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67 results for “Speciation: genetics”
Data from: New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)
Sustainable management of sea mullet (Mugil cephalus) fisheries needs to account for recent observations of regional-scale differentiation. Population genetic analysis is sought to assess the situation of this ecologically and economically important fish species in eastern Australian waters. Here, we report (i) new population genetic markers [single nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first estimates of spatial genetic differentiation and (iii) prospective power tests for designing more comprehensive studies. Six DNA samples from three sampling regions (North Queensland, South Queensland and central New South Wales) on the eastern coast of Australia were used to prepare restriction site associated DNA (RAD) tag libraries from genomic DNA digested with EcoRI and MseI. A pooled sample of regional RAD tag libraries was sequenced using the Roche GS-FLX Titanium platform. A total of 172 837 raw reads (17.4 Mbp) were retrieved, 95 500 of which were used to discover 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated based on 63 additional DNA samples genotyped using the Sequenom MassArray (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40% of these marking fixed variants between northern and southern sampling regions. Our preliminary findings indicate a multispecies fishery stock of M. cephalus in eastern Australian waters, but suggest that strong genetic differentiation occurs north of major fishing grounds. Low potential differentiation within major fishing grounds (e.g. FST = 0.0025) can be resolved with a likely power ≥67% by using standard sample sizes of 50 and validated subsets of available markers.
Data from: Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact
Background: Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane's Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. Results: Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane's Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. Conclusions: This study adds to a growing list of studies that support predictions of Haldane's Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane's Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumicrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat.
Data from: The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing
During speciation-with-gene-flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome-wide patterns of genetic differentiation, especially if the variance due to the previously mentioned factors is partitioned. In North American lake whitefish (Coregonus clupeaformis), glacial lineages that diverged in allopatry about 60,000 years ago and came into contact 12,000 years ago have independently evolved in several lakes into two sympatric species pairs (a normal benthic and a dwarf limnetic). Variable degrees of reproductive isolation between species pairs across lakes offer a continuum of genetic and phenotypic divergence associated with adaptation to distinct ecological niches. To disentangle the complex array of genetically based barriers that locally reduce the effective migration rate between whitefish species pairs, we compared genome-wide patterns of divergence across five lakes distributed along this divergence continuum. Using restriction site associated DNA (RAD) sequencing, we combined genetic mapping and population genetics approaches to identify genomic regions resistant to introgression and derive empirical measures of the barrier strength as a function of recombination distance. We found that the size of the genomic islands of differentiation was influenced by the joint effects of linkage disequilibrium maintained by selection on many loci, the strength of ecological niche divergence, as well as demographic characteristics unique to each lake. Partial parallelism in divergent genomic regions likely reflected the combined effects of polygenic adaptation from standing variation and independent changes in the genetic architecture of postzygotic isolation. This study illustrates how integrating genetic mapping and population genomics of multiple sympatric species pairs provide a window on the speciation-with-gene-flow mechanism.
Data from: Population genetics and speciation of yellow-bellied, red-naped, and red-breasted sapsuckers (Sphyrapicus varius, S. nuchalis, and S. ruber)
The root of understanding speciation lies in determining the forces which drive it. In many closely-related species, including Sphyrapicus varius, S. nuchalis, and S. ruber, it is assumed that speciation occurred due to isolation in multiple Pleistocene refugia. We used genetic data from 457 samples at the control region, COI, and CHD1Z to examine rangewide population genetic structure and differentiation amongst these three species across each species' breeding range. In addition, we modelled these species' ecological niches for the Holocene (~6,000 ya), Last Glacial Maximum (~22,000 ya), and Last Interglacial (~120,000-140,000 ya) to determine if Pleistocene glaciations could have contributed to allopatric distributions, therefore allowing these groups to differentiate. Population genetic data show a potential Pleistocene refugium in Haida Gwaii, an east-west split among S. varius, and low genetic differentiation within each species. Our control region data show some polyphyly, while COI and CHD1Z data show differentiation among species using composite genotypes. Ecological Niche Modelling shows a large amount of niche overlap at each time period suggesting that S. varius, S. nuchalis, and S. ruber may not have been completely allopatric, and these species likely had repeated intermittent contact. Our data support the growing body of research that suggests differentiation despite gene flow.
Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of measurements that define corallite architecture, and could partition additive and non-additive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h² estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h² were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.
Data from: Genetics of incipient speciation in Drosophila mojavensis. III. Life history divergence in allopatry and reproductive isolation
We carried out a three-tiered genetic analysis of egg-to-adult development time and viability in ancestral and derived populations of cactophilic D. mojavensis to test the hypothesis that evolution of these life history characters has shaped premating reproductive isolation in this species. First, a common garden experiment with 11 populations from Baja California and mainland Mexico and Arizona reared on two host cacti revealed significant host plant X region and population interactions for viability and development time. Second, replicated line crosses with cactus-reared flies revealed autosomal, X chromosome, cytoplasmic, and autosome X cactus influences on development time. Third, a QTL analysis of development time differences on 1688 Baja X mainland F2 males revealed eight QTL. Eight GxE interactions were also detected, caused by longer development times associated with mainland alleles reared a mainland host with smaller differences among Baja genotypes on a Baja host plant. Four QTL influenced both development time and cuticular hydrocarbon differences associated with courtship success, and there was a significant QTL-based correlation between development time and cuticular hydrocarbon variation. Thus, the regional shifts in life histories that evolved once D. mojavensis invaded mainland Mexico from Baja California by shifting host plants were genetically correlated with variation in cuticular hydrocarbon-based mate preferences.
Data from: Hybrid speciation in sparrows I: phenotypic intermediacy, genetic admixture and barriers to gene flow
Homoploid hybrid speciation is thought to require unusual circumstances to yield reproductive isolation from the parental species, and few examples are known from nature. Here we present genetic evidence for this mode of speciation in birds. Using Bayesian assignment analyses of 751 individuals genotyped for 14 unlinked, nuclear microsatellite loci, we show that the phenotypically intermediate Italian sparrow (Passer italiae) does not form a cluster of its own, but instead exhibits clear admixture (over its entire breeding range) between its putative parental species, the house sparrow (P. domesticus) and the Spanish sparrow (P. hispaniolensis). Further, the Italian sparrow possesses mitochondrial (mt) DNA haplotypes identical to both putative parental species (although mostly of house sparrow origin), indicating a recent hybrid origin. Today, the Italian sparrow has a largely allopatric distribution on the Italian peninsula and some Mediterranean islands separated from its suggested parental species by the Alps and the Mediterranean Sea, but occurs sympatrically with the Spanish sparrow on the Gargano peninsula in southeast Italy. No evidence of interbreeding was found in this sympatric population. However, the Italian sparrow hybridizes with the house sparrow in a sparsely populated contact zone in the Alps. Yet, the contact zone is characterized by steep clines in species-specific male plumage traits, suggesting that partial reproductive isolation may also have developed between these two taxa. Thus, geographic and reproductive barriers restrict gene flow into the nascent hybrid species. We propose that an origin of hybrid species where the hybrid lineage gets geographically isolated from the parental species, as seems to have happened here, might be more common in nature than previously assumed.
FIGURE 4 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 4. Inter- (gray) and intraspecific (open) genetic differences in Tettigonia species for CO1 calculated using the pdistance method and treatment of pairwise deletion for gaps with the range of genetic difference within clusters. The box plot displays the median (internal transverse thick line) and interquartile range (box). Short lines indicate maximum and minimum genetic differences. Asterisk denotes a sequence from NCBI; T. viridissima, JN609414–JN609420; T. hispania, EF515121; T. chinensis, HQ609468–HQ609470. (JJ-TU = Jeju Island population of T. ussuriana; JS-TU = Jeongseon population of T. ussuriana; PC-TU = Pyeongchang population of T. ussuriana; MJ-TU = Muju population of T. ussuriana; MG-TU = Mungyeong population of T. ussuriana)
FIGURE 3 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 3. Neighbor-joining tree inferred from the concatenated dataset of all five genetic loci: CO1, CO2, ND1, TA1, and ITS2. Neighbor-joining (left) and parsimony (right) bootstrap values are indicated above internodes; Bayesian posterior probabilities are shown below internodes.
FIGURE 2 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 2. Neighbor-joining (A), parsimony (B), and Bayesian inference (C) trees inferred from the combined dataset of three mtDNA loci (CO1 + CO2 + ND1). Numbers next to nodes are bootstrap or posterior probability values.
FIGURE 1 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 1. Neighbor-joining phylogenetic tree of each mtDNA gene analysis: (A) CO1, (B) CO2, (C) ND1. Numbers next to nodes are bootstrap values. Numbers on arrows are genetic differences between two clusters.
Genetic structure, phylogeography, adaptive variation and speciation in the tropical tree genus Symphonia
<p>S9.2.1. SNP genotypes of <em>Symphonia globulifera</em> samples generated by Genotyping-by-sequencing</p> <p>S9.4.2. SNP genotypes of <em>Symphonia globulifer</em>a and Malagasy <em>Symphonia </em>samples generated by Sequenom technology</p> <p> </p>
Figure 5 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 5. Example song spectrograms and photos for each of the three warbling vireo genetic groups used in our DFA of songs. The colours of the outlines of the spectrograms and photos correspond to DFA results in Figure 4. Photos were taken by the first author.
Figure 4 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 4. Plots of the first two canonical axes based on DFA of warbling vireo songs. Colours and shapes correspond to three of the four microsatellite genetic groups (Black Hills are not included): eastern (red/circle), north-western (green/ square) and south-western (blue/triangle). The largest shape represents the mean centroid for each genetic group.
Figure 3 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 3. Thirty-seven warbling vireo populations genotyped at 14 microsatellite loci. Colours correspond to the four genetic groups from STRUCTURE: eastern (red), north-western (green), south-western (blue) and the Black Hills (orange) (see Fig. 2). The eastern (Medicine Hat, M HAT; left circle) and north-western (Cypress Hills, C HILLS; right circle) groups from the SEAB population are shown separately. Refer to Table 1 for population abbreviations and sample sizes.
Figure 2 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 2. Hierarchical STRUCTURE plots (K = 2) based on genotypes from 14 microsatellite loci. Populations with additional hierarchical structure are in yellow. Each bar represents a single individual, and the Q value is the percent ancestry of that individual to each genetic group. (A) All populations (red = eastern group), (B) western populations and the Black Hills (orange), (C) remaining western populations (north-western = green; south-western = blue). Refer to Table 1 for population abbreviations and sample sizes.
Figure 1 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 1. Range distributions of the three warbling vireo subspecies in this study based on Phillips (1991) and American Ornithologists' Union (1998) in gray scale on the map. Circles on the map show sampling locations included in the cyt b analysis (top inset). Black circles are eastern haplotypes, whereas white circles are western haplotypes. The eastern (Medicine Hat, M HAT; left circle) and western (Cypress Hills, C HILLS; right circle) groups from the SEAB population are shown separately. The ATPase 6 and 8 results are not on the map (bottom inset) and do not include the eastern group. Colours in the haplotype networks correspond to our microsatellite genetic groups: eastern (black), north-western (grey), south-western (white) and the Black Hills (striped). Each circle is a haplotype, and its size is proportional to how many individuals share that haplotype. Cross hatches in the haplotype networks represent more than one nucleotide difference. Refer to Table 1 for population abbreviations and sample sizes.
Figure 6 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 6. Contemporary ecological niche models for three of the four warbling vireo microsatellite genetic groups (Black Hills are not included): north-western (top), south-western (middle) and eastern (bottom). The logarithmic scale on the left depicts the percent likelihood of habitat suitability based on climate variables.
Data from: Genetics of incipient speciation in Drosophila mojavensis. III. Life history divergence in allopatry and reproductive isolation
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Data from: Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact
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