Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World

Geographic range shifts can cause secondary contact and hybridization between closely related species, revealing mechanisms of species formation and integrity. These dynamics typically play out in restricted geographic regions, but highly vagile species may experience major distributional changes resulting in broad areas of contact. The Glossy Ibis (Plegadis falcinellus) is a dispersive waterbird of the Old World and Australia that colonized eastern North America in the early 19th century and came into contact with the native White‐faced Ibis (P. chihi). Putative hybrids between the two species have been observed across North America. To examine the population genomic consequences of this natural invasion, we sequenced 4,616 ultraconserved elements from 66 individuals sampled across the distributions of falcinellus, chihi, and the Puna Ibis (P. ridgwayi) of South America. We found genomic differentiation among the three species. Loci with high sequence divergence were often shared across all pairwise species comparisons, were associated with regions of high nucleotide diversity, and were concentrated on the Z chromosome. We detected signals of genetic admixture between chihi and falcinellus in individuals both near and far from their core area of sympatry. Genomic cline analyses revealed evidence of greater introgression into falcinellus from chihi, but we found little evidence for selection against hybrids. We also found signals of admixture between ridgwayi and South American populations of chihi. Our results indicate vagile species can experience pervasive introgression upon secondary contact, although we suggest these dynamics may be more ephemeral than the stable hybrid zones often observed in less dispersive organisms.     

Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants

Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change‐driven intracontinental range‐expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range‐expanding and four congeneric native species along a 2,000 km latitudinal transect from South‐Eastern to North‐Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range‐expanding plant species than in congeneric natives and that in their new range, range‐expanding plant species accumulate fewest root‐feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range‐expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range‐expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root‐feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range‐expanding and native plant species and that some range‐expanding plant species may become released from root‐feeding nematodes in the new range.     

Woody plant encroachment reduces species richness of herb‐rich woodlands in southern Australia

Abstract Woody plants have been increasing in many woodland and savanna ecosystems owing to land use changes in recent decades. We examined the effects of encroachment by the indigenous shrub Leptospermum scoparium (Myrtaceae) on herb‐rich Eucalyptus camaldulensis woodlands in southern Australia. Species richness and compositional patterns were examined under the canopy of L. scoparium and in surrounding open areas to determine the species most susceptible to structural changes. Richness was significantly lower in areas of moderate to high L. scoparium cover (>15%), suggesting that a threshold shrub cover caused major change in this ecosystem. Shrubs were associated with a significant reduction in above‐ground biomass of the ground‐layer flora and a significant shift in community composition. The few species that were positively associated with high L. scoparium cover were also common in the woodland flora; no new species were recorded under the shrub canopy. Important environmental changes associated with L. scoparium cover were decreased light availability and increased litter cover, which were likely a consequence of encroachment. Leptospermum scoparium cover was also associated with greater surface soil moisture, which may be a consequence of increased shading under the shrub canopy or indicate favourable soil conditions for L. scoparium establishment. Reductions in species richness and abundance of the germinable seed bank were found in soil samples taken from under L. scoparium. With ongoing recruitment of L. scoparium and consequent increases in shrub cover, ground‐layer diversity in these species‐rich woodlands should continue to decline over time.     

Transatlantic secondary contact in Atlantic Salmon,comparing microsatellites,a single nucleotide polymorphism array and restriction‐site associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re‐evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD‐seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans‐Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD‐seq based approaches for the resolution of complex spatial patterns, resolves a region of trans‐Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.     

Composition of mixed‐species flocks and shifts in foraging location of flocking species on Hainan Island,China

A total of 134 bird species were recorded at Jianfengling, Hainan Island, in China from May 2000 to September 2004, of which 44 participated in one or more of 134 mixed‐species flocks. These flocks averaged 3.8 ± 0.2 species and 20.3 ± 1.2 individuals. Flocking propensity in a given species ranged from 1.5 to 100%. For flocking species, frequency of flocking and number of individuals in flocks was positively correlated with frequency and number in point counts. Among all species pairs with flocking frequency above 5%, cluster and correlation analysis indicated there were two principal groups of flocking birds – canopy species and understorey species: associations were positive within a group, but negative between groups. Canopy birds had a higher flocking propensity than understorey birds. They also made significantly less use of inner branches and trunks and greater use of middle branches, and foraged at a significantly greater height when in mixed‐species flocks than when solitary. For understorey bird species, there were no significant differences in foraging locations between solitary and mixed‐species flocks. Higher flocking frequency occurred in the wet season for canopy birds, but in the dry season for understorey birds. Overall patterns were consistent with the explanation that flocking enables an expansion of foraging niche by reducing the risk of predation.     

Don’t stand so close to me: Microbiota‐facilitated enemy release dynamics in introduced Onthophagus taurus dung beetles

Microbial symbionts can influence their hosts in stunningly diverse ways. Emerging research suggests that an underappreciated facet of these relationships is the influence microbes can have on their host''s responses to novel, or stressful, environmental conditions. We sought to address these and related questions in populations resulting from the recent introduction and subsequent rapid range expansion of Onthophagus taurus dung beetles. Specifically, we manipulated both microbial communities and rearing temperature to detect signatures of developmental and life history differentiation in response to the local thermal conditions in two populations derived from the southern most (Florida) and northern most (Michigan) extremes of the exotic Eastern U.S. range of O. taurus. We then sought to determine the contributions, if any, of host‐associated microbiota to this differentiation. We found that when reared under common garden conditions individuals from Florida and Michigan populations differed significantly in developmental performance measures and life history traits, consistent with population divergence. At the same time, and contrary to our predictions, we failed to find support for the hypothesis that animals perform better if reared at temperatures that match their location of origin and that performance differences may be mediated by host‐associated microbiota. Instead, we found that microbiome swapping across host populations improved developmental performance in both populations, consistent with enemy release dynamics. We discuss the implications of our results for our understanding of the rapid spread of exotic O. taurus through the Eastern United States and the significance of symbiosis in host responses to novel environmental conditions more broadly.     

Antagonistic interactions subdue inter‐species green‐beard cooperation in bacteria

Cooperation can be favoured through the green‐beard mechanism, where a set of linked genes encodes both a cooperative trait and a phenotypic marker (green beard), which allows carriers of the trait to selectively direct cooperative acts to other carriers. In theory, the green‐beard mechanism should favour cooperation even when interacting partners are totally unrelated at the genome level. Here, we explore such an extreme green‐beard scenario between two unrelated bacterial species—Pseudomonas aeruginosa and Burkholderia cenocepacia, which share a cooperative locus encoding the public good pyochelin (an iron‐scavenging siderophore) and its cognate receptor (green beard) required for iron–pyochelin uptake. We show that pyochelin, when provided in cell‐free supernatants, can be mutually exchanged between species and provide fitness benefits under iron limitation. However, in co‐culture we observed that these cooperative benefits vanished and communities were dominated by P. aeruginosa, regardless of strain background and species starting frequencies. Our results further suggest that P. aeruginosa engages in interference competition to suppress B. cenocepacia, indicating that inter‐species conflict arising from dissimilarities at the genome level overrule the aligned cooperative interests at the pyochelin locus. Thus, green‐beard cooperation is subdued by competition, indicating that interspecific siderophore cooperation is difficult to evolve and to be maintained.     

Effect of Fluorination on Lithium Transport and Short‐Range Order in Disordered‐Rocksalt‐Type Lithium‐Ion Battery Cathodes

Fluorine substitution is a critical enabler for improving the cycle life and energy density of disordered rocksalt (DRX) Li‐ion battery cathode materials which offer prospects for high energy density cathodes, without the reliance on limited mineral resources. Due to the strong Li–F interaction, fluorine also is expected to modify the short‐range cation order in these materials which is critical for Li‐ion transport. In this work, density functional theory and Monte Carlo simulations are combined to investigate the impact of Li–F short‐range ordering on the formation of Li percolation and diffusion in DRX materials. The modeling reveals that F substitution is always beneficial at sufficiently high concentrations and can, surprisingly, even facilitate percolation in compounds without Li excess, giving them the ability to incorporate more transition metal redox capacity and thereby higher energy density. It is found that for F levels below 15%, its effect can be beneficial or disadvantageous depending on the intrinsic short‐range order in the unfluorinated oxide, while for high fluorination levels the effects are always beneficial. Using extensive simulations, a map is also presented showing the trade‐off between transition‐metal capacity, Li‐transport, and synthetic accessibility, and two of the more extreme predictions are experimentally confirmed.     

Habitat characteristics and species interference influence space use and nest‐site occupancy: implications for social variation in two sister species

Nest‐site selection is an important component of species socio‐ecology, being a crucial factor in establishment of group living. Consequently, nest‐site characteristics together with space‐use proxies may reveal the social organization of species, which is critical when direct observation of social interactions is hindered in nature. Importantly, nest‐site choice is expected to be under strong selective pressures and the object of intra‐ and interspecific competition. Although the bulk of research on sociality focuses on its ecological drivers, our study introduces interspecific competition as a potential factor that could influence social evolution. We investigated the influence of habitat and interspecific competition on the social organization of two sister species of the African four striped mouse, Rhabdomys dilectus dilectus and Rhabdomys bechuanae, in a similar macroenvironment. These species diverged in allopatry and occupy distinct environmental niches. We radiotracked 140 adults to identify their nest‐sites, determine nest characteristics and record groups that shared nest‐sites. Group cohesion was estimated from nest‐site fidelity, group association strength, and home range overlap within versus between group members. We compared the two species in sympatry versus parapatry to determine the impact of species interference on sociality. In parapatry, the two species selected distinct nest‐site types, interpreted as different anti‐predator strategies: R. bechuanae selected fewer, spaced, less concealed nest‐sites whereas R. d. dilectus selected clumped and less visible nest‐sites. Rhabdomys bechuanae also showed more cohesive and stable social groups than R. d. dilectus. In sympatry, compared to R. bechuanae, R. d. dilectus occupied similar nest‐sites, however slightly more exposed and clumped, and displayed similar nest‐site fidelity and group association strength. We conclude that although habitat selection may be an important driver of social divergence in Rhabdomys, species interference, by limiting R. d. dilectus movements and forcing nest‐site sharing may induce new ecological pressures that could influence its social evolution.     

State uncertainty models and mark‐resight models for understanding non‐breeding site use by Piping Plovers

Conservation of beach‐nesting medium‐distance migrants has focused on breeding areas because protection of nests is more tractable than protection of non‐breeding habitat. As breeding ground management has encountered diminishing returns, interest in understanding threats in non‐breeding areas has increased. However, robust estimates of non‐breeding demographic rates and abundance are generally lacking, hindering the study of limiting factors. Estimating such rates is made more difficult by complex population dynamics at non‐breeding sites. In South Carolina, endangered Piping Plovers Charadrius melodus start arriving in July and some depart prior to December (the autumn‐only population) while others remain through at least March (the wintering population). State uncertainty capture‐mark‐recapture models provide a means for estimating vital rates for such co‐occurring populations. We estimated the proportion of the population entering the study area per survey (entry probability) and proportion remaining per survey (persistence rate) for both populations during autumn, and abundance of the wintering population, at four sites in South Carolina in 2006/7 and 2007/8, taking advantage of birds previously colour‐ringed on the breeding grounds. We made fairly precise estimates of entry and persistence rates with small sample sizes. Cumulative entry probability was ~50% by the end of July and reached 95% for both populations by October. Estimated stopover duration for birds in the autumn‐only population was 35 days in year 1 and 42 days in year 2. We estimated a wintering super‐population size of 71 ± 16 se birds in the first year and 75 ± 16 in the second. If ringing programmes on the breeding grounds continue, standardized resighting surveys in the non‐breeding period and mark‐recapture models can provide robust estimates of entry and persistence rates and abundance. Habitat protection intended to benefit non‐breeding Piping Plovers at our coastal sites should be in effect by late summer, as many birds are resident from July to the end of winter.     

Seasonal changes in mixed‐species bird flocks and antipredator information

Animals acquire information produced by other species to reduce uncertainty and avoid predators. Mixed‐species flocks (MSFs) of birds are ubiquitous in forest ecosystems and structured, in part, around interspecific information transfer, with “nuclear” species providing information that other species eavesdrop on. We hypothesized that in a seasonal tropical forest, the amount of information produced by birds about predation would be dynamic and particularly would decrease inside MSFs when the nuclear species leave MSFs to breed. We obtained baseline information on MSF encounter rate and species composition along established sampling routes over 9 months near the Sino‐Vietnamese border. We also conducted three experiments to quantify information produced by different species in response to typical predator encounters, including a moving predator stimulus presented inside of MSFs, and a stationary predator model presented both inside and outside of MSFs. MSFs were much less frequent in the breeding season with fewer individuals of the nuclear species, David's Fulvetta (Alcippe davidi), participating, though the diversity of other species remained stable. Fulvettas were the dominant producer of alarm‐related information both to the moving and stationary stimuli in MSFs and were also among the most active mobbers to stimuli presented outside of MSFs. In the breeding season, they tended to call less to the moving stimulus, and substantially fewer individuals responded to the in‐flock stationary stimulus. Other species increased their own information production at stationary predator stimuli (inside and outside of MSFs) during the breeding season, perhaps due to their increased investment in offspring during this time. Yet even during the breeding season, David's Fulvetta remained the highest producer of information about predators in MSFs. Hence, while we show that information production in MSFs can be somewhat dynamic, we describe a continually asymmetric communication system, in which a nuclear species is important to the whole community.     

Global meta‐analysis of native and nonindigenous trophic traits in aquatic ecosystems

Ecologists have recently devoted their attention to the study of species traits and their role in the establishment and spread of nonindigenous species (NIS). However, research efforts have mostly focused on studies of terrestrial taxa, with lesser attention being dedicated to aquatic species. Aquatic habitats comprise of interconnected waterways, as well as exclusive introduction vectors that allow unparalleled artificial transport of species and their propagules. Consequently, species traits that commonly facilitate biological invasions in terrestrial systems may not be as represented in aquatic environments. We provide a global meta‐analysis of studies conducted in both marine and freshwater habitats. We selected studies that conducted experiments with native and NIS under common environmental conditions to allow detailed comparisons among species traits. In addition, we explored whether different factors such as species relatedness, functional feeding groups, latitude, climate, and experimental conditions could be linked to predictive traits. Our results show that species with traits that enhance consumption and growth have a substantially increased probability of establishing and spreading when entering novel ecosystems. Moreover, traits associated with predatory avoidance were more prevalent in NIS and therefore favour invasive species in aquatic habitats. When we analysed NIS interacting with taxonomically distinctive native taxa, we found that consumption and growth were particularly important traits. This suggests that particular attention should be paid to newly introduced species for which there are no close relatives in the local biota. Finally, we found a bias towards studies conducted in temperate regions, and thus, more studies in other climatic regions are needed. We conclude that studies aiming at predicting future range shifts should consider trophic traits of aquatic NIS as these traits are indicative of multiple interacting mechanisms involved in promoting species invasions.     

Bi‐parentally inherited species‐specific markers identify hybridization between rainbow trout and cutthroat trout subspecies

Eight polymerase chain reaction primer sets amplifying bi‐parentally inherited species‐specific markers were developed that differentiate between rainbow trout (Oncorhynchus mykiss) and various cutthroat trout (O. clarki) subspecies. The primers were tested within known F₁ and first generation hybrid backcrosses and were shown to amplify codominantly within hybrids. Heterozygous individuals also amplified a slower migrating band that was a heteroduplex, caused by the annealing of polymerase chain reaction products from both species. These primer sets have numerous advantages for native cutthroat trout conservation including statistical genetic analyses of known crosses and simple hybrid identification.     

Seventy years of stream‐fish collections reveal invasions and native range contractions in an Appalachian (USA) watershed

Aim

Knowledge of expanding and contracting ranges is critical for monitoring invasions and assessing conservation status, yet reliable data on distributional trends are lacking for most freshwater species. We developed a quantitative technique to detect the sign (expansion or contraction) and functional form of range‐size changes for freshwater species based on collections data, while accounting for possible biases due to variable collection effort. We applied this technique to quantify stream‐fish range expansions and contractions in a highly invaded river system.

Location

Upper and middle New River (UMNR) basin, Appalachian Mountains, USA.

Methods

We compiled a 77‐year stream‐fish collections dataset partitioned into ten time periods. To account for variable collection effort among time periods, we aggregated the collections into 100 watersheds and expressed a species’ range size as detections per watershed (HUC) sampled (DPHS). We regressed DPHS against time by species and used an information‐theoretic approach to compare linear and nonlinear functional forms fitted to the data points and to classify each species as spreader, stable or decliner.

Results

We analysed changes in range size for 74 UMNR fishes, including 35 native and 39 established introduced species. We classified the majority (51%) of introduced species as spreaders, compared to 31% of natives. An exponential functional form fits best for 84% of spreaders. Three natives were among the most rapid spreaders. All four decliners were New River natives.

Main conclusions

Our DPHS‐based approach facilitated quantitative analyses of distributional trends for stream fishes based on collections data. Partitioning the dataset into multiple time periods allowed us to distinguish long‐term trends from population fluctuations and to examine nonlinear forms of spread. Our framework sets the stage for further study of drivers of stream‐fish invasions and declines in the UMNR and is widely transferable to other freshwater taxa and geographic regions.

     

Expanding population edges: theories,traits, and trade‐offs

Recent patterns of global change have highlighted the importance of understanding the dynamics and mechanisms of species range shifts and expansions. Unique demographic features, spatial processes, and selective pressures can result in the accumulation and evolution of distinctive phenotypic traits at the leading edges of expansions. We review the characteristics of expanding range margins and highlight possible mechanisms for the appearance of phenotypic differences between individuals at the leading edge and core of the range. The development of life history traits that increase dispersal or reproductive ability is predicted by theory and supported with extensive empirical evidence. Many examples of rapid phenotypic change are associated with trade‐offs that may influence the persistence of the trait once expansion ends. Accounting for the effects of edge phenotypes and related trade‐offs could be critical for predicting the spread of invasive species and population responses to climate change.     

Honeybees Use Celestial and/or Terrestrial Compass Cues for Inter‐Patch Navigation

Foraging honeybees (Apis mellifera) are well known to fly straight from the hive, their primary hub, to distal goals as well as between familiar feeding sites. More recently, it was shown that a distal feeding site may be used as a secondary hub. If not fully satiated, the foraging bee may decide to depart the first feeding site in a new compass direction straight to one of many other feeding sites (inter‐patch foraging). Using a recently developed recording method, we discovered that the chosen departure direction at a secondary hub can be guided exclusively by either celestial or terrestrial compass cues. Given our data, we draw two theoretical inferences. First, the bees must be capable of learning and remembering multiple, spatially distinct, navigation vectors between the hive and among multiple feeding sites. Second, this documented and useful representation of multiple navigation vectors between multiple, identified target locations logically implies composite place‐vector mapping, stored in long‐term memory.