Importance of scale,land‐use,and stream network properties for riparian plant communities along an urban gradient

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Genome of an iconic Australian bird: High‐quality assembly and linkage map of the superb fairy‐wren (Malurus cyaneus)

The superb fairy‐wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high‐quality reference. To rectify that, we present the first high‐quality genome assembly of a Meliphagides representative: the superb fairy‐wren. We combined Illumina shotgun and mate‐pair sequences, PacBio long‐reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07‐Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high‐quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree‐based bird genetic maps, we find that the fairy‐wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high‐quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy‐wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.     

Territory configuration moderates the frequency of extra‐group mating in superb fairy‐wrens

The frequency of extra‐pair paternity (EPP) in socially monogamous birds varies substantially between and within species, but ecological drivers of this variation remain poorly understood. Habitat configuration could influence EPP by moderating access to extra‐pair mates, because species occupying territories in a clustered ‘honeycomb’ configuration have a larger pool of potential extra‐group mates in their immediate neighbourhood than those living in linearly arranged territories (e.g. along narrow strips of riparian or fragmented habitat). We exploited variation in the spatial arrangement of territories due to anthropogenic modification of habitat of the cooperatively breeding superb fairy‐wren Malurus cyaneus to test whether habitat configuration influenced the frequency of EPP. In this species, most paternity is obtained by males outside the social group [extra‐group paternity (EGP)]. We found that the frequency of EGP among groups living in linear strips of roadside vegetation (41% of 44 offspring) was lower than it was for groups living in clustered territories within continuous habitat (59% of 70 offspring). Differences in group size and pair relatedness did not explain differences in EGP associated with territory configuration, although the frequency of EGP was negatively correlated with pair relatedness. Our finding suggests that territory configuration can influence rates of EGP and that anthropogenic habitat fragmentation has the potential to limit access to extra‐pair mates, affecting mating systems and ultimately fitness.     

Geographical distribution and habitat occurrence of the Water Shrew (Neomys fodiens) in the Weald of South-East England

A survey of 96 sites in a range of riparian habitats in the catchments of five rivers during June–August 1998 used the bait tube method to investigate the geographical distribution and habitat occurrence of Water Shrews (Neomys fodiens) in the Weald of South‐East England. Water Shrews were found at 42% of sites, and were widely distributed in all river catchments except the Mole. They occurred in many riparian habitats, including rivers, streams, canals and ditches, with a range of physical and biotic characteristics. There were no signs of habitat avoidance in response to human disturbance but Water Shrews were absent from the river catchment with lowest water quality. Logistic regression analysis was used to model the effect of habitat variables on the presence of Water Shrews, with current speed, water depth, bank incline and bank‐side vegetation identified as important variables. Fast‐flowing shallow waters had a significant positive effect on their presence, whereas scarce herbaceous vegetation and a bank of low incline had a significant negative effect. These habitat variables appear to be reliable indicators of the probability of finding Water Shrews at a particular site, and have implications for habitat management and conservation.     

Non‐native salmonids affect amphibian occupancy at multiple spatial scales

Aim The introduction of non‐native species into aquatic environments has been linked with local extinctions and altered distributions of native species. We investigated the effect of non‐native salmonids on the occupancy of two native amphibians, the long‐toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), across three spatial scales: water bodies, small catchments and large catchments. Location Mountain lakes at ≥ 1500 m elevation were surveyed across the northern Rocky Mountains, USA. Methods We surveyed 2267 water bodies for amphibian occupancy (based on evidence of reproduction) and fish presence between 1986 and 2002 and modelled the probability of amphibian occupancy at each spatial scale in relation to habitat availability and quality and fish presence. Results After accounting for habitat features, we estimated that A. macrodactylum was 2.3 times more likely to breed in fishless water bodies than in water bodies with fish. Ambystoma macrodactylum also was more likely to occupy small catchments where none of the water bodies contained fish than in catchments where at least one water body contained fish. However, the probability of salamander occupancy in small catchments was also influenced by habitat availability (i.e. the number of water bodies within a catchment) and suitability of remaining fishless water bodies. We found no relationship between fish presence and salamander occupancy at the large‐catchment scale, probably because of increased habitat availability. In contrast to A. macrodactylum, we found no relationship between fish presence and R. luteiventris occupancy at any scale. Main conclusions Our results suggest that the negative effects of non‐native salmonids can extend beyond the boundaries of individual water bodies and increase A. macrodactylum extinction risk at landscape scales. We suspect that niche overlap between non‐native fish and A. macrodactylum at higher elevations in the northern Rocky Mountains may lead to extinction in catchments with limited suitable habitat.     

Reservoir water levels do not influence daily mass gain of warblers at a riparian stopover site

ABSTRACT Hydroelectric dam operations that lead to fluctuations in the water levels of reservoirs can influence the amount of riparian habitat available for migrating songbirds and may impact the use and quality of remaining habitat. Our objective was to determine if use of riparian habitats and mass gain by five warbler species at the Columbia River‐Revelstoke Migration Monitoring Station in British Columbia, Canada, were influenced by water levels in the surrounding Arrow Lakes Reservoir. We analyzed fall migration data collected from 1998 to 2006. Capture rates of American Redstarts (Setophaga ruticilla), Common Yellowthroats (Geothlypis trichas), Orange‐crowned Warblers (Vermivora celata), Wilson's Warblers (Wilsonia pusilla), and Yellow Warblers (Dendroica petechia) varied between years and weeks of the migration period, but were not affected by annual or weekly variation in water levels. Annual variation in capture rates was driven by hatch‐year birds (>80% of individuals captured were juveniles) and could reflect conditions on the breeding grounds that influence productivity. We found that mass gain by the five species of warblers varied between 0.32% and 0.98% of lean body mass/hour. Mass gain did not vary between years or across weeks of the migration period and was not influenced by annual or weekly variation in reservoir water levels. Although the amount of available riparian habitat was reduced when reservoir water levels were high, we found no evidence that this loss of habitat influenced either the number of warblers or the mass gain of warblers using the riparian habitat that remained. Body mass at the time of first capture varied between years and across weeks for all five species. For American Redstarts and Orange‐crowned Warblers, body mass declined as average weekly water levels increased, a pattern that could arise if water levels influenced either their settlement decisions or length of stay.     

The evolution of black plumage from blue in Australian fairy‐wrens (Maluridae): genetic and structural evidence

Genetic variation in the melanocortin‐1 receptor (MC1R) locus is responsible for color variation, particularly melanism, in many groups of vertebrates. Fairy‐wrens, Maluridae, are a family of Australian and New Guinean passerines with several instances of dramatic shifts in plumage coloration, both intra‐ and inter‐specifically. A number of these color changes are from bright blue to black plumage. In this study, we examined sequence variation at the MC1R locus in most genera and species of fairy‐wrens. Our primary focus was subspecies of the white‐winged fairy‐wren Malurus leucopterus in which two subspecies, each endemic to islands off the western Australian coast, are black while the mainland subspecies is blue. We found fourteen variable amino acid residues within M. leucopterus, but at only one position were alleles perfectly correlated with plumage color. Comparison with other fairy‐wren species showed that the blue mainland subspecies, not the black island subspecies, had a unique genotype. Examination of MC1R protein sequence variation across our sample of fairy‐wrens revealed no correlation between plumage color and sequence in this group. We thus conclude that amino acid changes in the MC1R locus are not directly responsible for the black plumage of the island subspecies of M. leucopterus. Our examination of the nanostructure of feathers from both black and blue subspecies of M. leucopterus and other black and blue fairy‐wren species clarifies the evolution of black plumage in this family. Our data indicate that the black white‐winged fairy‐wrens evolved from blue ancestors because vestiges of the nanostructure required for the production of blue coloration exist within their black feathers. Based on our phylogeographic analysis of M. leucopterus, in which the two black subspecies do not appear to be each other's closest relatives, we infer that there have been two independent evolutionary transitions from blue to black plumage. A third potential transition from blue to black appears to have occurred in a sister clade.     

Limited Effects of Large‐Scale Riparian Restoration on Seed Banks in Agriculture

I examined the effect of riparian forest restoration on plant abundance and diversity, including weed species, on agricultural lands along the Sacramento River in California (United States). Riparian forest restoration on the Sacramento River is occurring on a large‐scale, with a goal of restoring approximately 80,000 ha over 160 km of the river. In multiuse habitats, such as the Sacramento River, effects of adjoining habitat types and movement of species across these habitats can have important management implications in terms of landscape‐scale patterns of species distributions. Increased numbers of pest animals and weeds on agricultural lands associated with restored habitats could have negative economic impacts, and in turn affect support for restoration of natural areas. In order to determine the distribution and abundance of weeds associated with large‐scale restoration, I collected seed bank soil samples on orchards between 0 and 5.6 km from adjacent restored riparian, remnant riparian, and agricultural habitats. I determined the abundance, species richness, and dispersal mode of plant species in the seed bank and analyzed these variables in terms of adjacent habitat type and age of restored habitat. I found that agricultural weed species had higher densities at the edge of restored riparian habitat and that native plants had higher densities adjacent to remnant riparian habitat. Weed seed abundance increased significantly on walnut farms adjacent to restored habitat with time since restored. I supply strong empirical evidence that large areas of natural and restored habitats do not lead to a greater penetration of weed species into agricultural areas, but rather that weed penetration is both temporally and spatially limited.     

Life history and habitat preference in the Darling hardyhead,Craterocephalus amniculus (Teleostei,Atherinidae) in the northern Murray‐Darling Basin,Australia

The Darling hardyhead, Craterocephalus amniculus (Atherinidae), is a threatened fish species inhabiting upstream reaches of a number of northern Murray‐Darling Basin catchments. Little is known of its life history. Our goal was to determine patterns of seasonal size structure, interannual and spatial variation in diet, and habitat selection in this species across multiple sites and years in the upper Macintyre River, northern New South Wales. Preserved specimens from a separate study were used to obtain information on diet and size structure. Size structures suggested a single annual spawning season in late September or early October. Diets varied significantly, both between years at the downstream site and among the three sites although the underlying cause of this was untested. Dietary diversity increased with distance downstream. At the two upstream sites, aquatic invertebrates made up most of the diet while over half the gut contents at the downstream site was unidentified detritus. Preference was shown for pool habitats with a sand or cobble substrate, increased channel depth and width and distance from the bank, and reduced flow velocity. Overhanging exotic riparian vegetation and in‐stream woody debris were non‐preferred. This species may be vulnerable to further population decline in light of its restricted habitat preferences and narrow spawning season. However, comparable data from nearby catchments will be necessary to ascertain the species’ conservation status across its broader distribution.     

Determining fine‐scale migratory connectivity and habitat selection for a migratory songbird by using new GPS technology

Migratory aerial insectivores are among the fastest declining avian groups, but our understanding of these trends has been limited by poor knowledge of migratory connectivity and the identification of critical habitat across the vast distances they travel annually. Using new, archival GPS loggers, we tracked individual purple martins Progne subis from breeding colonies across North America to determine precise (< > 10 m) locations of migratory and overwintering roost locations in South America and to test hypotheses for fine‐scale migratory connectivity and habitat use. We discovered weak migratory connectivity at the roost scale, and extensive, fine‐scale mixing of birds in the Amazon from distant (> 2000 km) breeding sites, with some individuals sharing the same roosting trees. Despite vast tracts of contiguous forest in this region, birds occupied a much more limited habitat, with most (56%) roosts occurring on small habitat islands that were strongly associated with water. Only 17% of these roosts were in current protected areas. These data reflect a critical advance in our ability to remotely determine precise migratory connectivity and habitat selection across vast spatial scales, enhancing our understanding of population dynamics and enabling more effective conservation of species at risk.     

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

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

Habitat fragmentation influences genetic diversity and differentiation: Fine‐scale population structure of Cercis canadensis (eastern redbud)

Forest fragmentation may negatively affect plants through reduced genetic diversity and increased population structure due to habitat isolation, decreased population size, and disturbance of pollen‐seed dispersal mechanisms. However, in the case of tree species, effective pollen‐seed dispersal, mating system, and ecological dynamics may help the species overcome the negative effect of forest fragmentation. A fine‐scale population genetics study can shed light on the postfragmentation genetic diversity and structure of a species. Here, we present the genetic diversity and population structure of Cercis canadensis L. (eastern redbud) wild populations on a fine scale within fragmented areas centered around the borders of Georgia–Tennessee, USA. We hypothesized high genetic diversity among the collections of C. canadensis distributed across smaller geographical ranges. Fifteen microsatellite loci were used to genotype 172 individuals from 18 unmanaged and naturally occurring collection sites. Our results indicated presence of population structure, overall high genetic diversity (H_E = 0.63, H_O = 0.34), and moderate genetic differentiation (F_ST = 0.14) among the collection sites. Two major genetic clusters within the smaller geographical distribution were revealed by STRUCTURE. Our data suggest that native C. canadensis populations in the fragmented area around the Georgia–Tennessee border were able to maintain high levels of genetic diversity, despite the presence of considerable spatial genetic structure. As habitat isolation may negatively affect gene flow of outcrossing species across time, consequences of habitat fragmentation should be regularly monitored for this and other forest species. This study also has important implications for habitat management efforts and future breeding programs.     

Impacts of an invasive willow (Salix × rubens) on riparian bird assemblages in south‐eastern Australia

We explored how a woody plant invader affected riparian bird assemblages. We surveyed 15 200‐m‐long transects in riparian zones in a much‐changed landscape of eastern Victoria, Australia. Abundance, species‐richness, foraging‐guild richness and composition of birds were compared in transects in three habitat types: (i) riparian zones dominated by the invasive willow Salix × rubens; (ii) riparian zones lined with native woody species; and (iii) riparian zones cleared of almost all woody vegetation. We also measured abundance and richness of arthropods and habitat structure to explore further the effects of food resources and habitat on the avifauna. We observed 67 bird species from 14 foraging guilds. Native riparian transects had more birds, bird species and foraging guilds than willow‐invaded or cleared transects. Habitat complexity increased from cleared to willow‐invaded to native riparian transects, as did abundance of native and woodland‐dependent birds. Native shrub and trees species had more foliage and branch‐associated arthropods than did willows, consistent with a greater abundance and variety of foraging guilds of birds dependent on this resource. Willow spread into cleared areas is unlikely to facilitate greatly native bird abundance and diversity even though habitat complexity is increased. Willow invasion into the native riparian zone, by decreasing food resources and altering habitat, is likely to reduce native bird biodiversity and further disrupt connectivity of the riparian zone.     

Fine‐scale heterogeneity in beetle assemblages under co‐occurring Eucalyptus in the same subgenus

Aim Insect biodiversity is often positively associated with habitat heterogeneity. However, this relationship depends on spatial scale, with most studies focused on differences between habitats at large scales with a variety of forest tree species. We examined fine‐scale heterogeneity in ground‐dwelling beetle assemblages under co‐occurring trees in the same subgenus: Eucalyptus melliodora A. Cunn. ex Schauer and E. blakelyi Maiden (Myrtaceae). Location Critically endangered grassy woodland near Canberra, south‐eastern Australia. Methods We used pitfall traps and Tullgren funnels to sample ground‐dwelling beetles from the litter environment under 47 trees, and examined differences in diversity and composition at spatial scales ranging from 100 to 1000 m. Results Beetle assemblages under the two tree species had distinctive differences in diversity and composition. We found that E. melliodora supported a higher richness and abundance of beetles, but had higher compositional similarity among samples. In contrast, E. blakelyi had a lower abundance and species richness of beetles, but more variability in species composition among samples. Main conclusions Our study shows that heterogeneity in litter habitat under co‐occurring and closely related eucalypt species can influence beetle assemblages at spatial scales of just hundreds of metres. The differential contribution to fine‐scale alpha and beta diversity by each eucalypt can be exploited for conservation purposes by ensuring an appropriate mix of the two species in the temperate woodlands where they co‐occur. This would help not only to maximize biodiversity at landscape scales, but also to maintain heterogeneity in species richness, trophic function and biomass at fine spatial scales.     

Fine‐scale habitat preferences influence within‐river population connectivity: a case‐study using two sympatric New Zealand Galaxias fish species

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Thresholds of riparian forest use by terrestrial mammals in a fragmented Amazonian deforestation frontier

Species persistence in fragmented landscapes is intimately related to the quality, structure, and context of remaining habitat remnants. Riparian vegetation is legally protected within private landholdings in Brazil, so we quantitatively assessed occupancy patterns of terrestrial mammals in these remnants, examining under which circumstances different species effectively use them. We selected 38 riparian forest patches and five comparable riparian sites within continuous forest, at which we installed four to five camera-traps per site (199 camera-trap stations). Terrestrial mammal assemblages were sampled for 60 days per station during the dry seasons of 2013 and 2014. We modelled species occupancy and detection probabilities within riparian forest remnants, and examined the effects of patch size, habitat quality, and landscape structure on occupancy probabilities. We then scaled-up modelled occupancies to all 1915 riparian patches throughout the study region to identify which remnants retain the greatest potential to work as habitat for terrestrial vertebrates. Of the ten species for which occupancy was modelled, six responded to forest quality (remnant degradation, cattle intrusion, palm aggregations, and understorey density) or structure (remnant width, isolation, length, and area of the patch from which it originates). Patch suitability was lower considering habitat quality than landscape structure, and virtually all riparian remnants were unsuitable to maintain a high occupancy probability for all species that responded to forest patch quality or structure. Beyond safeguarding legal compliance concerning riparian remnant amount, ensuring terrestrial vertebrate persistence in fragmented landscapes will require curbing the drivers of forest degradation within private landholdings.     

ECOLOGICAL BARRIERS TO GENE FLOW BETWEEN RIPARIAN AND FOREST SPECIES OF AINSLIAEA (ASTERACEAE)

Understanding the role of habitat‐associated adaptation in reducing gene flow resulting in population differentiation and speciation is a major issue in evolutionary biology. We demonstrate a significant role for habitat divergence in species isolation between two naturally hybridizing riparian and nonriparian plants, Ainsliaea faurieana and A. apiculata (Asteraceae), on Yakushima Island, Japan. By analyzing the fine‐scale population structure at six sympatric sites, we found that variations in leaf shape, geography, light conditions, and genotype were strongly correlated across riverbank–forest transitions. No evidence of effective gene flow was found between the two species across the majority of the transition zones, although the NewHybrid clustering analysis confirmed interspecific hybridization. However, a relatively high level of gene flow was observed across one zone with a more diffuse ecotone and intermediate flooding and light conditions, possibly generated by human disturbances. These results suggest that the barriers to gene flow between the riparian and forest species are primarily ecological. Additional common garden experiments indicated that the two species are adaptively differentiated to contrasting flooding and light environments. Overall, our study suggests that adaptations to different habitats can lead to the formation of reproductive isolating barriers and the maintenance of distinct species boundaries.     

High‐resolution riparian vegetation mapping to prioritize conservation and restoration in an impaired desert river

In highly impaired watersheds, it is critical to identify both areas with desirable habitat as conservation zones and impaired areas with the highest likelihood of improvement as restoration zones. We present how detailed riparian vegetation mapping can be used to prioritize conservation and restoration sites within a riparian and instream habitat restoration program targeting 3 native fish species on the San Rafael River, a desert river in southeastern Utah, United States. We classified vegetation using a combination of object‐based image analysis (OBIA) on high‐resolution (0.5 m), multispectral, satellite imagery with oblique aerial photography and field‐based data collection. The OBIA approach is objective, repeatable, and applicable to large areas. The overall accuracy of the classification was 80% (Cohen's κ = 0.77). We used this high‐resolution vegetation classification alongside existing data on habitat condition and aquatic species' distributions to identify reaches' conservation value and restoration potential to guide management actions. Specifically, cottonwood (Populus fremontii) and tamarisk (Tamarix ramosissima) density layers helped to establish broad restoration and conservation reach classes. The high‐resolution vegetation mapping precisely identified individual cottonwood trees and tamarisk thickets, which were used to determine specific locations for restoration activities such as beaver dam analogue structures in cottonwood restoration areas, or strategic tamarisk removal in high‐density tamarisk sites. The site prioritization method presented here is effective for planning large‐scale river restoration and is transferable to other desert river systems elsewhere in the world.     

Cerulean Warblers in the Ozark region: habitat selection,breeding biology,survival, and space use

Cerulean Warblers (Setophaga cerulea) are a species with declining populations that exhibit regional variation in habitat selection and demographic rates. The Ozark region of the south‐central United States likely provides important habitat for Cerulean Warblers, but little is known about their breeding biology in that region. We studied Cerulean Warblers in riparian forests of the Ozarks of Arkansas from 2018 to 2020. We assessed multi‐scale habitat selection for vegetative and topographic features, documented their breeding biology, estimated within‐season and annual apparent survival, and estimated territory sizes. We found that Cerulean Warblers selected riparian habitat characterized by large‐diameter trees across all spatial scales. Contrary to the results of previous studies, males appeared to avoid white oaks (Quercus spp., Section Quercus) at the territory scale, but this avoidance may reflect an underlying preference for riparian habitat. Our logistic‐exposure estimate of nest survival (0.32; 85% confidence interval: 0.21–0.46) was similar to the median of estimates reported in previous studies. Our results indicate that maintaining riparian forests with large trees is important to provide suitable habitat for Cerulean Warblers in the Ozark region. Because of similarities in habitat selection among regions, some management practices from other populations, including retaining large trees and promoting a heterogeneous canopy structure, may be useful for managing for Cerulean Warblers in riparian areas of the Ozarks. However, selection for topography and tree species by Cerulean Warblers in our study also suggests that region‐specific management strategies will be beneficial. Finally, our demographic rate estimates for this population should prove valuable in future full‐annual‐cycle population modeling efforts.