Genetic effects of landscape,habitat preference and demography on three co‐occurring turtle species

Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life history strategies, habitat preferences and mobility. We sampled approximately 1500 individuals of three co‐occurring turtle species across a gradient of habitat change (including varying loss of wetlands and agricultural conversion of upland habitats) in the Midwestern USA. We used genetic clustering and multiple regression methods to identify associations between genetic structure and permanent landscape features, past landscape composition and landscape change in each species. Two aquatic generalists (the painted turtle, Chrysemys picta, and the snapping turtle Chelydra serpentina) both exhibited population genetic structure consistent with isolation by distance, modulated by aquatic landscape features. Genetic divergence for the more terrestrial Blanding's turtle (Emydoidea blandingii), on the other hand, was not strongly associated with geographic distance or aquatic features, and Bayesian clustering analysis indicated that many Emydoidea populations were genetically isolated. Despite long generation times, all three species exhibited associations between genetic structure and postsettlement habitat change, indicating that long generation times may not be sufficient to delay genetic drift resulting from recent habitat fragmentation. The concordances in genetic structure observed between aquatic species, as well as isolation in the endangered, long‐lived Emydoidea, reinforce the need to consider both landscape composition and demographic factors in assessing differential responses to habitat change in co‐occurring species.     

Seed production and germination in two rare and three common co‐occurring Acacia species from south‐east Australia

Abstract Seed set, size, viability and germination requirements were investigated for two rare (Acacia ausfeldii and A. willianisonii) and three common (A. pycnantha, A. genistifolia and A.paradoxa) co‐occurring congeners in box‐ironbark eucalypt forests near Bendigo, south‐east Australia to investigate correlates of rarity. Seed size was significantly smaller for the two rare species and germinants were less able to emerge from deeper sowing depths than were the larger seeded common congeners. All species had a strong heat‐stimulated germination response. While the rare A. ausfeldii showed strong germination only at the highest temperature treatment (100°C), the common and widespread A.pycnantha showed strong germination across a broad range of temperatures (60‐100°C), likely to be experienced by soil‐stored seeds during a fire. Seed viability, number of seeds per plant, and number of firm, aborted and eaten seeds per pod varied between species, but the pattern of variation was not related to rarity. Small seed size and a very specific temperature requirement for germination may help to explain rarity in A. ausfeldii, and to a lesser extent in A. willianisonii. Fires are often patchy and heating of the soil is likely to be highly spatially variable, so species with germination responses to a broad range of temperatures have an advantage over those that respond only to a narrow range. A narrower range of soil depths from which seeds can emerge will further reduce the proportion of the seed bank that might recruit following fire. Human impacts on species habitats, such as fragmentation, loss of topsoil through mining, timber harvesting, grazing and urbanization, and consequent reduction in fire intensity, are likely to have further contributed to rarity in these species. The role of pollination and other factors in relation to population size is the subject of further investigation.     

Environmental factors affecting patterns of distribution and co‐occurrence of two competing raptor species

Habitat selection is a complex process, that is affected by several factors, including habitat characteristics, environmental conditions, and both intra‐ and interspecific interactions. We analysed habitat preferences of two top avian predators, Peregrine Falcon Falco peregrinus, a medium‐sized diurnal raptor, and Eagle Owl Bubo bubo, a large nocturnal raptor. These two species are known to compete for preferred nest‐sites, and proximity to cliffs with Eagle Owls may reduce Peregrine breeding output through predation of young Falcons. We investigated the environmental factors affecting occurrence and coexistence of the two species and the potential role of habitat suitability in favouring co‐occurrence in 3519 km² of the central pre‐Alps of Italy, where the two species breed on cliffs and sometimes co‐occur on the same cliff. Peregrines settled on long, steep and favourably orientated cliffs in woodland landscapes close to urban areas. Eagle Owls settled on topographically similar cliffs, but in lower rainfall areas compared with cliffs occupied by Peregrines and cliffs unoccupied by either species. Sites where the two species co‐occurred were characterized by more horizontally extended cliffs compared with sites of exclusive occurrence of each species. An analysis of relative habitat suitability revealed that sites where the two species co‐occurred had the highest predicted probability of occupancy for both species, suggesting that those sites should be regarded as high‐quality sites. Breeding productivity of Eagle Owls was negatively affected by the co‐occurrence of Peregrines, whereas the effect of Eagle Owl proximity on Peregrine productivity varied according to cliff suitability for the Peregrines. Habitat selection had fitness consequences for Eagle Owls because breeding productivity increased with cliff length. Environmental conditions, particularly climatic factors, could allow the widespread coexistence of these competing raptors at the landscape scale, whereas at the local scale co‐occurrence could take place only on larger cliffs. These were preferred sites for both species, presumably because breeding at such sites offsets the costs of settling close to the competitor species.     

Discordant patterns of population structure for two co‐distributed snake species across a fragmented Ontario landscape

Aim The goal of our study was to investigate the effects of a fragmented landscape on the genetic population structure of two sympatric snake species that differ in habitat preference. The eastern garter snake (Thamnophis sirtalis sirtalis) is a common, habitat generalist, whereas the endangered eastern foxsnake (Mintonius [Elaphe] gloydi) is rarer, geographically restricted, and a marsh‐specialist. We were most interested in comparing the genetic population structure of both species and identifying any natural and human‐created features of the landscape that overlap with genetic disjunctions. Location Southwestern Ontario, Canada, surveying over half of the remaining range of the eastern foxsnake. Methods We utilized DNA microsatellite markers to examine genetic population structure of both species. The number of genetically distinct clusters for each species was determined using both Bayesian spatial assignment and spatial principal component analyses (sPCA). Genetic clusters were overlaid onto a habitat map to deduce possible physiognomic barriers to gene flow. Results Spatial assignment revealed three genetic clusters for garter snakes and five for foxsnakes. Each individual garter snake had a near equal probability of membership to two or more clusters with no cluster mapping onto a discrete geographic region, indicating that garter snakes comprise a single genetic population. The identified foxsnake clusters correspond to geographically circumscribed locations on the landscape, roughly coincident with isolated patches of suitable habitat. sPCAs revealed significant global allelic structure for foxsnakes, but not for garter snakes. No significant local structure was found for either species. Main Conclusions Our results imply that foxsnakes and garter snakes are differentially impacted by the same landscape or have dramatically different effective population sizes. Unsuitable intervening habitat such as agricultural tracts and roads between existing populations of foxsnakes appears to act as barriers to gene flow, while garter snake movement appears unrestricted by these features. Our findings have important implications for the management of eastern foxsnakes.     

Comparative phylogeography of two co‐distributed but ecologically distinct rainbowfishes of far‐northern Australia

Aim

To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co‐distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata).

Location

Fishes were sampled from far northern Australia (Queensland and Northern Territory).

Methods

We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity.

Results

Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10⁶ times coast length.

Main conclusions

Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species‐specific differences are epitomized here by the contrast between co‐distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.     

Multi‐scale oviposition site selection in two mosquito species

1. In organisms characterised by complex life cycles, habitat selection often occurs at multiple spatial scales. For instance, female mosquitoes searching for an appropriate aquatic habitat to oviposit their eggs should also consider the characteristics of the terrestrial landscape in which it is embedded. 2. In this study, a field experiment was conducted to test for multi‐scale oviposition site selection in two mosquito species. Artificial pools were placed in two adjacent landscapes, olive plantations and a citrus orchard, mainly differing in their blooming periods and nectar availability. Pools were organised in three pairs: predatory caged fish were present in both pools, in one pool, or in none. 3. Early during the season, most of the egg rafts were laid by Culiseta longiareolata females in pools located within the blooming citrus orchard. When blooming shifted to the olive plantation, C. longiareolata become opportunistic. Culex pipiens females appeared later on during the season, when egg rafts of C. longiareolata were scarce, and they exhibited a higher selectivity to the olive plantation, although its blooming ended. In addition, the selectivity of C. pipiens to fish‐free pools was stronger than that of C. longiareolata. 4. Culex pipiens was more selective, possibly due to its high dispersal ability, which can lower movement cost and enhance the ability to gather environmental information. A trade‐off among gonotrophic cycles, combined with a shorter breeding season and limited recognition ability of the predatory fish may have reduced C. longiareolata selectivity. These differential oviposition patterns can strongly affect the population and community dynamics of both species.     

Seasonal patterns of leaf production in co‐occurring trees with contrasting leaf phenology: time and quantitative divergences

Neotropical savannas (‘cerrados’) of Central Brazil are characterized by the coexistence of a large diversity of tree species with divergent phenological behaviors, which reflect a great diversity in growth strategies. In the present study time behavior and quantitative aspects of shoot growth, shoot mortality, and leaf longevity and production were analyzed in 12 woody species of contrasting leaf phenology, adopting a functional group approach where 12 species were categorized into three functional groups: evergreen, decidous and brevideciduous, according to their leaf phenology. Shoot growth and leaf production were seasonal for the three functional groups, differing in their time of occurrence, but being concentrated during the last months of the dry season. Shoot growth differed between evergreens and deciduous, as well leaf production. Evergreens had higher rates of shoot growth, produced a higher number of leaves and had longer leaf longevity (around 500 days against 300 days in deciduous and brevideciduous). Leaf longevity was associated with patterns of leaf production when accounting for all phenological groups studied. It was possible to identify different patterns of aerial growth in savanna phenological groups, providing evidence of great functional variability amongst the groups studied.     

Contrasting patterns of density‐dependent selection at different life stages can create more than one fast–slow axis of life‐history variation

There has been much recent research interest in the existence of a major axis of life‐history variation along a fast–slow continuum within almost all major taxonomic groups. Eco‐evolutionary models of density‐dependent selection provide a general explanation for such observations of interspecific variation in the "pace of life." One issue, however, is that some large‐bodied long‐lived “slow” species (e.g., trees and large fish) often show an explosive “fast” type of reproduction with many small offspring, and species with “fast” adult life stages can have comparatively “slow” offspring life stages (e.g., mayflies). We attempt to explain such life‐history evolution using the same eco‐evolutionary modeling approach but with two life stages, separating adult reproductive strategies from offspring survival strategies. When the population dynamics in the two life stages are closely linked and affect each other, density‐dependent selection occurs in parallel on both reproduction and survival, producing the usual one‐dimensional fast–slow continuum (e.g., houseflies to blue whales). However, strong density dependence at either the adult reproduction or offspring survival life stage creates quasi‐independent population dynamics, allowing fast‐type reproduction alongside slow‐type survival (e.g., trees and large fish), or the perhaps rarer slow‐type reproduction alongside fast‐type survival (e.g., mayflies—short‐lived adults producing few long‐lived offspring). Therefore, most types of species life histories in nature can potentially be explained via the eco‐evolutionary consequences of density‐dependent selection given the possible separation of demographic effects at different life stages.     

Life-history traits are correlated with geographical distribution patterns of western European forest herb species

Aim To investigate whether six plant life‐history traits that have been related to colonization ability at local scales are also related to the geographical range characteristics of 273 forest plant species. Location Continental western Europe, five countries in particular: France, Luxemburg, Belgium, the Netherlands and Germany. The region is situated between 42° and 55°N and 5°W and 15°E and has a summed total area of 971,404 km². Methods Distribution data were compiled from five national data bases and converted to a 10′ grid. Life‐history traits were taken from existing compilations of autecological information of European species. The spatial arrangement of occupied grid cells was investigated using Ripley's K. Cross‐species correlations and phylogenetically independent contrasts were used to investigate the relationships between plant life‐history traits and three range characteristics: area of occupancy, latitudinal extent and centroid latitude. Results For herbaceous species, seed dispersal mode, seed production and seed bank longevity exhibited significant associations with geographical range characteristics, including area of occupancy. Woody plant species exhibited fewer significant associations, although maximum height was positively associated with range centroid latitude within the study area. Furthermore, the ranges of species with limited dispersal ability were found to be more clustered than the ranges of species with morphological adaptations for long‐distance seed dispersal. Main conclusions For western European forest plant species, life‐history traits that are related to colonization ability at local scales are associated with variation in large‐scale geographical range characteristics. This finding implies that the distributions of some forest plant species in the study area may be limited by seed dispersal and colonization capacity rather than climate or other environmental factors.     

Effects of diet and host access on fecundity and lifespan in two fruit fly species with different life‐history patterns

The reproductive ability of female tephritids can be limited and prevented by denying access to host plants and restricting the dietary precursors of vitellogenesis. The mechanisms underlying the delayed egg production in each case are initiated by different physiological processes that are anticipated to have dissimilar effects on lifespan and reproductive ability later in life. The egg‐laying abilities of laboratory‐reared females of the Mediterranean fruit fly (Ceratitis capitata Wiedmann) and melon fly (Bactrocera cucurbitae Coquillett) from Hawaii are delayed or suppressed by limiting access to host fruits and dietary protein. In each case, this is expected to prevent the loss of lifespan associated with reproduction until protein or hosts are introduced. Two trends are observed in each species: first, access to protein at eclosion leads to a greater probability of survival and a higher reproductive ability than if it is delayed and, second, delayed host access reduces lifetime reproductive ability without improving life expectancy. When host access and protein availability are delayed, the rate of reproductive senescence is reduced in the medfly, whereas the rate of reproductive senescence is generally increased in the melon fly. Overall, delaying reproduction lowers the fitness of females by constraining their fecundity for the remainder of the lifespan without extending the lifespan. © 2013 The Royal Entomological Society     

Land use drivers of species re‐expansion: inferring colonization dynamics in Eurasian otters

Aim Land use intensity has been recognized as one of the major determinants of native species declines. The re‐expansion of species previously constrained by habitat degradation has been rarely investigated. Here, we use site occupancy models incorporating imperfect detection to identify the land use drivers of the re‐expansion of the Eurasian otter (Lutra lutra). Location Czech Republic. Methods We applied multi‐season occupancy models to otter presence–non‐detection data collected in three national surveys (1992, 2000, 2006) at 552 sites (11.2 × 12 km grid cells). Model parameters included site occupancy, colonization and extinction probabilities, and detection probability at a sub‐site level. We modelled changes in occupancy over time as a function of agricultural, urban and industrial land use and change in the extent of agricultural land use. Results Under the best fitting model, occupancy was estimated to be 34.6% in 1992, 51.3% in 2000 and 83.7% in 2006. Detection probability was neither perfect nor constant. Occupancy probability in 1992 was negatively related to land use gradients. Colonization was more likely to occur where a reduction in agricultural land was larger. Variation in extinction and colonization rates along land use gradients resulted in increased occupancy in industrial and especially urban landscapes. Conversely, occupancy remained almost unchanged along agricultural gradients. Main conclusions Dynamics of otter expansion were strongly associated with the two main patterns of the rapid environmental transition that has taken place in the Czech Republic since the early 1990s. Results show that a reduction in intensive agricultural land use led to an increase in otter distribution, providing evidence of the impact of agricultural land use on stream ecosystems. Moreover, otters recolonized urban and industrial landscapes, probably as a result of extensive reduction in water pollution from point sources. Our results suggest that active conservation of otter populations should focus on restoration of freshwater habitat at large scales, especially in agricultural landscapes.     

Stable isotopes reveal different patterns of inter‐crop dispersal in two ladybeetle species

1. Dispersal plays a key role in structuring the local population densities of many insect species, yet the movement patterns across the landscape of most species are poorly understood. By measuring the stable isotope of carbon (δ¹³C) from multiple tissues, a novel approach applied to field‐collected insects, we were able to infer differences in movement patterns of two species of mobile generalist insect predators. 2. Coccinella septempunctata L (7‐spot ladybeetle) and Harmonia axyridis Pallas (multicoloured Asian ladybeetle) were collected in agricultural habitats in 2003 and 2004, and were assayed for δ¹³C in the elytra (slow turnover) and fat/reproductive tissues (fast turnover). δ¹³C values were used to infer diet use of C3 versus C4 crops. 3. Coccinella septempunctata was relatively more faithful to a particular habitat and tended to stay in alfalfa and soybean (C3‐based photosynthetic crops) over long periods during the summer. This contrasts with H. axyridis which showed isotopic evidence consistent with frequent late‐season movement between C3 and C4 crops such as corn in the landscape. 4. These differing patterns suggest that in the late summer season H. axyridis individuals traverse the environment more extensively and utilise broadly dispersed aphid resources, whereas C. septempunctata adults are more specialised on alfalfa and soybean crops.     

Metastasis‐specific patterns of response and progression with anti‐PD‐1 treatment in metastatic melanoma

This study evaluated patterns of response as discerned by comprehensive metastasis‐specific analysis in metastatic melanoma patients receiving anti‐PD‐1 antibodies. Bi‐dimensional measurements of every metastasis in patients enrolled in the KEYNOTE‐001 trial at a single institution were obtained at baseline and throughout treatment. Twenty‐seven evaluable patients had 399 baseline metastases measurable on CT imaging. Complete response (CR) which occurred in 52.6% of metastases was smaller (mean 223 mm² versus 760 mm², p < .01) and occurred more frequently in the lungs (65% versus 39.4%, p < .01). Response was heterogenous (new/progressing metastases alongside CR metastases) at first assessment in 4/14 patients with objective response (OR) as opposed to 7/13 patients with non‐OR. CR of individual metastases is common and influenced by site and size. Most patients with OR demonstrate homogenous regression in all metastases at the first assessment. In contrast, patients with early heterogeneity had a poor outcome.     

Leaf wax n‐alkane patterns of six tropical montane tree species show species‐specific environmental response

It remains poorly understood how the composition of leaf wax n‐alkanes reflects the local environment. This knowledge gap inhibits the interpretation of plant responses to the environment at the community level and, by extension, inhibits the applicability of n‐alkane patterns as a proxy for past environments. Here, we studied the n‐alkane patterns of five Miconia species and one Guarea species, in the Ecuadorian Andes (653–3,507 m a.s.l.). We tested for species‐specific responses in the average chain length (ACL), the C₃₁/(C₃₁ + C₂₉) ratio (ratio), and individual odd n‐alkane chain lengths across an altitudinally driven environmental gradient (mean annual temperature, mean annual relative air humidity, and mean annual precipitation). We found significant correlations between the environmental gradients and species‐specific ACL and ratio, but with varying magnitude and direction. We found that the n‐alkane patterns are species‐specific at the individual chain length level, which could explain the high variance in metrics like ACL and ratio. Although we find species‐specific sensitivity and responses in leaf n‐alkanes, we also find a general decrease in “shorter” (<C₂₉) and an increase in “longer” (>C₃₁) chain lengths with the environmental gradients, most strongly with temperature, suggesting n‐alkanes are useful for reconstructing past environments.     

Long‐term mark‐and‐recapture study of a freshwater mussel reveals patterns of habitat use and an association between survival and river discharge

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Diversity and distribution of genetic variation in gammarids: Comparing patterns between invasive and non‐invasive species

Biological invasions are worldwide phenomena that have reached alarming levels among aquatic species. There are key challenges to understand the factors behind invasion propensity of non‐native populations in invasion biology. Interestingly, interpretations cannot be expanded to higher taxonomic levels due to the fact that in the same genus, there are species that are notorious invaders and those that never spread outside their native range. Such variation in invasion propensity offers the possibility to explore, at fine‐scale taxonomic level, the existence of specific characteristics that might predict the variability in invasion success. In this work, we explored this possibility from a molecular perspective. The objective was to provide a better understanding of the genetic diversity distribution in the native range of species that exhibit contrasting invasive propensities. For this purpose, we used a total of 784 sequences of the cytochrome c oxidase subunit I of mitochondrial DNA (mtDNA‐COI) collected from seven Gammaroidea, a superfamily of Amphipoda that includes species that are both successful invaders (Gammarus tigrinus, Pontogammarus maeoticus, and Obesogammarus crassus) and strictly restricted to their native regions (Gammarus locusta, Gammarus salinus, Gammarus zaddachi, and Gammarus oceanicus). Despite that genetic diversity did not differ between invasive and non‐invasive species, we observed that populations of non‐invasive species showed a higher degree of genetic differentiation. Furthermore, we found that both geographic and evolutionary distances might explain genetic differentiation in both non‐native and native ranges. This suggests that the lack of population genetic structure may facilitate the distribution of mutations that despite arising in the native range may be beneficial in invasive ranges. The fact that evolutionary distances explained genetic differentiation more often than geographic distances points toward that deep lineage divergence holds an important role in the distribution of neutral genetic diversity.