Ancestral genetic legacy of the extant population of Argentina as predicted by autosomal and X-chromosomal DIPs

The fungal pathogen Batrachochytrium dendrobatidis (Bd) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, the Bd epidemic wave hypothesis is supported by detection of Bd in historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood. Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread of Bd. To determine the presence and infection intensity of Bd on C. magnipes and sympatric amphibian species (which are also Bd hosts), we used a noninvasive sampling technique and qPCR assay to detect Bd on museum specimens of C. magnipes collected from 1952 to 2012, and from extant populations of C. magnipes and sympatric species of amphibians. We also tested for the presence of the recently discovered Batrachochytrium salamandivorans (Bsal), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific for Bsal. We did not detect Bd in populations of C. magnipes before 1969, while Bd was detected at low to moderate prevalence just prior to and during declines. This pattern is consistent with Bd-caused epizootics followed by host declines and extirpations described in other hosts. We did not detect Bsal in any extant population of C. magnipes. We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with the Bd epidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage of Bd, but our genotyping of the historical positive samples was unsuccessful. The lack of large samples from some years and the difficulty in genotyping historical Bd samples illustrate some of the difficulties inherent in assigning causality to historical amphibian declines. These data also provide an important historical baseline for actions to preserve the few known remaining populations of C. magnipes.

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Rescuing Christensenia aesculifolia (Marattiaceae), a plant species with an extremely small population in China

Oryx ◽

10.1017/s003060531800039x ◽

2018 ◽

Vol 53 (3) ◽

pp. 436-438

Author(s):

Lei Cai ◽

Guiliang Zhang ◽

Jianying Xiang ◽

Zhiling Dao ◽

Weibang Sun

Keyword(s):

Plant Species ◽

Small Population ◽

Provincial Government ◽

South East Asia ◽

Small Populations ◽

Species Status ◽

Field Surveys ◽

Field Investigations ◽

Threatened Habitat ◽

Extant Population

AbstractThe rare and threatened fern Christensenia aesculifolia of South-east Asia is listed in China as a second-ranked plant for national protection and is also categorized as one of 62 plant species with extremely small populations by the Yunnan provincial government. Field investigations during 2014–2017 failed to relocate one previously known population, and revealed that the single known extant population of C. aesculifolia contains only 10 individual plants. The most urgent conservation requirement for this species is to conserve the threatened habitat of the remnant population. Further field surveys and research are also required for an improved understanding of the species’ status.

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Factors affecting nest-site selection and nest success of translocated greater sage grouse

Wildlife Research ◽

10.1071/wr07185 ◽

2009 ◽

Vol 36 (6) ◽

pp. 479 ◽

Cited By ~ 5

Author(s):

Rick J. Baxter ◽

Jerran T. Flinders ◽

David G. Whiting ◽

Dean L. Mitchell

Keyword(s):

Nest Success ◽

Nest Site Selection ◽

Habitat Characteristics ◽

Theoretic Approach ◽

Embryo Viability ◽

Sage Grouse ◽

Crown Area ◽

Nest Sites ◽

Extant Population

Translocations have been used for decades to restore or augment wildlife populations, yet more often than not, little to no data and/or arbitrary means are used for determining translocation success. The objectives of our study were to describe nesting habitat utilised by the greater sage grouse translocated into an extant population and to identify factors related to nest success, thereby demonstrating the adaptability of the birds to their new environment and producing one measure of long-term translocation success. We trapped female grouse individuals during the spring on and near leks of source populations, fitted them with radio-transmitters, and released them in the morning onto an active lek in an extant population in Strawberry Valley, Utah. We monitored translocated females for nesting activity and documented nesting attempts, nest success, clutch size and embryo viability. Data were recorded on habitat variables associated with nest sites and paired-random sites, including factors known to be important for resident females that nested successfully. We used logistic regression and an a priori information-theoretic approach for modelling nest v. paired-random sites and successful v. unsuccessful nest sites. Our analyses suggested that crown area of the nest shrub and percentage grass cover were the two variables that discriminated between nest and paired-random sites. Females that nested successfully selected sites with more total shrub canopy cover, intermediate size-shrub crown area, aspects other than NW and SE, and steeper slopes than for unsuccessful nests. After being translocated from distant sites with differing habitat characteristics, these birds were able to initiate a nest, nest successfully, and select micro-habitat features similar to those selected by resident sage grouse across the species range. Our results demonstrate the adaptability of the translocated female sage grouse individuals and produce one tangible measure of long-term translocation success.

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Reconstructing the invasion route of DNA transposons using extant population samples

10.1101/729889 ◽

2019 ◽

Author(s):

Lukas Weilguny ◽

Christos Vlachos ◽

Divya Selvaraju ◽

Robert Kofler

Keyword(s):

P Element ◽

Model Organisms ◽

Migration Patterns ◽

Dna Transposons ◽

Time Points ◽

Wide Range ◽

Invasion Routes ◽

Geographic Regions ◽

Extant Population ◽

Shed Light

AbstractReconstructing invasion routes of transposable elements (TEs), so far, required capturing an ongoing invasion with population samples from different geographic regions and time points. Here, we propose a more accessible approach. Abundantly occurring internal deletions of DNA transposons allow to trace the direction as well as the path of an invasion, even hundreds of generations after the spread of a TE. We validated this hypothesis with computer simulations and by accurately reproducing the route of the P-element invasion in Drosophila melanogaster. Finally, we used our method to shed light on the controversial hobo invasion in D. melanogaster. Our approach solely requires sequenced samples from extant populations and sequences of TEs of interest. Hence, DNA transposons in a wide range of model and non-model organisms may be analyzed. Our approach will further our understanding of TE dynamics, migration patterns, and the ecology of species.

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Evaluation of two extant population sources of Clarias macrocephalus using liver transcriptomic profiles towards reintroduction

Israeli Journal of Aquaculture - Bamidgeh ◽

10.46989/001c.19030 ◽

2020 ◽

Author(s):

July B. Ariñez ◽

Apple G. Deallo ◽

Barry L.M. Tumbokon ◽

Augusto E. Serrano, Jr.

Keyword(s):

Clarias Macrocephalus ◽

Extant Population

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SimBA: simulation algorithm to fit extant-population distributions

BMC Bioinformatics ◽

10.1186/s12859-015-0525-0 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 3

Author(s):

Laxmi Parida ◽

Niina Haiminen

Keyword(s):

Simulation Algorithm ◽

Population Distributions ◽

Extant Population

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New populations of pampas deer Ozotoceros bezoarticus discovered in threatened Amazonian savannah enclaves

Oryx ◽

10.1017/s0030605318001539 ◽

2019 ◽

Vol 53 (4) ◽

pp. 748-751

Author(s):

Daniel G. Rocha ◽

Alexandre Vogliotti ◽

Diogo M. Gräbin ◽

Wilhan R. C. Assunção ◽

Bruno Contursi Cambraia ◽

...

Keyword(s):

Population Dynamics ◽

Genetic Structure ◽

Spatial Genetic Structure ◽

Conservation Status ◽

Red List ◽

Camera Traps ◽

Amazon Forest ◽

Ozotoceros Bezoarticus ◽

Extant Population ◽

Historical Range

AbstractThe savannah enclaves (i.e. patches) in the southern Brazilian Amazonia are among the most threatened and poorly surveyed sites in Amazonia. As part of an extensive mammal survey, we set camera traps in three of these savannah enclaves. We obtained 23 independent records of pampas deer Ozotoceros bezoarticus, a medium sized Neotropical cervid that is strongly associated with open habitats and categorized as Vulnerable on the Brazilian Red List of threatened species. These savannah enclaves with confirmed populations of pampas deer lie outside the species’ previously presumed historical range and are at least 350 km from any known extant population. Together, these savannah enclaves add c. 4,000 km2 to the pampas deer's currently known range. The small pampas deer populations in these enclaves are probably isolated by a matrix of Amazon forest, raising questions about spatial genetic structure and meta-population dynamics, and making them vulnerable to local extinction. We highlight the need for further studies, particularly genetic, to assess the conservation status of these populations, the results of which could potentially inform management decisions in other areas of the heavily fragmented range of this species.

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The use of grafted seedlings increases the success of conservation translocations of Manglietia longipedunculata (Magnoliaceae), a Critically Endangered tree

Oryx ◽

10.1017/s0030605315000423 ◽

2015 ◽

Vol 50 (3) ◽

pp. 437-445 ◽

Cited By ~ 5

Author(s):

Hai Ren ◽

Hong Liu ◽

Jun Wang ◽

Lianlian Yuan ◽

Xiaodong Cui ◽

...

Keyword(s):

Climate Change ◽

Critically Endangered ◽

Physiological Data ◽

Water Usage ◽

Flowering Stage ◽

Endangered Tree ◽

Physiological Properties ◽

Short Period ◽

Number Of Individuals ◽

Extant Population

AbstractThe distribution of the Critically Endangered tree Manglietia longipedunculata, of which there are only 11 known wild individuals, is restricted to the Nankunshan Nature Reserve in South China. The species is threatened with extinction because of its small number of individuals and the impediments to its reproduction (a combination of protogyny, a short period of stigma receptivity, and a lack of efficient pollinators). To reduce the risk of extinction we conducted two conservation translocation trials: one to augment the sole extant population, and the other 202 km north of the current range. The latter trial was a conservation introduction in which the goals were to increase the population and to buffer against the effects of climate change. We used emerged and grafted seedlings as translocation materials. We compared the survival, growth, and eco-physiological properties of emerged and grafted seedlings at the two sites. The survival rate and growth were higher for grafted seedlings than for emerged seedlings at both sites. Eco-physiological data indicated that grafted seedlings at both sites were as efficient or more so in light and water usage than wild individuals, whereas emerged seedlings were less efficient. Grafted seedlings attained the flowering stage sooner than emerged seedlings. Our study suggests that grafting can facilitate the augmentation and establishment of new populations of M. longipedunculata and perhaps of new populations of other threatened species facing reproductive difficulties and climate change.

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Status of the largest extant population of the critically endangered Aeolian lizard Podarcis raffonei (Capo Grosso, Vulcano island)

PLoS ONE ◽

10.1371/journal.pone.0253631 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0253631

Author(s):

Gentile Francesco Ficetola ◽

Iolanda Silva-Rocha ◽

Miguel A. Carretero ◽

Leonardo Vignoli ◽

Roberto Sacchi ◽

...

Keyword(s):

Mixture Models ◽

Monitoring Program ◽

Colour Pattern ◽

Single Male ◽

Vulcano Island ◽

Island Endemic ◽

Parallel Increase ◽

Podarcis Siculus ◽

Removal Sampling ◽

Extant Population

The Aeolian wall lizard Podarcis raffonei is an island endemic that survives only on three tiny islets, and on the Capo Grosso peninsula of the Vulcano island, thus is among the European vertebrates with the smallest range and one of the most threatened by extinction. This species is declining due to competition and hybridization with the non-native lizard Podarcis siculus, but a regular monitoring program is lacking. Here we assessed the size and status of the Capo Grosso population of P. raffonei on Vulcano. In September 2015 we captured 30 individuals showing the typical brown phenotype of P. raffonei, while one single male showed a green phenotype, apparently intermediate between P. raffonei and the non-native Podarcis siculus. In May 2017, only 47% of 131 individuals showed the typical brown phenotype (P. raffonei-like) and 53% showed the green phenotype (P. siculus-like). Based on N-mixture models and removal sampling the estimated size of the Capo Grosso population was of 800–1300 individuals in 2017, being similar to 2015; available data suggest that the total range of the species could be as small as 2 ha. The frequency of individuals with the typical P. raffonei phenotype dramatically dropped between two samplings with a parallel increase of individuals displaying the green phenotype. Observation on outdoor captive-bred individuals demonstrates plasticity for colouration in P. raffonei individuals from Capo Grosso, with several individuals showing the typical brown pattern in September 2017 and a green pattern in March 2021. Non-exclusive hypotheses, including hybridization with P. siculus and plasticity in colour pattern of P. raffonei, are discussed to explain the phenotypic shifts of the P. raffonei population of Capo Grosso. While genomic evidence is required to reach conclusions and investigate eventual hybridization, it is urgent to undertake a programme for the monitoring and management of this lizard.

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A century of decline: loss of genetic diversity in a southern African lion-conservation stronghold

10.1101/474940 ◽

2018 ◽

Author(s):

Simon G. Dures ◽

Chris Carbone ◽

Andrew J. Loveridge ◽

Glyn Maude ◽

Neil Midlane ◽

...

Keyword(s):

Genetic Diversity ◽

Protected Areas ◽

Large Scale ◽

Species Conservation ◽

Allelic Diversity ◽

Rapid Decline ◽

Conservation Area ◽

African Lion ◽

Loss Of Genetic Diversity ◽

Extant Population

AbstractAimThere is a dearth of evidence that determines the genetic diversity of populations contained within present-day protected areas compared with their historic state prior to large-scale species declines, making inferences about a species’ conservation genetic status difficult to assess. The aim of this paper is to demonstrate the use of historic specimens to assess the change in genetic diversity over a defined spatial area.LocationLike other species, African lion populations (Panthera leo) are undergoing dramatic contractions in range and declines in numbers, motivating the identification of a number of lion conservation strongholds across East and southern Africa. We focus on one such stronghold, the Kavango-Zambezi transfrontier conservation area (KAZA) of Botswana, Namibia, Zambia and Zimbabwe.MethodsWe compare genetic diversity between historical museum specimens, collected during the late 19th and early 20th century, with samples from the modern extant population. We use 16 microsatellite markers and sequence 337 base pairs of the hypervariable control region (HVR1) of the mitochondrial genome. We use bootstrap resampling to allow for comparisons between the historic and modern data.ResultsWe show that the genetic diversity of the modern population was reduced by 12% to 17%, with a reduction in allelic diversity of approximately 15%, compared to historic populations, in addition to having lost a number of mitochondrial haplotypes. We also identify reduced allelic diversity and a number of ‘ghost alleles’ in the historical samples no longer present in the extant population.Main ConclusionsWe argue a rapid decline in allelic richness after 1895 suggests the erosion of genetic diversity coincides with the rise of a European colonial presence and the outbreak of rinderpest in the region. Our results support the need to improved connectivity between protected areas in order to prevent further loss of genetic diversity in the region.

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