Individual heterozygosity predicts translocation success in threatened desert tortoises

Anthropogenic environmental modification is placing as many as 1 million species at risk of extinction. One management action for reducing extinction risk is translocation of individuals to locations from which they have disappeared or to new locations where biologists hypothesize they have a good chance of surviving. To maximize this survival probability, the standard practice is to move animals from the closest possible populations that contain presumably related individuals. In an empirical test of this conventional wisdom, we analyzed a genomic dataset for 166 translocated desert tortoises (Gopherus agassizii) that either survived or died over a period of two decades. We used genomic data to infer the geographic origin of translocated tortoises and found that individual heterozygosity predicted tortoise survival, whereas translocation distance or geographic unit of origin did not. Our results suggest a relatively simple indicator of the likelihood of a translocated individual’s survival: heterozygosity.

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Inferring the geographic origin of a range expansion: Latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program x -origin

Molecular Ecology ◽

10.1111/mec.14380 ◽

2017 ◽

Vol 26 (24) ◽

pp. 6908-6920 ◽

Cited By ~ 15

Author(s):

Qixin He ◽

Joyce R. Prado ◽

Laura Lacey Knowles

Keyword(s):

Range Expansion ◽

Geographic Origin ◽

Genomic Data

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Revisiting Orthotospovirus Phylogeny Using Whole Genomic Data and a Hypothesis for their Geographic Origin and Diversification

10.1101/2020.04.07.031120 ◽

2020 ◽

Author(s):

Anamarija Butković ◽

Rubén González ◽

Santiago F. Elena

Keyword(s):

Phylogenetic Relationships ◽

Geographic Origin ◽

Genome Shuffling ◽

Genomic Data ◽

Genomic Sequences ◽

Genome Database ◽

Evolutionary Forces ◽

The Family ◽

Plant Families ◽

Negative Sense

ABSTRACTThe family Tospoviridae, a member of the Bunyavirales order, is constituted of tri-segmented negative-sense single-stranded RNA viruses that infect plants and are also able of replicating in their insect vectors in a persistent manner. The family is composed of a single genus, the Orthotospovirus, whose type species is Tomato spotted wilt virus (TSWV). Previous studies assessing the phylogenetic relationships within this genus were based upon partial genomic sequences, thus resulting in unresolved clades and a poor assessment of the roles of recombination and genome shuffling during mixed infections. Complete genomic data for most Orthotospovirus species are now available at NCBI genome database. In this study we have used 62 complete genomes from 20 species. Our study confirms the existence of four phylogroups (A to D), grouped in two major clades (A-B and C-D), within the genus. We have estimated the split between the two major clades ∼3,100 years ago shortly followed by the split between the A and B phylogroups ∼2,860 years ago. The split between the C and D phylogroups happened more recently, ∼1,465 years ago. Segment reassortment has been shown to be important in the generation of novel viruses. Likewise, within-segment recombination events have been involved in the origin of new viral species. Finally, phylogeographic analyses of representative viruses suggests the Australasian ecozone as the possible origin of the genus, followed by complex patterns of migration, with rapid global spread and numerous reintroduction events.IMPORTANCEMembers of the Orthotospovirus genus infect a large number of plant families, including food crops and ornamentals, resulting in multimillionaire economical losses. Despite this importance, phylogenetic relationships within the genus were established years ago based in partial genomic sequences. A peculiarity of orthotospoviruses is their tri-segmented negative sense genomes, which makes segment reassortment and within-segment recombination, two forms of viral sex, potential evolutionary forces. Using full genomes from all described orthotospovirus species, we revisited their phylogeny and confirmed the existence of four major phylogroups with uneven geographic distribution. We have also shown a pervasive role of sex in the origin of new viral species. Finally, using Bayesian phylogeographic methods, we assessed the possible geographic origin and historical dispersal of representative viruses from the different phylogroups.

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Avoiding extinction under nonlinear environmental change: models of evolutionary rescue with plasticity

Biology Letters ◽

10.1098/rsbl.2021.0459 ◽

2021 ◽

Vol 17 (12) ◽

Author(s):

Philip B. Greenspoon ◽

Hamish G. Spencer

Keyword(s):

Phenotypic Plasticity ◽

Environmental Change ◽

Environmental Changes ◽

Extinction Risk ◽

Current Theory ◽

Species At Risk ◽

Adaptive Genetic Variation ◽

Change Models ◽

Numerous Species ◽

Evolutionary Rescue

Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here, we present a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change.

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Propuesta de evaluación para asignar tentativamente riesgo de extinción (ETRE): el caso de Peltogyne mexicana (Leguminosae)

Botanical Sciences ◽

10.17129/botsci.1971 ◽

2018 ◽

Vol 96 (4) ◽

pp. 609

Author(s):

Juan Carlos Montero-Castro ◽

José Antonio Zuñiga-Zuñiga ◽

Cuauhtémoc Sáenz-Romero ◽

Nahum Modesto Sánchez-Vargas

Keyword(s):

Extinction Risk ◽

Distribution Area ◽

Risk Category ◽

Species At Risk ◽

Tropical Timber ◽

Risk Of Extinction ◽

Timber Tree ◽

Speed Up ◽

Risk Situation ◽

Method Of Evaluation

Background: The rates of extinction evaluations are slow in relation to the magnitude of the problem. In the case of plants, just about 6 % of the species have been evaluated. On the other hand, it has been determined that the extension of the distribution area is a good predictor of the extinction risk.Questions: Is it possible to speed up the estimate of extinction risk of plant species? Can risk estimates that consider only the area of distribution converge with estimates from already established methods?Taxon: Peltogyne mexicanaStudy site: Guerrero, MexicoMethods: The Evaluation to Assign Tentatively Risk of Extinction (ETRE) was implemented comparing the area of occurrence (AOO), calculated with the GeoCat program, of the tropical timber tree Peltogyne mexicana against the AOO of other tropical trees (all Leguminosae) that are recognized with risk of extinction. The Method of Evaluation of Species at Risk (MER) was implemented and the results were compared.Results: With the implementation of the ETRE it was determined that Peltogyne mexicana has a high extinction risk, category that is confirmed with the MER implementation.Discussion: The suitability of the ETRE is based on the fact that several predictors of the risk of extinction are dependent on the size of the distribution area and that the estimate of the distribution area is amply accepted through the AOO. The ETRE is impartial, easily replicable, which can be implemented previously to evaluations more scrupulous, such as the MER. Actions are suggested to alleviate the risk situation of Peltogyne mexicana.

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Prediction of lithium response using genomic data

Scientific Reports ◽

10.1038/s41598-020-80814-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

William Stone ◽

Abraham Nunes ◽

Kazufumi Akiyama ◽

Nirmala Akula ◽

Raffaella Ardau ◽

...

Keyword(s):

Cross Validation ◽

Genomic Data ◽

Postsynaptic Membrane ◽

Classification Performance ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genomic Dataset ◽

Task Classification ◽

Lithium Response

AbstractPredicting lithium response prior to treatment could both expedite therapy and avoid exposure to side effects. Since lithium responsiveness may be heritable, its predictability based on genomic data is of interest. We thus evaluate the degree to which lithium response can be predicted with a machine learning (ML) approach using genomic data. Using the largest existing genomic dataset in the lithium response literature (n = 2210 across 14 international sites; 29% responders), we evaluated the degree to which lithium response could be predicted based on 47,465 genotyped single nucleotide polymorphisms using a supervised ML approach. Under appropriate cross-validation procedures, lithium response could be predicted to above-chance levels in two constituent sites (Halifax, Cohen’s kappa 0.15, 95% confidence interval, CI [0.07, 0.24]; and Würzburg, kappa 0.2 [0.1, 0.3]). Variants with shared importance in these models showed over-representation of postsynaptic membrane related genes. Lithium response was not predictable in the pooled dataset (kappa 0.02 [− 0.01, 0.04]), although non-trivial performance was achieved within a restricted dataset including only those patients followed prospectively (kappa 0.09 [0.04, 0.14]). Genomic classification of lithium response remains a promising but difficult task. Classification performance could potentially be improved by further harmonization of data collection procedures.

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Monitoring Extinction Risk and Threats of the World’s Fishes based on the Sampled Red List Index

10.21203/rs.3.rs-129206/v1 ◽

2020 ◽

Author(s):

Rafael Miranda ◽

Imanol Miqueleiz ◽

William Darwall ◽

Catherine Sayer ◽

Nicholas Dulvy ◽

...

Keyword(s):

Extinction Risk ◽

Conservation Status ◽

Marine Species ◽

Freshwater Ecosystems ◽

Red List ◽

Species At Risk ◽

Marine Systems ◽

Species Groups ◽

Global Biodiversity ◽

Over Time

Abstract Global biodiversity targets require us to identify species at risk of extinction and quantify status and trends of biodiversity. The Red List Index (RLI) tracks trends in the conservation status of entire species groups over time by monitoring changes in categories assigned to species. Here, we calculate this index for the world’s fishes in 2010, using a sampled approach to the RLI based on a randomly selected sample of 1,500 species, and also present RLI splits for freshwater and marine systems separately. We further compare specific traits of a worldwide fish list to our sample to assess its representativeness. Overall, 15.1% of species in the sample were estimated to be threatened with extinction, resulting in an sampled RLI of 0.914 for all species, 0.972 in marine and 0.860 in freshwater ecosystems. Our sample showed fishing as the principal threat for marine species, and pollution by agricultural and foresty effluents for freshwater fishes. The sampled list provides a robust representation for tracking trends in the conservation status of the world’s fishes, including disaggregated sampled indices for marine and freshwater fish. Reassessment and backcasting of this index is urgent to check the achievement of the commitments proposed in global biodiversity targets.

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The Importance of Assessing Climate Change Vulnerability to Address Species Conservation

Journal of Fish and Wildlife Management ◽

10.3996/052013-jfwm-039 ◽

2014 ◽

Vol 5 (2) ◽

pp. 450-462 ◽

Cited By ~ 4

Author(s):

Karen E. Bagne ◽

Megan M. Friggens ◽

Sharon J. Coe ◽

Deborah M. Finch

Keyword(s):

Climate Change ◽

At Risk ◽

Extinction Risk ◽

Species Conservation ◽

Biodiversity Loss ◽

Small Subset ◽

Species At Risk ◽

Terrestrial Vertebrates ◽

Climate Change Vulnerability ◽

Risk Of Extinction

Abstract Species conservation often prioritizes attention on a small subset of “special status” species at high risk of extinction, but actions based on current lists of special status species may not effectively moderate biodiversity loss if climate change alters threats. Assessments of climate change vulnerability may provide a method to enhance identification of species at risk of extinction. We compared climate change vulnerability and lists of special status species to examine the adequacy of current lists to represent species at risk of extinction in the coming decades. The comparison was made for terrestrial vertebrates in a regionally important management area of the southwestern United States. Many species not listed as special status were vulnerable to increased extinction risk with climate change. Overall, 74% of vulnerable species were not included in lists of special status and omissions were greatest for birds and reptiles. Most special status species were identified as additionally vulnerable to climate change impacts and there was little evidence to indicate the outlook for these species might improve with climate change, which suggests that existing conservation efforts will need to be intensified. Current special status lists encompassed climate change vulnerability best if climate change was expected to exacerbate current threats, such as the loss of wetlands, but often overlooked climate-driven threats, such as exceeding physiological thresholds.

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A 3500-year-old leaf from a Pharaonic tomb reveals that New Kingdom Egyptians were cultivating domesticated watermelon

10.1101/642785 ◽

2019 ◽

Cited By ~ 3

Author(s):

Susanne S. Renner ◽

Oscar A. Pérez-Escobar ◽

Martina V. Silber ◽

Mark Nesbitt ◽

Michaela Preick ◽

...

Keyword(s):

South Africa ◽

West Africa ◽

Stop Codon ◽

Citrullus Lanatus ◽

Geographic Origin ◽

Central Africa ◽

Genomic Data ◽

Nile Valley ◽

New Kingdom ◽

Extant Species

AbstractDomestication of the watermelon (Citrullus lanatus) has alternatively been placed in South Africa, the Nile valley, or more recently West Africa, with the oldest archeological evidence coming from Libya and Egypt. The geographic origin and domestication of watermelons has therefore remained unclear. Using extensive nuclear and plastid genomic data from a 3,560-year-oldCitrullusleaf from a mummy’s sarcophagus and skimmed genomes for representatives of the seven extant species ofCitrullus, we show that modern cultivars and the ancient plant uniquely share mutations in a lycopene metabolism gene (LYCB) affecting pulp color and a stop codon in a transcription factor regulating bitter cucurbitacin compounds. This implies that the plant we sequenced had red-fleshed and sweet fruits and that New Kingdom Egyptians were cultivating domesticated watermelons. The genomic data also identify extant Sudanese watermelons with white, sweet pulp as the closest relatives of domesticated watermelons.Significance statementWith some 197.8 million tons in 2017, watermelon,Citrullus lanatus, is among the World’s most important crops, yet its area of origin and domestication have remained unclear, with competing hypotheses favoring South Africa, West Africa, Central Africa, or the Nile valley. We generated extensive nuclear and plastid genomic data from a 3500-year-old leaf from a Pharaonic sarcophagus and performed genome skimming for representatives of all otherCitrullusspecies to compare key genes involved in fruit bitterness and color. White-fleshed, non-bitter melons from southern Sudan are the closest relatives of domesticated watermelon, and the ancient genome shares unique alleles with a red-fleshed, non-bitter domesticated form (but no wild forms), implying that 18thDynasty Egyptians were cultivating domesticated watermelon by 3500 years ago.

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Clarifying misconceptions of extinction risk assessment with the IUCN Red List

Biology Letters ◽

10.1098/rsbl.2015.0843 ◽

2016 ◽

Vol 12 (4) ◽

pp. 20150843 ◽

Cited By ~ 65

Author(s):

Ben Collen ◽

Nicholas K. Dulvy ◽

Kevin J. Gaston ◽

Ulf Gärdenfors ◽

David A. Keith ◽

...

Keyword(s):

Extinction Risk ◽

Iucn Red List ◽

Red List ◽

Species At Risk ◽

Iucn Red List Categories ◽

Use Of Data ◽

Risk Of Extinction ◽

Identification Of Species ◽

Extinction Risk Assessment ◽

Red Listing

The identification of species at risk of extinction is a central goal of conservation. As the use of data compiled for IUCN Red List assessments expands, a number of misconceptions regarding the purpose, application and use of the IUCN Red List categories and criteria have arisen. We outline five such classes of misconception; the most consequential drive proposals for adapted versions of the criteria, rendering assessments among species incomparable. A key challenge for the future will be to recognize the point where understanding has developed so markedly that it is time for the next generation of the Red List criteria. We do not believe we are there yet but, recognizing the need for scrutiny and continued development of Red Listing, conclude by suggesting areas where additional research could be valuable in improving the understanding of extinction risk among species.

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Exploring evolutionary relationships across the genome using topology weighting

10.1101/069112 ◽

2016 ◽

Cited By ~ 2

Author(s):

Simon H. Martin ◽

Steven M. Van Belleghem

Keyword(s):

Genomic Data ◽

Evolutionary Relationships ◽

Genomic Dataset ◽

Link Type ◽

Iterative Sampling ◽

Multiple Sequences

AbstractWe introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualising how these relationships change across the genome. A given set of taxa can be related in a limited number of ways, but if each taxon is represented by multiple sequences, the number of possible topologies becomes very large. Topology weighting reduces this complexity by quantifying the contribution of each ‘taxon topology’ to the full tree. We describe our method for topology weighting by iterative sampling of sub-trees (Twisst), and test it on both simulated and real genomic data. Overall, we show that this is an informative and versatile approach, suitable for exploring relationships in almost any genomic dataset.Scripts to implement the method described are available at github.com/simonhmartin/twisst.

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