Taxon Selection under Split Diversity

Minh, Bùi Quang; Klaere, Steffen; Haeseler, Arndt von

doi:10.1093/sysbio/syp058

Cited by 37 publications

(49 citation statements)

References 33 publications

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“…This includes 11 galliform species found in China of which ten were included in our phylogeny. There is substantial interest in using phylogenetic information to inform conservation priorities [11] and previous efforts to understand the use of phylogenetic information to establish conservation priorities have used galliforms as a model system [12], making a well-resolved galliform phylogeny even more critical.…”

Section: Introductionmentioning

confidence: 99%

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

et al. 2013

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Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups (“pheasants” and “partridges”) is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.

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Section: Introductionmentioning

confidence: 99%

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

et al. 2013

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“…, [24], [25], [36]). However, the PD complementarity scores that can be obtained from these methods are contingent, i.e.…”

Section: Discussionmentioning

confidence: 99%

“…Note that the overall PD for both trees [6], [39] and networks [24], [25], [36] is simply the sum of all split weights (Figure 1). …”

Section: Methodsmentioning

confidence: 99%

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Prioritizing Populations for Conservation Using Phylogenetic Networks

et al. 2014

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In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations.

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“…In the midst of the current biodiversity crisis, if prioritization is required, conservation efforts should be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history (Vane-Wright, Humphries & Williams, 1991). Methods first pioneered by Faith (1992) have been further developed and refined to evaluate the relative importance of species based on their contribution to total genetic diversity (Weitzman, 1992; Witting & Loeschcke, 1993; Redding, 2003; Steel, Mimoto & Mooers, 2007; Faith, 2008; Haake, Kashiwada & Su, 2008; Minh, Klaere & Von Haeseler, 2009; Hartmann, 2013). These methods were initially created for the analyses of phylogenetic trees, but have recently been extended for use with phylogenetic networks that better represent genetic diversity among populations and recently diverged species (Volkmann et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation

Jensen

Mooers

Caccone

et al. 2016

PeerJ

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In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization.

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Taxon Selection under Split Diversity

Cited by 37 publications

References 33 publications

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

Prioritizing Populations for Conservation Using Phylogenetic Networks

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation

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