http://www.mdpi.com/journal/diversity Latest open access articles published in Diversity at http://www.mdpi.com/journal/diversity/ http://www.mdpi.com/1424-2818/2/3/395/ Complex systems science has contributed to our understanding of ecology in important areas such as food webs, patch dynamics and population fluctuations. This has been achieved through the use of simple measures that can capture the difference between order and disorder and simple models with local interactions that can generate surprising behaviour at larger scales. However, close examination reveals that commonly applied definitions of complexity fail to accommodate some key features of ecological systems, a fact that will limit the contribution of complex systems science to ecology. We highlight these features of ecological complexity—such as diversity, cross-scale interactions, memory and environmental variability—that continue to challenge classical complex systems science. Further advances in these areas will be necessary before complex systems science can be widely applied to understand the dynamics of ecological systems. http://www.mdpi.com/1424-2818/2/3/395/ Mon, 15 Mar 2010 00:00:00 CET Diversity 2010-03-15 2 3 Article 395 410 1424-2818 Ecological Systems as Complex Systems: Challenges for an Emerging Science 2010-03-15 doi: 10.3390/d2030395 Anand Gonzalez Guichard Kolasa Parrott http://www.mdpi.com/1424-2818/2/3/370/ Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective) numbers of trait states (types). Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, β-diversity and fixation (inadvertently called differentiation) are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST ) refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered. http://www.mdpi.com/1424-2818/2/3/370/ Wed, 03 Mar 2010 00:00:00 CET Diversity 2010-03-03 2 3 Article 370 394 1424-2818 Linking Diversity and Differentiation 2010-03-03 doi: 10.3390/d2030370 Hans-Rolf Gregorius http://www.mdpi.com/1424-2818/2/3/353/ Several anthropologists of Amazonian societies in Ecuador have claimed that for Achuar [1] and Quichua speaking Runa [2-4] there is no fundamental distinction between humans on the one hand, and plants and animals on the other. A related observation is that Runa and Achuar people share an animistic cosmology whereby animals, plants, and even seemingly inert entities such as rocks and stones are believed to have a life force or essence with a subjectivity that can be expressed. This paper will focus on Quichua speaking Runa to seek linguistic evidence for animacy by examining the sound-symbolic properties of a class of expressions called ideophones. I argue that structural features of ideophones such as canonical length and diversity of sound segments as well as type of sound segments, help express the animism of the Runa lifeworld. Moreover, although these features are not indicative of any essential distinctions between plants and animals, they may be indicative of a scalar view of animacy, along the lines suggested by Descola who first proposed a continuum or ‘ladder of animacy’ for the Achuar [1, pp. 321-326]. Ideophones, then, may be understood as one set of linguistic tools for coming to terms with the diversity of their ecological setting, a setting which spans highly animate humans and animals, through less animate plants, trees, and rocks. http://www.mdpi.com/1424-2818/2/3/353/ Tue, 02 Mar 2010 00:00:00 CET Diversity 2010-03-02 2 3 Article 353 369 1424-2818 The Sound-Symbolic Expression of Animacy in Amazonian Ecuador 2010-03-02 doi: 10.3390/d2030353 Janis B. Nuckolls http://www.mdpi.com/1424-2818/2/3/331/ As in other parts of Amazonia, pre-Columbian Indians have profoundly modified the coast of the Guianas. Between 650 and 1650 AD, Arauquinoid people occupied a territory that was approximately 600 km long and used the raised field technique intensively before the European conquest. They erected thousands of raised fields of various shapes, dug canals, ditches, and pathways, and built artificial mounds to establish their villages. All these earthworks changed forever the face of the coastal flooded savannas and their ecology. Such labor was probably organized under the leadership of a central authority: it seems that Arauquinoid societies were organized in a chiefdom system. Statistical calculations, based on the known surface area of raised fields and on their estimated productivity, suggest a population density of 50 to 100 inhabitants per km2. Pre-Columbian inhabitants of the Guianas coast carefully organized, managed and “anthropisized” their territory following a specific pattern. http://www.mdpi.com/1424-2818/2/3/331/ Tue, 02 Mar 2010 00:00:00 CET Diversity 2010-03-02 2 3 Article 331 352 1424-2818 Pre-Columbian Earthworks in Coastal Amazonia 2010-03-02 doi: 10.3390/d2030331 Stéphen Rostain http://www.mdpi.com/1424-2818/2/3/314/ Infectious diseases caused by ranaviruses (RV, family Iridoviridae) not only affect wild amphibian populations but also agriculture and international animal trade. Although, the prevalence of RV infections and die offs has markedly increased over the last decade, it is still unclear whether these viruses are direct causal agents of extinction or rather are the resulting (secondary) consequences of weakened health of amphibian populations leading to increased susceptibility to viral pathogens. In either case, it is important to understand the critical role of host immune defense in controlling RV infections, pathogenicity, and transmission; this is the focus of this review. http://www.mdpi.com/1424-2818/2/3/314/ Fri, 26 Feb 2010 00:00:00 CET Diversity 2010-02-26 2 3 Review 314 330 1424-2818 Emerging Ranaviral Infectious Diseases and Amphibian Decline 2010-02-26 doi: 10.3390/d2030314 Jacques Robert http://www.mdpi.com/1424-2818/2/2/281/ As part of an overall decline in biodiversity, populations of many organisms are declining and species are being lost at unprecedented rates around the world. This includes many populations and species of amphibians. Although numerous factors are affecting amphibian populations, we show potential direct and indirect effects of climate change on amphibians at the individual, population and community level. Shifts in amphibian ranges are predicted. Changes in climate may affect survival, growth, reproduction and dispersal capabilities. Moreover, climate change can alter amphibian habitats including vegetation, soil, and hydrology. Climate change can influence food availability, predator-prey relationships and competitive interactions which can alter community structure. Climate change can also alter pathogen-host dynamics and greatly influence how diseases are manifested. Changes in climate can interact with other stressors such as UV-B radiation and contaminants. The interactions among all these factors are complex and are probably driving some amphibian population declines and extinctions. http://www.mdpi.com/1424-2818/2/2/281/ Thu, 25 Feb 2010 00:00:00 CET Diversity 2010-02-25 2 2 Article 281 313 1424-2818 Direct and Indirect Effects of Climate Change on Amphibian Populations 2010-02-25 doi: 10.3390/d2020281 Andrew R. Blaustein Susan C. Walls Betsy A. Bancroft Joshua J. Lawler Catherine L. Searle Stephanie S. Gervasi http://www.mdpi.com/1424-2818/2/2/256/ The origin and subsequent proliferation of malarias capable of infecting humans in South America remain unclear, particularly with respect to the role of Neotropical monkeys in the infectious chain. The evidence to date will be reviewed for Pre-Columbian human malaria, introduction with colonization, zoonotic transfer from cebid monkeys, and anthroponotic transfer to monkeys. Cultural behaviors (primate hunting and pet-keeping) and ecological changes favorable to proliferation of mosquito vectors are also addressed. http://www.mdpi.com/1424-2818/2/2/256/ Wed, 24 Feb 2010 00:00:00 CET Diversity 2010-02-24 2 2 Article 256 280 1424-2818 The Historical Ecology of Human and Wild Primate Malarias in the New World 2010-02-24 doi: 10.3390/d2020256 Loretta A. Cormier http://www.mdpi.com/1424-2818/2/2/233/ The area of the Aegean can be described as one of nature’s most active laboratories. The contemporary geomorphology of the Aegean is a result of diverse and still ongoing geological events, which coupled with climate changes, have created mountains and thousands of islands. The Aegean bridges three continents, where human activity has been recorded for at least 10,000 years. Herpetofauna diversity offered early researchers the possibility of describing patterns in the Aegean, especially as the distributional limit for several species and faunal elements. The patterns initially described at a rather coarse scale formed the frame on which the application of new techniques opened new views and permitted finer analyses. Here, we assess recent works on the Aegean’s herpetofauna, outlining the role of sea barriers, especially the Mid Aegean Trench (MAT). We propose four basic patterns (pre-MAT, post-MAT, newcomers, and that of an outlier) and discuss exceptions to these patterns, to interpret the diversity recorded. The interdisciplinary study of taxonomy helps explaining the observed diversity and provides powerful arguments for how exploring diversity can be used to explain more than biological processes. http://www.mdpi.com/1424-2818/2/2/233/ Tue, 16 Feb 2010 00:00:00 CET Diversity 2010-02-16 2 2 Article 233 255 1424-2818 Three Continents Claiming an Archipelago: The Evolution of Aegean’s Herpetofaunal Diversity 2010-02-16 doi: 10.3390/d2020233 Petros Lymberakis Nikos Poulakakis http://www.mdpi.com/1424-2818/2/2/207/ Contrary to common belief, decomposition of diversity into independent richness and evenness components is mathematically impossible. However, richness can be decomposed into independent diversity and evenness or inequality components. The evenness or inequality component derived in this way is connected to most of the common measures of evenness and inequality in ecology and economics. This perspective justifies the derivation of measures of relative evenness, which give the amount of evenness relative to the maximum and minimum possible for a given richness. Pielou’s [1] evenness measure J is shown to be such a measure. http://www.mdpi.com/1424-2818/2/2/207/ Thu, 11 Feb 2010 00:00:00 CET Diversity 2010-02-11 2 2 Article 207 232 1424-2818 The Relation between Evenness and Diversity 2010-02-11 doi: 10.3390/d2020207 Lou Jost http://www.mdpi.com/1424-2818/2/2/182/ Archaeology is a discipline that can offer a long term perspective on the impacts human societies have had on the environment. Landscape studies are critical for understanding these impacts, because they embrace a dialectical view regarding the relationship between humans and their immediate surroundings. Such studies are well suited to the Amazon basin, a region that has driven much media attention due to astonishing rates of deforestation in certain areas, with likely consequences on the planet’s climate, posing challenges to the survival of the human species for the coming decades. In fact, although much has been said about the impacts of contemporary societies on tropical forest environments, ancient landscape management practices have not yet been considered part of the equation. Thus far, we know that Amerindian societies have been actively transforming their surroundings for millennia. On the eve of European contact, large, complex societies were bringing about long-lasting transformations of landscapes throughout the basin. Conquest and colonization resulted in epidemics, enslavement, and changes to the indigenous economies that managed to survive the genocide. Afterwards, as colonizers would exploit traditional resources leading, in many instances, to their exhaustion, a huge quantity of information on sustainable ways of dealing with certain environments became lost. Traditional knowledge, however, still survives among certain indigenous, peasant (caboclo), and African-Brazilian populations. Documentation of surviving management practices together with the study of the archaeological record could provide valuable information for policy makers. This article examines historical transformations that took place on Marajó Island during the last two millennia and advocates the importance of archaeological research for understanding the historical ecology of landscape change. It is argued that ancient economic strategies, some still being practiced today, could be re-created in the present, since these may constitute opportunities for sustainable sources of income to local communities. http://www.mdpi.com/1424-2818/2/2/182/ Mon, 01 Feb 2010 00:00:00 CET Diversity 2010-02-01 2 2 Article 182 206 1424-2818 Long-Term Human Induced Impacts on Marajó Island Landscapes, Amazon Estuary 2010-02-01 doi: 10.3390/d2020182 Denise Schaan http://www.mdpi.com/1424-2818/2/2/163/ Behaviorally modern human beings have lived in Amazonia for thousands of years. Significant dynamics in species turnovers due to human-mediated disturbance were associated with the ultimate emergence and expansion of agrarian technologies in prehistory. Such disturbances initiated primary and secondary landscape transformations in various locales of the Amazon region. Diversity in these locales can be understood by accepting the initial premise of contingency, expressed as unprecedented human agency and human history. These effects can be accessed through the archaeological record and in the study of living languages. In addition, landscape transformation can be demonstrated in the study of traditional knowledge (TK). One way of elucidating TK distinctions between anthropic and nonanthropic landscapes concerns elicitation of differential labeling of these landscapes and more significantly, elicitation of the specific contents, such as trees, occurring in these landscapes. Freelisting is a method which can be used to distinguish the differential species compositions of landscapes resulting from human-mediated disturbance vs. those which do not evince records of human agency and history. The TK of the Ka’apor Indians of Amazonian Brazil as revealed in freelisting exercises shows differentiation of anthropogenic from high forests as well as a recognition of diversity in the anthropogenic forests. This suggests that the agents of human-mediated disturbance and landscape transformation in traditional Amazonia encode diversity and contingency into their TK, which encoding reflects past cultural influence on landscape and society over time. http://www.mdpi.com/1424-2818/2/2/163/ Mon, 01 Feb 2010 00:00:00 CET Diversity 2010-02-01 2 2 Article 163 181 1424-2818 Contingent Diversity on Anthropic Landscapes 2010-02-01 doi: 10.3390/d2020163 William Balée http://www.mdpi.com/1424-2818/2/2/142/ Rapid, global declines among amphibians are partly alarming because many occur for apparently unknown or enigmatic reasons. Moreover, the relationship between phylogeny and enigmatic declines in higher clades of the amphibian phylogeny appears at first to be an intractable problem. I present a working solution by assessing threatening processes potentially underlying enigmatic declines in the family, Hylidae. Applying comparative methods that account for various evolutionary scenarios, I find extreme concentrations of threatening processes, including pollution and habitat loss, in the clade Hylini, potentially influenced by traits under selection. The analysis highlights hotspots of declines under phylogenetic influence in the genera Isthmohyla, Plectrohyla and Ptychohyla, and geographically in Mexico and Guatemala. The conservation implications of concentrated phylogenetic influence across multiple threatening processes are twofold: Data Deficient species of threatened clades should be prioritized in future surveys and, perhaps, a greater vulnerability should be assigned to such clades for further consideration of clade-level conservation priorities. http://www.mdpi.com/1424-2818/2/2/142/ Wed, 27 Jan 2010 00:00:00 CET Diversity 2010-01-27 2 2 Article 142 162 1424-2818 Phylogenetic Signal of Threatening Processes among Hylids: The Need for Clade-Level Conservation Planning 2010-01-27 doi: 10.3390/d2020142 Sarah J. Corey http://www.mdpi.com/1424-2818/2/1/127/ In recent years, diversity, whether it be ecological, biological, cultural, or linguistic diversity, has emerged as a major cultural value. This paper analyzes whether a single concept of diversity can underwrite discussions of diversity in different disciplines. More importantly, it analyzes the normative justification for the endorsement of diversity as a goal in all contexts. It concludes that no more than a relatively trivial concept of diversity as richness is common to all contexts. Moreover, there is no universal justification for the endorsement of diversity. Arguments to justify the protection of diversity must be tailored to individual contexts. http://www.mdpi.com/1424-2818/2/1/127/ Tue, 26 Jan 2010 00:00:00 CET Diversity 2010-01-26 2 1 Article 127 141 1424-2818 Diversity: A Philosophical Perspective 2010-01-26 doi: 10.3390/d2010127 Sahotra Sarkar http://www.mdpi.com/1424-2818/2/1/115/ Research policies ensuing from the Convention on Biological Diversity made huge funds available to study biodiversity. These were mostly dedicated to projects aimed at providing services to taxonomy via information and technology, or to develop “modern”, i.e., molecular, approaches to taxonomy. Traditional taxonomy was overly neglected and is in serious distress all over the world. It is argued that both novel and traditional ways to study biodiversity are essential and that the demise of traditional taxonomy (based on phenotypes) in the era of biodiversity is the result of an unwise policy, mainly fostered by portions of the scientific community that aim at taking total advantage of the funds dedicated to the study of biodiversity. http://www.mdpi.com/1424-2818/2/1/115/ Fri, 22 Jan 2010 00:00:00 CET Diversity 2010-01-22 2 1 Communication 115 126 1424-2818 The Study of Species in the Era of Biodiversity: A Tale of Stupidity 2010-01-22 doi: 10.3390/d2010115 Ferdinando Boero http://www.mdpi.com/1424-2818/2/1/107/ The genetic diversity among Tunisian pomegranate cultivars has been investigated. Using universal primers, the random amplified polymorphic DNA (RAPD) method was used to generate banding profiles from a set of twelve cultivars. Data was then computed with appropriate programs to construct a dendrogram illustrating the relationships between the studied cultivars. Our data proved the efficiency of the designed method to examine the DNA polymorphism in this crop since the tested primers are characterized by a collective resolving power of 12.83. In addition, the cluster analysis has exhibited a parsimonious tree branching independent from the geographic origin of the cultivars. In spite of the relatively low number of primers and cultivars, RAPD constitutes an appropriate procedure to assess the genetic diversity and to survey the phylogenetic relationships in this crop. http://www.mdpi.com/1424-2818/2/1/107/ Mon, 18 Jan 2010 00:00:00 CET Diversity 2010-01-18 2 1 Communication 107 114 1424-2818 Molecular Polymorphisms in Tunisian Pomegranate (Punica granatum L.) as Revealed by RAPD Fingerprints 2010-01-18 doi: 10.3390/d2010107 Néjib Hasnaoui Messaoud Mars Jemni Chibani Mokhtar Trifi http://www.mdpi.com/1424-2818/2/1/72/ Molecular analyses are providing new elements to decipher the origin, domestication and dispersal of native Amazonian crops in an expanding archaeological context. Solid molecular data are available for manioc (Manihot esculenta), cacao (Theobroma cacao), pineapple (Ananas comosus), peach palm (Bactris gasipaes) and guaraná (Paullinia cupana), while hot peppers (Capsicum spp.), inga (Inga edulis), Brazil nut (Bertholletia excelsa) and cupuassu (Theobroma grandiflorum) are being studied. Emergent patterns include the relationships among domestication, antiquity (terminal Pleistocene to early Holocene), origin in the periphery, ample pre-Columbian dispersal and clear phylogeographic population structure for manioc, pineapple, peach palm and, perhaps, Capsicum peppers. Cacao represents the special case of an Amazonian species possibly brought into domestication in Mesoamerica, but close scrutiny of molecular data suggests that it may also have some incipiently domesticated populations in Amazonia. Another pattern includes the relationships among species with incipiently domesticated populations or very recently domesticated populations, rapid pre- or post-conquest dispersal and lack of phylogeographic population structure, e.g., Brazil nut, cupuassu and guaraná. These patterns contrast the peripheral origin of most species with domesticated populations with the subsequent concentration of their genetic resources in the center of the basin, along the major white water rivers where high pre-conquest population densities developed. Additional molecular genetic analyses on these and other species will allow better examination of these processes and will enable us to relate them to other historical ecological patterns in Amazonia. http://www.mdpi.com/1424-2818/2/1/72/ Wed, 06 Jan 2010 00:00:00 CET Diversity 2010-01-06 2 1 Review 72 106 1424-2818 Origin and Domestication of Native Amazonian Crops 2010-01-06 doi: 10.3390/d2010072 Charles R. Clement Michelly de Cristo-Araújo Geo Coppens d’Eeckenbrugge Alessandro Alves Pereira Doriane Picanço-Rodrigues http://www.mdpi.com/1424-2818/2/1/47/ It is well established that a decrease in genetic variation can lead to reduced fitness and lack of adaptability to a changing environment. Amphibians are declining on a global scale, and we present a four-point argument as to why this taxonomic group seems especially prone to such genetic processes. We elaborate on the extent of recent fragmentation of amphibian gene pools and we propose the term dissociated populations to describe the residual population structure. To put their well-documented loss of genetic diversity into context, we provide an overview of 34 studies (covering 17 amphibian species) that address a link between genetic variation and >20 different fitness traits in amphibians. Although not all results are unequivocal, clear genetic-fitness-correlations (GFCs) are documented in the majority of the published investigations. In light of the threats faced by amphibians, it is of particular concern that the negative effects of various pollutants, pathogens and increased UV-B radiation are magnified in individuals with little genetic variability. Indeed, ongoing loss of genetic variation might be an important underlying factor in global amphibian declines. http://www.mdpi.com/1424-2818/2/1/47/ Tue, 05 Jan 2010 00:00:00 CET Diversity 2010-01-05 2 1 Review 47 71 1424-2818 Global Amphibian Declines, Loss of Genetic Diversity and Fitness: A Review 2010-01-05 doi: 10.3390/d2010047 Morten E. Allentoft John O’Brien http://www.mdpi.com/1424-2818/2/1/28/ We have studied the population genetic structure of slightly admixed populations of crested newts (Triturus cristatus and T. carnifex) in a continuously fragmented landscape, located in northern Salzburg (Austria) and neighbouring Bavaria (Germany). Crested newts are listed as Critically Endangered in the provincial Red List of Salzburg and strictly protected by the EU Habitats Directive. We used seven polymorphic microsatellite loci to evaluate genetic diversity and processes that may determine the genetic architecture of populations. Genetic diversity was moderate, pairwise FST-values were comparatively high showing significant genetic differentiation and limited gene flow. Isolation by distance was significant for the whole data set, but not significant when calculated for T. cristatus- and T. carnifex-like populations separately. Bayesian analyses of population structure, using three different programs showed similar results. Spatial statistics reveal that the geographical isolation of populations is very high. http://www.mdpi.com/1424-2818/2/1/28/ Thu, 31 Dec 2009 00:00:00 CET Diversity 2009-12-31 2 1 Article 28 46 1424-2818 Conservation Genetics of Crested Newt Species Triturus cristatus and T. carnifex within a Contact Zone in Central Europe: Impact of Interspecific Introgression and Gene Flow 2009-12-31 doi: 10.3390/d2010028 Andreas Maletzky Roland Kaiser Peter Mikulíček http://www.mdpi.com/1424-2818/2/1/17/ Single Nucelotide Polymorphisms (SNPs) have become the most widely used markers in many current genetic applications. Here we report the discovery of nine new SNPs in olives by direct partial sequencing of two genes (OEX and OEW) in sixteen Tunisian cultivars. The SNP markers were then used to genotype 24 olive cultivars and assess the level of genetic diversity. Power of discrimination of SNP markers was then compared to that of microsatellites (SSRs). A combination of SSR and SNP markers was finally proposed that can be used for cultivars identification in juvenile step or for oil traceability. http://www.mdpi.com/1424-2818/2/1/17/ Wed, 30 Dec 2009 00:00:00 CET Diversity 2009-12-30 2 1 Article 17 27 1424-2818 Discovery and Potential of SNP Markers in Characterization of Tunisian Olive Germplasm 2009-12-30 doi: 10.3390/d2010017 Imen Rekik Hakim Naziha Grati Kammoun Emna Makhloufi Ahmed Rebaï http://www.mdpi.com/1424-2818/2/1/1/ Recent studies in Amazonia historical ecology have revealed substantial diversity and dynamic change in coupled natural human systems. In the southern Amazon, several headwater basins show evidence of substantial pre-Columbian landscape modification, particularly in areas historically dominated by speakers of the Arawak language family. The headwater basin of the Xingu River, the easternmost of these areas occupied by Arawak-speaking peoples, has revealed such a complex built environment. This discussion examines settlement pattern and land-use, which have implications for understanding the dynamics of natural-human systems in the Upper Xingu basin and other areas across the transitional forests of the southern Amazon. http://www.mdpi.com/1424-2818/2/1/1/ Thu, 24 Dec 2009 00:00:00 CET Diversity 2009-12-24 2 1 Article 1 16 1424-2818 Biocultural Diversity in the Southern Amazon 2009-12-24 doi: 10.3390/d2010001 Michael Heckenberger http://www.mdpi.com/1424-2818/1/2/182/ Biodiversity is one of the most fundamental properties of Nature. It underpins the stability of ecosystems, provides vast bioresources for economic use, and has important cultural significance for many people. The Pampa biome, located in the southernmost state of Brazil, Rio Grande do Sul, illustrates the direct and indirect interdependence of humans and biodiversity. The Brazilian Pampa lies within the South Temperate Zone where grasslands scattered with shrubs and trees are the dominant vegetation. The soil, originating from sedimentary rocks, often has an extremely sandy texture that makes them fragile—highly prone to water and wind erosion. Human activities have converted or degraded many areas of this biome. In this review we discuss our state-of-the-art knowledge of the diversity and the major biological features of this regions and the cultural factors that have shaped it. Our aim is to contribute toward a better understanding of the current status of this special biome and to describe how the interaction between human activities and environment affects the region, highlighting the fragility of the Brazilian Pampa. http://www.mdpi.com/1424-2818/1/2/182/ Mon, 21 Dec 2009 00:00:00 CET Diversity 2009-12-21 1 2 Review 182 198 1424-2818 The Brazilian Pampa: A Fragile Biome 2009-12-21 doi: 10.3390/d1020182 Luiz Fernando Wurdig Roesch Frederico Costa Beber Vieira Vilmar Alves Pereira Adriano Luis Schünemann Italo Filippi Teixeira Ana Julia Teixeira Senna Valdir Marcos Stefenon http://www.mdpi.com/1424-2818/1/2/166/ Amphibian declines have been reported in mountainous areas around the western USA. Few data quantify the extent of population losses in the Pacific Northwest, a region in which amphibian declines have received much attention. From 2001–2004, we resurveyed historical breeding sites of two species of conservation concern, the Western Toad (Bufo [=Anaxyrus] boreas) and Cascades Frog (Rana cascadae). We detected B. boreas breeding at 75.9% and R. cascadae breeding at 66.6% of historical sites. When we analyzed the data using occupancy models that accounted for detection probability, we estimated the current use of historically occupied sites in our study area was 84.9% (SE = 4.9) for B. boreas and 72.4% (SE = 6.6) for R. cascadae. Our ability to detect B. boreas at sites where they were present was lower in the first year of surveys (a low snowpack year) and higher at sites with introduced fish. Our ability to detect R. cascadae was lower at sites with fish. The probability that B. boreas still uses a historical site for breeding was related to the easting of the site (+) and the age of record (-). None of the variables we analyzed was strongly related to R. cascadae occupancy. Both species had increased odds of occupancy with higher latitude, but model support for this variable was modest. Our analysis suggests that while local losses are possible, these two amphibians have not experienced recent, broad population losses in the Oregon Cascades. Historical site revisitation studies such as ours cannot distinguish between population losses and site switching, and do not account for colonization of new habitats, so our analysis may overestimate declines in occupancy within our study area. http://www.mdpi.com/1424-2818/1/2/166/ Fri, 11 Dec 2009 00:00:00 CET Diversity 2009-12-11 1 2 Article 166 181 1424-2818 Evaluating Amphibian Declines with Site Revisits and Occupancy Models: Status of Montane Anurans in the Pacific Northwest USA 2009-12-11 doi: 10.3390/d1020166 Christopher A. Pearl Michael J. Adams R. Bruce Bury Wendy H. Wente Brome McCreary http://www.mdpi.com/1424-2818/1/2/151/ The arrival of Europeans in the Western Hemisphere (ca. AD 1500) is generally used as a convenient reference point for signaling the early appearance of invasive faunas. Although use of this date embraces an implicit belief in benign landscape management by pre-Columbian inhabitants of the Americas, substantial evidence for the anthropogenic movement of domesticated, wild, and synanthropic vertebrates throughout the Neotropics suggests that it may be an exaggerated and erroneous reference point for the aims of ecological restoration and biological conservation. http://www.mdpi.com/1424-2818/1/2/151/ Tue, 08 Dec 2009 00:00:00 CET Diversity 2009-12-08 1 2 Article 151 165 1424-2818 Adventive Vertebrates and Historical Ecology in the Pre-Columbian Neotropics 2009-12-08 doi: 10.3390/d1020151 Peter W. Stahl http://www.mdpi.com/1424-2818/1/2/133/ Extinction forecasting is one of the most important and challenging areas of conservation biology. Overestimates of extinction rates or the extinction risk of a particular species instigate accusations of hype and overblown conservation rhetoric. Conversely, underestimates may result in limited resources being allocated to other species/habitats perceived as being at greater risk. In this paper I review extinction models and identify the key sources of uncertainty for each. All reviewed methods which claim to estimate extinction probabilities have severe limitations, independent of if they are based on ecological theory or on rather subjective expert judgments. http://www.mdpi.com/1424-2818/1/2/133/ Thu, 26 Nov 2009 00:00:00 CET Diversity 2009-11-26 1 2 Review 133 150 1424-2818 Forecasting Extinctions: Uncertainties and Limitations 2009-11-26 doi: 10.3390/d1020133 Richard J. Ladle http://www.mdpi.com/1424-2818/1/2/118/ Coal extraction has been occurring in the Midwestern United States for over a century. Despite the pre-mining history of the landscape as woodlands, spent surface coalfields are often reclaimed to grasslands. We assessed amphibian and reptile species on a large tract of coal spoil prairie and found 13 species of amphibians (nine frog and four salamander species) and 19 species of reptiles (one lizard, five turtle, and 13 snake species). Two state-endangered and three state species of special concern were documented. The amphibian diversity at our study site was comparable to the diversity found at a large restored prairie situated 175 km north, within the historic prairie peninsula. http://www.mdpi.com/1424-2818/1/2/118/ Tue, 17 Nov 2009 00:00:00 CET Diversity 2009-11-17 1 2 Article 118 132 1424-2818 Mine Spoil Prairies Expand Critical Habitat for Endangered and Threatened Amphibian and Reptile Species 2009-11-17 doi: 10.3390/d1020118 Michael J. Lannoo Vanessa C. Kinney Jennifer L. Heemeyer Nathan J. Engbrecht Alisa L. Gallant Robert W. Klaver http://www.mdpi.com/1424-2818/1/2/102/ Although amphibians have been widely promoted as indicators of biodiversity and environmental change, rigorous tests are lacking. Here key indicator criteria are distilled from published papers, and a species that has been promoted as a bioindicator, the great crested newt, is tested against them. Although a link was established between the presence of great crested newts and aquatic plant diversity, this was not repeated with the diversity of macroinvertebrates. Equally, amphibians do not meet many of the published criteria of bioindicators. Our research suggests that a suite of indicators, rather than a single species, will usually be required. http://www.mdpi.com/1424-2818/1/2/102/ Fri, 13 Nov 2009 00:00:00 CET Diversity 2009-11-13 1 2 Article 102 117 1424-2818 Can a Single Amphibian Species Be a Good Biodiversity Indicator? 2009-11-13 doi: 10.3390/d1020102 David Sewell Richard A. Griffiths http://www.mdpi.com/1424-2818/1/2/89/ Commiphora wightii is an endangered, endemic species found in the Thar Desert of Rajasthan, India and adjoining areas of Pakistan. The populations of this plant are rapidly dwindling due to overexploitation for their medicinally important resin. Analysis of nucleotide sequences of the internal transcribed spacer of rDNAs revealed low genetic diversity (π = 0.03905; θw = 0.05418) and high population structure (ϕST = 0.206). Parsimony based assessment and Bayesian analyses were conducted on the dataset. Mantel’s test showed a statistically significant positive correlation between genetic and geographic distance (r2 = 0.3647; p = 0.023). Anthropogenic overexploitation of C. wightii for its natural resources has resulted in population fragmentation. Initiatives should be taken immediately to preserve the diversity of this important plant species. http://www.mdpi.com/1424-2818/1/2/89/ Mon, 26 Oct 2009 00:00:00 CET Diversity 2009-10-26 1 2 Article 89 101 1424-2818 Intraspecific Variation in Commiphora wightii Populations Based on Internal Transcribed Spacer (ITS1-5.8S-ITS2) Sequences of rDNA 2009-10-26 doi: 10.3390/d1020089 Inamul Haque Rajib Bandopadhyay Kunal Mukhopadhyay http://www.mdpi.com/1424-2818/1/1/67/ Although amphibians have experienced major global declines and an increasing extinction rate, recent results indicate that they are not as uniquely disadvantaged as previously supposed. Acquisition of robust data is evidently crucial to the determination of both absolute and relative rates of biodiversity declines, and thus in prioritising conservation actions. In Britain there is arguably a longer history of recording, and attempting to conserve, a wide range of species groups than anywhere else in the world. This stems from the early activities of Victorian naturalists in the nineteenth century, the establishment of natural history societies and, since the mid-twentieth century, a range of national recording schemes and organisations actively involved in conservation. In this review we summarise comparative evidence for British amphibians and reptiles concerning historical abundance, population trends and their causes, and outline how they relate to the situation elsewhere in Europe (and possibly the World). We discuss possible reasons why the plight of ectothermic vertebrates (fish, amphibians and reptiles) seems generally worse than that of endotherms (birds and mammals), as well as research priorities and factors likely to impact amphibians and reptile conservation in future. http://www.mdpi.com/1424-2818/1/1/67/ Thu, 24 Sep 2009 00:00:00 CEST Diversity 2009-09-24 1 1 Review 67 88 1424-2818 Amphibian Declines Are Not Uniquely High amongst the Vertebrates: Trend Determination and the British Perspective 2009-09-24 doi: 10.3390/d1010067 Trevor J. C. Beebee John W. Wilkinson John Buckley http://www.mdpi.com/1424-2818/1/1/52/ Species are being lost at increasing rates due to anthropogenic effects, leading to the recognition that we are witnessing the onset of a sixth mass extinction. Emerging infectious disease has been shown to increase species loss and any attempts to reduce extinction rates need to squarely confront this challenge. Here, we develop a procedure for identifying amphibian species that are most at risk from the effects of chytridiomycosis by combining spatial analyses of key host life-history variables with the pathogen's predicted distribution. We apply our rule set to the known global diversity of amphibians in order to prioritize pecies that are most at risk of loss from disease emergence. This risk assessment shows where limited conservation funds are best deployed in order to prevent further loss of species by enabling ex situ amphibian salvage operations and focusing any potential disease mitigation projects. http://www.mdpi.com/1424-2818/1/1/52/ Fri, 11 Sep 2009 00:00:00 CEST Diversity 2009-09-11 1 1 Article 52 66 1424-2818 Global Amphibian Extinction Risk Assessment for the Panzootic Chytrid Fungus 2009-09-11 doi: 10.3390/d1010052 Dennis Rödder Jos Kielgast Jon Bielby Sebastian Schmidtlein Jaime Bosch Trenton W. J. Garner Michael Veith Susan Walker Matthew C. Fisher Stefan Lötters http://www.mdpi.com/1424-2818/1/1/36/ The use of standardized and optimized protocols has been recently advocated for different arthropod taxa instead of ad-hoc sampling or sampling with protocols defined on a case-by-case basis. We present a comparison of both sampling approaches applied for spiders in a natural area of Portugal. Tests were made to their efficiency, over-collection of common species, singletons proportions, species abundance distributions, average specimen size, average taxonomic distinctness and behavior of richness estimators. The standardized protocol revealed three main advantages: (1) higher efficiency; (2) more reliable estimations of true richness; and (3) meaningful comparisons between undersampled areas. http://www.mdpi.com/1424-2818/1/1/36/ Tue, 01 Sep 2009 00:00:00 CEST Diversity 2009-09-01 1 1 Article 36 51 1424-2818 Ad-Hoc vs. Standardized and Optimized Arthropod Diversity Sampling 2009-09-01 doi: 10.3390/d1010036 Pedro Cardoso Luís C. Crespo Rui Carvalho Ana C. Rufino Sérgio S. Henriques http://www.mdpi.com/1424-2818/1/1/19/ This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologies. Molecular techniques have also had critical roles in studies of phylogeny and species evolution, and have been applied to increase our understanding of the distribution and extent of genetic variation within and between species. These techniques are well established and their advantages as well as limitations have been realized and described in this work. Recently, a new class of advanced techniques has emerged, primarily derived from a combination of earlier, more basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques, in order to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. Some of the advanced marker techniques utilize newer classes of DNA elements, such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The most important and recent advances made in molecular marker techniques are discussed in this review, along with their applications, advantages and limitations applied to plant sciences. http://www.mdpi.com/1424-2818/1/1/19/ Thu, 06 Aug 2009 00:00:00 CEST Diversity 2009-08-06 1 1 Review 19 35 1424-2818 Assessing Plant Genetic Diversity by Molecular Tools 2009-08-06 doi: 10.3390/d1010019 Linda Mondini Arshiya Noorani Mario A. Pagnotta http://www.mdpi.com/1424-2818/1/1/7/ In mammals, members of the TLR gene family play a primary role in the recognition of pathogen-associated molecular patterns from bacteria, viruses, protozoa and fungi. Recently, cattle TLR genes have been mapped to chromosomes using a radiation hybrid panel. Nucleotide sequences of bovine TLR2, TLR4 and TLR6 genes were screened to identify novel SNPs that can be used in studies of cattle resistance to diseases. In total, 8 SNPs were identified and were submitted to the NCBI dbSNP database. The frequencies of the SNPs were assessed in 16 different bovine European cattle breeds and a phylogenetic analysis carried out to describe the relationships between the breeds. Even if from our analysis the SNPs do not appear located in loci under selection, a deviation of three SNPs from Hardy Weinberg equilibrium was observed, and we hypothesize that some of the polymorphisms may be fixated since many generations. The described variations in immune function related genes will contribute to research on disease response in cattle. In fact, the SNPs can be used in association studies between polymorphisms and cattle resistance to diseases. http://www.mdpi.com/1424-2818/1/1/7/ Thu, 30 Jul 2009 00:00:00 CEST Diversity 2009-07-30 1 1 Article 7 18 1424-2818 Polymorphisms within the Toll-Like Receptor (TLR)-2, -4, and -6 Genes in Cattle 2009-07-30 doi: 10.3390/d1010007 Marco Mariotti John L. Williams Susana Dunner Alessio Valentini Lorraine Pariset http://www.mdpi.com/1424-2818/1/1/5/ After many years of careful planning, we are pleased to launch Diversity (ISSN 1424-2818), a new international and interdisciplinary Open Access journal. Among diversity topics, biodiversity has always been a key topic. In 1996, when I was establishing Molecular Diversity Preservation International (MDPI), an organization dedicated to the collection and distribution of rare molecular samples, I read several books on biodiversity. To promote the MDPI project, in 1996 the journal Molecules was launched, where authors are encouraged to deposit authentic samples of chemicals reported in the published articles. One of the topics covered by the journal Molecules was molecular diversity, and my own paper on diversity assessment published in volume 1 of Molecules cited some of the biodiversity books I had read [1] and Molecules still has a section called “Molecular Diversity” [2]. Our founding Editor-in-Chief, Prof. Dr. Michael Wink [3], also cites biological diversity as one of his main research interests. [...] http://www.mdpi.com/1424-2818/1/1/5/ Mon, 08 Jun 2009 00:00:00 CEST Diversity 2009-06-08 1 1 Editorial 5 6 1424-2818 Diversity – An International and Interdisciplinary Journal 2009-06-08 doi: 10.3390/d1010005 Shu-Kun Lin http://www.mdpi.com/1424-2818/1/1/1/ When we look at Planet Earth, its material and organisms, a prominent feature is the diversity of these components and the mechanisms underlying their functions. Biodiversity, which includes the diversity of the living organisms, their genes and the biomes, is a fascinating product of millions of years of evolution. Biodiversity is not static but in continuous change. In addition to the intrinsic natural causes, the biodiversity on Earth is increasingly challenged by human interference. Among the critical factors are the destruction of habitats (by agriculture or technical development, especially loss of rain forests and coral reefs), climate change, direct persecution and extermination of species (for traditional pharmaceutical use, game hunting or in fishery), as well as the introduction of invasive species and environmental pollution (some of them apparently influencing our climate) [1]. Global changes (land-use and climate) and human population growth (with a world population of more than 6.7 billion in 2009 and an annual increase of almost 80 million) are ultimately responsible for affecting biodiversity worldwide. The exact impact of human interference on the Earth’s diversity may not be realised until it is too late to save critical species. http://www.mdpi.com/1424-2818/1/1/1/ Fri, 05 Jun 2009 00:00:00 CEST Diversity 2009-06-05 1 1 Editorial 1 4 1424-2818 Towards a Better Understanding of Diversity 2009-06-05 doi: 10.3390/d1010001 Michael Wink