Population structure of the Chagas disease vector,Triatoma infestans,at the urban–rural interface

The increasing rate of biological invasions resulting from human transport or human‐mediated changes to the environment has had devastating ecological and public health consequences. The kissing bug, Triatoma infestans, has dispersed through the Peruvian city of Arequipa. The biological invasion of this insect has resulted in a public health crisis, putting thousands of residents of this city at risk of infection by Trypanosoma cruzi and subsequent development of Chagas disease. Here, we show that populations of Tria. infestans in geographically distinct districts within and around this urban centre share a common recent evolutionary history although current gene flow is restricted even between proximal sites. The population structure among the Tria. infestans in different districts is not correlated with the geographical distance between districts. These data suggest that migration among the districts is mediated by factors beyond the short‐range migratory capabilities of Tria. infestans and that human movement has played a significant role in the structuring of the Tria. infestans population in the region. Rapid urbanization across southern South America will continue to create suitable environments for Tria. infestans, and knowledge of its urban dispersal patterns may play a fundamental role in mitigating human disease risk.     

Photosynthesis and isoprene emission from trees along an urban–rural gradient in Texas

Isoprene emission is an important mechanism for improving the thermotolerance of plant photosystems as temperatures increase. In this study, we measured photosynthesis and isoprene emission in trees along an urban–rural gradient that serves as a proxy for climate change, to understand daily and seasonal responses to changes in temperature and other environmental variables. Leaf‐level gas exchange and basal isoprene emission of post oak (Quercus stellata) and sweet gum (Liquidambar styraciflua) were recorded at regular intervals over an entire growing season at urban, suburban, and rural sites in eastern Texas. In addition, the temperature and atmospheric carbon dioxide concentration experienced by leaves were experimentally manipulated in spring, early summer, and late summer. We found that trees experienced lower stomatal conductance and photosynthesis and higher isoprene emission, at the urban and suburban sites compared to the rural site. Path analysis indicated a daily positive effect of isoprene emission on photosynthesis, but unexpectedly, higher isoprene emission from urban trees was not associated with improved photosynthesis as temperatures increased during the growing season. Furthermore, urban trees experienced relatively higher isoprene emission at high CO₂ concentrations, while isoprene emission was suppressed at the other sites. These results suggest that isoprene emission may be less beneficial in urban, and potentially future, environmental conditions, particularly if higher temperatures override the suppressive effects of high CO₂ on isoprene emission. These are important considerations for modeling future biosphere–atmosphere interactions and for understanding tree physiological responses to climate change.     

Urbanization impacts apex predator gene flow but not genetic diversity across an urban‐rural divide

Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms (SNPs) were genotyped using double‐digest, restriction site‐associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome‐scale markers to document subtle impacts of urbanization on a wide‐ranging carnivore living near a large urban center.     

Exotic grasses and nitrate enrichment alter soil carbon cycling along an urban–rural tropical forest gradient

Urban areas are expanding rapidly in tropical regions, with potential to alter ecosystem dynamics. In particular, exotic grasses and atmospheric nitrogen (N) deposition simultaneously affect tropical urbanized landscapes, with unknown effects on properties like soil carbon (C) storage. We hypothesized that (H1) soil nitrate (NO₃^?) is elevated nearer to the urban core, reflecting N deposition gradients. (H2) Exotic grasslands have elevated soil NO₃^? and decreased soil C relative to secondary forests, with higher N promoting decomposer activity. (H3) Exotic grasslands have greater seasonality in soil NO₃^? vs. secondary forests, due to higher sensitivity of grassland soil moisture to rainfall. We predicted that NO₃^? would be positively related to dissolved organic C (DOC) production via changes in decomposer activity. We measured six paired grassland/secondary forest sites along a tropical urban‐to‐rural gradient during the three dominant seasons (hurricane, dry, and early wet). We found that (1) soil NO₃^? was generally elevated nearer to the urban core, with particularly clear spatial trends for grasslands. (2) Exotic grasslands had lower soil C than secondary forests, which was related to elevated decomposer enzyme activities and soil respiration. Unexpectedly, soil NO₃^? was negatively related to enzyme activities, and was lower in grasslands than forests. (3) Grasslands had greater soil NO₃^? seasonality vs. forests, but this was not strongly linked to shifts in soil moisture or DOC. Our results suggest that exotic grasses in tropical regions are likely to drastically reduce soil C storage, but that N deposition may have an opposite effect via suppression of enzyme activities. However, soil NO₃^? accumulation here was higher in urban forests than grasslands, potentially related to of aboveground N interception. Net urban effects on C storage across tropical landscapes will likely vary depending on the mosaic of grass cover, rates of N deposition, and responses by local decomposer communities.     

Shifts in reciprocal river‐riparian arthropod fluxes along an urban‐rural landscape gradient

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Sex‐biased transcriptome divergence along a latitudinal gradient

Sex‐dependent gene expression is likely an important genomic mechanism that allows sex‐specific adaptation to environmental changes. Among Drosophila species, sex‐biased genes display remarkably consistent evolutionary patterns; male‐biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex‐biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex‐specific selection and the evolution of sex‐biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male‐biased genes, there was no overrepresentation of X‐linked genes in males. By contrast, X‐linked divergence was elevated in females, especially for female‐biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro‐ and micro‐ecological spatial scales.     

Nitrogen deposition and forest nitrogen cycling along an urban–rural transect in southern China

There is increasing concern over the impact of atmospheric nitrogen (N) deposition on forest ecosystems in the tropical and subtropical areas. In this study, we quantified atmospheric N deposition and revealed current plant and soil N status in 14 forests along a 150 km urban to rural transect in southern China, with an emphasis on examining whether foliar δ¹⁵N can be used as an indicator of N saturation. Bulk deposition ranged from 16.2 to 38.2 kg N ha^?1 yr^?1, while the throughfall covered a larger range of 11.7–65.1 kg N ha^?1 yr^?1. Foliar N concentration, NO₃^? leaching to stream, and soil NO₃^? concentration were low and NO₃^? production was negligible in some rural forests, indicating that primary production in these forests may be limited by N supply. But all these N variables were enhanced in suburban and urban forests. Across the study transect, throughfall N input was correlated positively with soil nitrification and NO₃^? leaching to stream, and negatively with pH values in soil and stream water. Foliar δ¹⁵N was between ?6.6‰ and 0.7‰, and was negatively correlated with soil NO₃^? concentration and NO₃^? leaching to stream across the entire transect, demonstrating that an increased N supply does not necessarily increase forest δ¹⁵N values. We proposed several potential mechanism that could contribute to the δ¹⁵N pattern, including (1) increased plant uptake of ¹⁵N‐depleted soil NO₃^?, (2) foliage uptake of ¹⁵N‐depleted NH₄⁺, (3) increased utilization of soil inorganic N relative to dissolved organic N, and (4) increased fractionation during plant N uptake under higher soil N availability.     

Cryptic speciation along a bathymetric gradient

The deep ocean supports a highly diverse and mostly endemic fauna, yet little is known about how or where new species form in this remote ecosystem. How speciation occurs is especially intriguing in the deep sea because few obvious barriers exist that would disrupt gene flow. Geographic and bathymetric patterns of genetic variation can provide key insights into how and where new species form. We quantified the population genetic structure of a protobranch bivalve, Neilonella salicensis, along a depth gradient (2200–3800 m) in the western North Atlantic using both nuclear (28S and calmodulin intron) and mitochondrial (cytochrome c oxidase subunit I) loci. A sharp genetic break occurred for each locus between populations above 2800 m and below 3200 m, defining two distinct clades with no nuclear or mitochondrial haplotypes shared between depth regimes. Bayesian phylogenetic analyses provided strong support for two clades, separated by depth, within N. salicensis. Although no morphological divergence was apparent, we suggest that the depth‐related population genetic and phylogenetic divergence is indicative of a cryptic species. The frequent occurrence of various stages of divergence associated with species formation along bathymetric gradients suggests that depth, and the environmental gradients that attend changes in depth, probably play a fundamental role in the diversification of marine organisms, especially in deep water. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 897–913.     

Gene flow and range expansion in a mountain‐dwelling passerine with a fragmented distribution

We studied gene flow and bottleneck events in the population history of locally isolated citril finches endemic to European mountains. For the present study, we used two genetic markers with different rates of evolution: a fast evolving mitochondrial marker (ATPase6/8) and a more slowly evolving nuclear marker (02401). Populations north of the Pyrenees showed in general fewer haplotypes and a considerable lower nucleotide and gene diversity than the Iberian populations. Unexpectedly, we found very little genetic variability in the fast evolving mitochondrial marker, arguing for a strong and relatively recent bottleneck event in the species population history. This pattern potentially reflects a sudden decrease of crucial resources during Mid‐Holocene (mountain pine, Scots pine, and black pine) and a subsequent breakdown of the population. The bottleneck could also have been caused or coincide with a selective sweep in the mitochondrion. By contrast, the slowly evolving nuclear marker showed a much higher variability. This marker probably reflects major gene flow along a potential expansion pathway from the Eastern Pyrenees, northwards to the populations of Central Europe, and southwards to the more fragmented populations of central and southern Spain. The population of the Western Pyrenees (Navarra) appears to be cut‐off from this major gene flow and our data indicate a certain degree of partial isolation, probably reflecting more ancient events (e.g. the separation in distinct refuge sites during the last glacial maximum). © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 707–721.     

Application of plant metabarcoding to identify diverse honeybee pollen forage along an urban–agricultural gradient

Understanding animal foraging ecology requires large sample sizes spanning broad environmental and temporal gradients. For pollinators, this has been hampered by the laborious nature of morphologically identifying pollen. Identifying pollen from urban environments is particularly difficult due to the presence of diverse ornamental species associated with consumer horticulture. Metagenetic pollen analysis represents a potential solution to this issue. Building upon prior laboratory and bioinformatic methods, we applied quantitative multilocus metabarcoding to characterize the foraging ecology of honeybee colonies situated in urban, suburban, mixed suburban–agricultural and rural agricultural sites in central Ohio, USA. In cross‐validating a subset of our metabarcoding results using microscopic palynology, we find strong concordance between the molecular and microscopic methods. Our results suggest that forage from the agricultural site exhibited decreased taxonomic diversity and temporal turnover relative to the urban and suburban sites, though the generalization of this observation will require replication across additional sites and cities. Our work demonstrates the power of honeybees as environmental samplers of floral community composition at large spatial scales, aiding in the distinction of taxa characteristically associated with urban or agricultural land use from those distributed ubiquitously across the sampled landscapes. Observed patterns of high forage diversity and compositional turnover in our more urban sites are likely reflective of the fine‐grain heterogeneity and high beta diversity of urban floral landscapes at the scale of honeybee foraging. This provides guidance for future studies investigating how relationships between urbanization and measures of pollinator health are mediated by variation in floral resource dynamics across landscapes.     

Non-random distribution of individual genetic diversity along an environmental gradient

Improving our knowledge of the links between ecology and evolution is especially critical in the actual context of global rapid environmental changes. A critical step in that direction is to quantify how variation in ecological factors linked to habitat modifications might shape observed levels of genetic variability in wild populations. Still, little is known on the factors affecting levels and distribution of genetic diversity at the individual level, despite its vital underlying role in evolutionary processes. In this study, we assessed the effects of habitat quality on population structure and individual genetic diversity of tree swallows (Tachycineta bicolor) breeding along a gradient of agricultural intensification in southern Québec, Canada. Using a landscape genetics approach, we found that individual genetic diversity was greater in poorer quality habitats. This counter-intuitive result was partly explained by the settlement patterns of tree swallows across the landscape. Individuals of higher genetic diversity arrived earlier on their breeding grounds and settled in the first available habitats, which correspond to intensive cultures. Our results highlight the importance of investigating the effects of environmental variability on individual genetic diversity, and of integrating information on landscape structure when conducting such studies.     

The role of habitat choice in micro‐evolutionary dynamics: An experimental study on the Mediterranean killifish Aphanius fasciatus (Cyprinodontidae)

Habitat choice is defined as a nonrandom distribution of genotypes in different microhabitats. Therefore, it could exert a great impact on the genetic variance of natural populations by promoting genetic divergence, local adaptation, and may even lead to sympatric speciation. Despite this potential role in micro‐ and macro‐evolutionary processes, there is little empirical evidence that the various genotypes within a population may differ in habitat choice‐related behaviors. Here, we tested whether habitat choice may have contributed to genetic divergence within a local population of the Mediterranean killifish Aphanius fasciatus, which emerged between groups inhabiting microhabitats with different oxygen concentrations during previous field studies. In a first experiment, we studied the distribution of individuals in conditions of hypoxia and normoxia to test whether they had a different ability to shy away from a hypoxic environment; in a second experiment, we analyzed the individual behavior of fish separately in the two conditions, to verify whether they showed peculiar behavioral responses linked to a possible differential distribution. We then analyzed the six allozyme loci, whose allelic and genotypic frequencies were significantly divergent in the previous studies. In the first test, we found that the distribution of the two homozygote genotypes of the glucose‐6‐phosphate isomerase‐1 locus (GPI‐1) was significantly different between the hypoxic and the normoxic conditions. During the second test, all individuals were more active in hypoxic conditions, but the two GPI‐1 homozygotes showed a significant difference in time spent performing surface breathing, which was consistent with their distribution observed in the first experiment. These results provide evidence that individual behavioral traits, related to genetic features, may lead to a nonrandom distribution of genotypes in heterogeneous although contiguous microhabitats and, consequently, that habitat choice can play a significant role in driving the micro‐evolutionary dynamics of this species.     

Hawaiian picture‐winged Drosophila exhibit adaptive population divergence along a narrow climatic gradient on Hawaii Island

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Patterns of genetic and phenotypic variation in Iris haynei and I. atrofusca (Iris sect. Oncocyclus = the royal irises) along an ecogeographical gradient in Israel and the West Bank

Iris haynei and I. atrofusca are two closely related narrow endemics distributed vicariously along an ecogeographical north-south gradient in Israel and the West Bank. To obtain baseline information of the taxonomic status, conservation and population history of these taxa, we investigated patterns of phenotypic variation and the partitioning of genetic variation within and among populations using dominant random amplified polymorphic DNA (RAPD) markers. Multivariate (principal components analysis) and taxonomic distance analyses based on morphometric traits from eight populations revealed no unambiguous separation into two distinct groups. Results of genetic analyses for nine populations differed only slightly when either allele- or marker-based approaches were employed. Mean within-population diversity was high (0.258 for Nei's expected heterozygosity), but there was no significant relationship between genetic diversity and either population size or latitude. Although the range-wide estimate of GST ( approximately 0.20) revealed relatively high differentiation among populations this value was inflated because of a small, but significant, component of molecular variance among regions viz. taxa ( approximately 5%). Limited long-distance dispersal capabilities in conjunction with a linearized habitat distribution are proposed to contribute to the approximate isolation by distance pattern observed. It also appears that extant populations are currently deviating from equilibrium conditions because of primary divergence of a formerly more widespread ancestral population. Given the absence of deep genetic and phenotypic subdivision among northern (I. haynei) vs. central/southern (I. atrofusca) populations, we argue for a revision of their species status. Nonetheless, we recommend conservation attention to these geographically differentiated segments as separate management units, which can be seen as an instructive example of incipient species formation.     

Population structure in a saproxylic funnelweb spider (Hexathelidae: Hadronyche) along a forested rainfall gradient

We present research undertaken at Tallaganda State Forest, Australia, describing how current climatic conditions impact upon the saproxylic (decaying wood) habitat and the relationship between this habitat and the demography and morphology of a saproxylic funnelweb spider ( Hadronyche sp.). Climatic data support a north–south habitat cline and, to a lesser extent, a short-range, aspect-driven habitat cline. Rainfall and log moisture content increased with latitude through the forest, and aspect affected the amount of solar radiation penetrating to ground level. The distribution and abundance of Hadronyche varied among sites along both clines in response to several variables. The decay state of logs was highly influential, with wet, highly decayed logs favoured over dry, hard ones. Population density was highest in wetter, southern sites where these logs were abundant, but rare, suitably decomposed logs in dry, northern sites still typically hosted a comparable number of individuals. Morphological measurements showed some phenotypic variation along the north–south habitat gradient, but not over the short-range, aspect-driven gradients. Hadronyche would not be expected to show similarly strong patterns of molecular variation as seen in saproxylic Collembola and Onychophora within Tallaganda as it appears to be more vagile.     

Soil chemical properties,rather than landscape context,influence woodland fungal communities along an urban‐rural gradient

With the expansion of cities around the world there is a growing interest in the factors that influence biodiversity and ecosystem processes in urban areas. Fungi are exceptionally diverse and play key roles in ecosystem function, yet despite predictions of negative impacts due to urbanization, fungi have been generally overlooked in urban ecological studies. We surveyed fungi in 16 remnant river red gum (Eucalyptus camaldulensis: Myrtaceae) woodlands along a gradient of 4–35 km from the city of Melbourne (south‐east Australia). Using both sporocarp surveys and terminal restriction fragment length polymorphism (T‐RFLP; primer pair ITS1‐F‐ITS4), we examined relationships between fungal community composition, landscape context (i.e. urbanization) and soil physicochemical properties. Community compositions from sporocarp data were significantly correlated with those from T‐RFLP data, largely because of correlations with ectomycorrhizal sporocarps (Spearman rank correlation coefficients ρ 0.31–0.42) rather than saprotrophic fungi (ρ 0.18–0.21). Principal components analysis of soil properties and non‐metric multidimensional scaling ordinations of fungal community composition showed no clear separation of sites according to urbanization, and there were no significant correlations between fungal community composition and urbanization. However, fungal community composition was significantly correlated with soil chemical properties (ρ 0.41–0.55). These data suggest that site‐scale soil properties, and associated effects of past and current land management activities, were more important in determining fungal community composition than the landscape‐level influences of urbanization.     

Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance

Monarch butterflies are known for their spectacular annual migration in eastern North America, with millions of monarchs flying up to 4,500 km to overwintering sites in central Mexico. Monarchs also live west of the Rocky Mountains, where they travel shorter distances to overwinter along the Pacific Coast. It is often assumed that eastern and western monarchs form distinct evolutionary units, but genomic studies to support this notion are lacking. We used a tethered flight mill to show that migratory eastern monarchs have greater flight performance than western monarchs, consistent with their greater migratory distances. However, analysing more than 20 million SNPs in 43 monarch genomes, we found no evidence for genomic differentiation between eastern and western monarchs. Genomic analysis also showed identical and low levels of genetic diversity, and demographic analyses indicated similar effective population sizes and ongoing gene flow between eastern and western monarchs. Gene expression analysis of a subset of candidate genes during active flight revealed differential gene expression related to nonmuscular motor activity. Our results demonstrate that eastern and western monarchs maintain migratory differences despite ongoing gene flow, and suggest that migratory differences between eastern and western monarchs are not driven by select major‐effects alleles. Instead, variation in migratory distance and destination may be driven by environmentally induced differential gene expression or by many alleles of small effect.     

Estimates of gene flow, genetic substructure and population heterogeneity in bracken (Pteridium aquilinum)

Bracken [ Pteridium aquilinum (L.) Kuhn] is a cosmopolitan species and is a noxious weed in many areas. Because of its abundance, particularly in Britain, bracken affords an ideal system for investigating various aspects of population genetics and evolution. High mobility of dispersal units (spores) suggests that rates of gene flow among distant populations should be high. Gene flow is a major evolutionary force that influences the genetic structure of populations. To examine the effects of gene flow on population heterogeneity and population substructuring in bracken, starch gel electrophoresis of enzymes was used to provide the necessary genetic database. Allele frequency data at 21 loci were obtained for seven British populations, one Majorcan and one from the eastern United States. A model was employed to estimate the amount of gene flow ( Nm ) at several levels. Gene flow among British populations was extremely high ( Nm = 36.51), one of the highest estimates reported for plants. Among eight European populations gene flow was lower (but still considered high) at Nm = 2.47. Trans-Atlantic gene flow was low ( Nm = 0.0926).
F -statistics were used to assess population heterogeneity and substructuring. The data indicate that, compared with other species, there is very little genetic differentiation among British populations of bracken. Indeed, it appears that the whole island is behaving as a single randommating population. This result is consistent with high levels of gene flow. Only one population (on the Isle of Arran) showed statistically significant genetic substructuring. Habitat heterogeneity on the island and age structure are hypothesized as possible causes of this result.
The data reported here support previous studies demonstrating that bracken is genetically polymorphic and is an outcrossing species.     

Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow

Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub‐Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to humans and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180‐km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city (Morogoro). We sampled M. natalensis across 10 localities and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K‐invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the isolation‐with‐migration model implemented in IMa2, we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban source to rural sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2N_eM = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary.     

Isolation of polymorphic microsatellite loci from the red‐billed gull (Larus novaehollandiae scopulinus) and amplification in related species

We describe the isolation and characterization of seven dinucleotide microsatellite loci developed from the red‐billed gull (Larus novaehollandiae scopulinus). Locus‐specific primers were used to genotype individuals from 13 populations of this subspecies as well as individuals from closely related subspecies from Australia and New Caledonia. The primers were tested successfully on other species of gulls and shorebirds. The number of alleles observed within the red‐billed gull ranged from three to 17, and observed heterozygosity varied from 0.359 to 0.787. These microsatellites are likely to be useful for studies of mating systems and population genetics in a wide range of gull species.