Fine-scale genetic structure in a salamander with two reproductive modes: Does reproductive mode affect dispersal?

Reproduction is intimately linked with dispersal, but the effects of changes in reproductive strategies on dispersal have received little attention. Such changes have occurred in many taxonomic groups, resulting in profound alterations in life-history. In amphibians, many species shifted from oviparous/larviparous aquatic reproduction (deposition of eggs or pre-metamorphic larvae in water) to pueriparous terrestrial reproduction (parturition of terrestrial juveniles). The latter provides greater independence from water by skipping the aquatic larval stage; however, the eco-evolutionary implications of this evolutionary step have been underexplored, largely because reproductive modes rarely vary at the intraspecific level, preventing meaningful comparisons. We studied the effects of a transition to pueriparity on dispersal and fine-scale genetic structure in the fire salamander (Salamandra salamandra), a species exhibiting two co-occurring reproductive modes: larviparity and pueriparity. We performed genetic analyses (parentage and genetic spatial autocorrelation) using 11 microsatellite loci to compare dispersal and fine-scale genetic structure in three larviparous and three pueriparous populations (354 individuals in total). We did not find significant differences between reproductive modes, but in some larviparous populations movement patterns may be influenced by site-specific features (type of water bodies), possibly due to passive water-borne dispersal of larvae along streams. Additionally, females (especially larviparous ones) appeared to be more philopatric, while males showed greater variation in dispersal distances. This study also points to future avenues of research to better understand the eco-evolutionary implications of changes in reproductive modes in amphibians.     

Do common eiders nest in kin groups? Microgeographic genetic structure in a philopatric sea duck

We investigated local genetic associations among female Pacific common eiders (Somateria mollissima v‐nigrum) nesting in a stochastic Arctic environment within two groups of barrier islands (Simpson Lagoon and Mikkelsen Bay) in the Beaufort Sea, Alaska. Nonrandom genetic associations were observed among nesting females using regional spatial autocorrelation analyses for distance classes up to 1000 m in Simpson Lagoon. Nearest‐neighbour analyses identified clusters of genetically related females with positive lr values observed for 0–13% and 0–7% of the comparisons in Simpson Lagoon and Mikkelsen Bay, respectively, across years. These results indicate that a proportion of females are nesting in close proximity to more genetically related individuals, albeit at low frequency. Such kin groupings may form through active association between relatives or through natal philopatry and breeding site fidelity. Eiders nest in close association with driftwood, which is redistributed annually by seasonal storms. Yet, genetic associations were still observed. Microgeographic structure may thus be more attributable to kin association than natal philopatry and site fidelity. However, habitat availability may also influence the level of structure observed. Regional structure was present only within Simpson Lagoon and this island group includes at least three islands with sufficient driftwood for colonies, whereas only one island at Mikkelsen Bay has these features. A long‐term demographic study is needed to understand more fully the mechanisms that lead to fine‐scale genetic structure observed in common eiders breeding in the Beaufort Sea.     

Substrate preference in a colonial spider: is substrate choice affected by color morph?

Animals can show preference for a particular background as a way of decreasing visibility. Species with color polymorphism may have morph‐dependent background preference. I test this hypothesis on the orb‐weaving spider Parawixia bistriata. Adult females of P. bistriata present two distinct morphs characterized by brown and yellow opisthosomata. This nocturnal spider can be found in its retreat on the vegetation during the day. In order to examine whether females exhibit substrate preference dependent on their color morph, I first recorded the distribution of color morphs on different substrates (leaf and branch) and then performed a mark and release experiment. Field censuses indicated that the yellow morph was associated with leaves while the brown morph was found on either substrate type. The results of a mark and reciprocal release experiment agreed with the censuses and suggest that the two morphs differ in their association to substrate type: yellow females were associated with the leaf substrate, while brown females showed no association to a particular substrate type. Possible forces behind these differences in substrate choice are discussed.     

Is genetic structure of the southern pygmy mouse Baiomys musculus (Cricetidae) related to human-induced spatial landscape heterogeneity in a tropical dry forest?

Tropical dry forests are biologically important biomes sustaining a high rate of endemic species. However, these forests are highly threatened by human activities that negatively impact them on distinct levels, including the genetic diversity. Within the framework of landscape genetics (that seeks to evaluate the relation of characteristics of the environmental matrix with population genetics), we used ISSR markers to evaluate the relationship between the alteration of tropical dry forest by human-induced activities (conserved vs. disturbed) with the genetic structure of four breeding sites of the southern pygmy mouse Baiomys musculus. Averaging among the 105 loci used, the unbiased heterozygosis per population (0.247–0.305) was statistically similar among the four sites, as well as between conserved and disturbed conditions (2-way ANOVA F _(3,16)?=?1.47, P?=?0.1984). The genetic differentiation among the four breeding sites was high (F _ST?=?0.1122; 95?% CI 0.082–0.146) considering the geographical scale evaluated (ca. 4?km). Both, a factorial correspondence analysis and a model-based clustering analysis showed the existence of four genetic groups (one per breeding site). However, no association of genetic structure with disturbance conditions was revealed by these analyses. The absence of differences in mean genetic diversity and the lack of association of genetic structure with habitat transformation suggest that B. musculus has enough behavioral plasticity and enough genetic diversity to respond to environmental heterogeneity caused by human activities. We discussed conditions in which habitat transformation could indeed favor B. musculus.     

Do earthworms affect dynamics of functional response and genetic structure of microbial community in a lab-scale composting system?

Two laboratory-scale systems were set up (i) composting (without earthworms) and (ii) vermicomposting (with earthworms) and were monitored for 60 days after pre-composting. The physico-chemical parameters (pH, C/N, organic matter, NH(4)(+)-N and ash content) showed similar evolution in both systems except a higher NH(4)(+)-N in the initial vermicomposts. However, principle component analysis (PCA) of enzymatic activities and community level physiological profiles revealed differences in the functional response of microbial communities in compost and vermicompost during maturation. Dehydrogenase activity and bacterial counts indicated a steady decrease in biological activity and population during composting, whereas vermicomposting exhibited higher activity on day 30 and a reduction in bacterial counts on day 10. PCA of denatured gradient gel electrophoresis (DGGE) profiles showed divergent dynamics of bacterial communities in two processes. These results indicated differences in the functional response and genetic structure of microbial community in composts and vermicomposts despite similar changes in their physico-chemical parameters.     

Do polymorphic loci require large sample sizes to estimate genetic distances?

The coefficient of variation of estimates of three genetic distances (standard genetic distance of Nei, chord distance, FST) was examined with computer simulation to determine if large samples (per population) are necessary to precisely estimate genetic distances at loci with high levels of polymorphism. These simulations showed that loci with high mutation rates produce estimates of genetic distance with lower coefficients of variation than loci with lower mutation rates--without requiring larger sample sizes from each population. In addition, the rate at which increasing sample sizes decreases the coefficient of variation of estimates of genetic distances was shown to be approximately determined by the value of FST between the populations being sampled. When FST was greater than 0.05, sampling fewer than 20 individuals (per population) should be sufficient. When FST was less than 0.01, sampling 100 individuals (per population) or more will be useful.     

Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans?

Global tiger Panthera tigris populations mostly survive within the geographically fragmented forest patches, thereby limited genetic exchange between isolated populations. Assessing the genetic status of these populations can reveal the effects of dispersal barriers and provide critical insights to guide future conservation actions. Using non-invasively collected biological samples, we investigated fine-scale genetic structure of tigers in the Sundarbans mangrove forests intersected by the complex river systems, and which holds one of the largest global tiger populations. We genotyped 52 tiger samples at 10 polymorphic microsatellite loci, and sequenced 33 of them for a total of 1263 base-pairs at four mitochondrial gene fragments. Microsatellite analyses exhibit a signature of fine-scale genetic structure, which might have been the consequence of limited tiger dispersal due to wide rivers across the Sundarbans. Similarly, mitochondrial data show a historic pattern of population isolation that might be due to wider rivers across the entire Sundarbans shared by Bangladesh and India. Given the intrinsic nature of the mangrove habitat embedded with numerous rivers, increased commercial traffic and human activities may further impede tiger dispersal across wide rivers, escalating further genetic isolation of the Sundarbans tigers.     

Do group dynamics affect colour morph clines during a range shift?

Species exhibiting colour polymorphism are thought to have an ecological advantage at the landscape scale, because spatial segregation of alternatively adapted ecotypes into diverse habitats can increase the species' niche breadth and thus confer greater geographic range size. However, morph frequencies are also influenced by intrapopulational processes such as frequency‐ or density‐dependent social interactions. To identify how social feedback may affect clinal variation in morph frequencies, we investigated reciprocal interactions between morph‐specific thermal tolerance, local climatic conditions and social environments, in the context of a colour‐morph frequency cline associated with a recent range expansion in blue‐tailed damselflies (Ischnura elegans) in Sweden. Cold tolerances of gynochromes (female‐like female morph) were positively correlated with local gynochrome frequencies, suggesting a positive frequency‐dependent fitness benefit. In contrast, androchrome (male‐mimic female morph) cold tolerances were improved following recent exposure to cold weather, suggesting a beneficial environmental acclimation effect. Thus, according to an environment‐matching hypothesis for clinal variation, androchrome frequencies should therefore increase towards the (cooler) range limit. In contrast to this prediction, gynochrome frequencies increased at the expanding range limit, consistent with a positive frequency‐dependent social feedback that is beneficial when invading novel climates. Our results suggest that when phenotypes or fitnesses are affected by interactions with conspecifics, beneficial social effects on environmental tolerances may (i) facilitate range shifts, and (ii) reverse or counteract typical patterns of intraspecific interactions and environment‐matching clines observed in stable populations observed over broader geographic scales.     

Population genetic structure in Myrtus communis L. in a chronically fragmented landscape in the Mediterranean: can gene flow counteract habitat perturbation?

Ancient managed landscapes provide ideal opportunities to assess the consequences of habitat fragmentation on the patterns of genetic diversity and gene flow in long-lived plant species. Using amplified fragment length polymorphism (AFLP) and allozyme markers, we quantified seed-mediated gene flow and population genetic diversity and structure in 14 populations of Myrtus communis (myrtle), a common endozoochorous shrub species of forest patches in lowland agricultural Mediterranean areas. Overall, allozyme diversity for myrtle was low (P₉₅   =   25%; A   =   1.411; H_e = 0.085) compared to other known populations, and a significant portion of populations (57%) had lower levels of allelic diversity and/or heterozygosity than expected at random, as shown by simulated resampling of the whole diversity of the landscape. We found significant correlations between allozyme variability and population size and patch isolation, but no significant inbreeding in any population. Genetic differentiation among populations for both allozyme and AFLP markers was significant (Φ_ST = 0.144 and Φ_ST = 0.142, respectively) but an isolation-by-distance pattern was not detected. Assignment tests on AFLP data indicated a high immigration rate in the populations ( ca. 20–22%), likely through effective seed dispersal across the landscape by birds and mammals. Our results suggest that genetic isolation is not the automatic outcome of habitat destruction since substantial levels of seed-mediated gene flow are currently detectable. However, even moderate rates of gene flow seem insufficient in this long-lived species to counteract the genetic erosion and differentiation imposed by chronic habitat destruction.     

A regional analysis of Barí land use intensification and its impact on landscape heterogeneity

Since pacification 30 years ago, the Barí of northwest Venezuela have aggregated in villages and have begun to produce cattle and some crops for sale in regional markets. This research analyzes satellite imagery to compare patterns of land use among Barí settlements that differ in their population size, cattle holdings, and distance to nearest marketplace. These comparisons indicate that settlement history mediates the effect of population pressure and herd sizes on land use. Moreover, intensification of land use is associated with greater deforestation and a more heterogeneous landscape, but less biodiversity in woody species.     

Do competitive intraguild interactions affect space and habitat use by small carnivores in a forested landscape?

Complex interactions such as interference competition and predation, including intraguild predation, are now recognized as important components in animal community structure. At the lower end of a guild, weasels may be highly affected by other guild members due to small body size in relation to other predators. In 2000 and 2001, we radio-collared 24 ermines Mustela erminea and 25 long-tailed weasels M. frenata in 2 areas that differed in abundance of guild members. We tested the hypothesis that when faced with an increased density of other guild members, weasels would modify space and habitat use to reduce the risk of predation associated with encounters involving guild members. We predicted that weasels would increase use of specific habitats (such as refuges) to reduce encounter rates in the presence of a greater number of guild members. Because M. erminea is smaller than M. frenata and thus better able to take advantage of small rodent burrows as refuges from predators and as feeding grounds, we also predicted that M. frenata would show a stronger response to a higher abundance of guild members than M. erminea . Results were consistent with our predictions. Faced with an increased abundance of guild members, M. frenata showed increased habitat selectivity and reduced activity levels, which resulted in increased daily travel distances and increased home ranges. Mustela erminea responded to an increased abundance of guild members through reduced use of preferred habitat which M. frenata already occupied. The contrasting pattern of habitat selection observed between the 2 mustelid species suggested cascading effects, whereby large-predator pressure on M. frenata relaxed pressure of M. frenata on M. erminea . Our results draw attention to the likelihood that competitive intraguild interactions play a facilitating role in M. erminea – M. frenata coexistence.     

How does forest landscape structure explain tree species richness in a Mediterranean context?

Although the strong relationship between vegetation and climatic factors is widely accepted, other landscape composition and configuration characteristics could be significantly related with vegetation diversity patterns at different scales. Variation partitioning was conducted in order to analyse to what degree forest landscape structure, compared to other spatial and environmental factors, explained forest tree species richness in 278 UTM 10 × 10 km cells in the Mediterranean region of Catalonia (NE Spain). Tree species richness variation was decomposed through linear regression into three groups of explanatory variables: forest landscape (composition and configuration), environmental (topography and climate) and spatial variables. Additionally, the forest landscape characteristics which significantly contributed to explain richness variation were identified through a multiple regression model. About 60% of tree species richness variation was explained by the whole set of variables, while their joint effects explained nearly 28%. Forest landscape variables were those with a greater pure explanatory power for tree species richness (about 15% of total variation), much larger than the pure effect of environmental or spatial variables (about 2% each). Forest canopy cover, forest area and land cover diversity were the most significant composition variables in the regression model. Landscape configuration metrics had a minor effect on forest tree species richness, with the exception of some shape complexity indices, as indicators of land use intensity and edge effects. Our results highlight the importance of considering the forest landscape structure in order to understand the distribution of vegetation diversity in strongly human-modified regions like the Mediterranean.     

Yellow–green color polymorphism in males of a pea aphid clone and its genetic pattern

Although most aphid species living on leaves have a green body color, little is known regarding the biosynthetic pathways of green pigments. We found that a clone of the pea aphid, Acyrthosiphon pisum (Harris) produced both green- and yellow-colored males. The females of this clone were green in color, while 8.4% of the males produced were yellow. To date, yellow body color has been reported only in a single mutant clone in A. pisum. To explore the genetic pattern of yellow body color, green or yellow males were mated with green females of the same clone. The hatchability of the eggs sired by yellow males (26.2%) was less than half that of the eggs sired by green males (79.0%). The hatched foundresses of both groups were all green, with no yellow foundresses. Because aphids have an XX-XO sex determination system, color polymorphism in males suggests that male body color may be governed by an X-linked locus. If females possess heterozygosity at the putative locus, they can produce alternative phenotypes in males. The small proportion of yellow males and absence of yellow foundresses imply that the allele responsible for yellow body color has a deleterious effect. The present study suggests that this clone could be used to elucidate the biosynthetic pathways and underlying genetics of green pigments in aphids.     

Sexual dimorphism in a trophically polymorphic cichlid fish?

Sexual dimorphism in ecologically relevant traits is ubiquitous in animals. However, other types of intraspecific phenotypic divergence, such as trophic polymorphism, are less common. Because linkage to sex should often lead to balancing selection, understanding the association between sex and phenotypic divergence could help explain why particular species show high morphological variability. To determine if sexual dimorphism could be helping to maintain ecomorphological variation in a classic case of intraspecific trophic polymorphism, we examined the association between sex and morphological divergence in the cichlid Herichthys minckleyi. Although H. minckleyi with enlarged molariform teeth on their pharyngeal jaws have been reported to more commonly be male, we did not find an association between sex and pharyngeal morphotype. Sex was associated with divergence in body size (as measured through standard length). But, sex was not associated with any of the other trophic traits examined. However, pharyngeal morphotype did show an association with gut length, gape, and tooth number. Sexual dimorphism is not playing a central role in enhancing trophic diversity within H. minckleyi. J. Morphol. 276:1448–1454, 2015. © 2015 Wiley Periodicals, Inc.     

Does higher connectivity lead to higher genetic diversity? Effects of habitat fragmentation on genetic variation and population structure in a gypsophile

Habitat fragmentation is a major threat to the maintenance of genetic diversity in many plant populations. Genetic effects of population size have received far more attention than the effects of isolation—or connectivity—but both are key components of the fragmentation process. To analyze the consequences of fragment size and connectivity on the neutral genetic variation and population genetic structure of the dominant gypsophile Lepidium subulatum, we selected 20 fragments along two continuous gradients of size and degree of isolation in a fragmented gypsum landscape of Central Spain. We used eight polymorphic microsatellite markers, and analyzed a total of 344 individuals. Populations were characterized by high levels of genetic diversity and low inbreeding coefficients, which agrees with the mainly outcrossing system of L. subulatum and its high abundance in gypsum landscapes. Bayesian clustering methods, pairwise F _ST values and analysis of molecular variance revealed low among-population differentiation, with no significant isolation by distance. However, several genetic diversity indices such as allelic richness, number of effective alleles, expected heterozygosity and number of private alleles were negatively related to population isolation. The higher genetic diversity found on more connected fragments suggests higher rates of gene flow among more connected populations. Overall, our results highlight that fragmentation can have important effects on intra-population genetic processes even for locally abundant, dominant species. This, together with previously documented effects of connectivity on fitness of gypsophile species highlights the importance of including habitat connectivity in management and conservation strategies of this type of semiarid systems.     

Does landscape structure affect resource tracking by avian frugivores in a fragmented Afrotropical forest?

Frugivorous species heavily depend on patchy food resources and are believed to track these in space and time, thereby providing an important seed dispersal function that might be critical toward the regeneration of fruiting plants. However, isolation of suitable food patches due to habitat fragmentation or changes in landscape connectivity may hamper food tracking behaviour and adversely affect populations of both frugivores (through starvation) and food plants (through interruption of seed dispersal). We here test whether density fluctuations in four frugivorous Afrotropical bird species were larger and/or matched fluctuations in ripe fruit densities better in study plots embedded in large tracts of indigenous forest than in equally-sized plots embedded in cultivated lands. We compared these results with those of four non-frugivorous species (out-group) which were not expected to track fruit resources. Whereas densities of both frugivores and fruit crops strongly fluctuated in space and time, these fluctuations were not synchronised, nor did the level of synchrony differ in relation to matrix type. For some but not all bird species, lower densities and smaller temporal fluctuations in forest plots surrounded by cultivation may reflect decreased mobility. The observed fluctuations in bird densities most likely reflect exchange with the surrounding landscape matrix, suggesting that small pockets of fruiting trees in farmland may comprise critical food resources for frugivores inhabiting highly fragmented landscapes, apart from increasing connectivity for both bird and seed dispersal.