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34 results for “intraspecific divergence”
Figure 2 in Molecular evaluation of Conogethes punctiferalis (Guenée, 1854): Species status and intraspecific divergence
Figure 2. Median-joining network of mitochondrial haplotypes of refined Conogethes punctiferalis. Each node represents a unique haplotype identified from 420 mtCOI sequences. Node size is proportional to the frequency of relevant haplotypes, and branch length is proportional to the mutations that occurred between haplotypes. Color depicts the geographic origins of the harboring mtCOI sequences.
Figure 1 in Molecular evaluation of Conogethes punctiferalis (Guenée, 1854): Species status and intraspecific divergence
Figure 1. Species delimitation and phylogenetic relationship of Conogethes mitochondrial haplotypes. The ultrametric phylogenetic tree was inferred using BEAST with a strict molecular clock model and a speciation prior of Yule process. Strongly supported nodes with posteriors ≥ 0.95 and maximum likelihood bootstrapping support values ≥ 70 were indicated by black dots. The bars on the right depict the putative species delimited by different methods. Species names identified following Shashank et al. (2018).
Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination
<p>Polymorphisms can lead to speciation if there is differential mating success among conspecifics divergent for a trait. Polymorphism for sex determining system might be particularly expected to isolate gene pools, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane's rule). We investigated this question using a rare example of a species exhibiting polymorphism for sex determination: the viviparous snow skink <i>Carinascincus ocellatus</i>. While a coparatively high elevation population has entirely genotypic sex determination, in a lower elevation population there is an additional environmental component to sex determination. These systems also exhibit minor differences in sex-linked genotypes. Using 'Isolation with Migration' analysis of neutral loci, we estimated that these populations and their sex determining systems diverged in the absence of gene flow, across multiple periods of geographic proximity during Pleistocene glaciations. Our analysis suggests that populations of <i>C. ocellatus</i> with divergent sex determining systems are likely reproductively isolated, even though they are presently underlined by only subtle DNA differences. Given the influence of temperature on sex in one lineage, we also discuss the implications for the persistence of this polymorphism under climate change.</p>
Intraspecific trait variation shows the predominant influence of functional divergence on species co-occurrence
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Data from: Intraspecific divergence within Microcystis aeruginosa mediates the dynamics of freshwater harmful algal blooms under climate warming scenarios
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Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination
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Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait
<p>Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as "trichomes," on the dorsal cuticle of first-instar larvae of <i>Drosophila</i>. Most <i>Drosophila</i> species produce a dense lawn of trichomes, but a subset of dorsal trichomes were lost in <i>D. sechellia </i>and <i>D. ezoana </i>due entirely to regulatory evolution of the <i>shavenbaby</i> (<i>svb</i>) gene. Here we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of <i>D. virilis</i> that is similar to the trichome pattern variation identified previously between species.<b> </b>We found that 67% of this difference is explained by a QTL that contains <i>svb </i>and that <i>svb</i> expression correlates with trichome variation within <i>D. virilis</i> <i>.</i> Despite using an experimental design with reasonable power to detect a second locus accounting for the remainder of the variance in trichome number, only a single QTL could be mapped, suggesting that multiple other loci each make a small contribution to trichome patterning. Thus, the genetic architecture of intraspecific variation and interspecific differences exhibit similarities and differences that may reflect differences between short-term and long-term evolutionary processes.</p>
Data from: Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish
Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the south-western Atlantic and the other along the north-eastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations where found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intra-population genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.
Data from: Intraspecific divergence and evolution of a life-history trade-off along a successional gradient in Hawaii's Metrosideros polymorpha
The importance of environmental gradients in the diversification of long-lived tree species is poorly understood. Two morphologically distinct varieties of the endemic Hawaiian tree, 'ōhi'a lehua (Metrosideros polymorpha), are the canopy dominants at alternate extremes of a successional gradient formed by the recurring disturbance of lava flows on east Hawai'i Island. The maintenance of these varieties despite hybridization may be due to disruptive selection at either end of the successional gradient. To test this hypothesis, seeds from three, replicate monotypic stands of each variety on east Hawai'i Island were germinated and the resulting seedlings grown under four combinations of light and nitrogen levels in a greenhouse, and at early- and late-successional field sites. Growth and survivorship measures revealed differential fitness of these varieties in high- and low-light environments in the greenhouse with corresponding differential fitness in early- and late-successional field sites. Unique light-by-nitrogen interaction effects on growth were observed in each variety, and only the late-successional variety appeared to be nitrogen limited. These two varieties exhibit the classic plant life-history trade-off between fast growth in high light and high survivorship in shade, but notably within a single tree species. These findings strongly implicate a role for Hawaii's striking environmental heterogeneity in the emergence of at least two endemic forms of this woody genus.
Data from: Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis
The cactophilic fly Drosophila mojavensis exhibits considerable intraspecific genetic structure across allopatric geographic regions and shows associations with different host cactus species across its range. The divergence between these populations has been studied for more than 60 years, yet their exact historical relationships have not been resolved. We analysed sequence data from 15 intronic X-linked loci across populations from Baja California, mainland Sonora-Arizona and Mojave Desert regions under an isolation-with-migration model to assess multiple scenarios of divergence. We also compared the results with a pre-existing sequence dataset of 8 autosomal loci. We derived a population tree with Baja California placed at its base and link their isolation to Pleistocene climatic oscillations. Our estimates suggest the Baja California population diverged from an ancestral Mojave Desert/mainland Sonora-Arizona group around 230-270 Kya, while the split between the Mojave Desert and mainland Sonora-Arizona populations occurred one glacial cycle later, 117-135 Kya years ago. Although we found these three populations to be effectively allopatric, model ranking could not rule out the possibility of a low-level of gene flow between two of them. Finally, the Mojave Desert population showed a small effective population size, consistent with a historical population bottleneck. We show that model-based inference from multiple loci can provide accurate information on the historical relationships of closely related groups allowing us to set into historical context a classic system of incipient ecological speciation.
Data from: Intraspecific divergence and convergence of floral tube length in specialized pollination interactions
Floral tubes are often thought to be a consequence of adaptive specialization towards pollinator morphology. We explore floral tube length evolution within Tritoniopsis revoluta (Iridaceae), a species with considerable geographical tube length variation. We ask whether tube lengths of T. revoluta populations are associated with pollinator proboscis lengths, whether floral divergence occurs in the presence of different pollinators and whether floral convergence occurs between distantly related populations pollinated by the same pollinator. Finally, we ask whether tube length evolution is directional. Shifts between morphologically different pollinators were always associated with shifts in floral morphology, even when populations were very closely related. Distantly related populations had similar tube lengths when they were pollinated by the same pollinator. Shifts in tube length tended to be from short to long, although reversals were not infrequent. After correcting for the population-level phylogeny, there was a strong positive, linear relationship between floral tube length and pollinator proboscis length, suggesting that plants are functionally specialized on different pollinators at different sites. However, because tube length evolution in this system can be a bidirectional process, specialization to the local pollinator fauna is unlikely to result in evolutionary or ecological dead-ends such as canalization or range limitation.
Data from: Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau
A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their response to future environmental change. However, genetic signatures of such historical events are often weak at individual loci due to large effective population sizes and long generation times of forest trees. This problem can be overcome by analysing genetic variation across multiple loci. We used this approach to examine intraspecific divergence and past range dynamics in the conifer Picea likiangensis, a dominant tree of forests occurring in eastern and southern areas of the Qinghai-Tibet Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions and three plastid (chloroplast) DNA regions in 177 individuals sampled from 22 natural populations of this species, and tested the hypothesis that its evolutionary history was markedly affected by Pliocene QTP uplifts and Quaternary climatic oscillations. Consistent with the taxonomic delimitation of the three morphologically divergent varieties examined, all individuals clustered into three genetic groups with inter-variety admixture detected in regions of geographical overlap. Divergence between varieties was estimated to have occurred within the Pliocene and ecological niche modeling based on 20 ecological variables suggested that niche differentiation was high. Furthermore, modeling of population genetic data indicated that two of the varieties (var. rubescens and var. linzhiensis) expanded their population sizes after the largest Quaternary glaciation in the QTP, while expansion of the third variety (var. likiangensis) began prior to this, probably following the Pliocene QTP uplift. These findings point to the importance of geological and climatic changes during the Pliocene and Pleistocene as causes of intraspecific diversification and range shifts of dominant tree species in the QTP biodiversity hotspot region.
Data from: Repeated intraspecific divergence in life span and aging of African annual fishes along an aridity gradient
Life span and aging are substantially modified by natural selection. Across species, higher extrinsic (environmentally related) mortality (and hence shorter life expectancy) selects for the evolution of more rapid aging. However, among populations within species, high extrinsic mortality can lead to extended life span and slower aging as a consequence of condition-dependent survival. Using within-species contrasts of eight natural populations of Nothobranchius fishes in common garden experiments, we demonstrate that populations originating from dry regions (with short life expectancy) had shorter intrinsic life spans and a greater increase in mortality with age, more pronounced cellular and physiological deterioration (oxidative damage, tumor load), and a faster decline in fertility than populations from wetter regions. This parallel intraspecific divergence in life span and aging was not associated with divergence in early life history (rapid growth, maturation) or pace-of-life syndrome (high metabolic rates, active behavior). Variability across four study species suggests that a combination of different aging and life-history traits conformed with or contradicted the predictions for each species. These findings demonstrate that variation in life span and functional decline among natural populations are linked, genetically underpinned, and can evolve relatively rapidly.
Data from: Genotype by sequencing identifies natural selection as a driver of intraspecific divergence in Atlantic populations of the high dispersal marine invertebrate, Macoma petalum
Mitochondrial DNA analyses indicate that the Bay of Fundy population of the intertidal tellinid bivalve Macoma petalum is genetically divergent from coastal populations in the Gulf of Maine and Nova Scotia. To further examine the evolutionary forces driving this genetic break, we performed double digest genotype by sequencing (GBS) to survey the nuclear genome for evidence of both neutral and selective processes shaping this pattern. The resulting reads were mapped to a partial transcriptome of its sister species, M. balthica, to identify single nucleotide polymorphisms (SNPs) in protein-coding genes. Population assignment tests, principle components analyses, analysis of molecular variance, and outlier tests all support differentiation between the Bay of Fundy genotype and the genotypes of the Gulf of Maine, Gulf of St. Lawrence, and Nova Scotia. Although both neutral and non-neutral patterns of genetic subdivision were significant, genetic structure among the regions was nearly 20 times higher for loci putatively under selection, suggesting a strong role for natural selection as a driver of genetic diversity in this species. Genetic differences were the greatest between the Bay of Fundy and all other population samples, and some outlier proteins were involved in immunity-related processes. Our results suggest that in combination with limited gene flow across the mouth of the Bay of Fundy, local adaptation is an important driver of intraspecific genetic variation in this marine species with high dispersal potential.
Fig. 3 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 3. Maximum likelihood trees and population structuring of Apatania (A) and Limnephilus (B) based on ddRAD SNP data.ML trees were inferred from RAxML analysis with 1,000 bootstrap replicates. The bootstrap values are indicated near the branches. Results of population STRUCTURE analyses with posterior probability plots of individual assignments to the inferred genetic clusters for K = 6 and 7 for Apatania and K = 4 for Limnephilus.
Fig. 2 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 2. Maximum likelihood trees based on mitochondrial COI sequences of Apatania (A) and Limnephilus (B). The bootstrap values are indicated near the branches (only shown for nodes supported with more than 50% of BS).
intraspecific the to correspond. outgroups bold: grey in in Values; retzii. ) pb Microphis 605 ( : alignment red in; . I nov . subunit sp oxydase arrakisae c Microphis cytochrome: blue the in; on torrentius based) Microphis p-distances: green uncorrected in; (nicoleae matrix distance Microphis : Pairwise yellow In. . 2 divergence TABLE in A new freshwater pipefish species (Syngnathidae: Microphis) from the Sunda shelf islands, Indonesia
intraspecific the to correspond. outgroups bold: grey in in Values; retzii. ) pb Microphis 605 ( : alignment red in; . I nov . subunit sp oxydase arrakisae c Microphis cytochrome: blue the in; on torrentius based) Microphis p-distances: green uncorrected in; (nicoleae matrix distance Microphis : Pairwise yellow In. . 2 divergence TABLE
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
Data from: Repeated intraspecific divergence in life span and aging of African annual fishes along an aridity gradient
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Data from: Intraspecific phenotypic variation and morphological divergence of strains of Folsomia candida (Willem) (Collembola: Isotomidae), the "standard" test springtail
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