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Understanding genetic structure and diversity among remnant populations of rare species can inform conservation and recovery actions. We used a population genetic framework to spatially delineate gene pools and estimate gene flow and effective population sizes for the endangered California Freshwater Shrimp Syncaris pacifica. Tissues of 101 individuals were collected from 11 sites in 5 watersheds, using non-lethal tissue sampling. Single Nucleotide Polymorphism markers were developed de novo using ddRAD-seq methods, resulting in 433 unlinked loci scored with high confidence and low missing data. We found evidence for strong genetic structure across the species range. Two hierarchical levels of significant differentiation were observed: (i) five clusters (regional gene pools, FST = 0.38–0.75) isolated by low gene flow were associated with watershed limits and (ii) modest local structure among tributaries within a watershed that are not connected through direct downstream flow (local gene pools, FST = 0.06–0.10). Sampling sites connected with direct upstream-to-downstream water flow were not differentiated. Our analyses suggest that regional watersheds are isolated from one another, with very limited (possibly no) gene flow over recent generations. This isolation is paired with small effective population sizes across regional gene pools (Ne = 62.4–147.1). Genetic diversity was variable across sites and watersheds (He = 0.09–0.22). Those with the highest diversity may have been refugia and are now potential sources of genetic diversity for other populations. These findings highlight which portions of the species range may be most vulnerable to future habitat fragmentation and provide management consideration for maintaining local effective population sizes and genetic connectivity. [ABSTRACT FROM AUTHOR]

Human activities have widely disrupted the spatial ecological processes critical for population and ecosystem integrity. Local effects of altered sediment regimes in rivers are well explored, but how they impact connectivity at a catchment scale is less explored. In this paper we document evidence for altered metapopulation dynamics for a headwater specialist, blackspotted topminnow (Fundulus olivaceus) in catchments with geomorphically dynamic river mainstems.We quantified decade‐scale patterns of fluvial geomorphic activity via planform analysis of historical and recent aerial imagery, and patterns of gene flow in F. olivaceus via analysis of single nucleotide polymorphisms, identified by genotype‐by‐sequencing.Mainstem streams narrowed and increased in sinuosity, probably in recovery from historic flood events. Substantial variability in response indicated underlying differences due to differential disturbance history and catchment sensitivity to change.Multiple analytical approaches all found geography to be a major factor in genetic structuring among catchments. Metrics of genetic differentiation and heterozygosity for F. olivaceus within catchments were related to the degree of geomorphic change inferred from a multivariate composite metric. Catchments with more geomorphic change tended to have more population structuring.Five populations assigned to adjacent catchments. Analysis of heterozygosity in presumed donor, recipient, and mis‐assigned catchments indicated founder effects in recipient catchments and probable subsequent allopatric recolonisation following local extirpations.Our results demonstrate complex nonlocal effects of channel evolution on metapopulation dynamics in a pool‐dwelling non‐lithophilous headwater specialist. Our integrative approach allows strong insight into deeper effects of geomorphic processes on aquatic ecosystems. F. olivaceus is ecologically dissimilar to taxa traditionally anticipated to respond to sediment‐related disturbances and demonstrates how broader channel morphological change can affect habitats beyond sedimentation of the stream bed. [ABSTRACT FROM AUTHOR]

West-African populations of the African subspecies of leopards (Panthera pardus pardus) are very fragmented, particularly so in Nigeria, Africa’s most populous nation. We compile historical and recent information about the occurrence of these big cats in what is likely their last remaining stronghold: Gashaka Gumti National Park (GGNP) in Adamawa and Taraba States along the border with Cameroon. Leopards in GGNP’s northern Gumti sector are close to extinction, given that its open plains of savannah are heavily encroached upon by illegal cattle grazing. However, in GGNP’s southern Gashaka sector, leopards are better protected, given its often mountainous and densely forested landscape. We present specific data for a 30 km2 forest-savannah area around a research station at Kwano, which harbours sizeable populations of 35 species of prey species leopards target elsewhere. Here, direct evidence for leopard presence (e.g., footprints, scratchmarks, predation incidences, vocalizations, sightings, cameratrap images) amounts to 1 per year. Albeit this encounter rate is very low, it is relatively steady throughout the last 30 years and into the present. We assume that GGNP’s Gashaka sector represents one of the best chances for leopards to survive in Nigeria.

Genomic tools are now commonly used to assess the genetic diversity and genetic structure of species and populations, and they provide the ability to describe and address the negative effects of population declines and fragmentation. However, such studies are lacking for arboreal mammals despite their contribution to various ecosystem services, especially in uncommon and critically endangered ecosystems such as cloud forests. The aim of this work was to evaluate and compare the genetic diversity and population structure of two endemic arboreal mice from Mexican cloud forests that are associated with areas with different levels of impacts from human activities. We performed genotyping-by-sequencing in 47 Habromys schmidlyi and 17 Reithrodontomys wagneri individuals to evaluate genetic diversity and differentiation. In both species, the genetic diversity was low compared to other cricetid species, and we observed different population structure patterns, potentially linked to the different ecological associations. We detected two genetic groups in H. schmidlyi, that is a territorial species present in areas of low incline, while a single genetic group was found in R. wagneri, which forms family groups in areas with steep slopes. Overall, these results highlight how species' genetic diversity can be differentially impacted depending on differential ecological associations within the same ecosystem. This information is essential for the development of the adequate conservation and management of these species. [ABSTRACT FROM AUTHOR]

Relevance and purpose. Cenopopulations of deciduous tree species at the northern border of the range are of particular scientific interest as objects of biological diversity. The relevance of the work is associated with the need to organize monitoring of these rare objects in the forests of the Petrozavodsk Urban Okrug by cause of increasing anthropogenic pressure. Assessment of the state of valuable nature conservation objects has not only scientific, but also economic interest in the field of ecosystem services, taking into account those functions of natural ecosystems that ensure the quality of people’s living standards.Material and methods. During 2017–2018 a detailed study of the cenopopulations of Tilia cordata and Ulmus glabra was carried out on two model plots within the boundaries of the Petrozavodsk urban district. The area, abundance, ontogenetic structure of cenopopulations was determined using the standard technique of cenopopulation studies, taking into account the characteristics of specific species. Results and conclusions. The studied cenopopulations are isolated and small (up to 23 hectares). They were forming during the secondary succession anthropogenic felling and fires more than 100 years old. According to the ontogenetic spectrum, cenopopulations are normal mature, have an ontogenetic spectrum with a maximum on immature individuals, thus, cenopopulations are characterized by a normal turnover of generations. Generative reproduction and large generative trees high 16–24 m up to 120 years old are rare for the northern regions.

Abstract Background The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation. Results In this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, one of the few known reference genomes in genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. A phylogenetic tree was constructed using 4902 single-copy orthologous genes, which showed L. relictus had closest relative of L. smithsonianus, with divergence time of 14.7 Mya estimated between of them. PSMC analyses indicated that L. relictus had been undergoing a long-term population decline during 0.01-0.1 Mya with a small effective population size fom 8800 to 2200 individuals. Conclusions This genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and will help to establish a foundation for further studies investigating whether the breeding population is a complex population. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to alleviate the fragmentation of breeding populations.

One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affect behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg‐to‐adult viability and negative geotaxis behaviour—a locomotor response used to measure, e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F1 and F4 generation. The majority of inbred lines showed evidence for inbreeding depression for both egg‐to‐adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared with the locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F1 to F4. Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue. [ABSTRACT FROM AUTHOR]

The putatively positive association between host genetic diversity and the ability to defend against pathogens has long attracted the attention of evolutionary biologists. Chytridiomycosis, a disease caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has emerged in recent decades as a cause of dramatic declines and extinctions across the amphibian clade. Bd susceptibility can vary widely across populations of the same species, but the relationship between standing genetic diversity and susceptibility has remained notably underexplored so far. Here, we focus on a putatively Bd‐naive system of two mainland and two island populations of the common toad (Bufo bufo) at the edge of the species' range and use controlled infection experiments and dd‐RAD sequencing of >10 000 SNPs across 95 individuals to characterize the role of host population identity, genetic variation and individual body mass in mediating host response to the pathogen. We found strong genetic differentiation between populations and marked variation in their susceptibility to Bd. This variation was not, however, governed by isolation‐mediated genetic erosion, and individual heterozygosity was even found to be negatively correlated with survival. Individual survival during infection experiments was strongly positively related to body mass, which itself was unrelated to population of origin or heterozygosity. Our findings underscore the general importance of context‐dependency when assessing the role of host genetic variation for the ability of defence against pathogens. [ABSTRACT FROM AUTHOR]

Abstract Aim To infer relationships between populations of the semi‐arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia. Location Southeastern Australia. Taxon Eucalyptus behriana (Myrtaceae, Angiospermae). Methods We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site‐associated DNA sequencing (ddRAD‐seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species’ distribution. Results Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them. Conclusions Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial‐interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role.

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Background: The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation. Results: In this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, one of the few known reference genomes in genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. A phylogenetic tree was constructed using 4902 single-copy orthologous genes, which showed L. relictus had closest relative of L. smithsonianus, with divergence time of 14.7 Mya estimated between of them. PSMC analyses indicated that L. relictus had been undergoing a long-term population decline during 0.01-0.1 Mya with a small effective population size fom 8800 to 2200 individuals. Conclusions: This genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and will help to establish a foundation for further studies investigating whether the breeding population is a complex population. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to alleviate the fragmentation of breeding populations. [ABSTRACT FROM AUTHOR]

Estimating the effective population size and effective number of breeders per year (Nb) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one‐sample LDNe estimator of Nb in age‐structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5%–10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence Nb estimation. Precision was higher for 100 SNPs (H ≈ 0.30) than for 15 microsatellites (H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when Nb was small (Nb < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that Nb = 50 when the true Nb = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject Nb = 500 when the true Nb = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in Nb when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate Nb for age structured populations (https://github.com/popgengui/agestrucnb/), which should help biologists develop sensitive monitoring programmes for early detection of changes in Nb and population declines. [ABSTRACT FROM AUTHOR]

Species restricted to archipelagos are often range-restricted, dispersal limited, and persist as disjunct populations. These attributes can make island populations especially vulnerable to extinction from natural or anthropogenic processes. Ascertaining causes of habitat use, population impact, and range loss is fundamental to guiding effective conservation actions. The Komodo dragon (Varanus komodoensis) is an endangered, island-endemic species with a highly restricted range distribution limited to a small number of islands in Eastern Indonesia. Flores Island is the largest island (13,540 km2) within the species distribution. However, with relatively few and small-protected areas, alongside a much higher incidence of human-related habitat use, Komodo dragon habitat occupancy is suspected to decrease on Flores. Here over five years, we conducted systematic surveys to evaluate Komodo dragon habitat occupancy at 346 camera monitoring stations (CMS) distributed along the Flores coastline. We successfully detected Komodo dragons at 85 of the 346 CMS on Flores. The pattern of Komodo dragon site presence indicated their distribution was confined to three isolated and highly restricted habitat areas on the west, northwestern, and northern coastal regions of Flores. Ranking of competing models indicated that proximity to farms and villages had the strongest negative effects on Komodo dragon habitat occupancy. The current predicted Komodo dragon range distribution appeared to have undergone significant range area contraction (~ 44%) at multiple coastal areas known to be occupied by the Komodo dragon detected in previous decades (i.e., 1970–2000). We attribute decreased Komodo dragon habitat use and range loss to multiple and cascading human activities. To address these threats, we advocate a range of land use planning and community conservation actions to avoid a potential Komodo dragon extirpation on the largest island habitat within their distribution. [ABSTRACT FROM AUTHOR]

Estimating the effective population size and effective number of breeders per year (Nb) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one‐sample LDNe estimator of Nb in age‐structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5%–10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence Nb estimation. Precision was higher for 100 SNPs (H ≈ 0.30) than for 15 microsatellites (H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when Nb was small (Nb < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that Nb = 50 when the true Nb = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject Nb = 500 when the true Nb = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in Nb when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate Nb for age structured populations (https://github.com/popgengui/agestrucnb/), which should help biologists develop sensitive monitoring programmes for early detection of changes in Nb and population declines. [ABSTRACT FROM AUTHOR]

Aim: To infer relationships between populations of the semi‐arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia. Location: Southeastern Australia. Taxon: Eucalyptus behriana (Myrtaceae, Angiospermae). Methods: We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site‐associated DNA sequencing (ddRAD‐seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species' distribution. Results: Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them. Conclusions: Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial‐interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role. [ABSTRACT FROM AUTHOR]

Barbary macaques (Macaca sylvanus) are critically endangered primates. They are unique within their genus as the only African macaque. By the late Miocene, their habitat extended across Northern Africa and into Southern Europe. Aside from an introduced population in Gibraltar, their current distribution is reduced to disjointed forests in Algeria and Morocco. Our knowledge of the phylogeographic history and intra-specific diversity of this highly endangered species is also fragmented. In this study, we aimed to improve our understanding of the phylogeographic history and genetic diversity of the Barbary macaque by expanding the genetic data available on the Algerian populations. Moreover, we investigated captive populations of Barbary macaques for comparison to wild populations. The mtDNA hypervariable control region I was sequenced using DNA extracts from faecal and hair samples from wild and captive populations. The newly produced data (n = 157), from both Algerian and Moroccan populations, were combined with previously published data (n = 212) and used to characterize genetic variability and reconstruct phylogenetic relationships among wild and captive populations. We found that Algerian populations exhibit an increased genetic diversity relative to Moroccan populations. Phylogenetic relationships suggest that the Moroccan populations diversified after being isolated from the Algerian populations. Captive populations were found to be not fully representative of the genetic diversity exhibited in the species, but rather only of Moroccan populations. The findings in this study suggest that the fragmented Algerian populations should be managed in order to increase gene flow between them by increasing habitat connectivity where it is feasible to do so.

Dams alter river functioning and hinders the free movement of migratory fishes. We analysed the effects of a subtropical dam on the reproduction of migratory fishes using data from ichthyoplankton monitoring surveys. These were conducted at six sampling stations upstream, downstream and within the reservoir on a weekly basis during 6 years. The dam had a direct impact on fish movement, leading to the fragmentation of fish populations. Two different and independent reproductive areas became evident: one located in the reservoir headwater area and the other downstream of the dam. The long temporal scale of our study facilitated the detection of the impact of Salto Grande on the species of ichthyoplankton. Freshwater secondary fish species (mainly Lycengraulis grossidens) increased in abundance in the stations located inside the reservoir and closer to the dam, whereas most fishes found in the headwater of the reservoir corresponded to river migratory species (potamodromous fish). These differences are most likely due to changes in the physicochemical characteristics of the water induced by the transformation of a river into a reservoir. During rainy summers, Microcystis spp. densities were lower than 1,000 cells ml−1 and fish densities were higher than 4 ind. m−3, whereas in dry summers, there were important Microcystis spp. blooms (401,573 ± 112,559 cells ml−1) and fish larvae decreased sharply (<1 ind. m−3) in the reservoir headwater area. This could indicate that the discharge of water in the reservoir may also indirectly affect the regulation of fish reproduction. The alternating periods between dry and rainy summers associated with El Niño‐Southern Oscillation poses a challenge to ichthyofauna management in the reservoir. [ABSTRACT FROM AUTHOR]

Many species advertise their unique identity to conspecifics using dedicated individuality signals: one familiar example is human faces. But how unique in the global population do these signals need to be? While human faces are highly variable, each person interacts with many fewer individuals than are found in the total population. This raises the question of how evolutionary mechanisms drive up population‐wide diversity when selection occurs at such a local level. We use an individual‐based model in which individuals broadcast their identity and quality in separate, genetically‐coded signals. Mimicking, for example, scent marking mammal species, females in the model assess males using the quality signal, then attempt to relocate the highest quality male using his identity signal. We ask how population fragmentation affects genetic diversity in the individual identity‐signalling region under sexual selection, predicting one of two opposing outcomes: 1) divided populations evolve fewer signal variants globally, since repetition of signals is not costly when individuals interact only with local conspecifics, or 2) stochasticity in mutation and selection cause divergence among subpopulations, increasing the global number of signal variants. We show that local selection drives up global genetic diversity substantially in fragmented populations, even with extremely low rates of dispersal. Because new signal variants arise by mutation and then sweep through their subpopulation, a fragmented population has more global signal variation. This result furthers our understanding of how high levels of diversity in individuality signals are maintained. [ABSTRACT FROM AUTHOR]

The substitution of natural habitats with artificial structures, such as coastal defence structures, has significantly detrimental effects on the marine biological community. In this context, the application of ecological engineering to marine ecosystems presents an opportunity to mitigate these environmental impacts and enhance ecosystem services. There are proposals aimed at mimicking structures found in the natural environment to increase topographic complexity in artificial substrates, thereby promoting biodiversity and hindering the establishment of invasive species. The present study focuses on assessing change in the biological community of intertidal pools constructed on existing coastal defence structures and their influence on a halo (5 cm) of humidity created around the pools. Using an inexpensive method, the tidepools were created at the beginning of 2014 using a pneumatic hammer (DeWalt brand D25902K), imitating the tidepools of the adjacent natural substrate. The coastal defence structures (riprap) which were selected for the study host climax communities since they were built >8 years ago. After 7.5 years of the creation of this microhabitat, the value of species richness in the tidepool was 64.2% higher than in the control, Shannon diversity 41.54% and functional diversity 6.27%. The study of the effect on a halo (5 cm) of humidity produced around the pool shows that Shannon diversity is higher than in the control treatment, demonstrating that the microhabitat created mitigates the harsh environmental (high temperature and desiccation) conditions of the intertidal zone beyond the interior of the tidepool. The results showed that the species richness in the tidepools was bigger in the high intertidal than the low, therefore it is more beneficial to create this microhabitat in high intertidal zone. The created microhabitats serve as shelter and breeding sites for animal species that were not previously observed in the studied artificial structure, as detected for species such as Pisania striata, Ocenebra edwarasii , Stramonita haemastoma , Meralarhaphe neritoides , Siphonaria pectinata, Paracentrotus lividus and Spirorbis sp., thus contribute to reducing the fragmentation of their populations. In terms of "ecological succession", the current study demonstrated that typical species of a mature benthic biological community had colonised the created microhabitat 7.5 years later. These species included the Anthozoa Anemonia sulcata , Actinia equina and Exaiptasia diaphana or the endangered Mollusc Dendropoma lebeche. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity may help organisms persist in modified habitats. Yet, its adaptive value is frequently ignored because fitness consequences are not explored at the required time scale. Taking advantage of a 16-yr nest-box supplementation program, we explored effects of nest type and two social-ecological indices (breeding cluster size and distances between clusters) on adult and offspring survival of a non-excavator cavity-nesting bird species, the European roller (Coracias garrulus), a species of conservation concern. We also investigated site and habitat fidelity associated with different nest types. Apparent survival of rollers was mainly explained by age and sex. Social-ecological factors were more important than cavity type in apparent survival. Increases in apparent survival with decreasing distance to neighboring clusters were comparable for adult males and females but were stronger for juvenile males than for juvenile females. Nest type influenced residency patterns, so that males breeding in nest-boxes were more likely to be recaptured in subsequent years at the study site and in the same nest type compared with males associated with natural and semi-natural nest types. Whereas phenotypic plasticity in nest selection might favor rapid colonization of a novel nest type, widespread use of nest-boxes can decrease, through their effects on site and habitat fidelity, a species' responsiveness to environmental changes. We suggest that nest-box schemes should be applied to promote higher connectiveness of breeding populations and that nest-box programs may influence population dynamics and habitat selection criteria via their effect on social information and natal habitat preference induction.

Abstract Background Plasmodium falciparum malaria is one of the most widespread parasitic infections in humans and remains a leading global health concern. Malaria elimination efforts are threatened by the emergence and spread of resistance to artemisinin-based combination therapy, the first-line treatment of malaria. Promising molecular markers and pathways associated with artemisinin drug resistance have been identified, but the underlying molecular mechanisms of resistance remains unknown. The genomic data from early period of emergence of artemisinin resistance (2008–2011) was evaluated, with aim to define k13 associated genetic background in Cambodia, the country identified as epicentre of anti-malarial drug resistance, through characterization of 167 parasite isolates using a panel of 21,257 SNPs. Results Eight subpopulations were identified suggesting a process of acquisition of artemisinin resistance consistent with an emergence-selection-diffusion model, supported by the shifting balance theory. Identification of population specific mutations facilitated the characterization of a core set of 57 background genes associated with artemisinin resistance and associated pathways. The analysis indicates that the background of artemisinin resistance was not acquired after drug pressure, rather is the result of fixation followed by selection on the daughter subpopulations derived from the ancestral population. Conclusions Functional analysis of artemisinin resistance subpopulations illustrates the strong interplay between ubiquitination and cell division or differentiation in artemisinin resistant parasites. The relationship of these pathways with the P. falciparum resistant subpopulation and presence of drug resistance markers in addition to k13, highlights the major role of admixed parasite population in the diffusion of artemisinin resistant background. The diffusion of resistant genes in the Cambodian admixed population after selection resulted from mating of gametocytes of sensitive and resistant parasite populations.

Human‐induced transformations of ecosystems usually result in fragmented populations subject to increased extinction risk. Fragmentation is also often associated with novel environmental heterogeneity, which in combination with restricted gene flow may increase the opportunity for local adaptation. To manage at‐risk populations in these landscapes, it is important to understand how gene flow is changing, and how populations respond to habitat loss. We conducted a landscape genomics analysis using Restriction‐site Associated DNA sequencing to investigate the evolutionary response of the critically endangered Dahl's Toad‐headed turtle (Mesoclemmys dahli) to severe habitat modification. The species has lost almost all of its natural habitat in the southwestern part of its range and about 70% in the northeast. Based on least cost path analysis across different resistance surfaces for 3,211 SNPs, we found that the landscape matrix is restricting gene flow, causing the fragmentation of the species into at least six populations. Genome scans and allele‐environment association analyses indicate that the population fragments in the deforested grasslands of the southwest are adaptively different from those in the more forested northeast. Populations in areas with no forest had low levels of adaptive genetic diversity and the fixation of ancestrally‐polymorphic SNPs, consistent with directional selection in this novel environment. Our results suggest that this forest‐stream specialist is adapting to pond‐grassland conditions, but it is also suffering from negative consequences of habitat loss, including genetic erosion, isolation, small effective population sizes, and inbreeding. We recommend gene flow restoration via genetic rescue to counteract these threats, and provide guidance for this strategy. [ABSTRACT FROM AUTHOR]

Biodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali. The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions currently reported in the literature are inflated due to erroneous population assignments to the species level, and further highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok. [ABSTRACT FROM AUTHOR]

Sclerolaena napiformis is a perennial chenopod endemic to southeast Australia. Human-mediated habitat loss and fragmentation over the past century has caused a rapid decline in abundance and exacerbated reduced connectivity between remnant populations across three disjunct regions. To assess conservation requirements, we measured the genetic structure of 27 populations using double digest RADseq). We combined our genetic data with habitat models under projected climate scenarios to identify changes in future habitat suitability. There was evidence of regional differentiation that may pre-date (but also may be compounded) by recent habitat fragmentation. We also found significant correlation between genetic and geographic distance when comparing sites across regions. Overall, S. napiformis showed low genetic diversity and a relatively high proportion of inbreeding/selfing. Climate modelling, based on current occupancy, predicts a reduction in suitable habitat for S. napiformis under the most conservative climate change scenario. We suggest that the best conservation approach is to maximise genetic variation across the entire species range to allow dynamic evolutionary processes to proceed. We recommend a conservation strategy that encourages mixing of germplasm within regions and permits mixed provenancing across regions to maximise genetic novelty. This will facilitate shifts in genetic composition driven by individual plant fitness in response to the novel environmental conditions this species will experience over the next 50 years.

An investigation on morphometric and meristic variation of Zenarchopterus buffonis (Valenciennes, 1847) from coastal waters of Malaysia has been conducted between April 2011 and May 2013. A total of 300 fish specimens was collected from five different areas, viz. Tg. Belungkor, Johor; Sg. Likas, Sabah; Klang, Selangor; Matang, Perak and Langkawi, Kedah. The morphometric and meristic characters of Z. buffonis were analyzed in order to investigate the hypothesis population fragmentation in Malaysian coastal waters. Thirteen morphometric and six meristic characters were analyzed using Principal Component Analysis and Discriminant Function Analysis. Morphometric characters displayed considerably greater discriminatory power to distinguish individuals from different geographical areas compared to meristic characters. In the validation of the morphometric discriminant analysis, the most well defined population is Klang (96.9%), with only one misclassified individual. The most relevant morphometric characteristics for separation between these populations were the length of upper jaw, and length of lower jaw. Fish specimens from Matang area had longer upper and lower jaw was probably a result of the feeding strategy adopted by the fish in water bodies. Sg. Likas populations showed significant variations of anal ray counts compared to other regions that related to spawning season and juvenile development among Z. buffonis populations. The most well-defined group is Sg. Likas (92.3%), with only four misclassified individuals. Hence the findings of this study will be significant in differentiating the Z. buffonis population among different areas at least in Malaysia. [ABSTRACT FROM AUTHOR]

Background and Aims Dispersal is crucial due to its direct impact on dynamics of a species’ distribution as well as having a role in shaping adaptive potential through gene flow. In plants forming scarce and small populations, knowledge about the dispersal process is required to assess the potential for colonizing new habitats and connectivity of present and future populations. This study aimed to assess dispersal potential in Taxus baccata, a dioecious gymnosperm tree with a wide but highly fragmented distribution. Methods Seed and pollen dispersal kernels were estimated directly in the framework of the spatially explicit mating model, where genealogies of naturally established seedlings were reconstructed with the help of microsatellite markers. In this way, six differently shaped dispersal functions were compared. Key Results Seed dispersal followed a leptokurtic distribution, with the Exponential-Power, the Power-law and Weibull being almost equally best-fitting models. The pollen dispersal kernel appeared to be more fat-tailed than the seed dispersal kernel, and the Lognormal and the Exponential-Power function showed the best fit. The rate of seed immigration from the background sources was not significantly different from the rate of pollen immigration (13.1 % vs. 19.7 %) and immigration rates were in agreement with or below maximum predictions based on the estimated dispersal kernels. Based on the multimodel approach, 95 % of seeds travel <109 m, while 95 % of pollen travels <704 m from the source. Conclusions The results showed that, at a local spatial scale, yew seeds travel shorter distances than pollen, facilitating a rapid development of a kinship structure. At the landscape level, however, although yew exhibits some potential to colonize new habitats through seed dispersal, genetic connectivity between different yew remnants is strongly limited. Taking into account strong population fragmentation, the study suggests that gene dispersal may be a limiting factor of the adaptability of the species. [ABSTRACT FROM AUTHOR]

Background: Plasmodium falciparum malaria is one of the most widespread parasitic infections in humans and remains a leading global health concern. Malaria elimination efforts are threatened by the emergence and spread of resistance to artemisinin-based combination therapy, the first-line treatment of malaria. Promising molecular markers and pathways associated with artemisinin drug resistance have been identified, but the underlying molecular mechanisms of resistance remains unknown. The genomic data from early period of emergence of artemisinin resistance (2008-2011) was evaluated, with aim to define k13 associated genetic background in Cambodia, the country identified as epicentre of anti-malarial drug resistance, through characterization of 167 parasite isolates using a panel of 21,257 SNPs. Results: Eight subpopulations were identified suggesting a process of acquisition of artemisinin resistance consistent with an emergence-selection-diffusion model, supported by the shifting balance theory. Identification of population specific mutations facilitated the characterization of a core set of 57 background genes associated with artemisinin resistance and associated pathways. The analysis indicates that the background of artemisinin resistance was not acquired after drug pressure, rather is the result of fixation followed by selection on the daughter subpopulations derived from the ancestral population. Conclusions: Functional analysis of artemisinin resistance subpopulations illustrates the strong interplay between ubiquitination and cell division or differentiation in artemisinin resistant parasites. The relationship of these pathways with the P. falciparum resistant subpopulation and presence of drug resistance markers in addition to k13, highlights the major role of admixed parasite population in the diffusion of artemisinin resistant background. The diffusion of resistant genes in the Cambodian admixed population after selection resulted from mating of gametocytes of sensitive and resistant parasite populations. [ABSTRACT FROM AUTHOR]

Objectives Demographic crashes due to emerging diseases can contribute to population fragmentation and increase extinction risk of small populations. Ebola outbreaks in 2002-2004 are suspected to have caused a decline of more than 80% in some Western lowland gorilla ( Gorilla gorilla gorilla) populations. We investigated whether demographic indicators of this event allowed for the detection of spatial fragmentation in gorilla populations. Materials and Methods We collected demographic data from two neighbouring populations: the Lokoué population, suspected to have been affected by an Ebola outbreak (followed from 2001 to 2014), and the Romani population, of unknown demographic status before Ebola outbreaks (followed from 2005 to 2014). Results Ten years after the outbreak, the Lokoué population is slowly recovering and the short-term demographic indicators of a population crash were no longer detectable. The Lokoué population has not experienced any additional demographic perturbation over the past decade. The Romani population did not show any of the demographic indicators of a population crash over the past decade. Its demographic structure remained similar to that of unaffected populations. Discussion Our results highlighted that the Ebola disease could contribute to fragmentation of gorilla populations due to the spatially heterogeneous impact of its outbreaks. The demographic structure of populations (i.e., age-sex and group structure) can be useful indicators of a possible occurrence of recent Ebola outbreaks in populations without known history, and may be more broadly used in other emerging disease/species systems. Longitudinal data are critical to our understanding of the impact of emerging diseases on wild populations and their conservation. [ABSTRACT FROM AUTHOR]

Understanding dispersal traits and adaptive potential is critically important when assessing the vulnerability of freshwater species in highly modified ecosystems. The present study investigates the population genetic structure of the Murray crayfish Euastacus armatus in the southern Murray-Darling Basin. This species has suffered significant population declines in sections of the Murray River in recent years, prompting the need for information on natural recruitment processes to help guide conservation. We assessed allele frequencies from 10 polymorphic microsatellite loci across 20 sites encompassing the majority of the species' range. Low levels of gene flow were observed throughout hydrologically connected waterways, but significant spatial autocorrelation and low migration rate estimates reflect local genetic structuring and dispersal limitations, with home ranges limited to distances <50-km. Significant genetic differentiation of headwater populations upstream of barriers imposed by impoundments were also observed; however, population simulations demonstrate that these patterns likely reflect historical limitations to gene flow rather than contemporary anthropogenic impacts. Dispersal limitations, coupled with its biological traits, suggest that local populations are vulnerable to environmental disturbance with limited potential for natural recolonisation following population decline. We discuss the implications of these findings in the context of managing the recovery of the species. [ABSTRACT FROM AUTHOR]

A combination of directed amplification of minisatellite DNA (DAMD) and random amplification of polymorphic DNA (RAPD) primes were used to assess the genetic variation within and between three isolated populations of Indian sandalwood (Santalum album). Eleven primers used in this study amplified 65.99 % polymorphic bands. Analysis of molecular variance revealed a high genetic variation among these populations (ϕST = 0.549). There are indications of clonality within the existing Indian sandalwood populations which can be attributed to habitat fragmentation, isolation and vegetative reproduction.

Barbary macaques (Macaca sylvanus) are critically endangered primates. They are unique within their genus as the only African macaque. By the late Miocene, their habitat extended across Northern Africa and into Southern Europe. Aside from an introduced population in Gibraltar, their current distribution is reduced to disjointed forests in Algeria and Morocco. Our knowledge of the phylogeographic history and intra-specific diversity of this highly endangered species is also fragmented. In this study, we aimed to improve our understanding of the phylogeographic history and genetic diversity of the Barbary macaque by expanding the genetic data available on the Algerian populations. Moreover, we investigated captive populations of Barbary macaques for comparison to wild populations. The mtDNA hypervariable control region I was sequenced using DNA extracts from faecal and hair samples from wild and captive populations. The newly produced data (n = 157), from both Algerian and Moroccan populations, were combined with previously published data (n = 212) and used to characterize genetic variability and reconstruct phylogenetic relationships among wild and captive populations. We found that Algerian populations exhibit an increased genetic diversity relative to Moroccan populations. Phylogenetic relationships suggest that the Moroccan populations diversified after being isolated from the Algerian populations. Captive populations were found to be not fully representative of the genetic diversity exhibited in the species, but rather only of Moroccan populations. The findings in this study suggest that the fragmented Algerian populations should be managed in order to increase gene flow between them by increasing habitat connectivity where it is feasible to do so. [ABSTRACT FROM AUTHOR]