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

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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Conserving evolutionarily distinct species is critical to safeguard human well-being

Scientific Reports ◽

10.1038/s41598-021-03616-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Rafael Molina-Venegas

Keyword(s):

Related Species ◽

Phylogenetic Diversity ◽

Decisive Role ◽

Well Being ◽

Distinct Species ◽

Expected Number ◽

Phylogenetic Information ◽

Closely Related Species ◽

Number Of Species ◽

Evolutionary Distinctiveness

AbstractAlthough there is growing interest in safeguarding the Tree of Life to preserve the human benefits that are directly provided by biodiversity, their evolutionary distribution remains unknown, which has hampered our understanding of the potential of phylodiversity indicators to evince them. Here, I drew on a global review of plant benefits and comprehensive phylogenetic information to breakdown their evolutionary distribution and thereby show why the commonly used Phylogenetic Diversity and Evolutionary Distinctiveness indicators can unequivocally help to preserve these natural services. Beneficial species clumped within phylogenetically overdispersed genera and closely related species often contributed very few and redundant benefits, suggesting that multiple plant lineages are required to maintain a wide variety of services. Yet, a reduced number of species stood out as multi-beneficial and evolutionarily distinct plants relative to both the entire phylogeny and the subset of beneficial species, and they collectively contributed a higher-than-expected number of records for most types of benefits. In addition to providing a clear mechanistic understanding for the recently proved success of Phylogenetic Diversity in capturing plant benefits, these findings stress the decisive role that conservation programmes aimed at protecting evolutionarily distinct taxa will play in safeguarding the beneficial potential of biodiversity for the future.

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Trogia benghalensis (Marasmiaceae, Basidiomycota), a new species from India

Phytotaxa ◽

10.11646/phytotaxa.331.2.11 ◽

2017 ◽

Vol 331 (2) ◽

pp. 273 ◽

Cited By ~ 1

Author(s):

ARUN KUMAR DUTTA ◽

SUDESHNA NANDI ◽

ENTAJ TARAFDER ◽

RIMPA SIKDER ◽

ANIRBAN ROY ◽

...

Keyword(s):

New Species ◽

Related Species ◽

Internal Transcribed Spacer ◽

West Bengal ◽

Internal Transcribed Spacer Region ◽

Comprehensive Description ◽

Closely Related Species ◽

Molecular Sequence ◽

Region Data ◽

A New Species

A new species of Trogia (Marasmiaceae, Basidiomycota) is described from West Bengal, India. Analysis of the molecular sequence (nuclear ribosomal internal transcribed spacer region) data suggests that T. benghalesis is phylogenetically distinct from its closely related species. Comprehensive description based on macro- and microscopic characters, photographs and comparisons with morphologically similar and phylogenetically related species are provided.

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Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline

Genome ◽

10.1139/gen-2018-0067 ◽

2019 ◽

Vol 62 (9) ◽

pp. 585-595

Author(s):

D.A. Veldkornet ◽

J.B. Adams ◽

J.S. Boatwright ◽

A. Rajkaran

Keyword(s):

Dna Barcoding ◽

South African ◽

Phylogenetic Diversity ◽

Pairwise Distance ◽

Closely Related Species ◽

Phylogenetic Clustering ◽

Building Community ◽

Subtropical Estuaries ◽

Abiotic Interactions ◽

Conservation Prioritisation

Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.

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Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid Zone Specialist: The Yellow-Footed Rock-Wallaby

Genes ◽

10.3390/genes11020154 ◽

2020 ◽

Vol 11 (2) ◽

pp. 154

Author(s):

Sally Potter ◽

Linda E. Neaves ◽

Mark Lethbridge ◽

Mark D. B. Eldridge

Keyword(s):

Gene Flow ◽

Control Region ◽

Arid Zone ◽

Genetic Research ◽

Mitochondrial Control Region ◽

Genetic Connectivity ◽

Mountain Range ◽

Contemporary Gene Flow ◽

Region Data ◽

Demographic Processes

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogale xanthopus xanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x. xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.

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Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds

Genome ◽

10.1139/g04-009 ◽

2004 ◽

Vol 47 (3) ◽

pp. 535-545 ◽

Cited By ~ 19

Author(s):

Sergio L Pereira ◽

Erwin T Grau ◽

Anita Wajntal

Keyword(s):

Control Region ◽

Mitochondrial Control Region ◽

High Rate ◽

Molecular Organization ◽

Molecular Architecture ◽

Closely Related Species ◽

Protein Coding ◽

Dna Substitution ◽

Suitable Marker ◽

Composition Pattern

The control region (CR) plays an important role in replication and transcription in the mitochondrial genome. Its supposedly high rate of DNA substitution makes it a suitable marker for studies of population and closely related species. Three domains can be identified in CR, each having its own characteristics regarding base composition, pattern of variability and rate of DNA substitution. We sequenced the complete CR for 27 cracids, including all 11 genera to characterize its molecular organization, describe patterns of DNA substitution along the gene, and estimate absolute rates of DNA substitution. Our results show that cracid CR organization and patterns of DNA substitution are typical of other birds. Conserved blocks C and B, fused CSB2/3, and a putative segment for bidirectional replication not usually present in birds were identified in cracids. We also suggest a new delimitation for domains to allow better comparisons among CRs at different taxonomic ranking. Our estimates of absolute rates of DNA substitution show that, in general, CR evolves at a rate slower than that of two protein-coding genes (CR, 0.14%–0.3%; ND2, 0.37%–0.47%; and cytochrome b, 0.29%–0.35% per site per million years within genera). Within CR domains, rates within genera ranged from 0.05% to 0.8% per site per million years.Key words: mitochondrial control region, molecular evolution, Cracidae, Aves.

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Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

10.1101/2021.07.15.452170 ◽

2021 ◽

Author(s):

Michal Motyka ◽

Dominik Kusy ◽

Matej Bocek ◽

Renata Bilkova ◽

Ladislav Bocak

Keyword(s):

Phylogenetic Diversity ◽

Field Research ◽

Distribution Patterns ◽

Future Research ◽

Evidence Based ◽

Biodiversity Crisis ◽

Putative Species ◽

Α Diversity ◽

Very High ◽

Support Evidence

Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ~700 localities in three continents. The species-rich dataset included ~6,500 terminals, >2,300 putative species, more than a half of them unknown to science. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of α-diversity, very high species-level endemism, a biodiversity hotspot in New Guinea, and high phylogenetic diversity in the Sundaland. We suggest that ~20 person months of focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.

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Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities

10.1101/232991 ◽

2017 ◽

Author(s):

Rikki Gumbs ◽

Claudia L. Gray ◽

Oliver R. Wearn ◽

Nisha R. Owen

Keyword(s):

Extinction Risk ◽

Phylogenetic Analyses ◽

Iucn Red List ◽

New Method ◽

Conservation Priorities ◽

Conservation Action ◽

Biodiversity Crisis ◽

Data Limitations ◽

Evolutionary Distinctiveness ◽

Conservation Prioritisation

AbstractThe scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. The EDGE metric, which prioritises species based on their Evolutionary Distinctiveness (ED) and Global Endangerment (GE), relies on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic analyses of large clades are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to impute ED for species missing from a phylogeny whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogeny, the new method provided the closest estimates of their “true” score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous imputation methods. Previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogeny. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst limiting uncertainty and anticipating future phylogenetic advances.

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Balancing phylogenetic diversity and species numbers in conservation prioritization, using a case study of threatened species in New Zealand

Biological Conservation ◽

10.1016/j.biocon.2014.03.013 ◽

2014 ◽

Vol 174 ◽

pp. 47-54 ◽

Cited By ~ 33

Author(s):

Joseph R. Bennett ◽

Graeme Elliott ◽

Belinda Mellish ◽

Liana N. Joseph ◽

Ayesha I.T. Tulloch ◽

...

Keyword(s):

New Zealand ◽

Threatened Species ◽

Phylogenetic Diversity ◽

Species Numbers ◽

Conservation Prioritization

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Species boundaries in the Trichophyton mentagrophytes / T. interdigitale species complex

Medical Mycology ◽

10.1093/mmy/myy115 ◽

2018 ◽

Vol 57 (6) ◽

pp. 781-789 ◽

Cited By ~ 9

Author(s):

Ivan M Pchelin ◽

Daniil V Azarov ◽

Maria A Churina ◽

Sergey G Scherbak ◽

Svetlana V Apalko ◽

...

Keyword(s):

Species Delimitation ◽

Phylogenetic Network ◽

Taxonomic Status ◽

Epidemiological Data ◽

Trichophyton Mentagrophytes ◽

Species Boundaries ◽

Data Sets ◽

Internal Transcribed Spacer Region ◽

Closely Related Species ◽

The Status

AbstractThe fungi Trichophyton mentagrophytes and T. interdigitale are closely related species, causing superficial infections in humans and other mammals. The status of these taxa is a field of long-lasting debates. To clarify their phylogenetic relationships within the genus Trichophyton and sharpen the species boundaries, we performed sequencing of four T. mentagrophytes genomes and also evaluated three previously published multilocus data sets. We performed computational species delimitation analysis on all available in GenBank internal transcribed spacer region (ITS) sequences of Trichophyton spp. Phylogenomic data, phylogenetic network, and species delimitation analyses implied that T. mentagrophytes and T. interdigitale belong to the same phylogenetic species. However, we argue that taxonomic status quo should be retained, from the perspective of epidemiological data and the principle of taxonomic stability. Since there is a correlation between ITS genotype and epidemiological source of an isolate, restriction of T. interdigitale to purely anthropophilic ITS genotypes seems to be reasonable.

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Conserving Evolutionarily Distinct Species is Critical to Safeguard Human Well-Being

10.21203/rs.3.rs-544103/v1 ◽

2021 ◽

Author(s):

Rafael Molina-Venegas

Keyword(s):

Phylogenetic Diversity ◽

Decisive Role ◽

Well Being ◽

Distinct Species ◽

Tree Of Life ◽

Expected Number ◽

Phylogenetic Information ◽

Number Of Species ◽

Evolutionary Distinctiveness ◽

Mechanistic Understanding

Abstract Although there is growing interest in safeguarding the Tree of Life to preserve the human benefits that are directly provided by biodiversity, their evolutionary distribution remains unknown, which has hampered our understanding of the potential of phylodiversity indicators to evince them. Here, I drew on a global review of plant services and comprehensive phylogenetic information to breakdown their evolutionary distribution and thereby show why the commonly used Phylogenetic Diversity and Evolutionary Distinctiveness indicators can unequivocally help to preserve these natural benefits. Beneficial species clumped within phylogenetically overdispersed genera and closely related taxa often contributed very few and redundant services, suggesting that multiple plant lineages are required to maintain a wide variety of benefits. Yet, a reduced number of species stood out as multi-beneficial and evolutionarily distinct plants relative to both the entire phylogeny and the subset of beneficial species, and they collectively contributed a higher-than-expected number of records for most types of benefits. In addition to providing a clear mechanistic understanding for the recently proved success of Phylogenetic Diversity in capturing plant benefits, these findings stress the decisive role that conservation programmes aimed at protecting evolutionarily distinct taxa will pay in safeguarding the beneficial potential of biodiversity for the future.

Download Full-text