Contrasting coarse and fine scale genetic structure among isolated relic populations of Kmeria septentrionalis

Trees of the Magnoliaceae family are of scientific, cultural and socio-economic importance. Kmeria septentrionalis Dandy (Magnoliaceae) is a dioecious tree, found in small, isolated, relic populations in Southern China, and is subject to extensive protection due to its rarity and high economic values. To improve conservation outcomes and in particular, germplasm collection guidelines, information on spatial genetic structure of the species is required. In this study, we investigated the spatial genetic structure and genetic diversity of 161 individuals of K. septentrionalis collected from five natural populations using AFLP molecular markers. Within-population genetic variation was measured, with percentage of polymorphic bands (PPB) ranged from 63% to 87%, while H _S (genetic diversity within population) varied from 0.185 to 0.244 with a mean of 0.215 ± 0.025. Significant genetic differentiations were revealed between pairwise populations, indicating each population existing as an independent evolutionarily significant unit. Mantel test results showed no pattern of isolation-by-distance among populations separated by large distance. Fine scale spatial patterns of genetic variation suggested significant effects of isolation-by-distance within population at distances of 22 m. The results of contrasting genetic structure at coarse and fine scale in K. septentrionalis may indicate restricted pollen flow and seed dispersal at fine scales, and separated evolution in isolated populations over long period of time at coarser scales. Finally, we make several suggestions for improved management practices that may assist in the conservation of this species.     

Population genetic structure of the endangered Eastern Bristlebird, Dasyornis brachypterus; implications for conservation

For species that are habitat specialists or sedentary, population fragmentation may lead to genetic divergence between populations and reduced genetic diversity within populations, with frequent inbreeding. Hundreds of kilometres separate three geographical regions in which small populations of the endangered Eastern Bristlebird, Dasyornis brachypterus, a small, ground-dwelling passerine that occurs in fire-prone bushland in eastern Australia, are currently found. Here, we use mitochondrial and microsatellite DNA markers to: (i) assess the sub-specific taxonomy designated to northern range-edge, and central and southern range-edge D. brachypterus, respectively, and (ii) assess levels of standing genetic variation and the degree of genetic subdivision of remnant populations. The phylogenetic relationship among mtDNA haplotypes and their spatial distribution did not support the recognised subspecies boundaries. Populations in different regions were highly genetically differentiated, but in addition, the two largest, neighboring populations (located within the central region and separated by ~50 km) were moderately differentiated, and thus are likely closed to migration (microsatellites, F _ST = 0.06; mtDNA, F _ST = 0.12, ?? _ST = 0.08). Birds within these two populations were genotypically diverse and apparently randomly mating. A long-term plan for the conservation of D. brachypterus??s genetic diversity should consider individual populations as separate management units. Moreover, managers should avoid actively mixing birds from different populations or regions, to conserve the genetic integrity of local populations and avoid outbreeding depression, should further translocations be used as a recovery tool for this species.     

Local genetic structure of a montane herb among isolated grassland patches: implications for the preservation of genetic diversity under climate change

Habitat loss, fragmentation of meadow patches, and global climate change (GCC) threaten plant communities of montane grasslands. We analyzed the genetic structure of the montane herb Geranium sylvaticum L. on a local scale in order to understand the effects of habitat fragmentation and potential GCC impacts on genetic diversity and differentiation. Amplified fragment length polymorphism (AFLP) fingerprinting and cpDNA sequencing was performed for 295 individuals of 15 G. sylvaticum populations spanning the entire distribution range of the species in the Taunus mountain range in Germany. We found patterns of substantial genetic differentiation among populations using 150 polymorphic AFLP markers (mean F _ST = 0.105), but no variation in 896 bp of plastid DNA sequences. While populations in the center of their local distribution range were genetically diverse and less differentiated, higher F _ST values and reduced genetic variability was revealed for the populations at the low-altitudinal distribution margins. Projections of GCC effects on the distribution of G. sylvaticum in 2050 showed that GCC will likely lead to the extinction of most edge populations. To maintain regional genetic diversity, conservation efforts should focus on the diverse high-altitude populations, although a potential loss of unique variations in genetically differentiated peripheral populations could lower the overall genetic diversity and potentially the long-term viability in the study region. This study documents the usefulness of fine-scale assessments of genetic population structure in combination with niche modeling to reveal priority regions for the effective long-term conservation of populations and their genetic variation under climate change.     

Cryptic genetic subdivision in the San Benito evening primrose (Camissonia benitensis)

When rare plants are distributed across a range of habitats, ecotypic differentiation may arise requiring customized conservation measures. The rate of local adaptation may be accelerated in complex landscapes with numerous physical barriers to gene flow. In such cases, examining the distribution of genetic diversity is essential in determining conservation management units. We investigated the distribution of genetic diversity in the federally threatened Camissonia benitensis (Onagraceae), which grows in two distinct serpentine habitats across several watersheds in San Benito, Fresno, and Monterey Cos., CA, USA. We compared genetic diversity with that of its two widespread relatives, C. contorta and C. strigulosa, and examined the potential for hybridization with the latter species. Genotyping results using seven heterospecific microsatellite markers indicate that differentiation between habitat types was weak (F _ST = 0.0433) and in an AMOVA analysis, there was no significant partitioning of molecular variation between habitats. Watersheds accounted for 11.6 % of the molecular variation (pairwise F _ST = 0.1823–0.4275). Three cryptic genetic clusters were identified by InStruct and STRUCTURE that do not correlate with habitat or watershed. C. benitensis exhibits 5–11× higher inbreeding levels and 0.54× lower genetic diversity in comparison to its close relatives. We found no evidence of hybridization between C. benitensis and C. strigulosa. To maximize conservation of the limited amount of genetic diversity in C. benitensis, we recommend mixing seed representing the three cryptic genetic clusters across the species’ geographic range when establishing new populations.     

Geographic variation in relict populations: genetics and phenotype of bush-cricket Pholidoptera frivaldskyi (Orthoptera) in Carpathians

A decreasing population size is often causing species extinction, however, relict species persisting in small-sized populations counter this. We analysed spatial genetic variation and past changes in population size at the maternally-inherited mitochondrial DNA level to clarify the origin of all recently known isolated populations of Pholidoptera frivaldskyi occurring in the range of Carpathian Mountains. Along with that we analysed also morphological variation as some phenotypic traits can retain useful information on population genetic structure. We found a relatively low genetic diversity within isolated populations as 778 bp COI gene sequences revealed only 13 unique haplotypes (n = 173 individuals from 10 populations). The spatial analysis of molecular variance identified three geographically homogenous genetic clusters (one in Slovakia and two in Romania) with a high level of differentiation among them, suggesting restricted gene flow, whilst Bayesian skyline simulation reconstructed a negative demographic change through evolutionary time. Inferred genetic pattern clearly coincides with differences in males’ colour phenotype as the extent of pigmentation on the lateral pronotum varied significantly among genetic lineages. We suggest that geographical variation in the species populations has relict-like character and their isolated occurrence is not a result of recent introduction events. Identification of ‘evolutionary units’ may help in the conservation and management of this rare insect species.     

Genetic variation and conservation of the endangered endemic Anagyris latifolia Brouss. ex Willd. (Leguminosae) from the Canary Islands

Anagyris latifolia is an endemic and endangered species from the Canary Islands, whose distribution is limited to four islands, with less than 400 individuals in fragmented and isolated localities. RAPD markers have been used to assess the genetic diversity and genetic differentiation of its populations, in order to formulate appropriate management and conservation genetics strategies. Nine polymorphic primers generated 74 polymorphic DNA fragments. Genetic variation levels detected in Anagyris latifolia were significant high (H = 0.200; P% = 97.3), principal coordinates analysis and genetic differentiation coefficient showed a high degree of genetic differentiation between islands, without a define east-to-west stepping stone colonization route. AMOVA analysis showed that of the total genetic variation detected, 32.43% was maintained among islands, 20.73% contained among population within islands, and 46.84% resided within populations. According to these results, management strategies should be focused on each island separately.     

Dispersal ecology of the endangered woodland lichen Lobaria pulmonaria in managed hemiboreal forest landscape

Changes in the forest management practices have strongly influenced the distribution of species inhabiting old-growth forests. The epiphytic woodland lichen Lobaria pulmonaria is frequently used as a model species to study the factors affecting the population biology of lichens. We sampled 252 L. pulmonaria individuals from 12 populations representing three woodland types differing in their ecological continuity and management intensity in Estonia. We used eight mycobiont-specific microsatellite loci to quantify genetic diversity among the populations. We calculated the Sørensen distance to estimate genetic dissimilarity among individuals within populations. We revealed that L. pulmonaria populations have significantly higher genetic diversity in old-growth forests than in managed forests and wooded meadows. We detected a significant woodland-type-specific pattern of genetic dissimilarity among neighbouring L. pulmonaria individuals, which suggests that in wooded meadows and managed forests dominating is vegetative reproduction. The vegetative dispersal distance between the host trees of L. pulmonaria was found to be only 15–30 m. Genetic dissimilarity among individuals was also dependent on tree species and trunk diameter. Lobaria pulmonaria populations in managed forests included less juveniles compared to old-growth forests and wooded meadows, indicating that forest management influences life stage structure within populations. We conclude that as intensive stand management reduces the genetic diversity of threatened species in woodland habitats, particular attention should be paid to the preservation of remnant populations in old-growth habitats. Within managed habitats, conservation management should target on maintenance of the stand’s structural diversity and availability of potential host trees.     

Genetic diversity and population structure of the serpentine endemic Ni hyperaccumulator Alyssum lesbiacum

Alyssum lesbiacum is a well-established Ni hyperaccumulator, endemic to serpentine soils of Lesbos Island (Greece). A total of 95 individuals were collected from 17 plots encompassing the only four large populations of this species. ISSR (Inter-simple sequence repeat) markers were used to assess genetic diversity and population structure of A. lesbiacum to provide initial guidance for the development of successful management and conservation measures. A total of ten primers produced 82 bands, 96.34 % being polymorphic. The largest part of total diversity was found within populations, rather than among them. AMOVA analysis partitioned the largest part of diversity within plots (66 %), while 15 % contained among plots within populations and 19 % among populations. Principal coordinates analysis along with dendrogram based on genetic distances among populations showed a high degree of genetic differentiation of the isolated population Loutra. At a smaller scale, distance was not the most significant factor influencing the patterns of genetic diversity, but topography, ecosystem types and connectivity through streams. According to our results, conservation efforts should be organized at the level of watersheds and ecosystem types, considering them as management units. For ex situ conservation and restoration, seed samplings should be representative of the different habitats and watersheds as well as the patches of large and small populations while keeping the east population of Loutra separate from the other three central populations, to avoid any loss of genetic diversity and to preserve the character of the local adapted populations.     

Phylogeographic evidence links the threatened ‘Grampians’ Mountain Dragon (Rankinia diemensis Grampians) with Tasmanian populations: conservation implications in south-eastern Australia

The importance of protecting genetic diversity within a species is increasingly being recognised by conservation management authorities. However, discrepancies in conservation policy between authorities, such as state versus national bodies, can have significant implications for species management when they cross state boundaries. We conducted a phylogeographic study of the south-eastern Australian lizard Rankinia diemensis to identify evolutionary significant units (ESUs), including the endangered population from the Grampians National Park in western Victoria. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames. Based on criteria of genetic divergence and isolation, R. diemensis contains at least two ESUs that require specific management. We found that R. diemensis from the Grampians are closely related to Tasmanian populations, but that the divergence between these regions is great enough (3.7 % mtDNA) that they should be considered separate ESUs. However, we believe the close evolutionary ties between these two regions needs to be taken into account; yet under current practises, conservation management of subspecific ESUs relies on state-level efforts. We argue that another population that occurs on the Victorian coast also qualifies as an ESU and requires targeted conservation action. Rankinia diemensis provides a case-in-point of the discrepancy between the state-level approach of maintaining genetic variation within a species and the more conservative Commonwealth focus on conserving biodiversity at the species level.     

Population genetic structure of wild daffodils (Narcissus pseudonarcissus L.) at different spatial scales

We studied the population genetic and clonal structure of the endangered long-lived perennial plant Narcissus pseudonarcissus using random amplified polymorphic markers. Estimates for mean gene diversity within 15 populations of N. pseudonarcissus of three neighbouring geographical regions were high in comparison to other long-lived perennials (H _eN = 0.33). The genetic diversity of the two smallest populations (<200 plants) was significantly reduced, indicating loss of genetic variability due to drift. The analysis of the population genetic structure revealed a significant genetic differentiation both between regions (Φ_ST = 0.06) and between populations within regions (Φ_ST = 0.20). However, there was incomplete correspondence between geographical regions and the population genetic structure. In order to preserve the overall genetic variation in wild populations of N. pseudonarcissus, management measures should thus aim to protect many populations in each region. The spatial genetic structure within populations of N. pseudonarcissus was in agreement with an isolation by distance model indicating limited gene flow due to pollinator behaviour and restricted seed dispersal. The very restricted spatial extent of clonal growth (<5 cm) and the high level of clonal diversity indicate that clonal growth in N. pseudonarcissus is not an important mode of propagation and that management measures should favour sexual reproduction in order to avoid further reductions in the size and number of populations.     

Population genetics of a widely distributed small freshwater fish with varying conservation concerns: the southern purple-spotted gudgeon, <Emphasis Type="Italic">Mogurnda adspersa</Emphasis>

Genetic variation plays a pivotal role in species viability and the maintenance of population genetic variation is a main focus of conservation biology. Threatened species often show reduced genetic variation compared to non-threatened species, and this is considered indicative of lowered evolutionary potential, compromised reproductive fitness, and elevated extinction risk. The southern purple-spotted gudgeon, Mogurnda adspersa, is a small freshwater fish with poor dispersal potential that was once common throughout the Murray–Darling Basin (MDB) and along the central east coast of Australia. Its numbers and distribution have shrunk dramatically in the MDB due to flow alteration, degradation of habitat, decreasing water quality, and introduction of alien species. We used microsatellite DNA markers to assess population structure and genetic variation at both large (i.e. across basin) and fine (i.e. within river catchments) spatial scales using a substantial sampling effort across the species range (n = 579 individuals; 35 localities). The results consistently indicated very low levels of genetic variation throughout, including along the east coast where the species is relatively common. At the broader scale, three highly differentiated groups of populations were found, concordant with previously reported genealogical distinctiveness. Hence we propose each group as a distinct Evolutionarily Significant Unit. We also inferred a minimum of 12 management units in M. adspersa, with no appreciable gene flow between them. Our study discloses findings relevant for both long- and short-term management, as it informs on the geographic context in which conservation priorities should be defined and specifies biological units for population monitoring and translocations.     

Fine-scale spatial genetic structure in the frankincense tree <Emphasis Type="Italic">Boswellia papyrifera</Emphasis> (Del.) Hochst. and implications for conservation

The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a highly valued aromatic resin obtained from the bark of the tree. This study assessed the genetic diversity and fine-scale spatial genetic structure (FSGS) of two cohorts (adults and seedlings) from two populations (Guba-Arenja and Kurmuk) in Western Ethiopia and inferred intra-population gene dispersal in the species, using microsatellite markers. The expected heterozygosity (H _E) was 0.664–0.724. The spatial analyses based on kinship coefficient (F _ij) revealed a significant positive genetic correlation up to a distance of 130 m. Spatial genetic structure was relatively weak (Sp = 0.002–0.014) indicating that gene dispersal is extensive within the populations. Based on the FSGS patterns found, we estimate indirectly gene dispersal distances of 103 and 124 m for the two populations studied. The high heterozygosity, the low fixation index and the low Sp values found in this study are consistent with outcrossing as the (predominant) mating system in B. papyrifera. We suggest that seed collection for ex situ conservation and reforestation programmes of B. papyrifera should use trees separated by distances of at least 100 m but preferably 150 m to limit genetic relatedness among seeds from different trees.     

Reconstructing the introduction history of an invasive fish predator in South Africa

The Largemouth Bass (Micropterus salmoides) is a global invader with demonstrated ecological impacts on native fish communities. Introductions of fishes in freshwater ecosystems are often characterized as complex processes, yet an understanding of the nature of the introduction can inform management and conservation actions. Early in the twentieth century, two introductions of Largemouth Bass were made into South Africa for the establishment of a recreational fishery, and subsequent translocations have expanded their distribution to include much of southern Africa. In this study we quantified neutral genetic variation, modeled potential introduction scenarios, and identified potential source regions from within the native range. We documented limited levels of genetic diversity in nuclear microsatellite genotypes across populations (mean allelic richness = 1.80 and mean observed heterozygosity = 0.16) and observed low levels of genetic differentiation among four of the five focal populations (mean pairwise fixation index = 0.09), with a fifth population displaying greater levels of genetic divergence (mean pairwise fixation index = 0.27). A total of three cytochrome b haplotypes were recovered from South Africa samples and the single most common haplotype (93% of individuals) was identical to a haplotype from a population of Largemouth Bass in Maryland, USA. Using limited available stocking data along with outputs from Principal Component Analysis and approximate Bayesian evaluation of competing introduction scenarios we confirm the presence of multiple introductions. Despite evidence for multiple introductions, Largemouth Bass in South African water bodies harbor extremely low neutral genetic diversity, suggesting that even a very limited number of propagules can experience a high likelihood of success in invading nonnative waters.     

Genetic diversity analysis of the endangered slipper orchid Phragmipedium longifolium in Costa Rica

Phragmipedium longifolium is an endangered terrestrial orchid. In Costa Rica, these plants are found growing in small and isolated patches, some of them consisting of just four to six individuals. Information about the genetic variability within and among populations is very important for the conservation of this endangered species. A total of 160 samples were collected in six locations and analyzed with amplified fragment length polymorphism technique. The genetic diversity of P. longifolium in Costa Rica (Hw = 0.1711) is high and differentiation among sampled locations is moderate (φ_pt = 0.2013) in comparison with results of studies in some other terrestrial orchid species using the same technique. The percentage of polymorphic loci was, on average, 51.5. The analysis of molecular variance (AMOVA) indicated the main genetic variation was within sampled locations (80%), even though the variation among locations was also significant. In situ conservation is recommended because, in addition to protecting habitat and avoiding fragmentation, mycorrhizal fungi and pollinators are also protected. Close proximity between populations is required to maintain high genetic variability through a gene flow continuum. It is suggested that conservation of patches with higher genetic variability be prioritized as many are located in unprotected areas. A germplasm bank for ex situ conservation has been established in the living collection at Lankester Botanical Garden using the plants collected in this study. Finally, a search for new locations of this species is also suggested.     

Population genetic diversity and divergence of the halobiotic herb Limonium sinense estimated by AFLP and ISSR, and implications for conservation

Limonium sinense is a halobiotic herb endemic to China that has been traditionally used for hundreds of years for its good restorative function. Genetic variation and population structure of this species were investigated by using amplified fragment length polymorphisms (AFLPs) and inter simple sequence repeats (ISSRs). A high level of genetic diversity was detected [AFLP: H _E = 0.284, percentage of polymorphic loci (PPL) = 92.68 %; ISSR: H _E = 0.257, PPL = 85.71 %] at the species level with POPGENE. Based on analysis of molecular variation (AMOVA), the among-population component accounted for 29.03 % (AFLP) and 28.81 % (ISSR) of the genetic variation, indicating that most of the genetic variation was between individuals within populations. The Shannon diversity index (I) was higher for AFLP (0.432) than for ISSR (0.395). Five main clusters were shown in the unweighted pair-group method with arithmetic mean (UPGMA) dendrogram created using TFPGA, consistent with the result of principal coordinate analysis using NTSYS. In situ conservation is advocated first. Keeping a stable environment for this halobiotic herb is necessary. For ex situ conservation, it is important to establish a germplasm bank. AFLP and ISSR markers were proved to be efficient tools in assessing the genetic variation among populations of L. sinense. The patterns of variation appeared to be consistent for these two marker systems, and they can be used for management of genetic structure, protection of the halobiotic plant, and conservation of germplasm.     

Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas

Selective breeding often produces an improvement in phenotype. Much of the phenotypic change within a species is a consequence of genetic variation. However, there is growing evidence for phenotypic change even in the absence of DNA sequence polymorphisms, termed epigenetic variation. This study’s goal was to investigate the genetic and epigenetic variation in the mass selection populations of the Pacific oyster (Crassostrea gigas), determine if any correlation exists between the genetic and epigenetic variations. This can serve as a first step in investigating the potential role epigenetic variations have in selective breeding. Amplified fragment length polymorphism analysis and methylation-sensitive amplified polymorphism methodology were used to monitor genetic and epigenetic variation in two populations (the base stock and the third selected generation) from a mass selection line in the Pacific oyster. The correlation between genetic and epigenetic variation was evaluated by Co-Inertia Analysis. The genetic difference was mainly found in the gene frequency shift revealed by the F _ST value (0.0151, P < 0.01) and no significant reduction in genetic diversity was detected. The percentage of methylation in C. gigas was 26.4 %. No significant difference was observed on the average state of methylation, but a few bands showed different frequencies between the two populations. Co-Inertia Analysis revealed a significant association between the genetic and epigenetic profiles (P < 0.01).     

Extreme genetic depauperation and differentiation of both populations and species in Eurasian feather grasses (Stipa)

A highly selfing breeding system affects gene flow, which may have consequences for patterns of genetic variation and differentiation on both the population and species level. Feather grasses (Stipa spp.) are dominant elements of Eurasian steppes that persist in Central Europe in scattered isolated populations that are of great conservation interest. Cleistogamy is common in the Stipa pennata group, the phylogeny of which is largely unresolved. Intraspecific patterns of genetic variation can be characterised by lack of gene flow due to selfing, but also by large-scale historical migrations and long-term isolation. We analysed both 5 species within the S. pennata group and 33 populations of Stipa pulcherrima sampled across a large part of its range. Using AFLP markers we assessed phylogenetic relationships of the S. pennata group and patterns of genetic variation within and among populations. The S. pennata group formed a consistent clade separated from S. capillata. Stipa pulcherrima was sister to S. eriocaulis, but the relationships among S. pennata s. str., S. borysthenica., and S. tirsa remained unresolved. Within-population genetic variation was extremely low in all species of the S. pennata group (H _e = 0.0–0.013). In S. pulcherrima, genetic variation was consistently relatively high in the east (Romania, Russia) and declined toward western populations, with many populations at the western range edge lacking genetic variation entirely. Populations were strongly differentiated (F _ST = 0.762), and this differentiation did not follow a classical pattern of isolation by distance. Bayesian cluster analysis revealed nine gene pools in S. pulcherrima, which were mostly geographically clustered. Overall the results suggest that S. pulcherrima and species of the S. pennata group are characterised by a cleistogamous breeding system leading to extremely low levels of genetic variation and high levels of population differentiation at both the population and species level. Postglacial colonisation, current population isolation, and population bottlenecks at the western range periphery have further reduced genetic variation and obviated gene exchange. Thus, genetic variation can only be preserved by the conservation of multiple populations.     

Genome-wide SNP loci reveal novel insights into koala (<Emphasis Type="Italic">Phascolarctos cinereus</Emphasis>) population variability across its range

The koala (Phascolarctos cinereus) is an iconic Australian species that is currently undergoing a number of threatening processes, including disease and habitat loss. A thorough understanding of population genetic structuring and genomic variability of this species is essential to effectively manage populations across the species range. Using a reduced representation genome sequencing method known as double digest restriction-associated sequencing, this study has provided the first genome-wide SNP marker panel in the koala. In this study, 33,019 loci were identified in the koala and a filtered panel of 3060 high-utility SNP markers, including 95 sex-linked markers, were used to provide key insights into population variability and genomic variation in 171 koalas from eight populations across their geographic range. Broad-scale genetic differentiation between geographically separated populations (including sub-species) was assessed and revealed significant differentiation between all populations (F_ST range = 0.01–0.28), with the largest divergence observed between the three geographically distant subgroups (QLD, NSW and VIC) along the east coast of Australia (average F_ST range = 0.17–0.23). Sub-group divergence appears to be a reflection of an isolation by distance effect and sampling strategy rather than true evidence of sub-speciation. This is further supported by low proportions of AMOVA variation between sub-species groups (11.19 %). Fine-scale analysis using genome-wide SNP loci and the NETVIEW pipeline revealed cryptic genetic sub-structuring within localised geographic regions, which corresponded to the hierarchical mating system of the species. High levels of genome-wide SNP heterozygosity were observed amongst all populations (He = 0.25–0.35), and when evaluating across the species to other vertebrate taxa were amongst the highest values observed. This illustrates that the species as a whole still retains high levels of diversity which is comparable to other outbred vertebrate taxa for genome-wide SNPs. Insights into the potential for adaptive variation in the koala were also gained using outlier analysis of genome-wide SNPs. A total of 10 putative outlier SNPs were identified indicating the high likelihood of local adaptations within populations and regions. This is the first use of genome-wide markers to assess population differentiation at a broad-scale in the koala and the first time that sex-linked SNPs have been identified in this species. The application of this novel genomic resource to populations across the species range will provide in-depth information allowing informed conservation priorities and management plans for in situ koalas across Australia and ex situ around the world.     

Genetic diversity of the African poplar (<Emphasis Type="Italic">Populus ilicifolia</Emphasis>) populations in Kenya

We evaluated the genetic diversity of the African poplar (Populus ilicifolia) populations found in Kenya compared with reference samples of five poplar species from North America and one species introduced in Kenya from India (KEFRI-Kenya). Amplified fragment length polymorphism (AFLP) was used with the objective of providing important information for breeding and in situ/ex situ conservation of this species. Samples collected from three locations along the species’ natural range (Athi, Ewaso Nyiro, and Tana rivers) were compared with four samples of locally planted Populus deltoides stand introduced from India and ten reference samples from North America. Six AFLP primer combinations produced 521 clear bands for analysis. The percentage polymorphic loci were lowest in Tana (20.4 %) and highest in Athi (40.6 %). The average heterozygosity across the studied populations was between 0.07 and 0.3. AMOVA revealed more genetic variation partitioning within population (87 %; P?<?0.01) than among populations (13 %; P?<?0.01) suggesting significant genetic variation between populations. Further, UPGMA delineation showed two clusters of the Tana, Athi, and Ewaso Nyiro populations clustered together compared to the North America and India/KEFRI reference samples. Moreover, the study showed that the Athi population is more diverse than those of Tana and Ewaso Nyiro and may be important for conservation, domestication, and improvement studies. The genetic differentiation (F _ST ?=?0.134) among Kenyan P. ilicifolia populations suggests limited possibility of gene flow between these populations.     

Spatio-temporal effects of stray hatchery-reared Atlantic salmon Salmo salar on population genetic structure within a 21 km-long Icelandic river system

Although the tendency of Atlantic salmon Salmo salar to form differentiated populations among rivers and among tributaries within large river systems (>100 km-long) is well documented, much less is known about population structure within small river systems (<30 km-long). In the present study, we investigated the genetic effects of straying of hatchery-reared salmon on population structure and genetic composition within the Ellidaár river system, a small system (21 km total length) in SW Iceland. We analyzed spatial and temporal variation of wild and domesticated samples (farmed and ranched; n = 931) using seven microsatellite loci. Estimates of population differentiation [F _ST, genetic tree (D _A)] and Bayesian cluster analysis (STRUCTURE) revealed a significant population structure as well as relative long-term temporal stability of the genetic composition in the main river from 1948 to 2005. However, the genetic composition of the tributary populations was unstable and genetically homogenized in recent years. Wild-hatchery hybrids were detected during the influx of strays as well as few years after, suggesting that introgression has changed the genetic composition of the wild populations. More investigations are needed in Iceland and elsewhere on possible fine-scale population differentiation and factors leading to it. Fine-scale population differentiation as observed in the present study has implications for the resolution with which harvest and habitat management of salmon should be conducted. In addition, farming and ranching operations should be located to minimize potential negative effects of strays on wild fish.