scholarly journals What do we mean by diversity? The path towards quantification

2018 ◽  
Author(s):  
Lou Jost
Keyword(s):  
Biological Diversity ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Effective Number ◽  
Number Of Species ◽  
Mathematical Properties ◽  
Diversity Measures ◽  
Relative Abundances ◽  
Simple Count ◽  
Biological Reasoning

The concept of biological diversity has evolved from a simple count of species to more sophisticated measures that are sensitive to relative abundances and even to evolutionary divergence times between species. In the course of this evolution, diversity measures have often been borrowed from other disciplines. Biological reasoning about diversity often implicitly assumed that measures of diversity had certain mathematical properties, but most of biology’s traditional diversity measures did not actually possess these properties, a situation which often led to mathematically and biologically invalid inferences. Biologists now usually transform the traditional measures to «effective number of species», whose mathematics does support most of the rules of inference that biologists apply to them. Effective number of species, then, seems to capture most (though not all) of what biologists mean by diversity.

scholarly journals Reliable confidence intervals for RelTime estimates of evolutionary divergence times

2019 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Beatriz Mello ◽  
Sudhir Kumar
Keyword(s):  
Confidence Intervals ◽  
Divergence Time ◽  
Simulated Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Rate Variation ◽  
Evolutionary Divergence ◽  
Posterior Density ◽  
Divergence Time Estimates ◽  
Highest Posterior Density

AbstractConfidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in these analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density (HPD) intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, i.e., the true time is contained within the CIs with a 95% probability. These developments will encourage broader use of computationally-efficient RelTime approach in molecular dating analyses and biological hypothesis testing.

Impact of clonal evolution on the biological diversity of Trypanosoma cruzi

Parasitology ◽  
1997 ◽  
Vol 114 (3) ◽  
pp. 213-218 ◽  
Author(s):  
J.-P. LAURENT ◽  
C. BARNABE ◽  
V. QUESNEY ◽  
S. NOEL ◽  
M. TIBAYRENC
Keyword(s):  
Trypanosoma Cruzi ◽  
Biological Diversity ◽  
Clonal Evolution ◽  
Evolutionary Divergence ◽  
Biological Variability ◽  
Profound Impact ◽  
Applied Study ◽  
Biological Differences

Trypanosoma cruzi, the agent of Chagas' disease, exhibits considerable biological variability. Moreover, it has been postulated that populations of this protozoan are subdivided into natural clones, which can be separated from each other by considerable levels of evolutionary divergence. The authors have proposed that this long-term clonal evolution may have a profound impact on Trypanosoma cruzi biological diversity. In order to test this hypothesis, 16 T. cruzi stocks representing 3 major clonal genotypes of the parasite were analysed for 8 different in vitro biological parameters. The overall results show a strong statistical linkage between genetic and biological differences. This is in agreement with the working hypothesis, although a notable biological variability is observable among the stocks of each of the 3 major clonal genotypes. The authors propose that T. cruzi genetic variability must be taken into account in any applied study dealing with this parasite.

scholarly journals Necrophagous flies assemblages: Spatio-temporal patterns in a Neotropical urban environment

Caldasia ◽  
2018 ◽  
Vol 40 (2) ◽  
pp. 296-309 ◽  
Author(s):  
Moira Battan-Horenstein ◽  
Raquel Miranda Gleiser
Keyword(s):  
Species Composition ◽  
Forensic Sciences ◽  
The Sun ◽  
Effective Number ◽  
Bone Meal ◽  
Seasonal Differences ◽  
Local Factors ◽  
Relative Abundances ◽  
Spatio Temporal ◽  
Urban Sites

Species composition, richness, and relative abundance of the communities of Calliphoridae, Muscidae, and Fanniidae in Córdoba city, Argentina was assessed, and how these characteristics are affected by seasonal and anthropogenic conditions was studied. The study was carried out in thirteen sites with various levels of urbanization during 2014 and 2015, comparing two seasons: the warmer-wet summer and the cold-dry winter. Adult flies were collected in each site using two traps baited with hydrated bone meal. A total of 1683 flies were collected, belonging to twelve genera and 22 species. Several of the species collected are relevant to forensic sciences. The most frequent species were Hydrotaea aenescens (Muscidae) and Fannia fusconotata (Fanniidae). No differences in necrophagous fly richness or relative abundances between the central urban sites and the periphery suburban sites were observed; however, richness was significantly correlated with local (250 m buffer area) built-up density. Species composition differed between the urban and suburban sites. Seasonal differences were also detected: the relative abundances per species were more even in the summer. Dissimilarities in the assemblages were mainly due to differences in the relative abundances of some species, reflecting their adaptability to landscapes with different degree of urbanization. Regardless of season or urbanization density, species richness and effective number of species were higher in traps placed in the sun as opposed to shade. Taken together, these results suggest that in Córdoba city both landscape and local factors explain variations in the necrophagous fly community. 

Species structure in Zambian miombo woodland

1987 ◽  
Vol 3 (2) ◽  
pp. 109-118 ◽  
Author(s):  
E. N. Chidumayo
Keyword(s):  
Species Diversity ◽  
Biological Diversity ◽  
Diversity Index ◽  
Species Density ◽  
Species Structure ◽  
Miombo Woodland ◽  
Species Diversity Index ◽  
Old Growth ◽  
Number Of Species ◽  
The Mean

ABSTRACTMiombo woodland in Zambia is divided into wetter and drier types by the 1100 mm mean rainfall isohyet. In the present study two wetter (Northern, Northwestern) and three drier (Central, Eastern, Western) miombo subtypes were recognized.A survey of the woody flora of 94 old-growth and 58 coppice stands in the five miombo subtypes revealed some significant differences in species diversity among them. The floristic differentiantion of miombo subtypes was best achieved by the use of the Shannon species diversity index (H′) and species density (number of species 0.1 ha−1 or 0.4 ha−1). H′ in miombo decreased from 2.247 in Northwestern to 2.136 in Northern, 2.052 in Eastern, 1.918 in Central and 1.824 in Western subtypes. Although species density was not significantly different between wetter miombo subtypes, this decreased in a similar fashion from 18.78 0.1 ha−1 in Northwestern to 18.30 in Northern, 16.65 in Eastern, 14.79 in Central and 12.29 in Western subtypes. The low species diversity in Western drier miombo was attributed to the combined effects of low soil fertility and rainfall.Although the mean number of species per 0.1 ha plot was higher in coppice samples, species richness (d) and index of diversity (H′) were lower than in old-growth samples. These results indicate lower species diversity in regenerating miombo. The dynamic aspects of species structure should therefore be considered in the future conservation of biological diversity in miombo woodland.

scholarly journals Checklist of dragonflies and damselflies (Insecta: Odonata) of the Amazonas state, Brazil

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ricardo Koroiva ◽  
Ulisses Gaspar Neiss ◽  
Günther Fleck ◽  
Neusa Hamada
Keyword(s):  
Species Richness ◽  
Tropical Forest ◽  
Biological Diversity ◽  
Number Of Species ◽  
Southern Area ◽  
Brazilian State ◽  
Amazonas State

Abstract: Here we provide a checklist of the odonates from Amazonas state, Brazil. We registered 324 species and 101 genera, making Amazonas the Brazilian state with the most Odonata species recorded. The families with the highest number of species were Coenagrionidae with 32 genera and 101 species, followed by Libellulidae with 28 genera and 100 species and Gomphidae with 12 genera and 45 species. Some regions of Amazonas state remain poorly explored, such as the southern area, and large municipalities, such as São Gabriel da Cachoeira. This work underlines the importance of the biological diversity from Amazonas state and the Amazonian Biome for Odonata species richness in Brazil and shows that many areas in the world’s largest tropical forest have not yet been sampled.

Estimating number of species and relative abundances in stream-fish communities: effects of sampling effort and discontinuous spatial distributions

1995 ◽  
Vol 52 (5) ◽  
pp. 936-949 ◽  
Author(s):  
Paul L. Angermeier ◽  
Roy A. Smogor
Keyword(s):  
Fish Community ◽  
Sampling Effort ◽  
Fish Community Structure ◽  
Stream Length ◽  
Number Of Species ◽  
In Series ◽  
Species Similarity ◽  
Simulation Results ◽  
Relative Abundances ◽  
Negative Exponential

We sampled fishes and measured microhabitat in series of contiguous habitat units (riffles, runs, pools) in three Virginia streams. We used Monte Carlo simulations to construct hypothetical series of habitat units, then examined how number of species, similarity in relative abundances, and number of microhabitats accumulated with increasing number of habitat units (i.e., sampling effort). Proportions of all species and microhabitats represented were relatively low and variable at low sampling effort, but increased asymptotically and became less variable with greater sampling effort. To facilitate comparisons among streams, we fitted simulation results to negative exponential curves. The curves indicated that 90% of the species present were usually found by sampling 5 to 14 habitat units (stream length of 22–67 stream widths). Estimates of species relative abundances required less sampling effort for a given accuracy than estimates of number of species. Rates of species accumulation (with effort) varied among streams and reflected discontinuity in species distributions among habitat units. Most discontinuity seemed to be due to low population density rather than to habitat selectivity. Results from an Illinois stream corroborated our findings from Virginia, and suggested that greater sampling effort is needed to characterize fish community structure in more homogeneous stream reaches.

scholarly journals Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times

2019 ◽  
Vol 37 (1) ◽  
pp. 280-290 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Beatriz Mello ◽  
Sudhir Kumar
Keyword(s):  
Confidence Intervals ◽  
Divergence Time ◽  
Simulated Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Rate Variation ◽  
Evolutionary Divergence ◽  
Posterior Density ◽  
Divergence Time Estimates ◽  
Highest Posterior Density

Abstract Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in dating analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, that is, the actual time is contained within the CIs with a 94% probability. These developments will encourage broader use of computationally efficient RelTime approaches in molecular dating analyses and biological hypothesis testing.

RESEARCH ON THE FAUNA OF EARTHWORMS (OLIGOCHAETA, LUMBRICIDAE) IN ĐERDAP NATIONAL PARK

2021 ◽  
Author(s):  
Jovana Sekulić ◽  
◽  
Mirjana Stojanović ◽  
Tanja Trakić ◽  
Filip Popović
Keyword(s):  
Endemic Species ◽  
National Park ◽  
Biological Diversity ◽  
Southeastern Part ◽  
Central European ◽  
Northeastern Part ◽  
Intensive Research ◽  
Number Of Species

Đerdap National Park is located in the southeastern part of Europe, in the northeastern part of Serbia, on the border with Romania. This paper presents the currently known records on the diversity of earthworm fauna in Đerdap National Park. The number of species from family Lumbricidae known to be occurring in the studied region is 29 species from 11 genera. The genera with the largest number of the registered taxa are Dendrobaena (8) and Aporrectodea (7). A third of all species are peregrines (37.93%). Trans-Aegean species take part with 13.8%, followed by endemic, Central European, Balkanic-Alpine (10.34%). Then follow Illyric (6.90%) and slightly less Moesian, Circum- Mediterranean, and Southern-Alpine (3.45%). Endemic species take a part with three taxa. Only one species (Allolobophora mehadiensis boscaiui (Pop, 1948)) is Dacian endemic. The obtained results indicate a diverse Lumbricidae fauna. It is certainly necessary to continue with intensive research in order to preserve the biological diversity of this area.

Sign in / Sign up

Export Citation Format

Share Document