scholarly journals Phylogenetic diversity measures based on Hill numbers

2010 ◽  
Vol 365 (1558) ◽  
pp. 3599-3609 ◽  
Author(s):  
Anne Chao ◽  
Chun-Huo Chiu ◽  
Lou Jost
Keyword(s):  
Phylogenetic Diversity ◽  
Species Abundance ◽  
Taxonomic Diversity ◽  
Interval Length ◽  
Time Interval ◽  
Essential Property ◽  
Effective Number ◽  
Quadratic Entropy ◽  
Number Of Species ◽  
Hill Numbers

We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on ‘effective number of species’ or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on ‘total phylogenetic length’) to incorporate species abundances. The proposed measure quantifies ‘the mean effective number of species’ over any time interval of interest, or the ‘effective number of maximally distinct lineages’ over that time interval. The product of the measure and the interval length quantifies the ‘branch diversity’ of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.

Globally endangered butterflies (Lepidoptera) protected in the natural reserve «Dniprovsko-Orilsky»

2016 ◽  
Vol 27 (3-4) ◽  
pp. 47-54
Author(s):  
K. K. Holoborodko ◽  
V. O. Makhina ◽  
K. S. Buchnieva ◽  
O. E. Pakhomov
Keyword(s):  
Rare Species ◽  
Geographical Location ◽  
Taxonomic Diversity ◽  
Red List ◽  
River Valley ◽  
Number Of Species ◽  
Natural Reserve ◽  
Western Palearctic ◽  
Mediterranean Origin ◽  
Northern Species

Floodplain valley of the Dnieper river midstream is a unique natural complex, having a great bìogeographical, ecological, environmental, historical and recreational values. In 1990, the Natural reserve «Dniprovsko-Orilsky» was established within the area. The Natural reserve «Dniprovsko-Orilsky» is environmentally protected site within the Dnipropetrovsk region, Dnipropetrovsk oblast, Ukraine. This reserve occupies part of the Dnieper river valley and marshy and reedy banks of Protovch river (existing bed of Oril river). It was created by Regulation of the Council of Ministers of the USSR of 15 September 1990, No. 262, based on common zoological and ornitological Nature reserves «Taromskì plavni» and «Obukhovskie zaplavy». On the territory of the Natural reserve «Dniprovsko-Orilsky», they were registered 32 Lepidoptera species listed in the List of Threatened Species at different categories (5 species in IUCN Red List ; 18 in Red Data Book of Ukraine; 7 in European Red List of plants and animals endangered on a global scale; 31 in Red Book of Dnipropetrovsk oblast). The main scientific materials were author’s collections from area of research and materials of entomological funds, Department of Zoology and Ecology, Oles Honchar Dnipropetrovsk National University (mostly Memorial Collection of V. O. Barsov). Field surveys covered all the ecosystems basic on size and degree of protection. The author’s researches have conducted over the past decade during annual expeditions to the Reserve. Taxonomic structure of the complex is quite diverse, and represented by all the major families of higher millers and rhopalocera, having protectedstatus. In relation to taxonomy, this complex formed by representatives of five superfamilies (Zyganoidea, Noctuoidea, Bombycoidea, Hesperioidea, Papilionoidea) from 11 families (Zygaenidae, Saturniidae, Sphingidae, Noctuidae Arctiidae Hesperiidae, Papilionidae, Pieridae, Nymphalidae, Satyridae, Lycaenidae). High taxonomic diversity can be explained by unique geographical location of the reserve in azonal conditions of the Dnieper river valley. Such location allows to enter different zoogeographic Lepidoptera groups on the reserve territory. Zoogeographic analysis of species protected within the reserve territory selected 7 basic groups. It was found that most of the globally rare species have Mediterranean origin (39 %); species of Palearctic origin are in second place (22 %); Western Palearctic and Ponto-Kazakh types of areas are same of number of species, and come third (11 %); and others come 17 % (European, Euro-Siberian, and Holarctic). This fauna component is specific due to presence of so-called «northern» species that make up 40 % (representatives of Palearctic, Western Palearctic, Euro-Siberian, European and Holarctic groups). Their existence within the reserve territory is only possible due to development of boreal valley ecosystems. High taxonomic diversity can be explained by unique geographical location of the reserve in azonal conditions of the Dnieper river valley. Such location allows to enter different zoogeographic Lepidoptera groups on the reserve territory. Zoogeographic analysis of species protected within the reserve territory selected 7 basic groups. It was found that most of the globally rare species have Mediterranean origin (39 %); species of Palearctic origin are in second place (22 %); Western Palearctic and Ponto-Kazakh types of areas are same of number of species, and come third (11 %); and others come 17 % (European, Euro-Siberian, and Holarctic). This fauna component is specific due to presence of so-called «northern» species that make up 40 % (representatives of Palearctic, Western Palearctic, Euro-Siberian, European and Holarctic groups). Their existence within the reserve territory is only possible due to development of boreal valley ecosystems.

To the flora of сonjugates (Streptophyta, Conjugatophyceae) of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia)

2014 ◽  
Vol 48 ◽  
pp. 81-88
Author(s):  
A. F. Luknitskaya
Keyword(s):  
Species Distribution ◽  
National Park ◽  
Species Abundance ◽  
Water Bodies ◽  
Number Of Species ◽  
First Time

76 species, 3 varieties and 1 form from 21 genera of Streptophyta, Conjugatophyceae (Actinotaenium, Bambusina, Closterium, Cosmarium, Cylindrocystis, Euastrum, Gonatozygon, Haplotaenium, Micrasterias, Mougeotia, Netrium, Penium, Planotaenium, Pleurotaenium, Raphidiastrum, Spirogyra, Spirotaenia, Staurastrum, Staurodesmus, Tetmemorus, Xanthidium) were found in the basins of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia). The list of species is annotated with data on the species distribution in 55 collecting sites of 29 water bodies of the national park, and species abundance in collected samples according to Luknitskaya (2009). Among above mentioned genera, the genus Cosmarium is represented by the greatest number of species (20). Staurastrum chaetoceros has been found for the first time for the Novgorod Region.

scholarly journals INVENTÁRIO FLORESTAL PARA ADEQUAÇÃO AMBIENTAL DA FAZENDA SANTA RITA, MUNICÍPIO DE SANTARÉM, ESTADO DO PARÁ

FLORESTA ◽  
2010 ◽  
Vol 40 (3) ◽  
Author(s):  
João Ricardo Vasconcellos Gama ◽  
Josiel Carneiro Pinheiro
Keyword(s):  
Tree Species ◽  
Forest Inventory ◽  
Species Abundance ◽  
Sample Plot ◽  
Forest Fragment ◽  
Conservation Areas ◽  
Environmental Suitability ◽  
Number Of Species ◽  
Level Ii ◽  
Level I

O presente trabalho foi desenvolvido objetivando inventariar um fragmento florestal e indicar espécies arbóreas para a recuperação das áreas de reserva legal e preservação permanente da Fazenda Santa Rita, localizada na zona rural do município de Santarém, estado do Pará. Foram lançadas sistematicamente 18 parcelas de 20 x 50 m (1000 m²), totalizando uma área amostral de 18.000 m². Cada parcela foi dividida em dois níveis de inclusão: Nível I de inclusão, subparcela de 20 m x 25 m e mensuração de todas as árvores com DAP ≥ 10 cm e Nível II de inclusão, em parcelas de 20 x 50 m e medição de todas as árvores com DAP ³ 45 cm. Identificou-se 70 espécies e 33 famílias botânicas. As famílias que apresentaram maior riqueza de espécies foram: Lecythidaceae e Mimosaceae (7), Caesalpiniaceae e Sapotaceae (5) e Lauraceae (4). Estas famílias contribuíram com 40% das espécies amostradas, confirmando-se que poucas famílias botânicas representam grande parte da riqueza de espécies arbóreas em florestas de terra-firme.Palavras-chave: Inventário florestal; adequação ambiental; Amazônia. AbstractForest inventory for environmental adjustment in the Santa Rita farm, located in the County of Santarém, State of Pará, Brazil. This study was carried out aiming to identify a forest fragment and indicate tree species for recovering legal reserve and permanent conservation areas of the Santa Rita Farm. Eighteen sample plots, measuring 20 x50m each, were systematically distributed, totaling a sample area of 18.000 m². Each sample plot was divided into two levels. Level I: sub-plots of 20 x 25m, where all trees with DBH ≥ 10 cm were measured; Level II: plots of 20 x 50 m, where all trees with DAP ³ 45 cm were measured. A total of 70 tree species and 33 botanical families were identified. Families that presented higher number of species were: Lecythidaceae and Mimosaceae (7), Caesalpiniaceae and Sapotaceae (5) and Lauraceae (4). These families contributed with 40% of the species, confirming that few families represent a large part of the of tree species abundance in the Amazon high-land forests.Keywords: Forest inventory; environmental suitability; Amazon. 

scholarly journals Devonian bryozoan extinction and diversification

1992 ◽  
Vol 6 ◽  
pp. 136-136
Author(s):  
Alan S. Horowitz ◽  
Joseph F. Pachut
Keyword(s):  
Mass Extinction ◽  
Taxonomic Diversity ◽  
Mass Extinctions ◽  
Random Mass ◽  
Number Of Species ◽  
Rugose Corals ◽  
Nomina Dubia ◽  
Extinction Model ◽  
Permian Mass Extinction ◽  
Devonian Extinction

The names proposed world-wide for Devonian bryozoans have been evaluated with respect to replaced names, synonyms, and nomina dubia [Horowitz and Pachut (1993), Journal of Paleontology, in press]. The resulting list contains 1738 specific names assigned to 199 genera in 45 families. Approximately 75% of Devonian bryozoan species are reported from a single stage. Not more than 10%, and usually 4–6%, of the species reported in any Devonian stage are also reported in the succeeding stage.The largest decrease in observed bryozoan diversity occurs between the Givetian and Frasnian stages, reducing the number of species by 77%, genera by 64%, and families by 42%. These values are less than those reported for the range-through method for the entire fauna of the Permian mass extinction (Raup, 1979) but larger than percentage extinctions (presumably based on range-though data) for four other Phanerozoic mass extinctions tabulated by Valentine and Walker (1987).The range-through method dampens the observed differences in taxonomic diversity among Devonian stages at all taxonomic levels. The range-through number of species/stage is based upon both direct applications of the range-through method and on the assignment of ranges known only to early, middle and late Devonian to include appropriate Devonian stages. Generic and familial diversity increases monotonically from Lochkovian through Givetian stages. Thereafter (Givetian to Frasnian), range-through values for specific (69%), generic (31%), and familial diversity (10%) decrease. Specific and familial decreases across the Givetian-Frasnian boundary are comparable to those reported for non-Permian mass extinctions by Valentine and Walker, but the generic decrease is not as great. These results are consistent with Valentine and Walker's random mass extinction model.Observed bryozoan diversity across the Frasnian-Famennian boundary increases while values calculated using the range-through method decrease by approximately 5–15%. This does not suggest a major bryozoan extinction event. Conversely, the decrease in bryozoan diversity across the Givetian-Frasnian interval is similar to an important Devonian extinction among rugose corals. The reason(s) for these extinctions is not yet clear. With respect to Devonian bryozoans, our inadequate understanding of the cause(s) of mass extinctions and the relatively coarse resolution of the stadial timescale does not permit differentiating between gradual or catastrophic scenarios.

Discrete Mechanics and Optimal Control of Walking Gaits

2016 ◽  
Vol 12 (2) ◽  
Author(s):  
M. W. Koch ◽  
M. Ringkamp ◽  
S. Leyendecker
Keyword(s):  
Optimal Control ◽  
Time Span ◽  
Constrained Systems ◽  
Bipedal Walking ◽  
Interval Length ◽  
Time Interval ◽  
Discrete Mechanics ◽  
Flat Foot ◽  
Flat Feet ◽  
Heel Contact

In this work, we optimally control the upright gait of a three-dimensional symmetric bipedal walking model with flat feet. The whole walking cycle is assumed to occur during a fixed time span while the time span for each of the cycle phases is variable and part of the optimization. The implemented flat foot model allows to distinguish forefoot and heel contact such that a half walking cycle consists of five different phases. A fixed number of discrete time nodes in combination with a variable time interval length assure that the discretized problem is differentiable even though the particular time of establishing or releasing the contact between the foot and the ground is variable. Moreover, the perfectly plastic contact model prevents penetration of the ground. The optimal control problem is solved by our structure preserving discrete mechanics and optimal control for constrained systems (DMOCC) approach where the considered cost function is physiologically motivated and the obtained results are analyzed with regard to the gait of humans walking on a horizontal and an inclined plane.

Elasmobranch diversity, conservation and management along Wadge Bank, South India

2019 ◽  
Author(s):  
K. Karuppasamy ◽  
P. Jawahar ◽  
S. David Kingston ◽  
V. K. Venkataramani ◽  
V. Vidhya
Keyword(s):  
Species Richness ◽  
Phylogenetic Diversity ◽  
South India ◽  
Fish Communities ◽  
Taxonomic Diversity ◽  
Management Measures ◽  
Conservation And Management ◽  
D Value

The study was undertaken to document the elasmobranch diversity and their abundance along Wadge Bank. Species were collected fortnightly during June 2015 to May 2016 from three landing centres viz., Chinnamuttom,Colachel and Vizhinjam of Wadge Bank. A total of 1,575 specimens were collected during the period and 44 species were identified belonging to 8 orders, 13 families and 25 genera. Among the recorded \families,Carcharhinidae is the most dominant family with 12 species. The Colachel landing centre was rich in diversity with 43 species followed by Chinnamuttom 39 species and Vizhinjam26 species. The highest Shannon Weiner diversity (H’ value) was observed at Colachel (4.17) followed by Chinnamuttom (4.11) and Vizhinjam (3.76). The Margalef’s species richness (‘d’) value was assessed at Colachel (4.55) followed by Chinnamuttom (4.01) and Vizhinjam (2.91). The Pielou’s evenness (J’) estimated was 0.7786, 0.7700 and 0.8005respectively, for Chinnamuttom, Colachal and Vizhinjam. The highest taxonomic diversity value was observed at Colachel (60.33) and the lowest during at Vizhinjam (54.08). Among the three landing centres studied, the total phylogenetic diversity (sPhi+) was found to be the lowest at Vizhinjam (940) and highest at Colachel landing centre (1720). Bray Curtis similarities measure was also calculated, fish communities were separated into several clusters based on seasons. The conservation of elasmobranchs and the management measures to be followed along the Wadge Bank is also discussed.

The impact of trampling on feldmark vegetation in Kosciuszko National Park, New South Wales

2004 ◽  
Vol 52 (3) ◽  
pp. 315 ◽  
Author(s):  
K. L. McDougall ◽  
G. T. Wright
Keyword(s):  
National Park ◽  
New South ◽  
New South Wales ◽  
Species Abundance ◽  
Management Options ◽  
Cushion Plants ◽  
Number Of Species ◽  
South Wales ◽  
Westerly Winds ◽  
The Impact

A popular walking track in Kosciuszko National Park, New South Wales, passes through areas of feldmark vegetation, a windswept community of sparse dwarf shrubs, cushion plants and herbs. The prevailing westerly winds in this area prune the windward edges of the dominant Epacris gunnii shrubs. Layering on the protected side effectively means that the shrubs slowly move across the ridgetops. Twenty-five transects were placed perpendicular to the track in a patch of feldmark north of Mt Kosciuszko. The density of selected species and the total number of species were recorded in quadrats placed in the track centre, track edges and feldmark vegetation at 5 and 10 m from both sides of the track to determine whether the track has interrupted feldmark processes and affected species abundance. The abundance of all species and the number of species per quadrat was lowest in the track centre. Three species (including E. gunnii) were found to be less abundant on the leeward edge of the track than on the windward edge, suggesting that the track has indirectly interfered with feldmark processes. Two of the species were as abundant on track edges as at 5 and 10 m from the track. The area of affected vegetation is currently very small and it may take decades before the effect is obvious to people using the track. Management options for reducing or eliminating the impact are discussed.

scholarly journals Phylogenetic Diversity of Plant Metacommunity of the Dnieper River Arena Terrace Within the ‘Dnieper-Orilskiy ’ Nature Reserve

2017 ◽  
Vol 36 (4) ◽  
pp. 352-365
Author(s):  
Olexander Zhukov ◽  
Olga Kunah ◽  
Yulia Dubinina ◽  
Dmitry Ganga ◽  
Galina Zadorozhnaya
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Nature Reserve ◽  
Species Abundance ◽  
Remote Sensing Data ◽  
Principal Coordinate Analysis ◽  
Permutation Procedure ◽  
Additional Information ◽  
Plant Phylogeny ◽  
Steppe Meadow

Abstract This article presents the features of the phylogenetic organization of the plant communities of the Dnieper River terrace within the ‘Dnieper-Orilskiy’ Nature Reserve and the patterns of its spatial variation involving remote sensing data of the Earth’s surface. The research materials were collected in the period 2012−2016 from within the nature reserve. The research polygon is within the first terrace (arena) of the Dnieper valley. Sandy steppe, meadow, forest and marsh communities within the Protoch river floodplain and the Orlova ravine, as well as artificial pine plantations were the habitats present within the research polygon. The vegetation description was carried out on 10×10 m (100 m2) plots. A total of 94 geobotanical descriptions were made. Data on plant phylogeny was obtained by the Phylomatic service. Phylogenetic diversity of the communities was assessed by the Faith, Simpson and Shannon indices. Phylogenetic analysis was performed by means of a double principal coordinate analysis (DPCoA). The vegetation cover within the investigated polygon was represented by 189 species. Abundance Phylogenetic Deviation (APD) for the investigated metacommunity was evaluated to −0.53, which is statistically significantly different from random alternatives (p = 0.001). The APD negative value indicates that phylogenetic organization of the investigated metacommunity is overdispersed. The permutation procedure allowed us to establish that the eigenvalues of the DPCoA-axes obtained as a result of the real phylogenetic tree were significantly higher than their own number for the random phylogenetic trees for the first seven axes. This indicates that the first seven axes are useful for additional information on the ordination structure of the metacommunity.

scholarly journals The "neutral" community structure of planktonic herbivores, tintinnid ciliates of the microzooplankton, across the SE Tropical Pacific Ocean

2007 ◽  
Vol 4 (1) ◽  
pp. 561-593 ◽  
Author(s):  
J. R. Dolan ◽  
M. E. Ritchie ◽  
J. Ras
Keyword(s):  
Pacific Ocean ◽  
Chlorophyll Concentration ◽  
Neutral Theory ◽  
Species Abundance ◽  
Morphological Diversity ◽  
Taxonomic Diversity ◽  
Large Species ◽  
Community Characteristics ◽  
Phytoplankton Diversity ◽  
Mouth Size

Abstract. Across a species-rich area, the SE Pacific Ocean, the community characteristics of a group of planktonic herbivores was assessed. A series of 22 stations between the Marquise Islands (7° S 142° W) and the coast of Chile (35° S 73° W) was sampled during the BIOSOPE cruise in 2004. The relationships between taxonomic diversity, morphological diversity, patterns of tintinnid species assemblage, and phytoplankton abundance were examined. Tintinnid community characteristics were estimated from large volume (20–60 l) discrete depth sampling and phytoplankton were characterized based on HPLC pigment signatures. Across the transect, average water column concentrations of tintinnids ranged from 2–40 cells l−1or 8–40 ng C l−1, and were positively related to chlorophyll a concentrations which varied between 0.07–2 μg l−1. Large numbers of tintinnid taxa were found, 18–41 species per station, yielding a total of 149 species. Among stations, morphological and taxonomic diversity metrics co-varied but were not significantly related to phytoplankton diversity estimated using a pigment-based size-diversity metric. Taxonomic diversity of tintinnids, as H' or Fishers' alpha, was inversely related to chlorophyll concentration and positively to the depth of the chlorophyll maximum layer. For each station, species abundance distributions were compared to geometric, log-series and log-normal distributions. For most stations, the observed distribution most closely matched log-series, coherent with the neutral theory of random colonization from a large species pool. Occurrence rates of species were correlated with average abundance rather than specific characteristics of biomass or lorica oral diameter (mouth) size. Among stations, species richness was correlated with both the variety of mouth sizes (lorica oral diameters) as well as numbers of species per mouth size, also consistent with random colonization.

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