Stepping stones or stone dead? Fecundity, pollen dispersal and mating patterns of roadside Qualea grandiflora Mart. trees Abstract Forest fragmentation may affect mating and pollen dispersal patterns through conversion of continuous forests into small, spatially isolated remnant patches and individual trees in an anthropogenic landscape. We investigated reproductive investment and success, pollen dispersal, mating system, and genetic diversity and spatial structure of Qualea grandiflora trees in two environmental contexts: a continuous natural Cerrado area and isolated individuals on roadsides. Roadside trees produced more flowers and more fruit than Cerrado trees. Pollen dispersal kernels were fat-tailed in both contexts, indicating long-distance dispersal, but in Cerrado the mean pollen dispersal distance (524.7 m) and the effective number of pollen donors per mother-tree (Nep = 12.7) were higher than for roadside trees (60.9 m, Nep = 4.6). The levels and structure of genetic diversity, outcrossing rates ( \(t_{m}\) > 0.98), and mating among relatives ( \(t_{m} - t_{s}\) < 0.1) were similar in both environmental contexts. Allelic richness and number of private alleles were similar between the two environments. The fixation index was significantly lower in adults (minimum of 0.08) than in offspring (minimum of 0.23) in both contexts, suggesting selection against inbred individuals between offspring and adult stage. Our results indicate that the spatial isolation of roadside trees, by increasing the number of flowers produced, decreased pollinator movements, thereby reducing effective pollen flow and the number of pollen donors. All these results suggest that roadside trees can be used for harvesting seeds for recovery plans, and that these trees are a biological legacy, and reservoir of Q. grandiflora genetic diversity, from the original Cerrado forest.

Genome projects in invasion biology Abstract Advances in sequencing and informatics and rapidly falling costs have made genome sequencing projects far more accessible to researchers in all of the life sciences, including invasion biology. A complete genome is now the most efficient first step towards identifying and characterizing candidate genes that control invasiveness. At the genomic level, fundamental problems in invasion science can be pursued with great precision and rigor. This includes reconstruction of the history of invasions, analysis of demographic dynamics within colonizing populations, and study of the rapid, adaptive evolution of invasiveness. This update documents new developments in the emerging field of invasion genomics. Our review found that of 100 of the world’s most damaging invasive species, assembled genomes are available for 27—a minority but still a considerable resource. This calls for a larger investment in genomics, but also highlights publicly available genomic resources for invasive species that remain underutilized. We examine the value of reference genomes. We conclude that while some technologies (e.g. genotyping by Next Generation Sequencing) can be applied without reference genomes or with fragmented ones, investments in high quality genome assemblies will provide considerable long-term benefits in invasion and conservation genomics research programs.

Population dynamics of an endangered forest bird using mark–recapture models based on DNA-tagging Abstract Populations of vertebrates are built of individuals of different sex, age class or stage, which often affect distinctly the population dynamics. Such intrapopulation partitioning of vital rates needs to be identified to develop efficient conservation actions. Using DNA extracted from feces and feathers we combined DNA-tagging and mark–recapture analyses to evaluate sex-specific population dynamics of an endangered population of capercaillie (Tetrao urogallus; Phasianidae). We built encounter histories for 120 individuals in the mating seasons of 2009–2011, in a study area of about 424 km2. Minimum number of individuals per mating season and estimates of population size ranged 56–67 and 76–115, respectively. Estimates of population size were consistently lower in multiple-season, open-population models than in single-season closed-population models. The super-population in the study area was 149 individuals for the whole study period. Sex-ratio was notably male-biased. Probability of recapture p ranged 0.62–0.70, and was similar for males and females. Female apparent survival φ was lower than expected, and much lower than male apparent survival. It includes however movements in and out of the sampled population, thus comparison with previously reported values based on conventional tagging should be cautious. Females showed higher turnover, indicated by higher probability β of entering the sampled population, and higher number of entries from the super-population, Bgross. Realized population growth rate ʎ was > 1 for both females and males. The combination of non-intrusive DNA-tagging and the analytical framework of mark–recapture models provided inferences on population dynamics that would have been hardly feasible with conventional methods. Male-biased sex ratios, higher female turnover and seemingly low female apparent survival were our key findings. While the whole population needs continuous monitoring, we believe that adult females deserve priority attention in evaluation and design of conservation actions.

Effective population size and heterozygosity-fitness correlations in a population of the Mediterranean lagoon ecotype of long-snouted seahorse Hippocampus guttulatus Abstract The management of endangered species is complicated in the marine environment owing to difficulties to directly access, track and monitor in situ. Population genetics provide a genuine alternative to estimate population size and inbreeding using non-lethal procedures. The long-snouted seahorse, Hippocampus guttulatus, is facing multiple threats such as human disturbance or by-catch, and has been listed in the red list of IUCN. One large population is found in the Thau lagoon, in the south of France. A recent study has shown this population belongs to a genetic lineage only found in Mediterranean lagoons that can be considered as an Evolutionarily Significant Unit (ESU) and should be managed with dedicated conservation strategies. In the present study, we used genetic analysis of temporal samples to estimate the effective population size of the Thau population and correlations between individual multilocus heterozygosity and fitness traits to investigate the possible expression of inbreeding depression in the wild. Non-invasive sampling of 172 seahorses for which profiles were pictured and biometric data recorded were genotyped using 291 informative SNPs. Genetic diversity remained stable over a 7-year time interval. In addition, very low levels of close relatedness and inbreeding were observed, with only a single pair of related individuals in 2008 and two inbreds in 2013. We did not detect departure from identity equilibrium. The effective population size was estimated to be Ne = 2742 (~ 40 reproductive seahorses per km2), larger than previously thought. No correlation was observed between heterozygosity and fluctuating asymmetry or other morphometric traits, suggesting a population with low variance in inbreeding. Together these results suggest this population does not meet conventional genetic criteria of an endangered population, as the population seems sufficiently large to avoid inbreeding and its detrimental effects. This study paves the way for the genetic monitoring of this recently discovered ESU of a species with patrimonial and conservation concerns.

Metabarcoding-based dietary analysis of hen harrier ( Circus cyaneus ) in Great Britain using buccal swabs from chicks Abstract The hen harrier is a heavily persecuted bird of prey in Great Britain since its diet includes Red grouse, a game bird shot in driven and walked-up grouse shooting. Unlike walked-up shooting where shooters walk up moors and flush grouse with dogs, in driven grouse shooting the grouse are driven by beaters towards static shooters. Driven grouse moors (DGMs) are increasingly being managed to sustain high densities of Red grouse intensifying a long-standing conservation conflict between conservationists and grouse moor keepers. A metabarcoding approach was used with degenerate universal cytochrome oxidase I and cytochrome b primers along with hen harrier blocking primers. A novel sampling method was used to detect prey in buccal swab samples from chicks from broods across Great Britain from both managed and unmanaged moorland habitats. This resulted in detection of 62 species of prey across 51 broods with Meadow pipit, Red grouse, Wren, Skylark, and voles being most frequently detected. Frequency of occurrence data and species accumulation curves reveal high incidence of Red grouse and low prey species richness in the diet of hen harriers in DGMs but low incidence of Red grouse and high prey species richness in walked-up and unmanaged moors. Waders were only detected within walked-up and unmanaged moors and not within DGMs where they have been reported to occur at high densities. Regional species detected included endemic species such as the Orkney vole seen only in Orkney. This study represents the first metabarcoding-based dietary analysis in a raptor using buccal swabs.

Genetic status of the endangered plant species Gladiolus palustris in the western part of its distribution area Abstract Many endangered plant species suffer from the effects of ongoing fragmentation of their populations leading to a loss of genetic diversity through genetic drift. In addition, populations of rare plants may also be affected by hybridization with other plant species. We studied the genetic population structure of populations of the endangered Gladiolus palustris in the western limit of its distribution area using AFLP markers. In addition, we clarified the taxonomic status of populations where hybridization with the closely related G. imbricatus was suspected based on morphology by sequencing the ITS region of the nuclear ribosomal DNA as well as two regions of the chloroplast DNA. Our analysis of the genetic population structure of G. palustris revealed a strong differentiation among geographical regions, which was much higher than the differentiation among populations within regions. Most populations retained a considerable amount of genetic variation. To counteract the future loss of genetic diversity through drift, we recommend using the largest populations per region as seed source to increase genetic diversity in genetic depauperate populations of the same region. Our genetic analyses indicated that some French populations of G. palustris are of hybrid origin. These hybridization events are likely to be ancient as these populations are very isolated and some parent taxa went regionally extinct. As these hybrid populations may elucidate post-glacial distribution patterns of related Gladiolus taxa, we advocate that they deserve the same conservation efforts as purebred ones.

Isolation by a hydroelectric dam induces minimal impacts on genetic diversity and population structure in six fish species Abstract Reduced connectivity created by artificial barriers can influence the genetic integrity of isolated subpopulations by reducing local population sizes and altering patterns of gene flow. We investigated the genetic impacts of one such barrier, the Prairie du Sac dam, Wisconsin, USA, using microsatellite data from six fish species with varying life history traits sampled above and below the dam. Contrary to many past studies in other systems, we did not detect any significant differences in genetic diversity between populations found above and below the Prairie du Sac dam. Our results also revealed low genetic differentiation (FST = 0–0.008) between populations above and below the dam for all species. In fact, we found that more genetic variation was partitioned among sampling years than between above and below dam populations for all but one of the species. Results from coalescent simulations designed to model our study system indicated that the genetic impacts of the dam will likely be detectable approximately 40–60 generations after the dam was constructed, and that it is possible to largely mitigate these impacts with a fish passage strategy that facilitates a migration rate of ≥ 1% between above and below dam populations. In summary, our findings suggest the genetic impacts of dams can be relatively minimal on short time scales, and that fish passage strategies can significantly reduce genetic impacts if designed appropriately.

Hierarchical population structure of a rare lagomorph indicates recent fragmentation has disrupted metapopulation function Abstract An understanding of genetic diversity and population structure is important to the conservation of declining species within fragmented habitats. These issues become critical for small, isolated populations, in which stochasticity is a main driver of genetic change and possibly of population extinction. In eastern New York and New England the endemic New England cottontail has declined due to habitat loss and fragmentation. As a species that exhibits metapopulation dynamics, habitat fragmentation can have profound implications for its persistence. We examined genetic diversity, population structure, and effective population size (Ne) of New England cottontails in New York, a purported remnant stronghold for the species. We amplified ten microsatellite loci from tissues collected from live-captures and from fecal pellets. We investigated potential hierarchical population structuring using programs STRUCTURE and BAPS. STRUCTURE identified four hierarchical tiers consisting of nine clusters, and BAPS clustering was highly consistent with that given by STRUCTURE. Most populations displayed significant genetic differentiation (FST = 0.04–0.34) and little to no evidence of ongoing connectivity. Low genetic diversity was observed based on allelic richness (2.2–3.0), and all populations had critically low effective population sizes (Ne; 2.7–57.1). Observed trends in population subdivision, genetic diversity, and Ne were consistent with reported trends in the state-endangered Maine-New Hampshire populations, and not indicative of a genetic stronghold within New York. Instead, the small and isolated populations observed here imply a breakdown in metapopulation functionality indicative of conditions faced by the species range-wide and an immediate need for human intervention to restore connectivity and rebuild populations.

Recent large-scale landscape changes, genetic drift and reintroductions characterize the genetic structure of Norwegian wild reindeer Abstract Landscape changes, such as habitat loss and fragmentation, subdivide wild populations, reduce their size, and limit gene flow. These changes may further lead to depletion of genetic variation within populations as well as accelerating differentiation among populations. As a migratory species requiring large living areas, wild reindeer (Rangifer tarandus) is highly vulnerable to human activity. The number and continued presence of wild reindeer have been significantly reduced due to accelerating anthropogenic habitat modifications, as well as displacement in benefit of domesticated herds of the species. As a basis for future management strategies we assess genetic structure and levels of genetic variation in Norwegian wild reindeer by analysing 12 microsatellite loci and the mitochondrial control region in 21 management units with varying population sizes. Overall, both markers showed highly varying levels of genetic variation, with reduced variation in the smaller and more isolated populations. The microsatellite data indicated a relationship between population size and genetic variation. This relationship was positive and linear until a threshold for population size was reached at approximately 1500 reindeer. We found high levels of differentiation among most populations, indicating low levels of gene flow, but only a weak correlation between geographic and genetic distances. Our results imply that the genetic structure of Norwegian wild reindeer is mainly driven by recent colonization history, population size, as well as human-induced landscape fragmentation, restricting gene flow and leading to high levels of genetic drift. To sustain viable populations, conservation strategies should focus on genetic connectivity between populations.

Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail ( Cyrtonyx montezumae ) Abstract Population extirpations are often precursors to species extinctions. Anthropogenic activities often lead to smaller populations that are more prone to extirpations and advocates for active conservation management have recently called for the preservation and monitoring of genetic diversity, particularly with regard to the adaptive potential of vulnerable populations. We used genomics and curated arrays of molecular markers, including those expected to impact key fitness traits, to quantify evidence of genomic erosion in core and peripheral populations of a gallinaceous bird. The Montezuma quail (Cyrtonyx montezumae) is a game species considered vulnerable to extirpation in Texas, but core populations in Arizona and New Mexico are robust and have the potential to serve as genetic reservoirs. We sequenced the Montezuma quail genome then developed a single nucleotide polymorphism (SNP) assay to quantify genetic variation, effective population sizes, signatures of natural selection, and population structure. We genotyped SNPs from gene deserts and from genes associated with fitness traits and found the isolated Texas population exhibits an extremely small effective population size, is genetically distinct from our Arizona and New Mexico samples, and has reduced heterozygosity at the fitness-related markers. Thus, our samples from Texas exhibit symptoms of genetic erosion that could exacerbate future risk of local extirpation. Management agencies must decide if active conservation efforts such as assisted gene flow or genetic rescue are now warranted. This decision may not be straightforward because the current conservation status of the Texas population reflects its isolated geographic locale on the periphery of the species’ range.