Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

BACKGROUND: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. DEVELOPMENT AND TESTING OF THE ONTOLOGY: Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. RESULTS AND SIGNIFICANCE: Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

[Book Review] A database of North American tertiary mammals

Review of: Janis, C.M., Scott, K.M., & Jacobs, L.L. (eds.) 1998. Evolution of Tertiary Mammals of North America Volume 1: Terrestrial Carnivores, Ungulates, and Ungulatelike Mammals, i-x, 1491. Cambridge University Press, Cambridge, UK. £165

Mammals and agri-environment schemes: hare haven or pest paradise?

1. Agri-environment schemes (AESs) are designed to create landscape-scale improvements in biodiversity. While the specific aims of AESs do not always include the enhancement of species of conservation concern, associated conservation strategies, such as the UK Biodiversity Action Plan, often rest on the assumption that AESs enhance environmental conditions and thereby improve the conservation status of target species. However, there is little evidence for the general efficacy of AESs in this respect. 2. To evaluate the effects of the Environmentally Sensitive Area (ESA) scheme, a widespread AES in Northern Ireland, a spotlight survey of the relative abundance of three mammal species, Irish hare Lepus timidus hibernicus, European rabbit Oryctolagus cuniculus and red fox Vulpes vulpes, was conducted. Of these, the Irish hare is a priority species for conservation action and the focus of a species action plan, while rabbit and fox are commonly considered agricultural pests. The effects of ESA designation and habitat on each species were assessed at 150 ESA and 50 non-ESA sites, matched for landscape characteristics. 3. The ESA scheme had no demonstrable effect on the abundance of Irish hares, and this agri-environment scheme did not target the landscape and habitat variables associated with hares. 4. In contrast, the abundance of rabbits and foxes was significantly greater within ESAs than the wider countryside. Agricultural factors such as reduced livestock stocking density, reduced overgrazing and field boundary enhancements may create more favourable conditions for both species. Aside from the implications for farm economics, the proliferation of rabbit populations within conservation areas may raise issues concerning the grazing of important plant communities, while increases in fox populations may adversely affect ground-nesting birds and other animal species of conservation concern. 5. Synthesis and applications: The abundance of rabbits and foxes corroborates recent work that suggests AESs may benefit common species but can not be relied upon to encourage rarer species. The Irish hare species action plan relies on agri-environment schemes to enhance the species’ status and realize the target of increasing the hare population by 2010 by promoting suitable habitat. However, the ESA scheme is unlikely to help in achieving these objectives. Targeted and evidence-based agri-environment prescriptions are clearly required in order to ensure the realization of species-specific conservation targets.

The response of small mammals to natural and human-altered edges associated with Afromontane forests of South Africa

An increase in edge area reduces the effective size of habitat fragments and thus the area available for habitat-interior specialists. However, it is unclear how edge effects compare at different ecotones in the same system. We investigated the response of a small mammal community associated with Afromontane forests to edge effects at three different habitat transitions: natural forest to grassland (natural edge, structurally different vegetation types), natural forest to mature plantation (human-altered edge, structurally similar vegetation types) and natural forest to harvested plantation (human-altered edge, structurally different vegetation types). We predicted that edge effects should be less severe at natural ecotones and at similarly structured contiguous vegetation types than human-altered ecotones and differently structured contiguous vegetation types, respectively. We found that forest species seemed to avoid all habitat edges in our study area. Surprisingly, natural edges supported a less diverse small mammal community than human-altered forest edges. However, edge effects were observed deeper into native forests surrounded by mature alien plantations (and more so at harvested plantations) than into native forests surrounded by native grasslands. The net effect of mature plantations was therefore to reduce the functional size of the natural forest by creating a larger edge. We suggest that when plantations are established a buffer zone of natural vegetation be left between natural forests and newly established plantations to mitigate the negative effects of plantation forestry.

Origin of British and Irish mammals: disparate post-glacial colonisation and species introductions

Global climate changes during the Quaternary reveal much about broader evolutionary effects of environmental change. Detailed regional studies reveal how evolutionary lineages and novel communities and ecosystems, emerge through glacial bottlenecks or from refugia. There have been significant advances in benthic imaging and dating, particularly with respect to the movements of the British (Scottish) and Irish ice sheets and associated changes in sea level during and after the Last Glacial Maximum (LGM). Ireland has been isolated as an island for approximately twice as long as Britain with no evidence of any substantial, enduring land bridge between these islands after ca 15 kya. Recent biogeographical studies show that Britain's mammal community is akin to those of southern parts of Scandinavia, The Netherlands and Belgium, but the much lower mammal species richness of Ireland is unique and needs explanation. Here, we consider physiographic, archaeological, phylogeographical i.e. molecular genetic, and biological evidence comprising ecological, behavioural and morphological data, to review how mammal species recolonized western Europe after the LGM with emphasis on Britain and, in particular, Ireland. We focus on why these close neighbours had such different mammal fauna in the early Holocene, the stability of ecosystems after LGM subject to climate change and later species introductions.

There is general concordance of archaeological and molecular genetic evidence where data allow some insight into history after the LGM. Phylogeography reveals the process of recolonization, e.g. with respect to source of colonizers and anthropogenic influence, whilst archaeological data reveal timing more precisely through carbon dating and stratigraphy. More representative samples and improved calibration of the ‘molecular clock’ will lead to further insights with regards to the influence of successive glaciations. Species showing greatest morphological, behavioural and ecological divergence in Ireland in comparison to Britain and continental Europe, were also those which arrived in Ireland very early in the Holocene either with or without the assistance of people. Cold tolerant mammal species recolonized quickly after LGM but disappeared, potentially as a result of a short period of rapid warming. Other early arrivals were less cold tolerant and succumbed to the colder conditions during the Younger Dryas or shortly after the start of the Holocene (11.5 kya), or the area of suitable habitat was insufficient to sustain a viable population especially in larger species. Late Pleistocene mammals in Ireland were restricted to those able to colonize up to ca 15 kya, probably originating from adjacent areas of unglaciated Britain and land now below sea level, to the south and west (of Ireland). These few, early colonizers retain genetic diversity which dates from before the LGM. Late Pleistocene Ireland, therefore, had a much depleted complement of mammal species in comparison to Britain.

Mammal species, colonising predominantly from southeast and east Europe occupied west Europe only as far as Britain between ca 15 and 8 kya, were excluded from Ireland by the Irish and Celtic Seas. Smaller species in particular failed to colonise Ireland. Britain being isolated as an island from ca. 8 kya has similar species richness and composition to adjacent lowland areas of northwest continental Europe and its mammals almost all show strongest genetic affinity to populations in neighbouring continental Europe with a few retaining genotypes associated with earlier, western lineages.

The role of people in the deliberate introduction of mammal species and distinct genotypes is much more significant with regards to Ireland than Britain reflecting the larger species richness of the latter and its more enduring land link with continental Europe. The prime motivation of early people in moving mammals was likely to be resource driven but also potentially cultural; as elsewhere, people exploring uninhabited places introduced species for food and the materials they required to survive. It is possible that the process of introduction of mammals to Ireland commenced during the Mesolithic and accelerated with Neolithic people. Irish populations of these long established, introduced species show some unique genetic variation whilst retaining traces of their origins principally from Britain but in some cases, Scandinavia and Iberia. It is of particular interest that they may retain genetic forms now absent from their source populations. Further species introductions, during the Bronze and late Iron Ages, and Viking and Norman invasions, follow the same pattern but lack the time for genetic divergence from their source populations. Accidental introductions of commensal species show considerable genetic diversity based on numerous translocations along the eastern Atlantic coastline. More recent accidental and deliberate introductions are characterised by a lack of genetic diversity other than that explicable by more than one introduction.

The substantial advances in understanding the postglacial origins and genetic diversity of British and Irish mammals, the role of early people in species translocations, and determination of species that are more recently introduced, should inform policy decisions with regards to species and genetic conservation. Conservation should prioritise early, naturally recolonizing species and those brought in by early people reflecting their long association with these islands. These early arrivals in Britain and Ireland and associated islands show genetic diversity that may be of value in mitigating anthropogenic climate change across Europe. In contrast, more recent introductions are likely to disturb ecosystems greatly, lead to loss of diversity and should be controlled. This challenge is more severe in Ireland where the number and proportion of invasive species from the 19th century to the present has been greater than in Britain.

On the DNA of eleven mammals

This paper studies the DNA code of eleven mammals from the perspective of fractional dynamics. The application of Fourier transform and power law trendlines leads to a categorical representation of species and chromosomes. The DNA information reveals long range memory characteristics.

Statistical Analysis of Eco-Toxicologic Data of Mammals from a Polluted Area

Several eco-toxicological studies have shown that insectivorous mammals, due to their feeding habits, easily accumulate high amounts of pollutants in relation to other mammal species. To assess the bio-accumulation levels of toxic metals and their in°uence on essential metals, we quantified the concentration of 19 elements (Ca, K, Fe, B, P, S, Na, Al, Zn, Ba, Rb, Sr, Cu, Mn, Hg, Cd, Mo, Cr and Pb) in bones of 105 greater white-toothed shrews (Crocidura russula) from a polluted (Ebro Delta) and a control (Medas Islands) area. Since chemical contents of a bio-indicator are mainly compositional data, conventional statistical analyses currently used in eco-toxicology can give misleading results. Therefore, to improve the interpretation of the data obtained, we used statistical techniques for compositional data analysis to define groups of metals and to evaluate the relationships between them, from an inter-population viewpoint. Hypothesis testing on the adequate balance-coordinates allow us to confirm intuition based hypothesis and some previous results. The main statistical goal was to test equal means of balance-coordinates for the two defined populations. After checking normality, one-way ANOVA or Mann-Whitney tests were carried out for the inter-group balances

Mammals.

Describe las principales características físicas y de comportamiento, mecanismos de defensa, la atención y el desarrollo de los jóvenes, las especies en peligro y los esfuerzos de conservación se los mamíferos.Cada dos páginas hay tres entradas organizadas por temas. Las preguntas sobre los mamíferos son tanto generales como específicas, y se responden en breves párrafos. Los bloques son de de texto corto. En Ahora sé, se hace una revisión de los principales aspectos que refuerza lo aprendido. En Eso es asombroso, se ofrecen características destacadas de hechos increíbles de los mamíferos. Mira y encuentra, sirve para animar a los niños a identificar y asociar nombres con imágenes.

Land mammals : and those in danger of extinction.

Analiza los diferentes tipos de animales que se han extinguido naturalmente hace mucho tiempo y los que están en peligro actualmente por las actividades del hombre. Con un texto sencillo se explica por qué tantos se han extinguido y cómo se sabe que una vez existieron. Para edades comprendidas entre nueve y doce años.

Mammals.

Bajo la forma de preguntas y respuestas trata de despertar la curiosidad sobre las características, el comportamiento, ciclo de vida, y los hábitats de todo tipo de mamíferos, desde las musarañas a los elefantes. Para profundizar en su estudio y el respeto por su conservación. Recomendado para ocho a doce años.

Identifying important endemic areas using ecoregions: birds and mammals in the Indo-Pacific

Concentrations of large numbers of endemic species have been singled out in prioritization exercises as significant areas for global biodiversity conservation. This paper describes bird and mammal endemicity in Indo-Pacific ecoregions. An ecoregion is a relatively large unit of land or water that contains a distinct assemblage of natural communities. We prioritize 133 ecoregions according to their levels of endemicity, and explain how variables such as biome type, whether the ecoregion is on an island or continental mass, montane or non-montane, correlate with the proportion of the total species assemblage that are endemic. Following an exploratory principal components analysis we classify all ecoregions according to the relationship between numbers of endemics and overall species richness. Endemicity is negatively correlated with species richness. We show that plotting the logit transformation of the endemicity of birds and mammals against log of species richness is a more effective and useful way of identifying important ecoregions than simply ordering ecoregions by the proportion of endemic species, or any other single measure. The plot, divided into 16 regions corresponding to the quartiles of the two variables, was used to identify ecoregions of high conservation value. These are the ecoregions with the highest endemicity and lowest species richness. Further analysis shows that island and montane ecoregions, regardless of their biome type, are by far the most important for endemic species.

Determination of mitochondrial genetic diversity in mammals

Mitochondrial DNA (mtDNA) is one of the most Popular population genetic markers. Its relevance as an indicator Of Population size and history has recently been questioned by several large-scale studies in animals reporting evidence for recurrent adaptive evolution, at least in invertebrates. Here we focus on mammals, a more restricted taxonomic group for which the issue of mtDNA near neutrality is crucial. By analyzing the distribution of mtDNA diversity across species and relating 4 to allozyme diversity, life-history traits, and taxonomy, we show that (i) mtDNA in mammals (toes not reject the nearly neutral model; (ii) mtDNA diversity, however, is unrelated to any of the 14 life-history and ecological variables that we analyzed, including body mass, geographic range, and The World Conservation Union (IUCN) categorization; (iii) mtDNA diversity is highly variable between mammalian orders and families; (iv) this taxonomic effect is most likely explained by variations of mutation rate between lineages. These results are indicative of a strong stochasticity of effective population size in mammalian species. They Suggest that, even in the absence of selection, mtDNA genetic diversity is essentially unpredictable, knowing species biology, and probably uncorrelated to species abundance.