Biodiversity and systematics: the use and misuse of divergence information in assessing taxonomic diversity

1994 ◽  
Vol 1 (1) ◽  
pp. 53 ◽  
Author(s):  
Daniel P. Faith
Keyword(s):  
Phylogenetic Diversity ◽  
Conservation Management ◽  
Branch Length ◽  
Population Level ◽  
Taxonomic Diversity ◽  
Relative Advantage ◽  
Conservation Priorities ◽  
Mtdna Variation ◽  
Alternative Approach ◽  
Branch Lengths

Limited resources for conservation highlight the need for placing priorities on species or other taxa. While priorities or "weightings" based on taxonomic information are now well-established in principle, there is no agreement on a preferred approach. One set of methods attempts to use phylogenetic branch length or divergence information, when available. The "phylogenetic diversity" measure of Faith (1992) uses sums of branch lengths from phylogenetic estimates in order to predict underlying patterns of feature diversity among taxa. An alternative approach suggested by Altschul and Lipman also uses divergence information and would appear to yield results similar to phylogenetic diversity. However, it is demonstrated here that their method in fact can give results opposite to those required if feature diversity is to be maximized. A simple conservation management example, based on mtDNA variation at the population level, illustrates the relative advantage of using phylogenetic diversity to set conservation priorities.

scholarly journals Predicting the Impact of Describing New Species on Phylogenetic Patterns

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
D C Blackburn ◽  
G Giribet ◽  
D E Soltis ◽  
E L Stanley
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Length Variation ◽  
Tree Shape ◽  
Branch Lengths ◽  
Taxonomic History ◽  
Ecological Patterns ◽  
The Impact ◽  
Incomplete Sampling

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

scholarly journals Using a jumping spider fauna inventory (Araneae, Salticidae) as an indicator of the taxonomic diversity for Misiones, Argentina

2016 ◽  
Vol 64 (2) ◽  
pp. 875 ◽  
Author(s):  
Gonzalo D. Rubio
Keyword(s):  
Reference Data ◽  
Taxonomic Diversity ◽  
Diversity Indices ◽  
Conservation Priorities ◽  
Diversity Analysis ◽  
Jumping Spider ◽  
Future Studies

There is a clear connection between basic taxonomy and biodiversity issues. Faunistic studies with a taxonomically comprehensive inventory of species provide an important source of quantitative compiled information concerning several regions. This information can be used in diversity analysis and have great potential in setting conservation priorities. The salticid spider fauna of Misiones is relatively well known; here this knowledge is used to generate Clarke & Warwick taxonomic diversity indices. Different ecoregional diversities contributing to information about biodiversity levels of salticids in Misiones and providing reference data for future studies are analyzed. Differences between the three ecoregions of the province were found, mainly southern savannas regarding the forests of northern Misiones.

Three new cryptic species of the freshwater zooplankton genus Holopedium (Crustacea: Branchiopoda: Ctenopoda), revealed by genetic methods

Zootaxa ◽  
2007 ◽  
Vol 1656 (1) ◽  
pp. 1-50 ◽  
Author(s):  
CHAD L. ROWE ◽  
SARAH J. ADAMOWICZ ◽  
PAUL D. HEBERT
Keyword(s):  
North America ◽  
Large Scale ◽  
Amazon Basin ◽  
Morphological Variability ◽  
Morphological Differentiation ◽  
Population Level ◽  
Taxonomic Diversity ◽  
Coi Gene ◽  
Middle Latitudes ◽  
Molecular Approaches

Molecular approaches have greatly advanced our understanding of species diversity and biogeography in the cladoceran crustaceans. Here, we provide the first large-scale examination of taxonomic diversity in the genus Holopedium Zaddach, 1855, by characterizing patterns of allozyme, mtDNA, and morphological variation from a total of 193 sites from three continents, including collections from near the type localities for the two generally recognized species, Holopedium gibberum Zaddach, 1855, and Holopedium amazonicum Stingelin, 1904. Allozyme data were only available for North American samples but revealed the presence of four species. Divergence patterns in the mitochondrial cytochrome c oxidase subunit I (COI) gene supported those species, as well as a fifth taxon endemic to South America. The five putative species are separated by substantial sequence (8.7–24.5%) and allozyme (0.36–1.54 Nei’s distance) divergences, while intraspecific genetic diversity was generally limited in comparison. Although two of these species exhibited little morphological differentiation from their closest relatives, and diagnostic traits were not found among the characters considered, a population-level approach revealed significant morphological differences among all pairs of taxa. We therefore present both an allozyme key and a morphological/geographic key to all species, as well as new or augmented descriptions for all five species. H. gibberum s.s. is distributed in Europe and across arctic North America, while its cryptic sister species, H. glacialis n. sp., is widely distributed across temperate North America. H. amazonicum s.s. is apparently restricted to the Amazon basin, H. atlanticum n. sp. occurs in lakes along the eastern margin of North America, while H. acidophilum n. sp. occurs sporadically across North America along a narrow band of middle latitudes. Due to high morphological variability within species, as well as the detection of cryptic diversity, we suggest that genetic analyses should be performed on populations from other geographic regions and should always accompany the recognition of new species of Holopedium.

scholarly journals Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

2011 ◽  
Vol 21 (8) ◽  
pp. 3002-3013 ◽  
Author(s):  
Angela L. Strecker ◽  
Julian D. Olden ◽  
Joanna B. Whittier ◽  
Craig P. Paukert
Keyword(s):  
Phylogenetic Diversity ◽  
Freshwater Fishes ◽  
Conservation Priorities ◽  
Functional And Phylogenetic Diversity

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.

scholarly journals Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity

2017 ◽  
Author(s):  
Odile Maliet ◽  
Fanny Gascuel ◽  
Amaury Lambert
Keyword(s):  
Species Diversity ◽  
Phylogenetic Diversity ◽  
Extinction Risk ◽  
Simulated Data ◽  
Random Trees ◽  
Monte Carlo Algorithm ◽  
Conservation Priorities ◽  
Parameter Estimates ◽  
Relative Depth ◽  
As Species

AbstractPhylogenetic diversity (PD) is a measure of the evolutionary legacy of a group of species, which can be used to define conservation priorities. It has been shown that an important loss of species diversity can sometimes lead to a much less important loss of PD, depending on the topology of the species tree and on the distribution of its branch lengths. However, the rate of decrease of PD strongly depends on the relative depths of the nodes in the tree and on the order in which species become extinct. We introduce a new, sampling-consistent, three-parameter model generating random trees with covarying topology, clade relative depths and clade relative extinction risks. This model can be seen as an extension to Aldous’ one parameter splitting model β, which controls for tree balance) with two additional parameters: a new parameter α quantifying the correlation between the richness of a clade and its relative depth, and a parameter η quantifying the correlation between the richness of a clade and its frequency (relative abundance or range), taken herein as a proxy for its overall extinction risk. We show on simulated phylogenies that loss of PD depends on the combined effect of all three parameters, β, α and η. In particular, PD may decrease as fast as species diversity when high extinction risks are clustered within small, old clades, corresponding to a parameter range that we term the ‘thin ice zone’ (β < –1 or α < 0; η > 1). Besides, when high extinction risks are clustered within large clades, the loss of PD can be higher in trees that are more balanced (β > 0), in contrast to the predictions of earlier studies based on simpler models. We propose a Monte-Carlo algorithm, tested on simulated data, to infer all three parameters. Applying it to a real dataset comprising 120 bird clades (class Aves) with known range sizes, we show that parameter estimates precisely fall close to close to a ‘thin ice zone’: the combination of their ranking tree shape and non-random extinctions risks makes them prone to a sudden collapse of PD.

scholarly journals Phylogenetic species delimitation for crayfishes of the genusPacifastacus

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1915 ◽  
Author(s):  
Eric R. Larson ◽  
Magalie Castelin ◽  
Bronwyn W. Williams ◽  
Julian D. Olden ◽  
Cathryn L. Abbott
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Taxonomic Diversity ◽  
Pacifastacus Leniusculus ◽  
Phylogenetic Study ◽  
Conservation Priorities ◽  
Species Of Conservation Concern ◽  
Extant Species ◽  
Widely Invasive

Molecular genetic approaches are playing an increasing role in conservation science by identifying biodiversity that may not be evident by morphology-based taxonomy and systematics. So-called cryptic species are particularly prevalent in freshwater environments, where isolation of dispersal-limited species, such as crayfishes, within dendritic river networks often gives rise to high intra- and inter-specific genetic divergence. We apply here a multi-gene molecular approach to investigate relationships among extant species of the crayfish genusPacifastacus, representing the first comprehensive phylogenetic study of this taxonomic group. Importantly,Pacifastacusincludes both the widely invasive signal crayfishPacifastacus leniusculus,as well as several species of conservation concern like the Shasta crayfishPacifastacus fortis. Our analysis used 83 individuals sampled across the four extantPacifastacusspecies (omitting the extinctPacifastacus nigrescens), representing the known taxonomic diversity and geographic distributions within this genus as comprehensively as possible. We reconstructed phylogenetic trees from mitochondrial (16S, COI) and nuclear genes (GAPDH), both separately and using a combined or concatenated dataset, and performed several species delimitation analyses (PTP, ABGD, GMYC) on the COI phylogeny to propose Primary Species Hypotheses (PSHs) within the genus. All phylogenies recovered the genusPacifastacusas monophyletic, within which we identified a range of six to 21 PSHs; more abundant PSHs delimitations from GMYC and ABGD were always nested within PSHs delimited by the more conservative PTP method.Pacifastacus leniusculusincluded the majority of PSHs and was not monophyletic relative to the otherPacifastacusspecies considered. Several of these highly distinctP. leniusculusPSHs likely require urgent conservation attention. Our results identify research needs and conservation priorities forPacifastacuscrayfishes in western North America, and may inform better understanding and management ofP. leniusculusin regions where it is invasive, such as Europe and Japan.

Toward a Human-Centric Approach to Cybersecurity

2018 ◽  
Vol 32 (4) ◽  
pp. 411-424 ◽  
Author(s):  
Ronald J. Deibert
Keyword(s):  
National Security ◽  
Critical Infrastructure ◽  
World Politics ◽  
Relative Advantage ◽  
Access To Information ◽  
Freedom Of Association ◽  
Realist Theory ◽  
Planetary Scale ◽  
Alternative Approach ◽  
The Individual

AbstractA “national security–centric” approach currently dominates cybersecurity policies and practices. Derived from a realist theory of world politics in which states compete with each other for survival and relative advantage, the principal cybersecurity threats are conceived as those affecting sovereign states, such as damage to critical infrastructure within their territorial jurisdictions. As part of a roundtable on “Competing Visions for Cyberspace,” this essay presents an alternative approach to cybersecurity that is derived from the tradition of “human security.” Rather than prioritizing territorial sovereignty, this approach prioritizes the individual, and views networks as part of the essential foundation for the modern exercise of human rights, such as access to information, freedom of thought, and freedom of association. The foundational elements of a human-centric approach to cybersecurity are outlined and contrasted with the prevailing trends around national security–centric practices. A human-centric approach strives for indivisible network security on a planetary scale for the widest possible scope of human experience, and seeks to ensure that such principles are vigorously monitored and defended by multiple and overlapping forms of independent oversight and review.

scholarly journals Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference

2019 ◽  
Vol 37 (4) ◽  
pp. 1202-1210 ◽  
Author(s):  
David A Duchêne ◽  
K Jun Tong ◽  
Charles S P Foster ◽  
Sebastián Duchêne ◽  
Robert Lanfear ◽  
...  
Keyword(s):  
Empirical Data ◽  
Sequence Data ◽  
Branch Length ◽  
Data Sets ◽  
Gene Trees ◽  
Data Set ◽  
Branch Lengths ◽  
Statistical Support ◽  
Distinct Branch ◽  
Consistent Support

Abstract Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. In phylogenetics, the potential impacts of partitioning sequence data for the assignment of substitution models are well appreciated. In contrast, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci or subsets of loci. By analyzing a range of empirical data sets, we find consistent support for a model in which branch lengths are proportionate between subsets of loci: gene trees share the same pattern of branch lengths, but form subsets that vary in their overall tree lengths. These models had substantially better statistical support than models that assume identical branch lengths across gene trees, or those in which genes form subsets with distinct branch-length patterns. We show using simulations and empirical data that the complexity of the branch-length model with the highest support depends on the length of the sequence alignment and on the numbers of taxa and loci in the data set. Our findings suggest that models in which branch lengths are proportionate between subsets have the highest statistical support under the conditions that are most commonly seen in practice. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.

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