Population genetics of an invasive riparian species,<Emphasis Type="Italic"> Impatiens glandulifera</Emphasis>

We assess the population genetic structure of the invasive riparian weed Impatiens glandulifera, and where possible, determine whether natural or anthropogenic dispersal best explains the observed patterns. Results are compared with a similar contemporary analysis for Heracleum mantegazzianum undertaken in the same catchments, and we suggest that some of the observed differences in genetic structure could be because of life history differences between these species. Our results confirm the importance of at least occasional dispersal events mediated by human activity in the colonisation and subsequent spread of invasive plants in river catchments. However, processes related to river structure, dispersal range and genetic drift also appear to be structuring these populations over short temporal scales. The implication is that local populations can be established as small founders, and therefore eradication programs need to be thorough and undertaken at the catchment scale. Effective management needs to consider the natural spread of riparian species along rivers, but also prevent long-distance dispersal from sources outside the catchment. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Tracing the invasion history of mealy plum aphid, Hyalopterus pruni (Hemiptera: Aphididae), in North America: a population genetics approach

Biological invasions are typically the outcome of complex patterns of introduction, establishment, and spread, and genetic methods are excellent tools to resolve such histories for non-native organisms. The mealy plum aphid, Hyalopterus pruni, is an invasive pest of dried plum in California. We examined nine microsatellite loci and DNA sequences from three mitochondrial genes (1,148 bp) in populations throughout the native and invaded ranges of H. pruni to assess key invasion parameters, including geographic origins of invasive populations, number of introductions, and levels of genetic diversity and gene flow. Our results provide evidence for multiple invasions of H. pruni into North America, suggesting that aphids in California may have been introduced from Spain, and aphids in the eastern United States and Vancouver, Canada were likely introduced from central or northern Europe. H. pruni populations in California were characterized by low genetic diversity relative to native populations, while the two other North American populations were less genetically impoverished. Gene flow among introduced populations was low, but does appear to occur with some regularity. These findings provide a framework for more detailed studies of H. pruni, but also represent a model for how population genetics approaches can be used to study invasion biology and aid the development of optimized management methods for agricultural pests. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Estimating abundance with sparse data: tigers in northern Myanmar

As part of a national strategy for recovering tiger populations, the Myanmar Government recently proposed its first and the world’s largest tiger reserve in the Hukaung Valley, Kachin State. During November 2002–June 2004, camera-traps were used to record tigers, identify individuals, and, using capture–recapture approaches, estimate density in the reserve. Despite extensive (203 trap locations, 275–558 km² sample plots) and intensive (>4,500 trap nights, 9 months of sampling) survey efforts, only 12 independent detections of six individual tigers were made across three study sites. Due to the sparse data, estimates of tiger abundance generated by Program CAPTURE could not be made for all survey sites. Other approaches to estimating density, based on numbers of tigers caught, or derived from borrowed estimates of detection probability, offer an alternative to capture–recapture analysis. Tiger densities fall in the range of 0.2–2.2 tigers/100 km², with 7–71 tigers inside a 3,250 km² area of prime tiger habitat, where efforts to protect tigers are currently focused. Tiger numbers might be stabilized if strict measures are taken to protect tigers and their prey from seasonal hunting and to suppress illegal trade in wildlife. Efforts to monitor abundance trends in the tiger population will be expensive given the difficulty with which tiger data can be obtained and the lack of available surrogate indices of tiger density. Monitoring occupancy patterns, the subject of a separate ongoing study, may be more efficient.     

Accelerated failure time (AFT) modeling for the development and survival of Russian wheat aphid, <Emphasis Type="Italic">Diuraphis noxia</Emphasis> (Mordvilko)

Accelerated failure time model (AFT) and Cox’s proportional hazards model (PHM) are considered the two most significant models in survival analysis, which has become a de facto standard for biomedical data analysis and modeling. AFT not only plays an extremely significant role in survival analysis but also finds extensive applications in engineering reliability. Survival analysis studies a special type of random variables: time-to-event (also known as failure time, lifetime or survival time) random variables. Examples of time-to-event random variables include survival times of patients in a clinical trial and failure times of machine components. Since molting and death times of insect individuals are also perfect examples of time-to-event random variables, we argue that survival analysis including AFT modeling is ideal for analyzing insect development and survival data, and further for building dynamic models of insect development and survival. Here we demonstrate such an application with data collected by observing stage-to-stage development and survival of 1,800 Russian wheat aphids (RWA), Diuraphis noxia, reared in laboratory growth chambers arranged in 25 treatments (each with 72 individuals). The main advantages of survival analysis, including the unified modeling of survival and development as well as handling of information censoring, are also discussed.     

Polymorphic microsatellite loci in the Chinese pond turtle (Chinemys reevesii)

Eight novel polymorphic microsatellite loci developed from a microsatellite enriched genomic library, are presented for the Chinese pond turtle (Chinemys reevesii). We screened 30 individuals from three populations and detected high levels of polymorphism for all eight loci with the number of alleles/locus ranging from 7 to 17 (average = 10.88). The values of expected and observed heterozygosities ranged from 0.703 to 0.920 and 0.321 to 0.966, respectively. These highly variable loci will provide a powerful molecular toolkit for studies of population structure, gene flow, and paternity assignment.     

mtDNA indicates profound population structure in Indian tiger (Panthera tigris tigris)

We analyzed mtDNA polymorphisms (parts of control region, ND5, ND2, Cytb, 12S, together 902 bp) in 59 scat and 18 tissue samples from 13 Indian populations of the critically endangered Indian tiger (Panthera tigris tigris), along with zoo animals as reference. Northern tiger populations exhibit two unique haplotypes suggesting genetic isolation. Western populations from Sariska (extinct in 2004) and Ranthambore are genetically similar, such that Ranthambore could serve as a source for reintroduction in Sariska. Zoo populations maintain mitochondrial lineages that are rare or absent in the wild.     

Intra-population genetic diversity of two wheatgrass species along altitude gradients on the Qinghai-Tibetan Plateau: its implication for conservation and utilization

A fluorescence-based AFLP fingerprinting was applied to investigate genetic diversity in 22 natural populations of two wheatgrasses from Qinghai-Tibetan Plateau at different altitudes: the hexaploid Elymus nutans Griseb and the tetraploid E. burchan-buddae (Nevski) Tzvelev (Poaceae). Five selective primer combinations used in this study generated a total of 637 AFLP fragments across all the samples, with 612 fragments in E. nutans and 570 in E. burchan-buddae. About 45% of the scored fragments were <200 bp and about 13% of the fragments were >400 bp. Results showed that genetic diversity within populations of the two Elymus species increased gradually with the increase in altitudes from the lowest sampling sites (2800 m) and reached a plateau at the medium altitudes, and then started to decrease with the increase in altitudes. Regression analysis demonstrated a clear pattern between the expected heterozygosity (H _e) or Shannon index (I) and altitude variation, where the highest H _e values (0.3449 for E. nutans and 0.3167 E. burchan-buddae) and I values (0.5123 and 0.4759) were expected at the altitudes 3399 m and 3418 m across all sampling sites, respectively for E. nutans and E. burchan-buddae. In other words, higher genetic diversity was observed in populations occurring at the medium altitudes (3200–3600 m) than those at the low and high altitudes for the two Elymus species. Principal coordinate analysis (PCA) did not show clear association between genetic relationships of populations and their occurrences at a particular altitude. The above results suggest that efforts for conservation and utilization of two wheatgrasses species should focus more on populations occurring at the medium altitudes.     

Genetic structure of wild populations of the endangered Desert Pupfish complex (Cyprinodontidae: Cyprinodon)

Data from 10 microsatellite DNA loci were used to describe the genetic structure of the two extant species (Cyprinodon macularius and C. eremus) of the endangered Desert Pupfish complex of southwestern United States and northwestern Mexico. Variation at microsatellite loci was significantly correlated (Mantel test) with that of previous mtDNA results, both for the complex and for the relatively wide-ranging C. macularius alone. Both species showed unusually high levels of microsatellite diversity for non-marine fish (H _e = 0.84–0.93; A_R = 11.9–17.0). There was evidence (R _ST > F _ST) that the two extant populations of C. eremus have been isolated sufficiently long for mutation to contribute significantly to genetic divergence, whereas divergence among the nine assayed populations of C. macularius could be attributed to genetic drift alone. Correspondingly, 10% of the diversity in C. eremus was attributable to differences between the two populations, whereas, for C. macularius, only 2.7% was attributable to among-population variation. Within C. macularius, a small (0.8%), but statistically significant, portion was attributable to differences between populations in the Salton Sea area and those on the lower Colorado River delta. The two populations of C. eremus and five groups of populations of C. macularius are recommended as management units for conservation genetics management of the two species.     

Why sampling scheme matters: the effect of sampling scheme on landscape genetic results

There has been a recent trend in genetic studies of wild populations where researchers have changed their sampling schemes from sampling pre-defined populations to sampling individuals uniformly across landscapes. This reflects the fact that many species under study are continuously distributed rather than clumped into obvious “populations”. Once individual samples are collected, many landscape genetic studies use clustering algorithms and multilocus genetic data to group samples into subpopulations. After clusters are derived, landscape features that may be acting as barriers are examined and described. In theory, if populations were evenly sampled, this course of action should reliably identify population structure. However, genetic gradients and irregularly collected samples may impact the composition and location of clusters. We built genetic models where individual genotypes were either randomly distributed across a landscape or contained gradients created by neighbor mating for multiple generations. We investigated the influence of six different sampling protocols on population clustering using program STRUCTURE, the most commonly used model-based clustering method for multilocus genotype data. For models where individuals (and their alleles) were randomly distributed across a landscape, STRUCTURE correctly predicted that only one population was being sampled. However, when gradients created by neighbor mating existed, STRUCTURE detected multiple, but different numbers of clusters, depending on sampling protocols. We recommend testing for fine scale autocorrelation patterns prior to sample clustering, as the scale of the autocorrelation appears to influence the results. Further, we recommend that researchers pay attention to the impacts that sampling may have on subsequent population and landscape genetic results. The U.S. Government's right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

The scale of genetic differentiation in the Dunes Sagebrush-Lizard (Sceloporus arenicolus), an endemic habitat specialist

The Dunes Sagebrush-Lizard (Sceloporus arenicolus) is a North American species endemic to sand-shinnery oak habitats of the Mescalero and Monahans sand dunes in eastern New Mexico and western Texas. This lizard is listed as Endangered in New Mexico and exhibits habitat specificity at several geographic scales. Dunes Sagebrush-Lizards are only found in topographically complex shinnery oak (Quercus havardii) dominated landscapes within their small geographic distribution and are not found in surrounding human-altered landscapes. Within suitable sand-shinnery oak habitat, individuals predominantly occupy non-vegetated sand dune blowouts and utilize blowouts with particular physical characteristics due to thermoregulatory, reproduction, and foraging requirements. Here, we examined historical and contemporary patterns of genetic differentiation with respect to the current distribution of suitable habitat at multiple spatial scales using mitochondrial DNA sequences and microsatellite data from individuals throughout the entire range. We found three genetic clusters of individuals generally concordant with geographic regions and low sequence divergence at mitochondrial loci suggesting a recent origin of these populations. We also found high levels of genetic structure at microsatellite loci among populations within each of these groups indicating restricted gene flow at intermediate scales. Despite high habitat specificity, we did not detect genetic structure among sand blowouts at finer spatial scales. Within each population, matrices comprised of both sand blowouts and vegetated shinnery oak patches are necessary for genetic connectivity, but the fine scale spatial arrangement of blowouts may not be as critical. We discuss our results with respect to the scale of landscape heterogeneity and habitat connectivity and consider the conservation implications for this threatened taxon.