Molecular-genetic analyses reveal cryptic species of trematodes in the intertidal gastropod, Batillaria cumingi (Crosse)

Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philophthalmid, were detected using polymerase chain reaction-based restriction fragment-length polymorphism methodology and sequence analyses. These digeneans were all collected from the same species of gastropod first intermediate host, Batillaria cumingi (=Batillaria attramentaria). The mitochondrial cytochrome oxidase subunit 1 gene (approximately 800bp) and nuclear internal transcribed spacer 1 gene (approximately 400bp) were used for species level discrimination. Restriction fragment-length polymorphism analyses of cytochrome oxidase subunit 1 gene showed that C. batillariae included 10 distinguishable fragment patterns, and the philophthalmid included five patterns. On the basis of subsequent sequence analyses, the restriction fragment length polymorphism patterns of C. batillariae were grouped into eight phylogenetically distinct lineages and those of the philophthalmid into three phylogenetically distinct lineages. There was no evidence of gene flow among the different lineages due to the lack of heterozygosity within the observed internal transcribed spacer 1 gene fragment patterns. This suggests that all of these lineages are different species. Most of these species were widespread, but some exhibited restricted geographic distributions. We discuss the implications of these findings for host specificity of these trematodes. These results demonstrate the utility of genetic analysis to distinguish species of morphologically similar trematodes. Hence, trematode species diversity may often be underestimated when species identifications are limited to morphological features.     

Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc

The adaptive radiation of the seven‐spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.     

Exploring demographic, physical, and historical explanations for the genetic structure of two lineages of Greater Antillean bats

Observed patterns of genetic structure result from the interactions of demographic, physical, and historical influences on gene flow. The particular strength of various factors in governing gene flow, however, may differ between species in biologically relevant ways. We investigated the role of demographic factors (population size and sex-biased dispersal) and physical features (geographic distance, island size and climatological winds) on patterns of genetic structure and gene flow for two lineages of Greater Antillean bats. We used microsatellite genetic data to estimate demographic characteristics, infer population genetic structure, and estimate gene flow among island populations of Erophylla sezekorni/E. bombifrons and Macrotus waterhousii (Chiroptera: Phyllostomidae). Using a landscape genetics approach, we asked if geographic distance, island size, or climatological winds mediate historical gene flow in this system. Samples from 13 islands spanning Erophylla's range clustered into five genetically distinct populations. Samples of M. waterhousii from eight islands represented eight genetically distinct populations. While we found evidence that a majority of historical gene flow between genetic populations was asymmetric for both lineages, we were not able to entirely rule out incomplete lineage sorting in generating this pattern. We found no evidence of contemporary gene flow except between two genetic populations of Erophylla. Both lineages exhibited significant isolation by geographic distance. Patterns of genetic structure and gene flow, however, were not explained by differences in relative effective population sizes, island area, sex-biased dispersal (tested only for Erophylla), or surface-level climatological winds. Gene flow among islands appears to be highly restricted, particularly for M. waterhousii, and we suggest that this species deserves increased taxonomic attention and conservation concern.     

Determinants of distribution and prevalence of avian malaria in blue tit populations across Europe: separating host and parasite effects

Although avian malarial parasites are globally distributed, the factors that affect the geographical distribution and local prevalence of different parasite lineages across host populations or species are still poorly understood. Based on the intense screening of avian malarial parasites in nine European blue tit populations, we studied whether distribution ranges as well as local adaptation, host specialization and phylogenetic relationships can determine the observed prevalences within populations. We found that prevalence differed consistently between parasite lineages and host populations, indicating that the transmission success of parasites is lineage specific but is partly shaped by locality-specific effects. We also found that the lineage-specific estimate of prevalence was related to the distribution range of parasites: lineages found in more host populations were generally more prevalent within these populations. Additionally, parasites with high prevalence that were also widely distributed among blue tit populations were also found to infect more host species. These findings suggest that parasites reaching high local prevalence can also realize wide distribution at a global scale that can have further consequences for host specialization. Although phylogenetic relationships among parasites did not predict prevalence, we detected a close match between a tree based on the geographic distance of the host populations and the parasite phylogenetic tree, implying that neighbouring host populations shared a related parasite fauna.     

Phylogenetic Patterns of the Southeast Asian Tree Frog Chiromantis hansenae in Thailand

Although landscape features such as mountains and rivers are recognized often as limiting factors to amphibian dispersal and gene flow, a limited number of studies have investigated such patterns across Southeast Asia. A perfect example of this is Thailand, located in one of the world＇s biodiversity hotspot regions. Thailand represents the corridor between mainland Asia and the Sunda Shelf, a famous and widely recognized biogeographic region, and yet there are few studies on the genetic structure among populations of amphibian species distributed across Thailand. The Southeast Asian tree frog, Chiromantis hansenae has been reported to possess a geographic range that is restricted to Thailand and, presumably, Cambodia~ Here, we investigate phylogenetic relationships among C. hansenae populations using partial sequences of the mitochondrial 16S rRNA gene and nuclear POMC gene. Our results reveal two distinct evolutionary lineages within C. hansenae populations in Thailand. The genetic divergence among populations between these two clades is considerable, and results support inter-population divergence, and high genetic differentiation （pairwise FsT = 0.97）, between two localities sampled in western Thailand （TK1 and TK2）, separated from each other by 40 kilometers only. The results suggest that landscape features across Thailand may have a profound impact on patterns of diversification in the country, underscoring the urgent need for fine-scale investigations of genetic structure of endemic and ＂widespread＂ species.     

Testing the effect of transient Plio‐Pleistocene barriers in monsoonal Australo‐Papua: did mangrove habitats maintain genetic connectivity in the Black Butcherbird?

Changes in climate and sea level are hypothesized to have promoted the diversification of biota in monsoonal Australia and New Guinea by causing repeated range disjunctions and restricting gene flow between isolated populations. Using a multilocus (one mtDNA locus, five nuclear introns) phylogeographic approach, we test whether populations of the mangrove and rainforest restricted Black Butcherbird (Cracticus quoyi) have diverged across several geographic barriers defined a priori for this region. Phylogeographic structure and estimates of divergence times revealed Plio-Pleistocene divergences and long-term restricted gene flow of populations on either side of four major geographic barriers between and within Australia and New Guinea. Overall, our data are consistent with the hypothesis that mesic-adapted species did not disperse across the open dry woodlands and grasslands that dominated the transient palaeo-landbridges during the Plio-Pleistocene despite the presence of mangrove forests that might have acted as dispersal corridors for mesic-adapted species. Our study offers one of the first multilocus perspectives on the impact of changes in climate and sea level on the population history of widespread species with disjunct ranges in Australia and New Guinea.     

The distribution and evolutionary history of Wolbachia infection in native and introduced populations of the invasive argentine ant (Linepithema humile)

Wolbachia pipientis is a maternally transmitted bacterium that often alters the life history of its insect host to maximize transmission to subsequent generations. Here we report on the frequency and distribution of Wolbachia infection in a widespread invasive species, the Argentine ant (Linepithema humile). We screened 1175 individual Argentine ants from 89 nests on five continents and several islands, including numerous locations in both the native (South American) and introduced ranges. We detected Wolbachia in four of 11 native populations, but only one of 21 introduced populations was infected. In the Argentine ant's native range, the distribution of Wolbachia supergroups A and B was nonoverlapping. By coupling infection frequency data with behaviourally defined colony boundaries, we show that infected and uninfected colonies are often adjacent to one another, supporting the proposition that little female-mediated gene flow occurs among Argentine ant colonies. We also conduct a phylogenetic analysis, and show that the Wolbachia infecting both native and introduced populations of Argentine ants belong to two lineages that appear to be specialized on infecting New World ants. One other lineage of Wolbachia has undergone frequent, recent episodes of horizontal transmission between distantly related, introduced insect hosts.     

Species delimitation and biogeography of the Ryukyu ground geckos,Goniurosaurus kuroiwae ssp. (Squamata: Eublepharidae), by use of mitochondrial and nuclear DNA analyses

In the Ryukyu Archipelago, Japan, Goniurosaurus geckos are currently divided into six allopatric taxa among nearby islands. Recent studies suggested the occurrence of large genetic divergence within a single island and the possible non‐monophyly of a few taxa, but their species delimitation is not well resolved. We investigated the taxonomic relationships between the possibly geographically overlapped, highly diverged entities as well as other island populations via dense sampling. Our mitochondrial and nuclear DNA analyses showed that the two genetic groups were distributed in parapatry within Okinawajima Island and that they were hybridizing in narrow area around the contact zone. Geohistorical evidence suggests that the restricted gene flow has been caused by some intrinsic isolation mechanisms. Thus, we conclude that the two lineages represent full species. Mitochondrial analysis also showed that the genetic differences among other island populations were comparable to those between these species, thereby suggesting the presence of seven full species, including one unnamed taxon. We also discuss the possible cause of this divergence and why it has occurred at such a fine geographic scale.     

Ancient phylogeographic divergence in southeastern Australia among populations of the widespread common froglet, Crinia signifera

Geographic patterns of species diversity in southeast Australia have been attributed to changes in Pleistocene climate, but related phylogeographic patterns and processes are relatively understudied. 12S and 16S mitochondrial DNA sequences in Crinia signifera populations were used to infer historical patterns and processes in southeast Australia. Phylogenetic analysis identified three geographically restricted ancient lineages and several geographically restricted sub-clades. Present-day features that may prevent gene flow are absent between these geographic regions. Divergence among the three lineages corresponds to a late Miocene origin, approximately 9 million years ago (mya). The geographic breaks among the lineages are consistent with Miocene-Pliocene uplift in the Great Dividing Range and elevated sea levels in East Gippsland. Divergence among sub-clades in Victoria and South Australia is estimated to be within the early Pliocene, whereas sub-clades in New South Wales are estimated to have diverged near the Plio-Pleistocene boundary, approximately 2 mya. Geographic limits of sub-clades are consistent with geographic variation in advertisement calls, but are inconsistent with phylogeographic limits previously identified in other southeastern species.     

Less Pollen-Mediated Gene Flow for More Signatures of Glacial Lineages: Congruent Evidence from Balsam Fir cpDNA and mtDNA for Multiple Refugia in Eastern and Central North America

The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.     

Population genetics,conservation and evolution in salmonids and other widely cultured fishes: some perspectives over six decades

This paper explores my shifting understandings of interactions primarily between salmonid fish culture and fish conservation during the latter half of the 20th century. The idea that conspecific natural and cultured fish were largely interchangeable among phenotypically similar populations began to change with the advent of molecular genetic markers. With the gradual clarification of major geographic lineages beginning in the 1970s came awareness that translocations among anadromous lineages were generally destined for failure; in contrast, gene flow more readily occurred among non-anadromous lineages and sometimes, species. Within lineages, data concurrently were accumulating that showed adaptations to their respective environments distinguished cultured and wild populations. Reduced obstacles to gene flow at this level often resulted in homogenizations among wild and cultured fish in areas where widespread hatchery releases occurred; conversely, adaptive radiations in vacant habitats sometimes occurred over a few decades from single source hatchery releases. Current ideas relating to salmonid interbreeding, population substructure and culture evolved from these observations. Among lineages, resistance to gene flow is much greater between anadromous than purely freshwater populations or species. Within lineages, ease of gene flow in both anadromous and freshwater populations is problematical with regard to cultured and wild populations because large-scale supplementation programs erode local adaptations and fine-scale population substructures. At this level, a potential ability to regenerate natural substructure upon relaxation of supplementation is offset by uncertainties of time scales and intrinsic capabilities of homogenized populations. However, management that separates harvest and reproduction of wild and cultured subpopulations can minimize these losses. Some generality of this strategy to other fishes is supported by losses of local adaptations and outbreeding depression in black basses following population admixtures that parallel those observed in salmonids.     

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA‐seq analyses

Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ?a?i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ?a?i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).     

Ant-cultivated Chaetothyriales in hollow stems of myrmecophytic Cecropia sp. trees – diversity and patterns

Five Cecropia tree species occupied by four Azteca ant species from Costa Rica and French Guiana were investigated to assess the diversity and host specificity of chaetothyrialean fungal symbionts. The ITS rDNA region of the symbiotic fungi was sequenced either from pure culture isolation, or from environmental samples obtained from ant colonies nesting in hollow stems of the Cecropia host plants. The investigation revealed six closely related OTUs of Chaetothyriales. Neither the four Azteca species nor the six fungal OTUs were associated with specific Cecropia species. In contrast, ants and fungi showed an association. Azteca alfari was associated with a particular OTU, and often contained only one. Azteca coeruleipennis, Azteca constructor and Azteca xanthochroa were associated with a different set of OTUs and often had multiple OTUs within colonies. Possible reasons for these differences and the role of the fungi for the Azteca-Cecropia symbiosis are discussed.     

Phylogeny and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genes

Three nuclear genes, lsu-rDNA (encoding nuclear large subunit rDNA), ITS (encoding the rDNA internal transcribed spacers and 5.8 S rDNA) and rpb2 (encoding the second largest subunit of RNA polymerase II), and the mitochondrial gene atp6 (encoding the sixth subunit of ATP synthase), were sequenced from all recognized Sparassis lineages. Sparassis latifolia sp. nov. from boreal coniferous forests in China is described based on morphological, ecological, geographical and molecular data. The nuclear gene phylogeny strongly supported groups corresponding to morphological differences, geographic distribution and host shifts among species that produce clamp connections, such as S. crispa from Europe, S. radicata from western North America and S. latifolia from Asia. The atp6 phylogeny however showed no divergence among these three species. For clampless Sparassis species, such as S. spathulata from eastern North America, S. brevipes and a new species from Europe, the atp6 phylogeny was congruent with the nuclear gene phylogeny. Sparassis cystidiosa is basal in the nuclear tree but sister to S. brevipes-S. spathulata clade in the ATP6 tree. The differences between the phylogenetic inferences from the atp6 gene and those from nuclear genes within Sparassis species are discussed.     

Evolutionary diversification through hybridization in a wild host-pathogen interaction

Coevolutionary outcomes between interacting species are predicted to vary across landscapes, as environmental conditions, gene flow, and the strength of selection vary among populations. Using a combination of molecular, experimental, and field approaches, we describe how broad-scale patterns of environmental heterogeneity, genetic divergence, and regional adaptation have the potential to influence coevolutionary processes in the Linum marginale-Melampsora lini plant-pathogen interaction. We show that two genetically and geographically divergent pathogen lineages dominate interactions with the host across Australia, and demonstrate a hybrid origin for one of the lineages. We further demonstrate that the geographic divergence of the two lineages of M. lini in Australia is related to variation among lineages in virulence, life-history characteristics, and response to environmental conditions. When correlated with data describing regional patterns of variation in host resistance diversity and mating system these observations highlight the potential for gene flow and geographic selection mosaics to generate and maintain coevolutionary diversification in long-standing host-pathogen interactions.     

Comparative population genetic structures and local adaptation of two mutualists

Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.     

The geographic structure of morphological variation in eight species of fiddler crabs (Ocypodidae: genus Uca) from the eastern United States and Mexico

Species with larger geographic distributions are more likely to encounter a greater variety of environmental conditions and barriers to gene flow than geographically‐restricted species. Thus, even closely‐related species with similar life‐history strategies might vary in degree and geographic structure of variation if they differ in geographic range size. In the present study, we investigated this using samples collected across the geographic ranges of eight species of fiddler crabs (Crustacea: Uca) from the Atlantic and Gulf coasts of North America. Morphological variation in the carapace was assessed using geometric morphometric analysis of 945 specimens. Although the eight Uca species exhibit different degrees of intraspecific variation, widespread species do not necessarily exhibit more intraspecific or geographic variation in carapace morphology. Instead, species with more intraspecific variation show stronger morphological divergence among populations. This morphological divergence is partly a result of allometric growth coupled with differences in maximum body size among populations. On average, 10% of total within‐species variation is attributable to allometry. Possible drivers of the remaining morphological differences among populations include gene flow mediated by ocean currents and plastic responses to various environmental stimuli, with isolation‐by‐distance playing a less important role. The results obtained indicate that morphological divergence among populations can occur over shorter distances than expected based on dispersal potential. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 248–270.     

High genetic diversity and significant population structure in Cedrus brevifolia Henry, a narrow endemic Mediterranean tree from Cyprus

Endemic island plant species with a narrow distribution are often, but not always, linked to low genetic variation within populations and a lack of differentiation among populations. Cedrus brevifolia is a narrow endemic island tree species of Cyprus. Its range is restricted to a single forest, divided into five neighbouring sites. This study, using biparentally inherited nuclear microsatellites and paternally inherited plastid (chloroplast) microsatellites, assessed the genetic variation of C. brevifolia within its sole population and the level of genetic differentiation among formed sites. The results from both markers showed high diversity (nuclear H _T?=?0.70; plastid H _T?=?0.93), strongly suggesting that the species did not experience severe bottleneck events or extensive genetic drift. Besides, the maintenance of a high genetic diversity in C. brevifolia may suggest that it originates from a widespread congener species. Significant genetic differentiation at nuclear (G _ST?=?0.052) and plastid (G _ST?=?0.119) markers was found among the formed sites. Remarkably, the relatively high genetic differentiation found at plastid markers was comparable to values observed in two widespread congener cedar species. The genetic differentiation probably occurred due to fragmentation of a previously uniform population. This would lead to the shaping of different genetic groups (Bayesian analysis) and to significant population substructure. Furthermore, significant values observed for both isolation by distance and large-scale spatial genetic structure could indicate ineffective gene flow among sites and the early geographical isolation of the more isolated sites from the core population.     

Multiple cryptic species of sympatric generalists within the avian blood parasite Haemoproteus majoris

The avian haemosporidian parasite Haemoproteus majoris has been reported to infect a wide range of passerine birds throughout the Holarctic ecozone. Five cytochrome b (cyt b) lineages have been described as belonging to the morphological species H. majoris, and these form a tight phylogenetic cluster together with 13 undescribed lineages that differ from each other by < 1.2% in sequence divergence. Records in a database (MalAvi) that contains global findings of haemosporidian lineages generated by universal primers suggest that these lineages vary substantially in host distribution. We confirm this pattern in a data set collected at Lake Kvismaren, Sweden, where three of the generalist lineages have local transmission. However, whether these lineages represent intraspecific mitochondrial diversity or clusters of cryptic species has previously not been examined. In this study, we developed novel molecular markers to amplify the partial segments of four nuclear genes to determine the level of genetic diversity and gene phylogenies among the five morphologically described cyt b lineages of H. majoris. All five cyt b lineages were strongly associated with unique nuclear alleles at all four nuclear loci, indicating that each mitochondrial lineage represents a distinct biological species. Within lineages, there was no apparent association between nuclear alleles and host species, indicating that they form genetically unstructured populations across multiple host species.