Living on the edge: the role of geography and environment in structuring genetic variation in the southernmost populations of a tropical oak

Understanding the factors determining genetic diversity and structure in peripheral populations is a long‐standing goal of evolutionary biogeography, yet little empirical information is available for tropical species. In this study, we combine information from nuclear microsatellite markers and niche modelling to analyse the factors structuring genetic variation across the southernmost populations of the tropical oak Quercus segoviensis. First, we tested the hypothesis that genetic variability decreases with population isolation and increases with local habitat suitability and stability since the Last Glacial Maximum (LGM). Second, we employed a recently developed multiple matrix regression with randomisation (MMRR) approach to study the factors associated with genetic divergence among the studied populations and test the relative contribution of environmental and geographic isolation to contemporary patterns of genetic differentiation. We found that genetic diversity was negatively correlated with average genetic differentiation with other populations, indicating that isolation and limited gene flow have contributed to erode genetic variability in some populations. Considering the relatively small size of the study area (<120 km), analyses of genetic structure indicate a remarkable inter‐population genetic differentiation. Environmental dissimilarity and differences in current and past climate niche suitability and their additive effects were not associated with genetic differentiation after controlling for geographic distance, indicating that local climate does not contribute to explain spatial patterns of genetic structure. Overall, our data indicate that geographic isolation, but not current or past climate, is the main factor determining contemporary patterns of genetic diversity and structure within the southernmost peripheral populations of this tropical oak.     

Quantifying the roles of ecology and geography in spatial genetic divergence

Investigating the properties of ecological landscapes that influence gene flow among populations can provide key insights into the earliest stages of biological divergence. Both ecological and geographical factors can reduce gene flow, which can lead to population divergence, but we know little of the relative strengths of these phenomena in nature. Here, we use a novel application of structural equation modelling to quantify the contributions of ecological and geographical isolation to spatial genetic divergence in 17 species of Anolis lizards. Our comparative analysis shows that although both processes contributed significantly, geographical isolation explained substantially more genetic divergence than ecological isolation (36.3 vs. 17.9% of variance respectively), suggesting that despite the proposed ubiquity of ecological divergence, non‐ecological factors play the dominant role in the evolution of spatial genetic divergence.     

Species delimitation in native South American fire ants

The taxonomy of fire ants has been plagued by difficulties in recognizing species on the basis of morphological characters. We surveyed allozyme markers and sequences of the mtDNA COI gene in several closely related nominal species from two areas of sympatry in the native ranges to learn whether the morphology-based delimitation of these species is supported by genetic data. We found that Solenopsis invicta and Solenopsis richteri, pest species whose distinctiveness has been debated, appear to be fully reproductively isolated at both study sites. This isolation contrasts with the extensive hybridization occurring between them in the USA, where both have been introduced. We also found strong genetic differentiation consistent with barriers to gene flow between Solenopsis quinquecuspis and the other two species. However, several lines of evidence suggest that nuclear and mitochondrial genes of S. invicta and S. richteri are introgressing into S. quinquecuspis. The latter apparently is a recently derived member of the clade that includes all three species, suggesting that there has been insufficient time for its full development of intrinsic isolating mechanisms. Finally, our discovery of genetically distinct populations within both S. invicta and S. richteri suggests the presence of previously unrecognized (cryptic) species. Their existence, together with the difficulties in developing diagnostic morphological characters for described species, imply that the group is actively radiating species and that morphological divergence generally does not keep pace with the development of reproductive isolation and neutral genetic divergence in this process.     

Species delimitation through DNA barcoding of freshwater leeches of the Glossiphonia genus (Hirudinea: Glossiphoniidae) from Eastern Siberia,Russia

The study of biodiversity is a priority task of biological science. The structural unit of biodiversity is a species that has a clear identification in a taxonomic system. Morphological features are traditionally the main criteria for species discrimination in zoological studies. However, the presence of inter- and intraspecific polymorphism and phenotypic plasticity makes it difficult to identify species in many groups of invertebrates. To solve this problem, in this research, we analyzed morphological and genetic data in combination to delimit species among the Eastern Siberia Glossiphonia leeches using different approaches. Morphology analysis revealed phenetically distinct groups, suggesting the existence of at least two species in the region, G. verrucata, a rare Palaearctic species, and a potentially new species Glossiphonia sp. Moreover, sequence-based species delimitation methods congruently supported eight distinct species groups (including two Siberian species) within the available molecular dataset of the Glossiphonia world fauna, using phylogenetic (ML and BI), coalescent (ABGD and GMYC) methods, and pairwise analysis of sequences. The detected p-distances (modal value of 0.11) between these 8 groups and the level of genetic polymorphism (max. 0.0041) within groups indicate that the groups are 8 independent species according to the DNA barcoding. Our results once again proved the usefulness of molecular systematics. At the same time, we detected several inaccuracies in the leech species identification, as well as many ambiguous sites in sequences uploaded on GenBank, which affects the analysis and impedes progress of DNA barcoding technology.     

Genes mirror geography in Daphnia magna

Identifying the presence and magnitude of population genetic structure remains a major consideration in evolutionary biology as doing so allows one to understand the demographic history of a species as well as make predictions of how the evolutionary process will proceed. Next‐generation sequencing methods allow us to reconsider previous ideas and conclusions concerning the distribution of genetic variation, and what this distribution implies about a given species evolutionary history. A previous phylogeographic study of the crustacean Daphnia magna suggested that, despite strong genetic differentiation among populations at a local scale, the species shows only moderate genetic structure across its European range, with a spatially patchy occurrence of individual lineages. We apply RAD sequencing to a sample of D. magna collected across a wide swath of the species' Eurasian range and analyse the data using principle component analysis (PCA) of genetic variation and Procrustes analytical approaches, to quantify spatial genetic structure. We find remarkable consistency between the first two PCA axes and the geographic coordinates of individual sampling points, suggesting that, on a continent‐wide scale, genetic differentiation is driven to a large extent by geographic distance. The observed pattern is consistent with unimpeded (i.e. no barriers, landscape or otherwise) migration at large spatial scales, despite the fragmented and patchy nature of favourable habitats at local scales. With high‐resolution genetic data similar patterns may be uncovered for other species with wide geographic distributions, allowing an increased understanding of how genetic drift and selection have shaped their evolutionary history.     

History,geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei)

Divergent host use has long been suspected to drive population differentiation and speciation in plant‐feeding insects. Evaluating the contribution of divergent host use to genetic differentiation can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use double‐digest restriction‐associated DNA (ddRAD) sequencing to test the hypothesis that divergent host use contributes to genetic differentiation among populations of the redheaded pine sawfly (Neodiprion lecontei), a widespread pest that uses multiple Pinus hosts throughout its range in eastern North America. Because this species has a broad range and specializes on host plants known to have migrated extensively during the Pleistocene, we first assess overall genetic structure using model‐based and model‐free clustering methods and identify three geographically distinct genetic clusters. Next, using a composite‐likelihood approach based on the site frequency spectrum and a novel strategy for maximizing the utility of linked RAD markers, we infer the population topology and date divergence to the Pleistocene. Based on existing knowledge of Pinus refugia, estimated demographic parameters and patterns of diversity among sawfly populations, we propose a Pleistocene divergence scenario for N. lecontei. Finally, using Mantel and partial Mantel tests, we identify a significant relationship between genetic distance and geography in all clusters, and between genetic distance and host use in two of three clusters. Overall, our results indicate that Pleistocene isolation, dispersal limitation and ecological divergence all contribute to genomewide differentiation in this species and support the hypothesis that host use is a common driver of population divergence in host‐specialized insects.     

Species delimitation methods reveal cryptic diversity in the Hypnea cornuta complex (Cystocloniaceae,Rhodophyta)

The simple and convergent morphologies of many red algae make these species difficult to identify using traditional morphological characters. Many cryptic species have been described in recent years based on molecular datasets, and this has led to the application of an integrative taxonomy approach in species delimitation. Here, we performed several species delimitation methods (mBGD, ABGD, SPN, PTP, GMYCs and GMYCm) based on two different loci (COI-5P and rbcL) in species of the Hypnea cornuta complex. These methods were combined with morphological and phylogenetic data, extensive sampling, analysis of topotype material, and historically relevant herbarium samples. Our findings demonstrate that the groups morphologically assigned to H. cornuta and H. stellulifera consist of five different cryptic species. H. cornuta is a polyphyletic taxon composed of three well-separated lineages, thus requiring sequencing of type or topotype specimens to determine which one is Hypnea cornuta sensu stricto. We have revealed that the distribution of H. stellulifera is limited to Asia, while the Brazilian specimens initially assigned to this species were clarified as a new endemic species: Hypnea cryptica sp. nov. Our results indicated that only an integrative approach combining several lines of evidence, including morphology, nomenclature history, molecular data, biogeography and ecology can correctly solve the taxonomic status of widely distributed cryptic species.     

Species delimitation in a range-restricted group of cascudinhos (Loricariidae: Epactionotus) supports morphological and genetic differentiation across coastal rivers of southern Brazil

Epactionotus species are known for inhabiting the rocky-bottom stretches of fast-flowing rivers in a limited geographic area along the Atlantic coast of southern Brazil. These species are endemic to single coastal river drainages (two neighbouring drainages for Epactionotus bilineatus) isolated from each other by the coastal lacustrine environments or the Atlantic Ocean. E. bilineatus is from the Maquiné and Três Forquilhas River basins, both tributaries of the Tramandaí River system, whereas E. itaimbezinho is endemic to the Mampituba River drainage and Epactionotus gracilis to the Araranguá River drainage. Recent fieldwork in the Atlantic coastal drainages of southern Brazil revealed new populations in the Urussanga, Tubarão, d'Una and Biguaçu River drainages. Iterative species delimitation using molecular data (cytochrome c oxidase subunit I) and morphology (morphometrics and meristics) was applied to evaluate species recognition of isolated populations. With regard to new data, the genus was re-diagnosed, the status of Epactionotus species/populations was re-evaluated, formerly described species were supported and population structure was recognized. As for the newly discovered populations, both morphological and molecular data strongly support the population from the Biguaçu River drainage, in Santa Catarina State, as a new species. Molecular data revealed strong per-basin population structure, which may be related to species habitat specificity and low or no dispersal among drainages.     

Species delimitation: inferring gaps in morphology across geography

Species are commonly delimited on the basis of gaps in patterns of morphological variation, but there seems to be little recent work on methods to objectively assess such gaps. Here, we introduce a statistical approach that uses measurements of continuous morphological characters and geographic variation in those characters to (i) measure the strength of the evidence for the existence of a gap in morphological variation between two hypothesized species and (ii) examine if a gap in morphological variation between two hypothesized species can be explained by an alternative hypothesis of geographic variation within a species. This approach is based on recent developments in analyses of multivariate normal mixtures, estimates of multivariate tolerance regions, and principal coordinates of neighboring matrices. We demonstrate the application of the approach by examining previously proposed hypotheses of species limits in the plant genus Escallonia. We discuss the main features of the method, including potential limitations, in relation to other approaches that use gaps in morphological variation as a criterion for species delimitation. The method we propose can help strengthen the link between the theory and practice of species delimitation by increasing the transparency and consistency of taxonomic decisions based on morphology, thus contributing to integrative approaches for species delimitation that consider morphological and geographic data on an equal footing with other kinds of information.     

The relative influence of natural selection and geography on gene flow in guppies

Two general processes may influence gene flow among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes gene flow between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies (Poecilia reticulata). If selection is important, gene flow should be reduced between different selective environments. If geography is important, gene flow should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long-term gene flow, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long-term gene flow. Differences in predation or habitat features did not influence genetic divergence or gene flow. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies.     

Species delimitation based on multiple criteria: the Spotted Bush Warbler Bradypterus thoracicus complex (Aves: Megaluridae)

We demonstrate the importance of using multiple criteria in species delimitations, whatever the conceptual base for species delimitation. We do this by studying plumage, biometrics, egg coloration, song, mitochondrial DNA and habitat/altitudinal distribution in the Spotted Bush Warbler Bradypterus thoracicus (Blyth) complex, and by conducting playback experiments. Taxa that we suggest are best treated as separate species [B. thoracicus (Blyth), B. davidi (La Touche) and B. kashmirensis (Sushkin)] differ in most or all of these aspects, particularly in song and mitochondrial DNA, while those that we treat as subspecies (suschkini) or synonyms (przevalskii) differ slightly and only in morphology. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 291–307.     

Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences

The estimation of species diversity in fungal endophyte communities is based either on species counts or on the assignment of operational taxonomic units (OTUs). Consequently, the application of different species recognition criteria affects not only diversity estimates but also the ecological hypotheses that arise from those observations. The main objective of the study was to examine how the choice and number of genetic markers and species delimitation criteria influence biodiversity estimates. Here, we compare approaches to defining species boundaries in three dominant species complexes of tropical endophytes, specially Colletotrichum gloeosporioides agg., Pestalotiopsis microspora agg. and Trichoderma harzianum agg., from two Amazonian trees: Hevea brasiliensis and H. guianensis. Molecular tools were used to describe and compare the diversity of the different assemblages. Multilocus phylogenetic analyses [gpd, internal transcribed spacer (ITS) and tef1] and modern techniques for phylogenetic species delimitation were overlaid with ecological data to recognize putative species or OTUs. The results demonstrate that ITS alone generally underestimates the number of species predicted by other nuclear loci. These results question the use of ITS and arbitrary divergence thresholds for species delimitation.     

<Emphasis Type="Italic">Brachionus calyciflorus</Emphasis> is a Species Complex: Mating Behavior and Genetic Differentiation Among Four Geographically Isolated Strains

Four geographic strains of B. calyciflorus are investigated regarding their genetic similarity and ability to cross-mate. DNA sequence analysis of the mitochondrial cox1 gene (694 bp) and the nuclear ribosomal ITS region (735 bp) showed that the Florida and Georgia strains were very similar to each other (0.3% sequence divergence for the 1429 bp) and different from the Texas and Australia strains (~7% and 9% sequence divergence for the 1429 bp, respectively). Consistent with this genetic relatedness, cross-copulation occurred only between the Florida and Georgia strains. Thus, B. calyciflorus is a complex of cryptic species. While the Florida, Texas and Australia strains were reproductively isolated from one another, most combinations of cross-strain mating tests showed intense and prolonged male circling behavior following male–female encounters. This suggests that precopulatory male circling and copulation are two separate behaviors that may be controlled by different female chemicals and male coronal receptors. In some cross-strain mating tests, females regularly retracted their corona when circled by a male, indicating that they can recognize ‘foreign’ males and actively interfere with copulation.     

Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia

Isolation by spatial distance (IBD), environment (IBE), and historical climatic instability (IBI) are three common processes assessed in phylogeographic and/or landscape genetic studies. However, the relative contributions of these three processes with respect to spatial genetic patterns have seldom been compared. Moreover, whether the relative contribution differs in different regions or when assessed using different genetic markers has rarely been reported. Lindera obtusiloba has been found to have two sister genetic clades of chloroplast (cpDNA) and nuclear microsatellite (nSSR), both of which show discontinuous distribution in northern and southern East Asia. In this study, we used the Mantel test and multiple matrix regression with randomization (MMRR) to determine the relative contributions of IBD, IBE, and IBI with respect to L. obtusiloba populations. Independent Mantel tests and MMRR calculations were conducted for two genetic data sets (cpDNA and nSSR) and for different regions (the overall species range, and northern and southern subregions of the range). We found a significant IBI pattern in nSSR divergence for all assessed regions, whereas no clear IBI pattern was detected with respect to cpDNA. In contrast, significant (or marginal) divergent IBD patterns were detected for cpDNA in all regions, whereas although a significant IBE was apparent with respect to the overall range, the effect was not detected in the two subregions. The differences identified in nSSR and cpDNA population divergence may be related to differences in the heredity and ploidy of the markers. Compared with the southern region, the northern region showed less significant correlation patterns, which may be related to the shorter population history and restricted population range. The findings of this study serve to illustrate that comparing between markers or regions can contribute to gaining a better understanding the population histories of different genomes or within different regions of a species' range.     

Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera,Hydrophilidae)

The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius arcticus Kuwert, 1890, and three morphological variants of Hydrobius fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 & v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius fuscipes var. fuscipes and Hydrobius fuscipes var. subrotundus being sympatric. Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius fuscipes var. fuscipes from Hydrobius fuscipes var. subrotundus, but characters in the literature for Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii were diagnostic. Overall, morphological and molecular evidence strongly suggest that Hydrobius arcticus and the three morphological variants of Hydrobius fuscipes are separate species and Hydrobius rottenbergii Gerhardt, 1872, stat. n. and Hydrobius subrotundus Stephens, 1829, stat. n. are elevated to valid species. An identification key to northern European species of Hydrobius is provided.