenidium giganteum strains have increased. During 2013–2014, we conducted a phylogenetic study of 21 mammalian Lagenidium isolates; we found that 11 cannot be differentiated from L. giganteum strains that the US Environmental Protection Agency approved for biological control of mosquitoes; these strains were later unregistered and are no longer available. L. giganteum strains pathogenic to mammals formed a strongly supported clade with the biological control isolates, and both types experimentally infected mosquito larvae. However, the strains from mammals grew well at 25°C and 37°C, whereas the biological control strains developed normally at 25°C but poorly at higher temperatures. The emergence of heat-tolerant strains of L. giganteum pathogenic to lower animals and humans is of environmental and public health concern. PMID:25625190

  11. A new symmetrodont mammal from China and its implications for mammalian evolution.

    PubMed

    Hu, Y; Wang, Y; Luo, Z; Li, C

    1997-11-13

    A new symmetrodont mammal has been discovered in the Mesozoic era (Late Jurassic or Early Cretaceous period) of Liaoning Province, China. Archaic therian mammals, including symmetrodonts, are extinct relatives of the living marsupial and placental therians. However, these archaic therians have been mostly documented by fragmentary fossils. This newfossil taxon, represented by a nearly complete postcranial skeleton and a partial skull with dentition, is the best-preserved symmetrodont mammal yet discovered. It provides a new insight into the relationships of the major lineages of mammals and the evolution of the mammalian skeleton. Our analysis suggests that this new taxon represents a part of the early therian radiation before the divergence of living marsupials and placentals; that therians and multituberculates are more closely related to each other than either group is to other mammalian lineages; that archaic therians lacked the more parasagittal posture of the forelimb of most living therian mammals; and that archaic therians, such as symmetrodonts, retained the primitive feature of a finger-like promontorium (possibly with a straight cochlea) of the non-therian mammals. The fully coiled cochlea evolved later in more derived therian mammals, and is therefore convergent to the partially coiled cochlea of monotremes.

  12. Taxonicity of nonverbal learning disabilities in spina bifida.

    PubMed

    Ris, M Douglas; Ammerman, Robert T; Waller, Niels; Walz, Nicolay; Oppenheimer, Sonya; Brown, Tanya Maines; Enrile, Benedicta G; Yeates, Keith Owen

    2007-01-01

    As currently defined, it is not clear whether Nonverbal Learning Disabilities (NLD) should be considered a matter of kind or magnitude (Meehl, 1995). The taxonicity of NLD, or the degree to which it is best construed as discrete versus continuous, has not been investigated using methods devised for this purpose. Latent Class Analysis (LCA) is a method for finding subtypes of latent classes from multivariate categorical data. This study represents an application of LCA on a sample of children and adolescents with spina bifida myelomeningocele (SBM) (N = 44), those presenting with features of NLD (N = 28) but no medical condition, and control volunteers (N = 44). The two-class solution provided evidence for the presence of a taxon with an estimated base-rate in the SBM group of .57. Indicator validities (the conditional probabilities of indicator endorsement in each latent class) suggest a somewhat different priority for defining NLD than is typically used by researchers investigating this disorder. A high degree of correspondence between LCA classifications and those based on a more conventional algorithm provided evidence for the validity of this approach.

  13. Oligocene and early Miocene mammal biostratigraphy of the Valley of Lakes in Mongolia.

    PubMed

    Harzhauser, Mathias; Daxner-Höck, Gudrun; Erbajeva, Margarita A; López-Guerrero, Paloma; Maridet, Olivier; Oliver, Adriana; Piller, Werner E; Göhlich, Ursula B; Ziegler, Reinhard

    2017-01-01

    The Taatsiin Gol Basin in Mongolia is a key area for understanding the evolution and dispersal of Central Asian mammal faunas during the Oligocene and early Miocene. After two decades of intense fieldwork, the area is extraordinarily well sampled and taxonomically well studied, yielding a large dataset of 19,042 specimens from 60 samples. The specimens represent 176 species-level and 99 genus-level taxa comprising 135 small mammal species and 47 large mammals. A detailed lithostratigraphy and new magnetostratigraphic and radiometric datings provide an excellent frame for these biotic data. Therefore, we test and evaluate the informal biozonation scheme that has been traditionally used for biostratigraphic correlations within the basin. Based on the analysis of the huge dataset, a formalised biostratigraphic scheme is proposed. It comprises the Cricetops dormitor Taxon Range Zone (Rupelian), subdivided into the Allosminthus khandae Taxon Range Subzone and the Huangomys frequens Abundance Subzone, the Amphechinus taatsiingolensis Abundance Zone (early Chattian), the Amphechinus major Taxon Range Zone (late Chattian), subdivided into the Yindirtemys deflexus Abundance Subzone and the Upper Amphechinus major T. R. Z., and the Tachyoryctoides kokonorensis Taxon Range Zone (Aquitanian). In statistical analyses, samples attributed to these biozones form distinct clusters, indicating that each biozone was also characterised by a distinct faunal type.

  14. Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

    PubMed Central

    Kristensen, David M.; Waller, Alison S.; Yamada, Takuji; Bork, Peer; Mushegian, Arcady R.

    2013-01-01

    Viruses are the most abundant biological entities on earth and encompass a vast amount of genetic diversity. The recent rapid increase in the number of sequenced viral genomes has created unprecedented opportunities for gaining new insight into the structure and evolution of the virosphere. Here, we present an update of the phage orthologous groups (POGs), a collection of 4,542 clusters of orthologous genes from bacteriophages that now also includes viruses infecting archaea and encompasses more than 1,000 distinct virus genomes. Analysis of this expanded data set shows that the number of POGs keeps growing without saturation and that a substantial majority of the POGs remain specific to viruses, lacking homologues in prokaryotic cells, outside known proviruses. Thus, the great majority of virus genes apparently remains to be discovered. A complementary observation is that numerous viral genomes remain poorly, if at all, covered by POGs. The genome coverage by POGs is expected to increase as more genomes are sequenced. Taxon-specific, single-copy signature genes that are not observed in prokaryotic genomes outside detected proviruses were identified for two-thirds of the 57 taxa (those with genomes available from at least 3 distinct viruses), with half of these present in all members of the respective taxon. These signatures can be used to specifically identify the presence and quantify the abundance of viruses from particular taxa in metagenomic samples and thus gain new insights into the ecology and evolution of viruses in relation to their hosts. PMID:23222723

  15. Health risks for marine mammal workers.

    PubMed

    Hunt, Tania D; Ziccardi, Michael H; Gulland, Frances M D; Yochem, Pamela K; Hird, David W; Rowles, Teresa; Mazet, Jonna A K

    2008-08-19

    Marine mammals can be infected with zoonotic pathogens and show clinical signs of disease, or be asymptomatic carriers of such disease agents. While isolated cases of human disease from contact with marine mammals have been reported, no evaluation of the risks associated with marine mammal work has been attempted. Therefore, we designed a survey to estimate the risk of work-related injuries and illnesses in marine mammal workers and volunteers. The 17-question survey asked respondents to describe their contact with marine mammals, injuries sustained, and/or illnesses acquired during their period of marine mammal exposure. Most respondents, 88% (423/483), were researchers and rehabilitators. Of all respondents, 50% (243/483) reported suffering an injury caused by a marine mammal, and 23% (110/483) reported having a skin rash or reaction. Marine mammal work-related illnesses commonly reported included: 'seal finger' (Mycoplasma spp. or Erysipelothrix rhusiopathiae), conjunctivitis, viral dermatitis, bacterial dermatitis, and non-specific contact dermatitis. Although specific diagnoses could not be confirmed by a physician through this study, severe illnesses were reported and included tuberculosis, leptospirosis, brucellosis, and serious sequelae to seal finger. Risk factors associated with increased odds of injury and illness included prolonged and frequent exposure to marine mammals; direct contact with live marine mammals; and contact with tissue, blood, and excretions. Diagnosis of zoonotic disease was often aided by veterinarians; therefore, workers at risk should be encouraged to consult with a marine mammal veterinarian as well as a physician, especially if obtaining a definitive diagnosis for an illness becomes problematic.

  16. A Standardized Reference Data Set for Vertebrate Taxon Name Resolution

    PubMed Central

    Zermoglio, Paula F.; Guralnick, Robert P.; Wieczorek, John R.

    2016-01-01

    Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only once during accessioning of specimens, or have a history of label changes without clear provenance. Before records are reliably usable in research, it is critical that these issues be addressed. However, still missing is an assessment of the scope of the problem, the effort needed to solve it, and a way to improve effectiveness of tools developed to aid the process. We present a carefully human-vetted analysis of 1000 verbatim scientific names taken at random from those published via the data aggregator VertNet, providing the first rigorously reviewed, reference validation data set. In addition to characterizing formatting problems, human vetting focused on detecting misspelling, synonymy, and the incorrect use of Darwin Core. Our results reveal a sobering view of the challenge ahead, as less than 47% of name strings were found to be currently valid. More optimistically, nearly 97% of name combinations could be resolved to a currently valid name, suggesting that computer-aided approaches may provide feasible means to improve digitized content. Finally, we associated names back to biocollections records and fit logistic models to test potential drivers of issues. A set of candidate variables (geographic region, year collected, higher-level clade, and the institutional digitally accessible data volume) and their 2-way interactions all predict the probability of records having taxon name issues, based on model selection approaches. We strongly encourage further experiments to use this reference data set as a means to compare automated or computer-aided taxon name tools for their ability to resolve and improve the existing wealth of legacy data. PMID:26760296

  17. A Standardized Reference Data Set for Vertebrate Taxon Name Resolution.

    PubMed

    Zermoglio, Paula F; Guralnick, Robert P; Wieczorek, John R

    2016-01-01

    Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only once during accessioning of specimens, or have a history of label changes without clear provenance. Before records are reliably usable in research, it is critical that these issues be addressed. However, still missing is an assessment of the scope of the problem, the effort needed to solve it, and a way to improve effectiveness of tools developed to aid the process. We present a carefully human-vetted analysis of 1000 verbatim scientific names taken at random from those published via the data aggregator VertNet, providing the first rigorously reviewed, reference validation data set. In addition to characterizing formatting problems, human vetting focused on detecting misspelling, synonymy, and the incorrect use of Darwin Core. Our results reveal a sobering view of the challenge ahead, as less than 47% of name strings were found to be currently valid. More optimistically, nearly 97% of name combinations could be resolved to a currently valid name, suggesting that computer-aided approaches may provide feasible means to improve digitized content. Finally, we associated names back to biocollections records and fit logistic models to test potential drivers of issues. A set of candidate variables (geographic region, year collected, higher-level clade, and the institutional digitally accessible data volume) and their 2-way interactions all predict the probability of records having taxon name issues, based on model selection approaches. We strongly encourage further experiments to use this reference data set as a means to compare automated or computer-aided taxon name tools for their ability to resolve and improve the existing wealth of legacy data.

  18. Mammals in Our Lives.

    ERIC Educational Resources Information Center

    Naturescope, 1986

    1986-01-01

    Examines how humans have treated mammals throughout history. Identifies both the problems facing animals and the corrective efforts that are currently underway. Student activities include stories, games, a scavenger hunt, a mural, a puzzle, and a survey focusing on mammals. (ML)

  19. Small Mammal Intrigue.

    ERIC Educational Resources Information Center

    Cristol, Daniel A.

    1985-01-01

    Gives introductory information about the study of small mammals including the selection and use of harmless live-traps, handling and identification, techniques for observation and trapping in the wild, and safety measures. Suggests useful references for teachers wishing to develop a small mammal study program for their students. (JHZ)

  20. Small mammal communities of high elevation central Appalachian wetlands

    Treesearch

    Karen E. Francl; Steven B. Castleberry; W. Mark Ford

    2004-01-01

    We surveyed small mammal assemblages at 20 high-elevation wetlands in West Virginia and Maryland and examined relationships among mammal capture rates, richness and evenness and landscape features at multiple spatial scales. In 24,693 trap nights we captured 1451 individuals of 12 species. Small mammal species richness increased with wetland size and was negatively...

  1. Automatic Classification of a Taxon-Rich Community Recorded in the Wild

    PubMed Central

    Potamitis, Ilyas

    2014-01-01

    There is a rich literature on automatic species identification of a specific target taxon as regards various vocalizing animals. Research usually is restricted to specific species – in most cases a single one. It is only very recently that the number of monitored species has started to increase for certain habitats involving birds. Automatic acoustic monitoring has not yet been proven to be generic enough to scale to other taxa and habitats than the ones described in the original research. Although attracting much attention, the acoustic monitoring procedure is neither well established yet nor universally adopted as a biodiversity monitoring tool. Recently, the multi-instance multi-label framework on bird vocalizations has been introduced to face the obstacle of simultaneously vocalizing birds of different species. We build on this framework to integrate novel, image-based heterogeneous features designed to capture different aspects of the spectrum. We applied our approach to a taxon-rich habitat that included 78 birds, 8 insect species and 1 amphibian. This dataset constituted the Multi-label Bird Species Classification Challenge-NIPS 2013 where the proposed approach achieved an average accuracy of 91.25% on unseen data. PMID:24826989

  2. Allometry in dinosaurs and mammals

    NASA Astrophysics Data System (ADS)

    Lee, Scott

    2015-03-01

    The proportions of the leg bones change as the size of an animal becomes larger since the mass of the animal increases at a faster rate than the cross-sectional area of its leg bones. For the case of elastic similarity (in which the longitudinal stress in the legs remains constant in animals of all sizes), the diameter d and length L of the femur should be related as d = A L3/2. For geometric similarity (in which all dimensions are scaled by the same factor), d = A L. For animals with femora longer than 20 cm, we find the power law relationship to be d = A Lb with b = 1.13 +/- 0.06 for extant mammals (the largest mammal being Loxodonta africana with a 1.00-m-long femur) and b = 1.18 +/- 0.02 for dinosaurs (the largest dinosaur being Brachiosaurus brancai with a 2.03-m-long femur). These data show that extinct dinosaurs and extant animals scale in the same basic manner. The large sauropods (with femora twice as long as found in elephants) scale in a manner consistent with extrapolation of the scaling shown by extant mammals. These results argue that extinct dinosaurs moved in a manner very similar to extant mammals.

  3. The origins of multicellularity: a multi-taxon genome initiative.

    PubMed

    Ruiz-Trillo, Iñaki; Burger, Gertraud; Holland, Peter W H; King, Nicole; Lang, B Franz; Roger, Andrew J; Gray, Michael W

    2007-03-01

    The emergence of multicellular organisms from single-celled ancestors -- which occurred several times, independently in different branches of the eukaryotic tree -- is one of the most profound evolutionary transitions in the history of life. These events not only radically changed the course of life on Earth but also created new challenges, including the need for cooperation and communication between cells, and the division of labor among different cell types. However, the genetic changes that accompanied the several origins of multicellularity remain elusive. Recently, the National Human Genome Research Institute (NHGRI) endorsed a multi-taxon genome-sequencing initiative that aims to gain insights into how multicellularity first evolved. This initiative (which we have termed UNICORN) will generate extensive genomic data from some of the closest extant unicellular relatives of both animals and fungi. Here, we introduce this initiative and the biological questions that underpin it, summarize the rationale guiding the choice of organisms and discuss the anticipated benefits to the broader scientific community.

  4. Two issues in archaeological phylogenetics: taxon construction and outgroup selection.

    PubMed

    O'Brien, Michael J; Lyman, R Lee; Saab, Youssef; Saab, Elias; Darwent, John; Glover, Daniel S

    2002-03-21

    Cladistics is widely used in biology and paleobiology to construct phylogenetic hypotheses, but rarely has it been applied outside those disciplines. There is, however, no reason to suppose that cladistics is not applicable to anything that evolves by cladogenesis and produces a nested hierarchy of taxa. This includes cultural phenomena such as languages and tools recovered from archaeological contexts. Two methodological issues assume primacy in attempts to extend cladistics to archaeological materials: the construction of analytical taxa and the selection of appropriate outgroups. In biology the species is the primary taxonomic unit used, irrespective of the debates that have arisen in phylogenetic theory over the nature of species. Also in biology the phylogenetic history of a group of taxa usually is well enough known that an appropriate taxon can be selected as an outgroup. No analytical unit parallel to the species exists in archaeology, and thus taxa have to be constructed specifically for phylogenetic analysis. One method of constructing taxa is paradigmatic classification, which defines classes (taxa) on the basis of co-occurring, unweighted character states. Once classes have been created, a form of occurrence seriation-an archaeological method based on the theory of cultural transmission and heritability-offers an objective basis for selecting an outgroup.

  5. Ecotoxicology of wild mammals

    USGS Publications Warehouse

    Rattner, B.A.; Shore, R.F.

    2000-01-01

    An international group of 32 scientists has critically reviewed the scientific literature on exposure and effects of environmental contaminants in wild mammals. Although the absolute number of toxicological studies in domesticated and wild mammals eclipses that for birds, a detailed examination of scientific publications and databases reveal that information for 'wild' birds is actually greater than that for 'wild' mammals. Of the various taxa of mammals, ecotoxicological data is most noticeably lacking for marsupials and monotremes. In contrast, rodents (comprising 43% of all mammal species) have been studied extensively, despite evidence of their tolerance to some organochlorine compounds, rodenticides, and even radionuclides. Mammalian species at greatest risk of exposure include those that consume a high percentage of their body weight on a daily basis (e.g., shrews, moles and bats). Aquatic mammals tend to bioaccumulate tremendous burdens of lipophilic contaminants, although storage in their fat depots may actually limit toxicity. Carnivores appear to be more sensitive to adverse effects of environmental contaminants than herbivores. Remarkably few of the thousands of compounds manufactured worldwide have been toxicologically evaluated in wild mammals, and concentrations of even fewer have been monitored in tissues. Overarching research needs include: development of new exposure/effects models and better methods for estimation of species sensitivities; generation of comparative data on contaminant bioavailability, sublethal responses and detoxication mechanisms; enhanced understanding of pesticide, industrial contaminant and metal interactions; identification of endocrine disruptive contaminants and their overall ecological significance; and finally, estimating the relative contribution of environmental contamination as a factor affecting wild mammal populations.

  6. 7 CFR 360.501 - Petitions to remove a taxon from the noxious weed lists.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 5 2014-01-01 2014-01-01 false Petitions to remove a taxon from the noxious weed...) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.501 Petitions to remove a taxon from the noxious weed lists. A person may petition the Administrator to remove a...

  7. 7 CFR 360.501 - Petitions to remove a taxon from the noxious weed lists.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 5 2013-01-01 2013-01-01 false Petitions to remove a taxon from the noxious weed...) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.501 Petitions to remove a taxon from the noxious weed lists. A person may petition the Administrator to remove a...

  8. 7 CFR 360.501 - Petitions to remove a taxon from the noxious weed lists.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 5 2012-01-01 2012-01-01 false Petitions to remove a taxon from the noxious weed...) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.501 Petitions to remove a taxon from the noxious weed lists. A person may petition the Administrator to remove a...

  9. Phylogenomic analysis of ants, bees and stinging wasps: Improved taxon sampling enhances understanding of hymenopteran evolution

    USDA-ARS?s Scientific Manuscript database

    The importance of taxon sampling in phylogenetic accuracy is a topic of active debate. We investigated the role of taxon sampling in causing incongruent results between two recent phylogenomic studies of stinging wasps (Hymenoptera: Aculeata), a diverse lineage that includes ants, bees and the major...

  10. Pheromone reception in mammals.

    PubMed

    Bigiani, A; Mucignat-Caretta, C; Montani, G; Tirindelli, R

    2005-01-01

    Pheromonal communication is the most convenient way to transfer information regarding gender and social status in animals of the same species with the holistic goal of sustaining reproduction. This type of information exchange is based on pheromones, molecules often chemically unrelated, that are contained in body fluids like urine, sweat, specialized exocrine glands, and mucous secretions of genitals. So profound is the relevance of pheromones over the evolutionary process that a specific peripheral organ devoted to their recognition, namely the vomeronasal organ of Jacobson, and a related central pathway arose in most vertebrate species. Although the vomeronasal system is well developed in reptiles and amphibians, most mammals strongly rely on pheromonal communication. Humans use pheromones too; evidence on the existence of a specialized organ for their detection, however, is very elusive indeed. In the present review, we will focus our attention on the behavioral, physiological, and molecular aspects of pheromone detection in mammals. We will discuss the responses to pheromonal stimulation in different animal species, emphasizing the complicacy of this type of communication. In the light of the most recent results, we will also discuss the complex organization of the transduction molecules that underlie pheromone detection and signal transmission from vomeronasal neurons to the higher centers of the brain. Communication is a primary feature of living organisms, allowing the coordination of different behavioral paradigms among individuals. Communication has evolved through a variety of different strategies, and each species refined its own preferred communication medium. From a phylogenetic point of view, the most widespread and ancient way of communication is through chemical signals named pheromones: it occurs in all taxa, from prokaryotes to eukaryotes. The release of specific pheromones into the environment is a sensitive and definite way to send messages to

  11. Do Bird Friendly® Coffee Criteria Benefit Mammals? Assessment of Mammal Diversity in Chiapas, Mexico.

    PubMed

    Caudill, S Amanda; Rice, Robert A

    2016-01-01

    Biodiversity-friendly coffee certifications offer a viable way to protect wildlife habitat while providing a financial incentive to farmers. Most studies related to these certifications focus on avian habitat requirements and it is not known whether these standards also apply to other wildlife, such as mammals, that inhabit the coffee landscapes. We assessed the non-volant mammalian fauna and their associated habitat requirements in 23 sites representing forest, Bird Friendly® shade, conventional shade, and sun coffee habitats. We used Sherman trap-grids to measure small mammal abundance and richness, while camera traps were set for medium-sized and large mammals. We detected 17 species of mammals, representing 11 families. This preliminary study indicates that coffee farms in this region provide an important refuge for mammalian wildlife. Mammal species density ranked significantly higher in Bird Friendly® coffee sites than other coffee habitats, although there was no significant difference for species richness (using Chao2 estimator) among the habitat types. No significant difference was found in small mammal abundance among the habitat types. We found a higher species density of medium and large mammals in sites with larger, more mature shade trees associated with, but not required by Bird Friendly® certification standards. However, lower strata vegetation (5 cm to 1 m tall), the only vegetation parameter found to increase abundance and density for small mammals, is not specified in the Bird Friendly® standards. Our findings suggest that although the standards devised for avian habitat do benefit mammals, further study is needed on the requirements specific for mammals that could be included to enhance the coffee habitat for mammals that inhabit these coffee landscapes.

  12. Do Bird Friendly® Coffee Criteria Benefit Mammals? Assessment of Mammal Diversity in Chiapas, Mexico

    PubMed Central

    Caudill, S. Amanda; Rice, Robert A.

    2016-01-01

    Biodiversity-friendly coffee certifications offer a viable way to protect wildlife habitat while providing a financial incentive to farmers. Most studies related to these certifications focus on avian habitat requirements and it is not known whether these standards also apply to other wildlife, such as mammals, that inhabit the coffee landscapes. We assessed the non-volant mammalian fauna and their associated habitat requirements in 23 sites representing forest, Bird Friendly® shade, conventional shade, and sun coffee habitats. We used Sherman trap-grids to measure small mammal abundance and richness, while camera traps were set for medium-sized and large mammals. We detected 17 species of mammals, representing 11 families. This preliminary study indicates that coffee farms in this region provide an important refuge for mammalian wildlife. Mammal species density ranked significantly higher in Bird Friendly® coffee sites than other coffee habitats, although there was no significant difference for species richness (using Chao2 estimator) among the habitat types. No significant difference was found in small mammal abundance among the habitat types. We found a higher species density of medium and large mammals in sites with larger, more mature shade trees associated with, but not required by Bird Friendly® certification standards. However, lower strata vegetation (5 cm to 1 m tall), the only vegetation parameter found to increase abundance and density for small mammals, is not specified in the Bird Friendly® standards. Our findings suggest that although the standards devised for avian habitat do benefit mammals, further study is needed on the requirements specific for mammals that could be included to enhance the coffee habitat for mammals that inhabit these coffee landscapes. PMID:27880773

  13. Differences in the umbrella effects of African amphibians and mammals based on two estimators of the area of occupancy.

    PubMed

    Rondinini, Carlo; Boitani, Luigi

    2006-02-01

    Conservation organizations are collecting large-scale data regarding distribution and threats to vertebrate taxa. These data sets will enable planners to systematically identify large-scale conservation priorities; however, they will cover only a tiny proportion of living organisms. Therefore, it is essential to investigate to what extent the areas selected for conservation actions can provide protection for other species. We analyzed the umbrella effect between amphibians and mammals across mainland Africa. We built habitat suitability models within the geographic ranges of 1654 species, based on data collected in the framework of the World Conservation Union (IUCN) Global Amphibian Assessment and IUCN Global Mammal Assessment. We applied systematic reserve selection algorithms to two sets of estimators of the area of occupancy of amphibians and mammals (geographic ranges and estimated suitable areas) and thus selected four reserve systems. We then quantified the protection that each of the four systems provided for amphibians and mammals. Reserves selected for amphibians and mammals were comparable in area, with the former concentrated in the Afrotropical region and the latter more evenly dispersed. Mammal reserves left fewer gaps in species coverage among amphibians than the reverse, but amphibian reserves included a larger proportion of each mammal's area of occupancy than the reverse. For both taxa, setting reserves to include estimated suitable areas instead of ranges resulted in the clustering of reserves in the tropics. Furthermore, it efficiently protected hidden gaps (species with unsuitable portions of their range inside protected areas) in the other taxon and included a higher proportion of the area of occupancy of the other taxon. Overall, amphibians and mammals in Africa acted as an umbrella for a high proportion of species in the other taxon. Focusing on estimated suitable areas instead of ranges improved the umbrella effect of both taxa.

  14. Recovery trends in marine mammal populations.

    PubMed

    Magera, Anna M; Mills Flemming, Joanna E; Kaschner, Kristin; Christensen, Line B; Lotze, Heike K

    2013-01-01

    Marine mammals have greatly benefitted from a shift from resource exploitation towards conservation. Often lauded as symbols of conservation success, some marine mammal populations have shown remarkable recoveries after severe depletions. Others have remained at low abundance levels, continued to decline, or become extinct or extirpated. Here we provide a quantitative assessment of (1) publicly available population-level abundance data for marine mammals worldwide, (2) abundance trends and recovery status, and (3) historic population decline and recent recovery. We compiled 182 population abundance time series for 47 species and identified major data gaps. In order to compare across the largest possible set of time series with varying data quality, quantity and frequency, we considered an increase in population abundance as evidence of recovery. Using robust log-linear regression over three generations, we were able to classify abundance trends for 92 spatially non-overlapping populations as Significantly Increasing (42%), Significantly Decreasing (10%), Non-Significant Change (28%) and Unknown (20%). Our results were comparable to IUCN classifications for equivalent species. Among different groupings, pinnipeds and other marine mammals (sirenians, polar bears and otters) showed the highest proportion of recovering populations, likely benefiting from relatively fast life histories and nearshore habitats that provided visibility and protective management measures. Recovery was less frequent among cetaceans, but more common in coastal than offshore populations. For marine mammals with available historical abundance estimates (n = 47), larger historical population declines were associated with low or variable recent recoveries so far. Overall, our results show that many formerly depleted marine mammal populations are recovering. However, data-deficient populations and those with decreasing and non-significant trends require attention. In particular, increased study of

  15. Recovery Trends in Marine Mammal Populations

    PubMed Central

    Magera, Anna M.; Mills Flemming, Joanna E.; Kaschner, Kristin; Christensen, Line B.; Lotze, Heike K.

    2013-01-01

    Marine mammals have greatly benefitted from a shift from resource exploitation towards conservation. Often lauded as symbols of conservation success, some marine mammal populations have shown remarkable recoveries after severe depletions. Others have remained at low abundance levels, continued to decline, or become extinct or extirpated. Here we provide a quantitative assessment of (1) publicly available population-level abundance data for marine mammals worldwide, (2) abundance trends and recovery status, and (3) historic population decline and recent recovery. We compiled 182 population abundance time series for 47 species and identified major data gaps. In order to compare across the largest possible set of time series with varying data quality, quantity and frequency, we considered an increase in population abundance as evidence of recovery. Using robust log-linear regression over three generations, we were able to classify abundance trends for 92 spatially non-overlapping populations as Significantly Increasing (42%), Significantly Decreasing (10%), Non-Significant Change (28%) and Unknown (20%). Our results were comparable to IUCN classifications for equivalent species. Among different groupings, pinnipeds and other marine mammals (sirenians, polar bears and otters) showed the highest proportion of recovering populations, likely benefiting from relatively fast life histories and nearshore habitats that provided visibility and protective management measures. Recovery was less frequent among cetaceans, but more common in coastal than offshore populations. For marine mammals with available historical abundance estimates (n = 47), larger historical population declines were associated with low or variable recent recoveries so far. Overall, our results show that many formerly depleted marine mammal populations are recovering. However, data-deficient populations and those with decreasing and non-significant trends require attention. In particular, increased

  16. Ecotoxicology of Wild Mammals

    USGS Publications Warehouse

    2001-01-01

    An international group of 32 scientists has critically reviewed the scientific literature on exposure and effects of environmental contaminants in wild mammals. The underlying theme of this text is encompassed by the following four questions: What exactly do we know about environmental contaminants in mammals? What are the commonalities and differences between mammal orders/species in the effects that contaminants have? How and to what degree of accuracy can we predict the adverse effects of environmental contaminants on mammalian wildlife? How significant are contaminant insults compared with other density-independent and -dependent factors such as habitat loss, climatic factors and disease? The book is organized three topical sections including introductory chapters that provide a background on environmental contaminants and the mammalian orders, eight taxonomic chapters discussing all aspects of the exposure to and effects of contaminants in mammalian orders, and four thematic chapters that review and discuss generic issues including biomarkers, prediction and extrapolation of exposure and effects, hazard and risk assessment, and the relative significance of contaminants on mammals compared with other commonly encountered stressors. A final a summary chapter identifies phylogenetic trends, critical data gaps, and overarching research needs. Although the absolute number of toxicological studies in domesticated and wild mammals eclipses that wildlife species, a detailed examination of our knowledge base reveals that information for 'wild' birds is actually greater than that for 'wild' mammals. Of the various mammalian taxa, ecotoxicological data is most noticeably lacking for marsupials and monotremes. In contrast, rodents (comprising 43% of all mammal species) have been studied extensively, despite evidence of their tolerance to some organochlorine compounds, rodenticides, and even radionuclides. Mammalian species at greatest risk of exposure include those that

  17. Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.

    PubMed

    Cui, Hong; Xu, Dongfang; Chong, Steven S; Ramirez, Martin; Rodenhausen, Thomas; Macklin, James A; Ludäscher, Bertram; Morris, Robert A; Soto, Eduardo M; Koch, Nicolás Mongiardino

    2016-11-17

    Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the

  18. Accumulation of perfluorooctane sulfonate in marine mammals.

    PubMed

    Kannan, K; Koistinen, J; Beckmen, K; Evans, T; Gorzelany, J F; Hansen, K J; Jones, P D; Helle, E; Nyman, M; Giesy, J P

    2001-04-15

    Perfluorooctane sulfonate (PFOS) is a perfluorinated molecule that has recently been identified in the sera of nonindustrially exposed humans. In this study, 247 tissue samples from 15 species of marine mammals collected from Florida, California, and Alaskan coastal waters; and northern Baltic Sea; the Arctic (Spitsbergen); and Sable Island in Canada were analyzed for PFOS. PFOS was detected in liver and blood of marine mammals from most locations including those from Arctic waters. The greatest concentrations of PFOS found in liver and blood were 1520 ng/g wet wt in a bottlenose dolphin from Sarasota Bay, FL, and 475 ng/mL in a ringed seal from the northern Baltic Sea (Bothnian Sea), respectively. No age-dependent increase in PFOS concentrations in marine mammals was observed in the samples analyzed. The occurrence of PFOS in marine mammals from the Arctic waters suggests widespread global distribution of PFOS including remote locations.

  19. Global Patterns of Zoonotic Disease in Mammals.

    PubMed

    Han, Barbara A; Kramer, Andrew M; Drake, John M

    2016-07-01

    As the frequency and prevalence of zoonotic diseases increase worldwide, investigating how mammal host distributions determine patterns of human disease and predicting which regions are at greatest risk for future zoonotic disease emergence are two goals which both require better understanding of the current distributions of zoonotic hosts and pathogens. We review here the existing data about mammalian host species, comparing and contrasting these patterns against global maps of zoonotic hosts from all 27 orders of terrestrial mammals. We discuss the zoonotic potential of host species from the top six most species-rich mammal groups, and review the literature to identify analytical and conceptual gaps that must be addressed to improve our ability to generate testable predictions about zoonotic diseases originating from wild mammals.

  20. Osmoregulation in marine mammals

    NASA Technical Reports Server (NTRS)

    Ortiz, R. M.

    2001-01-01

    Osmoregulation in marine mammals has been investigated for over a century; however, a review of recent advances in our understanding of water and electrolyte balance and of renal function in marine mammals is warranted. The following topics are discussed: (i) kidney structure and urine concentrating ability, (ii) sources of water, (iii) the effects of feeding, fasting and diving, (iv) the renal responses to infusions of varying salinity and (v) hormonal regulation. The kidneys of pinnipeds and cetaceans are reniculate in structure, unlike those of terrestrial mammals (except bears), but this difference does not confer any greater concentrating ability. Pinnipeds, cetaceans, manatees and sea otters can concentrate their urine above the concentration of sea water, but only pinnipeds and otters have been shown to produce urine concentrations of Na+ and Cl- that are similar to those in sea water. This could afford them the capacity to drink sea water and not lose fresh water. However, with few exceptions, drinking is not a common behavior in pinnipeds and cetaceans. Water balance is maintained in these animals via metabolic and dietary water, while incidental ingestion and dietary salt may help maintain electrolyte homeostasis. Unlike most other aquatic mammals, sea otters commonly drink sea water and manatees frequently drink fresh water. Among the various taxonomic groups of marine mammals, the sensitivity of the renin-angiotensin-aldosterone system appears to be influenced by the availability of Na+. The antidiuretic role of vasopressin remains inconclusive in marine mammals, while the natriuretic function of atrial natriuretic peptide has yet to be examined. Ideas on the direction of future studies are presented.

  1. Venomous mammals: a review.

    PubMed

    Ligabue-Braun, Rodrigo; Verli, Hugo; Carlini, Célia Regina

    2012-06-01

    The occurrence of venom in mammals has long been considered of minor importance, but recent fossil discoveries and advances in experimental techniques have cast new light into this subject. Mammalian venoms form a heterogeneous group having different compositions and modes of action and are present in three classes of mammals, Insectivora, Monotremata, and Chiroptera. A fourth order, Primates, is proposed to have venomous representatives. In this review we highlight recent advances in the field while summarizing biochemical characteristics of these secretions and their effects upon humans and other animals. Historical aspects of venom discovery and evolutionary hypothesis regarding their origin are also discussed.

  2. Mammals in Winter.

    ERIC Educational Resources Information Center

    Wapner, Suzanne

    1985-01-01

    Mammals that tolerate the winter cold and stay active all year exploit the harsh northern climate to their advantage. By simple experiments and observation you can better understand their adaptations which include furry bodies, snowshoe feet, extra blubber, light coloration, and strategically distributed food caches. (JHZ)

  3. Morbilliviruses in marine mammals.

    PubMed

    Hall, A J

    1995-01-01

    Two of the three recently discovered aquatic morbilliviruses have been responsible for mass mortalities among marine mammals; both affect more than one host species, but susceptibility to infection varies considerably between species. Apparent differences between the dynamics of aquatic morbilliviruses and their terrestrial counterparts may be a consequence of high levels of interspecific transmission.

  4. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting.

    PubMed

    Delsuc, Frédéric; Scally, Mark; Madsen, Ole; Stanhope, Michael J; de Jong, Wilfried W; Catzeflis, François M; Springer, Mark S; Douzery, Emmanuel J P

    2002-10-01

    Extant xenarthrans (armadillos, anteaters and sloths) are among the most derived placental mammals ever evolved. South America was the cradle of their evolutionary history. During the Tertiary, xenarthrans experienced an extraordinary radiation, whereas South America remained isolated from other continents. The 13 living genera are relics of this earlier diversification and represent one of the four major clades of placental mammals. Sequences of the three independent protein-coding nuclear markers alpha2B adrenergic receptor (ADRA2B), breast cancer susceptibility (BRCA1), and von Willebrand Factor (VWF) were determined for 12 of the 13 living xenarthran genera. Comparative evolutionary dynamics of these nuclear exons using a likelihood framework revealed contrasting patterns of molecular evolution. All codon positions of BRCA1 were shown to evolve in a strikingly similar manner, and third codon positions appeared less saturated within placentals than those of ADRA2B and VWF. Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set rooted by three marsupial outgroups resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships. This topology was fully compatible with recent studies, dividing placentals into the Southern Hemisphere clades Afrotheria and Xenarthra and a monophyletic Northern Hemisphere clade (Boreoeutheria) composed of Laurasiatheria and Euarchontoglires. Partitioned likelihood statistical tests of the position of the root, under different character partition schemes, identified three almost equally likely hypotheses for early placental divergences: a basal Afrotheria, an Afrotheria + Xenarthra clade, or a basal Xenarthra (Epitheria hypothesis). We took advantage of the extensive sampling realized within Xenarthra to assess its impact on the location of the root on the placental tree. By resampling taxa

  5. Physiological Monitoring in Diving Mammals

    DTIC Science & Technology

    2010-09-30

    and Neurobiology, 2009. 165(28-39). 4. Fahlman, A., et al., Deep diving mammals : Dive behavior and circulatory adjustments contribute to bends...1 DISTRIBUTION STATEMENT A: Approved for public release; distribution is unlimited. Physiological Monitoring in Diving Mammals Peter L...NGO) scrutiny of the complex relationship between ocean noise, bubble injury and marine mammal strandings (http://www.awionline.org/oceans/Noise

  6. 76 FR 76949 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-09

    ... National Oceanic and Atmospheric Administration RIN 0648-XR52 Marine Mammals AGENCY: National Marine... Marine Mammal Protection Act of 1972, as amended (16 U.S.C. 1361 et seq.), the regulations governing the taking and importing of marine mammals (50 CFR part 216), the Endangered Species Act of 1973, as amended...

  7. 77 FR 2512 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-18

    ... National Oceanic and Atmospheric Administration RIN 0648-XA905 Marine Mammals AGENCY: National Marine...; receipt of application. SUMMARY: Notice is hereby given that Dorian Houser, Ph.D., National Marine Mammal... under the authority of the Marine Mammal Protection Act of 1972, as amended (MMPA; 16 U.S.C. 1361 et seq...

  8. 75 FR 68605 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-08

    ... National Oceanic and Atmospheric Administration RIN 0648-XX23 Marine Mammals AGENCY: National Marine... Marine Science Center, Newport, OR has been issued a permit to conduct research on marine mammals... authority of the Marine Mammal Protection Act of 1972, as amended (16 U.S.C. 1361 et seq.), the regulations...

  9. 76 FR 72681 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-25

    ... National Oceanic and Atmospheric Administration RIN 0648-XU87 Marine Mammals AGENCY: National Marine... Mammal Laboratory, (Responsible Party: Dr. John Bengtson, Director), Seattle, WA, has applied for an amendment to Scientific Research Permit No. 15126-01 for studies of marine mammals in Alaska. DATES: Written...

  10. 75 FR 76399 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-08

    ... National Oceanic and Atmospheric Administration RIN 0648-XK54 Marine Mammals AGENCY: National Marine...: The subject amendment to Permit No. 13602 was requested under the authority of the Marine Mammal... importing of marine mammals (50 CFR part 216), the Endangered Species Act of 1973, as amended (16 U.S.C...

  11. 76 FR 72680 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-25

    ... National Oceanic and Atmospheric Administration RIN 0648-XA078 Marine Mammals AGENCY: National Marine.... Environmental Research and Services, Fairbanks, AK, to conduct research on marine mammals in Alaska. ADDRESSES... authority of the Marine Mammal Protection Act of 1972, as amended (16 U.S.C. 1361 et seq.), the regulations...

  12. 76 FR 75524 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-02

    ... National Oceanic and Atmospheric Administration RIN 0648-XO45 Marine Mammals AGENCY: National Marine... conduct research on marine mammals. ADDRESSES: The application and related documents are available for... under the authority of the Marine Mammal Protection Act of 1972, as amended (16 U.S.C. 1361 et seq...

  13. 75 FR 77616 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-13

    ... National Oceanic and Atmospheric Administration RIN 0648-XP18 Marine Mammals AGENCY: National Marine... Marine Mammal Protection Act of 1972, as amended (16 U.S.C. 1361 et seq.), the regulations governing the taking and importing of marine mammals (50 CFR part 216), the Endangered Species Act of 1973, as amended...

  14. 77 FR 9627 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-17

    ... National Oceanic and Atmospheric Administration RIN 0648-XB005 Marine Mammals AGENCY: National Marine.../2\\ W. 4th Avenue, Olympia, WA 98501, has applied in due form for a permit to take marine mammals in... subject permit is requested under the authority of the Marine Mammal Protection Act of 1972, as amended...

  15. The changing fates of the world's mammals

    PubMed Central

    Hoffmann, Michael; Belant, Jerrold L.; Chanson, Janice S.; Cox, Neil A.; Lamoreux, John; Rodrigues, Ana S. L.; Schipper, Jan; Stuart, Simon N.

    2011-01-01

    A recent complete assessment of the conservation status of 5487 mammal species demonstrated that at least one-fifth are at risk of extinction in the wild. We retrospectively identified genuine changes in extinction risk for mammals between 1996 and 2008 to calculate changes in the International Union for Conservation of Nature (IUCN) Red List Index (RLI). Species-level trends in the conservation status of mammalian diversity reveal that extinction risk in large-bodied species is increasing, and that the rate of deterioration has been most accelerated in the Indomalayan and Australasian realms. Expanding agriculture and hunting have been the main drivers of increased extinction risk in mammals. Site-based protection and management, legislation, and captive-breeding and reintroduction programmes have led to improvements in 24 species. We contextualize these changes, and explain why both deteriorations and improvements may be under-reported. Although this study highlights where conservation actions are leading to improvements, it fails to account for instances where conservation has prevented further deteriorations in the status of the world's mammals. The continued utility of the RLI is dependent on sustained investment to ensure repeated assessments of mammals over time and to facilitate future calculations of the RLI and measurement against global targets. PMID:21844039

  16. Ectoparasites of African Mammals.

    DTIC Science & Technology

    1976-11-30

    This study consisted of ectoparasites from approximately 100,000 African small mammals, representing probably more than 500 species of which many are...study of ectoparasites may provide information concerning interactions among animal reservoirs of disease, and (3) an understanding of ecological...parameters for ectoparasites and their hosts may enhance understanding of epidemiological patterns. Of the four major groups dealt with, considerably more

  17. [Control of harmful mammals].

    PubMed

    van Eerdenburg, F J; Bouw, J; Zwart, P

    1987-07-15

    In the Netherlands, several millions of injurious small mammals are killed yearly. This concerns not only mice and rats but also moles, musk-rats and several other species of rodent. At the request of the Netherlands Society for the Protection of Animals, studies were done on the methods in killing these animals, the effectiveness of these methods and the possibilities of reducing the harm done to the animals. The most important results of these investigations are reported in the present paper.

  18. The genus Nonomuraea: A review of a rare actinomycete taxon for novel metabolites.

    PubMed

    Sungthong, Rungroch; Nakaew, Nareeluk

    2015-05-01

    The genus Nonomuraea is a rare actinomycete taxon with a long taxonomic history, while its generic description was recently emended. The genus is less known among the rare actinomycete genera as its taxonomic position was revised several times. It can be found in diverse ecological niches, while most of its member species were isolated from soil samples. However, new trends to discover the genus in other habitats are increasing. Generic abundance of the genus was found to be dependent on geographical changes. Novel sources together with selective and invented isolation techniques might increase a chance to explore the genus and its novel candidates. Interestingly, some of its members have been revealed as a valuable source of novel metabolites for medical and industrial purposes. Broad-range of potent bioactive compounds including antimicrobial, anticancer, and antipsychotic substances, broad-spectrum antibiotics and biocatalysts can be synthesized by the genus. In order to investigate biosynthetic pathways of the bioactive compounds and self-resistant mechanisms to these compounds, the links from genes to metabolites have yet been needed for further discovery and biotechnological development of the genus Nonomuraea. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. A Chinese triconodont mammal and mosaic evolution of the mammalian skeleton.

    PubMed

    Ji, Q; Luo, Z X; Ji, S A; Luo, Z

    1999-03-25

    Here we describe a new triconodont mammal from the Late Jurassic/Early Cretaceous period of Liaoning, China. This new mammal is represented by the best-preserved skeleton known so far for triconodonts which form one of the earliest Mesozoic mammalian groups with high diversity. The postcranial skeleton of this new triconodont shows a mosaic of characters, including a primitive pelvic girdle and hindlimb but a very derived pectoral girdle that is closely comparable to those of derived therians. Given the basal position of this taxon in mammalian phylogeny, its derived pectoral girdle indicates that homoplasies (similarities resulting from independent evolution among unrelated lineages) are as common in the postcranial skeleton as they are in the skull and dentition in the evolution of Mesozoic mammals. Limb structures of the new triconodont indicate that it was probably a ground-dwelling animal.

  20. Post-Jurassic mammal-like reptile from the Palaeocene.

    PubMed

    Fox, R C; Youzwyshyn, G P; Krause, D W

    1992-07-16

    Mammal-like reptiles of the order Therapsida document the emergence of mammals from more primitive synapsids and are of unique zoological and palaeontological interest on that account. Therapsids, first appearing in the Early Permian, were thought to become extinct in the Middle Jurassic, soon after the Late Triassic origin of mammals. Here, however, we report the discovery of a therapsid from the late Palaeocene, 100 million years younger than the youngest previous occurrence of the order. This discovery nearly doubles the stratigraphic range of therapsids and furnishes their first record from the Cenozoic. The documenting fossils, an incomplete dentary containing three teeth, and four isolated teeth from other, conspecific individuals (Fig. 1), are from the Paskapoo Formation, at Cochrane, Alberta, Canada, from beds yielding a diverse mammalian fauna of early Tiffanian age. These specimens are catalogued in the collections of the University of Alberta Laboratory for Vertebrate Paleontology (UALVP) and provide the basis for a new taxon, as named and described below: (see text)

  1. Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals.

    PubMed

    Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; King, Sarah R B; Di Marco, Moreno; Rondinini, Carlo; Boitani, Luigi

    2017-07-18

    Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation.

  2. Multiple ecological pathways to extinction in mammals

    PubMed Central

    Davidson, Ana D.; Hamilton, Marcus J.; Boyer, Alison G.; Brown, James H.; Ceballos, Gerardo

    2009-01-01

    As human population and resource demands continue to grow, biodiversity conservation has never been more critical. About one-quarter of all mammals are in danger of extinction, and more than half of all mammal populations are in decline. A major priority for conservation science is to understand the ecological traits that predict extinction risk and the interactions among those predictors that make certain species more vulnerable than others. Here, using a new database of nearly 4,500 mammal species, we use decision-tree models to quantify the multiple interacting factors associated with extinction risk. We show that the correlates of extinction risk vary widely across mammals and that there are unique pathways to extinction for species with different lifestyles and combinations of traits. We find that risk is relative and that all kinds of mammals, across all body sizes, can be at risk depending on their specific ecologies. Our results increase the understanding of extinction processes, generate simple rules of thumb that identify species at greatest risk, and highlight the potential of decision-tree analyses to inform conservation efforts. PMID:19528635

  3. Phylogenetic correlates of extinction risk in mammals: species in older lineages are not at greater risk.

    PubMed

    Verde Arregoitia, Luis Darcy; Blomberg, Simon P; Fisher, Diana O

    2013-08-22

    Phylogenetic information is becoming a recognized basis for evaluating conservation priorities, but associations between extinction risk and properties of a phylogeny such as diversification rates and phylogenetic lineage ages remain unclear. Limited taxon-specific analyses suggest that species in older lineages are at greater risk. We calculate quantitative properties of the mammalian phylogeny and model extinction risk as an ordinal index based on International Union for Conservation of Nature Red List categories. We test for associations between lineage age, clade size, evolutionary distinctiveness and extinction risk for 3308 species of terrestrial mammals. We show no significant global or regional associations, and three significant relationships within taxonomic groups. Extinction risk increases for evolutionarily distinctive primates and decreases with lineage age when lemurs are excluded. Lagomorph species (rabbits, hares and pikas) that have more close relatives are less threatened. We examine the relationship between net diversification rates and extinction risk for 173 genera and find no pattern. We conclude that despite being under-represented in the frequency distribution of lineage ages, species in older, slower evolving and distinct lineages are not more threatened or extinction-prone. Their extinction, however, would represent a disproportionate loss of unique evolutionary history.

  4. "Social Anxiety Disorder Carved at its Joints": evidence for the taxonicity of social anxiety disorder.

    PubMed

    Weeks, Justin W; Carleton, R Nicholas; Asmundson, Gordon J G; McCabe, Randi E; Antony, Martin M

    2010-10-01

    Previous findings suggest that social anxiety disorder may be best characterized as having a dimensional latent structure (Kollman et al., 2006; Weeks et al., 2009). We attempted to extend previous taxometric investigations of social anxiety by examining the latent structure of social anxiety disorder symptoms in a large sample comprised of social anxiety disorder patients (i.e., putative taxon members) and community residents/undergraduate respondents (i.e., putative complement class members). MAXEIG and MAMBAC were performed with indicator sets drawn from a self-report measure of social anxiety symptoms, the Social Interaction Phobia Scale (Carleton et al., 2009). MAXEIG and MAMBAC analyses, as well as comparison analyses utilizing simulated taxonic and dimensional datasets, yielded converging evidence that social anxiety disorder has a taxonic latent structure. Moreover, 100% of the confirmed social anxiety disorder patients in our overall sample were correctly assigned to the identified taxon class, providing strong support for the external validity of the identified taxon; and k-means cluster analysis results corroborated our taxometric base-rate estimates. Implications regarding the conceptualization, diagnosis, and assessment of social anxiety disorder are discussed.

  5. Large-brained mammals live longer.

    PubMed

    González-Lagos, C; Sol, D; Reader, S M

    2010-05-01

    Many mammals have brains substantially larger than expected for their body size, but the reasons for this remain ambiguous. Enlarged brains are metabolically expensive and require elongated developmental periods, and so natural selection should have favoured their evolution only if they provide counterbalancing advantages. One possible advantage is facilitating the construction of behavioural responses to unusual, novel or complex socio-ecological challenges. This buffer effect should increase survival rates and favour a longer reproductive life, thereby compensating for the costs of delayed reproduction. Here, using a global database of 493 species, we provide evidence showing that mammals with enlarged brains (relative to their body size) live longer and have a longer reproductive lifespan. Our analysis supports and extends previous findings, accounting for the possible confounding effects of other life history traits, ecological and dietary factors, and phylogenetic autocorrelation. Thus, these findings provide support for the hypothesis that mammals counterbalance the costs of affording large brains with a longer reproductive life.

  6. 75 FR 10216 - Marine Mammals; File No. 358-1787

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-05

    ...: 2010-4683] DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XR83 Marine Mammals; File No. 358-1787 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... taking and importing of marine mammals (50 CFR part 216). The amended permit allows an increase in the...

  7. Spatial scale and cross-taxon congruence of terrestrial vertebrate and vascular plant species richness in China.

    PubMed

    Qian, Hong; Kissling, W Daniel

    2010-04-01

    In ecology and biogeography it is often recognized that the species richness of different groups of organisms is spatially congruent (and thus positively correlated). However, ecological phenomena are often scale dependent and can change with spatial scale (i.e., grain size and extent). Because species richness gradients are also correlated with environmental gradients and plant species richness is thought to influence animal species richness, the relative roles of environment and plant richness in influencing cross-taxon congruence of animal richness at different spatial scales remain poorly explored. In this study, we examine the spatial concordance in species richness among terrestrial vertebrates and vascular plants at two spatial grain sizes (local and regional) across China. We hypothesize that (H1) cross-taxon richness relationships are weaker at the local scale; (H2) climatic predictors of species richness are stronger at the regional scale; (H3) effects of habitat heterogeneity on species richness are stronger at the local scale; (H4) plant richness positively affects vertebrate richness after accounting for environmental effects; and (H5) the plant-vertebrate richness relationship is weaker at the regional scale. We found significant and positive correlations between species richness of the groups, with correlations being stronger at the regional scale than at the local scale (supporting H1). Climate has weaker effects on species richness at the regional scale than at the local scale (rejecting H2), and for vertebrates (but not for plants) effects of habitat heterogeneity are stronger at the local scale (supporting hypothesis H3). Plant richness positively affects vertebrate richness after accounting for environmental effects (supporting H4), but the effect is stronger for the two endothermic groups (mammals and birds) than for the two ectothermic groups (reptiles and amphibians). In contrast to hypothesis H5, the effect of plant richness on species

  8. Dosage Compensation in Mammals

    PubMed Central

    Brockdorff, Neil; Turner, Bryan M.

    2015-01-01

    Many organisms show major chromosomal differences between sexes. In mammals, females have two copies of a large, gene-rich chromosome, the X, whereas males have one X and a small, gene-poor Y. The imbalance in expression of several hundred genes is lethal if not dealt with by dosage compensation. The male–female difference is addressed by silencing of genes on one female X early in development. However, both males and females now have only one active X chromosome. This is compensated by twofold up-regulation of genes on the active X. This complex system continues to provide important insights into mechanisms of epigenetic regulation. PMID:25731764

  9. Knowledge Management in Taxonomy and Biostratigraphy using TaxonConcept Software

    NASA Astrophysics Data System (ADS)

    Klump, J.; Huber, R.; Goetz, S.

    2005-12-01

    The use of fossils to constrain age models for geological samples is not as straightforward as it might seem. Even though index fossils have been defined as biostratigraphic time markers ambiguity arises from the synonymous use of taxonomic names. Progress in our understanding of the origin of certain species have sometimes lead to substantial changes in the taxonomic classification of these organisms. TaxonConcept was created as part of the Stratigraphy.net initiative as a tool to manage taxonomic information and complex knowledge networks to help resolve taxonomic ambiguities in biostratigraphy. Its workflow is based on the principles of open nomenclature. Open nomenclature allows researchers to comment on the identification of a specimen which cannot exactly be determined and is frequently used in synonymy lists. The use of such synonymy lists in TaxonConcept allows to work with taxonomic classifications that are uncertain, or where several versions exist. Every single taxonomic entity in TaxonConcept is recorded with its relevant citations in the literature. This allows to manage information on taxonomy. The members of working groups using TaxonConcept can record their opinion on the taxonomic classification of each taxon in the framework of open nomenclature and annotate it in free text. This managed and structured collection of taxonomic opinions is an example of knowledge management. Taxonomic opinions are otherwise dispersed throughout the literature, if recorded at all, and are only available to the specialist. Assembled as a collection, they represent our knowledge on the taxonomy of a certain group of organisms. In the terminology of computer science, the semantic relationships between taxonomic terms are an ontology. Open nomenclature offers a formal framework that lends itself very well to describe the nature of the relations between taxonomic terms. The use of such synonymy lists in a taxonomic information system allows interesting search options

  10. Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection.

    PubMed

    Wang, Huai-Chun; Susko, Edward; Roger, Andrew J

    2016-12-01

    Assessing the robustness of an inferred phylogeny is an important element of phylogenetics. This is typically done with measures of stabilities at the internal branches and the variation of the positions of the leaf nodes. The bootstrap support for branches in maximum parsimony, distance and maximum likelihood estimation, or posterior probabilities in Bayesian inference, measure the uncertainty about a branch due to the sampling of the sites from genes or sampling genes from genomes. However, these measures do not reveal how taxon sampling affects branch support and the effects of taxon sampling on the estimated phylogeny. An internal branch in a phylogenetic tree can be viewed as a split that separates the taxa into two nonempty complementary subsets. We develop several split-specific measures of stability determined from bootstrap support for quartets. These include BPtaxon_split (average bootstrap percentage [BP] for all quartets involving a taxon within a split), BPsplit (BPtaxon_split averaged over taxa), BPtaxon (BPtaxon_split averaged over splits) and RBIC-taxon (average BP over all splits after removing a taxon). We also develop a pruned-tree distance metric. Application of our measures to empirical and simulated data illustrate that existing measures of overall stability can fail to detect taxa that are the primary source of a split-specific instability. Moreover, we show that the use of many reduced sets of quartets is important in being able to detect the influence of joint sets of taxa rather than individual taxa. These new measures are valuable diagnostic tools to guide taxon sampling in phylogenetic experimental design. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Physiological Monitoring in Diving Mammals

    DTIC Science & Technology

    2015-09-30

    825-2025 email: andreas.fahlman@tamucc.edu Peter L. Tyack School of Biology Sea Mammal Research Unit Scottish Oceans Institute...OBJECTIVES This project is separated into three aims: Aim 1: Develop a new generation of tags/data logger for marine mammals that will...contain a sensor to be implanted into the muscle. The logger will collect physiological data from muscle tissue in freely diving marine mammals. The

  12. Unraveling the sequence information in COI barcode to achieve higher taxon assignment based on Indian freshwater fishes.

    PubMed

    Chakraborty, Mohua; Ghosh, Sankar Kumar

    2015-04-01

    Efficacy of cytochrome c oxidase subunit I (COI) DNA barcode in higher taxon assignment is still under debate in spite of several attempts, using the conventional DNA barcoding methods, to assign higher taxa. Here we try to understand whether nucleotide and amino acid sequence in COI gene carry sufficient information to assign species to their higher taxonomic rank, using 160 species of Indian freshwater fishes. Our results reveal that with increase in the taxonomic rank, sequence conservation decreases for both nucleotides and amino acids. Order level exhibits lowest conservation with 50% of the nucleotides and amino acids being conserved. Among the variable sites, 30-50% were found to carry high information content within an order, while it was 70-80% within a family and 80-99% within a genus. High information content shows sites with almost conserved sequence but varying at one or two locations, which can be due to variations at species or population level. Thus, the potential of COI gene in higher taxon assignment is revealed with validation of ample inherent signals latent in the gene.

  13. The maximum rate of mammal evolution.

    PubMed

    Evans, Alistair R; Jones, David; Boyer, Alison G; Brown, James H; Costa, Daniel P; Ernest, S K Morgan; Fitzgerald, Erich M G; Fortelius, Mikael; Gittleman, John L; Hamilton, Marcus J; Harding, Larisa E; Lintulaakso, Kari; Lyons, S Kathleen; Okie, Jordan G; Saarinen, Juha J; Sibly, Richard M; Smith, Felisa A; Stephens, Patrick R; Theodor, Jessica M; Uhen, Mark D

    2012-03-13

    How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.

  14. The maximum rate of mammal evolution

    NASA Astrophysics Data System (ADS)

    Evans, Alistair R.; Jones, David; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Fitzgerald, Erich M. G.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Okie, Jordan G.; Saarinen, Juha J.; Sibly, Richard M.; Smith, Felisa A.; Stephens, Patrick R.; Theodor, Jessica M.; Uhen, Mark D.

    2012-03-01

    How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.

  15. Global Warming Will Bring New Fungal Diseases for Mammals

    PubMed Central

    Garcia-Solache, Monica A.; Casadevall, Arturo

    2010-01-01

    ABSTRACT Fungi are major pathogens of plants, other fungi, rotifers, insects, and amphibians, but relatively few cause disease in mammals. Fungi became important human pathogens only in the late 20th century, primarily in hosts with impaired immunity as a consequence of medical interventions or HIV infection. The relatively high resistance of mammals has been attributed to a combination of a complex immune system and endothermy. Mammals maintain high body temperatures relative to environmental temperatures, creating a thermally restrictive ambient for the majority of fungi. According to this view, protection given by endothermy requires a temperature gradient between those of mammals and the environment. We hypothesize that global warming will increase the prevalence of fungal diseases in mammals by two mechanisms: (i) increasing the geographic range of currently pathogenic species and (ii) selecting for adaptive thermotolerance for species with significant pathogenic potential but currently not pathogenic by virtue of being restricted by mammalian temperatures. PMID:20689745

  16. Heterothermy in large mammals: inevitable or implemented?

    PubMed

    Hetem, Robyn S; Maloney, Shane K; Fuller, Andrea; Mitchell, Duncan

    2016-02-01

    Advances in biologging techniques over the past 20 years have allowed for the remote and continuous measurement of body temperatures in free-living mammals. While there is an abundance of literature on heterothermy in small mammals, fewer studies have investigated the daily variability of body core temperature in larger mammals. Here we review measures of heterothermy and the factors that influence heterothermy in large mammals in their natural habitats, focussing on large mammalian herbivores. The mean 24 h body core temperatures for 17 species of large mammalian herbivores (>10 kg) decreased by ∼1.3°C for each 10-fold increase in body mass, a relationship that remained significant following phylogenetic correction. The degree of heterothermy, as measured by the 24 h amplitude of body core temperature rhythm, was independent of body mass and appeared to be driven primarily by energy and water limitations. When faced with the competing demands of osmoregulation, energy acquisition and water or energy use for thermoregulation, large mammalian herbivores appear to relax the precision of thermoregulation thereby conserving body water and energy. Such relaxation may entail a cost in that an animal moves closer to its thermal limits for performance. Maintaining homeostasis requires trade-offs between regulated systems, and homeothermy apparently is not accorded the highest priority; large mammals are able to maintain optimal homeothermy only if they are well nourished, hydrated, and not compromised energetically. We propose that the amplitude of the 24 h rhythm of body core temperature provides a useful index of any compromise experienced by a free-living large mammal and may predict the performance and fitness of an animal. © 2014 Cambridge Philosophical Society.

  17. Global mammal distributions, biodiversity hotspots, and conservation

    PubMed Central

    Ceballos, Gerardo; Ehrlich, Paul R.

    2006-01-01

    Hotspots, which have played a central role in the selection of sites for reserves, require careful rethinking. We carried out a global examination of distributions of all nonmarine mammals to determine patterns of species richness, endemism, and endangerment, and to evaluate the degree of congruence among hotspots of these three measures of diversity in mammals. We then compare congruence of hotspots in two animal groups (mammals and birds) to assess the generality of these patterns. We defined hotspots as the richest 2.5% of cells in a global equal-area grid comparable to 1° latitude × 1° longitude. Hotspots of species richness, “endemism,” and extinction threat were noncongruent. Only 1% of cells and 16% of species were common to the three types of mammalian hotspots. Congruence increased with increases in both the geographic scope of the analysis and the percentage of cells defined as being hotspots. The within-mammal hotspot noncongruence was similar to the pattern recently found for birds. Thus, assigning global conservation priorities based on hotspots is at best a limited strategy. PMID:17164331

  18. Global mammal distributions, biodiversity hotspots, and conservation.

    PubMed

    Ceballos, Gerardo; Ehrlich, Paul R

    2006-12-19

    Hotspots, which have played a central role in the selection of sites for reserves, require careful rethinking. We carried out a global examination of distributions of all nonmarine mammals to determine patterns of species richness, endemism, and endangerment, and to evaluate the degree of congruence among hotspots of these three measures of diversity in mammals. We then compare congruence of hotspots in two animal groups (mammals and birds) to assess the generality of these patterns. We defined hotspots as the richest 2.5% of cells in a global equal-area grid comparable to 1 degrees latitude x 1 degrees longitude. Hotspots of species richness, "endemism," and extinction threat were noncongruent. Only 1% of cells and 16% of species were common to the three types of mammalian hotspots. Congruence increased with increases in both the geographic scope of the analysis and the percentage of cells defined as being hotspots. The within-mammal hotspot noncongruence was similar to the pattern recently found for birds. Thus, assigning global conservation priorities based on hotspots is at best a limited strategy.

  19. Genetic engineering of mammals.

    PubMed

    Wells, Kevin D

    2016-01-01

    Historically, genetic engineering for mammalian reproductive questions has been accomplished primarily in the mouse. However, all the genetic manipulations that can be done in the mouse can now be accomplished in most domesticated mammals. Random integration of transgenes, homologous recombination and gene editing are now routine for several mammalian species. For livestock, queries related to fertility can be asked directly for the species in question, without a need for a mouse model. For human clinical concerns, the most appropriate model should be selected based on physiology, anatomy, or even size. The mouse will continue to be a useful genetically engineered model. However, other species are now amenable to the full range of genetic manipulations and should be considered as possible models for human conditions when appropriate.

  20. Vacuoles in mammals

    PubMed Central

    2013-01-01

    A vacuole is a membrane-bound subcellular structure involved in intracellular digestion. Instead of the large “vacuolar” organelles that are found in plants and fungi, animal cells possess lysosomes that are smaller in size and are enriched with hydrolytic enzymes similar to those found in the vacuoles. Large vacuolar structures are often observed in highly differentiated mammalian tissues such as embryonic visceral endoderm and absorbing epithelium. Vacuoles/lysosomes share a conserved mechanism of biogenesis, and they are at the terminal of the endocytic pathways, Recent genetic studies of the mammalian orthologs of Vam/Vps genes, which have essential functions for vacuole assembly, revealed that the dynamics of vacuoles/lysosomes are important for tissue differentiation and patterning through regulation of various molecular signaling events in mammals. PMID:23572040

  1. DNA Methylation in Mammals

    PubMed Central

    Li, En; Zhang, Yi

    2014-01-01

    DNA methylation is one of the best characterized epigenetic modifications. In mammals it is involved in various biological processes including the silencing of transposable elements, regulation of gene expression, genomic imprinting, and X-chromosome inactivation. This article describes how DNA methylation serves as a cellular memory system and how it is dynamically regulated through the action of the DNA methyltransferase (DNMT) and ten eleven translocation (TET) enzymes. Its role in the regulation of gene expression, through its interplay with histone modifications, is also described, and its implication in human diseases discussed. The exciting areas of investigation that will likely become the focus of research in the coming years are outlined in the summary. PMID:24789823

  2. Genomic Imprinting in Mammals

    PubMed Central

    Barlow, Denise P.

    2014-01-01

    Genomic imprinting affects a subset of genes in mammals and results in a monoallelic, parental-specific expression pattern. Most of these genes are located in clusters that are regulated through the use of insulators or long noncoding RNAs (lncRNAs). To distinguish the parental alleles, imprinted genes are epigenetically marked in gametes at imprinting control elements through the use of DNA methylation at the very least. Imprinted gene expression is subsequently conferred through lncRNAs, histone modifications, insulators, and higher-order chromatin structure. Such imprints are maintained after fertilization through these mechanisms despite extensive reprogramming of the mammalian genome. Genomic imprinting is an excellent model for understanding mammalian epigenetic regulation. PMID:24492710

  3. 75 FR 27294 - Proposed Information Collection; Comment Request; Marine Mammal Stranding Report/Marine Mammal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... Mammal Stranding Report/Marine Mammal Rehabilitation Disposition Report AGENCY: National Oceanic and... mammal stranding report provides information on strandings so that the National Marine Fisheries Service... facilities. This information is submitted primarily by volunteer members of the marine mammal...

  4. 76 FR 25308 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-04

    ... National Oceanic and Atmospheric Administration RIN 0648-XA165 Marine Mammals AGENCY: National Marine... Anchorage, Biology Department, 3101 Science Circle, Anchorage, AK, has been issued a permit to conduct ] scientific research on marine mammal parts. ADDRESSES: The permit and related documents are available...

  5. Dimensionality vs Taxonicity of Schizotypy: Some New Data and Challenges Ahead

    PubMed Central

    Everett, Kirsty V.; Linscott, Richard J.

    2015-01-01

    Heterogeneity in the expression of schizotypy may arise from underlying dimensional processes or a taxonic population structure. In a 2-phase study, we tested the taxonicity of self-reported schizotypy within a general psychiatric sample (n = 109) and examined taxon validity by testing its association with clinical schizotaxia in follow-up subsamples. Taxometric analyses indicated a taxonic structure (schizotypy prevalence = 38.8%) provided the best description of the underlying population distribution. After a year, schizotypal (n = 14) and nonschizotypal (n = 14) subsamples returned for diagnosis of clinical schizotaxia by assessment of executive functioning, attention, memory, and negative symptoms. Seven patients met diagnostic criteria, all members of the schizotypy class. Schizotypy was associated with impaired attention and memory, more negative symptoms, poorer global functioning, and more extensive psychiatric histories. We reconcile inconsistencies in the literature by discussing threats to the validity of this and similar research on Meehl’s taxonomic model of schizotypy, including conceptual limitations of the lexical hypothesis and conventions of factor analysis. Scrutiny of Meehl’s model should involve disambiguation and better measurement of the schizotaxia-schizotypy phenotype. PMID:25810059

  6. Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island

    Treesearch

    Benjamin D. Cook; Catherine M. Pringle; Jane M. Hughes

    2008-01-01

    Taxon cycling, i.e. sequential phases of expansions and contractions in species’ distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae:...

  7. Psychopathy as a Taxon: Evidence That Psychopaths Are a Discrete Class.

    ERIC Educational Resources Information Center

    Harris, Grant T.; And Others

    1994-01-01

    Applied taxometric analyses to construct of psychopathy (as measured by Psychopathy Checklist) and to several variables reflecting antisocial childhood, adult criminality, and criminal recidivism. Findings from 653 serious offenders assessed or treated in maximum-security institution supported existence of taxon underlying psychopathy. Childhood…

  8. Psychopathy as a Taxon: Evidence That Psychopaths Are a Discrete Class.

    ERIC Educational Resources Information Center

    Harris, Grant T.; And Others

    1994-01-01

    Applied taxometric analyses to construct of psychopathy (as measured by Psychopathy Checklist) and to several variables reflecting antisocial childhood, adult criminality, and criminal recidivism. Findings from 653 serious offenders assessed or treated in maximum-security institution supported existence of taxon underlying psychopathy. Childhood…

  9. Road zone effects in small-mammal communities

    USGS Publications Warehouse

    Bissonette, J.A.; Rosa, S.A.

    2009-01-01

    Our study focused on the putative effects of roads on small-mammal communities in a high desert region of southern Utah. Specifically, we tested whether or not roads create adjacent zones characterized by lower small- mammal densities, abundance, and diversity. We sampled abundance of small mammals at increasing distances from Interstate 15 during two summers. We recorded 11 genera and 13 species. We detected no clear abundance, density, or diversity effects relative to distance from the road. Only two of 13 species were never captured near roads. The abundance of the remaining 11 small mammal species was either similar at different distances from the road or higher closer to the road. We conclude that although roads may act as barriers and possible sources of mortality, adjacent zones of vegetation often provide favorable microhabitat in the desert landscape for many small mammals. ?? 2009 by the author(s).

  10. Predicting above-ground density and distribution of small mammal prey species at large spatial scales

    Treesearch

    Lucretia E. Olson; John R. Squires; Robert J. Oakleaf; Zachary P. Wallace; Patricia L. Kennedy

    2017-01-01

    Grassland and shrub-steppe ecosystems are increasingly threatened by anthropogenic activities. Loss of native habitats may negatively impact important small mammal prey species. Little information, however, is available on the impact of habitat variability on density of small mammal prey species at broad spatial scales. We examined the relationship between small mammal...

  11. A new eutriconodont mammal and evolutionary development in early mammals.

    PubMed

    Luo, Zhe-Xi; Chen, Peiji; Li, Gang; Chen, Meng

    2007-03-15

    Detachment of the three tiny middle ear bones from the reptilian mandible is an important innovation of modern mammals. Here we describe a Mesozoic eutriconodont nested within crown mammals that clearly illustrates this transition: the middle ear bones are connected to the mandible via an ossified Meckel's cartilage. The connected ear and jaw structure is similar to the embryonic pattern in modern monotremes (egg-laying mammals) and placental mammals, but is a paedomorphic feature retained in the adult, unlike in monotreme and placental adults. This suggests that reversal to (or retention of) this premammalian ancestral condition is correlated with different developmental timing (heterochrony) in eutriconodonts. This new eutriconodont adds to the evidence of homoplasy of vertebral characters in the thoraco-lumbar transition and unfused lumbar ribs among early mammals. This is similar to the effect of homeobox gene patterning of vertebrae in modern mammals, making it plausible to extrapolate the effects of Hox gene patterning to account for homoplastic evolution of vertebral characters in early mammals.

  12. SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage

    PubMed Central

    Freyman, William A.

    2015-01-01

    The amount of phylogenetically informative sequence data in GenBank is growing at an exponential rate, and large phylogenetic trees are increasingly used in research. Tools are needed to construct phylogenetic sequence matrices from GenBank data and evaluate the effect of missing data. Supermatrix Constructor (SUMAC) is a tool to data-mine GenBank, construct phylogenetic supermatrices, and assess the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. SUMAC calculates a novel metric, Missing Sequence Decisiveness Scores (MSDS), which measures how much each individual missing sequence contributes to the decisiveness of the matrix. MSDS can be used to compare supermatrices and prioritize the acquisition of new sequence data. SUMAC constructs supermatrices either through an exploratory clustering of all GenBank sequences within a taxonomic group or by using guide sequences to build homologous clusters in a more targeted manner. SUMAC assembles supermatrices for any taxonomic group recognized in GenBank and is optimized to run on multicore computer systems by parallelizing multiple stages of operation. SUMAC is implemented as a Python package that can run as a stand-alone command-line program, or its modules and objects can be incorporated within other programs. SUMAC is released under the open source GPLv3 license and is available at https://github.com/wf8/sumac. PMID:26648681

  13. Protection of mammal diversity in Central America

    USGS Publications Warehouse

    Jenkins, Clinton N.; Giri, Chandra

    2008-01-01

    Central America is exceptionally rich in biodiversity, but varies widely in the attention its countries devote to conservation. Protected areas, widely considered the cornerstone of conservation, were not always created with the intent of conserving that biodiversity. We assessed how well the protected-area system of Central America includes the region's mammal diversity. This first required a refinement of existing range maps to reduce their extensive errors of commission (i.e., predicted presences in places where species do not occur). For this refinement, we used the ecological limits of each species to identify and remove unsuitable areas from the range. We then compared these maps with the locations of protected areas to measure the habitat protected for each of the region's 250 endemic mammals. The species most vulnerable to extinction—those with small ranges—were largely outside protected areas. Nevertheless, the most strictly protected areas tended toward areas with many small-ranged species. To improve the protection coverage of mammal diversity in the region, we identified a set of priority sites that would best complement the existing protected areas. Protecting these new sites would require a relatively small increase in the total area protected, but could greatly enhance mammal conservation.

  14. 50 CFR 216.25 - Exempted marine mammals and marine mammal products.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Exempted marine mammals and marine mammal... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS General Exceptions § 216.25 Exempted marine mammals and marine mammal...

  15. 50 CFR 216.25 - Exempted marine mammals and marine mammal products.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Exempted marine mammals and marine mammal... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS General Exceptions § 216.25 Exempted marine mammals and marine mammal...

  16. 50 CFR 216.25 - Exempted marine mammals and marine mammal products.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 10 2012-10-01 2012-10-01 false Exempted marine mammals and marine mammal... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS General Exceptions § 216.25 Exempted marine mammals and marine mammal...

  17. 50 CFR 216.25 - Exempted marine mammals and marine mammal products.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 10 2013-10-01 2013-10-01 false Exempted marine mammals and marine mammal... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS General Exceptions § 216.25 Exempted marine mammals and marine mammal...

  18. 50 CFR 216.25 - Exempted marine mammals and marine mammal products.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Exempted marine mammals and marine mammal... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS General Exceptions § 216.25 Exempted marine mammals and marine mammal...

  19. Species Richness Responses to Structural or Compositional Habitat Diversity between and within Grassland Patches: A Multi-Taxon Approach

    PubMed Central

    Lengyel, Szabolcs; Déri, Eszter; Magura, Tibor

    2016-01-01

    Habitat diversity (spatial heterogeneity within and between habitat patches in a landscape, HD) is often invoked as a driver of species diversity at small spatial scales. However, the effect of HD on species richness (SR) of multiple taxa is not well understood. We quantified HD and SR in a wet-dry gradient of open grassland habitats in Hortobágy National Park (E-Hungary) and tested the effect of compositional and structural factors of HD on SR of flowering plants, orthopterans, true bugs, spiders, ground beetles and birds. Our dataset on 434 grassland species (170 plants, 264 animals) showed that the wet-dry gradient (compositional HD at the between-patch scale) was primarily related to SR in orthopterans, ground-dwelling arthropods, and all animals combined. The patchiness, or plant association richness, of the vegetation (compositional HD at the within-patch scale) was related to SR of vegetation-dwelling arthropods, whereas vegetation height (structural HD at the within-patch scale) was related to SR of ground-dwelling arthropods and birds. Patch area was related to SR only in birds, whereas management (grazing, mowing, none) was related to SR of plants and true bugs. All relationships between HD and SR were positive, indicating increasing SR with increasing HD. However, total SR was not related to HD because different taxa showed similar positive responses to different HD variables. Our findings, therefore, show that even though HD positively influences SR in a wide range of grassland taxa, each taxon responds to different compositional or structural measures of HD, resulting in the lack of a consistent relationship between HD and SR when taxon responses are pooled. The idiosyncratic responses shown here exemplify the difficulties in detecting general HD-SR relationships over multiple taxa. Our results also suggest that management and restoration aimed specifically to sustain or increase the diversity of habitats are required to conserve biodiversity in

  20. Species Richness Responses to Structural or Compositional Habitat Diversity between and within Grassland Patches: A Multi-Taxon Approach.

    PubMed

    Lengyel, Szabolcs; Déri, Eszter; Magura, Tibor

    2016-01-01

    Habitat diversity (spatial heterogeneity within and between habitat patches in a landscape, HD) is often invoked as a driver of species diversity at small spatial scales. However, the effect of HD on species richness (SR) of multiple taxa is not well understood. We quantified HD and SR in a wet-dry gradient of open grassland habitats in Hortobágy National Park (E-Hungary) and tested the effect of compositional and structural factors of HD on SR of flowering plants, orthopterans, true bugs, spiders, ground beetles and birds. Our dataset on 434 grassland species (170 plants, 264 animals) showed that the wet-dry gradient (compositional HD at the between-patch scale) was primarily related to SR in orthopterans, ground-dwelling arthropods, and all animals combined. The patchiness, or plant association richness, of the vegetation (compositional HD at the within-patch scale) was related to SR of vegetation-dwelling arthropods, whereas vegetation height (structural HD at the within-patch scale) was related to SR of ground-dwelling arthropods and birds. Patch area was related to SR only in birds, whereas management (grazing, mowing, none) was related to SR of plants and true bugs. All relationships between HD and SR were positive, indicating increasing SR with increasing HD. However, total SR was not related to HD because different taxa showed similar positive responses to different HD variables. Our findings, therefore, show that even though HD positively influences SR in a wide range of grassland taxa, each taxon responds to different compositional or structural measures of HD, resulting in the lack of a consistent relationship between HD and SR when taxon responses are pooled. The idiosyncratic responses shown here exemplify the difficulties in detecting general HD-SR relationships over multiple taxa. Our results also suggest that management and restoration aimed specifically to sustain or increase the diversity of habitats are required to conserve biodiversity in

  1. Climate and species richness predict the phylogenetic structure of African mammal communities.

    PubMed

    Kamilar, Jason M; Beaudrot, Lydia; Reed, Kaye E

    2015-01-01

    We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.

  2. Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

    PubMed Central

    Kamilar, Jason M.; Beaudrot, Lydia; Reed, Kaye E.

    2015-01-01

    We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change. PMID:25875361

  3. Marine mammal harvests and other interactions with humans.

    PubMed

    Hovelsrud, Grete K; McKenna, Meghan; Huntington, Henry P

    2008-03-01

    The Arctic is currently undergoing rapid social and environmental changes, and while the peoples of the north have a long history of adapting, the current changes in climate pose unprecedented challenges to the marine mammal-human interactions in the Arctic regions. Arctic marine mammals have been and remain an important resource for many of the indigenous and nonindigenous people of the north. Changes in climate are likely to bring about profound changes to the environment in which these animals live and subsequently to the hunting practices and livelihoods of the people who hunt them. Climate change will lead to reduction in the sea ice extent and thickness and will likely increase shipping through the Northern Sea Route and the Northwest Passage and oil and gas activities in Arctic areas previously inaccessible. Such activities will lead to more frequent interactions between humans and marine mammals. These activities may also change the distribution of marine mammals, affecting the hunters. This paper has three parts. First, an overview of marine mammal harvesting activities in the different circumpolar regions provides a snapshot of current practices and conditions. Second, case studies of selected Arctic regions, indigenous groups, and species provide insight into the manner in which climate change is already impacting marine mammal harvesting activities in the Arctic. Third, we describe how climate change is likely to affect shipping and oil and gas exploration and production activities in the Arctic and describe the possible implications of these changes for the marine mammal populations. We conclude that many of the consequences of climate change are likely to be negative for marine mammal hunters and for marine mammals. Lack of adequate baseline data, however, makes it difficult to identify specific causal mechanisms and thus to develop appropriate conservation measures. Nonetheless, the future of Arctic marine mammals and human uses of them depends on

  4. Geographic Patterns in Intertidal Communities and Taxon Richness in Glacier Bay, Alaska: The Complex Spatial Interaction of Time since Deglaciation and Environmental Variables

    NASA Astrophysics Data System (ADS)

    Irvine, G. V.; Smeltz, T. S., Jr.

    2016-02-01

    Geographical patterns in species or taxon richness may illuminate processes producing or influencing the patterns. Historical factors such as deglaciation may leave a strong imprint on the communities that have since developed. The rapid and well-documented deglaciation of Glacier Bay, Alaska, following the Little Ice Age created an environment where rocky intertidal communities of varying ages (up to about 200 years) have developed. We used a multivariate approach to investigate the relationship of rocky intertidal community composition and richness to environmental gradients and time since deglaciation. Data for 25 rocky sites randomly selected from the entire bay was generated from sampling conducted from 1997 -2001. Is taxon richness significantly correlated with time since deglaciation? Yes. However, as might be expected from the legacy of melting glaciers in a fjord ecosystem, a number of oceanographic parameters are also highly correlated with taxon richness and community development. Which are the most important drivers of community composition throughout the bay? We investigated this using oceanographic data collected at a set of stations in Glacier Bay from 1993-2011, as well as time since deglaciation. The three physical parameters that showed the highest correlation to measures of community dissimilarity were July salinity, July sigma-t, and time since deglaciation. Principal components analysis (PCA) and bio-env analyses indicated that the oceanographic/geographic PCA component 1 was the most highly correlated with two measures of community dissimilarity. Increasing taxon richness was most positively correlated with high July salinity and position near the mouth of the bay. Cluster analyses indicated the similarity of communities at different sites, and provided further visual insight into the importance of geographical position in community development.

  5. Sex control in mammals.

    PubMed

    Bhattacharya, B C

    1958-01-01

    As a step toward control of sex of offspring in mammals, a method for separation of X- and Y-chromosome sperm, based on the differing specific gravity of the 2 types, is described. Sperm sinking to the bottom of an appropriate viscous medium are predominantly the denser X-Chromosome sperm. 99 female rabbits were inseminated with sperm that had been suspended for 24 hours in colloidial media: 38 females received sperm taken from the bottom of a dense medium, and 61 received sperm drawn from the top of a lighter medium. Only 18.2% of the does became pregnant, probably due to insufficient concentration of sperm. Offspring of 4 does impregnated with the lightest fraction were 85.7% male offspring of 7 does impregnated with the heaviest fraction were 77.3% female (vs. 48.2% normal female sex raio; p less than .05). For 7 does impregnanted with sperm taken from nearer the middle of the medium, offspring were 51.7% male.

  6. Decreased Taxon-Specific IgA Response in Relation to the Changes of Gut Microbiota Composition in the Elderly.

    PubMed

    Sugahara, Hirosuke; Okai, Shinsaku; Odamaki, Toshitaka; Wong, Chyn B; Kato, Kumiko; Mitsuyama, Eri; Xiao, Jin-Zhong; Shinkura, Reiko

    2017-01-01

    Gut microbiota is known to change with aging; however, the underlying mechanisms have not been well elucidated. Immunoglobulin A (IgA) is the dominant class of antibody secreted by the intestinal mucosa, and are thought to play a key role in the regulation of the gut microbiota. T cells regulate the magnitude and nature of microbiota-specific IgA responses. However, it is also known that T cells become senescent in elderly people. Therefore, we speculated that the age-related changes of IgA response against the gut microbiota might be one of the mechanisms causing the age-associated changes of gut microbiota composition. To prove our hypothesis, fecal samples from 40 healthy subjects (adult group: n = 20, an average of 35 years old; elderly group: n = 20, an average of 76 years old) were collected, and the gut microbiota composition and the response of IgA to gut microbiota were investigated. The relative abundance of Bifidobacteriaceae was significantly lower, whereas those of Clostridiaceae, Clostridiales;f__ and Enterobacteriaceae were significantly higher in the elderly group than in the adult group. There was no significant difference in the fecal IgA concentration between the adult and elderly groups. However, the taxon-specific IgA response to some bacterial taxa was different between the adult and elderly groups. To evaluate inter-group differences in the taxon-specific IgA response to each bacterial taxon, the IgA-indices were calculated, and the IgA-indices of Clostridiaceae and Enterobacteriaceae were found to be significantly lower in the elderly group than the adult group. In addition, Clostridiales;f__ and Enterobacteriaceae were significantly enriched in the IgA(+) fraction in the adult group but not in the elderly group, whereas Clostridiaceae was significantly enriched in the IgA(-) fraction in the elderly group but not in the adult group. Some species assigned to Clostridiaceae or Enterobacteriaceae are known to be pathogenic bacteria. Our results

  7. 77 FR 31537 - Taking and Importing Marine Mammals; Taking Marine Mammals Incidental to Coastal Commercial...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-29

    ... sight and sound of commercial fireworks. Fireworks displays are limited in duration by MBNMS... year and, as a result, marine mammals will be exposed to elevated levels of sound as well as increased... six of these species are likely to be present in the acute impact area (the area where sound, light...

  8. Inner architecture of vertebral centra in terrestrial and aquatic mammals: a two-dimensional comparative study.

    PubMed

    Dumont, Maitena; Laurin, Michel; Jacques, Florian; Pellé, Eric; Dabin, Willy; de Buffrénil, Vivian

    2013-05-01

    Inner vertebral architecture is poorly known, except in human and laboratory animals. In order to document this topic at a broad comparative level, a 2D-histomorphometric study of vertebral centra was conducted in a sample of 98 therian mammal species, spanning most of the size range and representing the main locomotor adaptations known in therian taxa. Eleven variables relative to the development and geometry of trabecular networks were extracted from CT scan mid-sagittal sections. Phylogeny-informed statistical tests were used to reveal the respective influences of phylogeny, size, and locomotion adaptations on mammalian vertebral structure. The use of random taxon reshuffling and squared change parsimony reveals that 9 of the 11 characteristics (the two exceptions are total sectional area and structural polarization) contain a phylogenetic signal. Linear discriminant analyses suggest that the sampled taxa can be arranged into three categories with respect to locomotion mode: a) terrestrial + flying + digging + amphibious forms, b) coastal oscillatory aquatic taxa, and c) pelagic oscillatory aquatic forms represented by oceanic cetaceans. Pairwise comparison tests and linear regressions show that, when specific size increases, the length of trabecular network (Tt.Tb.Le), as well as trabecular proliferation in total sections (Pr.Tb.Tt), increase with positive allometry. This process occurs in all locomotion categories but is particularly pronounced in pelagic oscillators. Conversely, mean trabecular width has a lesser increase with size in pelagic oscillators. Trabecular orientation is not influenced by size. All tests were corrected for multiple testing. By using six structural variables or indices, locomotion mode can be predicted with a 97.4% success rate for terrestrial forms, 66.7% for coastal oscillatory, and 81.3% for pelagic oscillatory. The possible functional meaning of these results and their potential use for paleobiological inference of locomotion in

  9. Comparative review of marine mammal guidance implemented during naval exercises.

    PubMed

    Dolman, Sarah J; Weir, Caroline R; Jasny, Michael

    2009-04-01

    This article reviews the types and effectiveness of marine mammal mitigation measures used during some naval activities worldwide. The three main standard methods used to mitigate the potential impacts of naval sonar sound on marine mammals are (1) time/area planning (of exercises/active sonar use) to avoid marine mammals; (2) implementation of operational procedures (e.g. 'soft start' - where sound levels are gradually increased over time); and (3) monitoring of animals for the purpose of maintaining an 'exclusion zone' around the sound source. Suggestions towards a minimum worldwide mitigation standard are made.

  10. Studies of Noise Compensation in Marine Mammals

    DTIC Science & Technology

    2011-04-30

    Mystic Aquarium to determine if captive beluga whales modify their calling behavior in increased noise during the summer of 2010. RESULTS Each of...mammals. OBJECTIVES The primary objective of this project is to test hypotheses regarding right whale vocal adjustment to compensate for noise with data...from Southern right whales (Eubalaena australis). APPROACH The approach for this study is to test hypotheses about common mechanisms of noise

  11. 75 FR 76399 - Marine Mammals

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-08

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XZ66 Marine Mammals AGENCY: National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Commerce. ACTION: Notice; receipt of...

  12. Reproductive cessation in female mammals.

    PubMed

    Packer, C; Tatar, M; Collins, A

    1998-04-23

    In female mammals, fertility declines abruptly at an advanced age. The human menopause is one example, but reproductive cessation has also been documented in non-human primates, rodents, whales, dogs, rabbits, elephants and domestic livestock. The human menopause has been considered an evolutionary adaptation, assuming that elderly women avoid the increasing complications of continued childbirth to better nurture their current children and grandchildren. But an abrupt reproductive decline might be only a non-adaptive by-product of life-history patterns. Because so many individuals die from starvation, disease and predation, detrimental genetic traits can persist (or even be favoured) as long as their deleterious effects are delayed until an advanced age is reached, and, for a given pattern of mortality, there should be an age by which selection would be too weak to prevent the onset of reproductive senescence. We provide a systematic test of these alternatives using field data from two species in which grandmothers frequently engage in kin-directed behaviour. Both species show abrupt age-specific changes in reproductive performance that are characteristic of menopause. But elderly females do not suffer increased mortality costs of reproduction, nor do post-reproductive females enhance the fitness of grandchildren or older children. Instead, reproductive cessation appears to result from senescence.

  13. Peroxisome degradation in mammals.

    PubMed

    Ezaki, Junji; Kominami, Eiki; Ueno, Takashi

    2011-11-01

    This review summarizes the historical aspects of the study of peroxisome degradation in mammalian cells. Peroxisomes have diverse metabolic roles in response to environmental changes and are degraded in a preferential manner, by comparison with cytosolic proteins. This review introduces three hypotheses on the degradation mechanisms: (a) the action of the peroxisome-specific Lon protease; (b) the membrane disruption effect of 15-lipoxygenase; and (c) autophagy that sequesters and degrades the organelles by lysosomal enzymes. Among these hypotheses, autophagy is now recognized as the most important mechanism for excess peroxisome degradation. One of the most striking characteristics of peroxisomes is that they are markedly proliferated in the liver by the administration of hypolipidemic drugs and industrial plasticizers. The effects of these substances were fully reversed after withdrawal of the substances, and most of the excess peroxisomes were selectively degraded and recovered to a normal number and size. Autophagic degradation of peroxisomes has been examined using this characteristic phenomenon. Excessive peroxisome degradation that occurs after cessation of hypolipidemic drugs has been extensively investigated biochemically and morphologically. The evidence shows that the degradation of excess peroxisomes and peroxisomal enzymes is inhibited by 3-methyladenine (3-MA), a specific inhibitor of autophagy. Furthermore, in liver-specific autophagy-deficient mice, rapid removal of peroxisomes was exclusively impaired, and degradation of peroxisomal enzymes was not detected. Thus, the significant contribution of autophagic machinery to peroxisomal degradation in mammals was confirmed. However, the important question of the mechanism for the selective recognition of peroxisomes by autophagosomes remains to be fully elucidated. Copyright © 2011 Wiley Periodicals, Inc.

  14. Physiological Monitoring in Diving Mammals

    DTIC Science & Technology

    2014-09-30

    isobestic point, the point where the spectra cross over (see below). Data from 5 marine mammal species (killer whale , 5 beluga whale , pilot whale ...spectra of HbO2 and HbR in several species of marine mammals (orcas, short-finned pilot whales , belugas , and northern elephant seals) and compare these...large, freely diving whales . We intend to use this data logger to measure muscle O2 saturation and determine how blood flow to muscle is altered during

  15. A cryptic taxon of Galápagos tortoise in conservation peril

    PubMed Central

    Russello, Michael A; Glaberman, Scott; Gibbs, James P; Marquez, Cruz; Powell, Jeffrey R; Caccone, Adalgisa

    2005-01-01

    As once boldly stated, ‘bad taxonomy can kill’, highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention. PMID:17148189

  16. A cryptic taxon of Galápagos tortoise in conservation peril.

    PubMed

    Russello, Michael A; Glaberman, Scott; Gibbs, James P; Marquez, Cruz; Powell, Jeffrey R; Caccone, Adalgisa

    2005-09-22

    As once boldly stated, 'bad taxonomy can kill', highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.

  17. Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

    PubMed Central

    Milani, Christian; Duranti, Sabrina; Lugli, Gabriele Andrea; Bottacini, Francesca; Strati, Francesco; Arioli, Stefania; Foroni, Elena; Turroni, Francesca; van Sinderen, Douwe

    2013-01-01

    Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by the food industry as health-promoting bacteria, although the genetic variability of members belonging to this taxon has so far not received much scientific attention. In this article, we describe the complete genetic makeup of the B. animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this strain with other sequenced strains belonging to this taxon. Moreover, a detailed comparative genomic analysis of B. animalis subsp. lactis genomes was performed, which revealed a closely related and isogenic nature of all currently available B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome structure of this bacterial group. PMID:23645200

  18. Invasive mammal eradication on islands results in substantial conservation gains

    PubMed Central

    Jones, Holly P.; Holmes, Nick D.; Butchart, Stuart H. M.; Tershy, Bernie R.; Kappes, Peter J.; Corkery, Ilse; Aguirre-Muñoz, Alfonso; Armstrong, Doug P.; Bonnaud, Elsa; Burbidge, Andrew A.; Campbell, Karl; Courchamp, Franck; Cowan, Philip E.; Cuthbert, Richard J.; Ebbert, Steve; Genovesi, Piero; Howald, Gregg R.; Keitt, Bradford S.; Kress, Stephen W.; Miskelly, Colin M.; Oppel, Steffen; Poncet, Sally; Rauzon, Mark J.; Rocamora, Gérard; Russell, James C.; Samaniego-Herrera, Araceli; Seddon, Philip J.; Spatz, Dena R.; Towns, David R.; Croll, Donald A.

    2016-01-01

    More than US$21 billion is spent annually on biodiversity conservation. Despite their importance for preventing or slowing extinctions and preserving biodiversity, conservation interventions are rarely assessed systematically for their global impact. Islands house a disproportionately higher amount of biodiversity compared with mainlands, much of which is highly threatened with extinction. Indeed, island species make up nearly two-thirds of recent extinctions. Islands therefore are critical targets of conservation. We used an extensive literature and database review paired with expert interviews to estimate the global benefits of an increasingly used conservation action to stem biodiversity loss: eradication of invasive mammals on islands. We found 236 native terrestrial insular faunal species (596 populations) that benefitted through positive demographic and/or distributional responses from 251 eradications of invasive mammals on 181 islands. Seven native species (eight populations) were negatively impacted by invasive mammal eradication. Four threatened species had their International Union for the Conservation of Nature (IUCN) Red List extinction-risk categories reduced as a direct result of invasive mammal eradication, and no species moved to a higher extinction-risk category. We predict that 107 highly threatened birds, mammals, and reptiles on the IUCN Red List—6% of all these highly threatened species—likely have benefitted from invasive mammal eradications on islands. Because monitoring of eradication outcomes is sporadic and limited, the impacts of global eradications are likely greater than we report here. Our results highlight the importance of invasive mammal eradication on islands for protecting the world's most imperiled fauna. PMID:27001852

  19. Invasive mammal eradication on islands results in substantial conservation gains.

    PubMed

    Jones, Holly P; Holmes, Nick D; Butchart, Stuart H M; Tershy, Bernie R; Kappes, Peter J; Corkery, Ilse; Aguirre-Muñoz, Alfonso; Armstrong, Doug P; Bonnaud, Elsa; Burbidge, Andrew A; Campbell, Karl; Courchamp, Franck; Cowan, Philip E; Cuthbert, Richard J; Ebbert, Steve; Genovesi, Piero; Howald, Gregg R; Keitt, Bradford S; Kress, Stephen W; Miskelly, Colin M; Oppel, Steffen; Poncet, Sally; Rauzon, Mark J; Rocamora, Gérard; Russell, James C; Samaniego-Herrera, Araceli; Seddon, Philip J; Spatz, Dena R; Towns, David R; Croll, Donald A

    2016-04-12

    More than US$21 billion is spent annually on biodiversity conservation. Despite their importance for preventing or slowing extinctions and preserving biodiversity, conservation interventions are rarely assessed systematically for their global impact. Islands house a disproportionately higher amount of biodiversity compared with mainlands, much of which is highly threatened with extinction. Indeed, island species make up nearly two-thirds of recent extinctions. Islands therefore are critical targets of conservation. We used an extensive literature and database review paired with expert interviews to estimate the global benefits of an increasingly used conservation action to stem biodiversity loss: eradication of invasive mammals on islands. We found 236 native terrestrial insular faunal species (596 populations) that benefitted through positive demographic and/or distributional responses from 251 eradications of invasive mammals on 181 islands. Seven native species (eight populations) were negatively impacted by invasive mammal eradication. Four threatened species had their International Union for the Conservation of Nature (IUCN) Red List extinction-risk categories reduced as a direct result of invasive mammal eradication, and no species moved to a higher extinction-risk category. We predict that 107 highly threatened birds, mammals, and reptiles on the IUCN Red List-6% of all these highly threatened species-likely have benefitted from invasive mammal eradications on islands. Because monitoring of eradication outcomes is sporadic and limited, the impacts of global eradications are likely greater than we report here. Our results highlight the importance of invasive mammal eradication on islands for protecting the world's most imperiled fauna.

  20. Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea.

    PubMed

    Steeves, Tammy E; Holdaway, Richard N; Hale, Marie L; McLay, Emma; McAllan, Ian A W; Christian, Margaret; Hauber, Mark E; Bunce, Michael

    2010-02-23

    Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an 'extinct' avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O'Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.

  1. Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea

    PubMed Central

    Steeves, Tammy E.; Holdaway, Richard N.; Hale, Marie L.; McLay, Emma; McAllan, Ian A. W.; Christian, Margaret; Hauber, Mark E.; Bunce, Michael

    2010-01-01

    Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an ‘extinct’ avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O'Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity. PMID:19675005

  2. Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala)

    PubMed Central

    Jønsson, Knud Andreas; Irestedt, Martin; Christidis, Les; Clegg, Sonya M.; Holt, Ben G.; Fjeldså, Jon

    2014-01-01

    Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles). PMID:24403319

  3. 50 CFR 14.18 - Marine mammals.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Marine mammals. 14.18 Section 14.18....18 Marine mammals. Any person subject to the jurisdiction of the United States who has lawfully taken a marine mammal on the high seas and who is authorized to import such marine mammal in accordance...

  4. 50 CFR 14.18 - Marine mammals.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Marine mammals. 14.18 Section 14.18....18 Marine mammals. Any person subject to the jurisdiction of the United States who has lawfully taken a marine mammal on the high seas and who is authorized to import such marine mammal in accordance...

  5. 50 CFR 14.18 - Marine mammals.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 1 2013-10-01 2013-10-01 false Marine mammals. 14.18 Section 14.18....18 Marine mammals. Any person subject to the jurisdiction of the United States who has lawfully taken a marine mammal on the high seas and who is authorized to import such marine mammal in accordance...

  6. 50 CFR 14.18 - Marine mammals.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 1 2014-10-01 2014-10-01 false Marine mammals. 14.18 Section 14.18....18 Marine mammals. Any person subject to the jurisdiction of the United States who has lawfully taken a marine mammal on the high seas and who is authorized to import such marine mammal in accordance...

  7. 50 CFR 14.18 - Marine mammals.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Marine mammals. 14.18 Section 14.18....18 Marine mammals. Any person subject to the jurisdiction of the United States who has lawfully taken a marine mammal on the high seas and who is authorized to import such marine mammal in accordance...

  8. Extensive intron gain in the ancestor of placental mammals.

    PubMed

    Kordiš, Dušan

    2011-11-23

    Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of de novo intron gain in domesticated genes from an analysis of their exon/intron structures. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. Gain of introns in domesticated genes has been reconstructed on well established mammalian, vertebrate and chordate phylogenies, and examined as to where and when the gain events occurred. The locations, sizes and amounts of de novo introns gained in the domesticated genes during the evolution of mammals and chordates has been analyzed. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Intron densities in Eutheria-specific domesticated genes and in older domesticated genes that originated early in vertebrates are lower than those for normal mammalian and vertebrate genes. Surprisingly, the majority of intron gains have occurred in the ancestor of placentals. This study provides the first evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution. The findings of this comprehensive

  9. Extensive intron gain in the ancestor of placental mammals

    PubMed Central

    2011-01-01

    Background Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of de novo intron gain in domesticated genes from an analysis of their exon/intron structures. Results A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. Gain of introns in domesticated genes has been reconstructed on well established mammalian, vertebrate and chordate phylogenies, and examined as to where and when the gain events occurred. The locations, sizes and amounts of de novo introns gained in the domesticated genes during the evolution of mammals and chordates has been analyzed. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Intron densities in Eutheria-specific domesticated genes and in older domesticated genes that originated early in vertebrates are lower than those for normal mammalian and vertebrate genes. Surprisingly, the majority of intron gains have occurred in the ancestor of placentals. Conclusions This study provides the first evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution. The

  10. Evolution of mammals and their gut microbes.

    PubMed

    Ley, Ruth E; Hamady, Micah; Lozupone, Catherine; Turnbaugh, Peter J; Ramey, Rob Roy; Bircher, J Stephen; Schlegel, Michael L; Tucker, Tammy A; Schrenzel, Mark D; Knight, Rob; Gordon, Jeffrey I

    2008-06-20

    Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.

  11. Evolution of mammals and their gut microbes

    PubMed Central

    Ley, Ruth E.; Hamady, Micah; Lozupone, Catherine; Turnbaugh, Peter; Ramey, Rob Roy; Bircher, J. Stephen; Schlegel, Michael. L.; Tucker, Tammy A.; Schrenzel, Mark D.; Knight, Rob; Gordon, Jeffrey I.

    2009-01-01

    Mammals are metagenomic in that they are composed not only of their own gene complements but also those of all of their associated microbes. To understand the co-evolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S rRNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory, that bacterial communities co-diversified with their hosts, and that the gut microbiota of humans living a modern lifestyle is typical of omnivorous primates. PMID:18497261

  12. Clonal diversity of the taxon Porphyromonas gingivalis assessed by random amplified polymorphic DNA fingerprinting.

    PubMed Central

    Ménard, C; Mouton, C

    1995-01-01

    A total of 97 strains of the periopathogen Porphyromonas gingivalis were collected. This collection included laboratory strains and clinical isolates of human origin with diverse clinical and geographical origins. Biological diversity was further increased by including 32 strains isolated from the oral cavities of nine different animal species. Genomic fingerprints of the 129 strains were generated as random amplified polymorphic DNAs (RAPDs) by the technique of PCR amplification with a single primer of arbitrary sequence. Four nonameric oligonucleotides were used as single primers, and the banding patterns of the DNA products separated on agarose gels were compared after ethidium ethidium bromide staining. Distance coeffients based on the positions of the major DNA fragments were calculated, and dendrograms were generated. We identified 102 clonal types (CTs) that could be assembled into three main groups by cluster analysis by the unweighted pair group method with mathematic averages. Group I (n = 79 CTs) included all 97 human strains and 6 monkey isolates. The strains in group II (n = 22 CTs) and III (n = 1 CT) were strongly differentiated from those in group I and included only strains of animal origin; they likely represent two cryptic species within the present P. gingivalis taxon. We observed that strains from Old World monkeys clustered together with the human genotype, whereas strains from New World monkeys clustered with the animal genotype. Our results with human strains also indicated that (i) the population structure is basically clonal, (ii) no dominant or widespread CT could be observed, and (iii) no relationship could be established between specific clusters of CTs and the periodontal status of the host. Our results corroborate previous findings by B. G. Loos, D. W. Dyer, T. S. Whittam, and R. K. Selander (Infect. Immun. 61:204-212, 1993) and suggest that P. gingivalis should be considered a commensal of the oral cavity acting as an opportunistic

  13. 50 CFR 18.25 - Exempted marine mammals or marine mammal products.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 8 2011-10-01 2011-10-01 false Exempted marine mammals or marine mammal... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.25 Exempted marine mammals or marine mammal products. (a) The provisions of the Act and these regulations shall not apply: (1...

  14. 50 CFR 18.25 - Exempted marine mammals or marine mammal products.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 9 2012-10-01 2012-10-01 false Exempted marine mammals or marine mammal... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.25 Exempted marine mammals or marine mammal products. (a) The provisions of the Act and these regulations shall not apply: (1...

  15. 50 CFR 18.25 - Exempted marine mammals or marine mammal products.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 9 2014-10-01 2014-10-01 false Exempted marine mammals or marine mammal... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.25 Exempted marine mammals or marine mammal products. (a) The provisions of the Act and these regulations shall not apply: (1...

  16. 50 CFR 18.25 - Exempted marine mammals or marine mammal products.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 9 2013-10-01 2013-10-01 false Exempted marine mammals or marine mammal... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.25 Exempted marine mammals or marine mammal products. (a) The provisions of the Act and these regulations shall not apply: (1...

  17. 50 CFR 18.25 - Exempted marine mammals or marine mammal products.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Exempted marine mammals or marine mammal... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.25 Exempted marine mammals or marine mammal products. (a) The provisions of the Act and these regulations shall not apply: (1...

  18. The evolution of mammal body sizes: responses to Cenozoic climate change in North American mammals.

    PubMed

    Lovegrove, B G; Mowoe, M O

    2013-06-01

    Explanations for the evolution of body size in mammals have remained surprisingly elusive despite the central importance of body size in evolutionary biology. Here, we present a model which argues that the body sizes of Nearctic mammals were moulded by Cenozoic climate and vegetation changes. Following the early Eocene Climate Optimum, forests retreated and gave way to open woodland and savannah landscapes, followed later by grasslands. Many herbivores that radiated in these new landscapes underwent a switch from browsing to grazing associated with increased unguligrade cursoriality and body size, the latter driven by the energetics and constraints of cellulose digestion (fermentation). Carnivores also increased in size and digitigrade, cursorial capacity to occupy a size distribution allowing the capture of prey of the widest range of body sizes. With the emergence of larger, faster carnivores, plantigrade mammals were constrained from evolving to large body sizes and most remained smaller than 1 kg throughout the middle Cenozoic. We find no consistent support for either Cope's Rule or Bergmann's Rule in plantigrade mammals, the largest locomotor guild (n = 1186, 59% of species in the database). Some cold-specialist plantigrade mammals, such as beavers and marmots, showed dramatic increases in body mass following the Miocene Climate Optimum which may, however, be partially explained by Bergmann's rule. This study reemphasizes the necessity of considering the evolutionary history and resultant form and function of mammalian morphotypes when attempting to understand contemporary mammalian body size distributions. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  19. Additional material of the enigmatic Early Miocene mammal Kelba and its relationship to the order Ptolemaiida

    PubMed Central

    Cote, Susanne; Werdelin, Lars; Seiffert, Erik R.; Barry, John C.

    2007-01-01

    Kelba quadeemae, a fossil mammal from the Early Miocene of East Africa, was originally named on the basis of three isolated upper molars. Kelba has previously been interpreted as a creodont, a pantolestid, an insectivoran, and a hemigaline viverrid. The true affinities of this taxon have remained unclear because of the limited material and its unique morphology relative to other Miocene African mammals. New material of Kelba from several East African Miocene localities, most notably a skull from the Early Miocene locality of Songhor in Western Kenya, permits analysis of the affinities of Kelba and documents the lower dentition of this taxon. Morphological comparison of this new material clearly demonstrates that Kelba is a member of the order Ptolemaiida, a poorly understood group whose fossil record was previously restricted to the Oligocene Fayum deposits of northern Egypt. Phylogenetic analysis supports the monophyly of the Ptolemaiida, including Kelba, and recovers two monophyletic clades within the order. We provide new family names for these groups and an emended diagnosis for the order. The discovery of ptolemaiidans from the Miocene of East Africa is significant because it extends the known temporal range of the order by >10 million years and the geographic range by >3,200 km. Although the higher-level affinities of the Ptolemaiida remain obscure, their unique morphology and distribution through a larger area of Africa (and exclusively Africa) lend support to the idea that Ptolemaiida may have an ancient African origin. PMID:17372202

  20. Distribution of Wild Mammal Assemblages along an Urban–Rural–Forest Landscape Gradient in Warm-Temperate East Asia

    PubMed Central

    Saito, Masayuki; Koike, Fumito

    2013-01-01

    Urbanization may alter mammal assemblages via habitat loss, food subsidies, and other factors related to human activities. The general distribution patterns of wild mammal assemblages along urban–rural–forest landscape gradients have not been studied, although many studies have focused on a single species or taxon, such as rodents. We quantitatively evaluated the effects of the urban–rural–forest gradient and spatial scale on the distributions of large and mid-sized mammals in the world's largest metropolitan area in warm-temperate Asia using nonspecific camera-trapping along two linear transects spanning from the urban zone in the Tokyo metropolitan area to surrounding rural and forest landscapes. Many large and mid-sized species generally decreased from forest landscapes to urban cores, although some species preferred anthropogenic landscapes. Sika deer (Cervus nippon), Reeves' muntjac (Muntiacus reevesi), Japanese macaque (Macaca fuscata), Japanese squirrel (Sciurus lis), Japanese marten (Martes melampus), Japanese badger (Meles anakuma), and wild boar (Sus scrofa) generally dominated the mammal assemblage of the forest landscape. Raccoon (Procyon lotor), raccoon dog (Nyctereutes procyonoides), and Japanese hare (Lepus brachyurus) dominated the mammal assemblage in the intermediate zone (i.e., rural and suburban landscape). Cats (feral and free-roaming housecats; Felis catus) were common in the urban assemblage. The key spatial scales for forest species were more than 4000-m radius, indicating that conservation and management plans for these mammal assemblages should be considered on large spatial scales. However, small green spaces will also be important for mammal conservation in the urban landscape, because an indigenous omnivore (raccoon dog) had a smaller key spatial scale (500-m radius) than those of forest mammals. Urbanization was generally the most important factor in the distributions of mammals, and it is necessary to consider the spatial

  1. Distribution of wild mammal assemblages along an urban-rural-forest landscape gradient in warm-temperate East Asia.

    PubMed

    Saito, Masayuki; Koike, Fumito

    2013-01-01

    Urbanization may alter mammal assemblages via habitat loss, food subsidies, and other factors related to human activities. The general distribution patterns of wild mammal assemblages along urban-rural-forest landscape gradients have not been studied, although many studies have focused on a single species or taxon, such as rodents. We quantitatively evaluated the effects of the urban-rural-forest gradient and spatial scale on the distributions of large and mid-sized mammals in the world's largest metropolitan area in warm-temperate Asia using nonspecific camera-trapping along two linear transects spanning from the urban zone in the Tokyo metropolitan area to surrounding rural and forest landscapes. Many large and mid-sized species generally decreased from forest landscapes to urban cores, although some species preferred anthropogenic landscapes. Sika deer (Cervus nippon), Reeves' muntjac (Muntiacus reevesi), Japanese macaque (Macaca fuscata), Japanese squirrel (Sciurus lis), Japanese marten (Martes melampus), Japanese badger (Meles anakuma), and wild boar (Sus scrofa) generally dominated the mammal assemblage of the forest landscape. Raccoon (Procyon lotor), raccoon dog (Nyctereutes procyonoides), and Japanese hare (Lepus brachyurus) dominated the mammal assemblage in the intermediate zone (i.e., rural and suburban landscape). Cats (feral and free-roaming housecats; Felis catus) were common in the urban assemblage. The key spatial scales for forest species were more than 4000-m radius, indicating that conservation and management plans for these mammal assemblages should be considered on large spatial scales. However, small green spaces will also be important for mammal conservation in the urban landscape, because an indigenous omnivore (raccoon dog) had a smaller key spatial scale (500-m radius) than those of forest mammals. Urbanization was generally the most important factor in the distributions of mammals, and it is necessary to consider the spatial scale of

  2. Regional Diversity and Diversification in Mammals.

    PubMed

    Machac, Antonin; Graham, Catherine H

    2017-01-01

    The effects of regional diversity on diversification remain controversial. The classic hypothesis that diversification decelerates as regional diversity increases has been recently revived. Yet, there is little geographic evidence for slower diversification across regions of high diversity, and diversity is often thought to promote diversification through its effects on ecological divergence and speciation. Here, we use the newest phylogeny for mammals (4,990 species) and two different methods to test the effects of regional diversity on diversification. We find that regions of high diversity are dominated by expanding clades that are far from their estimated carrying capacities. Regions of low diversity host clades that are small and mostly saturated. These results were supported across mammals and their six largest orders. They were corroborated by the two methods when controlling for clade relatedness, clade nestedness, and clade size. Together, these results reject the hypothesis that high geographic concentration of mammals effectively suppresses their further diversification. Instead, highly diverse regions (especially the tropics) seem to act as the engine of mammalian richness.

  3. Impact of Non-Native Terrestrial Mammals on the Structure of the Terrestrial Mammal Food Web of Newfoundland, Canada

    PubMed Central

    Strong, Justin S.; Leroux, Shawn J.

    2014-01-01

    The island of Newfoundland is unique because it has as many non-native terrestrial mammals as native ones. The impacts of non-native species on native flora and fauna can be profound and invasive species have been identified as one of the primary drivers of species extinction. Few studies, however, have investigated the effects of a non-native species assemblage on community and ecosystem properties. We reviewed the literature to build the first terrestrial mammal food web for the island of Newfoundland and then used network analyses to investigate how the timing of introductions and trophic position of non-native species has affected the structure of the terrestrial mammal food web in Newfoundland. The first non-native mammals (house mouse and brown rat) became established in Newfoundland with human settlement in the late 15th and early 16th centuries. Coyotes and southern red-backed voles are the most recent mammals to establish themselves on the island in 1985 and 1998, respectively. The fraction of intermediate species increased with the addition of non-native mammals over time whereas the fraction of basal and top species declined over time. This increase in intermediate species mediated by non-native species arrivals led to an overall increase in the terrestrial mammal food web connectance and generality (i.e. mean number of prey per predator). This diverse prey base and sources of carrion may have facilitated the natural establishment of coyotes on the island. Also, there is some evidence that the introduction of non-native prey species such as the southern red-backed vole has contributed to the recovery of the threatened American marten. Long-term monitoring of the food web is required to understand and predict the impacts of the diverse novel interactions that are developing in the terrestrial mammal food web of Newfoundland. PMID:25170923

  4. Impact of non-native terrestrial mammals on the structure of the terrestrial mammal food web of Newfoundland, Canada.

    PubMed

    Strong, Justin S; Leroux, Shawn J

    2014-01-01

    The island of Newfoundland is unique because it has as many non-native terrestrial mammals as native ones. The impacts of non-native species on native flora and fauna can be profound and invasive species have been identified as one of the primary drivers of species extinction. Few studies, however, have investigated the effects of a non-native species assemblage on community and ecosystem properties. We reviewed the literature to build the first terrestrial mammal food web for the island of Newfoundland and then used network analyses to investigate how the timing of introductions and trophic position of non-native species has affected the structure of the terrestrial mammal food web in Newfoundland. The first non-native mammals (house mouse and brown rat) became established in Newfoundland with human settlement in the late 15th and early 16th centuries. Coyotes and southern red-backed voles are the most recent mammals to establish themselves on the island in 1985 and 1998, respectively. The fraction of intermediate species increased with the addition of non-native mammals over time whereas the fraction of basal and top species declined over time. This increase in intermediate species mediated by non-native species arrivals led to an overall increase in the terrestrial mammal food web connectance and generality (i.e. mean number of prey per predator). This diverse prey base and sources of carrion may have facilitated the natural establishment of coyotes on the island. Also, there is some evidence that the introduction of non-native prey species such as the southern red-backed vole has contributed to the recovery of the threatened American marten. Long-term monitoring of the food web is required to understand and predict the impacts of the diverse novel interactions that are developing in the terrestrial mammal food web of Newfoundland.

  5. Eye shape and the nocturnal bottleneck of mammals.

    PubMed

    Hall, Margaret I; Kamilar, Jason M; Kirk, E Christopher

    2012-12-22

    Most vertebrate groups exhibit eye shapes that vary predictably with activity pattern. Nocturnal vertebrates typically have large corneas relative to eye size as an adaptation for increased visual sensitivity. Conversely, diurnal vertebrates generally demonstrate smaller corneas relative to eye size as an adaptation for increased visual acuity. By contrast, several studies have concluded that many mammals exhibit typical nocturnal eye shapes, regardless of activity pattern. However, a recent study has argued that new statistical methods allow eye shape to accurately predict activity patterns of mammals, including cathemeral species (animals that are equally likely to be awake and active at any time of day or night). Here, we conduct a detailed analysis of eye shape and activity pattern in mammals, using a broad comparative sample of 266 species. We find that the eye shapes of cathemeral mammals completely overlap with nocturnal and diurnal species. Additionally, most diurnal and cathemeral mammals have eye shapes that are most similar to those of nocturnal birds and lizards. The only mammalian clade that diverges from this pattern is anthropoids, which have convergently evolved eye shapes similar to those of diurnal birds and lizards. Our results provide additional evidence for a nocturnal 'bottleneck' in the early evolution of crown mammals.

  6. Eye shape and the nocturnal bottleneck of mammals

    PubMed Central

    Hall, Margaret I.; Kamilar, Jason M.; Kirk, E. Christopher

    2012-01-01

    Most vertebrate groups exhibit eye shapes that vary predictably with activity pattern. Nocturnal vertebrates typically have large corneas relative to eye size as an adaptation for increased visual sensitivity. Conversely, diurnal vertebrates generally demonstrate smaller corneas relative to eye size as an adaptation for increased visual acuity. By contrast, several studies have concluded that many mammals exhibit typical nocturnal eye shapes, regardless of activity pattern. However, a recent study has argued that new statistical methods allow eye shape to accurately predict activity patterns of mammals, including cathemeral species (animals that are equally likely to be awake and active at any time of day or night). Here, we conduct a detailed analysis of eye shape and activity pattern in mammals, using a broad comparative sample of 266 species. We find that the eye shapes of cathemeral mammals completely overlap with nocturnal and diurnal species. Additionally, most diurnal and cathemeral mammals have eye shapes that are most similar to those of nocturnal birds and lizards. The only mammalian clade that diverges from this pattern is anthropoids, which have convergently evolved eye shapes similar to those of diurnal birds and lizards. Our results provide additional evidence for a nocturnal ‘bottleneck’ in the early evolution of crown mammals. PMID:23097513

  7. Marine Mammal Impacts in Exploited Ecosystems: Would Large Scale Culling Benefit Fisheries?

    PubMed Central

    Morissette, Lyne; Christensen, Villy; Pauly, Daniel

    2012-01-01

    Competition between marine mammals and fisheries for marine resources—whether real or perceived—has become a major issue for several countries and in international fora. We examined trophic interactions between marine mammals and fisheries based on a resource overlap index, using seven Ecopath models including marine mammal groups. On a global scale, most food consumed by marine mammals consisted of prey types that were not the main target of fisheries. For each ecosystem, the primary production required (PPR) to sustain marine mammals was less than half the PPR to sustain fisheries catches. We also developed an index representing the mean trophic level of marine mammal's consumption (TLQ) and compared it with the mean trophic level of fisheries' catches (TLC). Our results showed that overall TLQ was lower than TLC (2.88 versus 3.42). As fisheries increasingly exploit lower-trophic level species, the competition with marine mammals may become more important. We used mixed trophic impact analysis to evaluate indirect trophic effects of marine mammals, and in some cases found beneficial effects on some prey. Finally, we assessed the change in the trophic structure of an ecosystem after a simulated extirpation of marine mammal populations. We found that this lead to alterations in the structure of the ecosystems, and that there was no clear and direct relationship between marine mammals' predation and the potential catch by fisheries. Indeed, total biomass, with no marine mammals in the ecosystem, generally remained surprisingly similar, or even decreased for some species. PMID:22970153

  8. Ectoparasites in small exotic mammals.

    PubMed

    Fehr, Michael; Koestlinger, Saskia

    2013-09-01

    Ectoparasites inhabiting the skin are responsible for significant problems in small mammals, owing to ingestion of blood, lymph, sebaceous secretions, and scavenging skin debris, as well as a hypersensitivity reaction to parasite antigen resulting in severe pruritus and subsequent self-trauma-induced lesions. In general practice, the most common diagnosis in exotic pets is an unspecified mite infestation, but other ectoparasites such as lice, fleas, insects, or even helminths may cause dermatologic diseases. If treatment with topical insecticides is planned, the small mammal should be isolated for a few hours to enable drying and spreading of the product.

  9. Evaluating and interpreting cross-taxon congruence: Potential pitfalls and solutions

    NASA Astrophysics Data System (ADS)

    Gioria, Margherita; Bacaro, Giovanni; Feehan, John

    2011-05-01

    Characterizing the relationship between different taxonomic groups is critical to identify potential surrogates for biodiversity. Previous studies have shown that cross-taxa relationships are generally weak and/or inconsistent. The difficulties in finding predictive patterns have often been attributed to the spatial and temporal scales of these studies and on the differences in the measure used to evaluate such relationships (species richness versus composition). However, the choice of the analytical approach used to evaluate cross-taxon congruence inevitably represents a major source of variation. Here, we described the use of a range of methods that can be used to comprehensively assess cross-taxa relationships. To do so, we used data for two taxonomic groups, wetland plants and water beetles, collected from 54 farmland ponds in Ireland. Specifically, we used the Pearson correlation and rarefaction curves to analyse patterns in species richness, while Mantel tests, Procrustes analysis, and co-correspondence analysis were used to evaluate congruence in species composition. We compared the results of these analyses and we described some of the potential pitfalls associated with the use of each of these statistical approaches. Cross-taxon congruence was moderate to strong, depending on the choice of the analytical approach, on the nature of the response variable, and on local and environmental conditions. Our findings indicate that multiple approaches and measures of community structure are required for a comprehensive assessment of cross-taxa relationships. In particular, we showed that selection of surrogate taxa in conservation planning should not be based on a single statistic expressing the degree of correlation in species richness or composition. Potential solutions to the analytical issues associated with the assessment of cross-taxon congruence are provided and the implications of our findings in the selection of surrogates for biodiversity are discussed.

  10. Competitive growth in a cooperative mammal.

    PubMed

    Huchard, Elise; English, Sinead; Bell, Matt B V; Thavarajah, Nathan; Clutton-Brock, Tim

    2016-05-26

    In many animal societies where hierarchies govern access to reproduction, the social rank of individuals is related to their age and weight and slow-growing animals may lose their place in breeding queues to younger 'challengers' that grow faster. The threat of being displaced might be expected to favour the evolution of competitive growth strategies, where individuals increase their own rate of growth in response to increases in the growth of potential rivals. Although growth rates have been shown to vary in relation to changes in the social environment in several vertebrates including fish and mammals, it is not yet known whether individuals increase their growth rates in response to increases in the growth of particular reproductive rivals. Here we show that, in wild Kalahari meerkats (Suricata suricatta), subordinates of both sexes respond to experimentally induced increases in the growth of same-sex rivals by raising their own growth rate and food intake. In addition, when individuals acquire dominant status, they show a secondary period of accelerated growth whose magnitude increases if the difference between their own weight and that of the heaviest subordinate of the same sex in their group is small. Our results show that individuals adjust their growth to the size of their closest competitor and raise the possibility that similar plastic responses to the risk of competition may occur in other social mammals, including domestic animals and primates.

  11. Adaptive evolution toward larger size in mammals.

    PubMed

    Baker, Joanna; Meade, Andrew; Pagel, Mark; Venditti, Chris

    2015-04-21

    The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope's rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both.

  12. Adaptive evolution toward larger size in mammals

    PubMed Central

    Baker, Joanna; Meade, Andrew; Pagel, Mark; Venditti, Chris

    2015-01-01

    The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope’s rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both. PMID:25848031

  13. Glucosylceramidases and malignancies in mammals.

    PubMed

    Astudillo, Leonardo; Therville, Nicole; Colacios, Céline; Ségui, Bruno; Andrieu-Abadie, Nathalie; Levade, Thierry

    2016-06-01

    Sphingolipids represent a major class of lipids that are essential constituents of eukaryotic cells. They are predominantly located in plasma membrane microdomains, and play an important structural role in regulating membrane fluidity. They are also bioactive effectors involved in diverse key cellular functions such as apoptosis and proliferation. The implication of some sphingolipids in cancer is well established whereas that of some others is still a matter of intense investigation. Glucosylceramide is the backbone of more than 300 structurally different glycosphingolipids including gangliosides and sulfatides, and is essential for mammalian development. Therefore, glucosylceramidases (also named GBA1, GBA2 and GBA3 β-glucosidases), the enzymes that hydrolyse β-glucosylceramide, play important functions. GBA1 is a lysosomal hydrolase whose deficiency causes Gaucher disease, the most prevalent inherited lysosomal storage disorder. GBA2 is a ubiquitous non-lysosomal glucosylceramidase whose mutations have been associated with some forms of hereditary spastic paraplegia. GBA3 is a cytosolic β-glucosidase, mostly present in the kidney, liver, spleen, intestine and lymphocytes of mammals, the function of which is still unclear. Whereas glucosylceramide synthase is implicated in multidrug resistance, the role of glucosylceramide breakdown in cancer is not yet fully appreciated. Defective GBA1 enzyme activity in humans, i.e., Gaucher disease, is associated with an increased risk of multiple myeloma and other malignancies. Putative molecular links between Gaucher disease and cancer, which might implicate the malignant cell and/or its microenvironment, are reviewed. The functions of GBA2 and GBA3 in cancer progression are also discussed. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  14. Solitary mammals provide an animal model for autism spectrum disorders.

    PubMed

    Reser, Jared Edward

    2014-02-01

    Species of solitary mammals are known to exhibit specialized, neurological adaptations that prepare them to focus working memory on food procurement and survival rather than on social interaction. Solitary and nonmonogamous mammals, which do not form strong social bonds, have been documented to exhibit behaviors and biomarkers that are similar to endophenotypes in autism. Both individuals on the autism spectrum and certain solitary mammals have been reported to be low on measures of affiliative need, bodily expressiveness, bonding and attachment, direct and shared gazing, emotional engagement, conspecific recognition, partner preference, separation distress, and social approach behavior. Solitary mammals also exhibit certain biomarkers that are characteristic of autism, including diminished oxytocin and vasopressin signaling, dysregulation of the endogenous opioid system, increased Hypothalamic-pituitary-adrenal axis (HPA) activity to social encounters, and reduced HPA activity to separation and isolation. The extent of these similarities suggests that solitary mammals may offer a useful model of autism spectrum disorders and an opportunity for investigating genetic and epigenetic etiological factors. If the brain in autism can be shown to exhibit distinct homologous or homoplastic similarities to the brains of solitary animals, it will reveal that they may be central to the phenotype and should be targeted for further investigation. Research of the neurological, cellular, and molecular basis of these specializations in other mammals may provide insight for behavioral analysis, communication intervention, and psychopharmacology for autism.

  15. Tyrosine metabolic enzymes from insects and mammals: a comparative perspective.

    PubMed

    Vavricka, Christopher John; Han, Qian; Mehere, Prajwalini; Ding, Haizhen; Christensen, Bruce M; Li, Jianyong

    2014-02-01

    Differences in the metabolism of tyrosine between insects and mammals present an interesting example of molecular evolution. Both insects and mammals possess fine-tuned systems of enzymes to meet their specific demands for tyrosine metabolites; however, more homologous enzymes involved in tyrosine metabolism have emerged in many insect species. Without knowledge of modern genomics, one might suppose that mammals, which are generally more complex than insects and require tyrosine as a precursor for important catecholamine neurotransmitters and for melanin, should possess more enzymes to control tyrosine metabolism. Therefore, the question of why insects actually possess more tyrosine metabolic enzymes is quite interesting. It has long been known that insects rely heavily on tyrosine metabolism for cuticle hardening and for innate immune responses, and these evolutionary constraints are likely the key answers to this question. In terms of melanogenesis, mammals also possess a high level of regulation; yet mammalian systems possess more mechanisms for detoxification whereas insects accelerate pathways like melanogenesis and therefore must bear increased oxidative pressure. Our research group has had the opportunity to characterize the structure and function of many key proteins involved in tyrosine metabolism from both insects and mammals. In this mini review we will give a brief overview of our research on tyrosine metabolic enzymes in the scope of an evolutionary perspective of mammals in comparison to insects. © 2013 Institute of Zoology, Chinese Academy of Sciences.

  16. Small Mammals, Reptiles, and Amphibians

    Treesearch

    Bryce Rickel

    2005-01-01

    This chapter focuses on small mammals, reptiles, and amphibians that inhabit the grasslands within the Southwestern Region of the USDA Forest Service. The chapter is not intended to be an all inclusive list of species, but rather to address the species that play important roles in grassland ecosystems and that often are associated with the management of grasslands....

  17. [Scabies among the Zoo mammals].

    PubMed

    Zuchowska, E

    1991-01-01

    Scabies was observed in 9 species of mammals at the Zoological Garden of Lódź in years 1957-1989. Sarcoptes scabiei spp. was found in capybaras, tapirs and camelids. Notoedres cati was recorded from the siberian tiger, but Notoedres sp. from the Erinaceus europaeus. Scabies was also found in a wild dead Tapla europaea at the Zoo area.

  18. Physiological Monitoring in Diving Mammals

    DTIC Science & Technology

    2011-09-30

    complex relationship between ocean noise, bubble injury and marine mammal strandings (http://www.awionline.org/ oceans /Noise/IONC/index.htm). During...first year, testing began using a fiber optic approach. Deoxygenated blood at various dilutions was used to test that the response was linear over the

  19. Detection and Polarization of Introgression in a Five-Taxon Phylogeny.

    PubMed

    Pease, James B; Hahn, Matthew W

    2015-07-01

    When multiple speciation events occur rapidly in succession, discordant genealogies due to incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of methods, including the [Formula: see text]-statistic (a.k.a. the "ABBA-BABA test"), have been proposed to infer introgression in the presence of ILS for a four-taxon clade. However, no integrated method exists to detect introgression using allelic patterns for more complex phylogenies. Here we explore the issues associated with previous systems of applying [Formula: see text]-statistics to a larger tree topology, and propose new [Formula: see text] tests as an integrated framework to infer both the taxa involved in and the direction of introgression for a symmetric five-taxon phylogeny. Using theory and simulations, we show that the [Formula: see text] statistics correctly identify the introgression donor and recipient lineages, even at low rates of introgression. [Formula: see text] is also shown to have extremely low false-positive rates. The [Formula: see text] tests are computationally inexpensive to calculate and can easily be applied to phylogenomic data sets, both genome-wide and in windows of the genome. In addition, we explore both the principles and problems of introgression detection in even more complex phylogenies. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Rediscovery and reclassification of the dipteran taxon Nothomicrodon Wheeler, an exclusive endoparasitoid of gyne ant larvae.

    PubMed

    Pérez-Lachaud, Gabriela; Jahyny, Benoit J B; Ståhls, Gunilla; Rotheray, Graham; Delabie, Jacques H C; Lachaud, Jean-Paul

    2017-03-31

    The myrmecophile larva of the dipteran taxon Nothomicrodon Wheeler is rediscovered, almost a century after its original description and unique report. The systematic position of this dipteran has remained enigmatic due to the absence of reared imagos to confirm indentity. We also failed to rear imagos, but we scrutinized entire nests of the Brazilian arboreal dolichoderine ant Azteca chartifex which, combined with morphological and molecular studies, enabled us to establish beyond doubt that Nothomicrodon belongs to the Phoridae (Insecta: Diptera), not the Syrphidae where it was first placed, and that the species we studied is an endoparasitoid of the larvae of A. chartifex, exclusively attacking sexual female (gyne) larvae. Northomicrodon parasitism can exert high fitness costs to a host colony. Our discovery adds one more case to the growing number of phorid taxa known to parasitize ant larvae and suggests that many others remain to be discovered. Our findings and literature review confirm that the Phoridae is the only taxon known that parasitizes both adults and the immature stages of different castes of ants, thus threatening ants on all fronts.

  1. TipMT: Identification of PCR-based taxon-specific markers.

    PubMed

    Rodrigues-Luiz, Gabriela F; Cardoso, Mariana S; Valdivia, Hugo O; Ayala, Edward V; Gontijo, Célia M F; Rodrigues, Thiago de S; Fujiwara, Ricardo T; Lopes, Robson S; Bartholomeu, Daniella C

    2017-02-11

    Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity. Here, we report the development of a Tool for Identification of Primers for Multiple Taxa (TipMT), which is a web application to search and design primers for genotyping based on genomic data. The tool identifies and targets single sequence repeats (SSR) or orthologous/taxa-specific genes for genotyping using Multiplex PCR. This pipeline was applied to the genomes of four species of Leishmania (L. amazonensis, L. braziliensis, L. infantum and L. major) and validated by PCR using artificial genomic DNA mixtures of the Leishmania species as templates. This experimental validation demonstrates the reliability of TipMT because amplification profiles showed discrimination of genomic DNA samples from Leishmania species. The TipMT web tool allows for large-scale identification and design of taxon-specific primers and is freely available to the scientific community at http://200.131.37.155/tipMT/ .

  2. Delineating Species with DNA Barcodes: A Case of Taxon Dependent Method Performance in Moths

    PubMed Central

    Kekkonen, Mari; Mutanen, Marko; Kaila, Lauri; Nieminen, Marko; Hebert, Paul D. N.

    2015-01-01

    The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work. PMID:25849083

  3. Rediscovery and reclassification of the dipteran taxon Nothomicrodon Wheeler, an exclusive endoparasitoid of gyne ant larvae

    PubMed Central

    Pérez-Lachaud, Gabriela; Jahyny, Benoit J. B.; Ståhls, Gunilla; Rotheray, Graham; Delabie, Jacques H. C.; Lachaud, Jean-Paul

    2017-01-01

    The myrmecophile larva of the dipteran taxon Nothomicrodon Wheeler is rediscovered, almost a century after its original description and unique report. The systematic position of this dipteran has remained enigmatic due to the absence of reared imagos to confirm indentity. We also failed to rear imagos, but we scrutinized entire nests of the Brazilian arboreal dolichoderine ant Azteca chartifex which, combined with morphological and molecular studies, enabled us to establish beyond doubt that Nothomicrodon belongs to the Phoridae (Insecta: Diptera), not the Syrphidae where it was first placed, and that the species we studied is an endoparasitoid of the larvae of A. chartifex, exclusively attacking sexual female (gyne) larvae. Northomicrodon parasitism can exert high fitness costs to a host colony. Our discovery adds one more case to the growing number of phorid taxa known to parasitize ant larvae and suggests that many others remain to be discovered. Our findings and literature review confirm that the Phoridae is the only taxon known that parasitizes both adults and the immature stages of different castes of ants, thus threatening ants on all fronts. PMID:28361946

  4. In search of the psychopathic sexuality taxon: indicator size does matter.

    PubMed

    Walters, Glenn D; Marcus, David K; Edens, John F; Knight, Raymond A; Sanford, Glenn M

    2011-01-01

    Recent research has suggested that a qualitatively distinct subtype of psychopathic sex offender can be identified via taxometric analyses (Harris et al., 2007). In this study we attempted to replicate the hypothesized psychopathic sexuality taxon in a group of 503 male sexual offenders using data from the Psychopathy Checklist-Revised (PCL-R:Hare, 2003) and five coercive and precocious sexuality items. Ambiguous to dimensional results were obtained when, in a replication of the Harris et al. (2007) study,dichotomized indicators were analyzed with summed input maximum covariance (MAXCOV). Clearly dimensional results, however, were obtained when higher correlating and more valid quasi-continuous indicators were analyzed with traditional (input variables not summed) MAXCOV, and both dichotomous and quasi-continuous indicators were analyzed with mean above minus below a cut (MAMBAC) and latent-mode factor analysis (L-Mode). These results suggest that Harris et al. (2007) may have mistaken the random fluctuations of weakly correlating and poorly differentiating indicators for a taxon. Consistent with the vast majority of earlier research,our results suggest that psychopathy (with or without coercive and precocious sexuality) is a dimensional construct.

  5. SMALL MAMMAL USE OF MICROHABITAT REVIEWED

    EPA Science Inventory

    Small mammal microhabitat research has greatly influenced vertebrate community ecologists. There exists a "microhabitat paradigm" that states that sympatry among small mammal species is enabled by differential use of microhabitat (i.e., microhabitat partitioning). However, seve...

  6. Hydrodynamic Flow Control in Marine Mammals

    DTIC Science & Technology

    2008-05-06

    Hydrodynamic flow control in marine mammals Frank E. Fish,1,* Laurens E. Howle† and Mark M. Murray§ Department of Biology, West Chester University...the flow of water around the body dictates the performance of marine mammals in the aquatic environment. Morphological specializations of marine mammals ...and maneuverability. The morphological features of marine mammals for flow control can be utilized in the biomimetic design of engineered structures

  7. Ocean Basin Impact of Ambient Noise on Marine Mammal Detectability, Distribution, and Acoustic Communication

    DTIC Science & Technology

    2015-09-30

    The ultimate goal of this research was to enhance the understanding of global ocean noise and how variability in sound level impacts marine mammal...detection as it relates to marine mammal active acoustic space and acoustic communication. This work increases the spatial range and time scale of prior...acoustic environment were then applied to the investigation of ocean noise issues related to general signal detection tasks, as well as marine mammal acoustic detection and impacts.

  8. Ocean Basin Impact of Ambient Noise on Marine Mammal Detectability, Distribution, and Acoustic Communication

    DTIC Science & Technology

    2015-07-06

    Technical Report 4. TITLE AND SUBTITLE Ocean Basin Impact of Ambient Noise on Marine Mammal Distribution, and Acoustic Communication 3. DATES...ultimate goal of this research is to enhance the understanding of global ocean noise and how variability in sound level impacts marine mammal acoustic...it relates to marine mammal active acoustic space and acoustic communication. This work increases the spatial range and time scale of prior

  9. First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism

    NASA Astrophysics Data System (ADS)

    Krause, David W.; Hoffmann, Simone; Wible, John R.; Kirk, E. Christopher; Schultz, Julia A.; von Koenigswald, Wighart; Groenke, Joseph R.; Rossie, James B.; O'Connor, Patrick M.; Seiffert, Erik R.; Dumont, Elizabeth R.; Holloway, Waymon L.; Rogers, Raymond R.; Rahantarisoa, Lydia J.; Kemp, Addison D.; Andriamialison, Haingoson

    2014-11-01

    Previously known only from isolated teeth and lower jaw fragments recovered from the Cretaceous and Palaeogene of the Southern Hemisphere, the Gondwanatheria constitute the most poorly known of all major mammaliaform radiations. Here we report the discovery of the first skull material of a gondwanatherian, a complete and well-preserved cranium from Upper Cretaceous strata in Madagascar that we assign to a new genus and species. Phylogenetic analysis strongly supports its placement within Gondwanatheria, which are recognized as monophyletic and closely related to multituberculates, an evolutionarily successful clade of Mesozoic mammals known almost exclusively from the Northern Hemisphere. The new taxon is the largest known mammaliaform from the Mesozoic of Gondwana. Its craniofacial anatomy reveals that it was herbivorous, large-eyed and agile, with well-developed high-frequency hearing and a keen sense of smell. The cranium exhibits a mosaic of primitive and derived features, the disparity of which is extreme and probably reflective of a long evolutionary history in geographic isolation.

  10. A multi-taxon approach reveals the effect of management intensity on biodiversity in Alpine larch grasslands.

    PubMed

    Nascimbene, Juri; Fontana, Veronika; Spitale, Daniel

    2014-07-15

    In the Alps, larch grasslands form one of the most pleasing aspects of the landscape. However, their effectiveness in contributing to biodiversity conservation may depend on the intensity of their management. We used a multi-taxon approach to evaluate the effects of the intensification of management practices and those of abandonment on the biodiversity of the main autotrophic organisms hosted in this habitat, including vascular plants, bryophytes, and lichens. The study was carried out in the eastern part of South Tyrol, in the Italian Alps, where the diversity patterns of these three organismal groups were compared among intensively managed, extensively managed, and abandoned stands. The management intensity was found to strongly influence the biodiversity of the organisms, with a general pattern indicating the best conditions in extensively managed stands. Both abandonment and management intensification were detrimental to biodiversity through different mechanisms that led to species loss or to major shifts in species composition. However, the most negative effects were related to management intensification, mainly due to the high nitrogen supply, providing evidence for the increasing impact of eutrophication on Alpine environments.

  11. Sequence of the canine herpesvirus thymidine kinase gene: taxon-preferred amino acid residues in the alphaherpesviral thymidine kinases.

    PubMed

    Rémond, M; Sheldrick, P; Lebreton, F; Foulon, T

    1995-12-01

    Multiple sequence alignments of evolutionarily related proteins are finding increasing use as indicators of critical amino acid residues necessary for structural stability or involved in functional domains responsible for catalytic activities. In the past, a number of alignments have provided such information for the herpesviral thymidine kinases, for which three-dimensional structures are not yet available. We have sequenced the thymidine kinase gene of a canine herpesvirus, and with a multiple alignment have identified amino acids preferentially conserved in either of two taxons, the genera Varicellovirus and Simplexvirus, of the subfamily Alphaherpesvirinae. Since some regions of the thymidine kinases show otherwise elevated levels of substitutional tolerance, these conserved amino acids are candidates for critical residues which have become fixed through selection during the evolutionary divergence of these enzymes. Several pairs with distinctive patterns of distribution among the various viruses occur in or near highly conserved sequence motifs previously proposed to form the catalytic site, and we speculate that they may represent interacting, co-ordinately variable residues.

  12. Morbillivirus infections in aquatic mammals.

    PubMed

    Visser, I K; van Bressem, M F; Barrett, T; Osterhaus, A D

    1993-01-01

    Infections with morbilliviruses have caused heavy losses among different populations of aquatic mammals during the last 5 years. Two different morbilliviruses were isolated from disease outbreaks among seals in Europe and Siberia: phocid distemper virus-1 (PDV-1) and phocid distemper virus-2 (PDV-2) respectively. PDV-1 was characterized as a newly identified morbillivirus, most related to canine distemper virus (CDV), whereas PDV-2 most probably is a strain of CDV. Morbilliviruses were also isolated from porpoises--porpoise morbillivirus (PMV)--and dolphins--dolphin morbillivirus (DMV)--which had stranded on the coasts of Europe. PMV and DMV proved to be closely related to, but distinct from 2 ruminant morbilliviruses, rinderpest virus (RPV) and peste-des-petits-ruminants virus (PPRV). Serological surveys carried out among pinniped and cetacean species in the seas of Europe and North America indicated that infections with these newly discovered morbilliviruses or closely related viruses commonly occur among aquatic mammal species.

  13. Ribosomes in the sea: a window on taxon-specific lysis

    NASA Astrophysics Data System (ADS)

    Suttle, C.; Zhong, X.; Wirth, J.

    2016-02-01

    Microbes are estimated to comprise more than 90% of the biomass in the world's oceans, are major drivers of biogeochemical cycles, and have turnover rates ranging from hours to days. Despite the central role that microbes play in marine ecosystems, there is no robust method to evaluate taxon-specific mortality rates. Here, we report a method that employs extracellular free-ribosomes as a proxy to evaluate taxon-specific microbial lysis. The method was validated with laboratory cultures of the marine heterotrophic bacterium Vibrio natriegens strain PWH3a and the photoautotroph Synechococcus strain DC2, with and without grazers or viruses, to identify the origin and fate of the extracellular free-ribosomes. Our results showed both viral lysis and programmed-cell-death (PCD) contribute to free-ribosome production. Ribosomes were not released when cells were grazed, but grazers could consume free-ribosomes. We show that extracellular free-ribosomes can be used to evaluate microbial mortality caused by viral lysis and PCD. This approach was applied to environmental samples by examining the taxonomic composition and relative abundance of free 16S-ribosomes in seawater samples collected from the Strait of Georgia and Saanich Inlet, British Columbia, Canada. Based on the presence of free ribosomes, lysis was detected in 2198 out of 4013 prokaryotic taxa, representing 22 bacterial and three archaeal phyla. Of these, lysis of 140 taxa could be detected in all nine samples. Based on the ratio of free ribosomes to cellular ribosomes, some taxa associated with specific ecological niches appeared to be subject to high rates of lysis, including the genera Achromobacter, Chryseobacterium, Clostridium, Delftia, Ferruginibacter, Lactobacillus, Marinomonas, Massilia, Microbacterium, Ochrobactrum, Paenibacillus, Phyllobacterium, Pseudomonas, Rhodobacter, and Stenotrophomonas. Our results showed high-lysis coupled with low-abundance, suggesting that taxa in lower abundance are subject

  14. Physiological Monitoring in Diving Mammals

    DTIC Science & Technology

    2012-09-30

    Fahlman Department of Life Sciences Texas A&M- Corpus Christi 6300 Ocean Dr Unit 5892 Corpus Christi, TX 78412 phone: (361) 825-3489 fax: (361...825-2025 email: andreas.fahlman@tamucc.edu Peter L. Tyack School of Biology, Sea Mammal Research Unit Scottish Oceans Institute University...Sciences Texas A&M- Corpus Christi 6300 Ocean Dr Unit 5892 Corpus Christi, TX 78412 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING

  15. Physiological Monitoring in Diving Mammals

    DTIC Science & Technology

    2011-09-30

    and Marine and Ocean Science 16. SECURITY CLASSIFICATION OF: a. REPORT b. ABSTRACT c. THIS PAGE 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES... ocean noise, bubble injury and marine mammal strandings (http://www.awionline.org/ oceans /Noise/IONC/index.htm). During a workshop held in Baltimore...fiber optic approach. Deoxygenated blood at various dilutions was used to test that the response was linear over the physiological range. y= 00957K

  16. Lung Mechanics in Marine Mammals

    DTIC Science & Technology

    2012-09-30

    lung mechanics in vivo during spontaneous breathing (dynamic) and mechanical ventilation (static), and the static compliance of the excised lung after...to depth. Physiological Zoology, 1982. 55(1): p. 105-111. 6. Fahlman, A., et al., Estimating the effect of lung collapse and pulmonary shunt on gas...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Lung Mechanics in Marine Mammals Andreas Fahlman

  17. Nomenclature and placental mammal phylogeny

    PubMed Central

    2010-01-01

    An issue arising from recent progress in establishing the placental mammal Tree of Life concerns the nomenclature of high-level clades. Fortunately, there are now several well-supported clades among extant mammals that require unambiguous, stable names. Although the International Code of Zoological Nomenclature does not apply above the Linnean rank of family, and while consensus on the adoption of competing systems of nomenclature does not yet exist, there is a clear, historical basis upon which to arbitrate among competing names for high-level mammalian clades. Here, we recommend application of the principles of priority and stability, as laid down by G.G. Simpson in 1945, to discriminate among proposed names for high-level taxa. We apply these principles to specific cases among placental mammals with broad relevance for taxonomy, and close with particular emphasis on the Afrotherian family Tenrecidae. We conclude that no matter how reconstructions of the Tree of Life change in years to come, systematists should apply new names reluctantly, deferring to those already published and maximizing consistency with existing nomenclature. PMID:20406454

  18. Anatomical adaptations of aquatic mammals.

    PubMed

    Reidenberg, Joy S

    2007-06-01

    This special issue of the Anatomical Record explores many of the anatomical adaptations exhibited by aquatic mammals that enable life in the water. Anatomical observations on a range of fossil and living marine and freshwater mammals are presented, including sirenians (manatees and dugongs), cetaceans (both baleen whales and toothed whales, including dolphins and porpoises), pinnipeds (seals, sea lions, and walruses), the sea otter, and the pygmy hippopotamus. A range of anatomical systems are covered in this issue, including the external form (integument, tail shape), nervous system (eye, ear, brain), musculoskeletal systems (cranium, mandible, hyoid, vertebral column, flipper/forelimb), digestive tract (teeth/tusks/baleen, tongue, stomach), and respiratory tract (larynx). Emphasis is placed on exploring anatomical function in the context of aquatic life. The following topics are addressed: evolution, sound production, sound reception, feeding, locomotion, buoyancy control, thermoregulation, cognition, and behavior. A variety of approaches and techniques are used to examine and characterize these adaptations, ranging from dissection, to histology, to electron microscopy, to two-dimensional (2D) and 3D computerized tomography, to experimental field tests of function. The articles in this issue are a blend of literature review and new, hypothesis-driven anatomical research, which highlight the special nature of anatomical form and function in aquatic mammals that enables their exquisite adaptation for life in such a challenging environment. 2007 Wiley-Liss, Inc.

  19. Dietary characterization of terrestrial mammals

    PubMed Central

    Pineda-Munoz, Silvia; Alroy, John

    2014-01-01

    Understanding the feeding behaviour of the species that make up any ecosystem is essential for designing further research. Mammals have been studied intensively, but the criteria used for classifying their diets are far from being standardized. We built a database summarizing the dietary preferences of terrestrial mammals using published data regarding their stomach contents. We performed multivariate analyses in order to set up a standardized classification scheme. Ideally, food consumption percentages should be used instead of qualitative classifications. However, when highly detailed information is not available we propose classifying animals based on their main feeding resources. They should be classified as generalists when none of the feeding resources constitute over 50% of the diet. The term ‘omnivore’ should be avoided because it does not communicate all the complexity inherent to food choice. Moreover, the so-called omnivore diets actually involve several distinctive adaptations. Our dataset shows that terrestrial mammals are generally highly specialized and that some degree of food mixing may even be required for most species. PMID:25009067

  20. Metabolism and toxicity of arsenicals in mammals.

    PubMed

    Sattar, Adeel; Xie, Shuyu; Hafeez, Mian Abdul; Wang, Xu; Hussain, Hafiz Iftikhar; Iqbal, Zahid; Pan, Yuanhu; Iqbal, Mujahid; Shabbir, Muhammad Abubakr; Yuan, Zonghui

    2016-12-01

    Arsenic (As) is a metalloid usually found in organic and inorganic forms with different oxidation states, while inorganic form (arsenite As-III and arsenate As-v) is considered to be more hazardous as compared to organic form (methylarsonate and dimethylarsinate), with mild or no toxicity in mammals. Due to an increasing trend to using arsenicals as growth promoters or for treatment purposes, the understanding of metabolism and toxicity of As gets vital importance. Its toxicity is mainly depends on oxi-reduction states (As-III or As-v) and the level of methylation during the metabolism process. Currently, the exact metabolic pathways of As have yet to be confirmed in humans and food producing animals. Oxidative methylation and glutathione conjugation is believed to be major pathways of As metabolism. Oxidative methylation is based on conversion of Arsenite in to mono-methylarsonic acid and di-methylarsenic acid in mammals. It has been confirmed that As is only methylated in the presence of glutathione or thiol compounds, suggesting that As is being methylated in trivalent states. Subsequently, non-conjugated trivalent arsenicals are highly reactive with thiol which converts the trivalent arsenicals in to less toxic pentavalent forms. The glutathione conjugate stability of As is the most important factor for determining the toxicity. It can lead to DNA damage by alerting enzyme profile and production of reactive oxygen and nitrogen species which causes the oxidative stress. Moreover, As causes immune-dysfunction by hindering cellular and humeral immune response. The present review discussed different metabolic pathways and toxic outcomes of arsenicals in mammals which will be helpful in health risk assessment and its impact on biological world.

  1. Sexual Selection of Protamine 1 in Mammals.

    PubMed

    Lüke, Lena; Tourmente, Maximiliano; Roldan, Eduardo R S

    2016-01-01

    Protamines have a crucial role in male fertility. They are involved in sperm chromatin packaging and influence the shape of the sperm head and, hence, are important for sperm performance. Protamine structure is basic with numerous arginine-rich DNA-binding domains. Postcopulatory sexual selection is thought to play an important role in protamine sequence evolution and expression. Here, we analyze patterns of evolution and sexual selection (in the form of sperm competition) acting on protamine 1 gene sequence in 237 mammalian species. We assessed common patterns as well as differences between the major mammalian subclasses (Eutheria, Metatheria) and clades. We found that a high arginine content in protamine 1 associates with a lower sperm head width, which may have an impact on sperm swimming velocity. Increase in arginine content in protamine 1 across mammals appears to take place in a way consistent with sexual selection. In metatherians, increase in sequence length correlates with sexual selection. Differences in selective pressures on sequences and codon sites were observed between mammalian clades. Our study revealed a complex evolutionary pattern of protamine 1, with different selective constraints, and effects of sexual selection, between mammalian groups. In contrast, the effect of arginine content on head shape, and the possible involvement of sperm competition, was identified across all mammals. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. The correct name of the taxon that contains the type strain of Rhodococcus equi.

    PubMed

    Tindall, B J

    2014-01-01

    Based on a nomenclatural point of view, the name Rhodococcus equi is associated, as required by the Bacteriological Code, with a defined position, rank and circumscription. A search of the literature indicates that the name Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 has also been shown to be a synonym of Corynebacterium equi Magnusson 1923, Corynebacterium hoagii (Morse 1912) Eberson 1918 and Nocardia restricta (Turfitt 1944) McClung 1974. Application of the rules of the Bacteriological Code together with the currently inferred taxonomic concept associated with the species bearing the name Rhodococcus equi indicates that this is not the correct name of this taxon and the use of that name in the context of a circumscription that includes the type strain of the species Corynebacterium hoagii is contrary to the Rules of the Code.

  3. An environmental bacterial taxon with a large and distinct metabolic repertoire.

    PubMed

    Wilson, Micheal C; Mori, Tetsushi; Rückert, Christian; Uria, Agustinus R; Helf, Maximilian J; Takada, Kentaro; Gernert, Christine; Steffens, Ursula A E; Heycke, Nina; Schmitt, Susanne; Rinke, Christian; Helfrich, Eric J N; Brachmann, Alexander O; Gurgui, Cristian; Wakimoto, Toshiyuki; Kracht, Matthias; Crüsemann, Max; Hentschel, Ute; Abe, Ikuro; Matsunaga, Shigeki; Kalinowski, Jörn; Takeyama, Haruko; Piel, Jörn

    2014-02-06

    Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such 'talented' producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus 'Entotheonella' with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. 'Entotheonella' spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum 'Tectomicrobia'. The pronounced bioactivities and chemical uniqueness of 'Entotheonella' compounds provide significant opportunities for ecological studies and drug discovery.

  4. 'Candidatus Phytoplasma hispanicum', a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus.

    PubMed

    Davis, Robert E; Harrison, Nigel A; Zhao, Yan; Wei, Wei; Dally, Ellen L

    2016-09-01

    Mexican periwinkle virescence (MPV) phytoplasma was originally discovered in diseased plants of Madagascar periwinkle (Catharanthus roseus) in Yucatán, Mexico. On the basis of results from RFLP analysis of PCR-amplified 16S rRNA gene sequences, strain MPV was previously classified as the first known member of phytoplasma group 16SrXIII, and a new subgroup (16SrXIII-A) was established to accommodate MPV phytoplasma. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MPV represents a lineage distinct from previously described 'CandidatusPhytoplasma' species. Nucleotide sequence alignments revealed that strain MPV shared less than 97.5 % 16S rRNA gene sequence similarity with all previously described 'Ca.Phytoplasma' species. Based on unique properties of the DNA, we propose recognition of Mexican periwinkle virescence phytoplasma strain MPV as representative of a novel taxon, 'CandidatusPhytoplasma hispanicum'.

  5. Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap.

    PubMed

    Gokul, Jarishma K; Hodson, Andrew J; Saetnan, Eli R; Irvine-Fynn, Tristram D L; Westall, Philippa J; Detheridge, Andrew P; Takeuchi, Nozomu; Bussell, Jennifer; Mur, Luis A J; Edwards, Arwyn

    2016-08-01

    Microbial colonization of glacial ice surfaces incurs feedbacks which affect the melting rate of the ice surface. Ecosystems formed as microbe-mineral aggregates termed cryoconite locally reduce ice surface albedo and represent foci of biodiversity and biogeochemical cycling. Consequently, greater understanding the ecological processes in the formation of functional cryoconite ecosystems upon glacier surfaces is sought. Here, we present the first bacterial biogeography of an ice cap, evaluating the respective roles of dispersal, environmental and biotic filtration occurring at local scales in the assembly of cryoconite microbiota. 16S rRNA gene amplicon semiconductor sequencing of cryoconite colonizing a Svalbard ice cap coupled with digital elevation modelling of physical parameters reveals the bacterial community is dominated by a ubiquitous core of generalist taxa, with evidence for a moderate pairwise distance-decay relationship. While geographic position and melt season duration are prominent among environmental predictors of community structure, the core population of taxa appears highly influential in structuring the bacterial community. Taxon co-occurrence network analysis reveals a highly modular community structured by positive interactions with bottleneck taxa, predominantly Actinobacteria affiliated to isolates from soil humus. In contrast, the filamentous cyanobacterial taxon (assigned to Leptolyngbya/Phormidesmis pristleyi) which dominates the community and binds together granular cryoconite are poorly connected to other taxa. While our study targeted one ice cap, the prominent role of generalist core taxa with close environmental relatives across the global cryosphere indicate discrete roles for cosmopolitan Actinobacteria and Cyanobacteria as respective keystone taxa and ecosystem engineers of cryoconite ecosystems colonizing ice caps. © 2016 John Wiley & Sons Ltd.

  6. Testing the Validity of Taxonic Schizotypy Using Genetic and Environmental Risk Variables.

    PubMed

    Morton, Sarah E; O'Hare, Kirstie J M; Maha, Jaimee L K; Nicolson, Max P; Machado, Liana; Topless, Ruth; Merriman, Tony R; Linscott, Richard J

    2017-05-01

    Meehl regarded schizotypy as a categorial liability for schizophrenia that is the product of genes, environment, and gene-environment interactions. We sought to test whether schizophrenia-related genotypes and environmental risk factors predict membership in classes defined by taxometric analyses of positive (cognitive-perceptual), negative (interpersonal), and disorganized schizotypy. Participants (n = 500) completed the Schizotypal Personality Questionnaire (SPQ) and provided information on the following risk factors: cannabis use, pregnancy and obstetric complications, social adjustment, and family history of psychosis. Saliva samples were obtained so that the frequency of single-nucleotide polymorphism (SNP) alleles associated with risk for developing schizophrenia could be determined. Genotyped SNPs were rs1625579 (MIR137), rs7004633 (MMP16), rs7914558 (CNNM2), and rs12966547 (CCDC68). Sets of SPQ items were subject to multiple coherent cut kinetic (CCK) analyses, including mean-above-minus-below-a-cut, maximum covariance, maximum eigenvalue, and latent modes analyses. CCK analyses indicated latent taxonicity of schizotypy across the 3 item sets. The cognitive-perceptual class had a base rate of 25%, and membership was predicted by the rs7004633 SNP (odds ratio = 2.33, 95% confidence interval = 1.15-4.72 in adjusted analyses). Poor social adjustment predicted memberships in the interpersonal (16%) and disorganized (21%) classes. Classes were found not to be mutually exclusive. Schizotypy is taxonic and schizotypy class membership is predicted by genetic and environmental factors that predict schizophrenia. The findings hold the promise that a more complete understanding of schizotypy as a schizophrenia liability state will come from investigation of other genes and environmental factors associated with schizophrenia.

  7. On the complexity of the Saccharomyces bayanus taxon: hybridization and potential hybrid speciation.

    PubMed

    Pérez-Través, Laura; Lopes, Christian A; Querol, Amparo; Barrio, Eladio

    2014-01-01

    Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99-100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.

  8. Development of taxon-specific sequences of common wheat for the detection of genetically modified wheat.

    PubMed

    Iida, Mayu; Yamashiro, Satomi; Yamakawa, Hirohito; Hayakawa, Katsuyuki; Kuribara, Hideo; Kodama, Takashi; Furui, Satoshi; Akiyama, Hiroshi; Maitani, Tamio; Hino, Akihiro

    2005-08-10

    Qualitative and quantitative Polymerase Chain Reaction (PCR) systems aimed at the specific detection and quantification of common wheat DNA are described. Many countries have issued regulations to label foods that include genetically modified organisms (GMOs). PCR technology is widely recognized as a reliable and useful technique for the qualitative and quantitative detection of GMOs. Detection methods are needed to amplify a target GM gene, and the amplified results should be compared with those of the corresponding taxon-specific reference gene to obtain reliable results. This paper describes the development of a specific DNA sequence in the waxy-D1 gene for common wheat (Triticum aestivum L.) and the design of a specific primer pair and TaqMan probe on the waxy-D1 gene for PCR analysis. The primers amplified a product (Wx012) of 102 bp. It is indicated that the Wx012 DNA sequence is specific to common wheat, showing homogeneity in qualitative PCR results and very similar quantification accuracy along 19 distantly related common wheat varieties. In Southern blot and real-time PCR analyses, this sequence showed either a single or a low number of copy genes. In addition, by qualitative and quantitative PCR using wx012 primers and a wx012-T probe, the limits of detection of the common wheat genome were found to be about 15 copies, and the reproducibility was reliable. In consequence, the PCR system using wx012 primers and wx012-T probe is considered to be suitable for use as a common wheat-specific taxon-specific reference gene in DNA analyses, including GMO tests.

  9. On the Complexity of the Saccharomyces bayanus Taxon: Hybridization and Potential Hybrid Speciation

    PubMed Central

    Pérez-Través, Laura; Lopes, Christian A.; Querol, Amparo; Barrio, Eladio

    2014-01-01

    Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99–100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains. PMID:24705561

  10. Macrochaete gen. nov. (Nostocales, Cyanobacteria), a taxon morphologically and molecularly distinct from Calothrix.

    PubMed

    Berrendero Gómez, Esther; Johansen, Jeffrey R; Kaštovský, Jan; Bohunická, Markéta; Čapková, Kateřina

    2016-08-01

    Historically, the genus Calothrix included all noncolonial, tapered, heterocytous filaments within the cyanobacteria. However, recent molecular phylogenies show that "Calothrix" defined in this sense represents five distinct clades. The type species of Calothrix is marine, with solitary basal heterocytes, no akinetes, and distal ends tapering abruptly into short hairs. We examined the morphology and phylogeny of 45 tapering cyanobacteria in the Rivulariaceae, including freshwater and marine representatives of both Calothrix (35 strains) and its sister taxon Rivularia (10 strains). The marine Calothrix fall into two lineages, but we lack the generitype and so cannot identify the clade corresponding to the type species. The freshwater and soil Calothrix fall into the C. parietina clade and are characterized by having a basal heterocyte, no akinetes, and gradual tapering-but not into a long hyaline hair. Macrochaete gen. nov. is a freshwater taxon sister to the Calothrix lineages but clearly separated from Rivularia. The species in this genus differ morphologically from Calothrix by their ability to produce two heteromorphic basal heterocytes and specific secondary structures of the 16S-23S ITS. An additional feature present in most species is the presence of a distal, long hyaline hair, but this character has incomplete penetrance due to its expression only under specific environmental conditions (low phosphate), and in one species appears to be lost. We recognize three species: M. psychrophila (type species) from cold environments (high mountains, Antarctica), M. santannae from wet walls of subtropical South America, and M. lichenoides, a phycobiont of lichens from Europe.

  11. The nocturnal bottleneck and the evolution of activity patterns in mammals.

    PubMed

    Gerkema, Menno P; Davies, Wayne I L; Foster, Russell G; Menaker, Michael; Hut, Roelof A

    2013-08-22

    In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.

  12. Using genomic data to unravel the root of the placental mammal phylogeny

    PubMed Central

    Murphy, William J.; Pringle, Thomas H.; Crider, Tess A.; Springer, Mark S.; Miller, Webb

    2007-01-01

    The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals ∼103 (95–114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny. PMID:17322288

  13. The nocturnal bottleneck and the evolution of activity patterns in mammals

    PubMed Central

    Gerkema, Menno P.; Davies, Wayne I. L.; Foster, Russell G.; Menaker, Michael; Hut, Roelof A.

    2013-01-01

    In 1942, Walls described the concept of a ‘nocturnal bottleneck’ in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail. PMID:23825205

  14. Problems with the claim of ecotype and taxon status of the wolf in the Great Lakes region

    USGS Publications Warehouse

    Cronin, Matthew A.; Mech, L. David

    2009-01-01

    Koblmuller et al. (2009) analysed molecular genetic data of the wolf in the Great Lakes (GL) region of the USA and concluded that the animal was a unique ecotype of grey wolf and that genetic data supported the population as a discrete wolf taxon. However, some of the literature that the researchers used to support their position actually did not, and additional confusion arises from indefinite use of terminology. Herein, we discuss the problems with designation of a wolf population as a taxon or ecotype without proper definition and assessment of criteria.

  15. Checklist of helminths found in Patagonian wild mammals.

    PubMed

    Fugassa, Martin H

    2015-09-03

    Using available reports, a checklist of the recorded helminth parasites of wild mammals from Patagonia was generated. Records of parasites found in Patagonia were included, together with records from mammals in áreas outside of Patagonia but whose range extends into Patagonia. Information about the host, localities, and references were also included. A total of 1323 records (224 Cestoda, 167 Trematoda, 894 Nematoda, 34 Acanthocephala, and 4 Pentastomida) belonging to 452 helminth species (77 Cestoda, 76 Trematoda, 277 Nematoda, 21 Acanthocephala, and 1 Pentastomida) found in 57 native mammals (22 Rodentia, 4 Didelphimorphia 1 Microbiotheria, 7 Chiroptera, 5 Cingulata, and 13 Carnivora) were listed. However, only 10.6 % of the reports were conducted on samples from Patagonia and corresponded to 25% of mammals in the region. In addition, many studies were made on a few species and, for example, 52% corresponded to studies made on Lama guanicoe. This suggests the need to increase efforts to know the parasitic fauna in a peculiar region as is the Patagonia. This is the first compilation of the helminth parasites of mammals in Argentine Patagonia and is important for parasitological and paleoparasitological studies.

  16. Status of marine mammals in the North sea

    NASA Astrophysics Data System (ADS)

    Reijnders, P. J. H.; Lankester, K.

    Information on the population status of marine mammals in the North Sea is rather scarce. For Grey Seals and Common Seals, which regularly come ashore, fairly accurate population estimates exist. However for whale species, even the more commonly observed dolphins and Harbour porpoise, no reliable data on stock areas or stock sizes can be provided. Nevertheless, it is assumed that most whale populations have decreased in numbers. And only after cessation of hunting, seal stocks have been increasing in most areas. Major recent and potential threats to marine mammals are interactions with fisheries and pollution. Several aspects of interactions considered are: drowning in nets, damage to nets or catch, 'competition' for fish and marine mammals as hosts for parasites. Most of these issues can only be answered by more intense population studies combined with multispecies fisheries assessments. Observer netwoeks and stranding data can provide useful indices for qualitative occurrence of marine mammals, but are of limited use for proper population analyses. Adequate management of an ecosystem requires understanding of interspecies relationships and the vulnerability of its components to changes in environmental conditions. Data on the status of marine mammals are urgently required to evaluate their role in the marine ecosystem.

  17. Communication masking in marine mammals: A review and research strategy.

    PubMed

    Erbe, Christine; Reichmuth, Colleen; Cunningham, Kane; Lucke, Klaus; Dooling, Robert

    2016-02-15

    Underwater noise, whether of natural or anthropogenic origin, has the ability to interfere with the way in which marine mammals receive acoustic signals (i.e., for communication, social interaction, foraging, navigation, etc.). This phenomenon, termed auditory masking, has been well studied in humans and terrestrial vertebrates (in particular birds), but less so in marine mammals. Anthropogenic underwater noise seems to be increasing in parts of the world's oceans and concerns about associated bioacoustic effects, including masking, are growing. In this article, we review our understanding of masking in marine mammals, summarise data on marine mammal hearing as they relate to masking (including audiograms, critical ratios, critical bandwidths, and auditory integration times), discuss masking release processes of receivers (including comodulation masking release and spatial release from masking) and anti-masking strategies of signalers (e.g. Lombard effect), and set a research framework for improved assessment of potential masking in marine mammals. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Age-related increase of reactive oxygen generation in the brains of mammals and birds: is reactive oxygen a signaling molecule to determine the aging process and life span?

    PubMed

    Sasaki, Toru; Unno, Keiko; Tahara, Shoichi; Kaneko, Takao

    2010-07-01

    Since Harman proposed the "free-radical theory of aging", oxidative stress has been postulated to be a major causal factor of senescence. The accumulation of oxidative stress-induced oxidatively modified macromolecules, including protein, DNA and lipid, were found in tissues during the aging process; however, it is not necessarily clear which factor is more critical, an increase in endogenous reactive oxygen and/or a decrease in anti-oxidative defense, to the age-related increase in oxidative damage. To clarify the increasing production of reactive oxygen with age, we examined reactive oxygen-dependent chemiluminescent (CL) signals in ex vivo brain slices prepared from different-aged animal brains during hypoxia-reoxygenation treatment using a novel photonic imaging method. The CL signal was intensified during reoxygenation. The signals in SAMP10 (short-life strain) and SAMR1 (control) brain slices increased with aging. The slope of the increase of CL intensity with age in P10 was steeper than in R1. Age-dependent increase of CL intensity was also observed in C57BL/6 mice, Wistar rats and pigeons; however, superoxide dismutase (SOD) activity in the brain did not change with age. These results suggest that reactive oxygen production itself increased with aging. The rate of age-related increases of CL intensity was inversely related to the maximum lifespan of animals. We speculate that reactive oxygen might be a signaling molecule and its levels in tissue might determine the aging process and lifespan. Decelerating age-related increases of reactive oxygen production are expected to be a potent strategy for anti-aging interventions.

  19. The evolution of maximum body size of terrestrial mammals.

    PubMed

    Smith, Felisa A; Boyer, Alison G; Brown, James H; Costa, Daniel P; Dayan, Tamar; Ernest, S K Morgan; Evans, Alistair R; Fortelius, Mikael; Gittleman, John L; Hamilton, Marcus J; Harding, Larisa E; Lintulaakso, Kari; Lyons, S Kathleen; McCain, Christy; Okie, Jordan G; Saarinen, Juha J; Sibly, Richard M; Stephens, Patrick R; Theodor, Jessica; Uhen, Mark D

    2010-11-26

    The extinction of dinosaurs at the Cretaceous/Paleogene (K/Pg) boundary was the seminal event that opened the door for the subsequent diversification of terrestrial mammals. Our compilation of maximum body size at the ordinal level by sub-epoch shows a near-exponential increase after the K/Pg. On each continent, the maximum size of mammals leveled off after 40 million years ago and thereafter remained approximately constant. There was remarkable congruence in the rate, trajectory, and upper limit across continents, orders, and trophic guilds, despite differences in geological and climatic history, turnover of lineages, and ecological variation. Our analysis suggests that although the primary driver for the evolution of giant mammals was diversification to fill ecological niches, environmental temperature and land area may have ultimately constrained the maximum size achieved.

  20. Polyandry Has No Detectable Mortality Cost in Female Mammals.

    PubMed

    Lemaître, Jean-François; Gaillard, Jean-Michel

    2013-01-01

    In several taxonomic groups, females mate with several males during a single reproductive cycle. Although there is evidence that polyandry provides some benefits to females, it often involves mortality costs. However, empirical evidences of mortality costs of polyandry have so far been reported only in invertebrates. Whether polyandry has mortality costs in vertebrates is currently unknown. In the present study, we aimed to fill the gap by investigating the relationships between the level of polyandry (measured either by male relative testes mass or the percentage of multiple paternities) and female patterns of mortality across mammals. While we found that the two metrics of female mortality co-varied with pace of life, we did not find any evidence that polyandry leads to either decreased median lifespan or increased aging rate in mammals. We discuss such an absence of detectable mortality costs of polyandry in female mammals in light of recent advances in the study of mammalian reproductive biology and life-history tactics.

  1. The Marine Mammal Protection Act at 40: status, recovery, and future of U.S. marine mammals.

    PubMed

    Roman, Joe; Altman, Irit; Dunphy-Daly, Meagan M; Campbell, Caitlin; Jasny, Michael; Read, Andrew J

    2013-05-01

    Passed in 1972, the Marine Mammal Protection Act has two fundamental objectives: to maintain U.S. marine mammal stocks at their optimum sustainable populations and to uphold their ecological role in the ocean. The current status of many marine mammal populations is considerably better than in 1972. Take reduction plans have been largely successful in reducing direct fisheries bycatch, although they have not been prepared for all at-risk stocks, and fisheries continue to place marine mammals as risk. Information on population trends is unknown for most (71%) stocks; more stocks with known trends are improving than declining: 19% increasing, 5% stable, and 5% decreasing. Challenges remain, however, and the act has generally been ineffective in treating indirect impacts, such as noise, disease, and prey depletion. Existing conservation measures have not protected large whales from fisheries interactions or ship strikes in the northwestern Atlantic. Despite these limitations, marine mammals within the U.S. Exclusive Economic Zone appear to be faring better than those outside, with fewer species in at-risk categories and more of least concern. © 2013 New York Academy of Sciences.

  2. Dental eruption in afrotherian mammals

    PubMed Central

    Asher, Robert J; Lehmann, Thomas

    2008-01-01

    Background Afrotheria comprises a newly recognized clade of mammals with strong molecular evidence for its monophyly. In contrast, morphological data uniting its diverse constituents, including elephants, sea cows, hyraxes, aardvarks, sengis, tenrecs and golden moles, have been difficult to identify. Here, we suggest relatively late eruption of the permanent dentition as a shared characteristic of afrotherian mammals. This characteristic and other features (such as vertebral anomalies and testicondy) recall the phenotype of a human genetic pathology (cleidocranial dysplasia), correlations with which have not been explored previously in the context of character evolution within the recently established phylogeny of living mammalian clades. Results Although data on the absolute timing of eruption in sengis, golden moles and tenrecs are still unknown, craniometric comparisons for ontogenetic series of these taxa show that considerable skull growth takes place prior to the complete eruption of the permanent cheek teeth. Specimens showing less than half (sengis, golden moles) or two-thirds (tenrecs, hyraxes) of their permanent cheek teeth reach or exceed the median jaw length of conspecifics with a complete dentition. With few exceptions, afrotherians are closer to median adult jaw length with fewer erupted, permanent cheek teeth than comparable stages of non-afrotherians. Manatees (but not dugongs), elephants and hyraxes with known age data show eruption of permanent teeth late in ontogeny relative to other mammals. While the occurrence of delayed eruption, vertebral anomalies and other potential afrotherian synapomorphies resemble some symptoms of a human genetic pathology, these characteristics do not appear to covary significantly among mammalian clades. Conclusion Morphological characteristics shared by such physically disparate animals such as elephants and golden moles are not easy to recognize, but are now known to include late eruption of permanent teeth, in

  3. Round table on morbilliviruses in marine mammals.

    PubMed

    Barrett, T; Blixenkrone-Møller, M; Domingo, M; Harder, T; Have, P; Liess, B; Orvell, C; Osterhaus, A D; Plana, J; Svansson, V

    1992-11-01

    Since 1988 morbilliviruses have been increasingly recognized and held responsible for mass mortality amongst harbour seals (Phoca vitulina) and other seal species. Virus isolations and characterization proved that morbilliviruses from seals in Northwest Europe were genetically distinct from other known members of this group including canine distemper virus (CDV), rinderpest virus, peste des petits ruminants virus and measles virus. An epidemic in Baikal seals in 1987 was apparently caused by a morbillivirus closely related to CDV so that two morbilliviruses have now been identified in two geographically distant seal populations, with only the group of isolates from Northwest Europe forming a new member of the genus morbillivirus: phocid distemper virus (PDV). Because of distemper-like disease, the Baikal seal morbillivirus was tentatively named PDV-2 in spite of its possible identity with CDV. The appearance of morbilliviruses in the Mediterranean Sea causing high mortality amongst dolphins should further increase the research activities on protection strategies for endangered species of marine mammals.

  4. Marine Mammals and Stress Workshop

    DTIC Science & Technology

    2012-09-30

    measuring indicators of stress, and 3) identify scientific or regional topics for future stress-related research involving marine mammals, including...concentrations vary by region of capture in free- ranging Steller sea lion pups”. Bechshoft, T., Sonne, C., Meyer, J.S., Novak, M.A., Henchey, E., Riget, F.F...concentrations vary by region of capture in free-ranging Steller sea lion pups.” 7. Bechshøft, Thea - “Cortisol in polar bear hair; results and applications

  5. Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling.

    PubMed

    Drummond, Christopher S; Eastwood, Ruth J; Miotto, Silvia T S; Hughes, Colin E

    2012-05-01

    Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth-death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18-0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48-1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89-3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36-1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these

  6. Effects of climate change on Arctic marine mammal health.

    PubMed

    Burek, Kathy A; Gulland, Frances M D; O'Hara, Todd M

    2008-03-01

    The lack of integrated long-term data on health, diseases, and toxicant effects in Arctic marine mammals severely limits our ability to predict the effects of climate change on marine mammal health. The overall health of an individual animal is the result of complex interactions among immune status, body condition, pathogens and their pathogenicity, toxicant exposure, and the various environmental conditions that interact with these factors. Climate change could affect these interactions in several ways. There may be direct effects of loss of the sea ice habitat, elevations of water and air temperature, and increased occurrence of severe weather. Some of the indirect effects of climate change on animal health will likely include alterations in pathogen transmission due to a variety of factors, effects on body condition due to shifts in the prey base/food web, changes in toxicant exposures, and factors associated with increased human habitation in the Arctic (e.g., chemical and pathogen pollution in the runoff due to human and domestic-animal wastes and chemicals and increased ship traffic with the attendant increased risks of ship strike, oil spills, ballast pollution, and possibly acoustic injury). The extent to which climate change will impact marine mammal health will also vary among species, with some species more sensitive to these factors than others. Baseline data on marine mammal health parameters along with matched data on the population and climate change trends are needed to document these changes.

  7. 75 FR 11132 - Marine Mammals; File No. 555-1870

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-10

    ... space as required by Animal Welfare Act regulations for the humane handling, care and treatment of... applicant. One project in the requested permit amendment (increasing the number of animals taken in the wild... did not present any unnecessary risks to the health and welfare of the marine mammals (50 CFR 216.34(1...

  8. New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia).

    PubMed

    Taylor, John D; Glover, Emily A; Smith, Lisa; Ikebe, Chiho; Williams, Suzanne T

    2016-11-23

    A new molecular phylogeny of the Lucinidae using 18S and 28S rRNA and cytochrome b genes includes many species from the tropical Western Atlantic as well as additional taxa from the Indo-West Pacific. This study provides a phylogenetic framework for a new taxonomy of tropical Western Atlantic lucinids. The analysis confirmed five major clades-Pegophyseminae, Leucosphaerinae, Myrteinae, Codakiinae and Lucininae, with Monitilorinae and Fimbriinae represented by single species. The Leucosphaerinae are expanded and include Callucina winckworthi and the W. Atlantic Myrtina pristiphora that groups with several Indo-West Pacific Myrtina species. Within the Codakiinae two abundant species of Ctena from the Western Atlantic with similar shells are discriminated as C. orbiculata and C. imbricatula, while in the Indo-West Pacific Ctena bella is a probable species complex. The Lucininae is the most species rich and disparate subfamily with several subclades apparent. Three species of Lucina are recognized in the W. Atlantic L. aurantia, L. pensylvanica and L. roquesana. Pleurolucina groups near to Cavilinga and Lucina, while Lucinisca muricata is more closely related to the E. Pacific L. fenestrata than to the Atlantic L. nassula. A new species of Parvilucina is identified from molecular analyses having been confounded with Parvilucina pectinata but differs in ligament structure. Also, the former Parvilucina clenchi is more distant and assigned to Guyanella.

  9. The placental mammal ancestor and the post-K-Pg radiation of placentals.

    PubMed

    O'Leary, Maureen A; Bloch, Jonathan I; Flynn, John J; Gaudin, Timothy J; Giallombardo, Andres; Giannini, Norberto P; Goldberg, Suzann L; Kraatz, Brian P; Luo, Zhe-Xi; Meng, Jin; Ni, Xijun; Novacek, Michael J; Perini, Fernando A; Randall, Zachary S; Rougier, Guillermo W; Sargis, Eric J; Silcox, Mary T; Simmons, Nancy B; Spaulding, Michelle; Velazco, Paúl M; Weksler, Marcelo; Wible, John R; Cirranello, Andrea L

    2013-02-08

    To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.

  10. A new symmetrodont mammal (Trechnotheria: Zhangheotheriidae) from the Early Cretaceous of China and trechnotherian character evolution

    PubMed Central

    Bi, Shundong; Zheng, Xiaoting; Meng, Jin; Wang, Xiaoli; Robinson, Nicole; Davis, Brian

    2016-01-01

    We report the discovery of Anebodon luoi, a new genus and species of zhangheotheriid symmetrodont mammal from the Lujiatun site of the Lower Cretaceous Yixian Formation, China. The fossil is represented by an associated partial skull and dentaries with a nearly complete dentition, and with a dental formula of I4/3 C1/1 P5/4 M3/4. This new taxon lacks the high molar count typical of derived symmetrodonts, differing from the well-represented zhangheotheriids Zhangheotherium and Maotherium in having a postcanine dental formula that resembles more primitive tinodontid symmetrodonts on the one hand, and sister taxa to therians such as Peramus on the other. Upper and lower distal premolars are strongly molariform and are captured undergoing replacement, clarifying positional homology among related taxa. We also describe the rostrum and, for the first time in a symmetrodont, much of the orbital mosaic. Importantly, our new taxon occupies a basal position within the Zhangheotheriidae and permits discussion of trechnotherian character evolution, ultimately shedding additional light on the evolution of therians. PMID:27215593

  11. Morbillivirus infections in aquatic mammals.

    PubMed

    Kennedy, S

    1998-10-01

    Morbillivirus infections which were not documented in aquatic mammals until 1988, have caused at least five epizootics in these species during the last 10 years. Affected populations include European harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) in 1998, Baikal seals (Phoca siberica) in Siberia from 1987-1988, striped dolphins (Stenella coeruleoalba) in the Mediterranean Sea from 1990-1992 and bottlenose dolphins (Tursiops truncatus) along the eastern coast of the United States from 1987-1988 and in the Gulf of Mexico from 1993-1994. Clinical signs and lesions in affected animals were similar to those of canine distemper. Lesions were mainly seen in lung, central nervous and lymphoid tissues and included formation of intranuclear and intracytoplasmic inclusion bodies. Syncytia were commonly found in lung and lymphoid tissues of cetaceans but not of pinnipeds. Antigenic and molecular biological studies indicate that a newly discovered morbillivirus, termed phocine distemper virus, and canine distemper virus were responsible for recent pinniped epizootics; cetacean die-offs were caused by strains of a second, newly recognized cetacean morbillivirus. Serological evidence of morbillivirus infection has been identified in a broad range of marine mammal populations and recent epizootics probably resulted from transfer of virus to immunologically-naive populations.

  12. Aestivation in mammals and birds.

    PubMed

    Geiser, Fritz

    2010-01-01

    Aestivation, which in the context of this paper refers to avian and mammalian torpor in summer/at high ambient temperatures (T (a)), does not appear to differ functionally from other forms of torpor, and to a large extent reflects the higher body temperatures (T (b)) caused by high T (a). However, from an ecological point of view, aestivation results in different challenges and requirements than does torpor use in winter, because heat can cause reduced food and water availability in many regions, but without the access to low T (a) for a substantial reduction of T (b). Aestivation is used by a diversity of adult mammals and birds both in the field and laboratory, as well as by growing young to reduce thermoregulatory energy expenditure. Torpor occurs at high T (a) including the thermo-neutral zone and even under these conditions the reduction in energy expenditure and water requirements or water loss is substantial. Although data from the laboratory and, especially, from the field are limited, they show that torpor at high T (a) is an effective survival strategy and suggest that it is employed by many mammals and birds in a diversity of habitats.

  13. A mammal-like reptile from Australia

    NASA Astrophysics Data System (ADS)

    Thulborn, Richard A.

    1983-05-01

    New fossil evidence indicates that a mammal-like reptile inhabited Australia in the early part of the Triassic period (~220 Myr ago). There are no previous reports of mammal-like reptiles from this continent, and the earliest known Australian mammals have been dated as no older than Oligocene (~23 Myr)1,2. The evidence is an isolated quadrate bone, recently discovered in Lower Triassic rocks of the Arcadia Formation, south-east Queensland. This bone has morphological peculiarities matched only in dicynodonts (mammal-like reptiles of the infraorder Dicynodontia, order Therapsida) and was probably derived from an animal similar or identical to the common African dicynodont Kannemeyeria.

  14. Farewell to life on land - thoracic strength as a new indicator to determine paleoecology in secondary aquatic mammals.

    PubMed

    Ando, Konami; Fujiwara, Shin-Ichi

    2016-12-01

    Habitat shifts from land to water have occurred independently in several mammal lineages. However, because we do not know completely about the relationship between skeletal morphology and function, both reliable life reconstructions of each extinct taxon and the timing of those shifts in locomotor strategies are yet to be fully understood. We estimated the strengths of rib cages against vertical compression in 26 extant and four extinct mammal specimens including cetartiodactyls, paenungulates, and carnivorans, representing 11 terrestrial, six semi-aquatic, and nine obligate aquatic taxa. Our analyses of extant taxa showed that strengths were high among terrestrial/semi-aquatic mammals, whose rib cages are subjected to vertical compression during the support on land, whereas strengths were low among obligate aquatic mammals, whose rib cages are not subjected to antigravity force in the water. We therefore propose rib strength as a new index to estimate the ability of an animal to be supported on land while being supported by either the forelimbs or thoracic region. According to our analyses of extinct taxa, this ability to be supported on land was rejected for a basal cetacean (Cetartiodactyla: Ambulocetus) and two desmostylians (Paenungulata: Paleoparadoxia and Neoparadoxia). However, this ability was not rejected for one desmostylian species (Desmostylus). Further study of the ribs of extant/extinct semi-aquatic taxa may help in understanding the ecological shifts in these groups.

  15. 76 FR 51352 - Taking and Importing Marine Mammals: Taking Marine Mammals Incidental to Navy Operations of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-18

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  1. L-pipecolic acid catabolism in mammals

    SciTech Connect

    Mihalik, S.J.

    1987-01-01

    The goal of the project was to study L-pipecolic acid metabolism in mammals. Initially, homogenized rabbit kidney cortices were incubated with L-(2,3,4,5,6-/sup 3/H)pipecolic acid. Anion exchange resin was used to separate the reaction product from the substrate. When the radioactive product eluted from the anion exchange column was separated by citrate buffer column chromatography, only one major radioactive peak was found. This peak coeluted with authentic ..cap alpha..-aminoadipic acid. When organelles from both kidney and liver were separated on Percoll gradients, L-pipecolic acid oxidation paralleled the mitochondrial marker glutamate dehydrogenase. L-Pipecolic acid oxidation was inhibited by rotenone and antimycin A and was found to occur in the soluble fraction of the mitochondria. FAD, glycerol, and phenazine ethosulfate all increased oxidative activity. L-Proline, and other compounds which are structurally similar to L-pipecolic acid did not inhibit oxidative activity.

  2. Mammal extinctions, body size, and paleotemperature

    USGS Publications Warehouse

    Bown, T.M.; Holroyd, P.A.; Rose, K.D.

    1994-01-01

    There is a general inverse relationship between the natural logarithm of tooth area (a body size indicator) of some fossil mammals and paleotemperature during approximately 2.9 million years of the early Eocene in the Bighorn Basin of northwest Wyoming. When mean temperatures became warmer, tooth areas tended to become smaller. During colder times, larger species predominated; these generally became larger or remained the same size. Paleotemperature trends also markedly affected patterns of local (and, perhaps, regional) extinction and immigration. New species appeared as immigrants during or near the hottest (smaller forms) and coldest (larger forms) intervals. Paleotemperature trend reversals commonly resulted in the ultimate extinction of both small forms (during cooling intervals) and larger forms (during warming intervals). These immigrations and extinctions mark faunal turnovers that were also modulated by sharp increases in sediment accumulation rate.

  3. Meiotic recombination in mammals: localization and regulation.

    PubMed

    Baudat, Frédéric; Imai, Yukiko; de Massy, Bernard

    2013-11-01

    During meiosis, a programmed induction of DNA double-strand breaks (DSBs) leads to the exchange of genetic material between homologous chromosomes. These exchanges increase genome diversity and are essential for proper chromosome segregation at the first meiotic division. Recent findings have highlighted an unexpected molecular control of the distribution of meiotic DSBs in mammals by a rapidly evolving gene, PR domain-containing 9 (PRDM9), and genome-wide analyses have facilitated the characterization of meiotic DSB sites at unprecedented resolution. In addition, the identification of new players in DSB repair processes has allowed the delineation of recombination pathways that have two major outcomes, crossovers and non-crossovers, which have distinct mechanistic roles and consequences for genome evolution.

  4. Influence of alternative silviculture on small mammals

    USGS Publications Warehouse

    Waldien, David L.; Hayes, John P.

    2006-01-01

    HIGHLIGHT: A variety of harvest methods promote diversity within forests while still generating income. For example, recent studies have shown that when dead wood is left on the forest floor during harvest, biodiversity increases. A new Cooperative Forest Ecosystem Research (CFER) program fact sheet summarizes how small mammals respond to dead wood in forests that are harvested with alternative methods. CFER is developing a series of fact sheets about responses to changes in young western Oregon forests. The fact sheets are designed to help resource managers balance management needs, including timber and wildlife. The USGS provides a primary source of financial support for CFER, a consortium of federal and state partners conducting research in support of the Northwest Forest Plan.

  5. Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology.

    PubMed

    Griesemer, James

    2013-12-01

    What gets integrated in integrative scientific practices has been a topic of much discussion. Traditional views focus on theories and explanations, with ideas of reduction and unification dominating the conversation. More recent ideas focus on disciplines, fields, or specialties; models, mechanisms, or methods; phenomena, problems. How integration works looks different on each of these views since the objects of integration are ontologically and epistemically various: statements, boundary conditions, practices, protocols, methods, variables, parameters, domains, laboratories, and questions all have their own structures, functions and logics. I focus on one particular kind of scientific practice, integration of "approaches" in the context of a research system operating on a special kind of "platform." Rather than trace a network of interactions among people, practices, and theoretical entities to be integrated, in this essay I focus on the work of a single investigator, David Wake. I describe Wake's practice of integrative evolutionary biology and how his integration of approaches among biological specialties worked in tandem with his development of the salamanders as a model taxon, which he used as a platform to solve, re-work and update problems that would not have been solved so well by non-integrative approaches. The larger goal of the project to which this paper contributes is a counter-narrative to the story of 20th century life sciences as the rise and march of the model organisms and decline of natural history.

  6. Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies.

    PubMed

    Mutanen, Marko; Wahlberg, Niklas; Kaila, Lauri

    2010-09-22

    Lepidoptera (butterflies and moths) represent one of the most diverse animals groups. Yet, the phylogeny of advanced ditrysian Lepidoptera, accounting for about 99 per cent of lepidopteran species, has remained largely unresolved. We report a rigorous and comprehensive analysis of lepidopteran affinities. We performed phylogenetic analyses of 350 taxa representing nearly 90 per cent of lepidopteran families. We found Ditrysia to be a monophyletic taxon with the clade Tischerioidea + Palaephatoidea being the sister group of it. No support for the monophyly of the proposed major internested ditrysian clades, Apoditrysia, Obtectomera and Macrolepidoptera, was found as currently defined, but each of these is supported with some modification. The monophyly or near-monophyly of most previously identified lepidopteran superfamilies is reinforced, but several species-rich superfamilies were found to be para- or polyphyletic. Butterflies were found to be more closely related to 'microlepidopteran' groups of moths rather than the clade Macrolepidoptera, where they have traditionally been placed. There is support for the monophyly of Macrolepidoptera when butterflies and Calliduloidea are excluded. The data suggest that the generally short diverging nodes between major groupings in basal non-tineoid Ditrysia are owing to their rapid radiation, presumably in correlation with the radiation of flowering plants.

  7. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate.

    PubMed

    Varaljay, Vanessa A; Robidart, Julie; Preston, Christina M; Gifford, Scott M; Durham, Bryndan P; Burns, Andrew S; Ryan, John P; Marin, Roman; Kiene, Ronald P; Zehr, Jonathan P; Scholin, Christopher A; Moran, Mary Ann

    2015-07-01

    The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community [corrected].These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.

  8. Biological richness of a large urban cemetery in Berlin. Results of a multi-taxon approach

    PubMed Central

    Blick, Theo; Hannig, Karsten; Kowarik, Ingo; Lemke, Andreas; Otte, Volker; Scharon, Jens; Schönhofer, Axel; Teige, Tobias; von der Lippe, Moritz; Seitz, Birgit

    2016-01-01

    Abstract Background Urban green spaces can harbor a considerable species richness of plants and animals. A few studies on single species groups indicate important habitat functions of cemeteries, but this land use type is clearly understudied compared to parks. Such data are important as they (i) illustrate habitat functions of a specific, but ubiquitous urban land-use type and (ii) may serve as a basis for management approaches. New information We sampled different groups of plants and animals in the Weißensee Jewish Cemetery in Berlin (WJC) which is one of the largest Jewish cemeteries in Europe. With a total of 608 species of plants and animals, this first multi-taxon survey revealed a considerable biological richness in the WJC. In all, 363 wild-growing vascular plant, 72 lichen and 26 bryophyte taxa were recorded. The sampling also yielded 34 bird and 5 bat species as well as 39 ground beetle, 5 harvestman and 64 spider species. Some species are new records for Berlin. PMID:27099549

  9. A macrophyte bioassessment approach linking taxon-specific tolerance and abundance in north temperate lakes.

    PubMed

    Mikulyuk, Alison; Barton, Martha; Hauxwell, Jennifer; Hein, Catherine; Kujawa, Ellen; Minahan, Kristi; Nault, Michelle E; Oele, Daniel L; Wagner, Kelly I

    2017-09-01

    Bioassessment methods are critically needed to evaluate and monitor lake ecological condition. Aquatic macrophytes are good candidate indicators, but few lake bioassessment methods developed in North America use them. The few macrophyte bioassessment methods that do exist suffer from problems related to subjectivity and discernibility along disturbance gradients. We developed and tested a bioassessment approach for 462 north temperate lakes. The approach links macrophyte abundance to lake ecological condition via estimates of taxon-specific abundance-weighted tolerance to anthropogenic disturbance. Using variables related to eutrophication, urban development and agriculture, we calculated abundance-weighted tolerance ranges for 59 macrophyte taxa and clustered them according to their tolerance to anthropogenic disturbance. We also created a composite index of anthropogenic disturbance using 20 variables related to population density, land cover and water chemistry. We used a statistical approach to set ecological condition thresholds based on the observed abundance of sensitive, moderately tolerant and tolerant taxa in each lake. The resulting lake condition categories were usually stable across multiple survey events and largely agreed with condition rankings assigned using expert judgment. We suggest using this macrophyte bioassessment method for federal water quality reports, restoration and management on north temperate lakes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. 'Candidatus Phytoplasma luffae', a novel taxon associated with witches' broom disease of loofah, Luffa aegyptica Mill.

    PubMed

    Davis, Robert E; Zhao, Yan; Wei, Wei; Dally, Ellen L; Lee, Ing-Ming

    2017-08-01

    The phytoplasma associated with witches' broom disease of loofah [Luffa aegyptica Mill., syn. Luffa cylindrica (L.) M.J. Roem.] in Taiwan was classified in group 16SrVIII, subgroup A (16SrVIII-A), based on results from actual and in silico RFLP analysis of 16S rRNA gene sequences. Nucleotide sequencing of PCR-amplified, cloned DNA segments revealed rrn interoperon sequence heterogeneity in the loofah witches' broom (LfWB) phytoplasma. Whereas the 16S-23S rRNA spacer region of rrnA contained a complete tRNA-Ile gene, the spacer of rrnB contained a nonfunctional remnant of a tRNA gene. Phylogenetic analysis of the rrnA and rrnB 16S rRNA genes revealed that the LfWB phytoplasma represented a distinct lineage within the phytoplasma clade, and the LfWB phytoplasma shared less than 97.5 % nucleotide sequence similarity of 16S rRNA genes with previously described 'CandidatusPhytoplasma' taxa. Based on unique properties of DNA, we propose recognition of loofah witches' broom phytoplasma strain LfWBR as representative of a novel taxon, 'CandidatusPhytoplasma luffae'.

  11. Trade-off between taxon diversity and functional diversity in European lake ecosystems.

    PubMed

    Grossmann, Lars; Beisser, Daniela; Bock, Christina; Chatzinotas, Antonis; Jensen, Manfred; Preisfeld, Angelika; Psenner, Roland; Rahmann, Sven; Wodniok, Sabina; Boenigk, Jens

    2016-12-01

    Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  12. Mycobacterial contamination of metalworking fluids: involvement of a possible new taxon of rapidly growing mycobacteria.

    PubMed

    Moore, J S; Christensen, M; Wilson, R W; Wallace, R J; Zhang, Y; Nash, D R; Shelton, B

    2000-01-01

    Contamination of air and metalworking fluid (MWF) systems with a rapidly growing mycobacterium (RGM) was detected in 1995 in a single manufacturing plant with recent cases of hypersensitivity pneumonitis (HP). Extensive environmental sampling was performed to determine the extent of the contamination and its variability over time. RGM were present in multiple indoor air samples, 100% of the central MWF storage tanks, and 75% of the freestanding cutting, drilling, and grinding machines. With one exception, contamination was limited to a recently introduced formulation (brand) of semisynthetic MWF used in 95% of the facility's machining operations. In general, the mycobacterial counts were stable over time, with the degree of contamination ranging from 10(2)-10(7) colony forming units (CFU)/mL. A few systems were culture positive for the mycobacterium (> 10(1) CFU/mL), changed to culture negative (< 10(1) CFU/mL), then changed back to culture positive without explanation. Samples obtained from diluted (5%) but unused MWF, a replenishment line with 2% unused MWF, an MWF pasteurizer, city water, and deionized water were culture negative for this species of mycobacterium. Inoculation and growth studies demonstrated that this mycobacterium does not grow in liquid samples of 5% unused MWF. By molecular techniques, the mycobacterial isolates consisted of a single strain and represented a previously undescribed taxon closely related to Mycobacterium chelonae/abscessus. The relationship of this mycobacterium to the cases of HP is unknown.

  13. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

    PubMed Central

    Varaljay, Vanessa A; Robidart, Julie; Preston, Christina M; Gifford, Scott M; Durham, Bryndan P; Burns, Andrew S; Ryan, John P; Marin III, Roman; Kiene, Ronald P; Zehr, Jonathan P; Scholin, Christopher A; Ann Moran, Mary

    2015-01-01

    The ‘bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the cleavage pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the demethylation pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated. PMID:25700338

  14. A New Taxon of Basal Ceratopsian from China and the Early Evolution of Ceratopsia

    PubMed Central

    Han, Fenglu; Forster, Catherine A.; Clark, James M.; Xu, Xing

    2015-01-01

    Ceratopsia is one of the best studied herbivorous ornithischian clades, but the early evolution of Ceratopsia, including the placement of Psittacosaurus, is still controversial and unclear. Here, we report a second basal ceratopsian, Hualianceratops wucaiwanensis gen. et sp. nov., from the Upper Jurassic (Oxfordian) Shishugou Formation of the Junggar Basin, northwestern China. This new taxon is characterized by a prominent caudodorsal process on the subtemporal ramus of the jugal, a robust quadrate with an expansive quadratojugal facet, a prominent notch near the ventral region of the quadrate, a deep and short dentary, and strongly rugose texturing on the lateral surface of the dentary. Hualianceratops shares several derived characters with both Psittacosaurus and the basal ceratopsians Yinlong, Chaoyangsaurus, and Xuanhuaceratops. A new comprehensive phylogeny of ceratopsians weakly supports both Yinlong and Hualianceratops as chaoyangsaurids (along with Chaoyangsaurus and Xuanhuaceratops), as well as the monophyly of Chaoyangosauridae + Psittacosaurus. This analysis also weakly supports the novel hypothesis that Chaoyangsauridae + Psittacosaurus is the sister group to the rest of Neoceratopsia, suggesting a basal split between these clades before the Late Jurassic. This phylogeny and the earliest Late Jurassic age of Yinlong and Hualianceratops imply that at least five ceratopsian lineages (Yinlong, Hualianceratops, Chaoyangsaurus + Xuanhuaceratops, Psittacosaurus, Neoceratopsia) were present at the beginning of the Late Jurassic. PMID:26649770

  15. Negevirus: a Proposed New Taxon of Insect-Specific Viruses with Wide Geographic Distribution

    PubMed Central

    Vasilakis, Nikos; Forrester, Naomi L.; Palacios, Gustavo; Nasar, Farooq; Savji, Nazir; Rossi, Shannan L.; Guzman, Hilda; Wood, Thomas G.; Popov, Vsevolod; Gorchakov, Rodion; González, Ana Vázquez; Haddow, Andrew D.; Watts, Douglas M.; da Rosa, Amelia P. A. Travassos; Weaver, Scott C.; Lipkin, W. Ian

    2013-01-01

    Six novel insect-specific viruses, isolated from mosquitoes and phlebotomine sand flies collected in Brazil, Peru, the United States, Ivory Coast, Israel, and Indonesia, are described. Their genomes consist of single-stranded, positive-sense RNAs with poly(A) tails. By electron microscopy, the virions appear as spherical particles with diameters of ∼45 to 55 nm. Based on their genome organization and phylogenetic relationship, the six viruses, designated Negev, Ngewotan, Piura, Loreto, Dezidougou, and Santana, appear to form a new taxon, tentatively designated Negevirus. Their closest but still distant relatives are citrus leposis virus C (CiLV-C) and viruses in the genus Cilevirus, which are mite-transmitted plant viruses. The negeviruses replicate rapidly and to high titer (up to 1010 PFU/ml) in mosquito cells, producing extensive cytopathic effect and plaques, but they do not appear to replicate in mammalian cells or mice. A discussion follows on their possible biological significance and effect on mosquito vector competence for arboviruses. PMID:23255793

  16. Widespread and Persistent Populations of a Major New Marine Actinomycete Taxon in Ocean Sediments

    PubMed Central

    Mincer, Tracy J.; Jensen, Paul R.; Kauffman, Christopher A.; Fenical, William

    2002-01-01

    A major taxon of obligate marine bacteria within the order Actinomycetales has been discovered from ocean sediments. Populations of these bacteria (designated MAR 1) are persistent and widespread, spanning at least three distinct ocean systems. In this study, 212 actinomycete isolates possessing MAR 1 morphologies were examined and all but two displayed an obligate requirement of seawater for growth. Forty-five of these isolates, representing all observed seawater-requiring morphotypes, were partially sequenced and found to share characteristic small-subunit rRNA signature nucleotides between positions 207 and 468 (Escherichia coli numbering). Phylogenetic characterization of seven representative isolates based on almost complete sequences of genes encoding 16S rRNA (16S ribosomal DNA) yielded a monophyletic clade within the family Micromonosporaceae and suggests novelty at the genus level. This is the first evidence for the existence of widespread populations of obligate marine actinomycetes. Organic extracts from cultured members of this new group exhibit remarkable biological activity, suggesting that they represent a prolific resource for biotechnological applications. PMID:12324350

  17. Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

    PubMed

    Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P; Carvalho, Valeria L; da Silva, Sandro Patroca; Cardoso, Jedson F; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G; Widen, Steven G; Vasconcelos, Pedro F C; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B

    2017-04-01

    The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses.

  18. 'Candidatus phytoplasma ziziphi', a novel phytoplasma taxon associated with jujube witches'-broom disease.

    PubMed

    Jung, Hee-Young; Sawayanagi, Toshimi; Kakizawa, Shigeyuki; Nishigawa, Hisashi; Wei, Wei; Oshima, Kenro; Miyata, Shin-ichi; Ugaki, Masashi; Hibi, Tadaaki; Namba, Shigetou

    2003-07-01

    Phylogenetic relationships of five jujube witches'-broom (JWB) phytoplasma isolates from four different districts, and other phytoplasmas, were investigated by 16S rDNA PCR amplification and sequence analysis. The 16S rDNA sequences of any pair of the five isolates of JWB phytoplasmas were > 99.5% similar. The JWB phytoplasma 16S rDNA sequences were most closely related to that of the elm yellows (EY) phytoplasma in 16S-group VIII. Phylogenetic analysis of the 16S rDNA sequences from the JWB phytoplasma isolates, together with sequences from most of the phytoplasmas archived in GenBank, produced a tree in which the JWB isolates clustered as a discrete subgroup. The uniqueness of the JWB phytoplasma appears to be correlated with a specific insect vector (Hishimonus sellatus) and the host plant (Zizyphus jujuba), or with a specific geographical distribution. The unique properties of the JWB phytoplasma sequences clearly indicate that it represents a novel taxon, 'Candidatus Phytoplasma ziziphi'.

  19. 'Candidatus Phytoplasma castaneae', a novel phytoplasma taxon associated with chestnut witches' broom disease.

    PubMed

    Jung, Hee-Young; Sawayanagi, Toshimi; Kakizawa, Shigeyuki; Nishigawa, Hisashi; Miyata, Shin-ichi; Oshima, Kenro; Ugaki, Masashi; Lee, Joon-Tak; Hibi, Tadaaki; Namba, Shigetou

    2002-09-01

    In Korea, Japanese chestnut trees (Castanea crenata Sieb. and Zucc.) showing symptoms indicative of witches' broom disease, including abnormally small leaves and yellowing of young leaves, were examined. Since the symptoms were suggestive of a phytoplasma infection, tissues were assayed for phytoplasmas by PCR analysis using a pair of universal primers that amplify a 1.4-kbp phytoplasma 16S rDNA fragment. The phytoplasma-specific fragment was amplified from diseased plants, but not from healthy plants, indicating that a phytoplasma was the causal agent of the chestnut witches' broom (CnWB) disease. The phylogenetic relationship of the CnWB phytoplasma to other phytoplasmas was examined by sequence analysis of the 16S rDNA. A phylogenetic analysis of 16S rDNA sequences of the phytoplasmas placed the CnWB phytoplasma within a distinct subgroup in the phytoplasma clade of the class Mollicutes. The phylogenetic tree indicated that the CnWB phytoplasma is related most closely to coconut phytoplasmas and suggested that they share a common ancestor. The unique properties of the CnWB phytoplasma sequences clearly establish that it represents a novel taxon, 'Candidatus Phytoplasma castaneae'.

  20. 'Candidatus Phytoplasma brasiliense', a new phytoplasma taxon associated with hibiscus witches' broom disease.

    PubMed

    Montano, H G; Davis, R E; Dally, E L; Hogenhout, S; Pimentel, J P; Brioso, P S

    2001-05-01

    Hibiscus rosa-sinensis is a valuable ornamental species widely planted in Brazil. Many plants are affected by witches' broom disease, which is characterized by excessive axillary branching, abnormally small leaves, and deformed flowers, symptoms that are characteristic of diseases attributed to phytoplasmas. A phytoplasma was detected in diseased Hibiscus by amplification of rRNA operon sequences by PCRs, and was characterized by RFLP and nucleotide sequence analyses of 16S rDNA. The collective RFLP patterns of amplified 16S rDNA differed from the patterns described previously for other phytoplasmas. On the basis of the RFLP patterns, the hibiscus witches' broom phytoplasma was classified in a new 16S rRNA RFLP group, designated group 16SrXV. A phylogenetic analysis of 16S rDNA sequences from this and other phytoplasmas identified the hibiscus witches' broom phytoplasma as a member of a distinct subclade (designated subclade xiv) of the class Mollicutes. A phylogenetic tree constructed on the basis of 16S rRNA gene sequences was consistent with the hypothesis that there was divergent evolution of hibiscus witches' broom phytoplasma and its closest relatives (members of 16S rRNA RFLP group 16SrII) from a common ancestor. On the basis of unique properties of the DNA from hibiscus witches' broom phytoplasma, it is proposed that it represents a new taxon, namely 'Candidatus Phytoplasma brasiliense'.

  1. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

    PubMed Central

    Song, Sen; Liu, Liang; Edwards, Scott V.; Wu, Shaoyuan

    2012-01-01

    The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity. PMID:22930817

  2. 76 FR 9250 - Taking of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-17

    ... the general goals listed below: (1) Avoidance or minimization of injury or death of marine mammals... mammals to levels of sound likely to result in injury or death of marine mammals; (3) several cautionary... injured or killed and the injury or death could be associated with the Navy's activity. The injury...

  3. Marine mammal impacts in exploited ecosystems: would large scale culling benefit fisheries?

    PubMed

    Morissette, Lyne; Christensen, Villy; Pauly, Daniel

    2012-01-01

    Competition between marine mammals and fisheries for marine resources-whether real or perceived-has become a major issue for several countries and in international fora. We examined trophic interactions between marine mammals and fisheries based on a resource overlap index, using seven Ecopath models including marine mammal groups. On a global scale, most food consumed by marine mammals consisted of prey types that were not the main target of fisheries. For each ecosystem, the primary production required (PPR) to sustain marine mammals was less than half the PPR to sustain fisheries catches. We also developed an index representing the mean trophic level of marine mammal's consumption (TL(Q)) and compared it with the mean trophic level of fisheries' catches (TL(C)). Our results showed that overall TL(Q) was lower than TL(C) (2.88 versus 3.42). As fisheries increasingly exploit lower-trophic level species, the competition with marine mammals may become more important. We used mixed trophic impact analysis to evaluate indirect trophic effects of marine mammals, and in some cases found beneficial effects on some prey. Finally, we assessed the change in the trophic structure of an ecosystem after a simulated extirpation of marine mammal populations. We found that this lead to alterations in the structure of the ecosystems, and that there was no clear and direct relationship between marine mammals' predation and the potential catch by fisheries. Indeed, total biomass, with no marine mammals in the ecosystem, generally remained surprisingly similar, or even decreased for some species.

  4. Introduced species: domestic mammals are more significant transmitters of parasites to native mammals than are feral mammals.

    PubMed

    Landaeta-Aqueveque, Carlos; Henríquez, Analía; Cattan, Pedro E

    2014-03-01

    The study of parasitism related to biological invasion has focused on attributes and impacts of parasites as invaders and the impact of introduced hosts on endemic parasitism. Thus, there is currently no study of the attributes of hosts which influence the invasiveness of parasites. We aimed to determine whether the degree of domestication of introduced mammalian species - feral introduced mammals, livestock or pets, hereafter 'D' - is important in the spillover of introduced parasites. The literature on introduced parasites of mammals in Chile was reviewed. We designed an index for estimating the relevance of the introduced host species to parasite spillover and determined whether the D of introduced mammals predicted this index. A total of 223 introduced parasite species were found. Our results indicate that domestic mammals have a higher number of introduced parasites and spillover parasites, and the index indicates that these mammals, particularly pets, are more relevant introducers than introduced feral mammals. Further analyses indicated that the higher impact is due to higher parasite richness, a longer time since introduction and wider dispersal, as well as how these mammals are maintained. The greater relevance of domestic mammals is important given that they are basically the same species distributed worldwide and can become the main transmitters of parasites to native mammals elsewhere. This finding also underlines the feasibility of management in order to reduce the transmission of parasites to native fauna through anti-parasitic treatment of domestic mammals, animal-ownership education and the prevention of importing new parasite species. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  5. 50 CFR 216.37 - Marine mammal parts.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 10 2013-10-01 2013-10-01 false Marine mammal parts. 216.37 Section 216... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Special Exceptions § 216.37 Marine mammal parts. With respect to marine mammal parts acquired by...

  6. 50 CFR 216.37 - Marine mammal parts.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Marine mammal parts. 216.37 Section 216... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Special Exceptions § 216.37 Marine mammal parts. With respect to marine mammal parts acquired by...

  7. 50 CFR 216.37 - Marine mammal parts.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 10 2012-10-01 2012-10-01 false Marine mammal parts. 216.37 Section 216... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Special Exceptions § 216.37 Marine mammal parts. With respect to marine mammal parts acquired by...

  8. 50 CFR 216.37 - Marine mammal parts.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Marine mammal parts. 216.37 Section 216.37..., DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Special Exceptions § 216.37 Marine mammal parts. With respect to marine mammal parts acquired by take or...

  9. 50 CFR 216.83 - Importation of birds or mammals.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Importation of birds or mammals. 216.83... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Pribilof Islands Administration § 216.83 Importation of birds or mammals. No mammals or birds...

  10. Report on marine mammal stranding

    NASA Astrophysics Data System (ADS)

    Kumar, Mohi

    2006-06-01

    The U.S. National Oceanic and Atmospheric Administration (NOAA) released a report on 27 April indicating that U.S. Navy sonar transmissions may have played a role in the stranding of more than 150 melon-headed whales on 3 July 2004 off the coast of Kauai, Hawaii. At the time of the stranding, which resulted in one whale death, the Navy was preparing to conduct sonar activities as part of a military exercise. The report notes that six naval surface vessels transiting to the area on the previous night intermittenly transmitted mid-frequency active sonar. That activity is ``a plausible, if not likely, contributing factor'' to the stranding event. There was no significant weather, natural oceanographic event, or known biological factors that would explain the animals' movement into the bay nor the group's continued presence in the bay, according to report lead author Teri Rowles, NOAA marine mammal veterinarian.

  11. Natural History of Oregon Coast Mammals

    Treesearch

    Chris Maser; Bruce R. Mate; Jerry F. Franklin; C.T. Dyrness

    1981-01-01

    The book presents detailed information on the biology, habitats, and life histories of the 96 species of mammals of the Oregon coast. Soils, geology, and vegetation are described and related to wildlife habitats for the 65 terrestrial and 31 marine species. The book is not simply an identification guide to the Oregon coast mammals but is a dynamic portrayal of their...

  12. MARINE MAMMAL DISEASES: PATHOGENS AND PROCESSES

    EPA Science Inventory

    The purpose of this chapter is to provide a concise overview of the pathogens and processes that alter the health of marine mammals. Viral disease is the most common etiology of significant mortality events in marine mammals. Discussion of viral disease focuses on effects in the ...

  13. MARINE MAMMAL DISEASES: PATHOGENS AND PROCESSES

    EPA Science Inventory

    The purpose of this chapter is to provide a concise overview of the pathogens and processes that alter the health of marine mammals. Viral disease is the most common etiology of significant mortality events in marine mammals. Discussion of viral disease focuses on effects in the ...

  14. The first multituberculate mammal from India

    NASA Astrophysics Data System (ADS)

    Parmar, Varun; Prasad, Guntupalli V. R.; Kumar, Deepak

    2013-06-01

    Mesozoic deposits of the former Gondwanaland are depauperate in early mammals, in general, and multituberculate mammals, in particular. Until now, the oldest multituberculate mammals known from the Gondwanan continents come from the Early Cretaceous of Morocco, NW Africa. Here, we report the presence of a new multituberculate mammal, Indobaatar zofiae gen. et sp. nov., from the Lower/Middle Jurassic Kota Formation, Pranhita-Godavari valley in peninsular India. This is the first record of a multituberculate from the Mesozoic rocks of India and possibly predates the oldest known multituberculates from Gondwanan continents. The new specimen, representing an upper premolar (P4), compares well with the upper premolar morphology of Eobaatariinae multituberculates known from the Early Cretaceous of Mongolia, China, England, and Spain. Together with the recent findings of cimolodontan multituberculates from the Early Cretaceous of Australia and Late Cretaceous of South America, the new discovery indicates a wide temporal and spatial distribution for multituberculate mammals in the former Gondwanaland.

  15. The first multituberculate mammal from India.

    PubMed

    Parmar, Varun; Prasad, Guntupalli V R; Kumar, Deepak

    2013-06-01

    Mesozoic deposits of the former Gondwanaland are depauperate in early mammals, in general, and multituberculate mammals, in particular. Until now, the oldest multituberculate mammals known from the Gondwanan continents come from the Early Cretaceous of Morocco, NW Africa. Here, we report the presence of a new multituberculate mammal, Indobaatar zofiae gen. et sp. nov., from the Lower/Middle Jurassic Kota Formation, Pranhita-Godavari valley in peninsular India. This is the first record of a multituberculate from the Mesozoic rocks of India and possibly predates the oldest known multituberculates from Gondwanan continents. The new specimen, representing an upper premolar (P(4)), compares well with the upper premolar morphology of Eobaatariinae multituberculates known from the Early Cretaceous of Mongolia, China, England, and Spain. Together with the recent findings of cimolodontan multituberculates from the Early Cretaceous of Australia and Late Cretaceous of South America, the new discovery indicates a wide temporal and spatial distribution for multituberculate mammals in the former Gondwanaland.

  16. Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use.

    PubMed

    Long, Ryan A; Wambua, Alois; Goheen, Jacob R; Palmer, Todd M; Pringle, Robert M

    2017-07-01

    Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey plants; (ii) how these effects vary with climatic context (here, seasonality in rainfall); and (iii) the extent to which behavioural responses of small mammals are contingent upon small-mammal density. We tested the effects of a diverse LMH community on small-mammal habitat use using 4 years of spatially explicit small-mammal trapping and vegetation data from the UHURU Experiment, a replicated set of LMH exclosures in semi-arid Kenyan savanna. Small-mammal habitat use was positively associated with tree density and negatively associated with bare (unvegetated) patches in all plots and seasons. In the presence of LMH, and especially during the dry season, small mammals consistently selected tree cover and avoided bare patches. In contrast, when LMH were excluded, small mammals were weakly associated with tree cover and did not avoid bare patches as strongly. These behavioural responses of small mammals were largely unaffected by changes in small-mammal density associated with LMH exclusion. Our results show that LMH indirectly affect small-mammal behaviour, and that these effects are influenced by climate and can arise via density-independent mechanisms. This raises the possibility that anthropogenic LMH declines might interact with changing patterns of rainfall to alter small-mammal distribution and behaviour, independent of numerical responses by small mammals to these perturbations. For example, increased rainfall in East

  17. A new perspective on adiposity in a naturally obese mammal

    NASA Technical Reports Server (NTRS)

    Ortiz, R. M.; Noren, D. P.; Litz, B.; Ortiz, C. L.

    2001-01-01

    Many mammals seasonally reduce body fat due to inherent periods of fasting, which is associated with decreased leptin concentrations. However, no data exist on the correlation between fat mass (FM) and circulating leptin in marine mammals, which have evolved large fat stores as part of their adaptation to periods of prolonged fasting. Therefore, FM was estimated (by tritiated water dilution), and serum leptin and cortisol were measured in 40 northern elephant seal (Mirounga angustirostris) pups early (<1 wk postweaning) and late (6-8 wk postweaning) during their natural, postweaning fast. Body mass (BM) and FM were reduced late; however, percent FM (early: 43.9 +/- 0.5, late: 45.5 +/- 0.5%) and leptin [early: 2.9 +/- 0.1 ng/ml human equivalents (HE), late: 3.0 +/- 0.1 ng/ml HE] did not change. Cortisol increased between early (9.2 +/- 0.5 microg/dl) and late (16.3 +/- 0.9 microg/dl) periods and was significantly and negatively correlated with BM (r = 0.426; P < 0.0001) and FM (r = 0.328; P = 0.003). FM and percent FM were not correlated (P > 0.10) with leptin at either period. The present study suggests that these naturally obese mammals appear to possess a novel cascade for regulating body fat that includes cortisol. The lack of a correlation between leptin and FM may reflect the different functions of fat between terrestrial and marine mammals.

  18. Spiny plants, mammal browsers, and the origin of African savannas.

    PubMed

    Charles-Dominique, Tristan; Davies, T Jonathan; Hempson, Gareth P; Bezeng, Bezeng S; Daru, Barnabas H; Kabongo, Ronny M; Maurin, Olivier; Muasya, A Muthama; van der Bank, Michelle; Bond, William J

    2016-09-20

    Savannas first began to spread across Africa during the Miocene. A major hypothesis for explaining this vegetation change is the increase in C4 grasses, promoting fire. We investigated whether mammals could also have contributed to savanna expansion by using spinescence as a marker of mammal herbivory. Looking at the present distribution of 1,852 tree species, we established that spinescence is mainly associated with two functional types of mammals: large browsers and medium-sized mixed feeders. Using a dated phylogeny for the same tree species, we found that spinescence evolved at least 55 times. The diversification of spiny plants occurred long after the evolution of Afrotherian proboscideans and hyracoids. However, it is remarkably congruent with diversification of bovids, the lineage including the antelope that predominantly browse these plants today. Our findings suggest that herbivore-adapted savannas evolved several million years before fire-maintained savannas and probably, in different environmental conditions. Spiny savannas with abundant mammal herbivores occur in drier climates and on nutrient-rich soils, whereas fire-maintained savannas occur in wetter climates on nutrient-poor soils.

  19. A new perspective on adiposity in a naturally obese mammal.

    PubMed

    Ortiz, R M; Noren, D P; Litz, B; Ortiz, C L

    2001-12-01

    Many mammals seasonally reduce body fat due to inherent periods of fasting, which is associated with decreased leptin concentrations. However, no data exist on the correlation between fat mass (FM) and circulating leptin in marine mammals, which have evolved large fat stores as part of their adaptation to periods of prolonged fasting. Therefore, FM was estimated (by tritiated water dilution), and serum leptin and cortisol were measured in 40 northern elephant seal (Mirounga angustirostris) pups early (<1 wk postweaning) and late (6-8 wk postweaning) during their natural, postweaning fast. Body mass (BM) and FM were reduced late; however, percent FM (early: 43.9 +/- 0.5, late: 45.5 +/- 0.5%) and leptin [early: 2.9 +/- 0.1 ng/ml human equivalents (HE), late: 3.0 +/- 0.1 ng/ml HE] did not change. Cortisol increased between early (9.2 +/- 0.5 microg/dl) and late (16.3 +/- 0.9 microg/dl) periods and was significantly and negatively correlated with BM (r = 0.426; P < 0.0001) and FM (r = 0.328; P = 0.003). FM and percent FM were not correlated (P > 0.10) with leptin at either period. The present study suggests that these naturally obese mammals appear to possess a novel cascade for regulating body fat that includes cortisol. The lack of a correlation between leptin and FM may reflect the different functions of fat between terrestrial and marine mammals.

  20. Spiny plants, mammal browsers, and the origin of African savannas

    PubMed Central

    Charles-Dominique, Tristan; Davies, T. Jonathan; Hempson, Gareth P.; Bezeng, Bezeng S.; Kabongo, Ronny M.; Maurin, Olivier; Muasya, A. Muthama; van der Bank, Michelle; Bond, William J.

    2016-01-01

    Savannas first began to spread across Africa during the Miocene. A major hypothesis for explaining this vegetation change is the increase in C4 grasses, promoting fire. We investigated whether mammals could also have contributed to savanna expansion by using spinescence as a marker of mammal herbivory. Looking at the present distribution of 1,852 tree species, we established that spinescence is mainly associated with two functional types of mammals: large browsers and medium-sized mixed feeders. Using a dated phylogeny for the same tree species, we found that spinescence evolved at least 55 times. The diversification of spiny plants occurred long after the evolution of Afrotherian proboscideans and hyracoids. However, it is remarkably congruent with diversification of bovids, the lineage including the antelope that predominantly browse these plants today. Our findings suggest that herbivore-adapted savannas evolved several million years before fire-maintained savannas and probably, in different environmental conditions. Spiny savannas with abundant mammal herbivores occur in drier climates and on nutrient-rich soils, whereas fire-maintained savannas occur in wetter climates on nutrient-poor soils. PMID:27601649

  1. Limits to captive breeding of mammals in zoos.

    PubMed

    Alroy, John

    2015-06-01

    Captive breeding of mammals in zoos is the last hope for many of the best-known endangered species and has succeeded in saving some from certain extinction. However, the number of managed species selected is relatively small and focused on large-bodied, charismatic mammals that are not necessarily under strong threat and not always good candidates for reintroduction into the wild. Two interrelated and more fundamental questions go unanswered: have the major breeding programs succeeded at the basic level of maintaining and expanding populations, and is there room to expand them? I used published counts of births and deaths from 1970 to 2011 to quantify rates of growth of 118 captive-bred mammalian populations. These rates did not vary with body mass, contrary to strong predictions made in the ecological literature. Most of the larger managed mammalian populations expanded consistently and very few programs failed. However, growth rates have declined dramatically. The decline was predicted by changes in the ratio of the number of individuals within programs to the number of mammal populations held in major zoos. Rates decreased as the ratio of individuals in programs to populations increased. In other words, most of the programs that could exist already do exist. It therefore appears that debates over the general need for captive-breeding programs and the best selection of species are moot. Only a concerted effort could create room to manage a substantially larger number of endangered mammals. © 2015, Society for Conservation Biology.

  2. Immunotoxic effects of environmental pollutants in marine mammals.

    PubMed

    Desforges, Jean-Pierre W; Sonne, Christian; Levin, Milton; Siebert, Ursula; De Guise, Sylvain; Dietz, Rune

    2016-01-01

    Due to their marine ecology and life-history, marine mammals accumulate some of the highest levels of environmental contaminants of all wildlife. Given the increasing prevalence and severity of diseases in marine wildlife, it is imperative to understand how pollutants affect the immune system and consequently disease susceptibility. Advancements and adaptations of analytical techniques have facilitated marine mammal immunotoxicology research. Field studies, captive-feeding experiments and in vitro laboratory studies with marine mammals have associated exposure to environmental pollutants, most notable polychlorinated biphenyls (PCBs), organochlorine pesticides and heavy metals, to alterations of both the innate and adaptive arms of immune systems, which include aspects of cellular and humoral immunity. For marine mammals, reported immunotoxicology endpoints fell into several major categories: immune tissue histopathology, haematology/circulating immune cell populations, functional immune assays (lymphocyte proliferation, phagocytosis, respiratory burst, and natural killer cell activity), immunoglobulin production, and cytokine gene expression. Lymphocyte proliferation is by far the most commonly used immune assay, with studies using different organic pollutants and metals predominantly reporting immunosuppressive effects despite the many differences in study design and animal life history. Using combined field and laboratory data, we determined effect threshold levels for suppression of lymphocyte proliferation to be between b0.001-10 ppm for PCBs, 0.002-1.3 ppm for Hg, 0.009-0.06 for MeHg, and 0.1-2.4 for cadmium in polar bears and several pinniped and cetacean species. Similarly, thresholds for suppression of phagocytosis were 0.6-1.4 and 0.08-1.9 ppm for PCBs and mercury, respectively. Although data are lacking for many important immune endpoints and mechanisms of specific immune alterations are not well understood, this review revealed a systemic suppression of

  3. Taxon-specific growth and selective microzooplankton grazing of phytoplankton in the Northeast Atlantic

    NASA Astrophysics Data System (ADS)

    Gaul, Wilhelm; Antia, Avan N.

    2001-10-01

    Taxon-specific microzooplankton dynamics were studied along a transect through the North Atlantic Drift from 70°N 04°E to 40°N 20°W during July 1997 using serial dilution and nutrient-enrichment experiments. Nutrient concentrations and microzooplankton composition indicated postbloom conditions at 40°N, 47°N, and 50°N, a transitional system at 54°N, and bloom conditions at 62°N and 70°N. The ratio of microzooplankton to phytoplankton biomass was inversely related to nitrate and phosphate concentrations. Potential grazing thresholds were observed in four of nine experiments at 40-66% of the initial phytoplankton concentration. Grazing losses were determined for six pigment-specific classes of phytoplankton. Selective grazing losses of phytoplankton taxa ranged from 73% to 248% of the nonselective grazing losses predicted according to their biomass contributions. The grazing selectivity varied considerably between communities, with the microherbivores showing positive selection for cyanobacteria and dinoflagellates and predominantly avoidance of chlorophyta and bacillariophyceae. Microzooplankton did not show a preference for the dominant phytoplankton taxa, but grazed preferentially on fast-growing phytoplankton with minor contributions (<15%) to the phytoplankton biomass. However, bacillariophyceae were the major contributors to phytoplankton biomass and accounted for major fractions of the total losses through microzooplankton grazing. Microzooplankton consumed the equivalent of 0.12-5.5 times their own biomass daily on a carbon basis, amounting to 65-197% of gross phytoplankton production. With the conservative assumption that 20% of the consumed phytoplankton was converted to microzooplankton biomass, the latter was estimated to contribute 27-381% to the net production of the entire microzooplankton community. We therefore conclude that the taxonomic structure and the net production of the microzooplankton communities were significantly affected by the

  4. Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?

    USGS Publications Warehouse

    Vandergast, Amy; Weissman, David B; Wood, Dustin; Rentz, David C F; Bazelet, Corinna S; Ueshima, Norihiro

    2017-01-01

    The relationships among and within the families that comprise the orthopteran superfamily Stenopelmatoidea (suborder Ensifera) remain poorly understood. We developed a phylogenetic hypothesis based on Bayesian analysis of two nuclear ribosomal and one mitochondrial gene for 118 individuals (84 de novo and 34 from GenBank). These included Gryllacrididae from North, Central, and South America, South Africa and Madagascar, Australia and Papua New Guinea; Stenopelmatidae from North and Central America and South Africa; Anostostomatidae from North and Central America, Papua New Guinea, New Zealand, Australia, and South Africa; members of the Australian endemic Cooloola (three species); and a representative of Lezina from the Middle East. We also included representatives of all other major ensiferan families: Prophalangopsidae, Rhaphidophoridae, Schizodactylidae, Tettigoniidae, Gryllidae, Gryllotalpidae and Myrmecophilidae and representatives of the suborder Caelifera as outgroups. Bayesian analyses of concatenated sequence data supported a clade of Stenopelmatoidea inclusive of all analyzed members of Gryllacrididae, Stenopelmatidae, Anostostomatidae, Lezina and Cooloola. We found Gryllacrididae worldwide to be monophyletic, while we did not recover a monophyletic Stenopelmatidae nor Anostostomatidae. Australian Cooloola clustered in a clade composed of Australian, New Zealand, and some (but not all) North American Anostostomatidae. Lezina was included in a clade of New World Anostostomatidae. Finally, we compiled and compared karyotypes and sound production characteristics for each supported group. Chromosome number, centromere position, drumming, and stridulation differed among some groups, but also show variation within groups. This preliminary trait information may contribute toward future studies of trait evolution. Despite greater taxon sampling within Stenopelmatoidea than previous efforts, some relationships among the families examined continue to remain elusive.

  5. A Cross-Taxon Analysis of Insect-Associated Bacterial Diversity

    PubMed Central

    Jones, Ryan Thomas; Sanchez, Leticia Gonzales; Fierer, Noah

    2013-01-01

    Although it is well known that plants and animals harbor microbial symbionts that can influence host traits, the factors regulating the structure of these microbial communities often remain largely undetermined. This is particularly true for insect-associated microbial communities, as few cross-taxon comparisons have been conducted to date. To address this knowledge gap and determine how host phylogeny and ecology affect insect-associated microbial communities, we collected 137 insect specimens representing 39 species, 28 families, and 8 orders, and characterized the bacterial communities associated with each specimen via 16S rRNA gene sequencing. Bacterial taxa within the phylum Proteobacteria were dominant in nearly all insects sampled. On average, the insect-associated bacterial communities were not very diverse, with individuals typically harboring fewer than 8 bacterial phylotypes. Bacterial communities also tended to be dominated by a single phylotype; on average, the most abundant phylotype represented 54.7% of community membership. Bacterial communities were significantly more similar among closely related insects than among less-related insects, a pattern driven by within-species community similarity but detected at every level of insect taxonomy tested. Diet was a poor predictor of bacterial community composition. Individual insect species harbored remarkably unique communities: the distribution of 69.0% of bacterial phylotypes was limited to unique insect species, whereas only 5.7% of phylotypes were detected in more than five insect species. Together these results suggest that host characteristics strongly regulate the colonization and assembly of bacterial communities across insect lineages, patterns that are driven either by co-evolution between insects and their symbionts or by closely related insects sharing conserved traits that directly select for similar bacterial communities. PMID:23613815

  6. A cross-taxon analysis of insect-associated bacterial diversity.

    PubMed

    Jones, Ryan Thomas; Sanchez, Leticia Gonzales; Fierer, Noah

    2013-01-01

    Although it is well known that plants and animals harbor microbial symbionts that can influence host traits, the factors regulating the structure of these microbial communities often remain largely undetermined. This is particularly true for insect-associated microbial communities, as few cross-taxon comparisons have been conducted to date. To address this knowledge gap and determine how host phylogeny and ecology affect insect-associated microbial communities, we collected 137 insect specimens representing 39 species, 28 families, and 8 orders, and characterized the bacterial communities associated with each specimen via 16S rRNA gene sequencing. Bacterial taxa within the phylum Proteobacteria were dominant in nearly all insects sampled. On average, the insect-associated bacterial communities were not very diverse, with individuals typically harboring fewer than 8 bacterial phylotypes. Bacterial communities also tended to be dominated by a single phylotype; on average, the most abundant phylotype represented 54.7% of community membership. Bacterial communities were significantly more similar among closely related insects than among less-related insects, a pattern driven by within-species community similarity but detected at every level of insect taxonomy tested. Diet was a poor predictor of bacterial community composition. Individual insect species harbored remarkably unique communities: the distribution of 69.0% of bacterial phylotypes was limited to unique insect species, whereas only 5.7% of phylotypes were detected in more than five insect species. Together these results suggest that host characteristics strongly regulate the colonization and assembly of bacterial communities across insect lineages, patterns that are driven either by co-evolution between insects and their symbionts or by closely related insects sharing conserved traits that directly select for similar bacterial communities.

  7. Two new cytotypes reinforce that Micronycteris hirsuta Peters, 1869 does not represent a monotypic taxon

    PubMed Central

    2013-01-01

    Background The genus Micronycteris is a diverse group of phyllostomid bats currently comprising 11 species, with diploid number (2n) ranging from 26 to 40 chromosomes. The karyotypic relationships within Micronycteris and between Micronycteris and other phyllostomids remain poorly understood. The karyotype of Micronycteris hirsuta is of particular interest: three different diploid numbers were reported for this species in South and Central Americas with 2n = 26, 28 and 30 chromosomes. Although current evidence suggests some geographic differentiation among populations of M. hirsuta based on chromosomal, morphological, and nuclear and mitochondrial DNA markers, the recognition of new species or subspecies has been avoided due to the need for additional data, mainly chromosomal data. Results We describe two new cytotypes for Micronycteris hirsuta (MHI) (2n = 26 and 25, NF = 32), whose differences in diploid number are interpreted as the products of Robertsonian rearrangements. C-banding revealed a small amount of constitutive heterochromatin at the centromere and the NOR was located in the interstitial portion of the short arm of a second pair, confirmed by FISH. Telomeric probes hybridized to the centromeric regions and weakly to telomeric regions of most chromosomes. The G-banding analysis and chromosome painting with whole chromosome probes from Carollia brevicauda (CBR) and Phyllostomus hastatus (PHA) enabled the establishment of genome-wide homologies between MHI, CBR and PHA. Conclusions The karyotypes of Brazilian specimens of Micronycteris hirsuta described here are new to Micronycteris and reinforce that M. hirsuta does not represent a monotypic taxon. Our results corroborate the hypothesis of karyotypic megaevolution within Micronycteris, and strong evidence for this is that the entire chromosome complement of M. hirsuta was shown to be derivative with respect to species compared in this study. PMID:24359225

  8. Sperm competition and the evolution of sperm design in mammals

    PubMed Central

    2011-01-01

    Background The influence of sperm competition upon sperm size has been a controversial issue during the last 20 years which remains unresolved for mammals. The hypothesis that, when ejaculates compete with rival males, an increase in sperm size would make sperm more competitive because it would increase sperm swimming speed, has generated contradictory results from both theoretical and empirical studies. In addition, the debate has extended to which sperm components should increase in size: the midpiece to accommodate more mitochondria and produce more energy to fuel motility, or the principal piece to generate greater propulsion forces. Results In this study we examined the influence of sperm competition upon sperm design in mammals using a much larger data set (226 species) than in previous analyses, and we corrected for phylogenetic effects by using a more complete and resolved phylogeny, and more robust phylogenetic control methods. Our results show that, as sperm competition increases, all sperm components increase in an integrated manner and sperm heads become more elongated. The increase in sperm length was found to be associated with enhanced swimming velocity, an adaptive trait under sperm competition. Conclusions We conclude that sperm competition has played an important role in the evolution of sperm design in mammals, and discuss why previous studies have failed to detect it. PMID:21232104

  9. Pelagic Ciliates in a Large Mesotrophic Lake: Seasonal Succession and Taxon-Specific Bacterivory in Lake Constance

    NASA Astrophysics Data System (ADS)

    Cleven, Ernst-Josef

    2004-07-01

    The taxonomic composition of the ciliate assemblage and their taxon-specific bacterial grazing rates in Lake Constance were investigated over the course of one year. Bacterial grazing rates were measured using natural fluorescently labelled bacteria (FLB) and compared to bacterial production. Small species such as Balanion planctonicum/Urotricha furcata and Rimostrombidium spp./Halteria sp. were the most numerous ciliates on the annual average. Larger ciliates such as Rimostrombidium lacustris and Limnostrombidium spp. contributed significantly to total ciliate biomass, but were relatively unimportant as bacterial grazers. Per capita ingestion rates ranged from 0-194 bacteria ciliate-1 h-1 and changed seasonally up to a hundredfold within a given taxon. Approximately 1% of the bacterial production were removed by the ciliate community on the annual average. (

  10. Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia.

    PubMed

    Beall, Clifford J; Campbell, Alisha G; Dayeh, Daniel M; Griffen, Ann L; Podar, Mircea; Leys, Eugene J

    2014-01-01

    The uncultivated bacterium Tannerella BU063 (oral taxon 286) is the closest relative to the periodontal pathogen Tannerella forsythia, but is not disease-associated itself. Using a single cell genomics approach, we isolated 12 individual BU063 cells by flow cytometry, and we amplified and sequenced their genomes. Comparative analyses of the assembled genomic scaffolds and their gene contents allowed us to study the diversity of this taxon within the oral community of a single human donor that provided the sample. Eight different BU063 genotypes were represented, all about 5% divergent at the nucleotide level. There were 2 pairs of cells and one group of three that were more highly identical, and may represent clonal populations. We did pooled assemblies on the nearly identical genomes to increase the assembled genomic coverage. The presence of a set of 66 "core" housekeeping genes showed that two of the single cell assemblies and the assembly derived from the three putatively identical cells were essentially complete. As expected, the genome of BU063 is more similar to Tannerella forsythia than any other known genome, although there are significant differences, including a 44% difference in gene content, changes in metabolic pathways, loss of synteny, and an 8-9% difference in GC content. Several identified virulence genes of T. forsythia are not found in BU063 including karilysin, prtH, and bspA. The absence of these genes may explain the lack of periodontal pathogenesis by this species and provides a new foundation to further understand the genome evolution and mechanisms of bacterial-host interaction in closely related oral microbes with different pathogenicity potential.

  11. Single Cell Genomics of Uncultured, Health-Associated Tannerella BU063 (Oral Taxon 286) and Comparison to the Closely Related Pathogen Tannerella forsythia

    PubMed Central

    Beall, Clifford J.; Campbell, Alisha G.; Dayeh, Daniel M.; Griffen, Ann L.; Podar, Mircea; Leys, Eugene J.

    2014-01-01

    The uncultivated bacterium Tannerella BU063 (oral taxon 286) is the closest relative to the periodontal pathogen Tannerella forsythia, but is not disease-associated itself. Using a single cell genomics approach, we isolated 12 individual BU063 cells by flow cytometry, and we amplified and sequenced their genomes. Comparative analyses of the assembled genomic scaffolds and their gene contents allowed us to study the diversity of this taxon within the oral community of a single human donor that provided the sample. Eight different BU063 genotypes were represented, all about 5% divergent at the nucleotide level. There were 2 pairs of cells and one group of three that were more highly identical, and may represent clonal populations. We did pooled assemblies on the nearly identical genomes to increase the assembled genomic coverage. The presence of a set of 66 “core” housekeeping genes showed that two of the single cell assemblies and the assembly derived from the three putatively identical cells were essentially complete. As expected, the genome of BU063 is more similar to Tannerella forsythia than any other known genome, although there are significant differences, including a 44% difference in gene content, changes in metabolic pathways, loss of synteny, and an 8–9% difference in GC content. Several identified virulence genes of T. forsythia are not found in BU063 including karilysin, prtH, and bspA. The absence of these genes may explain the lack of periodontal pathogenesis by this species and provides a new foundation to further understand the genome evolution and mechanisms of bacterial-host interaction in closely related oral microbes with different pathogenicity potential. PMID:24551246

  12. Multiple Continental Radiations and Correlates of Diversification in Lupinus (Leguminosae): Testing for Key Innovation with Incomplete Taxon Sampling

    PubMed Central

    Drummond, Christopher S.; Eastwood, Ruth J.; Miotto, Silvia T. S.; Hughes, Colin E.

    2012-01-01

    Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth–death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18–0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48–1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89–3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36–1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for “replicate adaptive radiations” in the sense of convergent morphological and ecological trajectories among species in different

  13. NITROGEN OUTPUTS OF SMALL MAMMALS FROM FECAL AND URINE DEPOSITION: IMPLICATIONS FOR NITROGEN CYCLING

    EPA Science Inventory

    The contribution of small mammals in nitrogen cycling is poorly understood and could have reverberations back to the producer community by maintaining or even magnifying increased nitrogen availability. Our objective was to model nitrogen outputs (deposition of feces and urine) ...

  14. NITROGEN OUTPUTS OF SMALL MAMMALS FROM FECAL AND URINE DEPOSITION: IMPLICATIONS FOR NITROGEN CYCLING

    EPA Science Inventory

    The contribution of small mammals in nitrogen cycling is poorly understood and could have reverberations back to the producer community by maintaining or even magnifying increased nitrogen availability. Our objective was to model nitrogen outputs (deposition of feces and urine) ...

  15. Implications of invasion by Juniperus virginiana on small mammals in the southern Great Plains

    USGS Publications Warehouse

    Horncastle, V.J.; Hellgren, E.C.; Mayer, P.M.; Ganguli, A.C.; Engle, David M.; Leslie, David M.

    2005-01-01

    Changes in landscape cover in the Great Plains are resulting from the range expansion and invasion of eastern red cedar (Juniperus virginiana). By altering the landscape and local vegetation, red cedar is changing the structure and function of habitat for small mammals. We examined effects of invasion by eastern red cedar on small mammals in 3 plant communities (tallgrass prairie, old field, and cross-timbers forest) in the cross-timbers ecoregion in Oklahoma. We sampled small mammals seasonally from May 2001 to August 2002 by using Sherman live traps and mark-recapture techniques on 3.24-ha, 450-trap grids in each plant community. We sampled vegetation in two hundred twenty-five 12 x 12-m cells within each grid. The structure of the small-mammal community differed among the 3 habitat types, with higher species diversity and richness in the tallgrass-prairie and old-field sites. Overall, the small-mammal community shifted along a gradient of increasing eastern red cedar. In the old-field and tallgrass-prairie plots, occurrence of grassland mammals decreased with increasing red cedar, whereas only 1 woodland mammal species increased. In the cross-timbers forest site, percent woody cover (<1 m in height), rather than cover of red cedar, was the most important factor affecting woodland mammal species. Examination of our data suggests that an increase in overstory cover from 0% to 30% red cedar can change a species-rich prairie community to a depauperate community dominated by 1 species, Peromyscus leucopus. Losses in species diversity and changes in mammal distribution paralleled those seen in avian communities invaded by eastern red cedar. Our results highlight ecological effects of invasion by eastern red cedar on diversity and function at multiple trophic levels. ?? 2005 American Society of Mammalogists.

  16. Large Mesozoic mammals fed on young dinosaurs.

    PubMed

    Hu, Yaoming; Meng, Jin; Wang, Yuanqing; Li, Chuankui

    2005-01-13

    Mesozoic mammals are commonly portrayed as shrew- or rat-sized animals that were mainly insectivorous, probably nocturnal and lived in the shadow of dinosaurs. The largest known Mesozoic mammal represented by substantially complete remains is Repenomamus robustus, a triconodont mammal from the Lower Cretaceous of Liaoning, China. An adult individual of R. robustus was the size of a Virginia opossum. Here we report a new species of the genus, represented by a skeleton with most of the skull and postcranium preserved in articulation. The new species is 50% larger than R. robustus in skull length. In addition, stomach contents associated with a skeleton of R. robustus reveal remains of a juvenile Psittacosaurus, a ceratopsian dinosaur. Our discoveries constitute the first direct evidence that some triconodont mammals were carnivorous and fed on small vertebrates, including young dinosaurs, and also show that Mesozoic mammals had a much greater range of body sizes than previously known. We suggest that Mesozoic mammals occupied diverse niches and that some large mammals probably competed with dinosaurs for food and territory.

  17. Seeking verisimilitude in a class: a systematic review of evidence that the criterial clinical symptoms of schizophrenia are taxonic.

    PubMed

    Linscott, Richard J; Allardyce, Judith; van Os, Jim

    2010-07-01

    This review examines whether there is evidence that the criterion symptoms of Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) (DSM-IV) schizophrenia are taxonic--that schizophrenia is not part of a single distribution of normality. Two taxometric methods, coherent cut kinetics (CCK) and latent variable modeling (LVM), are demonstrated to be sensitive to latent classes and, therefore, were regarded as providing relevant statistical evidence. A systematic literature search identified 24 articles describing analyses of 28 participant cohorts in which CCK or LVM methods were used with one or more criterion symptoms of schizophrenia. Virtually all analyses yielded results that, on first impression, favored taxonic over dimensional interpretations of the latent structure of schizophrenia. However, threats to the internal and external validity of these studies--including biased or inadequate analyses, violation of statistical assumptions, inadequate indicator screening, and the introduction of systematic error through recruitment and sampling--critically undermine this body of work. Uncertainties about the potential effects of perceptual biases, unimodal assessment, and item parceling are also identified, as are limitations in seeking to validate classes with single or double dissociations of outcomes. We conclude that there is no reason to seriously doubt a single-distribution model of schizophrenia because there is no evidence that provides a serious test of this null hypothesis. A second fundamental question remains outstanding: is schizophrenia truly a group of schizophrenias, with taxonic divisions separating its types? We make design and analysis suggestions for future research addressing these questions.

  18. Dengue infection in neotropical forest mammals.

    PubMed

    de Thoisy, Benoît; Lacoste, Vincent; Germain, Adeline; Muñoz-Jordán, Jorge; Colón, Candimar; Mauffrey, Jean-François; Delaval, Marguerite; Catzeflis, François; Kazanji, Mirdad; Matheus, Séverine; Dussart, Philippe; Morvan, Jacques; Setién, Alvaro Aguilar; Deparis, Xavier; Lavergne, Anne

    2009-04-01

    In South America, dengue is the arbovirus-transmitted disease with the highest incidence. Unlike other arboviruses, wild mammals have no confirmed role in the cycle of dengue in the neotropics, although serological studies have suggested a possible secondary amplification cycle involving mammals other than nonhuman primates. In French Guiana, where all four serotypes (DENV-1, DENV-2, DENV-3, DENV-4) are present, the disease is endemic with outbreak events. To determine whether wild mammals can be infected by DENV, rodents, marsupials, and bats were captured over several periods, from 2001 to 2007, at two sites. The first location is a secondary forest surrounded by an urban area where dengue is endemic. The second location is a forest edge site where the disease has not yet emerged. A total of 10,000 trap-nights were performed and 616 mammals were captured. RNAs representing the four DENV serotypes were detected at both sites by reverse-transcriptase polymerase chain reaction in the livers and/or sera of 92 mammals belonging to 14 out of 32 species distributed among all the orders investigated: Rodentia (33 positive/146 tested), Marsupialia (40/318), and Chiroptera (19/152). Sequence analyses of a portion of the capsid and premembrane junction revealed that mammal strains of DENV-1, DENV-2, DENV-3, and DENV-4 had only 92.6%, 89%, 95%, and 95.8% identity, respectively, with strains circulating in the human population during the same periods. Regarding DENV-2, strains related (99% identity) to those responsible for an epidemic event in humans in French Guiana concurrent to the capture sessions were also evidenced, suggesting that wild mammals in edge habitats can be infected by circulating human strains. Our results demonstrate, for the first time, that neotropical wild mammals can be infected with dengue virus. The question of whether mammals maintain DENV in enzootic cycles and can play a role in its reemergence in human populations remains to be answered.

  19. Reconsidering the evolution of brain, cognition, and behavior in birds and mammals

    PubMed Central

    Willemet, Romain

    2013-01-01

    Despite decades of research, some of the most basic issues concerning the extraordinarily complex brains and behavior of birds and mammals, such as the factors responsible for the diversity of brain size and composition, are still unclear. This is partly due to a number of conceptual and methodological issues. Determining species and group differences in brain composition requires accounting for the presence of taxon-cerebrotypes and the use of precise statistical methods. The role of allometry in determining brain variables should be revised. In particular, bird and mammalian brains appear to have evolved in response to a variety of selective pressures influencing both brain size and composition. “Brain” and “cognition” are indeed meta-variables, made up of the variables that are ecologically relevant and evolutionarily selected. External indicators of species differences in cognition and behavior are limited by the complexity of these differences. Indeed, behavioral differences between species and individuals are caused by cognitive and affective components. Although intra-species variability forms the basis of species evolution, some of the mechanisms underlying individual differences in brain and behavior appear to differ from those between species. While many issues have persisted over the years because of a lack of appropriate data or methods to test them; several fallacies, particularly those related to the human brain, reflect scientists' preconceptions. The theoretical framework on the evolution of brain, cognition, and behavior in birds and mammals should be reconsidered with these biases in mind. PMID:23847570

  20. The origin and early radiation of the therapsid mammal-like reptiles: a palaeobiological hypothesis.

    PubMed

    Kemp, T S

    2006-07-01

    The replacement of the basal synapsid pelycosaurs by the more 'mammal-like' therapsids in the Permian was an important event in the history of tetrapods because it initiated the eventual transition to the mammals. It is also an example of taxon replacement in the fossil record that is unusually amenable to explanation, based on a combination of analysis of the biological significance of the inferred character changes, with the stratigraphic, palaeogeographic and palaeoecological circumstances of the time. An hypothesis is presented in which the origin of the therapsids resulted from a correlated progression of character evolution leading to higher levels of metabolic activity and homeostatic regulation of the body. It was a response to the availability of a seasonally arid, savanna-like biome. The subsequent explosive radiation of therapsids was associated with habitat expansion made possible by the Mid-Permian development of geographical continuity between that biome and the temperate biomes. The final extinction of the pelycosaurs was a case of incumbent replacement by the new therapsid lineages.

  1. Assessing Mammal Exposure to Climate Change in the Brazilian Amazon

    PubMed Central

    Ribeiro, Bruno R.; Sales, Lilian P.; De Marco, Paulo; Loyola, Rafael

    2016-01-01

    Human-induced climate change is considered a conspicuous threat to biodiversity in the 21st century. Species’ response to climate change depends on their exposition, sensitivity and ability to adapt to novel climates. Exposure to climate change is however uneven within species’ range, so that some populations may be more at risk than others. Identifying the regions most exposed to climate change is therefore a first and pivotal step on determining species’ vulnerability across their geographic ranges. Here, we aimed at quantifying mammal local exposure to climate change across species’ ranges. We identified areas in the Brazilian Amazon where mammals will be critically exposed to non-analogue climates in the future with different variables predicted by 15 global circulation climate forecasts. We also built a null model to assess the effectiveness of the Amazon protected areas in buffering the effects of climate change on mammals, using an innovative and more realistic approach. We found that 85% of species are likely to be exposed to non-analogue climatic conditions in more than 80% of their ranges by 2070. That percentage is even higher for endemic mammals; almost all endemic species are predicted to be exposed in more than 80% of their range. Exposure patterns also varied with different climatic variables and seem to be geographically structured. Western and northern Amazon species are more likely to experience temperature anomalies while northeastern species will be more affected by rainfall abnormality. We also observed an increase in the number of critically-exposed species from 2050 to 2070. Overall, our results indicate that mammals might face high exposure to climate change and that protected areas will probably not be efficient enough to avert those impacts. PMID:27829036

  2. Assessing Mammal Exposure to Climate Change in the Brazilian Amazon.

    PubMed

    Ribeiro, Bruno R; Sales, Lilian P; De Marco, Paulo; Loyola, Rafael

    2016-01-01

    Human-induced climate change is considered a conspicuous threat to biodiversity in the 21st century. Species' response to climate change depends on their exposition, sensitivity and ability to adapt to novel climates. Exposure to climate change is however uneven within species' range, so that some populations may be more at risk than others. Identifying the regions most exposed to climate change is therefore a first and pivotal step on determining species' vulnerability across their geographic ranges. Here, we aimed at quantifying mammal local exposure to climate change across species' ranges. We identified areas in the Brazilian Amazon where mammals will be critically exposed to non-analogue climates in the future with different variables predicted by 15 global circulation climate forecasts. We also built a null model to assess the effectiveness of the Amazon protected areas in buffering the effects of climate change on mammals, using an innovative and more realistic approach. We found that 85% of species are likely to be exposed to non-analogue climatic conditions in more than 80% of their ranges by 2070. That percentage is even higher for endemic mammals; almost all endemic species are predicted to be exposed in more than 80% of their range. Exposure patterns also varied with different climatic variables and seem to be geographically structured. Western and northern Amazon species are more likely to experience temperature anomalies while northeastern species will be more affected by rainfall abnormality. We also observed an increase in the number of critically-exposed species from 2050 to 2070. Overall, our results indicate that mammals might face high exposure to climate change and that protected areas will probably not be efficient enough to avert those impacts.

  3. Running and Breathing in Mammals

    NASA Astrophysics Data System (ADS)

    Bramble, Dennis M.; Carrier, David R.

    1983-01-01

    Mechanical constraints appear to require that locomotion and breathing be synchronized in running mammals. Phase locking of limb and respiratory frequency has now been recorded during treadmill running in jackrabbits and during locomotion on solid ground in dogs, horses, and humans. Quadrupedal species normally synchronize the locomotor and respiratory cycles at a constant ratio of 1:1 (strides per breath) in both the trot and gallop. Human runners differ from quadrupeds in that while running they employ several phase-locked patterns (4:1, 3:1, 2:1, 1:1, 5:2, and 3:2), although a 2:1 coupling ratio appears to be favored. Even though the evolution of bipedal gait has reduced the mechanical constraints on respiration in man, thereby permitting greater flexibility in breathing pattern, it has seemingly not eliminated the need for the synchronization of respiration and body motion during sustained running. Flying birds have independently achieved phase-locked locomotor and respiratory cycles. This hints that strict locomotor-respiratory coupling may be a vital factor in the sustained aerobic exercise of endothermic vertebrates, especially those in which the stresses of locomotion tend to deform the thoracic complex.

  4. Passive electroreception in aquatic mammals.

    PubMed

    Czech-Damal, Nicole U; Dehnhardt, Guido; Manger, Paul; Hanke, Wolf

    2013-06-01

    Passive electroreception is a sensory modality in many aquatic vertebrates, predominantly fishes. Using passive electroreception, the animal can detect and analyze electric fields in its environment. Most electric fields in the environment are of biogenic origin, often produced by prey items. These electric fields can be relatively strong and can be a highly valuable source of information for a predator, as underlined by the fact that electroreception has evolved multiple times independently. The only mammals that possess electroreception are the platypus (Ornithorhynchus anatinus) and the echidnas (Tachyglossidae) from the monotreme order, and, recently discovered, the Guiana dolphin (Sotalia guianensis) from the cetacean order. Here we review the morphology, function and origin of the electroreceptors in the two aquatic species, the platypus and the Guiana dolphin. The morphology shows certain similarities, also similar to ampullary electroreceptors in fishes, that provide cues for the search for electroreceptors in more vertebrate and invertebrate species. The function of these organs appears to be very similar. Both species search for prey animals in low-visibility conditions or while digging in the substrate, and sensory thresholds are within one order of magnitude. The electroreceptors in both species are innervated by the trigeminal nerve. The origin of the accessory structures, however, is completely different; electroreceptors in the platypus have developed from skin glands, in the Guiana dolphin, from the vibrissal system.

  5. Marine mammals from the Miocene of Panama

    NASA Astrophysics Data System (ADS)

    Uhen, Mark D.; Coates, Anthony G.; Jaramillo, Carlos A.; Montes, Camilo; Pimiento, Catalina; Rincon, Aldo; Strong, Nikki; Velez-Juarbe, Jorge

    2010-12-01

    Panama has produced an abundance of Neogene marine fossils both invertebrate (mollusks, corals, microfossils etc.) and vertebrate (fish, land mammals etc.), but marine mammals have not been previously reported. Here we describe a cetacean thoracic vertebra from the late Miocene Tobabe Formation, a partial cetacean rib from the late Miocene Gatun Formation, and a sirenian caudal vertebra and rib fragments from the early Miocene Culebra Formation. These finds suggest that Central America may yet provide additional fossil marine mammal specimens that will help us to understand the evolution, and particularly the biogeography of these groups.

  6. Habitat patterns in a small mammal community

    SciTech Connect

    Kitchings, J.T.; Levy, D.J.

    1981-11-01

    Microhabitat relationships between four sympatric small mammal species (Peromyscus leucopus, Ochrotomys nuttalli, Blarina brevicauda, and Tamias striatus) were examined to determine if their discriminant analysis of small mammal habitat represented a unique habitat utilization pattern for a specific small mammal community. The authors concluded that habitat is only one of many dimensions to be considered when studying the interactions of sympatric species. Reproductive strategy, activity patterns, and other factors make up the n-dimensional hyperspace of an animal's niche. Thus differences in habitat usage alone cannot be used to determine niche overlap and competition between species. (JMT)

  7. Uncharted waters: nephrogenesis and renal regeneration in fish and mammals.

    PubMed

    Davidson, Alan J

    2011-09-01

    The major functions of the vertebrate kidney are the removal of metabolic waste and the balance of salt and water. These roles are fulfilled by nephrons, which generally comprise a blood filter (glomerulus) attached to an epithelial tubule. The number of nephrons in the mammalian kidney is set at the end of kidney organogenesis in the late fetal or neonatal period. Subsequent increases in nephron size and functionality then occur during postnatal growth to match increases in body mass/fluid. Because of this strategy of renal development, injuries or birth defects that reduce nephron number lead to a permanent nephron deficit and increase the risk of kidney disease. In contrast to mammals, fish kidneys continue to add nephrons throughout their lifespan. In response to renal injury, fish increase the rate of nephrogenesis, effectively replacing lost nephrons and maintaining their nephron endowment. A better understanding of the remarkable nephrogenic abilities of fish kidneys may lead to innovative ways to restore nephrogenesis in the adult mammalian kidney. This review examines our current understanding of nephrogenesis in mammals and fish and explores possible explanations for why fish, but not mammals, utilize a perpetual nephrogenesis strategy to grow and maintain their kidneys.

  8. 77 FR 6771 - Taking and Importing Marine Mammals: Taking Marine Mammals Incidental to U.S. Navy Operations of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-09

    ... Mammals: Taking Marine Mammals Incidental to U.S. Navy Operations of Surveillance Towed Array Sensor... harassment, incidental to conducting operations of Surveillance Towed Array Sensor System (SURTASS)...

  9. Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution

    PubMed Central

    2010-01-01

    alethinophidians. Conclusions Mitochondrial gene sequence data alone may not be able to robustly resolve basal divergences among alethinophidian snakes. Taxon sampling plays an important role in identifying mitogenomic evolutionary events within snakes, and in testing hypotheses explaining their origin. Dramatic rate shifts in mitogenomic evolution occur within Scolecophidia as well as Alethinophidia, thus falsifying the hypothesis that these shifts in snakes are associated exclusively with evolution of a non-burrowing lifestyle, macrostomatan feeding ecology and/or duplication of the control region, both restricted to alethinophidians among living snakes. PMID:20055998

  10. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?

    PubMed Central

    Stefanović, Saša; Rice, Danny W; Palmer, Jeffrey D

    2004-01-01

    Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots. Results We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered monocot sampling under the same analytical conditions used in their study. With Acorus alone representing monocots, strongly supported Amborella-sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella-sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella-sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea, whose position as a basal angiosperm was also, and very recently

  11. Asymmetric hybridization in Rhododendron agastum: a hybrid taxon comprising mainly F1s in Yunnan, China

    PubMed Central

    Zha, Hong-Guang; Milne, Richard I.; Sun, Hang

    2010-01-01

    Background and Aims Rhododendron (Ericaceae) is a large woody genus in which hybridization is thought to play an important role in evolution and speciation, particularly in the Sino-Himalaya region where many interfertile species often occur sympatrically. Rhododendron agastum, a putative hybrid species, occurs in China, western Yunnan Province, in mixed populations with R. irroratum and R. delavayi. Methods Material of these taxa from two sites 400 km apart (ZhuJianYuan, ZJY and HuaDianBa, HDB) was examined using cpDNA and internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) loci, to test the possibility that R. agastum was in fact a hybrid between two of the other species. Chloroplast trnL-F and trnS-trnG sequences together distinguished R. irroratum, R. delavayi and some material of R. decorum, which is also considered a putative parent of R. agastum. Key Results All 14 R. agastum plants from the HDB site had the delavayi cpDNA haplotype, whereas at the ZJY site 17 R. agastum plants had this haplotype and four had the R. irroratum haplotype. R. irroratum and R. delavayi are distinguished by five unequivocal point mutations in their ITS sequences; every R. agastum accession had an additive pattern (double peaks) at each of these sites. Data from AFLP loci were acquired for between ten and 21 plants of each taxon from each site, and were analysed using a Bayesian approach implemented by the program NewHybrids. The program confirmed the identity of all accessions of R. delavayi, and all R. irroratum except one, which was probably a backcross. All R. agastum from HDB and 19 of 21 from ZJY were classified as F1 hybrids; the other two could not be assigned a class. Conclusions Rhododendron agastum represents populations of hybrids between R. irroratum and R. delavayi, which comprise mostly or only F1s, at the two sites examined. The sites differ in that at HDB there was no detected variation in cpDNA type or hybrid class

  12. CARDIOVASCULAR RESPONSES OF DIVING AND NONDIVING MAMMALS TO APNEA.

    DTIC Science & Technology

    anesthetized nutria and cats. In the nutria , arterial blood pressure was maintained an average of 182 seconds after profound bradycardia developed despite a...bradycardia was observed. The increase in peripheral resistance during apnea in cats was less than 20% of that found in nutria . Evidence of cardiac...failure was found before bradycardia in the cat, but not in the nutria . It was concluded cardiovascular responses reported for diving mammals could be

  13. Sound's effects on marine mammals need investigation

    NASA Astrophysics Data System (ADS)

    Green, David M.

    Protecting marine mammals and conducting certain types of marine research, in particular, those that use sound in the ocean, have categorically come into conflict because of our lack of knowledge of the effects of low-frequency sound on marine mammals. Despite its intentions to improve Earth's overall environment, the proposed Acoustic Thermometry of Ocean Climate (ATOC) project, and by implication, other uses of sound in the ocean by oceanographers, are now under fire because of the dearth of data on this very issue.By passing the 1972 Marine Mammal Protection Act, the United States acknowledged that marine mammals are indeed a valuable national resource. Since World War II, the United States has developed and maintained a high-quality marine science research effort.

  14. Ocean Disposal of Marine Mammal Carcasses

    EPA Pesticide Factsheets

    Ocean dumping of marine mammal carcasses is allowed with a permit issued by EPA under the Marine Protection, Research and Sanctuaries Act. Includes permit information, potential environmental impacts, and instructions for getting the general permit.

  15. A Mesozoic gliding mammal from northeastern China.

    PubMed

    Meng, Jin; Hu, Yaoming; Wang, Yuanqing; Wang, Xiaolin; Li, Chuankui

    2006-12-14

    Gliding flight has independently evolved many times in vertebrates. Direct evidence of gliding is rare in fossil records and is unknown in mammals from the Mesozoic era. Here we report a new Mesozoic mammal from Inner Mongolia, China, that represents a previously unknown group characterized by a highly specialized insectivorous dentition and a sizable patagium (flying membrane) for gliding flight. The patagium is covered with dense hair and supported by an elongated tail and limbs; the latter also bear many features adapted for arboreal life. This discovery extends the earliest record of gliding flight for mammals to at least 70 million years earlier in geological history, and demonstrates that early mammals were diverse in their locomotor strategies and lifestyles; they had experimented with an aerial habit at about the same time as, if not earlier than, when birds endeavoured to exploit the sky.

  16. Microparasites and Placental Invasiveness in Eutherian Mammals

    PubMed Central

    Capellini, Isabella; Nunn, Charles L.; Barton, Robert A.

    2015-01-01

    Placental invasiveness—the number of maternal tissue layers separating fetal tissues from maternal blood—is variable across mammalian species. Although this diversity is likely to be functionally important, variation in placental invasiveness remains unexplained. Here we test the hypothesis that increased risk of transplacental transmission of pathogens from the mother to the fetus promotes the evolution of non-invasive placentation, the most likely derived condition in eutherian mammals. Specifically, we predict that non-invasive placentation is associated with increased microparasite species richness relative to more invasive placental types, based on the assumption that higher numbers of microparasites in a population reflects greater risk of transplacental transmission to fetuses. As predicted, higher bacteria species richness is associated with non-invasive placentation. Protozoa species richness, however, shows the opposite pattern. Because invasive placentae facilitate the transfer of maternal antibodies to the fetus, we propose that the ancestral condition of invasive placentation is retained under selection for protection of newborns from higher risk of postnatal protozoan infection. Hence, our findings suggest that a tradeoff exists between protection against bacterial infection prenatally and protozoan infection postnatally. Future studies are needed to investigate how maternal prevalence of infection and the relative pre- versus postnatal risk of fetal infection by different microparasite groups vary among mammalian hosts in relation to placental invasiveness. PMID:26168031

  17. Central control of thermogenesis in mammals

    PubMed Central

    Morrison, Shaun F.; Nakamura, Kazuhiro; Madden, Christopher J.

    2008-01-01

    Thermogenesis, the production of heat energy, is an essential component of the homeostatic repertoire to maintain body temperature in mammals and birds during the challenge of low environmental temperature and plays a key role in elevating body temperature during the febrile response to infection. The primary sources of neurally regulated metabolic heat production are mitochondrial oxidation in brown adipose tissue, increases in heart rate and shivering in skeletal muscle. Thermogenesis is regulated in each of these tissues by parallel networks in the central nervous system, which respond to feedforward afferent signals from cutaneous and core body thermoreceptors and to feedback signals from brain thermosensitive neurons to activate the appropriate sympathetic and somatic efferents. This review summarizes the research leading to a model of the feedforward reflex pathway through which environmental cold stimulates thermogenesis and discusses the influence on this thermoregulatory network of the pyrogenic mediator, prostaglandin E2, to increase body temperature. The cold thermal afferent circuit from cutaneous thermal receptors ascends via second-order thermosensory neurons in the dorsal horn of the spinal cord to activate neurons in the lateral parabrachial nucleus, which drive GABAergic interneurons in the preoptic area to inhibit warm-sensitive, inhibitory output neurons of the preoptic area. The resulting disinhibition of thermogenesis-promoting neurons in the dorsomedial hypothalamus and possibly of sympathetic and somatic premotor neurons in the rostral ventromedial medulla, including the raphe pallidus, activates excitatory inputs to spinal sympathetic and somatic motor circuits to drive thermogenesis. PMID:18469069

  18. Free D-aspartate in mammals.

    PubMed

    Furuchi, Takemitsu; Homma, Hiroshi

    2005-09-01

    D-Aspartate (D-Asp) is an endogenous amino acid present in nervous and endocrine tissues in mammals. A high concentration of D-Asp is observed in embryos, which disappears in nervous tissues after delivery, but increases temporarily in endocrine glands, particularly in the pituitary, pineal and adrenal glands at the specific stages. In the pineal gland, D-Asp that is apparently derived from other tissues suppresses melatonin secretion from parenchymal cells. Additionally, D-Asp levels increase in the testis just before birth and during maturation. The amino acid is presumed to be synthesized by the pituitary gland and testis. In the testis, D-Asp produced inside the seminiferous tubules acts on Leydig cells following release to enhance testosterone synthesis by activating the expression of Steroidogenic Acute Regulatory protein. Mammalian cells appear to contain all the molecular components required to regulate D-Asp homeostasis, as they can synthesize, release, take up, and degrade the amino acid. These findings collectively indicate that D-Asp is a novel type of messenger in the mammalian body.

  19. Central control of thermogenesis in mammals.

    PubMed

    Morrison, Shaun F; Nakamura, Kazuhiro; Madden, Christopher J

    2008-07-01

    Thermogenesis, the production of heat energy, is an essential component of the homeostatic repertoire to maintain body temperature in mammals and birds during the challenge of low environmental temperature and plays a key role in elevating body temperature during the febrile response to infection. The primary sources of neurally regulated metabolic heat production are mitochondrial oxidation in brown adipose tissue, increases in heart rate and shivering in skeletal muscle. Thermogenesis is regulated in each of these tissues by parallel networks in the central nervous system, which respond to feedforward afferent signals from cutaneous and core body thermoreceptors and to feedback signals from brain thermosensitive neurons to activate the appropriate sympathetic and somatic efferents. This review summarizes the research leading to a model of the feedforward reflex pathway through which environmental cold stimulates thermogenesis and discusses the influence on this thermoregulatory network of the pyrogenic mediator, prostaglandin E(2), to increase body temperature. The cold thermal afferent circuit from cutaneous thermal receptors ascends via second-order thermosensory neurons in the dorsal horn of the spinal cord to activate neurons in the lateral parabrachial nucleus, which drive GABAergic interneurons in the preoptic area to inhibit warm-sensitive, inhibitory output neurons of the preoptic area. The resulting disinhibition of thermogenesis-promoting neurons in the dorsomedial hypothalamus and possibly of sympathetic and somatic premotor neurons in the rostral ventromedial medulla, including the raphe pallidus, activates excitatory inputs to spinal sympathetic and somatic motor circuits to drive thermogenesis.

  20. Genomic Imprinting Mechanisms in Mammals

    PubMed Central

    Ideraabdullah, Folami Y.; Vigneau, Sebastien; Bartolomei, Marisa S.

    2008-01-01

    Genomic imprinting is a form of epigenetic gene regulation that results in expression from a single allele in a parent-of-origin-dependent manner. This form of monoallelic expression affects a small but growing number of genes and is essential to normal mammalian development. Despite extensive studies and some major breakthroughs regarding this intriguing phenomenon, we have not yet fully characterized the underlying molecular mechanisms of genomic imprinting. This is in part due to the complexity of the system in that the epigenetic markings required for proper imprinting must be established in the germline, maintained throughout development, and then erased before being re-established in the next generation’s germline. Furthermore, imprinted gene expression is often tissue or stage-specific. It has also become clear that while imprinted loci across the genome seem to rely consistently on epigenetic markings of DNA methylation and/or histone modifications to discern parental alleles, the regulatory activities underlying these markings vary among loci. Here, we discuss different modes of imprinting regulation in mammals and how perturbations of these systems result in human disease. We focus mostly on the mechanism of genomic imprinting mediated by insulators as is present at the H19/Igf2 locus, and by non-coding RNA present at the Igf2r and Kcnq1 loci. In addition to imprinting mechanisms at autosomal loci, what is known about imprinted X-chromosome inactivation and how it compares to autosomal imprinting is also discussed. Overall, this review summarizes the many years of imprinting research, while pointing out exciting new discoveries that further elucidate the mechanism of genomic imprinting, and speculating on areas that require further investigation. PMID:18778719

  1. Genomic imprinting mechanisms in mammals.

    PubMed

    Ideraabdullah, Folami Y; Vigneau, Sebastien; Bartolomei, Marisa S

    2008-12-01

    Genomic imprinting is a form of epigenetic gene regulation that results in expression from a single allele in a parent-of-origin-dependent manner. This form of monoallelic expression affects a small but growing number of genes and is essential to normal mammalian development. Despite extensive studies and some major breakthroughs regarding this intriguing phenomenon, we have not yet fully characterized the underlying molecular mechanisms of genomic imprinting. This is in part due to the complexity of the system in that the epigenetic markings required for proper imprinting must be established in the germline, maintained throughout development, and then erased before being re-established in the next generation's germline. Furthermore, imprinted gene expression is often tissue or stage-specific. It has also become clear that while imprinted loci across the genome seem to rely consistently on epigenetic markings of DNA methylation and/or histone modifications to discern parental alleles, the regulatory activities underlying these markings vary among loci. Here, we discuss different modes of imprinting regulation in mammals and how perturbations of these systems result in human disease. We focus on the mechanism of genomic imprinting mediated by insulators as is present at the H19/Igf2 locus, and by non-coding RNA present at the Igf2r and Kcnq1 loci. In addition to imprinting mechanisms at autosomal loci, what is known about imprinted X-chromosome inactivation and how it compares to autosomal imprinting is also discussed. Overall, this review summarizes many years of imprinting research, while pointing out exciting new discoveries that further elucidate the mechanism of genomic imprinting, and speculating on areas that require further investigation.

  2. 78 FR 28411 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-14

    ...NMFS received an application from Shell Gulf of Mexico Inc. (Shell) for an Incidental Harassment Authorization (IHA) to take marine mammals, by harassment only, incidental to a marine surveys program in the Chukchi Sea, Alaska, during the open water season of 2013. Pursuant to the Marine Mammal Protection Act (MMPA), NMFS is requesting comments on its proposal to issue an IHA to Shell to take, by Level B harassment, 13 species of marine mammals during the specified activity.

  3. 77 FR 49921 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-17

    ...NMFS received an application from ION Geophysical (ION) for an Incidental Harassment Authorization (IHA) to take marine mammals, by harassment only, incidental to a proposed marine seismic survey in the Beaufort and Chukchi Seas, Alaska, between October and December 2012. Pursuant to the Marine Mammal Protection Act (MMPA), NMFS is requesting comments on its proposal to issue an IHA to ION to take, by harassment, nine species of marine mammals during the specified activity.

  4. Advances in exotic mammal clinical therapeutics.

    PubMed

    Hawkins, Michelle G

    2015-05-01

    It is important that veterinarians treating exotic companion mammals stay abreast of the latest developments relating to medications and drug delivery approaches for safety, efficacy and welfare issues. Sustained release formulations of commonly used drugs as well as newer routes for administration of therapeutic agents allow the veterinarian treating exotic companion mammals to reduce the stress associated with drug administration. Interactions can occur between vehicle and drugs when formulations are compounded, therefore research studies are warranted regarding potential problems associated with these formulations.

  5. Ecological correlates of extra-group paternity in mammals.

    PubMed

    Isvaran, Kavita; Clutton-Brock, Tim

    2007-01-22

    Extra-group paternity (EGP) can form an important part of the mating system in birds and mammals. However, our present understanding of its extent and ecology comes primarily from birds. Here, we use data from 26 species and phylogenetic comparative methods to explore interspecific variation in EGP in mammals and test prominent ecological hypotheses for this variation. We found extensive EGP (46% of species showed more than 20% EGP), indicating that EGP is likely to play an important role in the mating system and the dynamics of sexual selection in mammals. Variation in EGP was most closely correlated with the length of the mating season. As the length of the mating season increased, EGP declined, suggesting that it is increasingly difficult for males to monopolize their social mates when mating seasons are short and overlap among females in oestrus is likely to be high. EGP was secondarily correlated with the number of females in a breeding group, consistent with the idea that as female clustering increases, males are less able to monopolize individual females. Finally, EGP was not related to social mating system, suggesting that the opportunities for the extra-group fertilizations and the payoffs involved do not consistently vary with social mating system.

  6. Impacts of roads and hunting on central African rainforest mammals.

    PubMed

    Laurance, William E; Croes, Barbara M; Tchignoumba, Landry; Lahm, Sally A; Alonso, Alfonso; Lee, Michelle E; Campbell, Patrick; Ondzeano, Claude

    2006-08-01

    Road expansion and associated increases in bunting pressure are a rapidly growing threat to African tropical wildlife. In the rainforests of southern Gabon, we compared abundances of larger (>1 kg) mammal species at varying distances from forest roads and between hunted and unhunted treatments (comparing a 130-km2 oil concession that was almost entirely protected from bunting with nearby areas outside the concession that had moderate hunting pressure). At each of 12 study sites that were evenly divided between hunted and unhunted areas, we established standardized 1-km transects at five distances (50, 300, 600, 900, and 1200 m) from an unpaved road, and then repeatedly surveyed mammals during the 2004 dry and wet seasons. Hunting had the greatest impact on duikers (Cephalophus spp.), forest buffalo (Syncerus caffer nanus), and red river hogs (Potamochoerus porcus), which declined in abundance outside the oil concession, and lesser effects on lowland gorillas (Gorilla gorilla gorilla) and carnivores. Roads depressed abundances of duikers, sitatungas (Tragelaphus spekei gratus), and forest elephants (Loxondonta africana cyclotis), with avoidance of roads being stronger outside than inside the concession. Five monkey species showed little response to roads or hunting, whereas some rodents and pangolins increased in abundance outside the concession, possibly in response to greater forest disturbance. Our findings suggest that even moderate hunting pressure can markedly alter the structure of mammal communities in central Africa. Roads had the greatest impacts on large and small ungulates, with the magnitude of road avoidance increasing with local hunting pressure.

  7. Species longevity in North American fossil mammals.

    PubMed

    Prothero, Donald R

    2014-08-01

    Species longevity in the fossil record is related to many paleoecological variables and is important to macroevolutionary studies, yet there are very few reliable data on average species durations in Cenozoic fossil mammals. Many of the online databases (such as the Paleobiology Database) use only genera of North American Cenozoic mammals and there are severe problems because key groups (e.g. camels, oreodonts, pronghorns and proboscideans) have no reliable updated taxonomy, with many invalid genera and species and/or many undescribed genera and species. Most of the published datasets yield species duration estimates of approximately 2.3-4.3 Myr for larger mammals, with small mammals tending to have shorter species durations. My own compilation of all the valid species durations in families with updated taxonomy (39 families, containing 431 genera and 998 species, averaging 2.3 species per genus) yields a mean duration of 3.21 Myr for larger mammals. This breaks down to 4.10-4.39 Myr for artiodactyls, 3.14-3.31 Myr for perissodactyls and 2.63-2.95 Myr for carnivorous mammals (carnivorans plus creodonts). These averages are based on a much larger, more robust dataset than most previous estimates, so they should be more reliable for any studies that need species longevity to be accurately estimated.

  8. A Jurassic mammal from South America.

    PubMed

    Rauhut, Oliver W M; Martin, Thomas; Ortiz-Jaureguizar, Edgardo; Puerta, Pablo

    2002-03-14

    The Jurassic period is an important stage in early mammalian evolution, as it saw the first diversification of this group, leading to the stem lineages of monotremes and modern therian mammals. However, the fossil record of Jurassic mammals is extremely poor, particularly in the southern continents. Jurassic mammals from Gondwanaland are so far only known from Tanzania and Madagascar, and from trackway evidence from Argentina. Here we report a Jurassic mammal represented by a dentary, which is the first, to our knowledge, from South America. The tiny fossil from the Middle to Late Jurassic of Patagonia is a representative of the recently termed Australosphenida, a group of mammals from Gondwanaland that evolved tribosphenic molars convergently to the Northern Hemisphere Tribosphenida, and probably gave rise to the monotremes. Together with other mammalian evidence from the Southern Hemisphere, the discovery of this new mammal indicates that the Australosphenida had diversified and were widespread in Gondwanaland well before the end of the Jurassic, and that mammalian faunas from the Southern Hemisphere already showed a marked distinction from their northern counterparts by the Middle to Late Jurassic.

  9. Climate change and seasonal reproduction in mammals

    PubMed Central

    Bronson, F. H.

    2009-01-01

    Seasonal reproduction is common among mammals at all latitudes, even in the deep tropics. This paper (i) discusses the neuroendocrine pathways via which foraging conditions and predictive cues such as photoperiod enforce seasonality, (ii) considers the kinds of seasonal challenges mammals actually face in natural habitats, and (iii) uses the information thus generated to suggest how seasonal reproduction might be influenced by global climate change. Food availability and ambient temperature determine energy balance, and variation in energy balance is the ultimate cause of seasonal breeding in all mammals and the proximate cause in many. Photoperiodic cueing is common among long-lived mammals from the highest latitudes down to the mid-tropics. It is much less common in shorter lived mammals at all latitudes. An unknown predictive cue triggers reproduction in some desert and dry grassland species when it rains. The available information suggests that as our climate changes the small rodents of the world may adapt rather easily but the longer lived mammals whose reproduction is regulated by photoperiod may not do so well. A major gap in our knowledge concerns the tropics; that is where most species live and where we have the least understanding of how reproduction is regulated by environmental factors. PMID:19833645

  10. Climate change and seasonal reproduction in mammals.

    PubMed

    Bronson, F H

    2009-11-27

    Seasonal reproduction is common among mammals at all latitudes, even in the deep tropics. This paper (i) discusses the neuroendocrine pathways via which foraging conditions and predictive cues such as photoperiod enforce seasonality, (ii) considers the kinds of seasonal challenges mammals actually face in natural habitats, and (iii) uses the information thus generated to suggest how seasonal reproduction might be influenced by global climate change. Food availability and ambient temperature determine energy balance, and variation in energy balance is the ultimate cause of seasonal breeding in all mammals and the proximate cause in many. Photoperiodic cueing is common among long-lived mammals from the highest latitudes down to the mid-tropics. It is much less common in shorter lived mammals at all latitudes. An unknown predictive cue triggers reproduction in some desert and dry grassland species when it rains. The available information suggests that as our climate changes the small rodents of the world may adapt rather easily but the longer lived mammals whose reproduction is regulated by photoperiod may not do so well. A major gap in our knowledge concerns the tropics; that is where most species live and where we have the least understanding of how reproduction is regulated by environmental factors.

  11. 78 FR 57368 - Taking and Importing Marine Mammals: Taking Marine Mammals Incidental to Navy Operations of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-18

    ... Marine Mammals Incidental to Navy Operations of Surveillance Towed Array Sensor System Low Frequency... Surveillance Towed Array Sensor System Low Frequency Active (SURTASS LFA) sonar within the northwest...

  12. 76 FR 35995 - Taking and Importing Marine Mammals; Taking Marine Mammals Incidental to Operation and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ..., upon application from Neptune LNG LLC (Neptune), issued regulations pursuant to the Marine Mammal... and recordkeeping requirements, Seafood, Transportation. Dated: June 14, 2011. John Oliver, Deputy...

  13. Deconstructing mammal dispersals and faunal dynamics in SW Europe during the Quaternary

    NASA Astrophysics Data System (ADS)

    Palombo, Maria Rita

    2014-07-01

    This research aims to investigate the relationships between climate change and faunal dynamics in south-west Europe, disentangling the asynchronous and diachronous dispersal bioevents of large mammals across geographical and ecological boundaries, analysing biodiversity and its changes through time. The analysis of local versus regional biological dynamics may shed new light on whether turnovers and ecological and evolutionary changes developed because of global climate changes and related phenomena, or because of intrinsic biological factors. The SW European Quaternary fossil record is particularly suitable for studying the role of climate change at local and regional levels because of the complex physiographic and climatic heterogeneity of the study area, the presence of important geographical/ecological barriers and the complex history of invasions of species of varying geographical origin and provenance. The data base consists of taxonomically revised lists of large mammal species from selected SW European local faunal assemblages ranging in age from the Early to the late Middle Pleistocene (middle Villafranchian to early Aurelian European Land Mammal Ages). The new biochronological scheme proposed here allows for the comparison of local turnovers and biodiversity trends, yielding a better understanding of the action of geographical/ecological barriers that either prevented the range of some taxa from reaching some regions or caused delays in the dispersal of a taxon in some territories. The results obtained provide evidence that major environmental perturbations, triggering dispersal events and removing keystone species, modified the structure of the pre-existing mammalian faunas, merging previously independently-evolved taxa into new palaeo-communities. The coupled action of climatic changes and internal biotic dynamics thus caused the Quaternary SW European faunal complexes to significantly restructure. Diachroneity in local turnover across the study area

  14. Mammals of Red Slough Wildlife Management Area, with comments on McCurtain County, Oklahoma

    USGS Publications Warehouse

    Roehrs, Zachary P.; Lack, Justin B.; Stanley, Craig E.; Seiden, Christopher J.; Bastarache, Robert; Arbour, W. David; Hamilton, Meredith J.; Leslie,, David M.; Van Den Bussche, Ronald A.

    2012-01-01

    Red Slough Wildlife Management Area (RSWMA) is located in the southeastern corner of Oklahoma, McCurtain County, and represents the extreme northwestern extent of the South Central Plains (SCP) ecoregion. Previous mammal research in southeastern Oklahoma has focused mostly on the Ouachita Mountains to the north of RSWMA. As a result, of the 69 species of mammals potentially occurring in McCurtain County, only 48 species represented by 599 voucher specimens reside in natural history collections. We present results from a mammal survey of RSWMA conducted from December 2009 to August 2010. We captured 574 non-volant small mammals in 9,115 trap-nights, 11 bats in 17 net-nights, and seven salvaged meso-mammals resulting in 157 voucher specimens of 22 mammal species, including the first specimen of Castor canadensis for McCurtain County, and photographic vouchers for eight additional species from RSWMA. These results provide a baseline for future studies on RSWMA and substantially increase our natural history knowledge for many relatively under-studied mammals in southeastern Oklahoma

  15. Negative effects of an exotic grass invasion on small-mammal communities.

    PubMed

    Freeman, Eric D; Sharp, Tiffanny R; Larsen, Randy T; Knight, Robert N; Slater, Steven J; McMillan, Brock R

    2014-01-01

    Exotic invasive species can directly and indirectly influence natural ecological communities. Cheatgrass (Bromus tectorum) is non-native to the western United States and has invaded large areas of the Great Basin. Changes to the structure and composition of plant communities invaded by cheatgrass likely have effects at higher trophic levels. As a keystone guild in North American deserts, granivorous small mammals drive and maintain plant diversity. Our objective was to assess potential effects of invasion by cheatgrass on small-mammal communities. We sampled small-mammal and plant communities at 70 sites (Great Basin, Utah). We assessed abundance and diversity of the small-mammal community, diversity of the plant community, and the percentage of cheatgrass cover and shrub species. Abundance and diversity of the small-mammal community decreased with increasing abundance of cheatgrass. Similarly, cover of cheatgrass remained a significant predictor of small-mammal abundance even after accounting for the loss of the shrub layer and plant diversity, suggesting that there are direct and indirect effects of cheatgrass. The change in the small-mammal communities associated with invasion of cheatgrass likely has effects through higher and lower trophic levels and has the potential to cause major changes in ecosystem structure and function.

  16. Negative Effects of an Exotic Grass Invasion on Small-Mammal Communities

    PubMed Central

    Freeman, Eric D.; Sharp, Tiffanny R.; Larsen, Randy T.; Knight, Robert N.; Slater, Steven J.; McMillan, Brock R.

    2014-01-01

    Exotic invasive species can directly and indirectly influence natural ecological communities. Cheatgrass (Bromus tectorum) is non-native to the western United States and has invaded large areas of the Great Basin. Changes to the structure and composition of plant communities invaded by cheatgrass likely have effects at higher trophic levels. As a keystone guild in North American deserts, granivorous small mammals drive and maintain plant diversity. Our objective was to assess potential effects of invasion by cheatgrass on small-mammal communities. We sampled small-mammal and plant communities at 70 sites (Great Basin, Utah). We assessed abundance and diversity of the small-mammal community, diversity of the plant community, and the percentage of cheatgrass cover and shrub species. Abundance and diversity of the small-mammal community decreased with increasing abundance of cheatgrass. Similarly, cover of cheatgrass remained a significant predictor of small-mammal abundance even after accounting for the loss of the shrub layer and plant diversity, suggesting that there are direct and indirect effects of cheatgrass. The change in the small-mammal communities associated with invasion of cheatgrass likely has effects through higher and lower trophic levels and has the potential to cause major changes in ecosystem structure and function. PMID:25269073

  17. Classification and identification of marine mammals by their click signatures

    NASA Astrophysics Data System (ADS)

    Goo, Gee-In

    2003-09-01

    In this paper, the author presents recent findings of applying passive Broadband Bionic Sonar technique to same data files with marine mammal "clicks". Using a resonance detection technique, a number of data files with mammal clicks were analyzed. From these data files, many unique mammal "click" signatures were observed. These results seem to indicate that individual marine mammals can be classified and possibly identified.

  18. 77 FR 47045 - Marine Mammals; File No. 16580

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... receive, import and export marine mammal parts for scientific research. ADDRESSES: The permit and related... specimens for scientific research had been submitted by the above-named applicant. The requested permit has... authorized marine mammal research for all marine mammal species under NMFS jurisdiction. Marine mammal parts...

  19. 50 CFR 216.83 - Importation of birds or mammals.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 10 2013-10-01 2013-10-01 false Importation of birds or mammals. 216.83 Section 216.83 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL OCEANIC AND ATMOSPHERIC... MAMMALS Pribilof Islands Administration § 216.83 Importation of birds or mammals. No mammals or birds...

  20. 50 CFR 216.83 - Importation of birds or mammals.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 10 2012-10-01 2012-10-01 false Importation of birds or mammals. 216.83 Section 216.83 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL OCEANIC AND ATMOSPHERIC... MAMMALS Pribilof Islands Administration § 216.83 Importation of birds or mammals. No mammals or birds...

  1. 50 CFR 216.83 - Importation of birds or mammals.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Importation of birds or mammals. 216.83 Section 216.83 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL OCEANIC AND ATMOSPHERIC... MAMMALS Pribilof Islands Administration § 216.83 Importation of birds or mammals. No mammals or birds...

  2. 50 CFR 216.83 - Importation of birds or mammals.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Importation of birds or mammals. 216.83 Section 216.83 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL OCEANIC AND ATMOSPHERIC... MAMMALS Pribilof Islands Administration § 216.83 Importation of birds or mammals. No mammals or birds...

  3. Chlorinated hydrocarbon contaminants in arctic marine mammals.

    PubMed

    Norstrom, R J; Muir, D C

    1994-09-16

    By 1976, the presence of chlorinated hydrocarbon contaminants (CHCs) had been demonstrated in fur seal (Callorhinus ursinus), ringed seal (Phoca hispida), hooded seal (Cystophora cristata), bearded seal (Erignathus barbatus), walrus (Obdobenus rosmarus divergens), beluga (Delphinapterus leucas), porpoise (Phocoena phocoena) and polar bear (Ursus maritimus) in various parts of the Arctic. In spite of this early interest, very little subsequent research on contaminants in Arctic marine mammals was undertaken until the mid-1980s. Since that time, there has been an explosion of interest, resulting in a much expanded data base on contaminants in Arctic marine mammals. Except in the Russian Arctic, data have now been obtained on the temporospatial distribution of PCBs and other contaminants in ringed seal, beluga and polar bear. Contaminants in narwhal (Monodon monoceros) have also now been measured. On a fat weight basis, the sum of DDT-related compounds (S-DDT) and PCB levels are lowest in walrus (< 0.1 microgram/g), followed by ringed seal, (0.1-1 microgram/g range). Levels are an order of magnitude higher in beluga and narwhal (1-10 micrograms/g range). It appears that metabolism and excretion of S-DDT and PCBs may be less efficient in cetaceans, leading to greater biomagnification. Polar bears have similar levels of PCBs as cetaceans (1-10 micrograms/g), but with a much simpler congener pattern. DDE levels are lowest in polar bear, indicating rapid metabolism. Effects of age and sex on residue levels are found for all species where this was measured. Among cetaceans and ringed seal, sexually mature females have lower levels than males due to lactation. Although PCB levels in adult male polar bears are about twice as high as females, there is only a trivial age effect in either sex apart from an initial decrease from birth to sexual maturity (age 0-5). Comparison of levels of S-DDT and PCBs in Arctic beluga and ringed seal with those in beluga in the Gulf of St

  4. Wet mammals shake at tuned frequencies to dry

    PubMed Central

    Dickerson, Andrew K.; Mills, Zachary G.; Hu, David L.

    2012-01-01

    In cold wet weather, mammals face hypothermia if they cannot dry themselves. By rapidly oscillating their bodies, through a process similar to shivering, furry mammals can dry themselves within seconds. We use high-speed videography and fur particle tracking to characterize the shakes of 33 animals (16 animals species and five dog breeds), ranging over four orders of magnitude in mass from mice to bears. We here report the power law relationship between shaking frequency f and body mass M to be f ∼ M−0.22, which is close to our prediction of f ∼ M−0.19 based upon the balance of centrifugal and capillary forces. We also observe a novel role for loose mammalian dermal tissue: by whipping around the body, it increases the speed of drops leaving the animal and the ensuing dryness relative to tight dermal tissue. PMID:22904256

  5. Cellular level brain imaging in behaving mammals: an engineering approach.

    PubMed

    Hamel, Elizabeth J O; Grewe, Benjamin F; Parker, Jones G; Schnitzer, Mark J

    2015-04-08

    Fluorescence imaging offers expanding capabilities for recording neural dynamics in behaving mammals, including the means to monitor hundreds of cells targeted by genetic type or connectivity, track cells over weeks, densely sample neurons within local microcircuits, study cells too inactive to isolate in extracellular electrical recordings, and visualize activity in dendrites, axons, or dendritic spines. We discuss recent progress and future directions for imaging in behaving mammals from a systems engineering perspective, which seeks holistic consideration of fluorescent indicators, optical instrumentation, and computational analyses. Today, genetically encoded indicators of neural Ca(2+) dynamics are widely used, and those of trans-membrane voltage are rapidly improving. Two complementary imaging paradigms involve conventional microscopes for studying head-restrained animals and head-mounted miniature microscopes for imaging in freely behaving animals. Overall, the field has attained sufficient sophistication that increased cooperation between those designing new indicators, light sources, microscopes, and computational analyses would greatly benefit future progress.

  6. The evolution of acoustic size exaggeration in terrestrial mammals

    PubMed Central

    Charlton, Benjamin D.; Reby, David

    2016-01-01

    Recent studies have revealed that some mammals possess adaptations that enable them to produce vocal signals with much lower fundamental frequency (F0) and formant frequency spacing (ΔF) than expected for their size. Although these adaptations are assumed to reflect selection pressures for males to lower frequency components and exaggerate body size in reproductive contexts, this hypothesis has not been tested across a broad range of species. Here we show that male terrestrial mammals produce vocal signals with lower ΔF (but not F0) than expected for their size in mating systems with greater sexual size dimorphism. We also reveal that males produce calls with higher than expected F0 and ΔF in species with increased sperm competition. This investigation confirms that sexual selection favours the use of ΔF as an acoustic size exaggerator and supports the notion of an evolutionary trade-off between pre-copulatory signalling displays and sperm production. PMID:27598835

  7. Enamel structure in some therapsids and mesozoic mammals.

    PubMed

    Osborn, J W; Hillman, J

    1979-11-01

    The distribution of enamel tubules, the shapes and arrangements of prisms, and the orientation of crystals in ground sections from several therapsids and mesozoic mammals have been investigated by conventional and polarizing microscopy. Along each of three separate phylogenetic lines which evolved occluding teeth, there was a progressive increase in the numbers of enamel tubules. In the investigation, the arcade-shaped prisms typical of recent mammals were first seen in material from the Cretaceous period. All the enamels investigated from the Triassic contained columns of crystals, which were deduced as hexagonal. The inner ends of the crystals within each column deviated towards the center of the column. It is concluded that the existence of an interprismatic region provides the most important distinction between prismatic enamels and the hexagonal columns of crystals in the Triassic material.

  8. Gene duplication and complex circadian clocks in mammals.

    PubMed

    Looby, Paul; Loudon, Andrew S I

    2005-01-01

    The circadian clock arose early in the evolution of life to enable organisms to adapt to the cycle of day and night. Recently, the extent and importance of circadian regulation of behaviour and physiology has come to be more fully realized. Core molecular cogs of circadian oscillators appear to have been largely conserved between such diverse organisms as Drosophila melanogaster and mammals. However, gene duplication events have produced multiple copies of many clock genes in mammals. Recent studies suggest that genome duplication has lead to increased circadian complexity and local tissue regulation. This has important implications for temporal regulation of behaviour via multiple clocks in the central nervous system, and also extends to the local physiology of major body organs and tissues.

  9. Absorption and ocular deposition of dietary lutein in marine mammals.

    PubMed

    Koutsos, Elizabeth A; Schmitt, Todd; Colitz, Carmen M H; Mazzaro, Lisa

    2013-01-01

    Cataracts and ocular disease are common lesions of marine mammals in zoological collections. Lutein, an oxygenated carotenoid, may have therapeutic or prophylactic effects on ocular disorder. Therefore, this study examined the ability of marine mammals to absorb dietary lutein. Two preliminary trials examined lutein in two forms (beadlet or ester) in a small sample size of marine mammals representing pinnipeds and cetaceans. Lutein was fed daily in tablets providing 0.89-3.6 mg lutein/kg body weight(0.75) per day for 15 days to 2 years. A third study was conducted using lutein beadlet fed at 3.6 mg lutein/kg body weight(0.75) per day for 15-21 days. Blood was analyzed for lutein pre- and postsupplementation. In the preliminary trials, lutein beadlet was observed to result in greater blood lutein levels than lutein esters, and cetaceans had more noticeable responses than pinnipeds. In Study 3, serum lutein and zeaxanthin increased postsupplementation in beluga whales (P < 0.05), and serum lutein tended to increase postsupplementation in dolphins (P < 0.10), but little change was seen in serum lutein in pinnipeds or manatee. Opportunistic retinal samples demonstrated some detectable lutein in the retina of a dolphin and several harp seals. The lutein levels in dolphins after supplementation are similar to those reported in free-ranging animals. Ocular lutein in harp seals demonstrates that ocular deposition occurs despite low circulating lutein levels.

  10. Corridors and olfactory predator cues affect small mammal behavior.

    SciTech Connect

    Brinkerhoff, Robert Jory; Haddad, Nick M.; Orrock, John L.

    2005-03-30

    Abstract The behavior of prey individuals is influenced by a variety of factors including, but not limited to, habitat configuration, risk of predation, and availability of resources, and these habitat-dependent factors may have interactive effects. We studied the responses of mice to an increase in perceived predation risk in a patchy environment to understand how habitat corridors might affect interactions among species in a fragmented landscape. We used a replicated experiment to investigate corridor-mediated prey responses to predator cues in a network of open habitat patches surrounded by a matrix of planted pine forest. Some of the patches were connected by corridors. We used mark–recapture techniques and foraging trays to monitor the movement, behavior, and abundance of small mammals. Predation threat was manipulated in one-half of the replicates by applying an olfactory predator cue. Corridors synchronized small mammal foraging activity among connected patches. Foraging also was inhibited in the presence of an olfactory predator cue but apparently increased in adjacent connected patches. Small mammal abundance did not change as a result of the predator manipulation and was not influenced by the presence of corridors. This study is among the 1st to indicate combined effects of landscape configuration and predation risk on prey behavior. These changes in prey behavior may, in turn, have cascading effects on community dynamics where corridors and differential predation risk influence movement and patch use.

  11. Apparatus for enhancing tissue repair in mammals

    NASA Technical Reports Server (NTRS)

    Goodwin, Thomas J. (Inventor); Parker, Clayton R. (Inventor)

    2007-01-01

    An apparatus is disclosed for enhancing tissue repair in mammals, with the apparatus comprising: a sleeve for encircling a portion of a mammalian body part, said sleeve comprising an electrically conductive coil capable of generating an electromagnetic field when an electrical current is applied thereto, means for supporting the sleeve on the mammalian body part; and means for supplying the electrically conductive coil with a square wave time varying electrical current sufficient to create a time varying electromagnetic force of from approximately 0.05 gauss to 0.05 gauss within the interior of the coil in order that when the sleeve is placed on a mammalian body part and the time varying electromagnetic force of from approximately 0.05 gauss to 0.05 gauss is generated on the mammalian body part for an extended period of time, tissue regeneration within the mammalian body part is increased to a rate in excess of the normal tissue regeneration rate that would occur without application of the time varying electromagnetic force.

  12. Annotated Bibliography of Publications from the U.S. Navy’s Marine Mammal Program.

    DTIC Science & Technology

    1987-11-01

    trematode from the California sea lion (Zalophus californianus). Bull. So. Calif. Acad. Sci. 68(2):82-85. Describes a new species of parasitic flatworm ...1980 Diagnostic key to the parasites of some marine mammals. NOSC TD 295, 37 pp. A key, with illustrations, for identification of parasites of marine...factor; less stressful capture procedures may increase captive life span. Johnston, D. G., and S. H. Ridgway 1969 Parasitism in some marine mammals

  13. Stress physiology in marine mammals: how well do they fit the terrestrial model?

    PubMed

    Atkinson, Shannon; Crocker, Daniel; Houser, Dorian; Mashburn, Kendall

    2015-07-01

    Stressors are commonly accepted as the causal factors, either internal or external, that evoke physiological responses to mediate the impact of the stressor. The majority of research on the physiological stress response, and costs incurred to an animal, has focused on terrestrial species. This review presents current knowledge on the physiology of the stress response in a lesser studied group of mammals, the marine mammals. Marine mammals are an artificial or pseudo grouping from a taxonomical perspective, as this group represents several distinct and diverse orders of mammals. However, they all are fully or semi-aquatic animals and have experienced selective pressures that have shaped their physiology in a manner that differs from terrestrial relatives. What these differences are and how they relate to the stress response is an efflorescent topic of study. The identification of the many facets of the stress response is critical to marine mammal management and conservation efforts. Anthropogenic stressors in marine ecosystems, including ocean noise, pollution, and fisheries interactions, are increasing and the dramatic responses of some marine mammals to these stressors have elevated concerns over the impact of human-related activities on a diverse group of animals that are difficult to monitor. This review covers the physiology of the stress response in marine mammals and places it in context of what is known from research on terrestrial mammals, particularly with respect to mediator activity that diverges from generalized terrestrial models. Challenges in conducting research on stress physiology in marine mammals are discussed and ways to overcome these challenges in the future are suggested.

  14. Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles

    PubMed Central

    Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C.

    2016-01-01

    High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments. PMID:27032533

  15. Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles

    NASA Astrophysics Data System (ADS)

    Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C.

    2016-04-01

    High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments.

  16. Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles.

    PubMed

    Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C

    2016-04-01

    High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments.

  17. Isotope analyses of fossil small mammals in karstic sites

    NASA Astrophysics Data System (ADS)

    Garcia Alix, Antonio; Delgado Huertas, Antonio

    2016-04-01

    Fossil skeletal accumulations in kartstic complexes, such as caves, are quite common, especially during the Pliocene and Quaternary. These fossil assemblages are sometimes difficult to study, as specimens from different ages can be found together (time averaging). The traditional approach to study this kind of paleontological sites was taphonomic (understanding the origin and other factors affecting the bone accumulation) and/or taxonomic (systematic description of the remains). However, other kinds of analyses, such as biogeochemical techniques to reconstruct past diets and environments, are being more frequently used. Small-mammals have a wide geographical distribution, and their remains (bones and teeth) are extensively represented in the fossil record; therefore, isotopic analyses in fossil small-mammals are a powerful tool to reconstruct paleoenvironments. Field samples for small-mammal studies yield large amounts of sediment-residues that need to be reduced in the laboratory (usually by means of diluted hydrochloric or acetic acid). Therefore, samples of fossil small-mammal for isotopic analyses usually receive two different acid treatments: one to reduce the carbonate residue of the sediment, and afterwards another one to remove digenetic carbonates from the ground sample. Those treatments, along with the small size of the remains, may increase the probability of chemical fractionation during those pre-treatment stages. Those acid treatments are even more aggressive in kasrtic fossil localities, as limestone has to be dissolved to extract the small mammal remains. In this abstract, we present the results of two different treatments carried out in limestone from the Pliocene karstic locality of Moreda (Guadix Basin, Spain) and a control sample. One batch of samples were treated with a solution of 1M acetic acid-acetate calcium buffer (ph 4,5), and the rest with diluted acetic acid (at 15% concentration, Ph 2,2), which is the most used to reduce the sediments

  18. Fecal Influenza in Mammals: Selection of Novel Variants

    PubMed Central

    Koçer, Zeynep A.; Obenauer, John; Zaraket, Hassan; Zhang, Jinghui; Rehg, Jerold E.; Russell, Charles J.

    2013-01-01

    In aquatic birds, influenza A viruses mainly replicate in the intestinal tract without significantly affecting the health of the host, but in mammals, they replicate in the respiratory tract and often cause disease. Occasionally, influenza viruses have been detected in stool samples of hospitalized patients and in rectal swabs of naturally or experimentally infected mammals. In this study, we compared the biological and molecular differences among four wild-type avian H1N1 influenza viruses and their corresponding fecal and lung isolates in DBA/2J and BALB/cJ mice. All fecal and lung isolates were more pathogenic than the original wild-type viruses, when inoculated into mice of both strains. The increased virulence was associated with the acquisition of genetic mutations. Most of the novel genotypes emerged as PB2E627K, HAF128V, HAF454L, or HAH300P variations, and double mutations frequently occurred in the same isolate. However, influenza virus strain- and host-specific differences were also observed in terms of selected variants. The avian H1N1 virus of shorebird origin appeared to be unique in its ability to rapidly adapt to BALB/cJ mice via the fecal route, compared to the adaptability of the H1N1 virus of mallard origin. Furthermore, a bimodal distribution in fecal shedding was observed in mice infected with the fecal isolates, while a normal distribution was observed after infection with the lung isolates or wild-type virus. Fecal isolates contained HA mutations that increased the activation pH of the HA protein. We conclude that influenza virus variants that emerge in fecal isolates in mammals might influence viral transmission, adaptation to mammals, and viral ecology or evolution. PMID:23966381

  19. 76 FR 35856 - Incidental Taking of Marine Mammals; Taking of Marine Mammals Incidental to the Explosive Removal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    ... accordance with the Marine Mammal Protection Act (MMPA) and implementing regulations, notification is hereby given that NMFS has issued a one-year Letter of Authorization (LOA) to take marine mammals incidental to... Incidental Taking of Marine Mammals; Taking of Marine Mammals Incidental to the Explosive Removal of Offshore...

  20. 77 FR 50289 - Taking and Importing Marine Mammals: Taking Marine Mammals Incidental to U.S. Navy Operations of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-20

    ... implement. SAG members will include recognized marine biology and marine bio-acoustic scientific subject... Part 218 Taking and Importing Marine Mammals: Taking Marine Mammals Incidental to U.S. Navy Operations... Marine Mammals: Taking Marine Mammals Incidental to U.S. Navy Operations of Surveillance Towed...

  1. Establishing a Marine Mammal Stranding Network in the Bahamas

    DTIC Science & Technology

    2008-01-01

    Marine Mammal Stranding Network in the Bahamas Diane Elaine Claridge Bahamas Marine Mammal Research Organisation P.O. Box AB...are to establish a marine mammal stranding network in the Bahamas to better understand the conservation needs of marine mammals in the Bahamas, with...well as the biology of marine mammals . The stranding network will be structured so that it will become self-sufficient and able to continue into

  2. 78 FR 35507 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-12

    ...NMFS received an application from TGS-NOPEC Geophysical Company ASA (TGS) for an Incidental Harassment Authorization (IHA) to take marine mammals, by harassment only, incidental to a marine 2- dimensional (2D) seismic survey program in the Chukchi Sea, Alaska, during the open water season of 2013. Pursuant to the Marine Mammal Protection Act (MMPA), NMFS is requesting comments on its proposal......

  3. 78 FR 47495 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-05

    ...In accordance with the Marine Mammal Protection Act (MMPA) regulations, notification is hereby given that NMFS has issued an Incidental Harassment Authorization (IHA) to Shell Gulf of Mexico Inc. (Shell) to take, by harassment, small numbers of 13 species of marine mammals incidental to a marine survey program in the Chukchi Sea, Alaska, during the 2013 Arctic open-water season. Pursuant to......

  4. 77 FR 27283 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-09

    ...In accordance with the Marine Mammal Protection Act (MMPA) regulations, notification is hereby given that NMFS has issued an Incidental Harassment Authorization (IHA) to Shell Offshore Inc. (Shell) to take marine mammals, by harassment, incidental to offshore exploration drilling on Outer Continental Shelf (OCS) leases in the Beaufort Sea, Alaska.

  5. 77 FR 27321 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-09

    ...In accordance with the Marine Mammal Protection Act (MMPA) regulations, notification is hereby given that NMFS has issued an Incidental Harassment Authorization (IHA) to Shell Gulf of Mexico Inc. (Shell) to take marine mammals, by harassment, incidental to offshore exploration drilling on Outer Continental Shelf (OCS) leases in the Chukchi Sea, Alaska.

  6. 78 FR 80385 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-31

    ...NMFS received an application from Apache Alaska Corporation (Apache) for an Incidental Harassment Authorization (IHA) to take marine mammals, by harassment, incidental to a proposed 3D seismic survey in Cook Inlet, Alaska, between March 1, 2014, and December 31, 2014. Pursuant to the Marine Mammal Protection Act (MMPA), NMFS requests comments on its proposal to issue an IHA to Apache to take,......

  7. 76 FR 46729 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-03

    ...In accordance with the Marine Mammal Protection Act (MMPA) regulations, notification is hereby given that NMFS has issued an Incidental Harassment Authorization (IHA) to Statoil USA E&P Inc. (Statoil) to take, by harassment, small numbers of 13 species of marine mammals incidental to shallow hazards and geotechnical surveys in the Chukchi Sea, Alaska, during the 2011 Arctic open-water season.

  8. 77 FR 2040 - Taking and Importing Marine Mammals: Taking Marine Mammals Incidental to Navy Training Exercises...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-13

    ... NMFS modify these LOAs to include taking of marine mammals incidental to mine neutralization training...; CHPT: 74 FR 28370). The potential effects of mine neutralization training on marine mammals were... neutralization training has been included in the specified activity in the associated 2009, 2010, and 2011 LOAs...

  9. 76 FR 330 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-04

    ... Specified Activities; Taking Marine Mammals Incidental to Polar Bear Captures AGENCY: National Marine...) to take marine mammals, by harassment, incidental to a capture- recapture program of polar bears in...-recapture program of polar bears in the U.S. Chukchi Sea. NMFS reviewed the USFWS' application...

  10. 77 FR 67797 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-14

    ... mortality of pinnipeds. Any harassment resulting from the bird mitigation research trial is expected to be...' research trial may result in the incidental take of small numbers of marine mammals, by Level B harassment... Specified Activities; Taking Marine Mammals Incidental to Bird Mitigation Research in the Farallon National...

  11. 78 FR 37209 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XC564 Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to Marine Seismic Survey in the Beaufort Sea,...

  12. 78 FR 18965 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-28

    ... Specified Activities; Taking Marine Mammals Incidental to an Exploration Drilling Program in the Chukchi Sea... harassment, incidental to conducting offshore exploration drilling on Outer Continental Shelf (OCS) leases in... small numbers of marine mammals, by harassment, incidental to conducting offshore exploration...

  13. 77 FR 31333 - Taking and Importing Marine Mammals: Taking Marine Mammals Incidental to Navy Training Exercises...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-25

    ... Marine Mammals Incidental to Navy Training Exercises in Three East Coast Range Complexes AGENCY: National...-2012 marine mammal monitoring report and the Navy's 2011-2012 exercise report are available by writing... training exercises. For detailed information on these actions, please refer to the June 15, 2009...

  14. SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT

    PubMed Central

    Baker, Robert J.; Bradley, Robert D.

    2009-01-01

    boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F1s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is “reproductively isolated species.” Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen–based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum. PMID:19890476

  15. [Amplitude modulation in sound signals by mammals].

    PubMed

    Nikol'skiĭ, A A

    2012-01-01

    Periodic variations in amplitude of a signal, or amplitude modulation (AM), affect the structure of communicative messages spectrum. Within the spectrum of AM-signals, side frequencies are formed both above and below the carrier frequency that is subjected to modulation. In case of harmonic signal structure they are presented near fundamental frequency as well as near harmonics. Thus, AM may by viewed as a relatively simple mechanism for controlling the spectrum of messages transmitted by mammals. Examples of AM affecting the spectrum structure of functionally different sound signals are discussed as applied to representatives of four orders of mammals: rodents (Reodentia), duplicidentates (Lagomorpha), pinnipeds (Pinnipedia), and paridigitates (Artiodactia). For the first time, the classification of AM in animals' sound signals is given. Five forms of AM are picked out in sound signals by mammals: absence of AM, continuous AM, fragmented, heterogeneous, and multilevel one. AM presence/absence is related neither with belonging to any specific order nor with some particular function of a signal. Similar forms of AM can occur in different orders of mammals in parallel. On the contrary, different forms of AM can be detected in signals meant for similar functions. The assumption is made about AM-signals facilitating information encoding and jamprotection of messages transmitted by mammals. Preliminry analysis indicates that hard-driving amplitude modulation is incompatible with hard-driving frequency modulation.

  16. Global habitat suitability models of terrestrial mammals.

    PubMed

    Rondinini, Carlo; Di Marco, Moreno; Chiozza, Federica; Santulli, Giulia; Baisero, Daniele; Visconti, Piero; Hoffmann, Michael; Schipper, Jan; Stuart, Simon N; Tognelli, Marcelo F; Amori, Giovanni; Falcucci, Alessandra; Maiorano, Luigi; Boitani, Luigi

    2011-09-27

    Detailed large-scale information on mammal distribution has often been lacking, hindering conservation efforts. We used the information from the 2009 IUCN Red List of Threatened Species as a baseline for developing habitat suitability models for 5027 out of 5330 known terrestrial mammal species, based on their habitat relationships. We focused on the following environmental variables: land cover, elevation and hydrological features. Models were developed at 300 m resolution and limited to within species' known geographical ranges. A subset of the models was validated using points of known species occurrence. We conducted a global, fine-scale analysis of patterns of species richness. The richness of mammal species estimated by the overlap of their suitable habitat is on average one-third less than that estimated by the overlap of their geographical ranges. The highest absolute difference is found in tropical and subtropical regions in South America, Africa and Southeast Asia that are not covered by dense forest. The proportion of suitable habitat within mammal geographical ranges correlates with the IUCN Red List category to which they have been assigned, decreasing monotonically from Least Concern to Endangered. These results demonstrate the importance of fine-resolution distribution data for the development of global conservation strategies for mammals.

  17. Responses of large mammals to climate change

    PubMed Central

    Hetem, Robyn S; Fuller, Andrea; Maloney, Shane K; Mitchell, Duncan

    2014-01-01

    Most large terrestrial mammals, including the charismatic species so important for ecotourism, do not have the luxury of rapid micro-evolution or sufficient range shifts as strategies for adjusting to climate change. The rate of climate change is too fast for genetic adaptation to occur in mammals with longevities of decades, typical of large mammals, and landscape fragmentation and population by humans too widespread to allow spontaneous range shifts of large mammals, leaving only the expression of latent phenotypic plasticity to counter effects of climate change. The expression of phenotypic plasticity includes anatomical variation within the same species, changes in phenology, and employment of intrinsic physiological and behavioral capacity that can buffer an animal against the effects of climate change. Whether that buffer will be realized is unknown, because little is known about the efficacy of the expression of plasticity, particularly for large mammals. Future research in climate change biology requires measurement of physiological characteristics of many identified free-living individual animals for long periods, probably decades, to allow us to detect whether expression of phenotypic plasticity will be sufficient to cope with climate change. PMID:27583293

  18. Responses of large mammals to climate change.

    PubMed

    Hetem, Robyn S; Fuller, Andrea; Maloney, Shane K; Mitchell, Duncan

    2014-01-01

    Most large terrestrial mammals, including the charismatic species so important for ecotourism, do not have the luxury of rapid micro-evolution or sufficient range shifts as strategies for adjusting to climate change. The rate of climate change is too fast for genetic adaptation to occur in mammals with longevities of decades, typical of large mammals, and landscape fragmentation and population by humans too widespread to allow spontaneous range shifts of large mammals, leaving only the expression of latent phenotypic plasticity to counter effects of climate change. The expression of phenotypic plasticity includes anatomical variation within the same species, changes in phenology, and employment of intrinsic physiological and behavioral capacity that can buffer an animal against the effects of climate change. Whether that buffer will be realized is unknown, because little is known about the efficacy of the expression of plasticity, particularly for large mammals. Future research in climate change biology requires measurement of physiological characteristics of many identified free-living individual animals for long periods, probably decades, to allow us to detect whether expression of phenotypic plasticity will be sufficient to cope with climate change.

  19. Global habitat suitability models of terrestrial mammals

    PubMed Central

    Rondinini, Carlo; Di Marco, Moreno; Chiozza, Federica; Santulli, Giulia; Baisero, Daniele; Visconti, Piero; Hoffmann, Michael; Schipper, Jan; Stuart, Simon N.; Tognelli, Marcelo F.; Amori, Giovanni; Falcucci, Alessandra; Maiorano, Luigi; Boitani, Luigi

    2011-01-01

    Detailed large-scale information on mammal distribution has often been lacking, hindering conservation efforts. We used the information from the 2009 IUCN Red List of Threatened Species as a baseline for developing habitat suitability models for 5027 out of 5330 known terrestrial mammal species, based on their habitat relationships. We focused on the following environmental variables: land cover, elevation and hydrological features. Models were developed at 300 m resolution and limited to within species' known geographical ranges. A subset of the models was validated using points of known species occurrence. We conducted a global, fine-scale analysis of patterns of species richness. The richness of mammal species estimated by the overlap of their suitable habitat is on average one-third less than that estimated by the overlap of their geographical ranges. The highest absolute difference is found in tropical and subtropical regions in South America, Africa and Southeast Asia that are not covered by dense forest. The proportion of suitable habitat within mammal geographical ranges correlates with the IUCN Red List category to which they have been assigned, decreasing monotonically from Least Concern to Endangered. These results demonstrate the importance of fine-resolution distribution data for the development of global conservation strategies for mammals. PMID:21844042

  20. Effects of corridors on home range sizes and interpatch movements of three small mammal species.

    SciTech Connect

    Mabry, Karen, E.; Barrett, Gary, W.

    2002-04-30

    Mabry, K.E., and G.W. Barrett. 2002. Effects of corridors on home range sizes and interpatch movements of three small mammal species. Landscape Ecol. 17:629-636. Corridors are predicted to benefit populations in patchy habitats by promoting movement, which should increase population densities, gene flow, and recolonization of extinct patch populations. However, few investigators have considered use of the total landscape, particularly the possibility of interpatch movement through matrix habitat, by small mammals. This study compares home range sizes of 3 species of small mammals, the cotton mouse, old field mouse and cotton rat between patches with and without corridors. Corridor presence did not have a statistically significant influence on average home range size. Habitat specialization and sex influenced the probability of an individual moving between 2 patches without corridors. The results of this study suggest that small mammals may be more capable of interpatch movement without corridors than is frequently assumed.

  1. Evidence for a Mid-Jurassic Adaptive Radiation in Mammals.

    PubMed

    Close, Roger A; Friedman, Matt; Lloyd, Graeme T; Benson, Roger B J

    2015-08-17

    A series of spectacular discoveries have transformed our understanding of Mesozoic mammals in recent years. These finds reveal hitherto-unsuspected ecomorphological diversity that suggests that mammals experienced a major adaptive radiation during the Middle to Late Jurassic. Patterns of mammalian macroevolution must be reinterpreted in light of these new discoveries, but only taxonomic diversity and limited aspects of morphological disparity have been quantified. We assess rates of morphological evolution and temporal patterns of disparity using large datasets of discrete characters. Rates of morphological evolution were significantly elevated prior to the Late Jurassic, with a pronounced peak occurring during the Early to Middle Jurassic. This intense burst of phenotypic innovation coincided with a stepwise increase in apparent long-term standing diversity and the attainment of maximum disparity, supporting a "short-fuse" model of early mammalian diversification. Rates then declined sharply, and remained significantly low until the end of the Mesozoic, even among therians. This supports the "long-fuse" model of diversification in Mesozoic therians. Our findings demonstrate that sustained morphological innovation in Triassic stem-group mammals culminated in a global adaptive radiation of crown-group members during the Early to Middle Jurassic.

  2. Ecological predictors of extinction risks of endemic mammals of China.

    PubMed

    Chen, You-Hua

    2014-07-01

    In this brief report, we analyzed ecological correlates of risk of extinction for mammals endemic to China using phylogenetic eigenvector methods to control for the effect of phylogenetic inertia. Extinction risks were based on the International Union for Conservation of Nature (IUCN) Red List and ecological explanatory attributes that include range size and climatic variables. When the effect of phylogenetic inertia were controlled, climate became the best predictor for quantifying and evaluating extinction risks of endemic mammals in China, accounting for 13% of the total variation. Range size seems to play a trivial role, explaining ~1% of total variation; however, when non-phylogenetic variation partitioning analysis was done, the role of range size then explained 7.4% of total variation. Consequently, phylogenetic inertia plays a substantial role in increasing the explanatory power of range size on the extinction risks of mammals endemic to China. Limitations of the present study are discussed, with a focus on under-represented sampling of endemic mammalian species.

  3. Bartonella infection in sylvatic small mammals of central Sweden.

    PubMed Central

    Holmberg, M.; Mills, J. N.; McGill, S.; Benjamin, G.; Ellis, B. A.

    2003-01-01

    Sylvatic small mammals were captured in rural habitats near Uppsala, Sweden, to measure the prevalence of bartonella infections, characterize bacterial isolates and identify their host range, and increase our understanding of host-pathogen ecology. During 7 nights of trapping at 3 localities, 236 small mammals were captured (trap success 30%). Bartonella were isolated from bloods of Apodemus flavicollis (19 of 110 tested), Apodemus sylvaticus (6/25), Clethrionomys glareolus (9/60), Microtus agrestis (1/3), Mus musculus (1/18), and Sorex araneus (3/20). Nucleotide sequencing (a 338 bp fragment of the gltA gene) of 40 isolates yielded 6 unique genotypes. Five of the 6 genotypes were most similar to other known bartonella isolated from Old World small-mammal hosts. The most frequent genotype (83%) was isolated from A. flavicollis and M. musculus and was identical to Bartonella grahamii, a recently demonstrated human pathogen. These two hosts were most frequently captured in and around human structures and work places, thus providing conditions that could potentially lead to frequent human infections. PMID:12613756

  4. Female promiscuity and maternally dependent offspring growth rates in mammals.

    PubMed

    Garratt, Michael; Brooks, Robert C; Lemaître, Jean-François; Gaillard, Jean-Michel

    2014-04-01

    Conflicts between family members are expected to influence the duration and intensity of parental care. In mammals, the majority of this care occurs as resource transfer from mothers to offspring during gestation and lactation. Mating systems can have a strong influence on the severity of familial conflict--where female promiscuity is prevalent, conflict is expected to be higher between family members, causing offspring to demand more resources. If offspring are capable of manipulating their mothers and receive resources in proportion to their demands, resource transfer should increase with elevated promiscuity. We tested this prediction, unexplored across mammals, using a comparative approach. The total durations of gestation and lactation were not related to testes mass, a reliable proxy of female promiscuity across taxa. Offspring growth during gestation, however, and weaning mass, were positively correlated with testes mass, suggesting that offspring gain resources from their mothers at faster rates when familial conflict is greater. During gestation, the relationship between offspring growth and testes mass was also related to placenta morphology, with a stronger relationship between testes mass and growth observed in species with a less invasive placenta. Familial conflict could have a pervasive influence on patterns of parental care in mammals.

  5. Functional constraints on tooth morphology in carnivorous mammals.

    PubMed

    Smits, Peter D; Evans, Alistair R

    2012-08-16

    The range of potential morphologies resulting from evolution is limited by complex interacting processes, ranging from development to function. Quantifying these interactions is important for understanding adaptation and convergent evolution. Using three-dimensional reconstructions of carnivoran and dasyuromorph tooth rows, we compared statistical models of the relationship between tooth row shape and the opposing tooth row, a static feature, as well as measures of mandibular motion during chewing (occlusion), which are kinetic features. This is a new approach to quantifying functional integration because we use measures of movement and displacement, such as the amount the mandible translates laterally during occlusion, as opposed to conventional morphological measures, such as mandible length and geometric landmarks. By sampling two distantly related groups of ecologically similar mammals, we study carnivorous mammals in general rather than a specific group of mammals. Statistical model comparisons demonstrate that the best performing models always include some measure of mandibular motion, indicating that functional and statistical models of tooth shape as purely a function of the opposing tooth row are too simple and that increased model complexity provides a better understanding of tooth form. The predictors of the best performing models always included the opposing tooth row shape and a relative linear measure of mandibular motion. Our results provide quantitative support of long-standing hypotheses of tooth row shape as being influenced by mandibular motion in addition to the opposing tooth row. Additionally, this study illustrates the utility and necessity of including kinetic features in analyses of morphological integration.

  6. Polyandry Has No Detectable Mortality Cost in Female Mammals

    PubMed Central

    Lemaître, Jean-François; Gaillard, Jean-Michel

    2013-01-01

    In several taxonomic groups, females mate with several males during a single reproductive cycle. Although there is evidence that polyandry provides some benefits to females, it often involves mortality costs. However, empirical evidences of mortality costs of polyandry have so far been reported only in invertebrates. Whether polyandry has mortality costs in vertebrates is currently unknown. In the present study, we aimed to fill the gap by investigating the relationships between the level of polyandry (measured either by male relative testes mass or the percentage of multiple paternities) and female patterns of mortality across mammals. While we found that the two metrics of female mortality co-varied with pace of life, we did not find any evidence that polyandry leads to either decreased median lifespan or increased aging rate in mammals. We discuss such an absence of detectable mortality costs of polyandry in female mammals in light of recent advances in the study of mammalian reproductive biology and life-history tactics. PMID:23825000

  7. Cool sperm: why some placental mammals have a scrotum.

    PubMed

    Lovegrove, B G

    2014-05-01

    Throughout the Cenozoic, the fitness benefits of the scrotum in placental mammals presumably outweighed the fitness costs through damage, yet a definitive hypothesis for its evolution remains elusive. Here, I present an hypothesis (Endothermic Pulses Hypothesis) which argues that the evolution of the scrotum was driven by Cenozoic pulses in endothermy, that is, increases in normothermic body temperature, which occurred in Boreotheria (rodents, primates, lagomorphs, carnivores, bats, lipotyphylans and ungulates) in response to factors such as cursoriality and climate adaptation. The model argues that stabilizing selection maintained an optimum temperature for spermatogenesis and sperm storage throughout the Cenozoic at the lower plesiomorphic levels of body temperature that prevailed in ancestral mammals for at least 163 million years. Evolutionary stasis may have been driven by reduced rates of germ-cell mutations at lower body temperatures. Following the extinction of the dinosaurs at the Cretaceous-Palaeogene boundary 65.5 mya, immediate pulses in endothermy occurred associated with the dramatic radiation of the modern placental mammal orders. The fitness advantages of an optimum temperature of spermatogenesis outweighed the potential costs of testes externalization and paved the way for the evolution of the scrotum. The scrotum evolved within several hundred thousand years of the K-Pg extinction, probably associated initially with the evolution of cursoriality, and arguably facilitated mid- and late Cenozoic metabolic adaptations to factors such as climate, flight in bats and sociality in primates.

  8. Cold and hunger induce diurnality in a nocturnal mammal.

    PubMed

    van der Vinne, Vincent; Riede, Sjaak J; Gorter, Jenke A; Eijer, Willem G; Sellix, Michael T; Menaker, Michael; Daan, Serge; Pilorz, Violetta; Hut, Roelof A

    2014-10-21

    The mammalian circadian system synchronizes daily timing of activity and rest with the environmental light-dark cycle. Although the underlying molecular oscillatory mechanism is well studied, factors that influence phenotypic plasticity in daily activity patterns (temporal niche switching, chronotype) are presently unknown. Molecular evidence suggests that metabolism may influence the circadian molecular clock, but evidence at the level of the organism is lacking. Here we show that a metabolic challenge by cold and hunger induces diurnality in otherwise nocturnal mice. Lowering ambient temperature changes the phase of circadian light-dark entrainment in mice by increasing daytime and decreasing nighttime activity. This effect is further enhanced by simulated food shortage, which identifies metabolic balance as the underlying common factor influencing circadian organization. Clock gene expression analysis shows that the underlying neuronal mechanism is downstream from or parallel to the main circadian pacemaker (the hypothalamic suprachiasmatic nucleus) and that the behavioral phenotype is accompanied by phase adjustment of peripheral tissues. These findings indicate that nocturnal mammals can display considerable plasticity in circadian organization and may adopt a diurnal phenotype when energetically challenged. Our previously defined circadian thermoenergetics hypothesis proposes that such circadian plasticity, which naturally occurs in nocturnal mammals, reflects adaptive maintenance of energy balance. Quantification of energy expenditure shows that diurnality under natural conditions reduces thermoregulatory costs in small burrowing mammals like mice. Metabolic feedback on circadian organization thus provides functional benefits by reducing energy expenditure. Our findings may help to clarify relationships between sleep-wake patterns and metabolic phenotypes in humans.

  9. Adaptive radiation of multituberculate mammals before the extinction of dinosaurs.

    PubMed

    Wilson, Gregory P; Evans, Alistair R; Corfe, Ian J; Smits, Peter D; Fortelius, Mikael; Jernvall, Jukka

    2012-03-14

    The Cretaceous-Paleogene mass extinction approximately 66 million years ago is conventionally thought to have been a turning point in mammalian evolution. Prior to that event and for the first two-thirds of their evolutionary history, mammals were mostly confined to roles as generalized, small-bodied, nocturnal insectivores, presumably under selection pressures from dinosaurs. Release from these pressures, by extinction of non-avian dinosaurs at the Cretaceous-Paleogene boundary, triggered ecological diversification of mammals. Although recent individual fossil discoveries have shown that some mammalian lineages diversified ecologically during the Mesozoic era, comprehensive ecological analyses of mammalian groups crossing the Cretaceous-Paleogene boundary are lacking. Such analyses are needed because diversification analyses of living taxa allow only indirect inferences of past ecosystems. Here we show that in arguably the most evolutionarily successful clade of Mesozoic mammals, the Multituberculata, an adaptive radiation began at least 20 million years before the extinction of non-avian dinosaurs and continued across the Cretaceous-Paleogene boundary. Disparity in dental complexity, which relates to the range of diets, rose sharply in step with generic richness and disparity in body size. Moreover, maximum dental complexity and body size demonstrate an adaptive shift towards increased herbivory. This dietary expansion tracked the ecological rise of angiosperms and suggests that the resources that were available to multituberculates were relatively unaffected by the Cretaceous-Paleogene mass extinction. Taken together, our results indicate that mammals were able to take advantage of new ecological opportunities in the Mesozoic and that at least some of these opportunities persisted through the Cretaceous-Paleogene mass extinction. Similar broad-scale ecomorphological inventories of other radiations may help to constrain the possible causes of mass extinctions.

  10. Current and Future Patterns of Global Marine Mammal Biodiversity

    PubMed Central

    Kaschner, Kristin; Tittensor, Derek P.; Ready, Jonathan; Gerrodette, Tim; Worm, Boris

    2011-01-01

    Quantifying the spatial distribution of taxa is an important prerequisite for the preservation of biodiversity, and can provide a baseline against which to measure the impacts of climate change. Here we analyse patterns of marine mammal species richness based on predictions of global distributional ranges for 115 species, including all extant pinnipeds and cetaceans. We used an environmental suitability model specifically designed to address the paucity of distributional data for many marine mammal species. We generated richness patterns by overlaying predicted distributions for all species; these were then validated against sightings data from dedicated long-term surveys in the Eastern Tropical Pacific, the Northeast Atlantic and the Southern Ocean. Model outputs correlated well with empirically observed patterns of biodiversity in all three survey regions. Marine mammal richness was predicted to be highest in temperate waters of both hemispheres with distinct hotspots around New Zealand, Japan, Baja California, the Galapagos Islands, the Southeast Pacific, and the Southern Ocean. We then applied our model to explore potential changes in biodiversity under future perturbations of environmental conditions. Forward projections of biodiversity using an intermediate Intergovernmental Panel for Climate Change (IPCC) temperature scenario predicted that projected ocean warming and changes in sea ice cover until 2050 may have moderate effects on the spatial patterns of marine mammal richness. Increases in cetacean richness were predicted above 40° latitude in both hemispheres, while decreases in both pinniped and cetacean richness were expected at lower latitudes. Our results show how species distribution models can be applied to explore broad patterns of marine biodiversity worldwide for taxa for which limited distributional data are available. PMID:21625431

  11. Current and future patterns of global marine mammal biodiversity.

    PubMed

    Kaschner, Kristin; Tittensor, Derek P; Ready, Jonathan; Gerrodette, Tim; Worm, Boris

    2011-01-01

    Quantifying the spatial distribution of taxa is an important prerequisite for the preservation of biodiversity, and can provide a baseline against which to measure the impacts of climate change. Here we analyse patterns of marine mammal species richness based on predictions of global distributional ranges for 115 species, including all extant pinnipeds and cetaceans. We used an environmental suitability model specifically designed to address the paucity of distributional data for many marine mammal species. We generated richness patterns by overlaying predicted distributions for all species; these were then validated against sightings data from dedicated long-term surveys in the Eastern Tropical Pacific, the Northeast Atlantic and the Southern Ocean. Model outputs correlated well with empirically observed patterns of biodiversity in all three survey regions. Marine mammal richness was predicted to be highest in temperate waters of both hemispheres with distinct hotspots around New Zealand, Japan, Baja California, the Galapagos Islands, the Southeast Pacific, and the Southern Ocean. We then applied our model to explore potential changes in biodiversity under future perturbations of environmental conditions. Forward projections of biodiversity using an intermediate Intergovernmental Panel for Climate Change (IPCC) temperature scenario predicted that projected ocean warming and changes in sea ice cover until 2050 may have moderate effects on the spatial patterns of marine mammal richness. Increases in cetacean richness were predicted above 40° latitude in both hemispheres, while decreases in both pinniped and cetacean richness were expected at lower latitudes. Our results show how species distribution models can be applied to explore broad patterns of marine biodiversity worldwide for taxa for which limited distributional data are available.

  12. Phosphatidylcholine composition of pulmonary surfactant from terrestrial and marine diving mammals

    PubMed Central

    Gutierrez, Danielle B.; Fahlman, Andreas; Gardner, Manuela; Kleinhenz, Danielle; Piscitelli, Marina; Raverty, Stephen; Haulena, Martin; Zimba, Paul V.

    2015-01-01

    Marine mammals are repeatedly exposed to elevated extra-thoracic pressure and alveolar collapse during diving and readily experience alveolar expansion upon inhalation – a unique capability as compared to terrestrial mammals. How marine mammal lungs overcome the challenges of frequent alveolar collapse and recruitment remains unknown. Recent studies indicate that pinniped lung surfactant has more anti-adhesive components compared to terrestrial mammals, which would aid in alveolar opening. However, pulmonary surfactant composition has not yet been investigated in odontocetes, whose physiology and diving behavior differ from pinnipeds. The aim of this study was to investigate the phosphatidylcholine (PC) composition of lung surfactants from various marine mammals and compare these to a terrestrial mammal. We found an increase in anti-adhesive PC species in harp seal (Pagophilus groenlandicus) and California sea lion (Zalophus californianus) compared to dog (Canus lupus familiaris), as well as an increase in the fluidizing PCs 16:0/14:0 and 16:0/16:1 in pinnipeds compared to odontocetes. The harbor porpoise (a representative of the odontocetes) did not have higher levels of fluidizing PCs compared to dog. Our preliminary results support previous findings that pinnipeds may have adapted unique surfactant compositions that allow them to dive at high pressures for extended periods without adverse effects. Future studies will need to investigate the differences in other surfactant components to fully assess the surfactant composition in odontocetes. PMID:25812797

  13. Phosphatidylcholine composition of pulmonary surfactant from terrestrial and marine diving mammals.

    PubMed

    Gutierrez, Danielle B; Fahlman, Andreas; Gardner, Manuela; Kleinhenz, Danielle; Piscitelli, Marina; Raverty, Stephen; Haulena, Martin; Zimba, Paul V

    2015-06-01

    Marine mammals are repeatedly exposed to elevated extra-thoracic pressure and alveolar collapse during diving and readily experience alveolar expansion upon inhalation - a unique capability as compared to terrestrial mammals. How marine mammal lungs overcome the challenges of frequent alveolar collapse and recruitment remains unknown. Recent studies indicate that pinniped lung surfactant has more anti-adhesive components compared to terrestrial mammals, which would aid in alveolar opening. However, pulmonary surfactant composition has not yet been investigated in odontocetes, whose physiology and diving behavior differ from pinnipeds. The aim of this study was to investigate the phosphatidylcholine (PC) composition of lung surfactants from various marine mammals and compare these to a terrestrial mammal. We found an increase in anti-adhesive PC species in harp seal (Pagophilus groenlandicus) and California sea lion (Zalophus californianus) compared to dog (Canus lupus familiaris), as well as an increase in the fluidizing PCs 16:0/14:0 and 16:0/16:1 in pinnipeds compared to odontocetes. The harbor porpoise (a representative of the odontocetes) did not have higher levels of fluidizing PCs compared to dog. Our preliminary results support previous findings that pinnipeds may have adapted unique surfactant compositions that allow them to dive at high pressures for extended periods without adverse effects. Future studies will need to investigate the differences in other surfactant components to fully assess the surfactant composition in odontocetes. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Differences in ligamenta flava among some mammals.

    PubMed Central

    Ponseti, I. V.

    1995-01-01

    The ligamenta flava of the thoracolumbar spine of mammals with great spinal mobility have a larger content of elastin than in animals with little spinal motion. The elastin content is also higher in the ligamenta flava of mammals with arched backs and prolonged sitting posture than in nonsitting mammals with the vertebral column in the shape of a flat bow. The ligamentum flavum appears to be important; a) in the control of intervertebra movements, b) in providing intrinsic stability to the spine in the sitting and standing postures and c) in maintaining a smooth surface in the posterior wall of the spinal canal and neural foraminae. Images Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 PMID:7634024

  15. Influenza Virus Infection of Marine Mammals.

    PubMed

    Fereidouni, Sasan; Munoz, Olga; Von Dobschuetz, Sophie; De Nardi, Marco

    2016-03-01

    Interspecies transmission may play a key role in the evolution and ecology of influenza A viruses. The importance of marine mammals as hosts or carriers of potential zoonotic pathogens such as highly pathogenic H5 and H7 influenza viruses is not well understood. The fact that influenza viruses are some of the few zoonotic pathogens known to have caused infection in marine mammals, evidence for direct transmission of influenza A virus H7N7 subtype from seals to man, transmission of pandemic H1N1 influenza viruses to seals and also limited evidence for long-term persistence of influenza B viruses in seal populations without significant genetic change, makes monitoring of influenza viruses in marine mammal populations worth being performed. In addition, such monitoring studies could be a great tool to better understand the ecology of influenza viruses in nature.

  16. The evolutionary diversification of parrots supports a taxon pulse model with multiple trans-oceanic dispersal events and local radiations.

    PubMed

    Schweizer, Manuel; Seehausen, Ole; Güntert, Marcel; Hertwig, Stefan T

    2010-03-01

    Vicariance is thought to have played a major role in the evolution of modern parrots. However, as the relationships especially of the African taxa remained mostly unresolved, it has been difficult to draw firm conclusions about the roles of dispersal and vicariance. Our analyses using the broadest taxon sampling of old world parrots ever based on 3219bp of three nuclear genes revealed well-resolved and congruent phylogenetic hypotheses. Agapornis of Africa and Madagascar was found to be the sister group to Loriculus of Australasia and Indo-Malayasia and together they clustered with the Australasian Loriinae, Cyclopsittacini and Melopsittacus. Poicephalus and Psittacus from mainland Africa formed the sister group of the Neotropical Arini and Coracopsis from Madagascar and adjacent islands may be the closest relative of Psittrichas from New Guinea. These biogeographic relationships are best explained by independent colonization of the African continent via trans-oceanic dispersal from Australasia and Antarctica in the Paleogene following what may have been vicariance events in the late Cretaceous and/or early Paleogene. Our data support a taxon pulse model for the diversification of parrots whereby trans-oceanic dispersal played a more important role than previously thought and was the prerequisite for range expansion into new continents. Copyright 2009 Elsevier Inc. All rights reserved.

  17. Seeking Verisimilitude in a Class: A Systematic Review of Evidence That the Criterial Clinical Symptoms of Schizophrenia Are Taxonic

    PubMed Central

    Linscott, Richard J.; Allardyce, Judith; van Os, Jim

    2010-01-01

    This review examines whether there is evidence that the criterion symptoms of Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) (DSM-IV) schizophrenia are taxonic—that schizophrenia is not part of a single distribution of normality. Two taxometric methods, coherent cut kinetics (CCK) and latent variable modeling (LVM), are demonstrated to be sensitive to latent classes and, therefore, were regarded as providing relevant statistical evidence. A systematic literature search identified 24 articles describing analyses of 28 participant cohorts in which CCK or LVM methods were used with one or more criterion symptoms of schizophrenia. Virtually all analyses yielded results that, on first impression, favored taxonic over dimensional interpretations of the latent structure of schizophrenia. However, threats to the internal and external validity of these studies—including biased or inadequate analyses, violation of statistical assumptions, inadequate indicator screening, and the introduction of systematic error through recruitment and sampling—critically undermine this body of work. Uncertainties about the potential effects of perceptual biases, unimodal assessment, and item parceling are also identified, as are limitations in seeking to validate classes with single or double dissociations of outcomes. We conclude that there is no reason to seriously doubt a single-distribution model of schizophrenia because there is no evidence that provides a serious test of this null hypothesis. A second fundamental question remains outstanding: is schizophrenia truly a group of schizophrenias, with taxonic divisions separating its types? We make design and analysis suggestions for future research addressing these questions. PMID:19176472

  18. 'Candidatus Phytoplasma tamaricis', a novel taxon discovered in witches'-broom-diseased salt cedar (Tamarix chinensis Lour.).

    PubMed

    Zhao, Yan; Sun, Qingrong; Wei, Wei; Davis, Robert E; Wu, Wei; Liu, Qingzhong

    2009-10-01

    Salt cedar trees with pronounced witches'-broom symptoms were observed in their natural habitat in China. 16S rRNA gene sequences unique to phytoplasmas were detected in every DNA sample extracted from stem and leaf tissues of the symptomatic trees, revealing a direct association between phytoplasma infection and the salt cedar witches'-broom (SCWB) disease. Phylogenetic analysis of the SCWB phytoplasma 16S rRNA gene sequence indicated that the SCWB phytoplasma belonged to a subclade consisting of several mutually distinct 'Candidatus Phytoplasma' taxa including 'Ca. Phytoplasma prunorum', 'Ca. Phytoplasma mali', 'Ca. Phytoplasma pyri' and 'Ca. Phytoplasma spartii'. Pairwise sequence similarity scores calculated from an alignment of near full-length 16S rRNA genes revealed that SCWB phytoplasma shared 96.6 % or less sequence similarity with each previously described or proposed 'Ca. Phytoplasma' taxon, justifying the recognition of SCWB phytoplasma as a novel taxon, 'Candidatus Phytoplasma tamaricis'. The distinct virtual RFLP pattern derived from the SCWB phytoplasma 16S rRNA gene sequence, together with its lower-than-threshold similarity coefficient values with RFLP patterns of any of the 29 previously established groups, supported the recognition of a new 16Sr group, designated 16SrXXX, salt cedar witches'-broom phytoplasma group.

  19. Revisiting the cost of carnivory in mammals.

    PubMed

    Tucker, M A; Ord, T J; Rogers, T L

    2016-11-01

    Predator-prey relationships play a key role in the evolution and ecology of carnivores. An understanding of predator-prey relationships and how this differs across species and environments provides information on how carnivorous strategies have evolved and how they may change in response to environmental change. We aim to determine how mammals overcame the challenges of living within the marine environment; specifically, how this altered predator-prey body mass relationships relative to terrestrial mammals. Using predator and prey mass data collected from the literature, we applied phylogenetic piecewise regressions to investigate the relationship between predator and prey size across carnivorous mammals (51 terrestrial and 56 marine mammals). We demonstrate that carnivorous mammals have four broad dietary groups: small marine carnivores (< 11 000 kg) and small terrestrial carnivores (< 11 kg) feed on prey less than 5 kg and 2 kg, respectively. On average, large marine carnivores (> 11 000 kg) feed on prey equal to 0.01% of the carnivore's body size, compared to 45% or greater in large terrestrial carnivores (> 11 kg). We propose that differences in prey availability, and the relative ease of processing large prey in the terrestrial environment and small prey in marine environment, have led to the evolution of these novel foraging behaviours. Our results provide important insights into the selection pressures that may have been faced by early marine mammals and ultimately led to the evolution of a range of feeding strategies and predatory behaviours. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  20. Resolving the relationships of Paleocene placental mammals.

    PubMed

    Halliday, Thomas J D; Upchurch, Paul; Goswami, Anjali

    2017-02-01

    The 'Age of Mammals' began in the Paleocene epoch, the 10 million year interval immediately following the Cretaceous-Palaeogene mass extinction. The apparently rapid shift in mammalian ecomorphs from small, largely insectivorous forms to many small-to-large-bodied, diverse taxa has driven a hypothesis that the end-Cretaceous heralded an adaptive radiation in placental mammal evolution. However, the affinities of most Paleocene mammals have remained unresolved, despite significant advances in understanding the relationships of the extant orders, hindering efforts to reconstruct robustly the origin and early evolution of placental mammals. Here we present the largest cladistic analysis of Paleocene placentals to date, from a data matrix including 177 taxa (130 of which are Palaeogene) and 680 morphological characters. We improve the resolution of the relationships of several enigmatic Paleocene clades, including families of 'condylarths'. Protungulatum is resolved as a stem eutherian, meaning that no crown-placental mammal unambiguously pre-dates the Cretaceous-Palaeogene boundary. Our results support an Atlantogenata-Boreoeutheria split at the root of crown Placentalia, the presence of phenacodontids as closest relatives of Perissodactyla, the validity of Euungulata, and the placement of Arctocyonidae close to Carnivora. Periptychidae and Pantodonta are resolved as sister taxa, Leptictida and Cimolestidae are found to be stem eutherians, and Hyopsodontidae is highly polyphyletic. The inclusion of Paleocene taxa in a placental phylogeny alters interpretations of relationships and key events in mammalian evolutionary history. Paleocene mammals are an essential source of data for understanding fully the biotic dynamics associated with the end-Cretaceous mass extinction. The relationships presented here mark a critical first step towards accurate reconstruction of this important interval in the evolution of the modern fauna.

  1. Precision genetic engineering in large mammals.

    PubMed

    Garrels, Wiebke; Ivics, Zoltan; Kues, Wilfried A

    2012-07-01

    Precision genetic engineering based on stable chromosomal insertion of exogenous DNA in the genomes of large mammals is immensely important for the development of improved biomedical models, pharmaceutical research and an accelerated breeding progress. Precision genetic engineering requires (i) a known locus of genomic integration, (ii) a defined status of foreign DNA, (iii) that transgene expression is unaffected by neighbouring chromosomal sequences, (iv) endogenous genes are not mutated and (v) no unwanted DNA sequences are present. Recently, advanced molecular techniques exploiting exogenous enzymes have opened the possibilities for more sophisticated genetic engineering. Here, we critically review current developments of enzyme-catalysed approaches for targeted transgenesis in large mammals.

  2. Oral biology and disorders of tusked mammals.

    PubMed

    Steenkamp, Gerhard

    2003-09-01

    Tusked mammals can be terrestrial or aquatic. Many of these magnificent animals are kept in captivity all over the world. Functions of tusks vary as much as the species in which they occur. Dental anomalies and disorders of tusks and the rest of the dentition in these mammals were discussed, with an emphasis on the elephant. The tusk anatomy, with its large, conically-shaped pulp, makes it an ideal tooth for partial pulpectomy treatment in trauma cases where the pulp is exposed. Surgical techniques for tusks have been developed and were discussed. Oral tumors occur, but are rare.

  3. Prestin and high frequency hearing in mammals

    PubMed Central

    Zhang, Shuyi; Liu, Yang

    2011-01-01

    Recent evidence indicates that the evolution of ultrasonic hearing in echolocating bats and cetaceans has involved adaptive amino acid replacements in the cochlear gene prestin. A substantial number of these changes have occurred in parallel in both groups, suggesting that particular amino acid residues might confer greater auditory sensitivity to high frequencies. Here we review some of these findings, and consider whether similar signatures of prestin protein sequence evolution also occur in mammals that possess high frequency hearing for passive localization and conversely, whether this gene has undergone less change in mammals that lack high frequency hearing. PMID:21655450

  4. New Specimens of the Rare Taeniodont Wortmania (Mammalia: Eutheria) from the San Juan Basin of New Mexico and Comments on the Phylogeny and Functional Morphology of “Archaic” Mammals

    PubMed Central

    Williamson, Thomas E.; Brusatte, Stephen L.

    2013-01-01

    Background Taeniodonta is a clade of Late Cretaceous – Paleogene mammals remarkable for their relatively extreme cranial, dental, and postcranial adaptations and notable for being among the first mammals to achieve relatively large size following the Cretaceous-Paleogene mass extinction. Previous workers have hypothesized that taeniodonts can be divided into two clades: Conoryctidae, a group of small-bodied taeniodonts with supposedly “generalized” postcranial skeletons, and Stylinodontidae, a group of large-bodied, robust animals with massive forelimbs and claws adapted for scratch-digging. However, many taeniodont taxa are poorly known and few are represented by postcranial material, leaving many details about their anatomy, biology, and evolution ambiguous. Methodology/Principal Findings In this paper, we describe three new specimens of the rare taxon Wortmaniaotariidens from the early Paleocene (Puercan) of New Mexico. Among these specimens is one that includes remarkably complete cranial and dental material, including associated upper and lower teeth, and another that consists of partial forelimbs. These specimens allow for an updated anatomical description of this unusual taxon, supply new data for phylogenetic analyses, and enable a more constrained discussion of taeniodont biology and functional morphology. Conclusions/Significance The new specimen of Wortmania that includes associated upper and lower teeth indicates that previous interpretations of the upper dentition of this taxon were not accurate and the taxon Robertschochiasullivani is a junior synonym of W. otariidens. New specimens that include partial forelimbs indicate that Wortmania is very similar to later, large-bodied taeniodonts, with marked and distinctive adaptations for scratch-digging. Comparisons with other taeniodont taxa that include postcranial material suggest that all taeniodonts may have had scratch-digging adaptations. A phylogenetic analysis shows that Schowalteria and

  5. 77 FR 25829 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-01

    ...NMFS received an application from BP Exploration (Alaska), Inc. (BP) for an Incidental Harassment Authorization (IHA) to take marine mammals, by harassment only, incidental to a proposed 3- dimensional (3D) ocean bottom cable (OBC) seismic survey in the Simpson Lagoon area of the Alaskan Beaufort Sea during the open water season of 2012. Pursuant to the Marine Mammal Protection Act (MMPA), NMFS is requesting comments on its proposal to issue an IHA to BP to take, by Level B harassment, 11 species of marine mammals during the specified activity.

  6. Predicting small mammal and flea abundance using landform and soil properties in a plague endemic area in Lushoto District, Tanzania.

    PubMed

    Meliyo, Joel L; Kimaro, Didas N; Msanya, Balthazar M; Mulungu, Loth S; Hieronimo, Proches; Kihupi, Nganga I; Gulinck, Hubert; Deckers, Jozef A

    2014-07-01

    Small mammals particularly rodents, are considered the primary natural hosts of plague. Literature suggests that plague persistence in natural foci has a root cause in soils. The objective of this study was to investigate the relationship between on the one hand landforms and associated soil properties, and on the other hand small mammals and fleas in West Usambara Mountains in Tanzania, a plague endemic area. Standard field survey methods coupled with Geographical Information System (GIS) technique were used to examine landform and soils characteristics. Soil samples were analysed in the laboratory for physico-chemical properties. Small mammals were trapped on pre-established landform positions and identified to genus/species level. Fleas were removed from the trapped small mammals and counted. Exploration of landform and soil data was done using ArcGIS Toolbox functions and descriptive statistical analysis. The relationships between landforms, soils, small mammals and fleas were established by generalised linear regression model (GLM) operated in R statistics software. Results show that landforms and soils influence the abundance of small mammals and fleas and their spatial distribution. The abundance of small mammals and fleas increased with increase in elevation. Small mammal species richness also increases with elevation. A landform-soil model shows that available phosphorus, slope aspect and elevation were statistically significant predictors explaining richness and abundance of small mammals. Fleas' abundance and spatial distribution were influenced by hill-shade, available phosphorus and base saturation. The study suggests that landforms and soils have a strong influence on the richness and evenness of small mammals and their fleas' abundance hence could be used to explain plague dynamics in the area.

  7. Ongoing unraveling of a continental fauna: Decline and extinction of Australian mammals since European settlement

    PubMed Central

    Woinarski, John C. Z.; Burbidge, Andrew A.; Harrison, Peter L.

    2015-01-01

    The highly distinctive and mostly endemic Australian land mammal fauna has suffered an extraordinary rate of extinction (>10% of the 273 endemic terrestrial species) over the last ∼200 y: in comparison, only one native land mammal from continental North America became extinct since European settlement. A further 21% of Australian endemic land mammal species are now assessed to be threatened, indicating that the rate of loss (of one to two extinctions per decade) is likely to continue. Australia’s marine mammals have fared better overall, but status assessment for them is seriously impeded by lack of information. Much of the loss of Australian land mammal fauna (particularly in the vast deserts and tropical savannas) has been in areas that are remote from human population centers and recognized as relatively unmodified at global scale. In contrast to general patterns of extinction on other continents where the main cause is habitat loss, hunting, and impacts of human development, particularly in areas of high and increasing human population pressures, the loss of Australian land mammals is most likely due primarily to predation by introduced species, particularly the feral cat, Felis catus, and European red fox, Vulpes vulpes, and changed fire regimes. PMID:25675493

  8. Blood flow to long bones indicates activity metabolism in mammals, reptiles and dinosaurs.

    PubMed

    Seymour, Roger S; Smith, Sarah L; White, Craig R; Henderson, Donald M; Schwarz-Wings, Daniela

    2012-02-07

    The cross-sectional area of a nutrient foramen of a long bone is related to blood flow requirements of the internal bone cells that are essential for dynamic bone remodelling. Foramen area increases with body size in parallel among living mammals and non-varanid reptiles, but is significantly larger in mammals. An index of blood flow rate through the foramina is about 10 times higher in mammals than in reptiles, and even higher if differences in blood pressure are considered. The scaling of foramen size correlates well with maximum whole-body metabolic rate during exercise in mammals and reptiles, but less well with resting metabolic rate. This relates to the role of blood flow associated with bone remodelling during and following activity. Mammals and varanid lizards have much higher aerobic metabolic rates and exercise-induced bone remodelling than non-varanid reptiles. Foramen areas of 10 species of dinosaur from five taxonomic groups are generally larger than from mammals, indicating a routinely highly active and aerobic lifestyle. The simple measurement holds possibilities offers the possibility of assessing other groups of extinct and living vertebrates in relation to body size, behaviour and habitat.

  9. Blood flow to long bones indicates activity metabolism in mammals, reptiles and dinosaurs

    PubMed Central

    Seymour, Roger S.; Smith, Sarah L.; White, Craig R.; Henderson, Donald M.; Schwarz-Wings, Daniela

    2012-01-01

    The cross-sectional area of a nutrient foramen of a long bone is related to blood flow requirements of the internal bone cells that are essential for dynamic bone remodelling. Foramen area increases with body size in parallel among living mammals and non-varanid reptiles, but is significantly larger in mammals. An index of blood flow rate through the foramina is about 10 times higher in mammals than in reptiles, and even higher if differences in blood pressure are considered. The scaling of foramen size correlates well with maximum whole-body metabolic rate during exercise in mammals and reptiles, but less well with resting metabolic rate. This relates to the role of blood flow associated with bone remodelling during and following activity. Mammals and varanid lizards have much higher aerobic metabolic rates and exercise-induced bone remodelling than non-varanid reptiles. Foramen areas of 10 species of dinosaur from five taxonomic groups are generally larger than from mammals, indicating a routinely highly active and aerobic lifestyle. The simple measurement holds possibilities offers the possibility of assessing other groups of extinct and living vertebrates in relation to body size, behaviour and habitat. PMID:21733896

  10. Scenarios of large mammal loss in Europe for the 21st century.

    PubMed

    Rondinini, Carlo; Visconti, Piero

    2015-08-01

    Distributions and populations of large mammals are declining globally, leading to an increase in their extinction risk. We forecasted the distribution of extant European large mammals (17 carnivores and 10 ungulates) based on 2 Rio+20 scenarios of socioeconomic development: business as usual and reduced impact through changes in human consumption of natural resources. These scenarios are linked to scenarios of land-use change and climate change through the spatial allocation of land conversion up to 2050. We used a hierarchical framework to forecast the extent and distribution of mammal habitat based on species' habitat preferences (as described in the International Union for Conservation of Nature Red List database) within a suitable climatic space fitted to the species' current geographic range. We analyzed the geographic and taxonomic variation of habitat loss for large mammals and the potential effect of the reduced impact policy on loss mitigation. Averaging across scenarios, European large mammals were predicted to lose 10% of their habitat by 2050 (25% in the worst-case scenario). Predicted loss was much higher for species in northwestern Europe, where habitat is expected to be lost due to climate and land-use change. Change in human consumption patterns was predicted to substantially improve the conservation of habitat for European large mammals, but not enough to reduce extinction risk if species cannot adapt locally to climate change or disperse. © 2015 Society for Conservation Biology.

  11. Alien mammals in Europe: updated numbers and trends, and assessment of the effects on biodiversity.

    PubMed

    Genovesi, Piero; Carnevali, Lucilla; Alonzi, Anna; Scalera, Riccardo

    2012-09-01

    This study provides an updated picture of mammal invasions in Europe, based on detailed analysis of information on introductions occurring from the Neolithic to recent times. The assessment considered all information on species introductions, known extinctions and successful eradication campaigns, to reconstruct a trend of alien mammals' establishment in the region. Through a comparative analysis of the data on introduction, with the information on the impact of alien mammals on native and threatened species of Europe, the present study also provides an objective assessment of the overall impact of mammal introductions on European biodiversity, including information on impact mechanisms. The results of this assessment confirm the constant increase of mammal invasions in Europe, with no indication of a reduction of the rate of introduction. The study also confirms the severe impact of alien mammals, which directly threaten a significant number of native species, including many highly threatened species. The results could help to prioritize species for response, as required by international conventions and obligations. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

  12. Effects of cattle grazing on small mammal communities in the Hulunber meadow steppe

    PubMed Central

    Xin, Xiao-Ping; Liu, Zhi-Tao; Song, Yan-Ling

    2016-01-01

    Small mammals play important roles in many ecosystems, and understanding their response to disturbances such as cattle grazing is fundamental for developing sustainable land use strategies. However, how small mammals respond to cattle grazing remains controversial. A potential cause is that most of previous studies adopt rather simple experimental designs based solely on the presence/absence of grazing, and are thus unable to detect any complex relationships between diversity and grazing intensity. In this study, we conducted manipulated experiments in the Hulunber meadow steppe to survey small mammal community structures under four levels of grazing intensities. We found dramatic changes in species composition in native small mammal communities when grazing intensity reached intermediate levels (0.46 animal unit/ha). As grazing intensity increased, Spermophilus dauricus gradually became the single dominant species. Species richness and diversity of small mammals in ungrazed and lightly grazed (0.23 animal unit/ha) area were much higher than in intermediately and heavily grazed area. We did not detect a humped relationship between small mammal diversity and disturbance levels predicted by the intermediate disturbance hypothesis (IDH). Our study highlighted the necessity of conducting manipulated experiments under multiple grazing intensities. PMID:27635323

  13. The impact of buffer strips and stream-side grazing on small mammals in southwestern Wisconsin

    USGS Publications Warehouse

    Chapman, Erik W.; Ribic, C.A.

    2002-01-01

    The practice of continuously grazing cattle along streams has caused extensive degradation of riparian habitats. Buffer strips and managed intensive rotational grazing (MIRG) have been proposed to protect and restore stream ecosystems in Wisconsin. However, the ecological implications of a switch from traditional livestock management to MIRG or buffer strip establishment have not been investigated. Differences in small mammal communities associated with riparian areas on continuously grazed and MIRG pastures, as well as vegetative buffer strips adjacent to row crops, were investigated in southwestern Wisconsin during May-September 1997 and 1998. More species (mean of 6-7) were found on the buffer sites than on the pasture sites (mean of 2-5). Total small mammal abundance on buffer sites was greater than on the pastures as well: there were 3-5 times as many animals on the buffer sites compared to the pasture sites, depending on year. There were no differences in species richness or total abundance between MIRG and continuously grazed pastures in either year. Total small mammal abundance was greater near the stream than away from the stream, regardless of farm management practice but there were no differences in species richness. Buffer strips appear to support a particularly rich and abundant small mammal community. Although results did not detect a difference in small mammal use between pasture types, farm-wide implications of a conversion from continuous to MIRG styles of grazing may benefit small mammals indirectly by causing an increase in the prevalence of pasture in the agricultural landscape.

  14. Effects of cattle grazing on small mammal communities in the Hulunber meadow steppe.

    PubMed

    Cao, Chan; Shuai, Ling-Ying; Xin, Xiao-Ping; Liu, Zhi-Tao; Song, Yan-Ling; Zeng, Zhi-Gao

    2016-01-01

    Small mammals play important roles in many ecosystems, and understanding their response to disturbances such as cattle grazing is fundamental for developing sustainable land use strategies. However, how small mammals respond to cattle grazing remains controversial. A potential cause is that most of previous studies adopt rather simple experimental designs based solely on the presence/absence of grazing, and are thus unable to detect any complex relationships between diversity and grazing intensity. In this study, we conducted manipulated experiments in the Hulunber meadow steppe to survey small mammal community structures under four levels of grazing intensities. We found dramatic changes in species composition in native small mammal communities when grazing intensity reached intermediate levels (0.46 animal unit/ha). As grazing intensity increased, Spermophilus dauricus gradually became the single dominant species. Species richness and diversity of small mammals in ungrazed and lightly grazed (0.23 animal unit/ha) area were much higher than in intermediately and heavily grazed area. We did not detect a humped relationship between small mammal diversity and disturbance levels predicted by the intermediate disturbance hypothesis (IDH). Our study highlighted the necessity of conducting manipulated experiments under multiple grazing intensities.

  15. Ongoing unraveling of a continental fauna: decline and extinction of Australian mammals since European settlement.

    PubMed

    Woinarski, John C Z; Burbidge, Andrew A; Harrison, Peter L

    2015-04-14

    The highly distinctive and mostly endemic Australian land mammal fauna has suffered an extraordinary rate of extinction (>10% of the 273 endemic terrestrial species) over the last ∼200 y: in comparison, only one native land mammal from continental North America became extinct since European settlement. A further 21% of Australian endemic land mammal species are now assessed to be threatened, indicating that the rate of loss (of one to two extinctions per decade) is likely to continue. Australia's marine mammals have fared better overall, but status assessment for them is seriously impeded by lack of information. Much of the loss of Australian land mammal fauna (particularly in the vast deserts and tropical savannas) has been in areas that are remote from human population centers and recognized as relatively unmodified at global scale. In contrast to general patterns of extinction on other continents where the main cause is habitat loss, hunting, and impacts of human development, particularly in areas of high and increasing human population pressures, the loss of Australian land mammals is most likely due primarily to predation by introduced species, particularly the feral cat, Felis catus, and European red fox, Vulpes vulpes, and changed fire regimes.

  16. [Current views on vision of mammals].

    PubMed

    Khokhlova, T V

    2012-01-01

    In the review, research data are presented on mammals' vision including visual pigments, color and contrast vision, and visual behaviour in different species. It is shown that in course of evolution mammals were gradually losing the elements of daylight cone vision system that are typical of other vertebrates. In monotremes, visual pigments SWS2 (cone blue-sensitive 2) and MWS/LWS (green/red-sensitive) are still present, as well as rod RH1. Theria, except some primates, also have two cone visual pigments: SWS1 (ultraviolet/violet or blue-sensitive 1) and MWS/LWS along with rod RH1. Humans and some other higher primates evolved the new visual pigment, MWS, and acquired trichromatic vision. Marine mammals (cetaceans and pinnipeds) and some species of other orders have lost also the visual pigment SWS1, probably due to specificity of processing the information received by these cones. Current view on mammals' vision with two cone pigments and rods is presented. Data on maximum spectral sensitivity of visual pigments in different species and orders are given along with data on spatial contrast sensation. High visual acuity has been acquired by ungulates, artiodactyls, and primates, while the highest one--by humans with their specialized fovea.

  17. Solid modeling of fossil small mammal teeth

    NASA Astrophysics Data System (ADS)

    Marschallinger, Robert; Hofmann, Peter; Daxner-Höck, Gudrun; Ketcham, Richard A.

    2011-09-01

    This paper presents an approach to create solid models of fossil small mammal teeth using a combination of microcomputed tomography, object based image analysis and voxel modeling. Small mammal teeth, because of their durability, are widely found in Cenozioc sediments the world over and play a key role in stratigraphy as well as in researching the rapid evolution and the paleogeographic spreading of small mammals. Recent advances in microcomputed tomography make this non-destructive analysis method an ideal data source for high-resolution 3D models of fossil small animal teeth. To derive internally consistent solid models of such fossils from micro-CT imagery, we propose a combination of 3D object based image analysis and solid modeling. Incorporating paleontological expert knowledge in the image processing cycle, object based image analysis yields topologically consistent image stacks classified by the main tooth components—enamel, dentine and pulp. Forwarding these data to a voxel modeling system, they can be quantitatively analyzed in an unprecedented manner: going beyond the possibilities of the state-of-art surface models, solid models are capable of unambiguously portraying the entire object volume—teeth can be peeled by material properties, subvolumes can be extracted and automatically analyzed by Boolean operations. The proposed method, which can be flexibly extended to handle a range of paleontological and geological micro-objects, is demonstrated with two typical fossil small mammal teeth.

  18. Internally coupled ears in living mammals.

    PubMed

    Mason, Matthew J

    2016-10-01

    It is generally held that the right and left middle ears of mammals are acoustically isolated from each other, such that mammals must rely on neural computation to derive sound localisation cues. There are, however, some unusual species in which the middle ear cavities intercommunicate, in which case each ear might be able to act as a pressure-difference receiver. This could improve sound localisation at lower frequencies. The platypus Ornithorhynchus is apparently unique among mammals in that its tympanic cavities are widely open to the pharynx, a morphology resembling that of some non-mammalian tetrapods. The right and left middle ear cavities of certain talpid and golden moles are connected through air passages within the basicranium; one experimental study on Talpa has shown that the middle ears are indeed acoustically coupled by these means. Having a basisphenoid component to the middle ear cavity walls could be an important prerequisite for the development of this form of interaural communication. Little is known about the hearing abilities of platypus, talpid and golden moles, but their audition may well be limited to relatively low frequencies. If so, these mammals could, in principle, benefit from the sound localisation cues available to them through internally coupled ears. Whether or not they actually do remains to be established experimentally.

  19. Mammals of the Savannah River Site

    SciTech Connect

    Cothran, E.G.; Smith, M.H.; Wolff, J.O.; Gentry, J.B.

    1991-12-31

    This book is designed to be used as a field guide, reference book, bibliography, and introduction to the basic biology and ecology of the 54 mammal species that currently or potentially exist on or near the Savannah River Site (SRS). For 50 of these species, we present basic descriptions, distinguishing morphological features, distribution and habitat preferences, food habits, reproductive biology, social behavior, ecological relationships with other species, and economic importance to man. For those species that have been studied on the SRS, we summarize the results of these studies. Keys and illustrations are provided for whole body and skull identification. A selected glossary defines technical terminology. Illustrations of tracks of the more common larger mammals will assist in field identifications. We also summarize the results of two major long-term SRS studies, ``The Forbearer Census`` and ``White-tailed Deer Studies``. A cross-indexed list of over 300 SRS publications on mammals classifies each publication by 23 categories such as habitat, reproduction, genetics, etc., and also for each mammal species. The 149 Master`s theses and Ph.D. dissertations that have been conducted at the Savannah River Ecology Laboratory are provided as additional references.

  20. Mammals of the Savannah River Site

    SciTech Connect

    Cothran, E.G.; Smith, M.H.; Wolff, J.O.; Gentry, J.B.

    1991-01-01

    This book is designed to be used as a field guide, reference book, bibliography, and introduction to the basic biology and ecology of the 54 mammal species that currently or potentially exist on or near the Savannah River Site (SRS). For 50 of these species, we present basic descriptions, distinguishing morphological features, distribution and habitat preferences, food habits, reproductive biology, social behavior, ecological relationships with other species, and economic importance to man. For those species that have been studied on the SRS, we summarize the results of these studies. Keys and illustrations are provided for whole body and skull identification. A selected glossary defines technical terminology. Illustrations of tracks of the more common larger mammals will assist in field identifications. We also summarize the results of two major long-term SRS studies, The Forbearer Census'' and White-tailed Deer Studies''. A cross-indexed list of over 300 SRS publications on mammals classifies each publication by 23 categories such as habitat, reproduction, genetics, etc., and also for each mammal species. The 149 Master's theses and Ph.D. dissertations that have been conducted at the Savannah River Ecology Laboratory are provided as additional references.

  1. A system for gathering small mammal data

    Treesearch

    Robert D. Neely; Robert W. Campbell

    1973-01-01

    As an aid to studying vertebrate predators of the gypsy moth, a radio telemetry system was designed to detect the death of small mammals and facilitate recovery of the remains. An intraperitoneally implanted radio transmitter is triggered by the drop in body temperature when the animal dies. The device was tested in white-footed mice.

  2. Ticks associated with wild mammals in Ghana.

    PubMed

    Ntiamoa-Baidu, Y; Carr-Saunders, C; Matthews, B E; Preston, P M; Walker, A R

    2005-06-01

    The host ranges of a collection of 21 tick species found on wild mammals in the savanna, forests and coastal zone of Ghana suggested that most species were adapted to feeding mainly on host species within a single mammalian order, i.e. on artiodactyls (bovids/suids), carnivores, rodents or pholidotes (pangolins). Only a few species were dispersed evenly across a range of orders. Seven out of ten of the most common ticks on forest mammals were significantly associated with a particular host species or a group of closely related host species, which could be viewed as their major host or hosts, but they were also recorded much less frequently on a wide range of host species. Two other species were confined to their major hosts. Only one species appeared to be widely dispersed on forest mammals and to lack a particular major host. The majority of tick species therefore occurred on hosts with very distinctive biological, behavioural and ecological characteristics. The study provided no evidence to support the view that host specificity is an artefact of sampling. Finding that the tick species on Ghanaian wild mammals occurred on particular hosts, as well as in distinct habitats, indicated that tick-host associations are important for tick survival and confirmed the importance of climate and vegetation in tick distribution.

  3. 78 FR 54867 - Proposed Information Collection; Comment Request; Marine Mammal Health and Stranding Response...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-06

    ... Mammal Health and Stranding Response Program, Level A Stranding and Rehabilitation Disposition Data Sheet... mammals while in rehabilitation status. The data from the marine mammal rehabilitation disposition report...

  4. Adaptive features of aquatic mammals' eye.

    PubMed

    Mass, Alla M; Supin, Alexander Ya

    2007-06-01

    The eye of aquatic mammals demonstrates several adaptations to both underwater and aerial vision. This study offers a review of eye anatomy in four groups of aquatic animals: cetaceans (toothed and baleen whales), pinnipeds (seals, sea lions, and walruses), sirenians (manatees and dugongs), and sea otters. Eye anatomy and optics, retinal laminar morphology, and topography of ganglion cell distribution are discussed with particular reference to aquatic specializations for underwater versus aerial vision. Aquatic mammals display emmetropia (i.e., refraction of light to focus on the retina) while submerged, and most have mechanisms to achieve emmetropia above water to counter the resulting aerial myopia. As underwater vision necessitates adjusting to wide variations in luminosity, iris muscle contractions create species-specific pupil shapes that regulate the amount of light entering the pupil and, in pinnipeds, work in conjunction with a reflective optic tapetum. The retina of aquatic mammals is similar to that of nocturnal terrestrial mammals in containing mainly rod photoreceptors and a minor number of cones (however, residual color vision may take place). A characteristic feature of the cetacean and pinniped retina is the large size of ganglion cells separated by wide intercellular spaces. Studies of topographic distribution of ganglion cells in the retina of cetaceans revealed two areas of ganglion cell concentration (the best-vision areas) located in the temporal and nasal quadrants; pinnipeds, sirenians, and sea otters have only one such area. In general, the visual system of marine mammals demonstrates a high degree of development and several specific features associated with adaptation for vision in both the aquatic and aerial environments.

  5. Effects of roads on small mammals

    USGS Publications Warehouse

    Adams, L.W.; Geis, A.D.

    1983-01-01

    (1) The study was designed to determine the effects of roads on the diversity, spatial distribution, and density of small mammals. (2) Forty species of small mammal (5859 individuals) were snap-trapped in the study. Data resulted from 144 360 trap-nights of effort for an average of 4.06 captures per 100 trap-nights. (3) Small mammal community structure and density were both influenced by roads. Community structure in right-of-way (ROW) habitat was different from that in adjacent habitat. Five species did not prefer ROW habitat: the golden mouse, dusky-footed woodrat, brush mouse, pinon mouse, and California red-backed vole. However, there were more species present in ROW habitat than in adjacent habitat. Grassland species generally preferred ROW habitat and many less habitat-specific species were distributed in ROW and adjacent habitat. (4) Small mammal density (all species combined) was greater in interstate ROW habitat than in adjacent habitat. This was also true individually for the eastern harvest mouse, white-footed mouse, meadow vole, prairie vole, vagrant shrew. Townsend's vole, and California vole. Small mammal density was less in county road ROWs than in adjacent habitat, probably because of the small size of these areas. The data indicate that ROW habitat and its accompanying edge are attractive no: only to grassland species but also to many less habitat-specific species that make use of the ROW-edge-adjacent habitat complex. (5) Mortality on interstate highways was greatest for those species with highest densities in ROW habitat, and did not appear to be detrimental to populations of these species.

  6. Paracellular Absorption: A Bat Breaks the Mammal Paradigm

    PubMed Central

    Caviedes-Vidal, Enrique; Karasov, William H.; Chediack, Juan Gabriel; Fasulo, Verónica; Cruz-Neto, Ariovaldo P.; Otani, Lye

    2008-01-01

    Bats tend to have less intestinal tissue than comparably sized nonflying mammals. The corresponding reduction in intestinal volume and hence mass of digesta carried is advantageous because the costs of flight increase with load carried and because take-off and maneuverability are diminished at heavier masses. Water soluble compounds, such as glucose and amino acids, are absorbed in the small intestine mainly via two pathways, the transporter-mediated transcellular and the passive, paracellular pathways. Using the microchiropteran bat Artibeus literatus (mean mass 80.6±3.7 g), we tested the predictions that absorption of water-soluble compounds that are not actively transported would be extensive as a compensatory mechanism for relatively less intestinal tissue, and would decline with increasing molecular mass in accord with sieve-like paracellular absorption. Using a standard pharmacokinetic technique, we fed, or injected intraperitonealy the metabolically inert carbohydrates L-rhamnose (molecular mass = 164 Da) and cellobiose (molecular mass = 342 Da) which are absorbed only by paracellular transport, and 3-O-methyl-D-glucose (3OMD-glucose) which is absorbed via both mediated (active) and paracellular transport. As predicted, the bioavailability of paracellular probes declined with increasing molecular mass (rhamnose, 90±11%; cellobiose, 10±3%, n = 8) and was significantly higher in bats than has been reported for laboratory rats and other mammals. In addition, absorption of 3OMD-glucose was high (96±11%). We estimated that the bats rely on passive, paracellular absorption for more than 70% of their total glucose absorption, much more than in non-flying mammals. Although possibly compensating for less intestinal tissue, a high intestinal permeability that permits passive absorption might be less selective than a carrier-mediated system for nutrient absorption and might permit toxins to be absorbed from plant and animal material in the intestinal

  7. Paracellular absorption: a bat breaks the mammal paradigm.

    PubMed

    Caviedes-Vidal, Enrique; Karasov, William H; Chediack, Juan Gabriel; Fasulo, Verónica; Cruz-Neto, Ariovaldo P; Otani, Lye

    2008-01-09

    Bats tend to have less intestinal tissue than comparably sized nonflying mammals. The corresponding reduction in intestinal volume and hence mass of digesta carried is advantageous because the costs of flight increase with load carried and because take-off and maneuverability are diminished at heavier masses. Water soluble compounds, such as glucose and amino acids, are absorbed in the small intestine mainly via two pathways, the transporter-mediated transcellular and the passive, paracellular pathways. Using the microchiropteran bat Artibeus literatus (mean mass 80.6+/-3.7 g), we tested the predictions that absorption of water-soluble compounds that are not actively transported would be extensive as a compensatory mechanism for relatively less intestinal tissue, and would decline with increasing molecular mass in accord with sieve-like paracellular absorption. Using a standard pharmacokinetic technique, we fed, or injected intraperitoneally the metabolically inert carbohydrates L-rhamnose (molecular mass = 164 Da) and cellobiose (molecular mass = 342 Da) which are absorbed only by paracellular transport, and 3-O-methyl-D-glucose (3OMD-glucose) which is absorbed via both mediated (active) and paracellular transport. As predicted, the bioavailability of paracellular probes declined with increasing molecular mass (rhamnose, 90+/-11%; cellobiose, 10+/-3%, n = 8) and was significantly higher in bats than has been reported for laboratory rats and other mammals. In addition, absorption of 3OMD-glucose was high (96+/-11%). We estimated that the bats rely on passive, paracellular absorption for more than 70% of their total glucose absorption, much more than in non-flying mammals. Although possibly compensating for less intestinal tissue, a high intestinal permeability that permits passive absorption might be less selective than a carrier-mediated system for nutrient absorption and might permit toxins to be absorbed from plant and animal material in the intestinal lumen.

  8. 76 FR 68974 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-07

    ... aircraft. Shell has requested an authorization to take 11 marine mammal species by Level B harassment... Interior, Bureau of Ocean Energy Management (BOEM, formerly the Minerals Management Service) Alaska OCS...

  9. 75 FR 16754 - Taking and Importing Marine Mammals; Taking of Marine Mammals Incidental to Conducting Precision...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-02

    ... of Marine Mammals Incidental to Conducting Precision Strike Weapons Testing and Training by Eglin Air... testing and training during Precision Strike Weapons (PSW) tests in the Gulf of Mexico (GOM), a...

  10. 76 FR 7548 - Taking and Importing Marine Mammals; Taking of Marine Mammals Incidental to Conducting Precision...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-10

    ... of Marine Mammals Incidental to Conducting Precision Strike Weapons Testing and Training by Eglin Air... testing and training during Precision Strike Weapons (PSW) testing and training in the Gulf of Mexico...

  11. 78 FR 63396 - Taking and Importing Marine Mammals; Taking Marine Mammals Incidental to Replacement of the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-24

    ... knowledge of the species and of the level of taking or impacts on populations of marine mammals that are... hours of the discovery. The Holder shall provide photographs or video footage or other documentation of...

  12. Challenges to natural resource monitoring in a small border park: terrestrial mammals at Coronado National Memorial, Cochise County, Arizona

    USGS Publications Warehouse

    Swann, Don E.; Bucci, Melanie; Kuenzi, Amy J.; Alberti, Barbara N.; Schwalbe, Cecil R.; Halvorson, William L.; van Riper, Charles; Schwalbe, Cecil R.

    2010-01-01

    Long-term monitoring in national parks is essential to meet National Park Service and other important public goals. Terrestrial mammals are often proposed for monitoring because large mammals are of interest to visitors and small mammals are important as prey. However, traditional monitoring strategies for mammals are often too expensive and complex to sustain for long periods, particularly in small parks. To evaluate potential strategies for long-term monitoring in small parks, we conducted an intensive one-year inventory of terrestrial mammals at Coronado National Memorial, located in Arizona on the U.S.-Mexico international border, then continued less-intensive monitoring at the site for 7 additional years. During 1996-2003 we confirmed 44 species of terrestrial mammals. Most species (40) were detected in the intensive first year of the study, but we continued to detect new species in later years. Mark-recapture data on small mammals indicated large inter-annual fluctuations in population size, but no significant trend over the 7-year period. Issues associated with the international border affected monitoring efforts and increased sampling costs. Our study confirms that sustained annual monitoring of mammals is probably not feasible in small park units like Coronado. However, comparisons of our data with past studies provide insight into important changes in the mammal community since the 1970s, including an increase in abundance and diversity of grassland rodents. Our results suggest that intensive inventories every 10-20 years may be a valuable and cost-effective approach for detecting long-term trends in terrestrial mammal communities in small natural areas.

  13. Avian sleep homeostasis: convergent evolution of complex brains, cognition and sleep functions in mammals and birds.

    PubMed

    Rattenborg, Niels C; Martinez-Gonzalez, Dolores; Lesku, John A

    2009-03-01

    Birds are the only taxonomic group other than mammals that exhibit high-amplitude slow-waves in the electroencephalogram (EEG) during sleep. This defining feature of slow-wave sleep (SWS) apparently evolved independently in mammals and birds, as reptiles do not exhibit similar EEG activity during sleep. In mammals, the level of slow-wave activity (SWA) (low-frequency spectral power density) during SWS increases and decreases as a function of prior time spent awake and asleep, respectively, and therefore reflects homeostatically regulated sleep processes potentially tied to the function of SWS. Although birds also exhibit SWS, previous sleep deprivation studies in birds did not detect a compensatory increase in SWS-related SWA during recovery, as observed in similarly sleep-deprived mammals. This suggested that, unlike mammalian SWS, avian SWS is not homeostatically regulated, and therefore might serve a different function. However, we recently demonstrated that SWA during SWS increases in pigeons following short-term sleep deprivation. Herein we summarize research on avian sleep homeostasis, and cast our evidence for this phenomenon within the context of theories for the function of SWS in mammals. We propose that the convergent evolution of homeostatically regulated SWS in mammals and birds was directly linked to the convergent evolution of large, heavily interconnected brains capable of performing complex cognitive processes in each group. Specifically, as has been proposed for mammals, the interconnectivity that forms the basis of complex cognition in birds may also instantiate slow, synchronous network oscillations during SWS that in turn maintain interconnectivity and cognition at an optimal level.

  14. Mammal assemblages in forest fragments and landscapes occupied by black howler monkeys.

    PubMed

    Rangel-Negrín, Ariadna; Coyohua-Fuentes, Alejandro; Canales-Espinosa, Domingo; Dias, Pedro Américo D

    2014-07-01

    Species assemblages in disturbed habitats vary as a function of the interaction between species requirements and the spatial configuration of the habitat. There are many reports accounting for the presence of howler monkeys in fragments where other mammals are absent, suggesting that they are more resilient. In the present study we explored this idea and predicted that if howler monkeys were more resilient to habitat loss and fragmentation than other mammals, mammal assemblages in fragments occupied by howler monkeys should include fewer species with decreasing amount of habitat (smaller fragment size and less habitat in the landscape) and increasing number of forest fragments. We explored these relationships by additionally considering the feeding and life habits of mammal species, as well as the isolation and proximity of each fragment to human settlements and roads. We sampled the presence of mammals in five fragments occupied by black howler monkeys (Alouatta pigra) in the Mexican state of Campeche. Through direct sights performed during 240 h in each fragment, we observed 23 species. At the landscape scale, higher fragmentation was associated with a decrease in herbivores, omnivores and total number of species. At the fragment scale semiarboreal, omnivore, and total number of species increased with increasing fragment size. This study supports the idea that howler monkeys are more resilient to forest loss and fragmentation than other native mammals, and our exploratory analyses suggest that the specific mammal assemblages that are found in fragments are related to both landscape and fragment scale spatial attributes, as well as with species-specific characteristics.

  15. 77 FR 48967 - Marine Mammals; File No. 17350

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-15

    ... marine mammals of the following species: bearded seal (Erignathus ] barbatus), ringed seal (Phoca hispida... National Oceanic and Atmospheric Administration RIN 0648-XC067 Marine Mammals; File No. 17350 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA),...

  16. 78 FR 23746 - Marine Mammals; File No. 17298

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-22

    ..., export, and receive marine mammal parts for scientific research. ADDRESSES: The permit and related... research on marine mammals parts had been submitted by the above-named applicant. The requested permit has...

  17. Molecular cloning and evolutionary analysis of GJB6 in mammals.

    PubMed

    Ru, Binghua; Han, Naijian; He, Guimei; Brayer, Kathryn; Zhang, Shuyi; Wang, Zhe

    2012-04-01

    GJB6 plays a crucial role in hearing. In mammals, bats use ultrasonic echolocation for orientation and locating prey. To investigate the evolution of GJB6 in mammals, we cloned the full-length coding region of GJB6 from 16 species of bats and 4 other mammal species and compared them with orthologous sequences in 11 other mammals. The results show purifying selection on GJB6 in mammals, as well as in the bat lineage, which indicates an important role for GJB6 in mammal hearing. We also found one unique amino acid substitution shared by 16 species of bats and 10 shared by two species of artiodactyls. This positioned the artiodactyls at an abnormal location in the gene tree. In addition, the cytoplasmic loop and carboxy terminus were more variable than other domains in all the mammals. These results demonstrate that GJB6 is basically conserved in mammals but has undergone relatively rapid evolution in particular lineages and domains.

  18. Effects of tillage practices and carbofuran exposure on small mammals

    USGS Publications Warehouse

    Albers, P.H.; Linder, G.; Nichols, J.D.

    1990-01-01

    We compared population estimates, body mass, movement, and blood chemistry of small mammals between conventionally tilled and no-till cornfields in Maryland and Pennsylvania to evaluate the effects of tillage practices and carbofuran exposure on small mammals.

  19. Lerneca inalata beripocone subsp. nov. (Orthoptera: Phalangopsidae; Luzarinae): a new taxon for the northern Pantanal of Brazil.

    PubMed

    Lima, Raysa Martins; Martins, Luciano De Pinho; Pereira, Marcelo Ribeiro; Ganchev, Todor D; Jahn, Olaf; Lhano, Marcos Gonçalves; Marques, Marinêz Isaac; Schuchmann, Karl-L

    2016-10-17

    The first record of the Orthoptera species Lerneca inalata for Brazil is presented here. The taxon is represented by a new subspecies Lerneca inalata beripocone subsp. nov. (Phalangopsidae, Luzarinae), collected in the Pantanal of Poconé, Mato Grosso, Brazil. This work includes morphological and morphometric data as well as descriptions of female genitalia and calling song. The new subspecies has as diagnostic features the male genitalia with six ventral spines on the B sclerite, the first spine having a subtle bifurcation; the mid-region of the strongly sclerotized pseudepiphallus; inclination of C sclerite with slightly concave curvature; tegmina-length ratio and the speculum (syn. mirror) width approximately three times the length of the apical area. The description of the female genitalia and the calling song is presented for the first time for the species Lerneca inalata. A distribution map covers the local occurrence of its subspecies.

  20. Molecular evidence for a single taxon, Anopheles nuneztovari s. l., from two endemic malaria regions in Colombia

    PubMed Central

    Jaramillo, Luz Marina; Gutiérrez, Lina A; Luckhart, Shirley; Conn, Jan E; Correa, Margarita M

    2012-01-01

    To elucidate the Anopheles nuneztovari s.l. taxonomic status at a microgeographic level in four malaria endemic localities from Antioquia and Córdoba, Colombia, fragments of the Cytochrome oxidase subunit I (COI) and the white gene were used. The COI analysis showed low genetic differentiation with FST levels between −0.02 and 0.137 and Nm values between 3 and infinity, indicating the presence of high gene flow among An. nuneztovari s.l. populations from the four localities. The COI network showed a single most common haplotype, 1 (n=55), present in all localities, as the likely ancestral haplotype. Analysis of the white gene showed that An. nuneztovari s.l. populations from both departments grouped with haplotypes 19 and 20, which are part of lineage 3 previously reported. The results of the present study suggest that An. nuneztovari s.l. is a single taxon in the area of the present study. PMID:22241127