Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 170-182 ◽  
Author(s):  
Mariam Adeoba ◽  
Solomon G. Tesfamichael ◽  
Kowiyou Yessoufou
Keyword(s):  
Threatened Species ◽  
Phylogenetic Diversity ◽  
Extinction Risk ◽  
Phylogenetic Signal ◽  
Distinct Species ◽  
Tree Of Life ◽  
Fish Family ◽  
The Face ◽  
Taxonomic Confusion ◽  
Coi Sequences

Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.

scholarly journals Phylogenetically informed spatial planning is required to conserve the mammalian tree of life

2017 ◽  
Vol 284 (1865) ◽  
pp. 20170627 ◽  
Author(s):  
Dan F. Rosauer ◽  
Laura J. Pollock ◽  
Simon Linke ◽  
Walter Jetz
Keyword(s):  
Conservation Planning ◽  
Phylogenetic Diversity ◽  
Informed Choice ◽  
Tree Of Life ◽  
Phylogenetic Information ◽  
Mammal Conservation ◽  
The Face ◽  
New Generation ◽  
The Impact ◽  
Effective Conservation

In the face of the current extinction crisis and severely limited conservation resources, safeguarding the tree of life is increasingly recognized as a high priority. We conducted a first systematic global assessment of the conservation of phylogenetic diversity (PD) that uses realistic area targets and highlights the key areas for conservation of the mammalian tree of life. Our approach offers a substantially more effective conservation solution than one focused on species. In many locations, priorities for PD differ substantially from those of a species-based approach that ignores evolutionary relationships. This discrepancy increases rapidly as the amount of land available for conservation declines, as does the relative benefit for mammal conservation (for the same area protected). This benefit is equivalent to an additional 5900 Myr of distinct mammalian evolution captured simply through a better informed choice of priority areas. Our study uses area targets for PD to generate more realistic conservation scenarios, and tests the impact of phylogenetic uncertainty when selecting areas to represent diversity across a phylogeny. It demonstrates the opportunity of using rapidly growing phylogenetic information in conservation planning and the readiness for a new generation of conservation planning applications that explicitly consider the heritage of the tree of life's biodiversity.

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

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.

scholarly journals For common community phylogenetic analyses, go ahead and use synthesis phylogenies

2018 ◽  
Author(s):  
Daijiang Li ◽  
Lauren Trotta ◽  
Hannah E. Marx ◽  
Julie M. Allen ◽  
Miao Sun ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Gene Sequence ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Pairwise Distance ◽  
Highly Correlated ◽  
Gene Sequence Data

AbstractShould we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel’s λ and Blomberg’s K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman’s ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blomberg’s K or close to Pagel’s λ from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

scholarly journals Genomic Approaches for Conservation Management in Australia under Climate Change

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 653
Author(s):  
Isabelle Onley ◽  
Katherine Moseby ◽  
Jeremy Austin
Keyword(s):  
Climate Change ◽  
Threatened Species ◽  
Management Practices ◽  
Conservation Management ◽  
Extinction Risk ◽  
Climate Change Scenarios ◽  
Genetic Management ◽  
Species Management ◽  
The Face ◽  
Analytical Approaches

Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.

scholarly journals Global extinction risk for seahorses, pipefishes and their near relatives (Syngnathiformes)

Oryx ◽  
2021 ◽  
pp. 1-10
Author(s):  
Riley A. Pollom ◽  
Gina M. Ralph ◽  
Caroline M. Pollock ◽  
Amanda C.J. Vincent
Keyword(s):  
Threatened Species ◽  
Habitat Degradation ◽  
Extinction Risk ◽  
Conservation Status ◽  
Field Research ◽  
Selective Extraction ◽  
Iucn Red List ◽  
Point Estimate ◽  
Conservation Action ◽  
Data Deficient

Abstract Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are seahorses (Hippocampus spp.: 14/42 species, with an additional 17 that are Data Deficient) or freshwater pipefishes of the genus Microphis (2/18 species, with seven additional that are Data Deficient). Two species are Near Threatened. Nearly one-third of syngnathiformes (97 species) are Data Deficient and could potentially be threatened, requiring further field research and evaluation. Most species (61%) were, however, evaluated as Least Concern. Primary threats to syngnathids are (1) overexploitation, primarily by non-selective fisheries, for which most assessments were determined by criterion A (Hippocampus) and/or (2) habitat loss and degradation, for which assessments were determined by criterion B (Microphis and some Hippocampus). Threatened species occurred in most regions but more are found in East and South-east Asia and in South African estuaries. Vital conservation action for syngnathids, including constraining fisheries, particularly non-selective extraction, and habitat protection and rehabilitation, will benefit many other aquatic species.

scholarly journals Conservation Status of Marine Biodiversity in Oceania: An Analysis of Marine Species on the IUCN Red List of Threatened Species

2011 ◽  
Vol 2011 ◽  
pp. 1-14 ◽  
Author(s):  
Beth A. Polidoro ◽  
Cristiane T. Elfes ◽  
Jonnell C. Sanciangco ◽  
Helen Pippard ◽  
Kent E. Carpenter
Keyword(s):  
Threatened Species ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Conservation Status ◽  
Marine Species ◽  
Iucn Red List ◽  
Red List ◽  
Marine Biodiversity ◽  
Conservation Priorities ◽  
Conservation Action

Given the economic and cultural dependence on the marine environment in Oceania and a rapidly expanding human population, many marine species populations are in decline and may be vulnerable to extinction from a number of local and regional threats. IUCN Red List assessments, a widely used system for quantifying threats to species and assessing species extinction risk, have been completed for 1190 marine species in Oceania to date, including all known species of corals, mangroves, seagrasses, sea snakes, marine mammals, sea birds, sea turtles, sharks, and rays present in Oceania, plus all species in five important perciform fish groups. Many of the species in these groups are threatened by the modification or destruction of coastal habitats, overfishing from direct or indirect exploitation, pollution, and other ecological or environmental changes associated with climate change. Spatial analyses of threatened species highlight priority areas for both site- and species-specific conservation action. Although increased knowledge and use of newly available IUCN Red List assessments for marine species can greatly improve conservation priorities for marine species in Oceania, many important fish groups are still in urgent need of assessment.

scholarly journals Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

2015 ◽  
Vol 370 (1662) ◽  
pp. 20140019 ◽  
Author(s):  
T. M. Brooks ◽  
A. Cuttelod ◽  
D. P. Faith ◽  
J. Garcia-Moreno ◽  
P. Langhammer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Threatened Species ◽  
Phylogenetic Diversity ◽  
Species Population ◽  
Threatened Taxa ◽  
Conservation Actions ◽  
Ecosystem Diversity ◽  
Species Specific ◽  
A Site ◽  
Specific Conservation

‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4 , 326–337. ( doi:10.1111/j.1752-4571.2010.00157.x )) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.

scholarly journals Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices

2018 ◽  
Vol 46 ◽  
pp. 192-198 ◽  
Author(s):  
Markus Gastauer ◽  
Cecílio Frois Caldeira ◽  
Ian Trotter ◽  
Silvio Junio Ramos ◽  
João Augusto Alves Meira Neto
Keyword(s):  
Phylogenetic Diversity ◽  
Tree Of Life ◽  
Dispersion Indices

Phylogenetic Diversity and Mycotoxin Potential of Emergent Phytopathogens within the Fusarium tricinctum Species Complex

2022 ◽  
Author(s):  
Imane Laraba ◽  
Mark Busman ◽  
David M. Geiser ◽  
Kerry O'Donnell
Keyword(s):  
Species Complex ◽  
Phylogenetic Diversity ◽  
Agricultural Research ◽  
Distinct Species ◽  
Culture Collections ◽  
Strain Collection ◽  
Food And Feed ◽  
Feed Safety ◽  
Large Survey ◽  
Fusarium Tricinctum

Recent studies on multiple continents indicate members of the Fusarium tricinctum species complex (FTSC) are emerging as prevalent pathogens of small-grain cereals, pulses, and other economically important crops. These understudied fusaria produce structurally diverse mycotoxins, among which enniatins (ENNs) and moniliformin (MON) are the most frequent and of greatest concern to food and feed safety. Herein a large survey of fusaria in the Fusarium Research Center and Agricultural Research Service culture collections was undertaken to assess species diversity and mycotoxin potential within the FTSC. A 151-strain collection originating from diverse hosts and substrates from different agroclimatic regions throughout the world was selected from 460 FTSC strains to represent the breadth of FTSC phylogenetic diversity. Evolutionary relationships inferred from a 5-locus dataset, using maximum likelihood and parsimony, resolved the 151 strains as 24 phylogenetically distinct species, including nine that are new to science. Of the five genes analyzed, nearly full-length phosphate permease sequences contained the most phylogenetically informative characters, establishing its suitability for species-level phylogenetics within the FTSC. Fifteen of the species produced ENNs, MON, the sphingosine analog 2-amino-14,16- dimethyloctadecan-3-ol (AOD), and the toxic pigment aurofusarin (AUR) on a cracked corn kernel substrate. Interestingly, the five earliest diverging species in the FTSC phylogeny (i.e., F. iranicum, F. flocciferum, F. torulosum, Fusarium spp. FTSC 8 and 24) failed to produce AOD and MON, but synthesized ENNs and/or AUR. Moreover, our reassessment of nine published phylogenetic studies on the FTSC identified 11 additional novel taxa, suggesting this complex comprises at least 36 species.

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