Multiple origins of invasive and ‘native’ water frogs (Pelophylax spp.) in Switzerland

The marsh frog (Pelophylax ridibundus) has been introduced in many areas in Central and Western Europe as a result of commercial trade with Eastern Europe, and is rapidly replacing the native pool frog (P. lessonae). A large number of Pelophylax species are distributed in Eastern Europe and the strong phenotypic similarity between these species is rendering their identification hazardous. Consequently, alien populations of Pelophylax might not strictly be composed of P. ridibundus as previously suspected. In the present study, we analysed the cytochrome‐b and NADH dehydrogenase subunit 3 genes of introduced and native Pelophylax species from Switzerland (299 individuals) in order to properly identify the source populations of the invaders and the genetic status of the native species. Our study highlighted the occurrence of several genetic lineages of invasive frogs in western Switzerland. Unexpectedly, we also showed that several populations of the native pool frog (P. lessonae) cluster with the Italian pool frog P. bergeri from central Italy (considered by some authors as a subspecies of P. lessonae). Hence, these populations are probably also the result of introductions, meaning that the number of native P. lessonae populations is fewer than expected in Switzerland. These findings have important implications concerning the conservation of the endemic pool frog populations, as the presence of multiple alien species could strongly affect their long‐term subsistence. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 442–449.     

Neglected native or undesirable alien? Resolution of a conservation dilemma concerning the pool frog Rana lessonae

Introduced species often pose serious threats to biodiversity, but occasionally confusion arises as to whether a species really is introduced or is in fact an overlooked native. A recent UK conservation dilemma has centred on the status of the pool frog Rana lessonae. This species has been the subject of documented introductions from central and southern Europe since the early 1800s, the accepted position being that all UK R. lessonae populations are descended from these introductions. However, a closer examination of early UK literature sources, and recent discoveries of isolated, native R. lessonae populations in Sweden and Norway, led some herpetologists to question whether the species was in fact present as a native at some locations prior to the introductions. Research was initiated along four major lines of enquiry: genetic, bioacoustic, archaeozoological and archival. A high degree of convergence among the genetic and bioacoustic investigations demonstrated that the potentially native UK pool frogs were closely related to Scandinavian frogs, thus ruling out introductions from further south as a potential origin. Subfossil evidence of pool frogs was found from ca. 1000 years before present, demonstrating that the species occurred in the UK prior to known introductions. Archival sources produced no historical support for introductions from northern Europe. The postglacial history inferred for these northern populations is consistent with the known climatic and geographical conditions. Taken together, the evidence for the native status of the pool frog is compelling, and furthermore the UK population appears to be part of a distinct northern clade.     

Fluvial range expansion, allopatry, and parallel evolution in a Danubian snail lineage (Neritidae: Theodoxus)

The snails Theodoxus danubialis and Theodoxus prevostianus form a single clade native to freshwaters of south-eastern Europe whose inter- and intraspecific relationships remain unresolved. The present study utilized a phylogeographical approach to clarify the relationship of these species as well as to reconstruct the evolutionary and demographic history of populations in the western portion of their range. Phylogenetic, population genetic, and nested clade analyses reveal a clade that has distributed itself upriver from a lower Danube River source population and become genetically distinct primarily through range expansion and localized allopatric divergence. Notably, this geographical pattern is replicated phylogenetically in the form of two cytochrome c oxidase subunit I (CO I) lineages that are present simultaneously in individual snails. Haplotypes from polymorphic individuals form two distinct clades, both of which show phylogenetic and nucleotide substitution patterns consistent with a mitochondrial origin, and whose common ancestor must have occurred in a lower Danube source population. Separated allopatrically from their Danubian relatives, populations of T. danubialis in northern Italy have also undergone substantial range expansion, much more recently than Danube watershed lineages. In addition to repeated patterns of range expansion, parallelism is found in T. prevostianus , which is shown to be a nonmonophyletic taxon of remarkable morphological and ecological similarity.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 603–617.     

Bioacoustic assessment of the taxonomic status of pool frog populations (Rana lessonae) with reference to a topotypical population

Six structural and temporal features of the mating calls of pool frogs recorded at eight localities in Italy, Germany, Yugoslavia and Albania were compared with those of the calls of topotypical Rana lessonae in northern Italy. All populations shared three out of six characters studied: call duration, intercall interval and call period. The pool frogs of three localities in peninsular Italy significantly differed in three characters from those of the other six localities, including the northern Italian one: pulses per pulse group, pulse groups per call, and pulse groups per second. This study demonstrates the existence of Rana bergeri , a pool frog species different from R. lessonae in peninsular Italy, but does not support the species status of the chemotaxonomically established R. shqiperica , which is considered as a synonym of R. lessonae .     

Crosses between frog populations reveal genetic divergence in larval life history at short geographical distance

A number of studies have documented interpopulation divergence in amphibian larval life-history traits across latitudes. Because many frogs are philopatric and have a patchy habitat distribution, genetic divergence could also exist on a much smaller geographical scale, revealed by recent estimates of population divergence using molecular markers. Whether this divergence is reflected in phenotypic traits is virtually unknown. Using artificial fertilization, individuals of the common frog, Rana temporaria , were crossed from two populations situated 130 km apart and differing in population size. The pattern of size at metamorphosis showed evidence of non-additive effects, as demonstrated by a significant interaction between male and female population of origin. Outbreeding resulted in an increase in metamorph size when eggs from the small population were fertilized with sperm from the large population. In the reciprocal cross, however, the pattern was in the opposite direction, with no significant effect of male population of origin. Genetic divergence of populations separated by a relatively short geographical distance may be more common in frogs than previously acknowledged, with potential implications for conservation of declining amphibian species.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 189–195.     

Asynchronous arrival pattern, operational sex ratio and occurrence of multiple paternities in a territorial breeding anuran, Rana dalmatina

Understanding why females mate multiply is a major issue in evolutionary ecology. We investigated the consequences of an asynchronous arrival pattern on male competition and multiple paternity in the apparently monoandrous agile frog ( Rana dalmatina ). The largest frogs arrived first and both males and females lost weight significantly during the spawning period. Asynchronous arrival at breeding sites resulted in a male-biased operational sex ratio (OSR). The OSR was more strongly male-biased at the beginning and at the end of the breeding period when the number of satellite males increased. All females mated only once, but multiple paternity within clutches occurred at the beginning and the end of the breeding period. The influence of asynchronous arrival and biased sex ratio suggests that reduced variance or bet-hedging promoting female fitness had only a reduced role in the evolution of polyandry, and polyandry is likely to be associated with male benefits. Polyandry in frogs can be explained either by forced mating as a result of sexual conflict or by clutch piracy. By modifying intrasexual competition, asynchronous arrival and changes in OSR may have a decisive influence upon the evolution of mating systems and favour both polyandry and stable coexistence of alternative mating behaviour.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 191–200.     

Pinus mugo (Pinaceae) in the Abruzzi Mountains: high morphological variation in isolated populations

Thirty-three individuals of Pinus mugo from the Abruzzian Apennines (Italy), the most isolated population of the species, were examined biometrically to verify the range of trait variation and compared with six other populations sampled in the north-eastern part of the species range. Ten needles and ten cones from each individual were measured and quantified on the basis of 31 traits. The interpopulation comparison revealed a close affinity of the Abruzzian population of P. mugo to three of the six other populations. The other three north-eastern populations, one from the Tatra Mountains and two from the Chornokhora Mountains, appeared to be different. This suggests that these populations originated from other Pleistocene centres of occurrence. The intrapopulation variation of the population from the Abruzzian Apennines is comparable with those of all six populations of P. mugo from the Sudety and Carpathian Mountains. These findings support the hypothesis that isolated but locally abundant plant populations do not necessarily show a reduction in variability resulting from isolation.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 309–316.     

Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene

The phylogeography of Atlantic brown trout ( Salmo trutta ) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 904–917.     

Geographical pattern of genetic variation in the Robertsonian system of Mus musculus domesticus in central Italy

The Robertsonian (Rb) system of Mus musculus domesticus in central Italy consists of three Rb races (CD, 2 n  = 22; CB, 2 n  = 22; ACR, 2 n  = 24), and additional Rb populations with new metacentrics have recently been reported. The aim of the present paper is to provide insight into the process of house mouse raciation in this area. Here we present new data concerning the geographical distribution of mtDNA haplotypes (control region sequence) in the three Rb races and in the surrounding standard populations. The presence of exclusive clades in all the three Rb races supports the idea of a past fragmentation event and a subsequent period of isolation. However, comparison of mtDNA polymorphism between Rb and standard races, and the shape of the mismatch distribution within the races, does not reveal any clear sign of a strong reduction in population size, at this geographical scale, related to race formation.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 395–405.     

Phylogenetic analyses of mtDNA sequences reveal three cryptic lineages in the widespread neotropical frog Leptodactylus fuscus (Schneider, 1799) (Anura, Leptodactylidae)

Leptodactylus fuscus is a neotropical frog ranging from Panamá to Argentina, to the east of the Andes mountains, and also inhabiting Margarita, Trinidad, and the Tobago islands. We performed phylogenetic analyses of 12S rRNA, 16S rRNA, tRNA-Leu, and ND1 mitochondrial (mt) DNA sequences from specimens collected across the geographic distribution of L. fuscus to examine two alternative hypotheses: (i) L. fuscus is a single, widely distributed species, or (ii) L. fuscus is a species complex. We tested statistically for geographic association and partitioning of genetic variation among mtDNA clades. The mtDNA data supported the hypothesis of several cryptic species within L. fuscus. Unlinked mtDNA and nuclear markers supported independently the distinctness of a 'northern' phylogenetic unit. In addition, the mtDNA data divided the southern populations into two clades that showed no sister relationship to each other, consistent with high differentiation and lack of gene flow among southern populations as suggested by allozyme data. Concordance between mtDNA and allozyme patterns suggests that cryptic speciation has occurred in L. fuscus without morphological or call differentiation. This study illustrates a case in which lineage splitting during the speciation process took place without divergence in reproductive isolation mechanisms (e.g. advertisement call in frogs), contrary to expectations predicted using a biological species framework.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 325–341. No claim to original US government works.     

Microsatellite DNA analysis of northern pike (Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations was high (overall θ_ST = 0.51; overall ρ_ST = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American and southern European populations were highly distinct. A population from Ireland was monomorphic at all loci, presumably reflecting founder events associated with introduction of the species to the island in the sixteenth century. Bayesian analysis of demographic parameters showed differences in θ (a product of effective population size and mutation rate) among populations from large and small water bodies, but the relative differences in θ were smaller than expected, which could reflect population subdivision within the larger water bodies. Finally, the analyses showed drastic population declines on a time scale of several thousand years within European populations, which we ascribe to either glacial bottlenecks or postglacial founder events.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 91–101.     

Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): genetic structure coincides with river systems in the Brazilian Atlantic Forest

Phylogenetic analyses based on mtDNA cytochrome  b were performed in 42 lizards of the Gymnodactylus darwinii complex from three regions within Brazil's Atlantic Forest. Mainland regions and continental shelf islands in the south-eastern range and mainland areas from the north-east were sampled. The criteria of maximum parsimony (MP), maximum likelihood (ML) and Bayesian methods were explored, with the robustness for nodes assessed by bootstrapping (MP and ML) and posterior probabilities (Bayesian searches). By all methods, three distinctive phylogroups were recovered: a south-eastern clade (SE) and two clades from northern regions (NE₁ and NE₂). The pattern of genetic structure of the major clades coincided with the presence of river systems in the Atlantic Forest, and based on corrected genetic distances between those clades, divergence times were tentatively estimated using mtDNA rates calibrated for squamate reptiles. The putative role of Atlantic Forest rivers in generating differentiation is discussed. We present a hypothesis of species limits for G. darwinii , based on concordant lines of evidence including cytogenetic and mtDNA analyses. Two chromosome races (cytotype A, 2n = 38; and cytotype B, 2n = 40) had distributions concordant with clades SE and NE₁ + NE₂, respectively. These races are interpreted to be full species on the basis of a number of empirical criteria.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 13–26.     

Molecular phylogenetic evidence for paraphyly of the genus Sooglossus, with the description of a new genus of Seychellean frogs

The Seychelles harbour an endemic frog family, the Sooglossidae, currently containing two genera: Sooglossus , with three species, and Nesomantis , with one species. These unique frogs are generally considered to be basal neobatrachians, although their relationships to other neobatrachian taxa, except the Nasikabatrachidae, remain unresolved. Our molecular phylogeny based on a dataset consisting of fragments of the nuclear rag-1 and rag-2 genes, as well as mitochondrial 16S rRNA in representatives of the major neobatrachian lineages, confirmed the previously postulated Sooglossidae + Nasikabatrachidae clade and the placement of the South American Caudiverbera with the Australian Myobatrachidae, but did not further resolve the position of sooglossids. Our results do, however, unambiguously show sooglossids to be monophyletic but the genus Sooglossus to be paraphyletic, with the type species Sooglossus sechellensis being more closely related to Nesomantis thomasseti than to Sooglossus gardineri and Sooglossus pipilodryas , in agreement with morphological, karyological, and bioacoustic data. As a taxonomic consequence, we propose to consider the genus name Nesomantis as junior synonym of Sooglossus , and to transfer the species thomasseti to Sooglossus . For the clade composed of the species gardineri and pipilodryas , here, we propose the new generic name Leptosooglossus . A significant genetic differentiation of 3% was found between specimens of Sooglossus thomasseti from the Mahé and Silhouette Islands, highlighting the need for further studies on their possible taxonomic distinctness.   © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 347–359.     

A molecular perspective on the evolutionary affinities of an enigmatic neotropical frog, Allophryne ruthveni

The phylogenetic relationships of neobatrachian frogs remain poorly resolved below the subordinal level. The neotropical frog Allophryne ruthveni (Gaige) illustrates the difficulty in evaluating phylogenetic relationships within the Neobatrachia. Since its discovery in 1926, it has been variously placed within five different anuran families: Bufonidae, Leptodactylidae, Centrolenidae, Hylidae and in its own monotypic family, Allophrynidae. Here we examine the evolutionary relationships of Allophryne ruthveni using DNA sequence data from two mitochondrial genes (16S and 12S rRNA). Our analyses suggest that Allophryne ruthveni is most closely allied to the glass frogs (Centrolenidae). Both 12S and combined data partitions support an Allophryne ruthveni–Cochranella midas– Centrolene geckoideum clade, with Allophryne ruthveni basally positioned. Considered alone, analyses of the 16S partition supports the placement of Allophryne ruthveni with the centrolenids only with neighbour-joining analyses. The placement of Allophryne ruthveni with the centrolenids supports Noble's (1931 ) hypothesis that Allophryne is an edentate centrolenid. More definitive statements of the evolutionary affinities of Allophryne ruthveni in particular, and the Neobatrachia in general, await greater sampling of taxa and both molecular and phenotypic (e.g. morphological and karyotypic) characters. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 335–346.     

Systematics of dusky salamanders, Desmognathus (Caudata: Plethodontidae), in the mountain and Piedmont regions of Virginia and North Carolina, USA

We analysed mitochondrial (cytochrome  b ) nucleotide sequences, nuclear allozyme markers, and morphometric characters to investigate species boundaries and phylogenetic relationships among dusky salamanders ( Desmognathus ) in the southern Blue Ridge and adjacent Piedmont Physiographic Provinces of Virginia and North Carolina. Our results revealed four distinct mitochondrial DNA clades that are also characterized by distinct allozyme markers. One clade consists of sequences derived from populations distributed from New England to south-western Virginia that are referable to Desmognathus fuscus Rafinesque, 1820, although there is considerable sequence and allozyme divergence within this clade. A second clade consists of sequences derived from populations referable to Desmognathus planiceps Newman, 1955, a form that we resurrect from its long synonymy under D. fuscus . Desmognathus planiceps and D. fuscus also differ in mandibular tooth shape. Two other cytochrome  b sequences recovered from populations along the Blue Ridge escarpment in southern Virginia are quite divergent from those of the previous two clades, and these populations may represent yet another distinct species. Sequences from a population in the Brushy Mountains in the Piedmont of northern North Carolina are similar to those of Desmognathus carolinensis . Population groupings indicated by allozyme data generally correspond to the cytochrome  b clades. Cryptic diversity in Appalachian desmognathan salamanders clearly requires further study. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 115–130.     

Relationships between the close congeners Anthoxanthum odoratum and A. alpinum (Poaceae, Pooideae) assessed by morphological and molecular methods

Anthoxanthum alpinum Löve & Löve has been described as a diploid perennial distributed in northern Eurasia and the high mountains of central and eastern Europe. Difficulties in finding reliable morphological differences between this taxon and the widespread tetraploid Anthoxanthum odoratum L. have resulted in taxonomists treating them as conspecific, despite the cytological differentiation. The purpose of this study was to use different approaches to assess the relationships between close congeners, such as the pair A. odoratum / A. alpinum . Macromorphological, micromorphological, and molecular data were gathered and analysed for 14 populations representing both taxa from Scandinavia and the Iberian Peninsula. Different cluster analyses were performed to study the relatedness between individuals and populations. Subsequently, a principal components analysis was computed on the basis of macromorphological quantitative traits, and principal coordinates analysis was used to analyse qualitative, micromorphological, and random amplification of polymorphic DNA (RAPD) data. An analysis of molecular variance was applied to the molecular data, and the genetic differentiation between samples was measured using the F _ST estimator. The results showed that the geographical origin was more important than the ploidy level in explaining the relatedness between specimens and populations. Moreover, a strong correlation was found between the micromorphological traits and environmental parameters. The results of the analyses do not support the assignment of a specific taxonomic rank to A. alpinum .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 237–252.     

Genetic diversity and phylogeography of the European roe deer: the refuge area theory revisited

The extant taxa of central and northern Europe are commonly believed to derive from Pleistocene ancestors, who moved to the north from three separate glacial refugia: the Iberian and Italian peninsulae, as well as the southern Balkans. The issue of postglacial dispersal patterns was addressed through the investigation of population structure and phylogeography of the European roe deer, Capreolus capreolus . The genetic diversity in 376 individuals representing 14 allegedly native populations across their European range was assessed, using ten autosomal microsatellite loci and restriction fragment length polymorphisms of the mitochondrial D-loop and NADH dehydrogenase 1 gene segments. Our results suggest the existence of three major genetic lineages of roe deer in Europe. One comprises populations in the south-western limit of the species' distribution (i.e. Iberia), where an internal substructure splits a northern from a southern sublineage. A second lineage includes populations of southern and eastern Europe, as well as a separate sublineage sampled in central-southern Italy, where the existence of the subspecies Capreolus c. italicus was supported. In central-northern Europe, a third lineage is present, which appeared genetically rather homogeneous, although admixed, and equally divergent from both the eastern and western lineages. Current patterns of intraspecific genetic variation suggest that postglacial recolonization routes of this cervid to northern Europe could be due to range expansion from one or more refugia in central-eastern Europe, rather than proceeding from the Mediterranean areas.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 85–100.     

Genetic variation and structure in native populations of the fire ant Solenopsis invicta: evolutionary and demographic implications

We studied population genetic variation and structure in the fire ant Solenopsis invicta using nuclear genotypic and mitochondrial DNA (mtDNA) sequence data obtained from samples collected throughout its native range. Geographic populations are strongly differentiated at both genomes, with such structure more pronounced in Brazil than in Argentina. Higher-level regional structure is evident from the occurrence of isolation-by-distance patterns among populations, the recognition of clusters of genetically similar, geographically adjacent populations by ordination analysis, and the detection of an mtDNA discontinuity between Argentina and Brazil coinciding with a previously identified landform of biogeographical relevance. Multiple lines of evidence from both genomes suggest that the ancestors of the ants we studied resembled extant northern Argentine S. invicta , and that existing Brazilian populations were established more recently by serial long-distance colonizations and/or range expansions. The most compelling evidence for this is the corresponding increase in F _K (a measure of divergence from a hypothetical ancestor) and decrease in genetic diversity with distance from the Corrientes population in northern Argentina. Relatively deep sequence divergence among several mtDNA clades, coupled with geographical partitioning of many of them, suggests prolonged occupation of South America by S. invicta in more-or-less isolated regional populations. Such populations appear, in some cases, to have come into secondary contact without regaining the capacity to freely interbreed. We conclude that nominal S. invicta in its native range comprises multiple entities that are sufficiently genetically isolated and diverged to have embarked on independent evolutionary paths.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 541–560.     

Infraspecific variation and phylogeography of the high-polyploid Iberian endemic Anthoxanthum amarum Brot. (Poaceae; Pooideae) assessed by random amplified polymorphic DNA markers (RAPDs) and morphology

High morphological and ecological diversity has been observed in the north-west Iberian Peninsula endemic Anthoxanthum amarum Brot., for which two different morphotypes (northern and southern) have been described on the basis of qualitative traits and geographical origin. In the present study, a combined molecular and morphological method was applied to ten populations of this species with the following aims: (1) to assess whether the variation observed was taxonomically meaningful; (2) to assess the influence of the environment on the variation in the morphological characters; and (3) to track the potential phylogeographical information deduced from our random amplified polymorphic DNA marker (RAPD) data in order to draw inferences about the past history of this species in the north-west Iberian Peninsula. To achieve these aims, 26 macromorphological characters were recorded in 279 specimens, and 77 RAPD phenotypes were identified in the 79 plants studied. The association analyses performed using the morphological and molecular data showed that no clear separation existed between the morphs, and a strong correlation between qualitative characters and the environment was detected. Moreover, both the multivariate analyses and the assignment test based on RAPD data revealed that the genetic variation was hierarchically structured, and three genetically distinct groups could be identified. Two of these clusters might correspond to different expansion routes proposed in the literature for different plant species in the north-west Iberian Peninsula.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 179–192.