Habitat‐driven diversification,hybridization and cryptic diversity in the Fork‐tailed Drongo (Passeriformes: Dicruridae: Dicrurus adsimilis)

Species complexes of widespread African vertebrates that include taxa distributed across different habitats are poorly understood in terms of their phylogenetic relationships, levels of genetic differentiation and diversification dynamics. The Fork‐tailed Drongo (Dicrurus adsimilis) species complex includes seven Afrotropical taxa with parapatric distributions, each inhabiting a particular bioregion. Various taxonomic hypotheses concerning the species limits of the Fork‐tailed Drongo have been suggested, based largely on mantle and upperpart coloration, but our understanding of diversity and diversification patterns remains incomplete. Especially given our lack of knowledge about how well these characters reflect taxonomy in a morphologically conservative group. Using a thorough sampling across Afrotropical bioregions, we suggest that the number of recognized species within the D. adsimilis superspecies complex has likely been underestimated and that mantle and upperpart coloration reflects local adaptation to different habitat structure, rather than phylogenetic relationships. Our results are consistent with recent phylogeographic studies of sub‐Saharan African vertebrates, indicating that widespread and often morphologically uniform species comprise several paraphyletic lineages, often with one or more of the lineages being closely related to phenotypically distinct forms inhabiting a different, yet geographically close, biome.     

Evaluation of species boundaries in sympatric and parapatric populations of Mesoamerican toads

Approaches that integrate multiple independent, yet complimentary, lines of evidence have been effectively utilized to identify and evaluate species diversity. Integrative approaches are especially useful in taxa that exhibit cryptic diversity and are highly morphologically conserved, as well as organisms whose distributions may be sympatric or parapatric. The Incilius coccifer complex in Honduras is comprised of three putative taxa: I. coccifer, I. ibarrai and I. porteri. The taxonomy of the I. coccifer complex has been a source of debate among specialists, with some recognizing three species, while others choose to recognize one widespread taxon. To assess species boundaries and evaluate the taxonomic structure for the I. coccifer complex, we utilized a combination of comprehensive field sampling, molecular phylogenetics and macroecological modelling. Using 58 samples representing all three putative taxa, we generated sequence data from the mitochondrial loci 16S and COI in order to assess genetic diversity and phylogenetic relationships, and tested putative species boundaries using General Mixed Yule‐Coalescent models. To evaluate macroecological differences in the distribution of putative taxa, we utilized maximum entropy modelling and identified areas of suitable and non‐suitable habitat, as well as identifying potential areas of overlap between species habitats. We recovered three clades that broadly correspond to the three named taxa that, while being monophyletic, are separated by relatively small genetic distances. Species distribution models revealed that I. coccifer is macroecologically different than the other two taxa, but that I. ibarrai and I. porteri are highly similar. We uncovered cases of sympatry between pairs of species in at least three localities in Honduras, suggesting the potential for hybridization in these closely related lineages.     

The impact of species-specific traits and phylogenetic relatedness on allozyme diversity inCarex sect.Phyllostachys (Cyperaceae)

Allozyme variation was examined inCarex sect.Phyllostachys (Cyperaceae) to study the effects of species-specific traits and phylogenetic relatedness on genetic structure. In contrast to the findings of similar studies, genetic variability in thePhyllostachys is poorly correlated with geographic range and putative differences in breeding systems (as inferred from morphology). This suggests that other patterns of evolution, colonization, and gene flow characterize the species found in this section. Fixation indices are negative for all populations suggesting that mechanisms such as disassortative mating and selection are maintaining heterozygous excess within populations. Closely related taxa often exhibit different genetic variability statistics. In some instances, however, clades (e.g.C. jamesii andC. juniperorum) display very similar levels of genetic variability despite marked differences in species-specific traits. Recent speciation coupled with the ability to maintain historical levels of variation within populations may be factors accounting for this phenomenon. Contrary to similar studies, species restricted to known glacial refugia have lower genetic diversity than those species that underwent mass migrations in response to deglaciation. Narrowly endemic species were found to partition their genetic diversity within, as opposed to between populations. The opposite trend was evident in wider ranging congeners.     

Correlated patterns of genetic diversity and differentiation across an avian family

Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology and migratory behaviour, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole‐genome pooled sequencing of 262 individuals from five taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked whether these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g. areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation.     

Comparative mitochondrial genetics of North American and Eurasian mergansers with an emphasis on the endangered scaly-sided merganser (Mergus squamatus)

The scaly-sided merganser, Mergus squamatus, is considered one of the most threatened sea duck species in the Palearctic with limited breeding and wintering distribution in China and Russia. To provide information for future conservation efforts, we sequenced a portion of the mitochondrial (mt) DNA control region in four species of mergansers and three additional sea duck taxa to characterize the evolutionary history of the scaly-sided merganser, infer population trends that may have led to its limited geographic distribution, and to compare indices of genetic diversity among species of mergansers. Scaly-sided mergansers exhibit substantially lower levels of mtDNA genetic diversity (h = 0.292, π = 0.0007) than other closely related sea ducks and many other avian taxa. The four haplotypes observed differed by a single base pair suggesting that the species has not experienced a recent population decline but has instead been at a low population level for some time. A phylogenetic analysis placed the scaly-sided merganser basal to North American and European forms of the common merganser, M. merganser. Our inclusion of a small number of male samples doubled the number of mtDNA haplotypes observed, suggesting that additional genetic variation likely exists within the global population if there is immigration of males from unsampled breeding areas.     

Comparative Analysis of Phylogenetic Relationships of Grain Amaranths and Their Wild Relatives (Amaranthus; Amaranthaceae) Using Internal Transcribed Spacer, Amplified Fragment Length Polymorphism, and Double-Primer Fluorescent Intersimple Sequence Repeat Markers

The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among these closely related taxa. Internal transcribed spacer (ITS) of nuclear ribosomal DNA, amplified fragment length polymorphism (AFLP), and double-primer fluorescent intersimple sequence repeat (ISSR) were employed to reexamine the taxonomic status and phylogenetic relationships of grain amaranths and their wild relatives. Low ITS divergence in these taxa resulted in poorly resolved phylogeny. However, extensive polymorphisms exist at AFLP and ISSR loci both within and among species. In phylogenetic trees based on either AFLP or ISSR or the combined data sets, nearly all intraspecific accessions can be placed in their corresponding species clades, indicating that these taxa are well-separated species. The AFLP trees share many features in common with the ISSR trees, both showing a close relationship between A. caudatus and A. quitensis, placing A. hybridus in the same clade as all grain amaranths, and indicating that A. powellii is the most divergent taxon in the A. hybridus species complex. This study has demonstrated that both AFLP and double-primer fluorescent ISSR have a great potential for generating a large number of informative characters for phylogenetic analysis of closely related species, especially when ITS diversity is insufficient.     

Habitat predictors of genetic diversity for two sympatric wetland‐breeding amphibian species

Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond‐breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata; and Southern Leopard frogs, Lithobates sphenocephalus) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond‐breeding amphibian species.     

A phylogeographic framework for the conservation of Saharan and Arabian Dorcas gazelles (Artiodactyla: Bovidae)

Many species of gazelles (Gazella spp.) are nowadays threatened by hunting, poaching, habitat loss and habitat deterioration. Conservation efforts for this group not only face the problem of maintaining remnant populations, but often natural populations have been extirpated from the wild. In some cases, though, captive breeding programs exist that might provide a valuable source for future reintroductions. A major problem in this context is that phylogeographic relationships among different (potentially locally adapted) populations, and even basic phylogenetic relationships between species, are poorly understood, thus hampering the assignment of management units, breeding groups or stocks for reintroduction projects. Our present study focused on Dorcas gazelles (G. dorcas and G. saudiya) from the species’ entire distribution range, with samples originating from western Saharan Africa into Saudi Arabia. In stark contrast to previous studies reporting on pronounced genetic structure in taxa such as Mountain gazelles (G. gazella), we detected low genetic diversity and no evidence for major phylogenetic lineages when analyzing two mitochondrial genetic markers. Using a coalescent approach we infer a steep population decline that started approximately 25,000 years before present and is still ongoing, which coincides with human activities in Saharan Africa. Our phylogenetic analyses, statistical parsimony network analysis and inferred colonization patterns shed doubt on the validity of various described subspecies of G. dorcas.     

Does the Reproductive Strategy Affect the Transmission and Genetic Diversity of Bionts in Cyanolichens? A Case Study Using Two Closely Related Species

Observed levels of population genetic diversity are often associated with differences in species dispersal and reproductive strategies. In symbiotic organisms, the genetic diversity level of each biont should also be highly influenced by biont transmission. In this study, we evaluated the influence of the reproductive strategies of cyanolichen species on the current levels of population genetic diversity of bionts. To eliminate any phylogenetic noise, we selected two closely related species within the genus Degelia, which only differ in their reproductive systems. We sampled all known populations of both species in central Spain and genotyped the fungal and cyanobacterial components of lichen samples using DNA sequences as molecular markers. We applied population genetics approaches to evaluate the genetic diversity and population genetic structure of the symbiotic components of both lichen species. Our results indicate that fungal and cyanobiont genetic diversity is highly influenced by the reproductive systems of lichen fungus. We detected higher bionts genetic diversity values in the sexual species Degelia plumbea. By contrast, the levels of fungal and cyanobiont genetic diversity in the asexual species Degelia atlantica were extremely low (almost clonal), and the species shows a high specificity towards its cyanobiont. Our results indicate that reproduction by vegetative propagules, in species of the genus Degelia, favors vertical transmission and clonality, which affects the species’ capacity for resources and competition, thereby limiting the species to restricted niches.     

花蔺和黄花蔺居群遗传结构比较研究

采用垂直板型聚丙烯酰胺凝胶电泳技术,分别通过１９和２１个等位酶位点测定了花蔺３个居群和黄花蔺４个居群的遗传结构与基因流。两类群都维持较高水平的遗传多样性。花蔺居群期望杂合度、固定指数、异交率和遗传分化分别为０．１４４、０．１７４、９４．０％和０．２００,显示出异交繁育系统类型。黄花蔺居群期望杂合度、固定指数、异交率和遗传分化分别为０．０７６、０．４１５、５８．５％和０．３９１。表明其异交＋自交的敏     

Molecular and morphological variation of rare endemic oncocyclus irises (Iridaceae) of Lebanon

Oncocyclus irises endemic to Lebanon form a complex of three closely related taxa replacing each other over short geographical distances in a linear habitat. In order to characterize the appropriate taxonomic levels and to assess their conservation status, we investigated patterns of phenotypic variability and the partitioning of genetic variation within and among populations using random amplified polymorphic DNA (RAPD) markers. Multivariate analysis (principal components analysis and multiple correspondence analysis), based on 16 quantitative and six qualitative characters, revealed no separation between populations or taxa. Moreover, no morphological character could be used to define clear boundaries between populations/taxa. The genetic characterization revealed high levels of polymorphism and diversity (H_s). Principal components analysis showed population delimitations, but no groupings reflecting the currently defined taxa could be identified. Both morphological and genetic data showed that Lebanese oncocyclus irises could not be fitted into clear taxonomic boundaries. Consequences for conservation are discussed. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 123–135.     

Hybridization between two parapatric ranid frog species in the northern Sierra Nevada,California, USA

Contact zones between species provide a unique opportunity to test whether taxa can hybridize or not. Cross‐breeding or hybridization between closely related taxa can promote gene flow (introgression) between species, adaptation, or even speciation. Though hybridization events may be short‐lived and difficult to detect in the field, genetic data can provide information about the level of introgression between closely related taxa. Hybridization can promote introgression between species, which may be an important evolutionary mechanism for either homogenization (reversing initial divergence between species) or reproductive isolation (potentially leading to speciation). Here, we used thousands of genetic markers from nuclear DNA to detect hybridization between two parapatric frog species (Rana boylii and Rana sierrae) in the Sierra Nevada of California. Based on principal components analysis, admixture, and analysis of heterozygosity at species diagnostic SNPs, we detected two F1 hybrid individuals in the Feather River basin, as well as a weak signal of introgression and gene flow between the frog species compared with frog populations from two other adjacent watersheds. This study provides the first documentation of hybridization and introgression between these two species, which are of conservation concern.     

Investigating niche and lineage diversification in widely distributed taxa: phylogeography and ecological niche modeling of the Peromyscus maniculatus species group

The relationship between lineage formation and variation in the ecological niche is a fundamental evolutionary question. Two prevailing hypotheses reflect this relationship: niche conservatism and niche divergence. Niche conservatism predicts a pattern where sister taxa will occupy similar niche spaces; whereas niche divergence predicts that sister taxa will occupy different niche spaces. Widely distributed species often show distinct phylogeographic structure, but little research has been conducted on how the environment may be related to these phylogenetic patterns. We investigated the relationship between lineage divergence and environmental space for the closely related species Peromyscus maniculatus and P. polionotus utilizing phylogenetic techniques and ecological niche modeling (ENM). We estimated the phylogenetic relationship among individuals based on complete cytochrome b sequences that represent individuals from a majority of the species ranges. Niche spaces that lineages occupy were estimated by using 12 environmental layers. Differences in niche space were tested using multivariate statistics based on location data, and ENMs were employed using maximum entropy algorithms. Two similarity indices estimated significant divergence in environmental space based on the ENM. Six geographically structured lineages were identified within P. maniculatus. Nested within P. maniculatus we found that P. polionotus recently diverged from a clade occupying central and western United States. We estimated that the majority of the genetic lineages occupy distinct environmental niches, which supports a pattern of niche divergence. Two sister taxa showed niche divergence and represent different ecomorphs, suggesting morphological, genetic and ecological divergence between the two lineages. Two other sister taxa were observed in the same environmental space based on multivariate statistics, suggesting niche conservatism. Overall our results indicate that a widely distributed species may exhibit both niche conservatism and niche divergence, and that most lineages seem to occupy distinct environmental niches.     

AFLP and breeding system studies indicate vicariance origin for scattered populations and enigmatic low fecundity in the Moroccan endemic Hypochaeris angustifolia (Asteraceae), sister taxon to all of the South American Hypochaeris species

We used Amplified Fragment Length Polymorphism markers (AFLP) and breeding system studies to investigate the population structure and reproductive biology of Hypochaeris angustifolia (Asteraceae: Cichorieae). This species is endemic to altiplanos of the Atlas Mountains (Morocco) where it occurs in scattered populations, and it is the sister species to c. 40 species of this genus in South America. PCoA, NJ, and Bayesian clustering, revealed that the populations are very isolated whilst AFLP parameters show that almost all populations have marked genetic divergence. We contend that these features are more in accord with a vicariance origin for the scattered populations of H. angustifolia, rather than establishment by long-distance dispersal. The breeding system studies revealed that H. angustifolia is a self-incompatible species, with low fecundity in natural and in experimental crosses, probably due to a low frequency of compatible phenotypes within and between the populations.     

Evolutionary patterns and genetic structure in localized and widespread species in the Stylidium caricifolium complex (Stylidiaceae)

The Stylidium caricifolium (Stylidiaceae) complex consists of seven currently recognized species and a taxon of putative hybrid origin endemic to southwest Western Australia. These taxa vary in geographical distribution from widespread, extending over a range of 500 km, to extremely localized, covering a range of only 0.5 km. Patterns of allozyme variation were investigated in 61 populations covering all taxa and two closely related species. Measures of genetic diversity were consistently lower and in some cases significantly lower in four rare and geographically restricted taxa compared with their widespread relatives. In contrast, genetic diversity in two other localized taxa was comparable or higher than in the widespread taxa. The level of divergence among populations was moderate to high, with a significant trend of higher F(ST) values for the widespread species to lower values for the geographically restricted and rare taxa. Phylogenetic relationships and levels of divergence indicate that most taxa are probably relictual rather than recently evolved. Geographical localization and rarity in this complex can be attributed to a range of factors associated with habitat specificity, historical and ecological processes that characterize the southwest region, and mode of origin.     

Morphological similarity and molecular divergence of Trochulus striolatus and T. montanus,and their relationship to sympatric congeners (Gastropoda: Pulmonata: Hygromiidae)

Shell morphology has played an important role in the differentiation of mollusc species. However, extensive morphological variation and the lack of readily available diagnostic characters often lead to confusion and controversy in taxonomy of closely related species, such as the genus Trochulus. Two nominal species Trochulus striolatus and T. montanus show only subtle differences in their reproductive systems and are indistinguishable on the basis of sole conchological traits. Therefore, we performed molecular and morphological analyses to establish robust species limits among the taxa. The canonical discriminant analysis (CDA) of shell characters confirmed strong similarity between the species. It also revealed high intraspecific variability of the shell morphology, which allowed the distinguishing of some populations as two extremely distinct forms, while simultaneously making it difficult to discriminate between the two species. Analysis of the genital morphology indicated that differences were continuous and practically negligible among the species. In contrast, phylogenetic analyses based on newly obtained 114 Trochulus sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and 55 homologues retrieved from the GenBank database showed clear genetic divergence between T. striolatus and T. montanus. Moreover, they revealed a close relationship between some T. montanus, some T. caelatus and T. clandestinus samples, which formed a monophyletic group. Some of their haplotypes were even identical. It suggested that their recent common origin or recurrent gene flow occurred between these populations. However, T. sericeus sequences were split into independent diverged lineages, which were separated by many unidentified Trochulus species. It suggested that this taxon may represent a paraphyletic species complex.     

Ecology,song similarity and phylogeny predict natural hybridization in an avian family

Hybridization is important in the evolution of many animal groups; however, broad scale patterns of natural hybridization are still poorly understood. Using phylogenetic comparative analyses, we tested for relationships between demographic, ecological, phenotypic and phylogenetic variables and the incidence of natural hybridization among 45 species of North American wood warbler. Since 1980, hybrids have been documented in 24 species (53 %). We detected negative relationships between the incidence of hybridization and both breeding range size and phylogenetic distance, and positive relationships between the incidence of hybridization and (1) song similarity, (2) the extent of breeding sympatry of species pairs and (3) the number of additional heterospecific warbler species that co-occur during breeding. Neither population size nor breeding habitat quality (as measured by threats to survival or reproduction in breeding areas) explained variation in the incidence of hybridization. Our results suggest a potential role of limited breeding habitat in wood warbler hybridization events and a net positive effect of breeding sympatry. They also support the hypothesis that mating signal similarity facilitates hybridization events and are consistent with an increase in reproductive isolation with increasing genetic divergence. Our results also suggest the presence of phylogenetic signal in wood warbler hybridization. By investigating natural hybridization at the taxonomic level of family, we have identified several previously undocumented patterns of natural hybridization. This study demonstrates the utility of examining the combined effects of ecology, demography, phenotype and phylogeny when studying variation in the expression of natural hybridization among taxa.     

The unexpected genetic mating system of the red‐backed toadlet (Pseudophryne coriacea): A species with prolonged terrestrial breeding and cryptic reproductive behaviour

Molecular technologies have revolutionized our classification of animal mating systems, yet we still know very little about the genetic mating systems of many vertebrate groups. It is widely believed that anuran amphibians have the highest reproductive diversity of all vertebrates, yet genetic mating systems have been studied in <1% of all described species. Here, we use single nucleotide polymorphisms to quantify the genetic mating system of the terrestrial breeding red‐backed toadlet Pseudophryne coriacea. In this species, breeding is prolonged (approximately 5 months), and males construct subterranean nests in which females deposit eggs. We predicted that females would display extreme sequential polyandry because this mating system has been reported in a closely related species (P. bibronii). Parentage analysis revealed that mating success was heavily skewed towards a subset of males (30.6% of potential sires) and that nearly all females (92.6%) mated with one male. In a high percentage of occupied nests (37.1%), the resident male was not the genetic sire, and very few nests (4.3%) contained clutches with multiple paternity. Unexpectedly, these results show that sequential polyandry is rare. They also show that there is a high frequency of nest takeover and extreme competition between males for nest sites, but that males rarely sneak matings. Genetic analysis also revealed introgressive hybridization between P. coriacea and the red‐crowned toadlet (Pseudophryne australis). Our study demonstrates a high level of mating system complexity, and it shows that closely related anurans can vary dramatically in their genetic mating system.