scholarly journals Who’s who in the western Hermann’s tortoise conservation: a STR toolkit and reference database for wildlife forensic genetic analyses

2018 ◽  
Author(s):  
Biello Roberto ◽  
Zampiglia Mauro ◽  
Corti Claudia ◽  
Deli Gianluca ◽  
Biaggini Marta ◽  
...  
Keyword(s):  
Dna Typing ◽  
Geographic Origin ◽  
Unknown Origin ◽  
Reference Database ◽  
Illegal Trade ◽  
Wild Populations ◽  
Long Distance ◽  
Testudo Hermanni ◽  
Forensic Genetic ◽  
Area Of Origin

ABSTRACTIllegal trade is threatening tortoise populations worldwide since decades. Nowadays, however, DNA typing and forensic genetic approaches allow to investigate geographic origin of confiscated animals and to relocate them into the wild, provided that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise Testudo hermanni hermanni. We used the microsatellite panel to (i) increase the understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70% of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origin of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show the role for reintroduction projects of the microsatellite panel, which was useful to re-assign most of the confiscated individuals to the respective macro-area of origin. At the same time, the microsatellite panel can assist future forensic genetic applications to detect illegal trade and possess of Testudo hermanni individuals.

scholarly journals Genetic Assignment Tests to Identify the Probable Geographic Origin of a Captive Specimen of Military Macaw (Ara militaris) in Mexico: Implications for Conservation

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 245
Author(s):  
Francisco A. Rivera-Ortíz ◽  
Jessica Juan-Espinosa ◽  
Sofía Solórzano ◽  
Ana M. Contreras-González ◽  
María del C. Arizmendi
Keyword(s):  
Genetic Markers ◽  
Geographic Origin ◽  
Unknown Origin ◽  
Positive Control ◽  
Reference Database ◽  
Genetic Assignment ◽  
Sierra Madre Oriental ◽  
Assignment Tests ◽  
Sierra Madre ◽  
Positive Controls

The Military Macaw (Ara militaris) faces a number of serious conservation threats. The use of genetic markers and assignment tests may help to identify the geographic origin of captive individuals and improve conservation and management programs. The purpose of this study was to identify the possible geographic origin of a captive individual using genetic markers. We used a reference database of genotypes of 86 individuals previously shown to belong to two different genetic groups to determine the genetic assignment of the captive individual of unknown origin (captive specimen) and five individuals of known geographic origin (as positive controls). We evaluated the accuracy of three assignment/exclusion criteria to determine the success of correct assignment of the individual of unknown origin and the five positive control individuals. WICHLOCI estimated that eight loci were required to achieve an assignment success of 83%. The correct geographic origin of positive controls was identified with 83% confidence. All of the analyses assigned the captive individual to the genetic group from the Sierra Madre Oriental. Bayesian assignment tests, tests for genetic distance and allele frequency tests assigned the unknown individual to the locations from the Sierra Madre Oriental with a probability of 71.2–82.4%. We show that the use of genetic markers provides a promising tool for determining the origin of pets and individuals seized from the illegal animal trade to better inform decisions on reintroduction and improve conservation programs.

scholarly journals From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

2021 ◽  
Author(s):  
Roberto Biello ◽  
Mauro Zampiglia ◽  
Silvia Fuselli ◽  
Giulia Fabbri ◽  
Roberta Bisconti ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Low Cost ◽  
Geographic Origin ◽  
Unknown Origin ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
In The Wild ◽  
Testudo Hermanni ◽  
Source Populations

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3,182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.

Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

BMC Zoology ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gabriela Padilla-Jacobo ◽  
Tiberio C. Monterrubio-Rico ◽  
Horacio Cano-Camacho ◽  
María Guadalupe Zavala-Páramo
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Coastal Region ◽  
Central American ◽  
Illegal Trade ◽  
Wild Populations ◽  
High Genetic Diversity ◽  
Genealogical Relationship ◽  
Genetic Pool

Abstract Background The Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets. Results Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico. Conclusions Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

scholarly journals Morphological Traits and Phenolic Compounds in Tunisian Wild Populations and Cultivated Varieties of Portulaca oleracea L.

Agronomy ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 948 ◽  
Author(s):  
Dorra Sdouga ◽  
Ferdinando Branca ◽  
Souhir Kabtni ◽  
Maria Concetta Di Bella ◽  
Neila Trifi-Farah ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Geographic Origin ◽  
Sinapic Acid ◽  
Principal Component ◽  
Portulaca Oleracea ◽  
Array Detector ◽  
Wild Populations ◽  
Antioxidant Power ◽  
Morphological Heterogeneity ◽  
Freeze Dried

This study aims to evaluate the bio-morphological and biochemical variability of three Tunisian wild populations and one growing cultivar of purslane (Portulaca oleracea L.). The studied varieties should be easily distinguished by the color and the habitus of the plant as mentioned in literature, but the various analyses have shown a strong morphological heterogeneity within and among the wild and cultivated accessions as presented by the variance analysis test (ANOVA) and the PCA (Principal component analysis). We found high intrapopulation variability through the wild populations that make it hard to differentiate them only on the base of morphology. We analyzed the biochemical profile of those populations based on the analysis of freeze-dried samples of leaves and stems. We identified and quantified twelve different phenolic compounds by the HPLC-diode array detector (DAD) technique. Six phenolic acids and flavonoids were identified in the leaves and stems of the wild and cultivated populations. Sinapic acid and myricetin are the majors identified compounds through our samples. The results were significantly different in relation to the plant organs and to the geographic origin for most of the compounds. The obtained results highlighted the importance of Portulaca as a medicinal plant by showing its richness in phenols and flavonoids that have multi-medicinal effects besides their antioxidant power.

scholarly journals Complete Genome Analysis of 33 Ecologically and Biologically Diverse Rift Valley Fever Virus Strains Reveals Widespread Virus Movement and Low Genetic Diversity due to Recent Common Ancestry

2006 ◽  
Vol 81 (6) ◽  
pp. 2805-2816 ◽  
Author(s):  
Brian H. Bird ◽  
Marina L. Khristova ◽  
Pierre E. Rollin ◽  
Thomas G. Ksiazek ◽  
Stuart T. Nichol
Keyword(s):  
Genetic Diversity ◽  
Rift Valley ◽  
Complete Genome ◽  
Rift Valley Fever ◽  
Geographic Origin ◽  
Recent Common Ancestor ◽  
Virus Movement ◽  
Long Distance ◽  
Valley Fever ◽  
Virus Strains

ABSTRACT Rift Valley fever (RVF) virus is a mosquito-borne RNA virus responsible for large explosive outbreaks of acute febrile disease in humans and livestock in Africa with significant mortality and economic impact. The successful high-throughput generation of the complete genome sequence was achieved for 33 diverse RVF virus strains collected from throughout Africa and Saudi Arabia from 1944 to 2000, including strains differing in pathogenicity in disease models. While several distinct virus genetic lineages were determined, which approximately correlate with geographic origin, multiple exceptions indicative of long-distance virus movement have been found. Virus strains isolated within an epidemic (e.g., Mauritania, 1987, or Egypt, 1977 to 1978) exhibit little diversity, while those in enzootic settings (e.g., 1970s Zimbabwe) can be highly diverse. In addition, the large Saudi Arabian RVF outbreak in 2000 appears to have involved virus introduction from East Africa, based on the close ancestral relationship of a 1998 East African virus. Virus genetic diversity was low (∼5%) and primarily involved accumulation of mutations at an average of 2.9 × 10−4 substitutions/site/year, although some evidence of RNA segment reassortment was found. Bayesian analysis of current RVF virus genetic diversity places the most recent common ancestor of these viruses in the late 1800s, the colonial period in Africa, a time of dramatic changes in agricultural practices and introduction of nonindigenous livestock breeds. In addition to insights into the evolution and ecology of RVF virus, these genomic data also provide a foundation for the design of molecular detection assays and prototype vaccines useful in combating this important disease.

Nothing to laugh about – the ongoing illegal trade in laughingthrushes (Garrulax species) in the bird markets of Java, Indonesia

2016 ◽  
Vol 26 (4) ◽  
pp. 524-530 ◽  
Author(s):  
CHRIS R. SHEPHERD ◽  
JAMES A. EATON ◽  
SERENE C. L. CHNG
Keyword(s):  
Native Species ◽  
Ad Hoc ◽  
Conservation Status ◽  
Iucn Red List ◽  
Red List ◽  
Illegal Trade ◽  
Wild Populations ◽  
Protected Species ◽  
Species List ◽  
Numerous Species

SummaryIn ad hoc survey inventories of eight major bird markets in Java in 2014 and 2015, 615 individuals from nine species of the Garrulax genus were found for sale. The most numerous species was Sunda Laughingthrush Garrulax palliatus (215 individuals), followed by Chinese Hwamei G. canorus and Chestnut-capped Laughingthrush G. mitratus. Prices collected in Jakarta revealed that non-native species were the most expensive. Information from these and previous surveys indicate that prices for Sumatran Laughingthrush Garrulax bicolor appeared to have soared since 2007, suggesting increasing rarity of the species. We urge the Indonesian Government to take action against the illegal trade in laughingthrushes under existing laws, especially for the Rufous-fronted Laughingthrush Garrulax rufifrons which is listed on the national protected species list. We also recommend that the Sumatran Laughingthrush Garrulax bicolor be listed as a protected species under Indonesian law. As wild populations of Rufous-fronted Laughingthrush and Sumatran Laughingthrush are threatened by trade, we recommend an urgent review of the conservation status of both species on the IUCN Red List.

scholarly journals In vitro development of the Mexican endemic twig epiphyte Erycina hyalinobulbon (Orchidaceae) to promote its conservation

2021 ◽  
Author(s):  
José Tonatiuh Gutiérrez Zavala ◽  
Irebe Ávila Díaz ◽  
Rosa Elia Magaña Lemus
Keyword(s):  
Carbon Source ◽  
Culture Media ◽  
Low Cost ◽  
Illegal Trade ◽  
Wild Populations ◽  
Short Life ◽  
In Vitro Development ◽  
Basal Salts ◽  
Vitro Development

Background and Aims: Orchids in Mexico are mainly threatened by deforestation, changes in land use, illegal trade, deficiencies in environmental policy and legislation, and a lack of community participation in the conservation of their forests. Erycina hyalinobulbon is an endemic twig epiphyte orchid with a short life cycle and with large flowers in relation to its size, for which it has been harvested from its wild populations. The objectives of this work were to evaluate the in vitro development of E. hyalinobulbon in culture media with organic supplements, to compare sucrose vs. N’Joy Stevia® as a carbon source for its initial stages of development, and to evaluate the development of its seedlings in media enriched with plant growth regulators (PGR).Methods: For the sowing of seeds, PhytamaxTM and MS medium at 30% of its basal salts were used in combination with organic supplement (coconut milk, pineapple puree and banana puree), along with the Phy medium used as control. In order to measure the effect of sucrose vs. N´Joy Stevia® as a carbon source, these two treatments were used, with the PhytamaxTM medium. To evaluate the development of seedlings with PGR, three treatments were tested: the 100% PhytamaxTM control, 30% PhytamaxTM with 1.166 ml/l of Maxi-grow and the medium Chiu.Key results: PhytamaxTM medium added with banana promoted germination by 9.3%, being a low cost and easy production option. Ninety days after sowing, N´Joy Stevia® as a carbon source promoted germination by 8%. The best development of the seedlings was registered in the medium PhytamaxTM without PGR.Conclusions: With this study, it was possible to develop an accessible in vitro propagation system for E. hyalinobulbon, in order to sustainably manage it and favor its conservation.

scholarly journals Spatial and temporal invasion dynamics of the 2014–2017 Zika and chikungunya epidemics in Colombia

2021 ◽  
Vol 17 (7) ◽  
pp. e1009174
Author(s):  
Kelly Charniga ◽  
Zulma M. Cucunubá ◽  
Marcela Mercado ◽  
Franklyn Prieto ◽  
Martha Ospina ◽  
...  
Keyword(s):  
Zika Virus ◽  
Temporal Dynamics ◽  
Virus Disease ◽  
Geographic Distance ◽  
Geographic Origin ◽  
Gravity Models ◽  
Long Distance ◽  
Spatial Spread ◽  
Invasion Dynamics ◽  
Logistic Regression Models

Zika virus (ZIKV) and chikungunya virus (CHIKV) were recently introduced into the Americas resulting in significant disease burdens. Understanding their spatial and temporal dynamics at the subnational level is key to informing surveillance and preparedness for future epidemics. We analyzed anonymized line list data on approximately 105,000 Zika virus disease and 412,000 chikungunya fever suspected and laboratory-confirmed cases during the 2014–2017 epidemics. We first determined the week of invasion in each city. Out of 1,122, 288 cities met criteria for epidemic invasion by ZIKA and 338 cities by CHIKV. We analyzed risk factors for invasion using linear and logistic regression models. We also estimated that the geographic origin of both epidemics was located in Barranquilla, north Colombia. We assessed the spatial and temporal invasion dynamics of both viruses to analyze transmission between cities using a suite of (i) gravity models, (ii) Stouffer’s rank models, and (iii) radiation models with two types of distance metrics, geographic distance and travel time between cities. Invasion risk was best captured by a gravity model when accounting for geographic distance and intermediate levels of density dependence; Stouffer’s rank model with geographic distance performed similarly well. Although a few long-distance invasion events occurred at the beginning of the epidemics, an estimated distance power of 1.7 (95% CrI: 1.5–2.0) from the gravity models suggests that spatial spread was primarily driven by short-distance transmission. Similarities between the epidemics were highlighted by jointly fitted models, which were preferred over individual models when the transmission intensity was allowed to vary across arboviruses. However, ZIKV spread considerably faster than CHIKV.

scholarly journals Natural epialleles of Arabidopsis SUPERMAN display superwoman phenotypes

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Ramesh Bondada ◽  
Saravanakumar Somasundaram ◽  
Mohan Premanand Marimuthu ◽  
Mohammed Afsal Badarudeen ◽  
Vaishak Kanjirakol Puthiyaveedu ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Epigenetic Regulation ◽  
Gene Function ◽  
Cytosine Methylation ◽  
Unknown Origin ◽  
Chromatin Modifications ◽  
Wild Populations ◽  
Dna Cytosine Methylation

AbstractEpimutations are heritable changes in gene function due to loss or gain of DNA cytosine methylation or chromatin modifications without changes in the DNA sequence. Only a few natural epimutations displaying discernible phenotypes are documented in plants. Here, we report natural epimutations in the cadastral gene, SUPERMAN(SUP), showing striking phenotypes despite normal transcription, discovered in a natural tetraploid, and subsequently in eleven diploid Arabidopsis genetic accessions. This natural lois lane(lol) epialleles behave as recessive mendelian alleles displaying a spectrum of silent to strong superwoman phenotypes affecting only the carpel whorl, in contrast to semi-dominant superman or supersex features manifested by induced epialleles which affect both stamen and carpel whorls. Despite its unknown origin, natural lol epialleles are subjected to the same epigenetic regulation as induced clk epialleles. The existence of superwoman epialleles in diverse wild populations is interpreted in the light of the evolution of unisexuality in plants.

scholarly journals Multidisciplinary fingerprints: forensic reconstruction of an insect reinvasion

2009 ◽  
Vol 7 (45) ◽  
pp. 677-686 ◽  
Author(s):  
Kyung Seok Kim ◽  
Gretchen D. Jones ◽  
John K. Westbrook ◽  
Thomas W. Sappington
Keyword(s):  
Trajectory Analysis ◽  
Insect Pest ◽  
Geographic Origin ◽  
Tropical Storm ◽  
Anthonomus Grandis ◽  
Long Distance Dispersal ◽  
Forensic Evidence ◽  
Long Distance ◽  
Central Texas ◽  
Better Than

An unexpected outbreak of boll weevils, Anthonomus grandis , an insect pest of cotton, across the Southern Rolling Plains (SRP) eradication zone of west-central Texas, USA, was detected soon after passage of Tropical Storm Erin through the Winter Garden district to the south on 16 August 2007. The synchrony and broad geographic distribution of the captured weevils suggest that long-distance dispersal was responsible for the reinvasion. We integrated three types of assessment to reconstruct the geographic origin of the immigrants: (i) DNA fingerprinting; (ii) pollen fingerprinting; and (iii) atmospheric trajectory analysis. We hypothesized the boll weevils originated in the Southern Blacklands zone near Cameron, or in the Winter Garden district near Uvalde, the nearest regions with substantial populations. Genetic tests broadly agree that the immigrants originated southeast of the SRP zone, probably in regions represented by Uvalde or Weslaco. The SRP pollen profile from weevils matched that of Uvalde better than that of Cameron. Wind trajectories supported daily wind-aided dispersal of weevils from the Uvalde region to the SRP from 17 to 24 August, but failed to support migration from the Cameron region. Taken together the forensic evidence strongly implicates the Winter Garden district near Uvalde as the source of reinvading boll weevils.

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