Post-2020 goals overlook genetic diversity Laikre, Linda; Hoban, Sean; Bruford, Michael W ...
Science (American Association for the Advancement of Science),
03/2020, Letnik:
367, Številka:
6482
Journal Article
The use of ecological replacements (analogue species to replace extinct taxa) to restore ecosystem functioning is a promising conservation tool. However, this approach is controversial, in part due ...to a paucity of data on interactions between analogue species and established taxa in the ecosystem.
We conducted ecological surveys, comprehensively DNA barcoded an ecosystem's flora and inferred the diet of the introduced Aldabra giant tortoise, acting as an ecological replacement, to understand how it might have modified island plant communities on a Mauritian islet. Through further dietary analyses, we investigated consequential effects on the threatened endemic Telfair's skink.
Dietary overlap between tortoises and skinks was greater than expected by chance. However, there was a negative correlation between tortoise and skink preferences in herbivory and minimal overlap in the plants most frequently consumed by the reptiles.
Changes in the plant community associated with 7 years of tortoise grazing were characterised by a decrease in the percentage cover of native herbs and creepers, and an increase in the cover of an invasive herb when compared to areas without tortoises. However, tortoise dietary preferences themselves did not directly drive changes in the plant community.
Tortoises successfully dispersed the seeds of an endemic palm, which in time may increase the extent of unique palm‐rich habitat. We found no evidence that tortoises have increased the extent of plant species hypothesised to be part of a lost Mauritian tortoise grazed community.
Synthesis and applications. Due to a negative correlation in tortoise and skink dietary preferences and minimal overlap in the most frequently consumed taxa, the presence of tortoises is unlikely to have detrimental impacts on Telfair's skinks. Tortoise presence is likely to be beneficial to skinks in the long term by increasing the extent of palm‐rich habitat. Although tortoises are likely to play a role in controlling invasive plants, they are not a panacea for this challenge. After 7 years, tortoises have not resurrected a lost tortoise grazed community that we hypothesise might have existed in limited areas on the islet, indicating that further interventions may be required to restore this plant community.
Résumé
L'utilisation de remplacements écologiques (espèces analogues pour remplacer les taxons éteints) pour restaurer le fonctionnement d'un écosystème est un outil de conservation prometteur. Cependant, cette approche est controversée, en partie à cause d'un manque de données sur les interactions entre les espèces analogues et les taxons présents dans l'écosystème.
Nous avons mené des études écologiques, codé l’ADN de la flore d'un écosystème et déduit le régime alimentaire de la tortue géante d'Aldabra, espèce introduite agissant comme un remplacement écologique, pour comprendre comment elle aurait potentiellement modifié les communautés végétales insulaires sur un îlot mauricien. Grâce à d'autres analyses alimentaires, nous avons étudié les effets résultants sur le scinque de Telfair, une espèce endémique menacée.
Le chevauchement entre l'alimentation des tortues et les scinques était plus important que prévu. Cependant, il y avait une corrélation négative entre les préférences des tortues et des scinques au niveau de l'herbivorie et un chevauchement minime pour les plantes les plus fréquemment consommées par ces reptiles.
Les changements dans la communauté végétale associés à sept années de broutage des tortues ont été caractérisés par une diminution du pourcentage de couverture d'herbes et de plantes grimpantes indigènes, et une augmentation de la couverture d'une herbe envahissante par rapport aux zones sans tortues. Cependant, les préférences alimentaires des tortues elles‐mêmes n'ont pas directement entraîné de changements dans la communauté végétale.
Les tortues ont réussi à disperser les graines d'un palmier endémique, ce qui, avec le temps, pourrait augmenter l'étendue de l'habitat riche en palmiers. Nous n'avons trouvé aucune preuve que les tortues ont augmenté l'étendue des espèces végétales supposées faire partie d'une communauté végétale disparue qui existait dû au broutage des tortues mauriciennes.
Synthèse et applications. En raison d'une corrélation négative dans les préférences alimentaires des tortues et des scinques et d'un chevauchement minimal dans les taxons les plus fréquemment consommés, il est peu probable que la présence de tortues ait des effets néfastes sur les scinques de Telfair. La présence de tortues est susceptible d'être bénéfique pour les scinques à long terme en augmentant l'étendue de l'habitat riche en palmiers. Bien que les tortues soient susceptibles de jouer un rôle dans le contrôle des plantes envahissantes, elles ne sont pas une panacée pour ce défi. Après sept ans, les tortues n'ont pas ressuscité la communauté végétale disparue qui existait dû au broutage des tortues endémique qui, selon nous, aurait pu exister dans des zones limitées de l'îlot, ce qui indique que d'autres interventions pourraient être nécessaires pour restaurer cette communauté végétale.
Due to a negative correlation in tortoise and skink dietary preferences and minimal overlap in the most frequently consumed taxa, the presence of tortoises is unlikely to have detrimental impacts on Telfair's skinks. Tortoise presence is likely to be beneficial to skinks in the long term by increasing the extent of palm‐rich habitat. Although tortoises are likely to play a role in controlling invasive plants, they are not a panacea for this challenge. After 7 years, tortoises have not resurrected a lost tortoise grazed community that we hypothesise might have existed in limited areas on the islet, indicating that further interventions may be required to restore this plant community.
Aim
The British Isles have been worked for millennia to extract metal ores to feed industrial development, leaving a legacy of mine water pollution that continues to impact freshwater communities in ...many regions. Brown trout (Salmo trutta L.) have long been observed to persist in these metal‐impacted systems as apex predators, with previous studies showing a small number of impacted populations to be highly genetically divergent. We sought to understand the scale of genetic diversity across regions and the repeatability of genetic divergence in trout populations affected by metal pollution.
Location
We examined four mine water‐impacted regions across the British Isles: west Wales, northeast England, southwest England and southeast Ireland.
Methods
We employed a panel of 95 SNP loci to screen 1236 individuals from 71 sites representing paired metal‐impacted and clean sites from across the four regions. From these, we obtained diversity statistics, assessed genetic structuring of populations and modelled historical demographic scenarios to understand which factors most credibly explain genetic variation in divergent populations.
Results
We evidenced hierarchical population structure in the regions studied, in line with expectations from phylogeographic history. However, in a hierarchical analysis of genetic structuring the first level of differentiation was driven by the divergence of the metal‐impacted trout of Cornwall in southwest England. Within regions we observed reduced genetic diversity and repeated patterns of local genetic sub‐structuring between paired samples from metal‐impacted and relatively clean sites. Demographic history analyses suggested the timing of these splits to be relatively recent and to be associated with periods of peak mining activity.
Main conclusions
Our findings demonstrate distinct patterns of genetic isolation and reduced diversity arising from legacy pollution in freshwater ecosystems, with impacts being most apparent where both chemical pollution and physical barriers are present. Management should focus on the amelioration of mine water wash‐out and the removal of barriers to fish movement to safeguard genetic diversity in impacted populations.
Understanding the interaction between life history, demography and population genetics in threatened species is critical for the conservations of viable populations. In the context of habitat loss ...and fragmentation, identifying the factors that underpin the structuring of genetic variation within populations can allow conservationists to evaluate habitat quality and connectivity and help to design dispersal corridors effectively. In this study, we carried out a detailed, fine‐scale landscape genetic investigation of a giant panda population from the Qinling Mountains for the first time. With a large microsatellite data set and complementary analysis methods, we examined the role of isolation‐by‐barriers (IBB), isolation‐by‐distance (IBD) and isolation‐by‐resistance (IBR) in shaping the pattern of genetic variation in this giant panda population. We found that the Qinling population comprises one continuous genetic cluster, and among the landscape hypotheses tested, gene flow was found to be correlated with resistance gradients for two topographic factors, slope aspect and topographic complexity, rather than geographical distance or barriers. Gene flow was inferred to be facilitated by easterly slope aspect and to be constrained by topographically complex landscapes. These factors are related to benign microclimatic conditions for both the pandas and the food resources they rely on and more accessible topographic conditions for movement, respectively. We identified optimal corridors based on these results, aiming to promote gene flow between human‐induced habitat fragments. These findings provide insight into the permeability and affinities of giant panda habitats and offer important reference for the conservation of the giant panda and its habitat.
Species delimitation is one of the most contested areas in modern biology, with widespread disagreement about almost every aspect of the definition and implementation of the “species” label. While ...this debate is intellectually stimulating, it also has real implications for conservation, where its impacts on taxonomic inflation or inertia can mean that specific populations receive adequate conservation measures or are ignored. Recently, the rise of next generation sequencing and phylogenomics has revolutionised phylogenetic understanding of many organismal groups but has simultaneously highlighted the porosity of genomes in terms of admixture across previously delineated species barriers. The extraordinary power of genomic data is increasingly being used to delineate species, and several publications in this domain have recently attracted significant attention and criticism. Here we revisit the question of species delimitation, but from a genomic context. We ask how and whether the large amounts of data provided by genomic methods can resolve the longstanding discussion on the validity and application of phylogenetic and allied species concepts, and how some recent examples can inform this debate. We argue that conserving adaptive potential is a priority for conservation, and no single species concept currently does that adequately on its own. Genomic data holds the potential to add unprecedented detail, but frequently falls short of this potential.
The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has ...taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.
Livestock production both contributes to and is affected by global climate change, and substantial modifications will be required to increase its climate resilience. In this context, reliance on ...dominant commercial livestock breeds, featuring small effective population sizes, makes current production strategies vulnerable if their production is restricted to environments, which may be too costly to support under future climate scenarios. The adaptability of animal populations to future environments will therefore become important. To help evaluate the role of genetics in climate adaptation, we compared selection strategies in dairy cattle using breeding simulations, where genomic selection was used on two negatively correlated traits for production (assumed to be moderately heritable) and adaptation (assumed to have low heritability). Compared with within-population breeding, genomic introgression produced a more positive genetic change for both production and adaptation traits. Genomic introgression from highly adapted but low production value populations into highly productive but low adaptation populations was most successful when the adaptation trait was given a lower selection weight than the production trait. Genomic introgression from highly productive population to highly adapted population was most successful when the adaptation trait was given a higher selection weight than the production trait. Both these genomic introgression schemes had the lowest risk of inbreeding. Our results suggest that both adaptation and production can potentially be improved simultaneously by genomic introgression.
Abstract
Africa’s black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. ...Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa’s Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.
Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its ...numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
Landscape genetics is increasingly being used in landscape planning for biodiversity conservation by assessing habitat connectivity and identifying landscape barriers, using intraspecific genetic ...data and quantification of landscape heterogeneity to statistically test the link between genetic variation and landscape variability. In this study we used genetic data to understand how landscape features and environmental factors influence demographic connectedness in Europe's largest brown bear population and to assist in mitigating planned infrastructure development in Romania. Model-based clustering inferred one large and continuous bear population across the Carpathians suggesting that suitable bear habitat has not become sufficiently fragmented to restrict movement of individuals. However, at a finer scale, large rivers, often located alongside large roads with heavy traffic, were found to restrict gene flow significantly, while eastern facing slopes promoted genetic exchange. Since the proposed highway infrastructure development threatens to fragment regions of the Carpathians where brown bears occur, we develop a decision support tool based on models that assess the landscape configuration needed for brown bear conservation using wildlife corridor parameters. Critical brown bear corridors were identified through spatial mapping and connectivity models, which may be negatively influenced by infrastructure development and which therefore require mitigation. We recommend that current and proposed infrastructure developments incorporate these findings into their design and where possible avoid construction measures that may further fragment Romania's brown bear population or include mitigation measures where alternative routes are not feasible.
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