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19 results for “intraspecific differentiation”
Non-genetically-based intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae
<p>We used next-generation sequencing to study DNA methylation and gene expression changes in plants from four clonal populations of the metallophyte moss <em>Scopelophila cataractae</em> experimentally exposed to either Cd or Cu. For this we performed reduced representation bisulfite DNA sequencing and RNA sequencing. </p>
Population differentiation and intraspecific genetic admixture in two Eucryptorrhynchus weevils (Coleoptera: Curculionidae) across northern China
<p><span>Inreasing damage of pests in agriculture and forestry can arise both as a consequence of changes in local species and through the introduction of alien species. In this study, we used population genetics approaches to examine population processes of two pests of the tree-of-heaven trunk weevil (TTW), <em>Eucryptorrhynchus brandti</em> (Harold) and the tree-of-heaven root weevil (TRW), <em>E. scrobiculatus</em> (Motschulsky) on the tree-of-heaven across their native range of China. We analyzed the population genetics of the two weevils based on ten highly polymorphic microsatellite markers. Population genetic diversity analysis showed strong population differentiation among populations of each species, with FST ranges from 0.0197 to 0.6650 and from -0.0724 to 0.6845, respectively. Populations from the same geographical areas can be divided into different genetic clusters, and the same genetic cluster contained populations from different geographical populations, pointing to dispersal of the weevils possibly being human-mediated. Redundancy analysis showed that the independent effects of environment and geography could account for 93.94% and 29.70% of the explained genetic variance in TTW, and 41.90% and 55.73% of the explained genetic variance in TRW, respectively, indicating possible impacts of local climates on population genetic differentiation. Our study helps to uncover population genetic processes of these local pest species with relevance to control methods.</span></p>
Population differentiation and intraspecific genetic admixture in two Eucryptorrhynchus weevils (Coleoptera: Curculionidae) across northern China
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Blow to the Northeast? Intraspecific differentiation of Populus davidiana suggests a northeastward skew of a phylogeographic break boundary in East Asia
<p><b><span>Aim: </span></b>There is increasing interest in the role that biological traits, and historical and biogeographic processes, play in the formation of phylogeographic patterns. An arid belt that once existed in northern China might have affected many plants, but this has yet to be untested in an arid-tolerant, wind-dispersed species. Here we tested how intrinsic and extrinsic factors have affected the phylogeography of <i><span>Populus davidiana</span></i>.</p> <p><b><span>Location: </span></b>East Asia</p> <p><b><span>Methods: </span></b>Genetic variation was surveyed across 40 populations (555 individuals) covering the Chinese range of <i><span>P. davidiana</span></i>, using 16 nuclear microsatellite loci (nSSRs) and four chloroplast fragments (cpDNA). Demographic and migration hypotheses were tested using coalescent-based approaches, and the present and past potential distributions were predicted using species distribution modelling.</p> <p><span><span><b><span>Results: </span></b>Molecular data divides <i><span>P. davidiana </span></i>into two lineages, northeastern China (NECR), and central and northern China (CNCR); however, the dividing line is around 118ºE for nSSRs, but 122ºE for cpDNA. The range and habitat of the two lineages barely overlap at present, and their ecological separation may have initiated around the Pliocene-Quaternary boundary, when major infraspecific cpDNA clades diverged. NECR and CNCR experienced postglacial northeastward and northward range shifts, respectively. Bi-directional historical gene flow was detected between NECR and CNCR for both bi-parentally inherited nSSRs and maternally inherited cpDNA. Demographic inferences suggest a severe bottleneck for CNCR and especially NECR, around the latest Pleistocene.</span></span></p> <p><b><span>Main conclusions: </span></b>The phylogeographic break within <i><span>P. davidiana</span></i> reflects the impacts of biogeographic history, climate and biological traits. Its plumed, wind-dispersed seeds might be especially significant, because prevailing southwestern spring winds may have moved the NECR-CNCR boundary further east than similar phylogenetic breaks in other species, and also moved the cpDNA boundary relative to that for nuclear markers. Biological traits, therefore, should also be considered when examining the genetic and ecological differentiation between closely related taxa.</p>
Data from: Facultative paedomorphosis as a mechanism promoting intraspecific niche differentiation
Organisms with complex life cycles are characterized by a metamorphosis that allows for a major habitat shift and the exploitation of alternative resources. However, metamorphosis can be bypassed in some species through a process called paedomorphosis, resulting in the retention of larval traits at the adult stage and is considered important at both micro- and macroevolutionary scales. In facultatively paedomorphic populations of newts, some individuals retain gills and a fully aquatic life at the adult stage (paedomorphs), while others undergo complete metamorphosis (metamorphs), allowing for a terrestrial life-stage. Because facultative paedomorphosis affects trophic structures and feeding mechanism of newts, one hypothesis is that it may be maintained as a trophic polymorphism, with the advantage to lessen intraspecific competition during the shared aquatic life-stage. Here, we tested this hypothesis combining stomach content data with stable isotope techniques, using carbon and nitrogen stable isotopes, in facultatively paedomorphic alpine newts (Ichthyosaura alpestris). Both stomach content and stable isotope analyses showed that paedomorphs had smaller trophic niches and were more reliant on pelagic resources, while metamorphs relied more on littoral resources, corresponding to a polyphenism along the littoral-pelagic axis and the extension of the population's trophic niche to otherwise 'underused' pelagic resources by paedomorphs. Interestingly, stable isotopes revealed that the trophic polyphenism was less marked in males than in females and potentially linked to sexual activity. Although paedomorphosis and metamorphosis are primarily seen as results of trade-offs between the advantages of using aquatic versus terrestrial habitats, this study provides evidence that additional forces, such as intraspecific trophic niche differences between morphs and trophic niche expansion, may play an important role in the persistence of this dimorphism in heterogeneous environments. Moreover, the different patterns found in males and females show the importance of considering sex to understand the evolutionary ecology of trophic polymorphisms.
Data from: Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes
Linking intraspecific and interspecific divergence is an important challenge in speciation research. X chromosomes are expected to evolve faster than autosomes and disproportionately contribute to reproductive barriers, and comparing genetic variation on X and autosomal markers within and between species can elucidate evolutionary processes that shape genome variation. We performed RADseq on a 16-population transect of two closely-related Australian cricket species, Teleogryllus commodus and T. oceanicus, covering allopatry and sympatry. This classic study system for sexual selection provides a rare exception to Haldane's rule, as hybrid females are sterile. We found no evidence of recent introgression, despite the fact that the species co-exist in overlapping habitats in the wild and interbreed in the laboratory. Putative X-linked loci showed greater differentiation between species compared to autosomal loci. However, population differentiation within species was unexpectedly lower on X-linked markers than autosomal markers, and relative X-to-autosomal genetic diversity was inflated above neutral expectations. Populations of both species showed genomic signatures of recent population expansions, but these were not strong enough to account for the inflated X/A diversity. Instead, most of the excess polymorphism on the X could better be explained by sex-biased processes that increase the relative effective population size of the X, such as interspecific variation in the strength of sexual selection among males. Taken together, the opposing patterns of diversity and differentiation at X versus autosomal loci implicate a greater role for sex-linked genes in maintaining species boundaries in this system.
FIGURE 6. T in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 6. T-test results for morphological indicators. (F = females, M = males, N = northern Xinjiang, S = south Xinjiang)
FIGURE 5 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 5. The morphology and tail of Laudakia stoliczkana subspecies. (A & a: L. s. altaica; B & b: L. s. stoliczkana)
FIGURE 4 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 4. The estimation of divergence time for Laudakia. (Note: Values are estimated divergence times, and the blue bars are 95% confidence intervals HPD)
FIGURE 3 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 3. Bayesian phylogenetic trees of Laudakia species on tandem sequences (CO1 and 16S). (note: the values of nodes near is BPP/BS).
FIGURE 2 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 2. Bayesian phylogenetic trees of Laudakia on the sequenced of COI. (note: the values of nodes near is BPP/BS).
FIGURE 1 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 1. Bayesian phylogenetic trees of Laudakia on the sequenced of 16S. (note: the values of nodes near is BPP/BS).
Data from: The Near East as a cradle of biodiversity: a phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation
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Data from: Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes
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Data from: Facultative paedomorphosis as a mechanism promoting intraspecific niche differentiation
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Blow to the Northeast? Intraspecific differentiation of Populus davidiana suggests a northeastward skew of a phylogeographic break boundary in East Asia
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Testing small scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding
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Drivers of intraspecific differentiation of the alpine cold tolerant herb Notopterygium oviforme: the roles of isolation by distance and ecological factors
<p>Determining the driver mechanisms of phenotypic and genetic divergence of species have long been the central topic in evolutionary biology. However, the relative roles of isolation by distance (IBD) and environment factors in contributing to species divergence is largely undetermined in perennial herbs in East Asia. In this study, we collected population genetic samples of a cold-tolerant perennial herb <i>Notopterygium oviforme</i> in central China. We integrated the population transcriptomes, whole chloroplast genomes, genotyping-by-sequencing, microsatellite markers and ecological environment factors to determine the relative contributions of geography, climatic and soil factors on genetic, chemical and phenotypic trait divergence. The clearly genetic distinction was identified between the west Qinling (WQ) and east Qinling Mountains (EQ) geographical groups within<i> N. oviforme</i>. Interestingly, the two groups have existed the obviously niche conservatism, which might have caused the similarity of most leaf functional traits. Multiple matrix regression with randomization analysis showed that the spatial pattern of intraspecific divergence mainly resulted from effect of IBD, not isolation by environment. Meanwhile, transcriptomic expression divergence and some ecological factors have played the key roles in differentiation of intraspecific lineage. Approximate Bayesian Computation showed that both lineages have experienced the historically population expansion, and the recent range contraction. Molecular dating suggested that the intraspecific divergence was closely associated with the dramatically uplifts of the Qinling Mountains in East Asia. These results demonstrated that the geography, geological and environmental factors together shaped the cryptic intraspecific diversification and population dynamics shifts of<i> </i>perennial cold tolerant herb.</p>
Drivers of intraspecific differentiation of the alpine cold tolerant herb Notopterygium oviforme: the roles of isolation by distance and ecological factors
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