Ecological correlates of the spatial co‐occurrence of sympatric mammalian carnivores worldwide

The composition of local mammalian carnivore communities has far‐reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108 087 trap days across 12 countries spanning five continents. We estimate local probabilities of co‐occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co‐occurrence. Within individual study areas, species pairs co‐occurred more frequently than expected at random. Co‐occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co‐occurrence decreased as compared to other species pairs when the pair included a large‐bodied carnivore. Our results suggest that a combination of shared traits and top‐down regulation by large carnivores shape local carnivore communities globally.     

Large‐scale introduction of the Indo‐Pacific damselfish Abudefduf vaigiensis into Hawai'i promotes genetic swamping of the endemic congener A. abdominalis

Hybridization in the ocean was once considered rare, a process prohibited by the rapid evolution of intrinsic reproductive barriers in a high‐dispersal medium. However, recent genetic surveys have prompted a reappraisal of marine hybridization as an important demographic and evolutionary process. The Hawaiian Archipelago offers an unusual case history in this arena, due to the recent arrival of the widely distributed Indo‐Pacific sergeant (Abudefduf vaigiensis), which is hybridizing with the endemic congener, A. abdominalis. Surveys of mtDNA and three nuclear loci across Hawai'i (N = 396, Abudefduf abdominalis and N = 314, A. vaigiensis) reveal that hybridization is significantly higher in the human‐perturbed southeast archipelago (19.8%), tapering off to 5.9% in the pristine northwest archipelago. While densities of the two species varied throughout Hawai'i, hybridization was highest in regions with similar species densities, contradicting the generalization that the rarity of one species promotes interspecific mating. Our finding of later generation hybrids throughout the archipelago invokes the possibility of genetic swamping of the endemic species. Exaptation, an adaptation with unintended consequences, may explain these findings: the endemic species has transient yellow coloration during reproduction, whereas the introduced species has yellow coloration continuously as adults, in effect a permanent signal of reproductive receptivity. Haplotype diversity is higher in Hawaiian A. vaigiensis than in our samples from the native range, indicating large‐scale colonization almost certainly facilitated by the historically recent surge of marine debris. In this chain of events, marine debris promotes colonization, exaptation promotes hybridization, and introgression invokes the possible collapse of an endemic species.     

Geographic variation in hybridization and ecological differentiation between three syntopic,morphologically similar species of montane lizards

To understand factors shaping species boundaries in closely related taxa, a powerful approach is to compare levels of genetic admixture at multiple points of contact and determine how this relates to intrinsic and extrinsic factors, such as genetic, morphological and ecological differentiation. In the Australian Alps, the threatened alpine bog skink Pseudemoia cryodroma co‐occurs with two morphologically and ecologically similar congeners, P. entrecasteauxii and P. pagenstecheri, and all three species are suspected to hybridize. We predicted that the frequency of hybridization should be negatively correlated with genetic divergence, morphological differentiation and microhabitat separation. We tested this hypothesis using a mitochondrial locus, 13 microsatellite loci, morphological and microhabitat data and compared results across three geographically isolated sites. Despite strong genetic structure between species, we detected hybridization between all species pairs, including evidence of backcrossed individuals at the two sites where all three species are syntopic. Hybridization frequencies were not consistently associated with genetic, morphological or ecological differentiation. Furthermore, P. entrecasteauxii and P. pagenstecheri only hybridized at the two sites where they are syntopic with P. cryodroma, but not at the largest site where P. cryodroma was not recorded, suggesting that P. cryodroma may serve as a bridging species. This study reveals the complex dynamics within a three species hybrid zone and provides a baseline for assessing the impact of climate change and anthropogenic habitat modification on future hybridization frequencies.     

Hybridization and speciation in the carabid beetles of the subgenusOhomopterus (Coleoptera, Carabidae, genusCarabus)

Natural hybridization among wingless carabid beetles of the subgenusOhomopterus (Carabidae, genusCarabus) is reviewed, and its significance in the evolution of this subgenus discussed. Natural hybridization occurs between parapatric species of similar size. Two case studies of natural hybridization suggest that natural hybridization could have affected the evolution of this subgenus in different ways. When there is a large difference in genital morphology between hybridizing species, interspecific copulation often results in genital injuries that causes mortality of copulating individuals, and hence reduces the fitness of hybridizing individuals greatly. In such a case, hybridization may be effective in maintaining the parapatric distribution of the two species, and in the long term, may promote reinforcement selection for traits which are effective in prezygotic reproductive isolation. When the morphological difference in genitalia is not so large as to cause genital injury, a hybrid population may be established at the intermediate zone between two parental species, provided that the immigration rates of the two species into the intermediate zone are small. Thus, natural hybridization may have contributed to both divergence and reticulate evolution in this subgenus.     

Anonymous nuclear markers for cetacean species

Here we report the development and characterization of 17 anonymous nuclear markers for cetacean species. These markers were isolated from a genomic library built from a common dolphin (genus Delphinus), and tested across several families within Cetacea. An average of 1 SNP per 272 bp was found in 10 anonymous markers screened for polymorphism within the genus Delphinus (total of 6,537 bp sequenced). These markers represent a significant addition to the set of tools used in genetic studies of cetaceans where population and species boundaries have to be inferred in order to implement proper conservation strategies.     

Massive invasion of exotic Barbus barbus and introgressive hybridization with endemic Barbus plebejus in Northern Italy: where,how and why?

Biological invasions and introgressive hybridization are major drivers for the decline of native freshwater fish. However, the magnitude of the problem across a native species range, the mechanisms shaping introgression as well as invader's dispersal and the relative role of biological invasions in the light of multiple environmental stressors are rarely described. Here, we report extensive (N = 665) mtDNA sequence and (N = 692) microsatellite genotypic data of 32 Northern Adriatic sites aimed to unravel the invasion of the European Barbus barbus in Italy and the hybridization and decline of the endemic B. plebejus. We highlight an exceptionally fast breakthrough of B. barbus within the Po River basin, leading to widespread introgressive hybridization with the endemic B. plebejus within few generations. In contrast, adjacent drainage systems are still unaffected from B. barbus invasion. We show that barriers to migration are inefficient to halt the invasion process and that propagule pressure, and not environmental quality, is the major driver responsible for B. barbus success. Both introgressive hybridization and invader's dispersal are facilitated by ongoing fisheries management practices. Therefore, immediate changes in fisheries management (i.e. stocking and translocation measures) and a detailed conservation plan, focussed on remnant purebred B. plebejus populations, are urgently needed.     

Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact

Hybrid zones allow the measurement of gene flow across the genome, producing insight into the genomic architecture of speciation. Such analysis is particularly powerful when applied to multiple pairs of hybridizing species, as patterns of genomic differentiation can then be related to age of the hybridizing species, providing a view into the build‐up of differentiation over time. We examined 33 809 single nucleotide polymorphisms (SNPs) in three hybridizing woodpecker species: Red‐breasted, Red‐naped and Yellow‐bellied sapsuckers (Sphyrapicus ruber, Sphyrapicus nuchalis and Sphyrapicus varius), two of which (ruber and nuchalis) are much more closely related than each is to the third (varius). To identify positions of SNPs on chromosomes, we developed a localization method based on comparative genomics. We found narrow clines, bimodal distributions of hybrid indices and genomic regions with decreased rates of introgression. These results suggest moderately strong reproductive isolation among species and selection against specific hybrid genotypes. We found 19 small regions of strong differentiation between species, partly shared among species pairs, but no large regions of differentiation. An association analysis revealed a single strong‐effect candidate locus associated with plumage, possibly explaining mismatch among the three species in genomic relatedness and plumage similarity. Our comparative analysis of species pairs of different age and their hybrid zones showed that moderately strong reproductive isolation can occur with little genomic differentiation, but that reproductive isolation is incomplete even with much greater genomic differentiation, implying there are long periods of time when hybridization is possible if diverging populations are in geographic contact.     

Assessing the taxonomic status of Osmoderma cristinae (Coleoptera: Scarabaeidae), endemic to Sicily,by genetic,morphological and pheromonal analyses

Resolving complexes of closely related and cryptic insect species can be challenging, especially when dealing with rare and protected taxa that are difficult to collect for genetic and morphological analyses. Until recently, populations of the genus Osmoderma (Scarabaeidae), widespread in Europe, were treated as a single species O. eremita (Scopoli, 1763) in spite of observed geographic variation in morphology. A previous survey using sequence data from the mtDNA cytochrome C oxidase I gene (COI) revealed the occurrence of at least two distinct lineages within this species complex: O. eremita in the west and O. barnabita Motschulsky, 1845, in the east. Interestingly, beetles confined to Sicily have been described as a distinct species, O. cristinae Sparacio, 1994, based on morphological traits. Only few Sicilian specimens were included in the former genetic analysis, and the results led to a still questionable taxonomic rank for these populations. To explore the robustness of the previous taxonomic arrangement for O. cristinae, a combination of genetic, morphological and pheromonal analyses was used. A 617‐bp fragment of the COI gene, aligned with O. cristinae and O. eremita sequences already available in GenBank, showed a clear genetic divergence between the two species (interspecific mean distance = 6.6%). Moreover, results from AFLP markers sustained the distinction of the two species. In addition, geometric morphometric analyses of the shape of male genitalia revealed a clear differentiation between the two species. Via scent analysis and field trapping, we demonstrated the production of the sex pheromone (R)‐(+)‐γ‐decalactone by males of O. cristinae, the attraction by conspecific individuals (mostly females) to this compound, and a lack of antagonistic effect of (S)‐(–)‐γ‐decalactone. The fact that O. eremita and O. eremita use the same compound for mate finding suggests that this sex pheromone has not undergone a differentiation and probably the allopatry of these two species compensates for the absence of a mechanism to avoid cross‐attraction. Our genetic and morphological data support the divergence of the two species and confirm the species status for O. cristinae, while sex pheromones are confirmed to be invariant among different species of the genus Osmoderma.     

Females drive asymmetrical introgression from rare to common species in Darwin's tree finches

The consequences of hybridization for biodiversity depend on the specific ecological and evolutionary context in which it occurs. Understanding patterns of gene flow among hybridizing species is crucial for determining the evolutionary trajectories of species assemblages. The recently discovered hybridization between two species of Darwin's tree finches (Camarhynchus parvulus and C. pauper) on Floreana Island, Galápagos, presents an exciting opportunity to investigate the mechanisms causing hybridization and its potential evolutionary consequences under conditions of recent habitat disturbance and the introduction of invasive pathogens. In this study, we combine morphological and genetic analysis with pairing observations to explore the extent, direction and drivers of hybridization and to test whether hybridization patterns are a result of asymmetrical pairing preference driven by females of the rarer species (C. pauper). We found asymmetrical introgression from the critically endangered, larger‐bodied C. pauper to the common, smaller‐bodied C. parvulus, which was associated with a lack of selection against heterospecific males by C. pauper females. Examination of pairing data showed that C. parvulus females paired assortatively, whereas C. pauper females showed no such pattern. This study shows how sex‐specific drivers can determine the direction of gene flow in hybridizing species. Furthermore, our results suggest the existence of a hybrid swarm comprised of C. parvulus and hybrid birds. We discuss the influence of interspecific abundance differences and susceptibility to the invasive parasite Philornis downsi on the observed hybridization and recommend that the conservation of this iconic species group should be managed jointly rather than species‐specific.     

Isolation and characterization of twelve polymorphic microsatellite markers for the invasive ascidian Styela clava (Tunicata)

The invasive solitary ascidian Styela clava has spread extensively along European coasts since its first occurrence in the early 1950s. In order to characterize spatial and temporal patterns of genetic change during its establishment and subsequent spread, we developed 12 species‐specific loci from an enriched microsatellite library. Polymorphism was explored in one native and two introduced populations (N = 31 ± 1). Number of alleles per locus varied from two to 13 (mean = 7). The average expected heterozygosity within populations ranged from 0.539 to 0.580.     

Spatial and seasonal variations in fish assemblages of the Yangtze River estuary

This study aimed to test the hypothesis that biotic influences play a role in determining estuarine fish assemblages. Thus the mechanisms that regulate the observed spatial niche segregation between fish species with morphological and ecological similarities within estuaries were investigated. Fishes were sampled seasonally at 30 stations along an entire salinity gradient of the Yangtze River estuary from spring 2010 to winter 2011, using bottom trawling (10 mm mesh size in the cod end). A total of 62 species belonging to 28 families were collected. Marine migrants (21) and estuarine species (19) dominated the assemblage and accounted for the highest abundances (marine migrants = 42.5%, estuarine species = 38.3%), with the marine migrants having the highest biomass (57.2%). Canonical correspondence analyses indicated that chlorophyll a, salinity, temperature, and geographic distance were the four main variables influencing the occurrence of fishes within the system. A stable fish assemblage in the upper zone during the wet season (spring and summer) was more obvious than in the dry season. The Pianka index showed a clear spatial segregation in four pairs of tonguesoles species (Cygonobius), and in most pairs of gobiids (Gobiidae), and a high degree of overlapping (>0.60) in only four pairs of gobiid species during the wet season. However, according to the results of the null model the observed segregating or pattern sharing was not caused by interspecific competition.     

Highlighting convergent evolution in morphological traits in response to climatic gradient in African tropical tree species: The case of genus Guibourtia Benn.

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Red shiner invasion and hybridization with blacktail shiner in the upper Coosa River,USA

Human disturbance increases the invasibility of lotic ecosystems and the likelihood of hybridization between invasive and native species. We investigated whether disturbance contributed to the invasion of red shiner (Cyprinella lutrensis) and their hybridization with native blacktail shiner (C. venusta stigmatura) in the Upper Coosa River System (UCRS). Historical records indicated that red shiners and hybrids rapidly dispersed in the UCRS via large, mainstem rivers since the mid to late 1990s. We measured the occurrence and abundance of parental species and hybrids near tributary-mainstem confluences and characterized populations at these incipient contact zones by examining variation across morphological traits and molecular markers. Red shiners represented only 1.2% of total catch in tributaries yet introgression was widespread with hybrids accounting for 34% of total catch. Occurrence of red shiners and hybrids was highly correlated with occurrence of blacktail shiners, indicating that streams with native populations are preferentially colonized early in the invasion and that hybridization is a key process in the establishment of red shiners and their genome in new habitats. Tributary invasion was driven by post-F1 hybrids with proportionately greater genomic contributions from blacktail shiner. Occurrence of red shiners and hybrids and the relative abundance of hybrids significantly increased with measures of human disturbance including turbidity, catchment agricultural land use, and low dissolved oxygen concentration. Red shiners are a significant threat to Southeast Cyprinella diversity, given that 41% of these species hybridize with red shiner, that five southeastern drainages are invaded, and that these drainages are increasingly disturbed by urbanization.     

Hybridization relics complicate barcode‐based identification of species in earthworms

Introgressive hybridization results in mito‐nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early‐generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation.     

When morphological identification meets genetic data: the case of Lucanus cervus and L. tetraodon (Coleoptera,Lucanidae)

The European stag beetle Lucanus cervus, widely distributed across Europe and in some Near East countries, is one of the best known coleopteran species listed in the European Habitats Directive 92/43/EEC and it is considered a flagship species for conservation of saproxylic fauna. Lucanus tetraodon is a closely related species whose geographical distribution is still poorly known and debated. The two species have a sympatric occurrence in central Italy, and in some localities of these areas, many individuals show a mosaic of morphological traits that makes species assignment nearly impossible. We used both mitochondrial and nuclear markers to analyse these specimens. The mitochondrial results evidenced that the two species represent well‐defined genetic entities with mitochondrial DNA introgression. This pattern could be the result of either hybridization or of a convergence of morphological characters under local selective pressures in areas of sympatric occurrence. The nuclear marker was polymorphic across the two species and therefore did not reveal hybridization, even if many are the supports to this phenomenon. The most plausible explanation for this genetic pattern is a very recent divergence of the two species which share a common origin and thus a common wg genotype.     

Using genetic and morphological analysis to distinguish endangered taxa from their hybrids with the cultivated exotic pest plant <Emphasis Type="Italic">Lantana strigocamara</Emphasis> (syn: <Emphasis Type="Italic">Lantana camara</Emphasis>)

Because highly invasive species can rapidly assimilate rare taxa, we questioned whether two Florida endangered Lantana depressa varieties existed 21 years after Sanders documented their widespread hybridization with exotic Lantana strigocamara, and whether morphological traits could accurately discriminate genetic individuals. Stepwise discriminant analysis of morphological characters discriminated the three taxa, correctly classifying 98, 91, 89% of L. strigocamara, L. depressa var. depressa, and var. floridana. Hybrids blurred taxonomic distinctions of varieties and reduced classification accuracy by 7–17%. Species-specific Random Fragment Length Polymorphism (RFLP-PCR) confirmed hybridization has occurred. Intersimple Sequence Repeat (ISSR) fingerprints analyzed with STRUCTURE identified three groups indicating introgression. Morphological traits significantly, but weakly correlated with q ratios (P = 0.0001; r ² = 0.45). Although L. strigocamara introgression is widespread and ongoing, wild populations contain individuals that are predominantly L. depressa genome, supporting actions to remove adventive L. strigocamara, prevent its sale, and promote sales of genetically confirmed natives.     

Needle morphological evidence of the homoploid hybrid origin of Pinus densata based on analysis of artificial hybrids and the putative parents,Pinus tabuliformis and Pinus yunnanensis

Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P. densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P. densata were seeded in a high‐altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P. densata and between the two parental species, P. tabuliformis and P. yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92%, which was very similar to P. densata. The eight needle traits (needle length, the mean number of stomata in sections 2 mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P. densata. The similar needle features between the artificial hybrids and P. densata could be used to verify the homoploid hybrid origin of P. densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.     

A population genetics perspective on the evolutionary histories of three clonal,endemic, and dominant grass species of the Qinghai–Tibet Plateau: Orinus (Poaceae)

We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai–Tibet Plateau (QTP). Here, we used eight selectively obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among‐species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. Thus, we tested explicit models of hybridization using a Bayesian approach within NewHybrids software. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a Mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, p < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them.     

Weak coordination among petiole,leaf, vein,and gas‐exchange traits across Australian angiosperm species and its possible implications

Close coordination between leaf gas exchange and maximal hydraulic supply has been reported across diverse plant life forms. However, it has also been suggested that this relationship may become weak or break down completely within the angiosperms. We examined coordination between hydraulic, leaf vein, and gas‐exchange traits across a diverse group of 35 evergreen Australian angiosperms, spanning a large range in leaf structure and habitat. Leaf‐specific conductance was calculated from petiole vessel anatomy and was also measured directly using the rehydration technique. Leaf vein density (thought to be a determinant of gas exchange rate), maximal stomatal conductance, and net CO₂ assimilation rate were also measured for most species (n = 19–35). Vein density was not correlated with leaf‐specific conductance (either calculated or measured), stomatal conductance, nor maximal net CO₂ assimilation, with r² values ranging from 0.00 to 0.11, P values from 0.909 to 0.102, and n values from 19 to 35 in all cases. Leaf‐specific conductance calculated from petiole anatomy was weakly correlated with maximal stomatal conductance (r² = 0.16; P = 0.022; n = 32), whereas the direct measurement of leaf‐specific conductance was weakly correlated with net maximal CO₂ assimilation (r² = 0.21; P = 0.005; n = 35). Calculated leaf‐specific conductance, xylem ultrastructure, and leaf vein density do not appear to be reliable proxy traits for assessing differences in rates of gas exchange or growth across diverse sets of evergreen angiosperms.