Early stages of speciation with gene flow in the Amazilia Hummingbird (Amazilis amazilia) subspecies complex of Western South America

Disentangling the factors underlying the diversification of geographically variable species with a wide geographical range is essential to understanding the initial stages and drivers of the speciation process. The Amazilia Hummingbird, Amazilis amazilia, is found along the Pacific coast from northern Ecuador down to the Nazca Valley of Peru, and is currently classified as six phenotypically differentiated subspecies. We aimed to resolve the evolutionary relationships of the six subspecies, to assess the geographical pattern and extent of evolutionary divergence, and to test for introgression using both a mtDNA marker and a genome‐by‐sequencing dataset from 86 individuals from across the species range. The consensus phylogenetic tree separated the six subspecies into three distinct clades, corresponding with the Ecuador lowlands (A. amazilia dumerilii), the Ecuador highlands (A. amazilia alticola and A. amazilia azuay), and the Peruvian coast (A. amazilia leucophoea, A. amazilia amazilia, and A. amazilia caeruleigularis). However, an unresolved mtDNA network suggests that the diversification of the subspecies was recent and rapid. We found evidence of gene flow among the subspecies A. amazilia dumerilii, A. amazilia alticola, and A. amazilia leucophoea, with strong genetic isolation of the subspecies A. amazilia azuay in the isolated Yunguilla Valley of Ecuador. Finally, environmental data from each subspecies’ capture locations were concordant with the three distinct clades. Overall, our results suggest that both expansions into new habitats and geographic isolation shaped the present‐day phylogeny and range of the A. amazilia subspecies, and that A. amazilia azuay may be genetically divergent enough to be considered a separate species.     

Range expansion of the Asian native giant resin bee Megachile sculpturalis (Hymenoptera,Apoidea, Megachilidae) in France

In 2008, a new species for the French bee fauna was recorded in Allauch near Marseille: the giant resin bee, Megachile sculpturalis (Smith, 1853). This was the first European record of this species that is native to East Asia. To our knowledge, it is the first introduced bee species in Europe. Here, we provide an overview of the current distribution of M. sculpturalis in France and we describe the history of its range expansion. Besides our own observations, information was compiled from literature and Internet websites, and by contacting naturalist networks. We collected a total of 117 records (locality × year combinations) for the 2008–2016 period. The geographical range of M. sculpturalis has extended remarkably, now occupying a third of continental France, with the most northern and western records located 335 and 520 km from Allauch, respectively. Information on its phenology, feeding, and nesting behavior is also provided. We report several events of nest occupation or eviction of Osmia sp. and Xylocopa sp. individuals by M. sculpturalis. Our results show that M. sculpturalis is now well established in France. Given its capacity to adapt and rapidly expand its range, we recommend amplifying the monitoring of this species to better anticipate the changes in its geographical range and its potential impacts on native bees.     

The Genus Cerion (Gastropoda: Cerionidae) in the Florida Keys

The systematic relationships and phylogeography of Cerion incanum, the only species of Cerion native to the Florida Keys, are reviewed based on partial sequences of the mitochondrial COI and 16S genes derived from 18 populations spanning the range of this species and including the type localities of all four described subspecies. Our samples included specimens of Cerion casablancae, a species introduced to Indian Key in 1912, and a population of C. incanum x C. casablancae hybrids descended from a population of C. casablancae introduced onto Bahia Honda Key in the same year. Molecular data did not support the partition of C. incanum into subspecies, nor could populations be apportioned reliably into subspecies based on morphological features used to define the subspecies. Phylogenetic analyses affirmed the derived relationship of C. incanum relative to other cerionids, and indicated a Bahamian origin for the Cerion fauna of southern Florida. Relationships among the populations throughout the Keys indicate that the northernmost populations, closest to the Tomeu paleoislands that had been inhabited by Cerion petuchi during the Calabrian Pleistocene, are the oldest. The range of Cerion incanum expanded as the archipelago that is the Florida Keys was formed since the lower Tarantian Pleistocene by extension from the northeast to the southwest, with new islands populated as they were formed. The faunas of the High Coral Keys in the northeast and the Oölite Keys in the southwest, both with large islands that host multiple discontinuous populations of Cerion, are each composed of well supported clades that are characterized by distinctive haplotypes. In contrast, the fauna of the intervening Low Coral Keys consist of a heterogeneous series of populations, some with haplotypes derived from the High Coral Keys, others from the Oölite Keys. Individuals from the C. incanum x C. casablancae hybrid population inhabiting the southeastern coast of Bahia Honda Key were readily segregated based on their mitogenome lineage, grouping either with C. incanum or with C. casablancae from Indian Key. Hybrids with C. casablancae mitogenomes had haplotypes that were more divergent from their parent mitogenome than were hybrids with C. incanum mitogenomes.     

To the knowledge of the leaf beetle genus Cystocnemis (Coleoptera, Chrysomelidae)

Four subspecies of Cystocnemis discoidea are distinguished; two subspecies are described as new to science based on investigation of intraspecific variation in different parts of the species range, and ssp. gebleri was resurrected from synonymy. The ways of speciation in highland-hollow landscapes are discussed. The alpine subspecies C. discoidea oreas ssp. n. has an altibiome disjunction with the nominotypical subspecies. Similarity of the alpine subspecies of C. discoidea to the species from the subgenus Entomomela was found to be the reason of permanent confusion of representatives of these taxa. The subgenus Entomomela is transferred from the genus Oreomela to the genus Cystocnemis. A key to species and subspecies of the genus Cystocnemis is given.     

European hare (Lepus europaeus) invasion ecology: implication for the conservation of the endemic Irish hare (Lepus timidus hibernicus)

European hare Lepus europaeus populations have undergone recent declines but the species has successfully naturalised in many countries outside its native range. It was introduced to Ireland during the mid-late nineteenth century for field sport and is now well established in Northern Ireland. The native Irish hare Lepus timidus hibernicus is an endemic subspecies of mountain hare L. timidus and has attracted major conservation concern following a long-term population decline during the twentieth century and is one of the highest priority species for conservation action in Ireland. Little is known about the European hare in Ireland or whether it poses a significant threat to the native mountain hare subspecies by compromising its ecological security or genetic integrity. We review the invasion ecology of the European hare and examine evidence for interspecific competition with the mountain hare for habitat space and food resources, interspecific hybridisation, disease and parasite transmission and possible impacts of climate change. We also examine the impact that introduced hares can have on native non-lagomorph species. We conclude that the European hare is an emerging and significant threat to the conservation status of the native Irish hare. Invasive mammal species have been successfully eradicated from Ireland before and immediate action is often the only opportunity for cost-effective eradication. An urgent call is issued for further research whilst the need for a European hare invasive Species Action Plan (iSAP) and Eradication strategy are discussed.     

Assessment of Daucus carota L. (Apiaceae) subspecies by chemotaxonomic and DNA content analyses

For a clearer distinction between the four subspecies of Daucus carota native from Portugal (subsp. carota, subsp. maximus, subsp. gummifer and subsp. halophilus), morphological features of the fruits, DNA content analyses by flow cytometry, and chemical characterization of the essential oils were undertaken.We found chemotaxonomic evidences to consider D. carota subsp. maximus as a separate species rather than a subspecies of D. carota. This separation is based on the morphometric analysis of the fruits and in the high levels of asarone present only in the essential oil of the subsp. maximus. The remaining subspecies are difficult to distinguish from each other based on the morphology of the fruits and in DNA content. However, based on the essential oils, it was possible to distinguish the subspecies halophilus from the other two (subsp. gummifer and subsp. carota) because of its high content of elemicin, with the other two having high levels of geranyl acetate.Based on these results, the subspecies maximus is proposed as a different species (Daucus maximus Desf.) and the taxonomic status of other three subspecies (subsp. carota, subsp. gummifer and subsp. halophilus) is maintained. Still, the latter three taxa need to be further studied for a more precise taxonomic characterization.     

Phylogeography of the Eurasian green woodpecker (Picus viridis)

Aim In this paper we investigate the evolutionary history of the Eurasian green woodpecker (Picus viridis) using molecular markers. We specifically focus on the respective roles of Pleistocene climatic oscillations and geographical barriers in shaping the current population genetics within this species. In addition, we discuss the validity of current species and subspecies limits. Location Western Palaearctic: Europe to western Russia, and Africa north of the Sahara. Methods We sequenced two mitochondrial genes and five nuclear introns for 17 Eurasian green woodpeckers. Multilocus phylogenetic analyses were conducted using maximum likelihood and Bayesian algorithms. In addition, we sequenced a fragment of the cytochrome b gene (cyt b, 427 bp) and of the Z‐linked BRM intron 15 for 113 and 85 individuals, respectively. The latter data set was analysed using population genetic methods. Results Our phylogenetic results support the monophyly of Picus viridis and suggest that this taxon comprises three allopatric/parapatric lineages distributed in North Africa, the Iberian Peninsula and Europe, respectively. The North African lineage split from the Iberian/European clade during the early Pleistocene (1.6–2.2 Ma). The divergence event between the Iberian and the European lineages occurred during the mid‐Pleistocene (0.7–1.2 Ma). Our results also support a post‐glacial range expansion of these two lineages from distinct refugia located in the Iberian Peninsula and possibly in eastern Europe or Anatolia, which led to the establishment of a secondary contact zone in southern France. Main conclusions Our results emphasize the crucial role of both Pleistocene climatic oscillations and geographical barriers (Strait of Gibraltar, Pyrenees chain) in shaping the current genetic structure of the Eurasian green woodpecker. Our molecular data, in combination with diagnosable plumage characters, suggest that the North African green woodpecker (Levaillant’s woodpecker) merits species rank as Picus vaillantii (Malherbe, 1847). The two European lineages could be distinguished by molecular and phenotypic characters over most of their respective geographical ranges, but they locally exchange genes in southern France. Consequently, we prefer to treat them as subspecies (P. viridis viridis, P. viridis sharpei) pending further studies.     

Factors affecting the establishment of the invasive crayfish Procambarus clarkii (Crustacea, Decapoda) in the Mediterranean rivers of the northeastern Iberian Peninsula

It is essential to find the combination of factors associated with ecosystem invasibility, as this forms part of basic knowledge on biological invasions and provides important information to guide management and conservation decisions. We surveyed 325 sampling sites in Catalonia to investigate relationships between crayfish presence and a series of biotic and abiotic factors, including fish abundance and species richness, geographical features, and water mineralization and eutrophication. Abiotic data provided by 29 environmental variables were studied by principal-components analysis. We then used a combination of three statistical approaches (comparison of average scores, general linear mixed models, and hierarchical partitioning analysis) to determine the potential relationship between crayfish occurrence and predictors. Our findings seem to indicate that the presence of crayfish was associated with geographical features, water mineralization and eutrophication, and the introduction of non-indigenous fish species to Catalonia. Our results also suggest that re-establishment of the natural hydrology of Mediterranean streams could hinder the spread of Procambarus clarkii. This, combined with preservation of headwater streams and attempts at local extirpation of P. clarkii, would favour native species and, potentially, enable the successful reintroduction of the native white-clawed crayfish (Austropotamobius pallipes species complex).     

Low genetic diversity of the successful invasive African clawed frog Xenopus laevis (Pipidae) in Chile

In Africa, the genus Xenopus presents cryptic species and diverse hybrids between species. It has been assumed that the invasive populations of this genus correspond to X. laevis and that they are derived from the subspecies that inhabits the Mediterranean Cape region of South Africa. In part, this is supported by the successful establishment of this species in several Mediterranean regions of the world. In Mediterranean Chile, Xenopus has invaded an area of about 21,000 km², with scarce attention to genetic aspects underlying its invasion. Using mitochondrial DNA sequences we determined that Xenopus laevis laevis from the Cape region of South Africa is the subspecies that invaded Chile. The analysis indicated that the invaders have low genetic diversity (only two haplotypes, compared to 10 in two localities of their native range), and that probably the invasion in Chile occurred only once. Landscape genetics revealed that factors such as aridity and elevation have determined the spread of the species, both from the ecological and genetic points of view. Our results show that the invasion of the African clawed frog in Chile has been successful for at least 30 years, in spite of low genetic variability, few events of introduction, low propagule pressure, and bottlenecks in the founding population.     

Reduced SNP Panels for Genetic Identification and Introgression Analysis in the Dark Honey Bee (Apis mellifera mellifera)

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham’s F_ST, an F_ST-based outlier test, Delta, informativeness (I_n), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs.     

Examination of the effects of largemouth bass (Micropterus salmoides) and bluegill (Lepomis macrochirus) on the ecosystem attributes of lake Kawahara-oike,Nagasaki, Japan

The introduction of largemouth bass (Micropterus salmoides) and bluegill sunfish (Lepomis macrochirus) into the freshwater ecosystems of Japan has resulted in the suppression and/or replacement of native species, generating considerable concerns among resource managers. The impacts of largemouth bass and bluegill on native fauna have been examined in aquaria and isolated farm ponds, but there is limited work examining the likelihood to fundamentally modifying Japan's lakes. The objective of the present study is to examine the direct and synergistic ecological effects of largemouth bass and bluegill on the biotic communities of Lake Kawahara-oike, Nagasaki, Japan, using an ecosystem (Ecopath) modeling approach. Specifically, we examine whether the two fish species have played a critical role in shaping the trophodynamics of the lake. We attempt to shed light on the trophic interactions between largemouth bass and bluegill and subsequently evaluate to what extent these interactions facilitate their establishment at the expense of native species. We also examine how these changes propagate through the Lake Kawahara-oike food web. Our study suggests that the introduction of bluegill has induced a range of changes at multiple trophic levels. The present analysis also provides evidence that largemouth bass was unable to exert significant top-down control on the growth rates of the bluegill population. Largemouth bass and bluegill appear to prevail over the native fish species populations and can apparently coexist in large numbers in invaded lakes. Future management strategies controlling invasive species are urgently required, if the integrity of native Japanese fish communities is to be protected.     

Facilitation of the non-native annual plant Mesembryanthemum crystallinum (Aizoaceae) by the endemic cactus Eulychnia acida (Cactaceae) in the Atacama Desert

The Atacama Desert is one of the most stressful environments worldwide and represents a strong barrier for the establishment of native and non-native plants. In this study, we report the establishment of a non-native annual plant through facilitation by a native endemic cactus in a relatively undisturbed coastal area in north-central Chile. Soil collected under Eulychnia acida contained more available nutrients (N, P and K), water, and soluble salts than soils collected away from E. acida. Co-occurrence analyses showed a strong positive spatial association (facilitation) between the native cactus E. acida and the non-native annual, Mesembryanthemum crystallinum. The aboveground biomass of M. crystallinum individuals was 4-fold higher under the influence of E. acida. Native halophytes occasionally shared the cactus understory with the non-native species, but dominant native shrubs and perennial herbs did not co-occur with the cactus at scales of 1 and 4 m². All these results support facilitation of the native cactus on the non-native herb. The combination of direct and indirect positive effects could explain the assembly of the non-native annual plant in these undisturbed areas of the Atacama Desert and have major implications on M. crystallinum capacity to colonize new areas.     

Molecular phylogeny,taxonomy, and distribution of French Unio species (Bivalvia,Unionidae)

A plethora of unionid names was established in the nineteenth century by the “Nouvelle Ecole”. Although naiad morphological plasticity is well documented, the currently recognized fauna, with 17 species and subspecies included in the French checklist for the Unio genus, is still based upon morphological characters only. Insights have been provided from molecular data elsewhere in Europe and North Africa, but the French fauna remains unstudied. We present a molecular phylogeny of the Unio genus in France based on COI, 16S and 28S genes; taking up all available data in Europe plus 273 specimens collected in all main French drainages. The results show that there are either three valid species in France, with U. pictorum and U. mancus synonymized, or five, with the subspecies U. crassus courtillieri elevated to species level. Subspecies were generally not recovered, which questions the evolutionary units tacitly implied by subspecific names. Although sampling topotypes is the most reliable way to evaluate the status of a nominal subspecies, major human-induced changes in aquatic hydrosystems challenge the method. Nevertheless, operational taxonomy has to rely on ground-truthed data and we propose to reduce the actual number of valid taxa in France to the seven observed operational taxonomic units.     

Invasion history of Caprella scaura Templeton, 1836 (Amphipoda: Caprellidae) in the Iberian Peninsula: multiple introductions revealed by mitochondrial sequence data

The caprellid Caprella scaura, native to the western Indian Ocean, is one striking example of a successful invader. It was first recorded in the Iberian Peninsula in Gerona (north-eastern coast of Spain), in 2005, and has recently been reported throughout the Mediterranean and Atlantic coasts of this region. The most likely vector of introduction and distribution is within the hull-fouling community on recreational craft. However, beyond the dates of detection, the introduction history of C. scaura remains unclear. Direct sequencing of mitochondrial DNA (cytochrome c oxidase subunit I) was used to compare genetic composition in native and introduced populations in order to infer the invasion history of this species. In addition, 18S rDNA sequences were used to resolve phylogenetic relationships within this species and with the morphologically closest species Caprella californica and Caprella scauroides. The high genetic divergence and population subdivision found between non-native Iberian populations together with a high level of genetic diversity in some populations indicate multiple geographical sources and introduction points for this caprellid. Our data suggest that Iberian populations may derive from at least two sources: (1) Pacific Australian, and (2) Indian Ocean, either directly, or, more likely, through stepping-stone events from central Mediterranean population(s). Atlantic Iberian populations seem to be the most recently established populations. On the other hand, this is the first study providing molecular evidence confirming C. scaura, C. californica and C. scauroides as distinct species. It also provides strong molecular evidence that C. scaura typica and C. scaura scaura correspond to the same subspecies, and the Japanese C. scaura diceros and the Chilean C. scaura spinirostris could merit specific rank.     

The complete mitochondrial genome sequence analysis of Tibetan argali (Ovis ammon hodgsoni): Implications of Tibetan argali and Gansu argali as the same subspecies

The genus Ovis (Bovidae, Artiodactyla) includes six species, i.e. Ovis ammon, Ovis aries, Ovis canadensis, Ovis dalli, Ovis nivicola and Ovis vignei. Based on morphology, geographical location, habitat, etc., the species O. ammon is divided into nine subspecies. The near threatened Tibetan argali is distributed across the Tibetan Plateau and its peripheral mountains, and believed to be one of the O. ammon subspecies (O. a. hodgsoni). However, considering its morphological features and distributions, a question has been proposed by some researchers about the subspecies status of Tibetan argali. In this study, we employed complete mitochondrial DNA (mtDNA) to explore the phylogenetic relationship and population genetic structure of Tibetan argali. The results revealed that the nucleotide composition, gene arrangement and codon usage pattern of the mitochondrial genome of Tibetan argali are similar to those of other caprines. Phylogenetic analyses showed that Tibetan argali was clustered with O. ammon. Interestingly, five Tibetan argali individuals and one of the three Gansu argali (O. a. dalailamae) individuals were clustered in the same branch, which is a sister group to other two Gansu argali individuals. Together with morphological characteristics, our results suggested that Tibetan argali and Gansu argali may belong to the same subspecies (O. a. hodgsoni) of O. ammon, rather than two different subspecies.     

Geographical range as predictor of spatial expansion of invading birds

Many studies have been carried out on predictive traits, such as geographical range, but most of them were related to introduced species and considered the invasion as a whole. The contrasting results previously obtained suggest that studies should take into account the dynamics of the invasion process (immigration, establishment, spread). We hypothesise that the geographical range reflects the species tolerance to new environments, and is related especially to the establishment and spread of the invasion process. First, data on spontaneous invasive birds in France since 1950 were collected to determine the relation between geographical range and spontaneous invasions of French biogeographical areas. Second, the urban context, assumed to be free of immigration, was used to focus on this relation during the establishment and spread of species. For all species recorded, we determined the geographical range from an atlas, measured as the distribution range area RA (occupied area in km²) and the latitudinal range LR (km from north to south). Our results on spontaneous invaders show that the geographical range, especially RA, could help to predict the extent of an invasion once it has started. In the urban context, RA and LR discriminated urban colonists from urban avoiders, which supported the link between the geographical range and establishment/spread success. The geographical range participates, with other traits, in defining an ‘ideal invader’. We suggest that the dynamics of the invasion process i.e., considering each step of invasion rather than an entity, should be an important conceptual tool for future predictive studies.     

Chemical and molecular identification of the invasive termite <Emphasis Type="Italic">Zootermopsis nevadensis</Emphasis> (Isoptera: Archotermopsidae) in Japan

Numerous termite species have been introduced outside their native ranges by human transport, and some have become invasive. The dampwood termite Zootermopsis nevadensis (Hagen), which is native to western North America, has been introduced to and become established in Kawanishi City, Hyogo Prefecture, Japan. Zootermopsis nevadensis is subdivided into two subspecies based on cuticular hydrocarbon (CHC) phenotypes: Z. nevadensis nevadensis and Z. nevadensis nuttingi (Haverty and Thorne). Here, we identified Z. nevadensis in Japan as hybrids between the two subspecies. Chemical analysis showed the presence of 7,15-dimethylhenicosane and 5,17-dimethylhenicosane in the CHCs of Z. nevadensis in Japan, corresponding to the CHC phenotype of Z. n. nevadensis. Conversely, all mitochondrial cytochrome c oxidase subunit I sequences of Z. nevadensis in Japan were identical to sequences from Z. n. nuttingi and hybrids between the two subspecies from a native hybrid zone in California, USA. In addition, phylogenetic analysis showed that Z. nevadensis in Japan formed a clade with Z. n. nuttingi and hybrids between the two subspecies. Our results show discordance between the chemical and genetic features of Z. nevadensis in Japan, indicating that individuals of Z. nevadensis in Japan are hybrids between the two subspecies.     

The Role of Geographical and Ecological Factors on Population Divergence of the Neotropical otter <Emphasis Type="Italic">Lontra longicaudis</Emphasis> (Carnivora,Mustelidae)

The geographic distribution of the populations of a species are influenced by the spatial structure of the ecosystems, the environmental factors and the presence of geographic barriers. The Neotropical otter, Lontra longicaudis, is widely distributed throughout the Americas, where a wide range of environmental conditions and geographical features could promote genetic and morphological variation on the three currently recognized subspecies. In this study, we combined phylogeographic, morphometric and environmental niche modelling analyses to examine whether: (1) genetic variation is associated with the presence of barriers to gene flow and/or hydrography; (2) genetic and morphologic variation are associated with environmental variation; and (3) the observed variation in L. longicaudis populations corresponds to the previously defined subspecies. We found strong phylogeographic structure between the northern (L. l. annectens) and the two-southern subspecies (L. l. longicaudis and L. l. enudris), and although shallower, we also detected genetic differentiation between the two South American subspecies. Such genetic differentiation corresponds to the hydrography and to the geographical barriers characteristic of the distributional area of the species. We found a correlation between the shape of the skull and mandible with the environmental variation through the distribution of the species, and we rejected the hypothesis of niche equivalency and similarity between the three identified genetic lineages, suggesting adaptations to different environmental conditions. Our results support that the variation in environmental conditions, in concert with geographical barriers to gene flow and hydrography, have led to population divergence of L. longicaudis along the Neotropics. These results have important taxonomic implications for the species and its conservation.