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Individuals identified as Aricidea assimilis Tebble, 1959 were collected from ten localities across the Mediterranean Sea from 0.5 to 225 m depth in order to have a wide coverage of the species habitats and geographic range and to assess the effects of environmental factors and biogeographical barriers on molecular and morphological diversity. Two mitochondrial and one nuclear markers were used to reconstruct phylogenetic relationships and test the occurrence of cryptic species. We observed two highly divergent lineages, one including all individuals from shallow, sandy environments (

Plant domestication and movement are large contributors to the success of new diseases. The introduction of new host species can result in accelerated evolutionary changes in pathogens, affecting long-established coevolutionary dynamics. This has been observed in poplarswhere severe epidemics of pathogens that were innocuous in their natural pathosystems occurred following host domestication. The North American fungus Sphaerulina musiva is responsible for endemic leaf spots on Populus deltoides. We showthat the expansion of poplar cultivation resulted in the emergence of a new lineage of this pathogen that causes stem infections on a new host, P. balsamifera. This suggests a host shift since this is not a known host. Genome analysis of this emerging lineage reveals a mosaic pattern with islands of diversity separated by fixed genome regions, which is consistent with a homoploid hybridization event between two individuals that produced a hybrid swarm. Genome regions of extreme divergence and lowdiversity are enriched in genes involved in host-pathogen interactions. The specialization of this emerging lineage to a new host and its clonal propagation represents a serious threat to poplars and could affect both natural and planted forests. This work provides a clear example of the changes created by the intensification of tree cultivation that facilitate the emergence of specialized pathogens, jeopardizing the natural equilibrium between hosts and pathogens. [ABSTRACT FROM AUTHOR]

Individuals identified as Aricidea assimilis Tebble, 1959 were collected from ten localities across the Mediterranean Sea from 0.5 to 225 m depth in order to have a wide coverage of the species habitats and geographic range and to assess the effects of environmental factors and biogeographical barriers on molecular and morphological diversity. Two mitochondrial and one nuclear markers were used to reconstruct phylogenetic relationships and test the occurrence of cryptic species. We observed two highly divergent lineages, one including all individuals from shallow, sandy environments (<10 m depth) and the other with the individuals from deeper muddy bottoms (30–225 m depth). Less pronounced divergence was detected between morphologically distinct brackish-water individuals and the remaining shallow-water individuals. The divergence observed between deep-water and shallow-water lineages is consistent with the hypothesis of distinct species. The ambiguous results of species delimitation tests applied to the two shallow-water sub-lineages might instead suggest a process of incipient speciation, even if this hypothesis needs additional evidence. These results suggest that sediment represents the main factor driving genetic divergence and ultimately cryptic speciation in A. assimilis, while other depth-associated factors and geographical barriers do not seem to significantly contribute to the genetic architecture of this species, suggesting the occurrence of wide-range larval dispersal. [ABSTRACT FROM AUTHOR]

Abstract Countershading, characterized by a darker dorsal surface and lighter ventral surface, is common among many animals. This dorsoventral pigment polarity is often thought to be adaptive coloration for camouflage. By contrast, noncountershaded (melanistic) morphs often occur within a species due to genetic color polymorphism in terrestrial animals. However, the polymorphism with either countershaded or melanistic morphs is poorly known in wild aquatic animals. This study explored the genetic nature of diverged color morphs of a lineage of gudgeon fish (genus Sarcocheilichthys) in the ancient Lake Biwa and propose this system as a novel model for testing hypotheses of functional aspects of countershading and its loss in aquatic environments. This system harbors two color morphs that have been treated taxonomically as separate species; Sarcocheilichthys variegatus microoculus which occurs throughout the littoral zone and Sarcocheilichthys biwaensis which occurs in and around rocky areas. First, we confirmed that the divergence of dorsoventral color patterns between the two morphs is under strict genetic control at the levels of chromatophore distribution and melanin‐related gene expression under common garden rearing. The former morph displayed sharp countershading coloration, whereas the latter morph exhibited a strong tendency toward its loss. The crossing results indicated that this divergence was likely controlled by a single locus in a two‐allele Mendelian inheritance pattern. Furthermore, our population genomic and genome‐wide association study analyses detected no genome‐wide divergence between the two morphs, except for one region near a locus that may be associated with the color divergence. Thus, these morphs are either in a state of intraspecific color polymorphism or two incipient species. Evolutionary forces underlying this polymorphism appear to be associated with heterogeneous littoral environments in this lake. Future ecological genomic research will provide insight into adaptive functions of this widespread coloration, including the eco‐evolutionary drivers of its loss, in the aquatic world.

The complete mitochondrial genomes are sequenced in two individuals representing two morphological forms, 'usual' (U) and 'gray' (G), of the short-spined sea urchin Strongylocentrotus intermedius. The genome sequences are 15,705 bp in size, and the gene arrangement, composition, and size are very similar to the other sea urchin mitochondrial genomes published previously. A low level of sequence divergence (D xy = 0.0083 ± 0.0007) is detected between the forms. The GenBank (KC490912) mt genome of S. intermedius is much closer to the U form (D xy = 0.0013 ± 0.0003) than to the G form (D xy = 0.0085 ± 0.0006), demonstrating unique evolutionary trajectories for each form, which we previously suggested based on the bindin gene and symbiont analyses.

Natural selection along elevational gradients has potential to drive predictable adaptations across distinct lineages, but the extent of such repeated evolution remains poorly studied for many widespread alpine taxa. We present parallel genomic analyses of two recently evolved flightless alpine insect lineages to test for molecular signatures of repeated alpine adaptation. Specifically, we compare low‐elevation vs. alpine stonefly ecotypes from parallel stream populations in which flightless upland ecotypes have been independently derived. We map 67,922 polymorphic genetic markers, generated across 176 Zelandoperla fenestrata specimens from two independent alpine stream populations in New Zealand's Rock and Pillar Range, to a newly developed plecopteran reference genome. Genome‐wide scans revealed 31 regions with outlier single nucleotide polymorphisms (SNPs) differentiating lowland vs. alpine ecotypes in Lug Creek, and 37 regions with outliers differentiating ecotypes in Six Mile Creek. Of these regions, 13% (8/60) yielded outlier SNPs across both within‐stream ecotype comparisons, implying comparable genomic shifts contribute to this repeated alpine adaptation. Candidate genes closely linked to repeated outlier regions include several with documented roles in insect wing‐development (e.g., dishevelled), suggesting that they may contribute to repeated alpine wing reduction. Additional candidate genes have been shown to influence insect fecundity (e.g., ovo) and lifespan (e.g., Mrp4), implying that they might contribute to life history differentiation between upland and lowland ecotypes. Additional outlier genes have potential roles in the evolution of reproductive isolation among ecotypes (hedgehog and Desaturase 1). These results demonstrate how replicated outlier tests across independent lineages can potentially contribute to the discovery of genes underpinning repeated adaptation. [ABSTRACT FROM AUTHOR]

Morphology‐based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination‐activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus‐like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions. [ABSTRACT FROM AUTHOR]

Countershading, characterized by a darker dorsal surface and lighter ventral surface, is common among many animals. This dorsoventral pigment polarity is often thought to be adaptive coloration for camouflage. By contrast, noncountershaded (melanistic) morphs often occur within a species due to genetic color polymorphism in terrestrial animals. However, the polymorphism with either countershaded or melanistic morphs is poorly known in wild aquatic animals. This study explored the genetic nature of diverged color morphs of a lineage of gudgeon fish (genus Sarcocheilichthys) in the ancient Lake Biwa and propose this system as a novel model for testing hypotheses of functional aspects of countershading and its loss in aquatic environments. This system harbors two color morphs that have been treated taxonomically as separate species; Sarcocheilichthys variegatus microoculus which occurs throughout the littoral zone and Sarcocheilichthys biwaensis which occurs in and around rocky areas. First, we confirmed that the divergence of dorsoventral color patterns between the two morphs is under strict genetic control at the levels of chromatophore distribution and melanin‐related gene expression under common garden rearing. The former morph displayed sharp countershading coloration, whereas the latter morph exhibited a strong tendency toward its loss. The crossing results indicated that this divergence was likely controlled by a single locus in a two‐allele Mendelian inheritance pattern. Furthermore, our population genomic and genome‐wide association study analyses detected no genome‐wide divergence between the two morphs, except for one region near a locus that may be associated with the color divergence. Thus, these morphs are either in a state of intraspecific color polymorphism or two incipient species. Evolutionary forces underlying this polymorphism appear to be associated with heterogeneous littoral environments in this lake. Future ecological genomic research will provide insight into adaptive functions of this widespread coloration, including the eco‐evolutionary drivers of its loss, in the aquatic world. [ABSTRACT FROM AUTHOR]

Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We sequenced mitochondrial DNA (mtDNA) from 20 subspecies of M. pennsylvanicus and contextualized infraspecific variation through comparison of pairwise genetic distances derived from an extended data set of 63 species of Microtus. We found strong support for at least three divergent clades within M. pennsylvanicus, with observed intraspecific clade divergence exceeding that between several pairwise comparisons of sister species within Microtus. Six nuclear genes were then sequenced to test the validity of mtDNA structure and to further evaluate the possibility of cryptic, species-level diversity using Bayes factor species delimitation (BFD) analyses. BFD consistently and decisively supported multiple species based on the multilocus approach. We propose that taxonomic revision of the meadow vole is required, with the eastern clade now identified as M. pennsylvanicus (Ord 1815), the western clade as M. drummondii (Audubon and Bachman 1853), and the coastal Florida clade as M. dukecampbelli (Woods, Post, and Kilpatrick 1982). We suggest that such an arrangement would more closely reflect evolutionary history and provide critical context for further examination of distinctive southern peripheral populations that harbor novel evolutionary legacies and adaptive potential. [ABSTRACT FROM AUTHOR]

Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We sequenced mitochondrial DNA (mtDNA) from 20 subspecies of M. pennsylvanicus and contextualized infraspecific variation through comparison of pairwise genetic distances derived from an extended data set of 63 species of Microtus. We found strong support for at least three divergent clades within M. pennsylvanicus , with observed intraspecific clade divergence exceeding that between several pairwise comparisons of sister species within Microtus. Six nuclear genes were then sequenced to test the validity of mtDNA structure and to further evaluate the possibility of cryptic, species-level diversity using Bayes factor species delimitation (BFD) analyses. BFD consistently and decisively supported multiple species based on the multilocus approach. We propose that taxonomic revision of the meadow vole is required, with the eastern clade now identified as M. pennsylvanicus (Ord 1815), the western clade as M. drummondii (Audubon and Bachman 1853), and the coastal Florida clade as M. dukecampbelli (Woods, Post, and Kilpatrick 1982). We suggest that such an arrangement would more closely reflect evolutionary history and provide critical context for further examination of distinctive southern peripheral populations that harbor novel evolutionary legacies and adaptive potential. [ABSTRACT FROM AUTHOR]

A recent study demonstrated that British red foxes introduced to the mid-Atlantic coastal plain (ACP) of the eastern United States during the late 18th century successfully interbred with indigenous American red foxes despite half a million year's divergence. However, a large disparity in frequency of European mitochondria (27%) versus Y chromosomes (1%) left unclear the magnitude of genetic exchange. We sought to quantify genomic introgression using 35 autosomal and 5 X-chromosome ancestry-informative markers (AIMs) in conjunction with diagnostic Y chromosome single nucleotide polymorphism (Y-SNP) markers to characterize the modern state of red foxes in the eastern United States and to gain insight into the potential role of reproductive barriers. European admixture was highest in the ACP and apparently restricted to the central eastern United States. We estimated only slightly (and nonsignificantly) European ancestry in autosomal than X-chromosome markers. European ancestry from autosomal and X-chromosome markers (36.4%) was higher than the corresponding mitochondrial (mt) DNA estimate (26.4%) in the ACP. Only 1 of 124 males (<1%) in the ACP had European Y chromosomes, which was similar to the neighboring regions, in which 2 of 99 (2%) males carried a European Y chromosome (the same haplotype). Although we could not rule out drift as the cause of low European Y-chromosome frequency, results were also consistent with F1 male infertility. In the future, more extensive genomic sequencing will enable a more thorough investigation of possible barrier genes on the X chromosome as well as throughout the genome. [ABSTRACT FROM AUTHOR]

Speciation traits of paramere, paraproct and aedeagus were applied to find initial split criteria with fine structure analysis in order to prepare diverged trait matrices for delimiting phylogenetic incipient species of unsettled limnephilid taxa in the early stages of reproductive isolation. A brief history is presented how this phenotypic taxonomic tool of the speciation traits was discovered and applied in caddisfly taxonomy. The theoretical basis was elaborated for the phenotypic speciation trait by reviewing several relevant topics in the sciences of taxonomy, molecular genetics and phylogenetics. Perspectives of integrative taxonomy is discussed in context of phenotype versus genotype, immensely complex phenotype versus phenomic challenge, taxonomic impediment versus genetic expedient, taxonomic adaptation of genetic vocabulary versus genetic sophistication and virtualization, New Systematics of Huxley and Mayr versus New Taxonomy of Wheeler. Debates on magic trait, speciation phenotype, speciation trait and super traits are discussed concluding that evolution works with phenotype and why the cryptic species concept is irrelevant. Briefly summarized how speciation traits evolve in sexual selection, through accelerated reproductive isolation with genital evolution through sex-limited speciation traits, including minor sex chromosomes. Why neutral molecular markers are blind compared to the adaptive speciation traits sensitized by fine structure analysis and backed by the potential of high-tech and high-throughput phenotyping and cyber-infrastructure broadly accessible and fed by computable phenotype descriptions. What sort of genetics could really help taxonomy to describe biodiversity of the over 100 million unknown taxa? Collecting new and re-examining old type materials deposited in various collections, the following taxonomic actions were elaborated by speciation traits. Drusus bolivari new species complex has been erected with redescription of Drusus bolivari (McLachlan, 1876), with species status resurrection of D. estrellensis (McLachlan, 1884) stat. restit., with description of five new species: D. carmenae Oláh, sp. nov., D. gonzalezi Oláh, sp. nov., D. grafi Oláh, sp. nov., D. gredosensis Oláh, sp. nov., D. jesusi Oláh, sp. nov., D. pyrenensis Oláh & Coppa, sp. nov. Genus Isogamus is revised with description of two new species: I. baloghi Oláh, sp. nov., I. balinti Oláh, sp. nov. Melampophylax genus revised with one new species cluster: M. nepos, with two new species descriptions: M. keses Coppa & Oláh, sp. nov. M. szczesnyorum Oláh & Chvojka, sp. nov., with three new species status: M. banaticus Botosaneanu, 1995 stat. nov., M. gutinicus Botosaneanu, 1995 stat. nov., M. triangulifera Botosaneanu, 1957 stat. nov. Rhadicoleptus genus revised with redescription of R. alpestris (Kolenati, 1848), with three new species status: R. macedonicus Botosaneanu & Riedel, 1965 stat. nov. R. meridiocarpaticus Botosaneanu & Riedel, 1965 stat. nov. R. sylvanocarpaticus Botosaneanu & Riedel, 1965 stat. nov., with one species status resurrection: R. spinifer (McLachlan, 1875) stat. restit. Based on paramere evolution the Rhadicoleptus genus is transferred from the tribe Limnephilini to Stenophylacini. Annitella kosciuszkii new species complex has been erected and revised with redescription of A. chomiacensis (Dziędzielewicz, 1908), A. lateroproducta (Botosaneanu, 1952), with one species status resurrection: A. kosciuszkii Klapálek, 1907 stat. restit., with description of a new species: A. wolosatka Oláh &Szczęsny, sp. nov., with two new synonyms: A. dziedzielewiczi Schmid, 1952 synonym of A. kosciuszkii. syn. nov., A. transylvanica Murgoci, 1957 synonym of A. kosciuszkii. syn. nov. Chaetopteryx rugulosa species group revised with description of five new species: C. balcanica Oláh, sp. nov., C. karima Oláh, sp. nov., C. kozarensis Oláh, sp. nov., C. psunjensis Oláh, sp. nov., C. tompa Oláh, sp. nov., with three species status resurrections: C. papukensis Oláh & Szivák, 2012 stat. restit., C. prealpensis Oláh, 2012 stat. restit., C. zalaensis Oláh, 2012 stat. restit. Psilopteryx psorosa new species group erected and revised with three new sibling species complexes: P. bohemosaxonica, P. carpathica, P. psorosa, with two new species descriptions: P. javorensis Oláh, sp. nov., P. harmas Oláh & Chvojka, sp. nov. with one species status resurrection: P. carpathica Schmid, 1952 stat. restit., with three new species status: P. bohemosaxonica Mey & Botosaneanu, 1985 stat. nov., P. retezatica Botosaneanu & Schneider, 1978 stat. nov., P. transylvanica Mey & Botosaneanu, 1985 stat. nov.

Abstract: Parasitism has been proposed as a factor in host speciation, as an agent affecting coexistence of host species in species‐rich communities and as a driver of post‐speciation diversification. Young adaptive radiations of closely related host species of varying ecological and genomic differentiation provide interesting opportunities to explore interactions between patterns of parasitism, divergence and coexistence of sympatric host species. Here, we explored patterns in ectoparasitism in a community of 16 fully sympatric cichlid species at Makobe Island in Lake Victoria, a model system of vertebrate adaptive radiation. We asked whether host niche, host abundance or host genetic differentiation explains variation in infection patterns. We found significant differences in infections, the magnitude of which was weakly correlated with the extent of genomic divergence between the host species, but more strongly with the main ecological gradient, water depth. These effects were most evident with infections of Cichlidogyrus monogeneans, whereas the only host species with a strictly crevice‐dwelling niche, Pundamilia pundamilia, deviated from the general negative relationship between depth and parasitism. In accordance with the Janzen–Connell hypothesis, we also found that host abundance tended to be positively associated with infections in some parasite taxa. Data on the Pundamilia sister species pairs from three other islands with variable degrees of habitat (crevice) specialization suggested that the lower parasite abundance of P. pundamilia at Makobe could result from both habitat specialization and the evolution of specific resistance. Our results support influences of host genetic differentiation and host ecology in determining infections in this diverse community of sympatric cichlid species. [ABSTRACT FROM AUTHOR]

Abstract: Phylogenetic relationships within the helcionelloid molluscs have been difficult to establish. One of the reasons for this is that qualitative approaches to investigating morphological variation in this group have struggled to identify clear patterns. An alternative method of identifying these patterns is to study these organisms quantitatively. Here this approach is exemplified by employing morphometric methods to investigate patterns of subtle morphological variation in two species of Mackinnonia Runnegar in Bengtson et al. from Cambrian Series 2, Stages 3–4. Specifically, a combination of elliptical Fourier and multivariate analyses were conducted to study intra‐ and interspecific variation in protoconch form as well as variation in ontogenetic trajectory of the teleoconch of two species of Mackinnonia. The material used consists of two assemblages of Mackinnonia rostrata (Zhou & Xiao), from the Shackleton Limestone of Antarctica and Ajax Limestone of Australia, and an assemblage of Mackinnonia taconica (Landing & Bartowski) from the Bastion Formation of Greenland. Results of this study show significant (p < 0.0001) differences in protoconch shape between all three groups. Ontogenetic sequences of outline curves truncated at successive rugae significantly (p < 0.05) discriminate between M. rostrata and M. taconica. These techniques uncovered significant intraspecific morphological variation of disparate assemblages of M. rostrata despite shared qualitative features and structure a conceptual framework for understanding such patterns of variation and put this in the context of the incipient species concept. [ABSTRACT FROM AUTHOR]

[Display omitted] • Hidden introgression is detected through a large geographical cline spanning through approximately 150 km. • Sample choice, small population sizes, and linking population sizes in SNAPP can influence species tree reconstructions. • Species delimitation methods yield contrasting results within Trachydactylus hajarensis. • Dataset down sampling and species delimitation methods need to be cautiously implemented and validated to avoid contributing to taxonomic inflation. With the advent of molecular phylogenetics and the implementation of Multispecies Coalescent-based (MSC) species delimitation methods (SDM), the number of taxonomic studies unveiling and describing cryptic sibling species has greatly increased. However, speciation between early divergent lineages is often defined without evaluating population structure or gene flow, which can lead to false claims of species status and, subsequently, taxonomic inflation. In this study, we focus on the intriguing case of the Arabian gecko Trachydactylus hajarensis (Squamata: Gekkonidae). We generated mitochondrial data (12S rDNA) and genome-wide SNP data (ddRADseq) for 52 specimens to determine phylogenomic relationships, population structure and genetic diversity within this species. Then, we applied a set of different SDMs to evaluate several competing species hypotheses through the MSC. Results show that T. hajarensis is comprised by three well-defined population lineages, two of them in the Hajar Mountains of eastern Arabia, and one in Masirah Island, on the southeastern coast of Oman. Strong mito-nuclear discordances were found between populations inhabiting the Hajar Mountains, but we did not find evidence of current gene flow between them. Surprisingly, discordances in species tree topology were found when different downsampled datasets were used, and especially when linking population sizes, a commonly implemented feature in species tree reconstruction with genomic data. Different SDMs yielded different results, supporting from four species within the group, to T. hajarensis being a single species. With such contrasting results we suggest caution before splitting T. hajarensis. Overall, this study highlights the importance of sample and prior choice and the integration of several SDMs to not incur into taxonomic inflation, providing a set of already available tools to assess population structure, genetic diversity, and SDMs before describing new species. [ABSTRACT FROM AUTHOR]

Abstract Background Published data revealed that two of the 243 structural cuticular proteins of Anopheles gambiae, CPLCG3 and CPLCG4, are implicated in insecticide resistance and a third, CPF3, has far higher transcript levels in M than in S incipient species. We studied the distribution of transcripts for these three genes in the tissues of An. gambiae and the location of the proteins in the cuticle itself to gain information about how these cuticular proteins contribute to their important roles. Our data are consistent with CPLCG3/4 contributing to a thicker cuticle thus slowing penetration of insecticides and CPF3 possibly having a role in the greater desiccation tolerance of the M form. Methods Using RT-qPCR, we established the temporal expression of the genes and by in situ hybridization we revealed the main tissues where their mRNAs are found. Electron microscopy immunolocalization, using secondary antibodies labeled with colloidal gold, allowed us to localize these proteins within different regions of the cuticle. Results The temporal expression of these genes overlaps, albeit with higher levels of transcripts from CPF3 in pharate adults and both CPLCG3 and CPLCG4 are higher in animals immediately after adult eclosion. The main location of mRNAs for all three genes is in appendages and genitalia. In contrast, the location of their proteins within the cuticle is completely different. CPF3 is found exclusively in exocuticle and CPLCG3/4 is restricted to the endocuticle. The other CPF gene expressed at the same times, CPF4, in addition to appendages, has message in pharate adult sclerites. Conclusions The temporal and spatial differences in transcript abundance and protein localization help to account for An. gambiae devoting about 2% of its protein coding genes to structural cuticular proteins. The location of CPLCG3/4 in the endocuticle may contribute to the thickness of the cuticle, one of the recently appreciated components of insecticide resistance, while the location of CPF3 might be related to the greater desiccation resistance of the M form.

Identifying the molecular changes that lead to ecological specialization during speciation is one of the major goals of molecular evolution. One question that remains to be thoroughly investigated is whether ecological specialization derives strictly from adaptive changes and their associated trade-offs, or from conditionally neutral mutations that accumulate under relaxed selection. We used whole-genome sequencing, genome annotation and computational analyses to identify genes that have rapidly diverged between two incipient species of Saccharomyces paradoxus that occupy different climatic regions along a south-west to north-east gradient. As candidate loci for ecological specialization, we identified genes that show signatures of adaptation and accelerated rates of amino acid substitutions, causing asymmetric evolution between lineages. This set of genes includes a glycyl-tRNA-synthetase, GRS2, which is known to be transcriptionally induced under heat stress in the model and sister species S. cerevisiae. Molecular modelling, expression analysis and fitness assays suggest that the accelerated evolution of this gene in the Northern lineage may be caused by relaxed selection. GRS2 arose during the whole-genome duplication (WGD) that occurred 100 million years ago in the yeast lineage. While its ohnolog GRS1 has been preserved in all post-WGD species, GRS2 has frequently been lost and is evolving rapidly, suggesting that the fate of this ohnolog is still to be resolved. Our results suggest that the asymmetric evolution of GRS2 between the two incipient S. paradoxus species contributes to their restricted climatic distributions and thus that ecological specialization derives at least partly from relaxed selection rather than a molecular trade-off resulting from adaptive evolution. [ABSTRACT FROM AUTHOR]

To understand how new species form and what causes their collapse, we examined how reproductive isolation evolves during the speciation process, considering species pairs with little to extensive divergence, including a recently collapsed pair. We estimated many reproductive barriers in each of five sets of stickleback fish species pairs using our own data and decades of previous work. We found that the types of barriers important early in the speciation process differ from those important late. Two premating barriers-habitat and sexual isolation-evolve early in divergence and remain two of the strongest barriers throughout speciation. Premating isolation evolves before postmating isolation, and extrinsic isolation is far stronger than intrinsic. Completing speciation, however, may require postmating intrinsic incompatibilities. Reverse speciation in one species pair was characterized by significant loss of sexual isolation. We present estimates of barrier strengths before and after collapse of a species pair; such detail regarding the loss of isolation has never before been documented. Additionally, despite significant asymmetries in individual barriers, which can limit speciation, total isolation was essentially symmetric between species. Our study provides important insight into the order of barrier evolution and the relative importance of isolating barriers during speciation and tests fundamental predictions of ecological speciation. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genomes are sequenced in two individuals representing two morphological forms, ‘usual’ (U) and ‘gray’ (G), of the short-spined sea urchin Strongylocentrotus intermedius. The genome sequences are 15,705 bp in size, and the gene arrangement, composition, and size are very similar to the other sea urchin mitochondrial genomes published previously. A low level of sequence divergence (Dxy = 0.0083 ± 0.0007) is detected between the forms. The GenBank (KC490912) mt genome of S. intermedius is much closer to the U form (Dxy = 0.0013 ± 0.0003) than to the G form (Dxy = 0.0085 ± 0.0006), demonstrating unique evolutionary trajectories for each form, which we previously suggested based on the bindin gene and symbiont analyses.

1. Although divergence via host-plant shifting is a common theme in the speciation of some phytophagous insects, it is not clear whether host shifts are typically initiators of speciation or if they instead contribute to divergence events already in progress. While host shifts appear to be generally associated with speciation events for flies in the genus Strauzia, three sympatric varieties of the sunflower fly [ Strauzia longipennis ( Wiedemann)] co-occur on the same host plant in the Midwestern United States and may have evolved reproductive barriers without a host shift. 2. The strength of two prezygotic reproductive barriers was compared among the three S. longipennis varieties: one barrier that is often associated with divergent ecological selection (allochronic isolation), and another that is more likely to be independent of ecological selection (pre-copulatory sexual isolation). The presence and relative strength of each barrier between fly varieties were evaluated using microsatellites, no choice mating experiments, studies of allochronic isolation, and field collection data. 3. Evidence for both allochronic isolation and pre-copulatory sexual isolation was detected between the three varieties of S. longipennis. The measure of isolation calculated for each barrier between the three varieties was lower than measures calculated between different species of Strauzia found on different hosts, suggesting that subsequent host shifts may increase the degree of reproductive isolation. For Strauzia and other specialist insects, some reproductive isolation may evolve prior to, and indeed may facilitate, host shifts. [ABSTRACT FROM AUTHOR]

The Carambola fruit fly, Bactrocera carambolae, is an invasive pest in Southeast Asia. It has been introduced into areas in South America such as Suriname and Brazil. Bactrocera carambolae belongs to the B. dorsalis species complex, and seems to be separated from B. dorsalis based on morphological and multilocus phylogenetic studies. Even though the Carambola fruit fly is an important quarantine species and has an impact on international trade, knowledge of the molecular ecology of B. carambolae, concerning species status and pest management aspects, is lacking. Seven populations sampled from the known geographical areas of B. carambolae including Southeast Asia (i.e., Indonesia, Malaysia, Thailand) and South America (i.e., Suriname), were genotyped using eight microsatellite DNA markers. Genetic variation, genetic structure, and genetic network among populations illustrated that the Suriname samples were genetically differentiated from Southeast Asian populations. The genetic network revealed that samples from West Sumatra (Pekanbaru, PK) and Java (Jakarta, JK) were presumably the source populations of B. carambolae in Suriname, which was congruent with human migration records between the two continents. Additionally, three populations of B. dorsalis were included to better understand the species boundary. The genetic structure between the two species was significantly separated and approximately 11% of total individuals were detected as admixed (0.100 ≤ Q ≤ 0.900). The genetic network showed connections between B. carambolae and B. dorsalis groups throughout Depok (DP), JK, and Nakhon Sri Thammarat (NT) populations. These data supported the hypothesis that the reproductive isolation between the two species may be leaky. Although the morphology and monophyly of nuclear and mitochondrial DNA sequences in previous studies showed discrete entities, the hypothesis of semipermeable boundaries may not be rejected. Alleles at microsatellite loci could be introgressed rather than other nuclear and mitochondrial DNA. Bactrocera carambolae may be an incipient rather than a distinct species of B. dorsalis. Regarding the pest management aspect, the genetic sexing Salaya5 strain (SY5) was included for comparison with wild populations. The SY5 strain was genetically assigned to the B. carambolae cluster. Likewise, the genetic network showed that the strain shared greatest genetic similarity to JK, suggesting that SY5 did not divert away from its original genetic makeup. Under laboratory conditions, at least 12 generations apart, selection did not strongly affect genetic compatibility between the strain and wild populations. This knowledge further confirms the potential utilization of the Salaya5 strain in regional programs of area-wide integrated pest management using SIT. [ABSTRACT FROM AUTHOR]

Parasitic wasps are among the most speciose of all animals yet the drivers and mechanisms underlying their remarkable diversity are not well understood. Cotesia congregata (Say) and host, Manduca sexta (L.), have long-served as a model system for host-parasite and tritrophie interactions at multiple levels, as well as the evolution of symbiotic coevolved bracoviruses that suppress host defenses to parasitism. We investigated potential barriers to reproduction between two genetically differentiated host-foodplant complex sources of C. congregata originating from caterpillar hosts, M. sexta on tobacco ("MsT wasps") or Ceratomia catalpae (Boisduval) on catalpa ("CcC wasps"). Both MsT and CcC wasps displayed ~30% lower responses to cuticular washes of females from the alternate complex. Male courtship songs differed with respect to frequency, absolute amplitude, and duration of song elements. Despite differences in courtship behaviors, MsT and CcC wasps mated and produced offspring in the laboratory. However, mating success of F1 MsT♂ × CcC♀ wasps was lower and fitness of F1 CcC♂ × MsT♀ hybrids was greatly reduced due to encapsulation and melanization of wasp eggs in M. sexta. Heritable differences in brood size and secondary sex ratios of emergent adults indicate hostspecific adaptations. Overall, results demonstrate the evolution and accumulation of both pre- and postzygotic barriers to reproduction, two of which are asymmetrical, and offer additional support that MsT and CcC wasp are incipient species. [ABSTRACT FROM AUTHOR]

Grebes (Aves: Podicipedidae) are a threatened family containing species that vary widely in demography. Podicipedidae includes several species that are either rare and confined to a single lake basin, or abundantly distributed across several continents. The most speciose genus, Podiceps, particularly the eared grebe lineage, best reflects this curious demographic pattern by representing the most abundant of extant grebes, several critically endangered species, and a recently extinct species. Here, we obtained genetic data from 3 mitochondrial markers to make phylogenetic and population genetic inferences about the eared grebe clade. Using DNA from tissue, feather, skin, and toe pads, our sampling encompassed all species and subspecies, including the extinct Colombian Grebe ( Podiceps andinus) and migratory and resident populations of the North American Black-necked Grebe ( P. nigricollis californicus). Bayesian inference yielded novel insights into the dynamics of this group, particularly the recent ecological isolation and incipient speciation of the Colombian and Junin ( P. taczanowskii) grebes, as determined from limited genetic divergence and rapid evolution of plumage color and bill shape (elongation, deepening of the culmen). DNA barcode and cytochrome b distances supported these inferences. Population genetic and divergence time analyses further revealed that the abundance of the North American Black-necked Grebe is likely associated with mid-Pleistocene dispersal from South America followed by late Pleistocene expansion during a time when hypersaline lake habitat accommodated large populations of staging birds. In conclusion, the demographic variation among species in the eared grebe group can be explained by recent ecological speciation of both a sympatric and an allopatric nature. Future investigation is warranted to determine whether this pattern of speciation and associated rapid phenotypic divergence can be extended to other grebe taxa. Los Podicipedidae son una familia amenazada que incluye especies que varían enormemente en su demografía. Los Podicipedidae incluyen varias especies que o son raras y están confinadas a una única cuenca de un lago, o están distribuidas abundantemente a lo largo de varios continentes. El género Podiceps, que es el que contiene más especies, particularmente el linaje 'con penachos', es el que mejor refleja este curioso patrón demográfico, pues incluye las especies actuales más abundantes, varias especies en peligro crítico y las especies recientemente extintas. En este estudio, obtuvimos datos genéticos a partir de tres marcadores mitocondriales para hacer inferencias filogenéticas y de genética poblacional sobre los Podiceps con penachos. Usamos ADN proveniente de tejidos, plumas, piel y almohadillas de los dedos para abarcar a todas las especies y subespecies, incluyendo la especie extinta P. andinus y las poblaciones residentes y migratorias de P. nigricollis californicus. Las inferencias bayesianas brindaron nuevas ideas sobre la dinámica de este grupo, particularmente sobre el aislamiento ecológico reciente y la incipiente especiación de P. andinus y P. taczanowskii, determinada por una divergencia genética limitada y la rápida evolución del color del plumaje y la forma del pico (elongación y profundización del culmen). El código de barras de ADN y las distancias del cytochrome b apoyan estas inferencias. La genética poblacional y los análisis del tiempo de divergencia revelan adicionalmente que la abundancia de P. nigricollis californicus está probablemente asociada con una dispersión a mediados del Pleistoceno desde América del Sur seguida por una expansión a fines del Pleistoceno durante un período en que el hábitat hipersalino del lago soportó grandes poblaciones de aves. En conclusión, la variación demográfica entre las especies de Podiceps con penachos puede explicarse por especiación ecológica reciente de naturaleza tanto simpátrica como alopátrica. Es necesario realizar futuras investigaciones para determinar si este patrón de especiación y de divergencia fenotípica rápida asociado puede extenderse a otros taxa de los Podicipedidae. Palabras clave: especies incipientes, expansión demográfica, filogenia, forma del pico, Podicipedidae [ABSTRACT FROM AUTHOR]

The taxonomic status and biogeography of the North American Raphia species is reviewed using adult morphology, larval host plants, geographic phenotypic variation, and variation of mtDNA COI barcode sequences. Lack of diagnostic morphological differences, combined with relatively low mtDNA barcode divergences and clinal phenotypic variation in key geographic regions indicate that the six previously recognized species of North American Raphia are best interpreted as parapatric subspecies. Raphia frater abrupta Grote, stat. n., R. f. coloradensis Putnam-Cramer, stat. r., R. f. piazzi Hill, stat. n., and R. f. elbea Smith, stat. n., are accordingly revised to subspecies of R. frater Grote. Type locality restrictions are provided for Raphia abrupta and Raphia frater and a neotype is designated for Raphia frater var. coloradensis. [ABSTRACT FROM AUTHOR]

Predation is a major evolutionary force driving speciation. The threat-sensitive response hypothesis predicts that prey adjust and balance the time spent on a costly antipredator response with other activities that enhance their fitness. Thus, prey able to develop an antipredator response proportional to risk intensity should have a selective advantage., Knowledge on how evolution has shaped threat sensitivity among closely related species exposed to different predation pressures is scarce, prompting investigations to better predict and explain its effect on communities., We explored and compared the antipredator response of aquatic mosquito larvae in three sibling species of the Anopheles gambiae complex, with contrasting larval biologies in Burkina Faso. Anopheles arabiensis and An. gambiae sensu stricto breed in temporary water collections where predator densities are low, whereas Anopheles coluzzii is able to thrive in permanent pools where the predation pressure is much higher. We hypothesized that the increase and decline of behavioural antipredator responses might differ between the three species over time. To test this hypothesis, progenies of field-collected mosquitoes were experimentally exposed to a range of soluble predation cues and their response was monitored for up to 48 h., The three species were all threat sensitive but their reaction norms differed. For the range of concentrations tested, An. coluzzii larvae gradually increased in antipredator response, whereas An. gambiae larvae readily displayed antipredator behaviour at low concentrations leading to a saturation of the response for high cue concentrations. An. arabiensis displayed a narrower reaction norm with low response intensity. Larval instars did not differ in their threat sensitivity. The antipredator behaviour of the three species waned after about 1 h of exposure. Early instars tended to express antipredation behaviour for longer than did older instars., This study provides information on how aquatic prey species with an aerial adult stage manage larval predation risk over time according to cue concentrations and suggests that different predation pressures might play a role as a disruptive selective force fostering habitat segregation and speciation within the An. gambiae complex. The evolution of phenotypic plasticity is further discussed in the light of divergent predation pressures. [ABSTRACT FROM AUTHOR]

Background Published data revealed that two of the 243 structural cuticular proteins of Anopheles gambiae, CPLCG3 and CPLCG4, are implicated in insecticide resistance and a third, CPF3, has far higher transcript levels in M than in S incipient species. We studied the distribution of transcripts for these three genes in the tissues of An. gambiae and the location of the proteins in the cuticle itself to gain information about how these cuticular proteins contribute to their important roles. Our data are consistent with CPLCG3/4 contributing to a thicker cuticle thus slowing penetration of insecticides and CPF3 possibly having a role in the greater desiccation tolerance of the M form. Methods Using RT-qPCR, we established the temporal expression of the genes and by in situ hybridization we revealed the main tissues where their mRNAs are found. Electron microscopy immunolocalization, using secondary antibodies labeled with colloidal gold, allowed us to localize these proteins within different regions of the cuticle. Results The temporal expression of these genes overlaps, albeit with higher levels of transcripts from CPF3 in pharate adults and both CPLCG3 and CPLCG4 are higher in animals immediately after adult eclosion. The main location of mRNAs for all three genes is in appendages and genitalia. In contrast, the location of their proteins within the cuticle is completely different. CPF3 is found exclusively in exocuticle and CPLCG3/4 is restricted to the endocuticle. The other CPF gene expressed at the same times, CPF4, in addition to appendages, has message in pharate adult sclerites. Conclusions The temporal and spatial differences in transcript abundance and protein localization help to account for An. gambiae devoting about 2% of its protein coding genes to structural cuticular proteins. The location of CPLCG3/4 in the endocuticle may contribute to the thickness of the cuticle, one of the recently appreciated components of insecticide resistance, while the location of CPF3 might be related to the greater desiccation resistance of the M form. [ABSTRACT FROM AUTHOR]

Aim Previous work on the tidepool copepod Tigriopus californicus revealed a curious case of incipient speciation at the southern end of the species' range in Baja California, Mexico. The present study expands on the geography of this pattern and tests for congruence between reproductive and phylogenetic patterns. Location The Pacific coast of North America, from central Baja California to south-eastern Alaska (27-57° N), including the full range of T. californicus. Methods Primary techniques included mating experiments (> 4000 crosses), phylogeny reconstruction (mitochondrial cytochrome c oxidase subunit I) and screening of single nucleotide polymorphisms ( SNPs, 42 loci). Analyses used > 8000 copepods for the mating experiments, 86 copepods for the phylogeny and 41 copepods for the SNP assays. Phylogenies were constructed using Bayesian, maximum likelihood and maximum parsimony methods. Results Populations were found to fall into three reproductive groups: northern and southern groups that were reproductively isolated from each other, and an intermediate group that could serve as a conduit for gene flow. The northern and intermediate populations fell into one clade while all southern populations fell into a second clade. These two clades are now separated by less than 12 km at latitude 29.35° N. Nuclear SNP data for a subset of locations confirmed striking divergence between populations on either side of this boundary. The second (southern) clade was further subdivided into two clades separated by the lagoon region of Guerrero Negro (latitude 28° N). Main conclusions Reproductive assays and molecular data (both mitochondrial and nuclear) reveal a sharp break at 29.35° N, a region with no obvious barriers to dispersal, with no evidence for mixing across this narrow transition zone. Results also showed a milder break at the Guerrero Negro Lagoon (28° N), a location where breaks have been reported for other taxa. [ABSTRACT FROM AUTHOR]

Early in speciation, as populations undergo the transition from local adaptation to incipient species, is when a number of transient, but potentially important, processes appear to be most easily detected. These include signatures of selective sweeps that can point to asymmetry in selection between habitats, divergence hitchhiking, and associations of adaptive genes with environments. In a genomic comparison of ecotypes of the prairie sunflower, Helianthus petiolaris, occurring at Great Sand Dunes National Park and Preserve (Colorado), we found that selective sweeps were mainly restricted to the dune ecotype and that there was variation across the genome in whether proximity to the nondune population constrained or promoted divergence. The major regions of divergence were few and large between ecotypes, in contrast with an interspecific comparison between H. petiolaris and a sympatric congener, Helianthus annuus. In general, the large regions of divergence observed in the ecotypic comparison swamped locus-specific associations with environmental variables. In both comparisons, regions of high divergence occurred in portions of the genetic map with high marker density, probably reflecting regions of low recombination. The difference in genomic distributions of highly divergent regions between ecotypic and interspecific comparisons highlights the value of studies spanning the spectrum of speciation in related taxa. [ABSTRACT FROM AUTHOR]

The ecological interactions parasitic insects have with their hosts may contribute to their prodigious diversity, which is unrivaled among animals. Many insects assumed to be polyphagous generalists have been shown to consist of several differentiated races, each occupying a different host-niche. The sunflower maggot fly, Strauzia longipennis, has long been thought to consist of two or more races due to its substantial intra-specific morphological variation. Here, we use nuclear and mitochondrial markers to test the hypothesis that S. longipennis is a complex of two or more partially reproductively isolated races. We collected S. longipennis flies as pupae from roots of Jerusalem artichoke ( Helianthus tuberosus) and as adults swept from leaves of mature H. tuberosus across the breadth of a field season. Flies were scored for morphological variety ( typica or vittigera), mitochondrial haplotype (A or B) and a panel of 176 AFLP loci. Bayesian clustering and neighbor-joining phylogenetic analyses of AFLP data supported the existence of at least three, possibly four, genetic races of Strauzia (clusters I, II, III, and V), as well as a small number of putative interracial hybrids (cluster IV). Clusters I and III each consisted of flies of both morphological varieties and both haplotype groups, while flies in cluster II were all of variety typica and all but one was of mitochondrial haplotype B. Flies in cluster II were also collected only as adults on H. tuberosus and not among flies reared from pupae collected from H. tuberosus roots, suggesting that they use a different plant as their larval host. Mean capture date was significantly different between flies of each genetic race, indicating that partial allochronic isolation may be one contemporary barrier to gene flow between races. Evidence that mitochondrial genomes and morphological traits have moved between lineages implies a model of speciation-with-gene-flow for S. longipennis races. [ABSTRACT FROM AUTHOR]

Predation is a major evolutionary force driving speciation. Identifying the stimuli prompting anti-predator responses is essential for unravelling the proximate mechanisms of anti-predator adaptations and for understanding how predation impacts species diversification., Here, we explore for the first time the divergence in the use of cues of predation risk by different incipient species of mosquitoes within the Anopheles gambiae complex. We examined the anti-predator responses to various predation cues by the aquatic larvae of Anopheles arabiensis and the two molecular forms, M and S, of Anopheles gambiae s.s. sampled from wild populations in Burkina Faso naturally exposed to different predator densities., The larvae altered their behaviour in response to various predation cues, shifting from the surface of the water to a less exposed location on the walls of the experimental arena. There were important differences in the use of predation cues between populations sharing the same larval development sites and, within the M form, related to predation pressure at their site of origin. Anopheles arabiensis larvae, which develop in small temporary waterbodies, relied only on physical cues signalling the presence of a predator to mount a vigilance response, whereas the sympatric larvae of the M and S forms of An. gambiae used both physical and chemical cues to fine-tune their response. M-form larvae, developing in permanent aquatic habitats with high densities of predators, responded chiefly to chemical stimuli ensuing from acute predation., Our results suggest that predation might play a role as a disruptive selective force promoting ecological divergence within the An. gambiae complex and, more recently, between the M and S molecular forms. Notably, beyond interspecific differences in the use of predation cues, our study also documented phenotypic differences within the M form based on predation pressure at their site of origin, suggesting that a process of ecological divergence is generating species 'forerunners' within the An. gambiae complex in the wild. [ABSTRACT FROM AUTHOR]

In a genome alignment of five individuals of the ascomycete fungus Zymoseptoria pseudotritici, a close relative of the wheat pathogen Z. tritici (synonym Mycosphaerella graminicola), we observed peculiar diversity patterns. Long regions up to 100 kb without variation alternate with similarly long regions of high variability. The variable segments in the genome alignment are organized into two main haplotype groups that have diverged ∼3% from each other. The genome patterns in Z. pseudotritici are consistent with a hybrid speciation event resulting from a cross between two divergent haploid individuals. The resulting hybrids formed the new species without backcrossing to the parents. We observe no variation in 54% of the genome in the five individuals and estimate a complete loss of variation for at least 30% of the genome in the entire species. A strong population bottleneck following the hybridization event caused this loss of variation. Variable segments in the Z. pseudotritici genome exhibit the two haplotypes contributed by the parental individuals. From our previously estimated recombination map of Z. tritici and the size distribution of variable chromosome blocks untouched by recombination we estimate that the hybridization occurred ∼380 sexual generations ago. We show that the amount of lost variation is explained by genetic drift during the bottleneck and by natural selection, as evidenced by the correlation of presence/ absence of variation with gene density and recombination rate. The successful spread of this unique reproductively isolated pathogen highlights the strong potential of hybridization in the emergence of pathogen species with sexual reproduction. [ABSTRACT FROM AUTHOR]

Ecology Letters (2010) 13: 716–727 Understanding the maintenance and origin of biodiversity is a formidable task, yet many ubiquitous ecological patterns are predicted by a surprisingly simple and widely studied neutral model that ignores functional differences between species. However, this model assumes that new species arise instantaneously as singletons and consequently makes unrealistic predictions about species lifetimes, speciation rates and number of rare species. Here, we resolve these anomalies – without compromising any of the original model's existing achievements and retaining computational and analytical tractability – by modelling speciation as a gradual, protracted, process rather than an instantaneous event. Our model also makes new predictions about the diversity of ‘incipient’ species and rare species in the metacommunity. We show that it is both necessary and straightforward to incorporate protracted speciation in future studies of neutral models, and argue that non-neutral models should also model speciation as a gradual process rather than an instantaneous one. [ABSTRACT FROM AUTHOR]

Abstract: Relationships of the 133 species of the subfamily Carduelinae (Fringillidae) are poorly resolved. For a more robust phylogenetic resolution, we sequenced two mitochondrial protein-coding genes (ATPase 6 and ND3), two nuclear introns (myoglobin intron 2 and transforming growth factor-β2 intron 5) and one nuclear protein-coding gene (c-mos) from 50 cardueline taxa representing especially the large genera Serinus and Carduelis. A total of 2934bp obtained was subjected to maximum likelihood and Bayesian inference. Three of the five loci, as well as the combined dataset recovered the monophyly of the basal placement of Fringilla in the monophyletic Fringillidae, and the monophyly of the Carduelinae. While relationships within this group are moderately resolved by some individual gene trees (myoglobin and c-mos loci), high nodal support is provided in other individual gene trees and the combined tree. Among the well resolved terminal cardueline groups, Linurgus, Loxia and Pyrrhula are found to be monophyletic while genera Carpodacus, Carduelis and Serinus appear para- or polyphyletic. Within Serinus and Carduelis, the obtained phylogenetic structure corresponds well with the subdivisions suggested by H.E. Wolters, based on traditional methods. Thus, we support his generic subdivision (Ochrospiza, Dendrospiza and Crithagra for Serinus, and Chloris, Spinus, Sporagra, Pseudomitris, Acanthis and Linaria for Carduelis). Otherwise, we notice several cases of significant genetic divergence within traditional species suggesting incipient speciation in Linurgus olivaceus, Loxia curvirostra, Serinus mozambicus and Serinus burtoni. Some of these cases need a further phylogeographical study with a denser geographical sampling but for the case the most noteworthy, that of Serinus burtoni, we suggest a taxonomic change in this study. [Copyright &y& Elsevier]

Many vertebrate taxa show genetic differentiation between populations in northern and southern California. This genetic pattern may reflect a common environmental history for these species. For example, a previous study of the California vole (Microtus californicus) showed morphological divergence between populations in northern and southern California and decreased fertility in crosses between the populations. To investigate phylogeographic differences in this species, we assessed variation in mitochondrial and nuclear DNA throughout much of its distribution from Oregon to Baja California. We generated molecular data (mitochondrial cytochrome b and nuclear acid phosphatase V intron [AP5]) for 178 individuals. Examination of these data suggests 2 phylogeographic groups that are largely discordant with the boundaries of 17 currently recognized subspecies. Estimates of pairwise genetic divergence between these groups for cytochrome b are as high as 4.46% uncorrected p. Sequence data for AP5 also indicate a division between populations of M. californicus in northern and southern California. Examination of data from the mitochondrial and nuclear markers together suggests limited gene flow between clades. These data are concordant with other studies that suggest that mountain ranges in California were important in within- and possibly between-species divergence and subsequent contact. The general distribution of each clade, combined with a geographic information system analysis of known capture sites, suggests that clade divergence may be correlated with ecological differences. Our study creates a new framework for reevaluating morphological and ecological diversity in this species, and with more diverse markers, possibly the recognition of 2 species of California voles. [ABSTRACT FROM AUTHOR]

Abstract: While models of sympatric speciation are motivated in part by multi-species adaptive radiations such as the Cameroon crater lake cichlids, existing models have focused on bifurcation into a single pair of daughter species. This paper shows that a familiar model of sympatric speciation, driven by intraspecific competition and assortative mating based on ecological characters values, can yield multiple daughter species if individual niche widths are sufficiently restricted. Surprisingly, the multi-species outcome is not produced by successive bifurcation events, but by simultaneous divergence resulting in a hard polytomy. This result is sensitive to a number of assumptions, whose violation may prevent speciation. In some cases when speciation fails, the population instead ends in a state that closely resembles incipient species pairs, with an ecological polymorphism and partial reproductive isolation. However, this polymorphism is stable and does not lead to complete reproductive isolation, suggesting that empirical cases of incipient species pairs may not always end in speciation. [Copyright &y& Elsevier]

Incipient species groups or young adaptive radiations such as crossbills (Aves: Loxia) present the opportunity to investigate directly the processes occurring during speciation. New World crossbills include white-winged crossbills ( Loxia leucoptera), Hispaniolan crossbills ( Loxia megaplaga), and red crossbills ( Loxia curvirostra complex), the last of which is comprised of at least nine morphologically and vocally differentiated forms (‘call types’) where divergent natural selection for specialization on different conifer resources has been strongly implicated as driving diversification. Here we use amplified fragment length polymorphism (AFLP) markers to investigate patterns of genetic variation across populations, call types, and species of New World crossbills. Tree-based analyses using 440 AFLP loci reveal strongly supported clustering of the formally recognized species, but did not separate individuals from the eight call types in the red crossbill complex, consistent with recent divergence and ongoing gene flow. Analyses of genetic differentiation based on inferred allele frequency variation however, reveal subtle but significant levels of genetic differentiation among the different call types of the complex and indicate that between call-type differentiation is greater than that found among different geographic locations within call types. Interpreted in light of evidence of divergent natural selection and strong premating reproductive isolation, the observed genetic differentiation suggests restricted gene flow among sympatric call types consistent with the early stages of ecological speciation. [ABSTRACT FROM AUTHOR]

The desaturase-2 (desat2) locus of Drosophila melanogaster has two alleles whose frequencies vary geographically: one (the "Z" allele) is found primarily in east Africa and the Caribbean, and the other (the "M" allele) occurs in other parts of the world. It has been suggested that these alleles not only cause sexual isolation between races, but that their distribution reflects differential adaptation to climate: Z alleles are supposedly adapted to tropical conditions and M alleles to temperate ones. This has thus been viewed as a case of reproductive isolation evolving as a pleiotropic byproduct of adaptation. Here we reinvestigate this presumed climatic adaptation, using transgenic lines differing in the nature of their desat2 alleles. We were unable to replicate earlier results showing that carriers of M alleles are uniformly more cold resistant and less starvation resistant than carriers of Z alleles. It is thus doubtful whether the distribution of these alleles reflects natural selection involving climate. Mating studies of transgenic lines show some evidence for sexual isolation due to desat2. However, work on other, wild-type lines, as well as observations on the nature of sexual isolation, suggest that this conclusion--and thus the relationship between this locus and mating discrimination between races of D. melanogaster--may also be doubtful. [ABSTRACT FROM AUTHOR]

Polymorphic SINE insertions can be useful markers for assessing population structure and differentiation. Maque is a family of SINE elements which, based on bioinformatic analysis, was suggested to have been active recently in Anopheles gambiae, the major vector of malaria. Here, we report the development of polymorphic Maque insertions as population genetic markers in A. gambiae, and the use of these markers to better characterize divergence on the X chromosome between A. gambiae M and S molecular forms in populations from Burkina Faso and Mali. Our data are consistent with the recent activity of Maque. Phylogenetic analysis suggests that at least two recently active lineages may have a role in mediating genome evolution. We found differences in element insertion frequency and sequence between the M and S populations analysed. Significant differentiation was observed between these two groups across a 6 Mb region at the proximal (centromeric) end of the X chromosome. Locus-specific FST values ranged from 0.14 to 1.00 in this region, yet were not significantly different from zero in more distal locations on the X chromosome; the trend was consistent in populations from both geographical locales suggesting that differentiation is not due to local adaptation. Strong differentiation between M and S at the proximal end of the X chromosome, but not outside this region, suggests the action of selection counteracting limited gene flow between these taxa and supports their characterization as incipient species. [ABSTRACT FROM AUTHOR]

Anopheles funestus Giles is one of the most important vectors of malaria in sub-Saharan Africa. The population structure of this mosquito in Burkina Faso, West Africa based on chromosomal inversion data led to the description of two chromosomal forms, Kiribina and Folonzo. Because both forms co-occur in the same locales yet differ significantly, both in the frequency of inverted arrangements on chromosome arms 3R and 2R and in vectorial capacity, they were hypothesized to be emerging species with at least partial barriers to gene flow. This hypothesis would be strengthened by molecular evidence of differentiation between Kiribina and Folonzo at loci outside chromosomal inversions. We surveyed molecular variation in sympatric populations of the two forms using sequences from the mitochondrial ND5 gene and genotypes at sixteen microsatellite loci distributed across the genome. Both classes of marker revealed slight but significant differentiation between the two forms (mtDNA FST = 0.023, P < 0.001; microsatellite FST = 0.004, P<0.001; Rst = 0.009, P = 0.002). Locus-by-locus analysis of the microsatellite data showed that significant differentiation was not genome-wide, but could be attributed to five loci on chromosome 3R ( FST = 0.010, P<0.001; Rst = 0.016, P = 0.002). Importantly, three of these loci are outside of, and in linkage equilibrium with, chromosomal inversions, suggesting that differentiation between chromosomal forms extends beyond the inversions themselves. The slight overall degree of differentiation indicated by both marker classes is likely an underestimate because of recent population expansion inferred for both Folonzo and Kiribina. The molecular evidence from this study is consistent with the hypothesis of incipient speciation between Kiribina and Folonzo. [ABSTRACT FROM AUTHOR]

We analysed insertion-deletion patterns in 159 published sequences of ITS1 for Caulerpa taxifolia (Vahl) C. Agardh collected from 55 localities throughout the species' range. Five indelotypes (I) were identified that represented a sequential loss of insertions from the ancestral type (I 3 ) to the most derived type (I 0 ). The I 3 consists of the complete ITS1 sequence, which is also characteristic of three outgroup species. In contrast, the I 0 has lost three inserts from the complete sequence and is associated with the invasive forms found in the Mediterranean, California and southeastern Australia. The I 2 was found in samples from the Red Sea and Jakarta, whereas the I 1 was associated with samples from Australia and New Caledonia. When mapped onto location and habitat, these ordered character-states reveal a widespread distribution of I 3 and (probably) I 2 , which are associated with offshore coral reefs and clear oligotrophic waters. The I 1 and I 0 comprise a paraphyletic assemblage of the more derived types harbouring two or three deletions and occurring together along mainland Australian coasts in more turbid environments. The presence of I 0 , I 1a and I 1b along the Australian coast indicates that the ecological transition that gave rise to the coastal ecotype has been present at least since the time of the mutation between I 2 and I 1 . These types of fixed differences confirm that C. taxifolia consists of at least two incipient species--the coastal form being an offshoot derived from the clear-water ecotypes. The finding of indelotype I 1a in an isolate from Sousse (Tunisia) confirms a second Mediterranean introduction and highlights the urgency for further research in the evolutionary diversification of one of the most intriguing and troublesome seaweeds. [ABSTRACT FROM AUTHOR]

Evolution Canyon in Lower Nahal Oren, Mount Carmel, Israel has been identified as a location promoting sympatric speciation. Several previous studies on Drosophila melanogaster populations from the two disparate slopes of the canyon suggest that these two populations are experiencing incipient speciation. However, recent microsatellite data did not reveal the expected level of population differentiation. Given the importance of this system for studying speciation, we set out to test two predictions of the incipient speciation hypothesis--genetic differentiation and sexual isolation. We sequenced six different Acp genes from isofemale lines from the south-facing slope (11 lines) and northfacing slope (nine lines) of Evolution Canyon. We found no evidence of genetic differentiation between the two slopes (F[subST] = -0.03). We also conducted mate choice tests, using intraslope F[sub1] hybrids between different isofemale lines. There was no significant departure from random mating in mixtures of flies from the two slopes. Our results provide further indication that it is unlikely these two populations are experiencing incipient speciation. We discuss our results in light of the discrepancies that have been published on this enigmatic D. melanogaster system from Evolution Canyon. [ABSTRACT FROM AUTHOR]

Abstract. The mosquito Anopheles gambiae Giles sensu stricto (Diptera: Culicidae), the principal vector of malaria in West Africa, comprises several chromosomal forms (e.g. Bissau, Forest, Mopti, Savanna) associated with climatic zones. Here we show how climate data can be used to map the geographical distribution of these chromosomal forms. The climate at 144 sites surveyed for mosquitoes in West Africa between 1971 and 92 was determined using computerized climate surfaces. Forest and Bissau forms occurred at relatively wet sites: median annual precipitation 1325 mm and 1438 mm, respectively, interquartile ranges (IQR) 1144–1858 mm and 1052–1825 mm), whilst the Mopti form was found at dry sites (annual 938 mm, IQR 713–1047 mm) and the Savanna form at sites intermediate between the wet and dry forms (annual 1067 mm, IQR 916–1279). Logistic regression analyses of the climate variables were carried out on a stratified random sample of half the sites. The resulting models correctly classified over 80% of the sites for presence or absence of each chromosomal form. When these models were tested against excluded sites they were also correct at over 80% of sites. The combined data produced models that were correct at over 86% of sites. Mean annual precipitation, evapotranspiration, minimum temperature and maximum temperature were the most important climate variables correlated with the distribution of these forms of An. gambiae. We used the logistic models to map the distribution of each chromosomal form within the reported range for An. gambiae s.s. in West Africa employing a geographical information system. Our maps indicate that each chromosomal form favours particular climate envelopes in well-defined ecoclimatic zones, although these forms are sympatric at the edges of their ranges. This study demonstrates that climate can be used to map the distribution of chromosomal forms of insects across large areas. [ABSTRACT FROM AUTHOR]