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1.
PLoS One ; 19(4): e0300383, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38574082

RESUMO

Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple "yes" or "no" result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.


Assuntos
Tubarões , Animais , Tubarões/genética , Espécies em Perigo de Extinção , Alimentos Marinhos , Carne , DNA/genética
2.
Animals (Basel) ; 13(6)2023 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-36978581

RESUMO

The survival of endangered felids is becoming increasingly dependent on the successful management and breeding of reserve populations in captivity. While most felid species are reported to be solitary in the wild, increasing evidence suggests that some big cats have greater social plasticity than is currently acknowledged. This social plasticity allows felids to be sometimes socially housed in environments such as zoos and rescue centers. While the effects of such shared enclosures remain in question, many reports provide evidence of several welfare benefits of maintaining these large carnivores in pairs or even groups. Since 2019, Le Parc des Félins has housed a breeding pair of Malaysian tigers (Panthera tigris jacksoni) alongside their offspring. The purpose of this study was to quantify the social affiliation between the male tiger and his cubs and to investigate the female's tolerance toward him. The data were collected using video recordings in the outdoor enclosure when social interactions were observed. The data were coded and categorized in the open-source software BORIS, from which behavioral activity budgets were calculated. Data were analyzed using the chi-squared test for association to determine differences in affiliative frequency, with directed and undirected sociograms created to visualize individual relationships. Overall, the male regularly engaged in affiliative behaviors with the cubs, with no significant difference found in the frequency of interactions with them compared to the female. No physical aggression was directed by the male toward the cubs. Although the female maintained a stronger bond with the cubs compared to the male, he displayed a greater range of affiliative behaviors toward them than male tigers are thought to exhibit. Both adults showed a high degree of tolerance toward their conspecifics, suggesting that maintaining breeding pairs with their offspring is a viable management strategy in zoological collections. This study could therefore improve husbandry and conservation practices by developing our understanding of felid sociality and the potential welfare benefits of social housing, allowing for evidence-based captive management decisions.

3.
Ecol Evol ; 12(11): e9490, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-36381392

RESUMO

Growth in the global development of cities, and increasing public interest in beekeeping, has led to increase in the numbers of urban apiaries. Towns and cities can provide an excellent diet for managed bees, with a diverse range of nectar and pollen available throughout a long flowering season, and are often more ecologically diverse than the surrounding rural environments. Accessible urban honeybee hives are a valuable research resource to gain insights into the diet and ecology of wild pollinators in urban settings. We used DNA metabarcoding of the rbcL and ITS2 gene regions to characterize the pollen community in Apis mellifera honey, inferring the floral diet, from 14 hives across an urban gradient around Greater Manchester, UK. We found that the proportion of urban land around a hive is significantly associated with an increase in the diversity of plants foraged and that invasive and non-native plants appear to play a critical role in the sustenance of urban bees, alongside native plant species. The proportion of improved grassland, typical of suburban lawns and livestock farms, is significantly associated with decreases in the diversity of plant pollen found in honey samples. These findings are relevant to urban landscape developers motivated to encourage biodiversity and bee persistence, in line with global bio-food security agendas.

4.
PLoS One ; 17(9): e0274895, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36170271

RESUMO

Coral reefs species represent one-third of all marine species described in the ocean. They are also responsible for providing habitat and support to different species. Recently, Caribbean coral reefs ecosystems have suffered an alarming decrease in their populations as a result of overexploitation. Madracis auretenra in particular, is a widespread shallow coral in marine protected areas (MPAs) of the Caribbean. Due to the important role of MPAs as a biodiversity conservation tool, this species can be used as a model to estimate its dispersion/migration among Caribbean reefs through the use of informative genetic markers (microsatellites) specifically designed for it. Seventeen new polymorphic microsatellites markers for M. auretenra were developed and tested in 330 samples from Colombia, Guatemala, Curacao and Barbados. The gene diversity (1-D) ranged from 0.482 to 0.903, while the evenness ranged from 0.456 to 0.884 after clone removal. The expected heterozygosity (He) ranged from 0.347 to 0.742, while the observed heterozygosity (Ho) ranged from 0.078 to 0.578. The specificity of our microsatellites shows the potential use of these markers in a-posteriori analysis to detect population structure at different spatial scales, where M. auretenra is reported.


Assuntos
Antozoários , Animais , Antozoários/genética , Região do Caribe , Recifes de Corais , Ecossistema , Marcadores Genéticos , Repetições de Microssatélites/genética
5.
Sci Rep ; 12(1): 13193, 2022 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-35915204

RESUMO

In 2013 Colombia made an important step towards the construction and management of Marine Protected Areas (MPAs) by establishing the first Deep Corals National Park (PNNCP). Inside this MPA, the coral Madracis myriaster (Cnidaria: Pocilloporidae) was found as the main reef builder, offering habitat for many species of fish and invertebrates. In order to improve the study of deep-sea coral habitats, their connectivity and prospective management, nine new genetic markers (microsatellites) were developed for M. myriaster and tested in samples from PNNCP. We present the assessment of these markers, with a specificity for the deep coral, and its prospective use in future analysis for the PNNCP and other areas in the Caribbean and the Atlantic, where M. myriaster is reported. We also include an additional taxonomic analysis performed on samples of M. myriaster using scanning electron microscopy.


Assuntos
Antozoários , Animais , Antozoários/genética , Recifes de Corais , Ecossistema , Peixes , Invertebrados , Repetições de Microssatélites/genética
6.
Commun Biol ; 5(1): 770, 2022 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-35908086

RESUMO

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0-30%). Fish gut microbiomes were significantly more variable at degraded reefs, a pattern driven by changes in the relative abundance of the most common taxa potentially associated with stress. We also demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which may suggest a less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions may be vulnerable to severe coral degradation.


Assuntos
Antozoários , Microbioma Gastrointestinal , Microbiota , Animais , Bactérias/genética , Peixes
7.
Ecol Evol ; 12(4): e8744, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35386872

RESUMO

Over the last 20 years, ecological restoration of degraded habitats has become common in conservation practice. Mountain hares (Lepus timidus scoticus) were surveyed during 2017-2021 using 830 km of line transects in the Peak District National Park, England. Historically degraded bog areas were previously reported having low hare numbers. Following bog restoration, we found hare densities of 32.6 individuals km-2, notably higher than neighboring degraded (unrestored) bog with 24.4 hares km-2. Hare density on restored peatland was 2.7 times higher than on bogs managed for grouse shooting at 12.2 hares km-2 and 3.3 times higher than on heather moorland managed for grouse shooting at 10.0 hares km-2. Yearly estimates varied most on habitats managed for grouse, perhaps indicative of the impact of habitat management, for example, heather burning and/or possible hare culling to control potential tick-borne louping ill virus in gamebirds. Acid grassland used for sheep farming had a similar density to grouse moorland at 11.8 hares km-2. Unmanaged dwarf shrub heath had the lowest density at 4.8 hares km-2. Hare populations are characterized by significant yearly fluctuations, those in the study area increasing by 60% between 2017 and 2018 before declining by ca. 15% by 2020 and remaining stable to 2021. During an earlier survey in 2002, total abundance throughout the Peak District National Park was estimated at 3361 (95% CI: 2431-4612) hares. The present study estimated 3562 (2291-5624) hares suggesting a stable population over the last two decades despite fluctuations likely influenced by weather and anthropogenic factors. Mountain hares in the Peak District favored bog habitats and were associated with restored peatland habitat. Wildlife management should be cognizant of hare density variation between habitats, which may have implications for local extinction risk.

8.
Sci Rep ; 12(1): 1695, 2022 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-35105909

RESUMO

Mangroves form coastal tropical forests in the intertidal zone and are an important component of shoreline protection. In comparison to other tropical forests, mangrove stands are thought to have relatively low genetic diversity with population genetic structure gradually increasing with distance along a coastline. We conducted genetic analyses of mangrove forests across a range of spatial scales; within a 400 m2 parcel comprising 181 Rhizophora mangle (red mangrove) trees, and across four sites ranging from 6-115 km apart in Honduras. In total, we successfully genotyped 269 R. mangle trees, using a panel of 677 SNPs developed with 2b-RAD methodology. Within the 400 m2 parcel, we found two distinct clusters with high levels of genetic differentiation (FST = 0.355), corresponding to trees primarily located on the seaward fringe and trees growing deeper into the forest. In contrast, there was limited genetic differentiation (FST = 0.027-0.105) across the sites at a larger scale, which had been predominantly sampled along the seaward fringe. Within the 400 m2 parcel, the cluster closest to the seaward fringe exhibited low genetic differentiation (FST = 0.014-0.043) with the other Honduran sites, but the cluster further into the forest was highly differentiated from them (FST = 0.326-0.414). These findings contradict the perception that genetic structure within mangroves forests occurs mainly along a coastline and highlights that there is greater genetic structure at fine spatial scales.

9.
Animals (Basel) ; 12(4)2022 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-35203127

RESUMO

Human-animal interaction (HAI) can be valuable for captive animals, and many zoo-housed species benefit from interactions with their keepers. There is also an increasing body of evidence that some animal species possess personalities that are temporally consistent. However, the majority of zoo research, particularly on personality and HAI, traditionally has focused on mammals, and there are comparatively fewer studies on reptiles. Research was undertaken at the Faunistic Park Le Cornelle, Italy, to investigate the effects of approach tests and food interaction events on 5 male and 5 female Aldabra tortoise (Aldrabrachelys gigantea) behavior. During human-tortoise interactions, continuous focal sampling of behavior took place. The behavioral differences between individual tortoises, interaction type (approach or training) and person involved in the interaction (keeper, vet, or observer) were analysed using general linear mixed-effects models. The personality components of the tortoises were also quantified using principal component analysis. Overall, the study revealed that individuals acted significantly differently to one another, and that while females initially appeared to display a greater number of shy behaviors, this was not consistent across the group. PCA revealed two personality dimensions in the tortoises: boldness and avoidance. Overall, the study revealed that the tortoises possessed personalities that were independent of sex or scenario. The study also revealed that many tortoises chose to interact with their keepers during training and approach tests: this suggests that human-tortoise interactions may have some enrichment value. Future research could quantify tortoise personality in other scenarios such as in social interactions with other tortoises.

10.
Proc Biol Sci ; 288(1957): 20210552, 2021 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-34403636

RESUMO

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.


Assuntos
Microbiota , Micobioma , Animais , Bactérias/genética , Interações entre Hospedeiro e Microrganismos , Filogenia
11.
Am J Bot ; 108(8): 1331-1342, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34458987

RESUMO

PREMISE: Host-plant genetic variation can shape associated communities of organisms. These community-genetic effects include (1) genetically similar hosts harboring similar associated communities (i.e., the genetic similarity rule) and (2) host-plant heterozygosity increasing associated community diversity. Community-genetic effects are predicted to be less prominent in plant systems with limited genetic variation, such as those at distributional range limits. Yet, empirical evidence from such systems is limited. METHODS: We sampled a natural population of a mangrove foundation species (Avicennia germinans) at an expanding range limit in Florida, USA. We measured genetic variation within and among 40 host trees with 24 nuclear microsatellite loci and characterized their foliar endophytic fungal communities with internal transcribed spacer (ITS1) gene amplicon sequencing. We evaluated relationships among host-tree genetic variation, host-tree spatial location, and the associated fungal communities. RESULTS: Genetic diversity was low across all host trees (mean: 2.6 alleles per locus) and associated fungal communities were relatively homogeneous (five sequence variants represented 78% of all reads). We found (1) genetically similar host trees harbored similar fungal communities, with no detectable effect of interhost geographic distance. (2) Host-tree heterozygosity had no detectable effect, while host-tree absolute spatial location affected community alpha diversity. CONCLUSIONS: This research supports the genetic similarity rule within a range limit population and helps broaden the current scope of community genetics theory by demonstrating that community-genetic effects can occur even at expanding distributional limits where host-plant genetic variation may be limited. Our findings also provide the first documentation of community-genetic effects in a natural mangrove system.


Assuntos
Avicennia , Avicennia/genética , Florida , Fungos/genética , Repetições de Microssatélites/genética , Plantas , Árvores
12.
Sci Rep ; 11(1): 3523, 2021 02 10.
Artigo em Inglês | MEDLINE | ID: mdl-33568733

RESUMO

Amongst the global decline of coral reefs, hope spots such as Cordelia Bank in Honduras, have been identified. This site contains dense, remnant thickets of the endangered species Acropora cervicornis, which local managers and conservation organizations view as a potential source population for coral restoration projects. The aim of this study was to determine the genetic diversity of colonies across three banks within the protected area. We identified low genetic diversity (FST = 0.02) across the three banks, and genetic similarity of colonies ranged from 91.3 to 95.8% between the banks. Clonality rates were approximately 30% across the three banks, however, each genotype identified was unique to each bank. Despite the low genetic diversity, subtle genetic differences within and among banks were demonstrated, and these dense thickets were shown not to be comprised of a single or a few genotypes. The presence of multiple genotypes suggests A. cervicornis colonies from these banks could be used to maintain and enhance genetic diversity in restoration projects. Management of hope spots, such as Cordelia Bank, and the incorporation of genetic information into restoration projects to ensure genetic diversity within out-planted populations, will be critical in the ongoing challenge of conserving and preserving coral reefs.


Assuntos
Antozoários/genética , Conservação dos Recursos Naturais , Estruturas Genéticas/genética , Dinâmica Populacional , Animais , Recifes de Corais , Espécies em Perigo de Extinção , Genótipo
13.
Heredity (Edinb) ; 126(1): 63-76, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32699391

RESUMO

Understanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.


Assuntos
Estruturas Genéticas , Oceanografia , Região do Caribe , Humanos
14.
Mar Pollut Bull ; 160: 111701, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33181965

RESUMO

This review represents a comprehensive analysis on pollutants in elasmobranchs including meta-analysis on the most studied pollutants: mercury, cadmium, PCBs and DDTs, in muscle and liver tissue. Elasmobranchs are particularly vulnerable to pollutant exposure which may pose a risk to the organism as well as humans that consume elasmobranch products. The highest concentrations of pollutants were found in sharks occupying top trophic levels (Carcharhiniformes and Lamniformes). A human health risk assessment identified that children and adults consuming shark once a week are exposed to over three times more mercury than is recommended by the US EPA. This poses a risk to local fishing communities and international consumers of shark-based products, as well as those subject to the widespread mislabelling of elasmobranch products. Wider screening studies are recommended to determine the risk to elasmobranchs from emerging pollutants and more robust studies are recommended to assess the risks to human health.


Assuntos
Elasmobrânquios , Poluentes Ambientais , Mercúrio , Tubarões , Rajidae , Poluentes Químicos da Água , Animais , Criança , Humanos , Mercúrio/análise , Alimentos Marinhos , Poluentes Químicos da Água/análise
15.
Mol Ecol ; 29(14): 2583-2597, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32573031

RESUMO

Expansion of many tree species lags behind climate change projections. Extreme storms can rapidly overcome this lag, especially for coastal species, but how will storm-driven expansion shape intraspecific genetic variation? Do storms provide recruits only from the nearest sources, or from more distant sources? Answers to these questions have ecological and evolutionary implications, but empirical evidence is absent from the literature. In 2017, Hurricane Irma provided an opportunity to address this knowledge gap at the northern range limit of the neotropical black mangrove (Avicennia germinans) on the Atlantic coast of Florida, USA. We observed massive post-hurricane increases in beach-stranded A. germinans propagules at, and past, this species' present day range margin when compared to a previously surveyed nonhurricane year. Yet, propagule dispersal does not guarantee subsequent establishment and reproductive success (i.e., effective dispersal). We also evaluated prior effective dispersal along this coastline with isolated A. germinans trees identified beyond the most northern established population. We used 12 nuclear microsatellite loci to genotype 896 hurricane-driven drift propagules from nine sites and 10 isolated trees from four sites, determined their sources of origin, and estimated dispersal distances. Almost all drift propagules and all isolated trees came from the nearest sources. This research suggests that hurricanes are a prerequisite for poleward range expansion of a coastal tree species and that storms can shape the expanding gene pool by providing almost exclusively range-margin genotypes. These insights and empirical estimates of hurricane-driven dispersal distances should improve our ability to forecast distributional shifts of coastal species.


Assuntos
Avicennia/genética , Tempestades Ciclônicas , Variação Genética , Mudança Climática , Florida , Repetições de Microssatélites , Dispersão Vegetal
16.
Animals (Basel) ; 10(2)2020 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-32085568

RESUMO

Etorphine-azaperone immobilisation was evaluated for translocation of Masai giraffes. Nine giraffes were darted with 0.012 ± 0.001 mg/kg etorphine and 0.07 ± 0.01 mg/kg azaperone. Once ataxic, giraffes were roped for recumbency and restrained manually. Naltrexone (3 mg/mg etorphine) was immediately given intravenously to reverse etorphine-related side effects. Protocol evaluation included physiological monitoring, blood-gas analyses, anaesthetic times, and quality scores (1 = excellent, 4 = poor). Sedation onset and recumbency were achieved in 2.6 ± 0.8 and 5.6 ± 1.4 min. Cardio-respiratory function (HR = 70 ± 16, RR = 32 ± 8, MAP = 132 ± 16) and temperature (37.8 ± 0.5) were stable. Arterial gas analysis showed hypoxaemia in some individuals (PaO2 = 67 ± 8 mmHg) and metabolic acidosis (pH = 7.23 ± 0.05, PaCO2 = 34 ± 4 mmHg, HCO3- = 12.9 ± 1.2 mmol/l). Minor startle response occurred, while higher induction-induced excitement correlated to longer inductions, worse restraint, and decreased HCO3-. After 19 ± 3.5 min of restraint, giraffes were allowed to stand and were loaded onto a chariot. Immobilisations were good and scored 2 (1-3). Inductions and recoveries were smooth and scored 1 (1-2). Translocations were uneventful and no complications occurred in 14-days boma follow-up.

17.
Mol Ecol ; 29(4): 704-719, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31990426

RESUMO

The central-marginal hypothesis (CMH) posits that range margins exhibit less genetic diversity and greater inter-population genetic differentiation compared to range cores. CMH predictions are based on long-held "abundant-centre" assumptions of a decline in ecological conditions and abundances towards range margins. Although much empirical research has confirmed CMH, exceptions remain almost as common. We contend that mangroves provide a model system to test CMH that alleviates common confounding factors and may help clarify this lack of consensus. Here, we document changes in black mangrove (Avicennia germinans) population genetics with 12 nuclear microsatellite loci along three replicate coastlines in the United States (only two of three conform to underlying "abundant-centre" assumptions). We then test an implicit prediction of CMH (reduced genetic diversity may constrain adaptation at range margins) by measuring functional traits of leaves associated with cold tolerance, the climatic factor that controls these mangrove distributional limits. CMH predictions were confirmed only along the coastlines that conform to "abundant-centre" assumptions and, in contrast to theory, range margin A. germinans exhibited functional traits consistent with greater cold tolerance compared to range cores. These findings support previous accounts that CMH may not be a general rule across species and that reduced neutral genetic diversity at range margins may not be a constraint to shifts in functional trait variation along climatic gradients.


Assuntos
Avicennia/genética , Ecossistema , Genética Populacional , Avicennia/crescimento & desenvolvimento , Mudança Climática , Fluxo Gênico/genética , Variação Genética/genética , Repetições de Microssatélites/genética
18.
Mol Ecol Resour ; 19(6): 1672-1680, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31339632

RESUMO

Bespoke microsatellite marker panels are increasingly affordable and tractable to researchers and conservationists. The rate of microsatellite discovery is very high within a shotgun genomic data set, but extensive laboratory testing of markers is required for confirmation of amplification and polymorphism. By incorporating shotgun next-generation sequencing data sets from multiple individuals of the same species, we have developed a new method for the optimal design of microsatellite markers. This new tool allows us to increase the rate at which suitable candidate markers are selected by 58% in direct comparisons and facilitate an estimated 16% reduction in costs associated with producing a novel microsatellite panel. Our method enables the visualisation of each microsatellite locus in a multiple sequence alignment allowing several important quality checks to be made. Polymorphic loci can be identified and prioritised. Loci containing fragment-length-altering mutations in the flanking regions, which may invalidate assumptions regarding the model of evolution underlying variation at the microsatellite, can be avoided. Priming regions containing point mutations can be detected and avoided, helping to reduce sample-site-marker specificity arising from genetic isolation, and the likelihood of null alleles occurring. We demonstrate the utility of this new approach in two species: an echinoderm and a bird. Our method makes a valuable contribution towards minimising genotyping errors and reducing costs associated with developing a novel marker panel. The Python script to perform our method of multi-individual microsatellite identification (MiMi) is freely available from GitHub (https://github.com/graemefox/mimi).


Assuntos
Genoma/genética , Repetições de Microssatélites/genética , Alelos , Marcadores Genéticos/genética , Genômica/métodos , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Mutação Puntual/genética , Polimorfismo Genético/genética
19.
J Anim Ecol ; 88(11): 1684-1695, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31325164

RESUMO

Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.


Assuntos
Microbiota , Poríferos , Animais , Florida , Geografia , Filogenia , RNA Ribossômico 16S
20.
Animals (Basel) ; 9(6)2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31226801

RESUMO

Understanding animal personalities has notable implications in the ecology and evolution of animal behavior, but personality studies can also be useful in optimizing animal management, with the aim of improving health and well-being, and optimizing reproductive success, a fundamental factor in the species threatened with extinction. Modern zoos are increasingly being structured with enclosures that host different species, which permanently share spaces. This condition has undeniable positive aspects, but, in some species, it could determine the appearance of collective or synchronized behaviors. The aim of this study was to verify, in a colony of three species of communally housed penguins (Pygoscelis papua, Aptenodytes patagonicus and Eudyptes moseleyi), through a trait-rating assessment, if interspecific group life impacts on the expression of personality traits, and if it is possible to highlight specie-specific expression of personality traits, despite the influence of forced cohabitation. For many of the personality traits we analyzed, we have observed that it was possible to detect an expression that differed, according to the species. From a practical point of view, these data could ameliorate the management of the animals, allowing to design animal life routines, according to the different behavioral characteristics of the cohabiting species.

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