Fine Geographic Scale Research Articles

Fine-Scale Population Genetic Structure of Zhikong Scallop (Chlamys farreri): Do Local Marine Currents Drive Geographical Differentiation?

Marine scallops, with extended planktonic larval stages which can potentially disperse over large distances when advected by marine currents, are expected to possess low geographical differentiation. However, the sessile lifestyle as adult tends to form discrete "sea beds" with unique population dynamics and structure. The narrow distribution of Zhikong scallop (Chlamys farreri), its long planktonic larval stage, and the extremely hydrographic complexity in its distribution range provide an interesting case to elucidate the impact of marine currents on geographical differentiation for marine bivalves at a fine geographical scale. In this study, we analyzed genetic variation at nine microsatellite DNA loci in six locations throughout the distribution of Zhikong scallop in the Northern China. Very high genetic diversity was present in all six populations. Two populations sampled from the same marine gyre had no detectable genetic differentiation (F (ST) = 0.0013); however, the remaining four populations collected from different marine gyres or separated by strong marine currents showed low but significant genetic differentiation (F (ST) range 0.0184-0.0602). Genetic differentiation was further analyzed using the Monmonier algorithm to identify genetic barriers and using the assignment test conducted by software GeneClass2 to ascertain population membership of individuals. The genetic barriers fitting the orientation of marine gyres/currents were clearly identified, and the individual assignment analysis indicated that 95.6% of specimens were correctly allocated to one of the six populations sampled. The results support the hypothesis that significant population structure is present in Zhikong scallop at a fine geographical scale, and marine currents can be responsible for the genetic differentiation.

Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs) are appealing genetic markers due to several beneficial attributes, but uncertainty remains about how many of these bi-allelic markers are necessary to have sufficient power to differentiate populations, a task now generally accomplished with highly polymorphic microsatellite markers. In this study, we tested the utility of 37 SNPs and 13 microsatellites for differentiating 29 broadly distributed populations of Chinook salmon (n = 2783). Information content of all loci was determined by In and G'(ST), and the top 12 markers ranked by In were microsatellites, but the 6 highest, and 7 of the top 10 G'(ST) ranked markers, were SNPs. The mean ratio of random SNPs to random microsatellites ranged from 3.9 to 4.1, but this ratio was consistently reduced when only the most informative loci were included. Individual assignment test accuracy was higher for microsatellites (73.1%) than SNPs (66.6%), and pooling all 50 markers provided the highest accuracy (83.2%). When marker types were combined, as few as 15 of the top ranked loci provided higher assignment accuracy than either microsatellites or SNPs alone. Neighbour-joining dendrograms revealed similar clustering patterns and pairwise tests of population differentiation had nearly identical results with each suite of markers. Statistical tests and simulations indicated that closely related populations were better differentiated by microsatellites than SNPs. Our results indicate that both types of markers are likely to be useful in population genetics studies and that, in some cases, a combination of SNPs and microsatellites may be the most effective suite of loci.

Evidence for fine geographical scale heterogeneity in gene frequencies in yellowfin tuna ( Thunnus albacares) from the north Indian Ocean around Sri Lanka

Yellowfin tuna are currently considered by the member nations of the Indian Ocean Tuna Commission to constitute a single stock in the Indian Ocean due to a lack of knowledge about yellowfin tuna population structure in this region. Previous studies of Indian Ocean yellowfin tuna based on morphology and fisheries data have hinted at the presence of multiple stocks in the region, and further, that stocks may mix in the north western Indian Ocean around Sri Lanka. To better understand the genetic stock structure of yellowfin tuna in the north western Indian Ocean, we examined genetic variation in 285 yellowfin individuals collected over a period of 4 years from six fishing grounds around Sri Lanka and a single fishing ground in the Maldive Islands. We screened variation in both the mitochondrial ATP ase 6 and 8 region (498 bp) and three microsatellite loci. Significant genetic differentiation was detected among sites for mitochondrial DNA ( Φ ST = 0.1285, P < 0.001) and at two microsatellite loci ( F ST = 0.0164, P < 0.001 and F ST = 0.0064, P < 0.001), while spatial analysis of molecular variance of mtDNA data identified three genetically heterogenous groups namely; western, south eastern and all remaining sites. These results suggest the possibility that genetically discrete yellowfin tuna populations may be present in the north western Indian Ocean.

Genetic identification of native populations of fluvial white-spotted charr Salvelinus leucomaenis in the upper Tone River drainage

Stocking of exogenous, hatchery-reared white-spotted charr Salvelinus leucomaenis has been conducted throughout much of their range in Honshu Island, Japan, to increase angling opportunities. Although the native char populations are thought to have declined because of hybridization with introduce fish, their distribution and genetic status have been uncertain. Fine population structures of charr in the upper Tone River drainage were examined using mitochondrial DNA and microsatellite analyses so as to clarify the presence of native populations. One common mtDNA haplotype was detected in all populations in the Ohashi River and Watarase River, and four and one tributary populations were monomorphic for such haplotypes, respectively. However, several haplotypes, considered to have originated from stocked hatchery fish, were observed in the stocked and the remaining populations. Judging from the genetic integrity over a fine geographic scale, the former were considered as indicative of native populations and the latter as admixtures with hatchery fish. Comparisons of genetic diversity, deviations from the Hardy-Weinberg equilibrium, principal component analysis, and relatedness estimations based on microsatellite DNA can also provide evidence for distinguishing native populations from those influenced by hatchery fish.

Mapping Carbon Monoxide Using GPS Tracked Sensors

In this paper we discuss a pilot study where we have mapped urban air pollution using mobile carbon monoxide (CO) sensors. Our objective is to use inexpensive Global Positioning System (GPS) receivers to track the sensors and explore CO variations at a fine geographic scale. The critical issue in data processing is the treatment of the imprecise logs from the GPS. By using knowledge about the route and the geometry of the buildings, we are able to increase the position accuracy significantly, while at the same time showing that certain events, such as CO profiles while crossing roads, can be detected with a high degree of accuracy. Comparisons between data from our own mobile sensors and a fixed sensor site show good agreement in the vicinity of the fixed sensor, while at the same time identifying significant CO peaks within 100 m of this location. Using the mobile sensors to collect data along two of the main roads in the area, we are able to show CO variations along an urban canyon for parallel and perpendicular wind directions. Finally, a number of significant sources of CO were discovered during the course of the study, which suggest possible locations for fixed sensor sites in the future. We conclude by discussing the results in the context of the push towards large sensor networks and mobile communications. The potential for ad hoc mobile sensor networks may be very large.

Unobserved diversity, depletion and irreversibility The importance of subpopulations for management of cod stocks

Diversity is often associated with resilience but in this model, unobserved genetic or behavioral diversity can explain the collapse of supposedly regulated fish stocks such as cod. Recent studies have shown the existence of separate sub stocks of cod even at a very fine geographical scale. We show that modeling a group of distinct stocks as if it were one large stock will tend to over-estimate the growth and harvest potential. If quotas are based on such over-estimates, the unobserved stock diversity can explain sudden stock collapses and unexpectedly slow recovery as observed for Canadian cod. It is a lack of information concerning diversity that leads to irreversibility. The differences between the various stocks may be behavioral or genetic but cannot be observed by the fishermen or regulators who believe that there is a gradual decline in one big stock while in fact they are witnessing the successive disappearance of a series of sub stocks.

MODELING HANTAVIRUS RESERVOIR SPECIES DOMINANCE IN HIGH SEROPREVALENCE AREAS ON THE AZUERO PENINSULA OF PANAMA

Habitat fragmentation commonly influences distribution of zoonotic disease reservoirs. In Panama, populations of rodent hosts of hantaviruses are favored by small habitat fragments isolated by agricultural lands. We expected a similar relationship between landscape characteristics and host distribution at fine geographical scales in southern Panama. The relative abundance of Zygodontomys brevicauda, the primary host for "Calabazo" virus, and other rodents was assessed at 24 sites within the Azuero Peninsula. We used satellite imagery to produce several spatial variables that described landscape; however, only slope was consistently related to abundances of the two most dominant rodent species. Using regression, we constructed a spatial model of areas of Z. brevicauda dominance, which in turn relates to higher infection rates. The model predicts highest abundances of Z. brevicauda in flat areas, where humans also dominate. These predictions have important ecological and conservation implications that associate diversity loss, topography, and human land use.

Genetic and Demographic Criteria for Defining Population Units for Conservation: The Value of Clear Messages

Abstract In a recent paper on Harlequin Duck (Histrionicus histrionicus) interannual site fidelity (Iverson et al. 2004), we concluded that wintering populations were demographically structured at a finer geographic scale than that at which genetic differentiation was observed and that conservation efforts should recognize this degree of demographic independence. In a critique of our study, Pearce and Talbot (2006) contend that our measures of fidelity were not robust and imply that in the face of “mixed messages” we failed to appreciate the role of genetic data in defining population units. We recognize, as we did in our original paper, that our methods for quantifying site fidelity have some limitations; however, the patterns in our data are consistent with a considerable body of literature indicating high winter site fidelity in Harlequin Ducks. Moreover, we do not consider differences in the scales at which genetic and demographic structure are expressed to be “mixed messages,” given the different spatial and temporal scales at which genetic and contemporary demographic processes operate. We emphasize that a lack of genetic differentiation does not necessarily preclude the existence of contemporary demographic structure with relevance for conservation.

Shell growth of sea scallops (Placopecten magellanicus) in the southern and northern Great South Channel, USA

Abstract Shell growth of sea scallops in two commercially productive regions of the Great South Channel (GSC) (41°4′N 69°16′W) was studied using tag–recapture experiments. Commercial fishers captured and returned 9.7% of the 11 704 sea scallops tagged in the southern GSC study area, and 7.9% of the 18 274 sea scallops tagged in the northern GSC study area. Scallop density and shell height distribution were sampled with underwater video in the two study areas. In the southern GSC tagged scallops grew faster, reached larger asymptotic size, and had higher growth performance (Φ′) than in the northern GSC study area. Mean sea scallop density in the southern GSC was 0.117 scallops m−2 (s.e. = 0.01), and 2.601 scallops m−2 (s.e. = 0.28) in the northern GSC. Environmental factors, fishing pressure, and sea scallop density all influence shell growth on a fine geographic scale (1–100 km2) and should be considered in area-specific management strategies, such as that currently used in the USA sea scallop fishery.

GENETIC AND DEMOGRAPHIC CRITERIA FOR DEFINING POPULATION UNITS FOR CONSERVATION: THE VALUE OF CLEAR MESSAGES

Abstract In a recent paper on Harlequin Duck (Histrionicus histrionicus) interannual site fidelity (Iverson et al. 2004), we concluded that wintering populations were demographically structured at a finer geographic scale than that at which genetic differentiation was observed and that conservation efforts should recognize this degree of demographic independence. In a critique of our study, Pearce and Talbot (2006) contend that our measures of fidelity were not robust and imply that in the face of “mixed messages” we failed to appreciate the role of genetic data in defining population units. We recognize, as we did in our original paper, that our methods for quantifying site fidelity have some limitations; however, the patterns in our data are consistent with a considerable body of literature indicating high winter site fidelity in Harlequin Ducks. Moreover, we do not consider differences in the scales at which genetic and demographic structure are expressed to be “mixed messages,” given the different spa...

Temporal and spatial diversification of Circum‐Mediterranean Compositae‐Anthemideae

AbstractA combination of dispersal‐vicariance analysis (DIVA) and molecular clock dating of a calibrated, ratesmoothed maximum‐likelihood tree based on sequence information from the internal transcribed spacer region of the ribosomal repeat (nrDNA ITS) was used to reconstruct the biogeographical history of the Circum‐Mediterranean clade of Compositae‐Anthemideae. The reconstructions suggest that the ancestor of this clade diverged from the basal African lineages in the late Early Miocene (18 Myr), presumably in conjunction with the collision of the African and Eurasian platform through the Arabian plate. Recurrent dispersal/vicariance events during the Middle and Late Miocene (16–11 Myr) both between the eastern and western Mediterranean regions and (in the latter region) between the northern and southern Peri‐Tethys platforms caused the further diversification of the clade and may have been triggered by episodes of marine regression/transgression events on the Eurasian platform and in the area of the Strait of Gibraltar, respectively. The analyses further show that both the western part of the North African platform and the Anatolian region played a paramount role in the radiation of different subclades of the Circum‐Mediterranean Anthemideae, leading to the present day genus‐richness of the western subclade and to the species‐richness in the large genera (Achillea, Anthemis, Cota, Tanacetum, Tripleurospermum) of the eastern subclade. Whereas in the present analyses these radiations are reconstructed as sympatric speciation events, they may actually correspond to allopatric speciation events on a finer geographical scale within the two main centres of diversification (NW Africa, Anatolia). The Messinian salinity crisis (5.96–5.33 Myr) and the following re‐inundation of the Mediterranean basin (Early Pliocene) triggered dispersal/vicariance events observable today on the level of species or species groups, as did the climatic changes during the Pleistocene.

Processes of diversification and dispersion of Rice yellow mottle virus inferred from large‐scale and high‐resolution phylogeographical studies

Phylogeography of Rice yellow mottle virus (RYMV) was reconstructed from the coat protein gene sequences of a selection of 173 isolates from the 14 countries of mainland Africa where the disease occurred and from the full sequences of 16 representative isolates. Genetic variation was linked to geographical distribution and not to host species as isolates from wild rice always clustered with isolates from cultivated rice of the same region. Genetic variation was not associated to agro-ecology, viral interference and insect vector species. Distinct RYMV lineages occurred in East, Central and West Africa, although the Central African lineage included isolates from Benin, Togo and Niger at the west, adjacent to countries of the West African lineage. Genetic subdivision at finer geographical scales was apparent within lineages of Central and West Africa, although less pronounced than in East Africa. Physical obstacles, but also habitat fragmentation, as exemplified by the small low-lying island of Pemba offshore Tanzania mainland, explained strain localization. Three new highly divergent strains were found in eastern Tanzania. By contrast, intensive surveys in Cote d'Ivoire and Guinea at the west of Africa did not reveal any new variant. Altogether, this supported the view that the Eastern Arc Mountains biodiversity hotspot was the centre of origin of RYMV and that the virus spread subsequently from east to west across Africa. In West Africa, specific strains occurred in the Inner Niger Delta and suggested it was a secondary centre of diversification. Processes for diversification and dispersion of RYMV are proposed.

First upper molar and mandible shape of wood mice ( Apodemus sylvaticus) from northern Germany: ageing, habitat and insularity

The patterns of shape variation of the first upper molar and mandible have been investigated within and among wood mice ( Apodemus sylvaticus) populations from northern Germany. Some factors such as sex and age of the animals could be a source of within-group morphological variability interfering with among-groups patterns of differentiation. The relative importance of both sources of shape variation was investigated, in order to evaluate the robustness of patterns of fine-scale geographic differentiation. The increasing age of the animals, estimated by wear stages of the upper tooth row, caused significant variations in size and shape of the molars due to progressive abrasion of the cusps. It also involved shape changes of the mandible due to bone remodelling. However, these intrapopulational effects are of limited importance compared to geographic differentiation. Gene flow among populations should be favoured across mainland populations but lowered between mainland and islands, and to a lesser extent among close islands. Shape differences in molars are in agreement with this expected pattern of gene flow. Patterns of mandible differentiation rather match local variations in habitats. At this fine geographic scale, molar shape would vary according to the amount of genetic exchange among populations whereas mandible shape might be under local selective and/or functional constraints.

Local adaptation in the rock pocket mouse (Chaetodipus intermedius): natural selection and phylogenetic history of populations

Elucidating the causes of population divergence is a central goal of evolutionary biology. Rock pocket mice, Chaeotdipus intermedius, are an ideal system in which to study intraspecific phenotypic divergence because of the extensive color variation observed within this species. Here, we investigate whether phenotypic variation in color is correlated with local environmental conditions or with phylogenetic history. First, we quantified variation in pelage color (n=107 mice) and habitat color (n=51 rocks) using a spectrophotometer, and showed that there was a correlation between pelage color and habitat color across 14 sampled populations (R2=0.43). Analyses of mtDNA sequences from these same individuals revealed strong population structure in this species across its range, where most variation (63%) was partitioned between five geographic regions. Using Mantel tests, we show that there is no correlation between color variation and mtDNA phylogeny, suggesting that pelage coloration has evolved rapidly. At a finer geographical scale, high levels of gene flow between neighboring melanic and light populations suggest the selection acting on color must be quite strong to maintain habitat-specific phenotypic distributions. Finally, we raise the possibility that, in some cases, migration between populations of pocket mice inhabiting different lava flows may be responsible for similar melanic phenotypes in different populations. Together, the results suggest that color variation can evolve very rapidly over small geographic scales and that gene flow can both hinder and promote local adaptation.

Bioclimate envelope models: what they detect and what they hide

Bioclimate envelope models: what they detect and what they hide

Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex

Species with fragmented distributions are particularly useful models for investigating processes underlying biological diversification in the Neotropics. The Phaeothlypis wood-warbler complex (Aves: Parulidae) is comprised of six disjunct or parapatric populations. The geographic distribution of these six populations mirrors the classic map of Neotropical areas of endemism that were originally proposed as putative Pleistocene forest refugia, but the magnitude of mitochondrial DNA divergence between these populations suggests that they are each substantially older, with origins in the late Pliocene. Phylogenetic reconstructions based on long mtDNA coding sequences show that the Guiana Shield and Atlantic Forest populations are sister lineages, and group this combined lineage and the remaining four population-specific lineages in a five-way hard polytomy. MtDNA-based phylogenetic reconstructions provide no evidence that the three populations with conspicuous yellow rump and tail feathers currently grouped as the Buff-rumped Warbler ( P. fulvicauda) form a monophyletic group. Furthermore, there is a broad discordance between mtDNA and plumage along a transect just east of the Andes, where the contact zone between highly divergent mtDNA clades is more than 1000 km north of the phenotypic hybrid zone between the bright and dark plumage forms. This discordance between mtDNA genotype and plumage phenotype is similar to patterns seen on a finer geographic scale in other avian hybrid zones and may result from asymmetric introgression of the bright plumage trait.

Urban sprawl as a risk factor in motor vehicle occupant and pedestrian fatalities.

We sought to determine the association between urban sprawl and traffic fatalities. We created a sprawl index by applying principal components analysis to data for 448 US counties in the largest 101 metropolitan areas. Regression analysis was used to determine associations between the index and traffic fatalities. For every 1% increase in the index (i.e., more compact, less sprawl), all-mode traffic fatality rates fell by 1.49% (P <.001) and pedestrian fatality rates fell by 1.47% to 3.56%, after adjustment for pedestrian exposure (P <.001). Urban sprawl was directly related to traffic fatalities and pedestrian fatalities. Subsequent studies should investigate relationships at a finer geographic scale and should strive to improve on the measure of exposure used to adjust pedestrian fatality rates.

MONKEYS AND TOADS DEFINE AREAS OF ENDEMISM ON SULAWESI

Ecological or geological phenomena can impose limits on geographic diversification that cause biogeographical patterns of distantly related but sympatrically occurring taxa to be similar. Concordant patterns of diversity facilitate conservation management because strategic designation of protected areas can capture complementary rather than redundant components of variation. Here we demonstrate that on the biodiverse Indonesian island of Sulawesi, seemingly idiosyncratic distributions of diversity in endemic monkeys (Macaca species) and toads (Bufo celebensis) are actually virtually identical on a fine geographic scale. It appears that range fragmentation has generated seven multi‐taxon areas of genetic endemism, each of which should be targeted for conservation. Joint consideration of molecular phylogeography, morphology, and demography helps resolve apparent contradictions in paraphyletic macaque mitochondrial DNA and in undifferentiated toad morphology, and facilitates an understanding of biogeography and conservation genetics of Sulawesi fauna.

A Review of Northern Pike Population Genetics Research andIts Implications for Management

Abstract Conserving genetic diversity within and among populations of northern pike Esox lucius is important for maintaining their short-term fitness and long-term evolutionary potential. Northern pike have consistently shown low within-population variation, as detected by allozymes, mitochondrial DNA, and randomly amplified polymorphic DNA. Microsatellite DNA loci reveal considerably greater variation in northern pike, yet microsatellite variation tends to be less than that in other fish species. Low genetic variation within populations may result from compounding factors of low effective population size and bottlenecks. Allozyme, randomly amplified polymorphic DNA, and microsatellite markers have revealed significant differentiation of populations located in different continents and major drainages, but only microsatellites have differentiated populations on finer geographic scales. Within the north-central United States, analyses with microsatellites have detected genetic differences among most populat...

Seasonal and Spatial Patterns of "Green Tides" (Ulvoid Algal Blooms) and Related Water Quality Parameters in the Coastal Waters of Washington State, USA

Eutrophication-induced macroalgal blooms can impact marine communities, yet little is known about this phenomenon in the northeastern Pacific region. Changes in ulvoid biomass and water quality parameters (nutrients, transparency, temperature, salinity, and oxygen concentrations) were monitored at 6 sites on Blakely Island, Washington State, USA for two years. Observed ulvoid biomass varied from 0 to 441 g dw m−2. Biomass peaked in summer and autumn and was greatest at sites with the highest water-column nitrogen concentrations. Intertidal ulvoid communities were dominated by Ulva fenestrata Postels et Ruprecht while Ulvaria obscura (Kützing) Gayral dominated the subtidal zone near Blakely Island. In contrast with these observations, prior quantitative studies describe Ulvaria as rare or ephemeral. Fifteen additional sites were examined for species composition patterns. Similar patterns were seen at sites in Puget Sound, while Enteromorpha spp. were more common and U. obscura absent at sites in Hood Canal, Willapa Bay, and Grays Harbor. Green tides and other macroalgal blooms are typically reported to be monospecific, while in the present study two or more species are in close association, albeit at different tidal elevations. Enteromorpha spp. and Ulva spp. are known as important components of green tides, but relatively little is known about the biology of Ulvaria. Substantial variation in biomass on a fine geographic scale indicates the need for fine scale monitoring of the green tide phenomenon in the northeastern Pacific region.