A ‘fast-food approach’ to the standardization of quadratic diversity

Abstract

Intuitively, a community composed of ecologically dissimilar taxa is more diverse than a community composed of more similar taxa. However, since traditional diversity indices such as Shannon's entropy or Simpson's diversity are computed solely from the relative abundances of a given species assemblage, they cannot account for ecological differences between species. There have been recent developments regarding the use of quadratic entropy, a diversity index that incorporates both species relative abundances and a measure of the pairwise ecological differences between species. In this paper we firstly show that under some specific circumstances quadratic entropy can be additively decomposed into α- β- and γ-diversities, a property that renders it a desirable measure of diversity in the ecological practice. Next, we suggest a quick and simple method for obtaining a standardized version of quadratic entropy that may allow an easier interpretation of the resulting diversity values.     

Heterogeneity in shore flies – the case of Glenanthe Haliday (Diptera: Ephydridae) in the Old World

Old World species of the genus Glenanthe are treated comprehensively with an emphasis on the unusually diverse morphological heterogeneity discovered in structures of the male terminalia. As perspective for this treatment, the tribe Lipochaetini, in which Glenanthe is placed, is characterized and discussed, and an annotated key to the four included genera is provided to facilitate their identification. Glenanthe is demonstrated to be a monophyletic lineage within Lipochaetini. Seven Old World species of Glenanthe are now known, including two new Afrotropical species as follows (type locality in parenthesis): G. namibia n. sp. (Namibia. Mukwe: Divuju: Okavango River [18°04’04”S, 21°28’51”E] and G. danielssoni n. sp. (Republic of South Africa. Cape Province: De Hoop Nature Reserve [34°27’S, 28°25’E]. The identity of G. fuscinervis Becker, revised status (raised from synonymy with G. ripicola (Haliday)), is clarified, and found to be conspecific with Hydrina ochracea Oldenberg, which is recognized as a junior synonym. Papp’s synonymy of Glenanthe fasciventris Becker with Hydrellia (Glenanthe) ripicola Haliday is confirmed, and herein we relegate G. iranica Canzoneri & Rampini also as junior synonym of G. ripicola. The remarkable diverse structures of the male terminalia of all included species are described and illustrated and distribution maps are also provided.     

Annandale’s collection of freshwater fishes from Inle Lake,Myanmar, housed in the Kyoto University Museum

Ichthyological Research -     

The Alps as barrier to dispersal in cold-adapted freshwater fishes? Phylogeographic history and taxonomic status of the bullhead in the Adriatic freshwater drainage

The freshwater faunas of the Italian peninsula are isolated from the rest of Europe by the geographic barrier of the Alps and consequently have developed many endemic forms and contain few non-endemic species. However, some 'non-endemics' may either represent recent invaders of the Adriatic basin or cryptic endemic species. To test these two hypotheses against each other, we studied the origin and phylogenetic relationships of bullheads, cold adapted freshwater fishes of the genus Cottus, from both sides of the Alps and Dinaric Mountains. From the Adriatic basin, Cottus ferrugineus () was described as an endemic species, but the present analyses of sequences of the complete mitochondrial control region of 146 individuals from 43 localities showed no major differentiation between bullheads from both sides of the Alps. The very low diversification between representatives across the Alps suggests active transfers of haplotypes across this geographic barrier from the glacial cycles up to recent times. The transfers are most likely based on stream capture, since the cold-adapted bullhead is able to colonise the highest stretches of the water courses. No other freshwater fish in Europe is known to have experienced such an extensive gene flow across the highest European Mountains. In contrast, the Dinaric Mountains seem to have been a much more effective barrier between the Danube and the Adriatics. Our data reject the hypothesis of C. ferrugineus as an endemic species in the whole Adriatic drainage.     

The origin of the salmonid fishes: marine,freshwater... or neither?

Reviews in Fish Biology and Fisheries - The evolutionary origins of the salmonidfishes, whether in freshwater or the sea, havebeen debated for centuries. Early viewsfavoured a group of marine...     

Tree diversity,congruence and endemism: Himalaya ‘The land of diversity’

Trees are acknowledged as most valued gift of nature and saviour of earth, enhancing and protecting landscapes, ecosystems and production systems. An authentic database of tree flora missing from local to global scale has immense value. Formulation of conservation and management policies are difficult owing to huge variation in number of species, lack of tree cover and quantification of tree diversity. To endow with a pragmatic groundwork for quantification of tree diversity of IHR, we had published an inventory of 1466 tree species (Angiosperms and Gymnosperms) along with their taxonomically vetted scientific name, distributional range, phenological attributes (leaf persistence and flower colour), use value, congruence, endemism and threatened species. One more database on tree diversity of Western Himalaya was also published with an annotated list of tree flora compiled from unrestricted literature and e-floras related to the regions. The present paper is an attempt to bring out the overall representation of tree flora of IHR, its distributional pattern, congruence, and endemism criterion in Western and Eastern Himalaya along with correlation between the regions as well as states.

     

What governs the functional diversity patterns of fishes in the headwater streams of the humid forest enclaves: environmental conditions,taxonomic diversity or biotic interactions?

The relationship between functional and taxonomic diversity is a major issue in ecology. Biodiversity in aquatic environments is strongly influenced by environmental gradients that act as dispersion and niche barriers. Environmental conditions act as filters to select functional traits, but biotic interactions also play a role in assemblage structure. In headwater streams, the relationship between functional and taxonomic diversity remains unclear. In this study we investigated how environmental conditions, taxonomic diversity and biotic interactions influence the spatial distribution of traits and functional diversity in stream fish species. Standardized sampling of fish species was carried out in 50 m sections of 16 streams located in rainforest enclaves in a semiarid region of Brazil (Caatinga biome). The functional diversity indices displayed different responses to the predictor variables used. Functional richness was mainly influenced by environmental conditions, while functional evenness was mostly determined by taxonomic diversity. On the other hand, functional dispersion was explained by a combination of environmental conditions and taxonomic diversity. The spatial distribution of fish species with the same functional traits was random, indicating that biotic interactions are not a strong predictor in these ecosystems. Channel width, pH and substrate were the most important variables in the spatial distribution of the functional traits of the fish species. Our results suggest that the functional structure of fish assemblages in headwater streams depends mainly on environmental conditions and taxonomic diversity.     

Longwave-sensitive visual pigments in some deep-sea fishes: segregation of ‘paired’ rhodopsins and porphyropsins

Summary Microspectrophotometric examination of individual rods, and partial bleaching of visual pigment extracts from three species of deep-sea fish,Aristostomias grimaldii, Malacosteus niger andPachystomias microdon, suggest the presence of a rhodopsin-porphyropsin system of paired pigments.Aristostomias andMalacosteus have a P552₂-P517₁ pair, whilePachystomias has a P544₂-P513₁ pair. In contrast to most pigmentpair systems, each pigment is restricted to a single class of rod, thus giving the fish two spectrally distinct classes of photoreceptor. It is suggested that the longwave sensitive rods are an adaptation enabling these species to perceive their own deep-red bioluminescence. The astaxanthin-based red tapetum inMalacosteus, and a chlorin-like pigment, possibly acting as a photosensitizer and found in the rod outer segments ofMalacosteus, may also act to increase longwave sensitivity.     

Hovering sunbirds in the Old World: occasional behaviour or evolutionary trend?

The nectarivory of sunbirds in the Old World and hummingbirds in the New World evolved independently. While both groups are specialised in their feeding apparatuses, hummingbirds are moreover famous for their adaptations to sustained hovering flight. Recently, an example of a pollination system of the invasive plant Nicotiana glauca has been used to show that less adapted sunbirds also are frequently able to hover. Nevertheless, the question has remained why plants adapted to bird hovering pollination do not occur outside the New World. In this paper we show that the long‐peduncle Cameroonian Impatiens sakeriana is not capable of autonomous selfing and can be pollinated only by two often hovering sunbirds, the Cameroon sunbird Cyanomitra oritis and the northern double‐collared sunbird Cinnyris reichenowi. Our study revealed that this plant is highly specialised for pollination by C. oritis. Cinnyris reichenowi hovers less frequently and often thieves nectar by piercing the flower spur when perching. This study shows that pollination systems occurring in the Old World follow similar evolutionary trends as systems including hovering hummingbirds in the New World.     

Taxonomy-testing and the ‘Goldilocks Hypothesis’: morphometric analysis of species diversity in living and extinct Hispaniolan hutias

Understanding the dynamics of the Late Quaternary Caribbean mammal extinction event is complicated by continuing uncertainty over the taxonomic status of many species. Hispaniola is one of the few Caribbean islands to retain native non-volant mammals; however, there has been little consensus over past or present levels of diversity in Hispaniolan hutias (Capromyidae: Plagiodontinae). Craniodental measurement data from modern hutia specimens, previously classified as both Plagiodontia aedium and P. hylaeum, display morphological differences between Hispaniola's northern and southern palaeo-islands using MANOVA and PCA. Although attempts to amplify mitochondrial DNA from the holotype of P. aedium were unsuccessful, this specimen is morphometrically associated with southern palaeo-island specimens. The mandibular size distribution of recent Plagiodontia specimens is unimodal, but the Late Quaternary mandibular size distribution is multimodal and displays much broader measurement spread, representing multiple extinct species. Finite Mixture Analysis was used to assess the best fit of different taxonomic hypotheses to the fossil mandibular size distribution. All retained FMA models include living hutias and P. spelaeum as distinct taxa; PCA further demonstrates that levels of morphological variation between modern hutia populations are lower than levels between living hutias and P. spelaeum, so that living hutias are interpreted as the single species P. aedium. Taxonomic differentiation for larger-bodied hutias is less well defined, but most retained models show only one larger species, for which the only available name is P. velozi. ‘Plagiodontia’ araeum is morphologically distinct from other species and is reassigned to Hyperplagiodontia. Hispaniola's plagiodontine fauna has lost its largest and smallest representatives; similar trends of body size selectivity in extinction risk are shown more widely across the Caribbean mammal fauna, possibly due to different regional anthropogenic threats (invasive mammals, hunting) affecting small-bodied and large-bodied mammals during the recent past. This apparent pattern of extinction selectivity is named the ‘Goldilocks Hypothesis’.     

Functional Morphology in Paleobiology: Origins of the Method of ‘Paradigms’

From the early nineteenth century, the successful use of fossils in stratigraphy oriented paleontology (and particularly the study of fossil invertebrates) towards geology. The consequent marginalising of biological objectives was countered in the twentieth century by the rise of ‘Paläobiologie’, first in the German cultural area and only later, as ‘paleobiology’, in the anglophone world. Several kinds of paleobiological research flourished internationally after the Second World War, among them the novel field of ‘paleoecology’. Within this field there were attempts to apply functional morphology to the problematical cases of fossil organisms, for which functions cannot be observed directly. This article describes the origins of the kind of functional inference for fossils that I proposed in 1961 as the method of ‘paradigms’ (a year before Thomas Kuhn made that word more widely familiar with a quite different meaning). Here I summarize some of my ‘worked exemplars’, which were intended to show the paradigm method in action. These case-studies were all taken from the paleontologically important phylum of the Brachiopoda, but the method was claimed to have much wider implications for the interpretation of the fossil record in terms of adaptive evolution. This article takes the history of the paradigm method as far as the late 1960s. I hope to trace, in a sequel, its ambivalent fate during the 1970s and beyond, when for example Gould’s critique of ‘the adaptationist programme’ and the rise of computer-based quantitative methods for the evolutionary interpretation of the fossil record led to the relative eclipse of functional morphology in paleontology.     

Deterministic diversity changes in freshwater phytoplankton in the Yunnan–Guizhou Plateau lakes in China

Diversity measures reflect different aspects of a community, which are determined by different ecological processes. However, information is still limited on the ecological processes that are represented by different measures of species diversity. In this study, the primary driving factors for richness and diversity indices were tested. The possible ecological processes represented by each index were analyzed. First, the type of ecological process that governed the phytoplankton community in the Yunnan–Guizhou Plateau lakes, either deterministic or stochastic, was identified by Caswell's neutral model. The results indicate that a deterministic process governs the phytoplankton community. Second, the driving factors of richness and diversity indices were screened with mixed models. The results suggest that the variation of phytoplankton richness in different lakes or sites was primarily related to bottom-up factors. The variations in evenness and other measures based on the relative abundance were driven by both top-down and bottom-up factors, such as zooplankton biomass, and pH and mean light, respectively. Finally, although the different measures of diversity may respond to specific bottom-up or top-down processes, the responses to the two processes were not independent of each other. These findings will increase our understanding of the relationships between ecological processes and diversity measures for freshwater phytoplankton.     

The diversity of soil communities, the ‘poor man's tropical rainforest’

This paper reviews the various factors that facilitate the high biodiversity of soil communities, concentrating on soil animals. It considers the problems facing soil ecologists in the study of soil communities and identifies the important role such communities play in terrestrial ecosystems. The review also considers diversity and abundance patterns. A range of factors are identified that may contribute to the biodiversity of soil and their role is reviewed. These include diversity of food resources and trophic specialization, habitat favourableness, habitat heterogeneity in space and time, scale and spatial extent of the habitat, niche dynamics and resource partitioning, productivity, disturbance and aggregation.Biodiversity of soil organisms appears high, largely attributable to the nested set of ecological worlds in the soil — the relationship between the range of size groupings of soil organisms relative to the spatial heterogeneity perceived by these various groups — that provide a large area for life for the micro- and mesofauna. The role of aggregation and how it relates to the spatial scale under consideration and to species interactions amongst soil animals is largely unknown at present. The role of disturbance is equivocal and man's activities more often than not seem to lead to a reduced biodiversity of soil communities. This paper also identifies areas where further work is desirable to improve our understanding of the structure and functioning of soil communities.     

Endangered species diversity ‘hot spots’ in Russia and centers of endemism

Geographic distributions of all 125 endangered and threatened animals and all 70 endangered flowering plant species were compiled and mapped by administrative territory (republics, states, provinces, and districts) of the Russian Federation, based on distributional data in the official Red Data Books of the R.S.F.S.R. [Eliseev et al. (eds) (1985) Red Book of the R.S.F.S.R.: Animals. Rosleskhoz Publishing, Moscow; Golovanov et al. (eds). (1988). Red Book of the R.S.F.S.R.: Plants. Rosagprom Publishing, Moscow]. Territories were ranked using an algorithm that gives highest rank to the single territory with the greatest number of endangered species present, then iteratively assigns the next highest rank to the territory containing the greatest number of species not found in a territory of higher rank. This algorithm minimizes the number of territories necessary to include one population of each endangered species, but may designate very low rank to a territory that holds high numbers of endangered species if many of those species are found in a territory of higher rank. When different sets of species were used to determine territory rank with this algorithm the only significant correlation between rank lists was between ranks generated when all species are used and when only species endemic to single territories were used. Mountainous territories on Russia's southern borders held the greatest numbers of endangered species and were highly ranked whether or not species occurring outside of Russia were excluded from the ranking algorithm. The Maritime state, Krasnodar state, Dagestan republic, Sakhalin province and the Jewish province all are centers of endangered species diversity that together contain 50 or more of endangered species for multiple taxonomic groups; this was the Dobson et al. [(1997) Science 275: 550–553] definition of an endangered species hot spot. These are all mountainous territories on Russia's southern border. Precise territorial ranking within the mountainous southern regions of the Southern Far East, Caucasus, and Altai/Sayan regions of southern Siberia was highly influenced by species endemic to single territories.