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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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

Abstract Patterns of DNA sequence variation in the ribosomal DNA (rDNA) second internal transcribed spacer (ITS2) and five unlinked single-copy nuclear loci were examined for evidence of reproductive isolation among four chromosomally recognized taxa of Anopheles gambiae from West Africa: Savanna, Bamako, Mopti and Forest, as well as sibling species An. arabiensis and An. merus. Included among the single-copy loci were three sequence-tagged random amplified polymorphic DNA (RAPD) loci, two of which (R15 and R37) had been reported as discriminating between Mopti and other chromosomal forms. Each of the five single-copy sequences were highly polymorphic in most samples. However, the R15 and R37 loci had no diagnostic value, and therefore are not recommended as tools in recognition of field-collected An. gambiae chromosomal forms. Although pairwise comparisons between species generally revealed significant levels of differentiation at all five loci, variation was not partitioned by chromosomal form within An. gambiae at any single-copy locus examined. The few exceptions to these trends appear related to a location either inside or nearby chromosomal inversions. At the tryptophan oxygenase locus inside inversion 2Rb, variation was structured only by inversion orientation and not by taxonomic designation even between An. gambiae and An. arabiensis, providing the first molecular evidence that the 2Rb inversion was transferred between species by introgressive hybridization. By contrast, the rDNA showed fixed differences between species and a difference diagnostic for Mopti, consistent with effective, if not complete, reproductive isolation. The apparent disagreement between the data from this locus and multiple single-copy loci within An. gambiae may be explained by the much lower effective population size of rDNA, owing to concerted evolution, which confers increased sensitivity at much shorter divergence times. Taken together with the accompanying reports by, and,... [ABSTRACT FROM AUTHOR]