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1.
Hypoxia is a key factor determining survival, and haemoglobins are targets of selection in species native to high-altitude regions. We studied population genetic structure and evaluated evidence for local adaptation in the crested duck (Lophonetta specularioides). Differentiation, gene flow and time since divergence between highland and lowland populations were assessed for three haemoglobin genes (α(A) , α(D) , β(A) ) and compared to seven reference loci (six autosomal introns and mtDNA). Four derived amino acid replacements were found in the globin genes that had elevated Φ(ST) values between the Andean highlands and Patagonian lowlands. A single β(A) -globin polymorphism at a site known to influence O(2) affinity was fixed for different alleles in the two populations, whereas three α(A) - and α(D) -globin polymorphisms exhibited high heterozygosity in the highlands but not in the lowlands. Coalescent analyses supported restricted gene flow for haemoglobin alleles and mitochondrial DNA but nonzero gene flow for the introns. Simulating genetic data under a drift-migration model of selective neutrality, the β(A) -globin fell outside the 95% confidence limit of simulated data, suggesting that directional selection is maintaining different variants in the contrasting elevational environments, thereby restricting migration of β(A) -globin alleles. The α(A) - and α(D) -globins, by contrast, did not differ from the simulated values, suggesting that variants in these genes are either selectively neutral, or that the effects of selection could not be differentiated from background levels of population structure and linkage disequilibrium. This study illustrates the combined effects of selection and population history on inferring levels of population divergence for a species distributed across an altitudinal gradient in which selection for hypoxia resistance has likely played an important role.  相似文献   

2.
Several lines of evidence suggest that recent long‐distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi‐Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (im and migrate ) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average FST = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long‐range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000–289 000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi‐Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.  相似文献   

3.
Theory predicts that parallel evolution should be common when the number of beneficial mutations is limited by selective constraints on protein structure. However, confirmation is scarce in natural populations. Here we studied the major haemoglobin genes of eight Andean duck lineages and compared them to 115 other waterfowl species, including the bar-headed goose ( Anser indicus ) and Abyssinian blue-winged goose ( Cyanochen cyanopterus ), two additional species living at high altitude. One to five amino acid replacements were significantly overrepresented or derived in each highland population, and parallel substitutions were more common than in simulated sequences evolved under a neutral model. Two substitutions evolved in parallel in the αA subunit of two (Ala-α8) and five (Thr-α77) taxa, and five identical βA subunit substitutions were observed in two (Ser-β4, Glu-β94, Met-β133) or three (Ser-β13, Ser-β116) taxa. Substitutions at adjacent sites within the same functional protein region were also observed. Five such replacements were in exterior, solvent-accessible positions on the A helix and AB corner of the αA subunit. Five others were in close proximity to inositolpentaphosphate binding sites, and two pairs of independent replacements occurred at two different α1β1 intersubunit contacts. More than half of the substitutions in highland lineages resulted in the acquisition of serine or threonine (18 gains vs. 2 losses), both of which possess a hydroxyl group that can hydrogen bond to a variety of polar substrates. The patterns of parallel evolution observed in these waterfowl suggest that adaptation to high-altitude hypoxia has resulted from selection on unique but overlapping sets of one to five amino acid substitutions in each lineage.  相似文献   

4.
    
Many methods for fitting demographic models to data sets of aligned sequences rely upon an assumption that the data have a branching coalescent history without recombination within regions or loci. To mitigate the effects of the failure of this assumption, a common approach is to filter data and sample regions that pass the four‐gamete criterion for recombination, an approach that allows data to run, but that is expected to detect only a minority of recombination events. A series of empirical tests of this approach were conducted using computer simulations with and without recombination for a variety of isolation‐with‐migration (IM) model for two and three populations. Only the IMa3 program was used, but the general results should apply to related genealogy‐sampling‐based methods for IM models or subsets of IM models. It was found that the details of sampling intervals that pass a four‐gamete filter have a moderate effect, and that schemes that use the longest intervals, or that use overlapping intervals, gave poorer results. A simple approach of using a random nonoverlapping interval returned the smallest difference between results with and without recombination, with the mean difference between parameter estimates usually less than 20% of the true value (usually much less). However, the posterior probability distributions for migration rates were flatter with recombination, suggesting that filtering based on the four‐gamete criterion, while necessary for methods like these, leads to reduced resolution on migration. A distinct, alternative approach, of using a finite sites mutation model and not filtering the data, performed quite poorly.  相似文献   

5.
    
The integration of fossil and molecular data can provide a synthetic understanding of the ecological and evolutionary history of an organism. We analysed range‐wide maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA sequence data with coalescent simulations and traditional population genetic methods to test hypotheses of population divergence generated from the fossil record of Douglas‐fir (Pseudotsuga menziesii), an ecologically and economically important western North American conifer. Specifically, we tested (i) the hypothesis that the Pliocene orogeny of the Cascades and Sierra Nevada caused the divergence of coastal and Rocky Mountain Douglas‐fir varieties; and (ii) the hypothesis that multiple glacial refugia existed on the coast and in the Rocky Mountains. We found that Douglas‐fir varieties diverged about 2.11 Ma (4.37 Ma–755 ka), which could be consistent with a Pliocene divergence. Rocky Mountain Douglas‐fir probably resided in three or more glacial refugia. More variable molecular markers would be required to detect the two coastal refugia suggested in the fossil record. Comparison of mitochondrial DNA and chloroplast DNA variation revealed that gene flow via pollen linked populations isolated from seed exchange. Postglacial colonization of Canada from coastal and Rocky Mountain refugia near the ice margin at the Last Glacial Maximum produced a wide hybrid zone among varieties that formed almost exclusively by pollen exchange and chloroplast DNA introgression, not seed exchange. Postglacial migration rates were 50–165 m/year, insufficient to track projected 21st century warming in some regions. Although fossil and genetic data largely agree, each provides unique insights.  相似文献   

6.
    
Two monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time‐calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This suggests a mid‐late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089–0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present‐day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.  相似文献   

7.
    
Assessing the geographic structure of populations has relied heavily on Sewell Wright's F‐statistics and their numerous analogues for many decades. However, it is well appreciated that, due to their nonlinear relationship with gene flow, F‐statistics frequently fail to reject the null model of panmixia in species with relatively high levels of gene flow and large population sizes. Coalescent genealogy samplers instead allow a model‐selection approach to the characterization of population structure, thereby providing the opportunity for stronger inference. Here, we validate the use of coalescent samplers in a high gene flow context using simulations of a stepping‐stone model. In an example case study, we then re‐analyze genetic datasets from 41 marine species sampled from throughout the Hawaiian archipelago using coalescent model selection. Due to the archipelago's linear nature, it is expected that most species will conform to some sort of stepping‐stone model (leading to an expected pattern of isolation by distance), but F‐statistics have only supported this inference in ~10% of these datasets. Our simulation analysis shows that a coalescent sampler can make a correct inference of stepping‐stone gene flow in nearly 100% of cases where gene flow is ≤100 migrants per generation (equivalent to FST = 0.002), while F‐statistics had mixed results. Our re‐analysis of empirical datasets found that nearly 70% of datasets with an unambiguous result fit a stepping‐stone model with varying population sizes and rates of gene flow, although 37% of datasets yielded ambiguous results. Together, our results demonstrate that coalescent samplers hold great promise for detecting weak but meaningful population structure, and defining appropriate management units.  相似文献   

8.
    
Haemoglobin from the bar‐headed goose (Anser indicus) has higher oxygen affinity than that from its lowland relatives such as greylag goose (A. anser). The crystal structure of bar‐headed goose aquomet haemoglobin was determined at 2.3 Å resolution and compared with the structures of the goose oxy, human, horse and other avian haemoglobins and the sequences of other avian haemoglobins. Four amino‐acid residues differ between greylag goose and bar‐headed goose haemoglobins, among which Alaα119 and Aspβ125 in bar‐headed goose haemoglobin reduces the contacts between the α1 and β1 subunits compared with Pro and Glu, respectively, and therefore may increase the oxygen affinity by loosening the α1β1 interface. Compared with human oxy haemoglobin, the relative orientation of two αβ dimers in the bar‐headed goose aquomet and oxy Hbs are rotated by about 4°, indicating a unique quaternary structural difference from the typical R state. This new `RH' state is probably correlated with the higher oxygen affinity of bar‐headed goose haemoglobin.  相似文献   

9.
    
Living humans from the highland Andes exhibit antero-posteriorly and medio-laterally enlarged chests in response to high-altitude hypoxia. This study hypothesizes that morphological responses to high-altitude hypoxia should also be evident in pre-Contact Andean groups. Thoracic skeletal morphology in four groups of human skeletons (N = 347) are compared: two groups from coastal regions (Ancón, Peru, n = 79 and Arica, Chile, n = 123) and two groups from high altitudes (San Pedro de Atacama, Chile, n = 102 and Machu Picchu and Cuzco, Peru, n = 43). Osteometric variables that represent proportions of chest width and depth include sternal and clavicular lengths and breadths and rib length, curvature, and area. Each variable was measured relative to body size, transformed into logarithmic indices, and compared across sex-specific groups using ANOVA and Tukey multiple comparison tests. Atacama highlanders have the largest sternal and clavicular proportions and ribs with the greatest area and least amount of curvature, features that suggest an antero-posteriorly deep and mediolaterally wide thoracic skeleton. Ancón lowlanders exhibit proportions indicating narrower and shallower chests. Machu Picchu and Cuzco males cluster with the other highland group in rib curvature and area at the superior levels of the thorax, whereas chest proportions in Machu Picchu and Cuzco females resemble those of lowlanders. The variation in Machu Picchu and Cuzco males and females is interpreted as the result of population migrations. The presence of morphological traits indicative of enlarged chests in some highland individuals suggests that high-altitude hypoxia was an environmental stressor shaping the biology of highland Andean groups during the pre-Contact period.  相似文献   

10.
    
Understanding local adaptation and population differentiation is vital to the success of re‐introduction initiatives. As other mammals living on islands, Arabian gazelles (G. arabica) show reduced body size on the Farasan archipelago, which we corroborated in this study through morphometric analyses of skulls. In the light of the steep population decline on the Arabian Peninsula – but stable population development on the archipelago – we tested the potential suitability of Farasan gazelles as a source for re‐introductions on the mainland. We therefore investigated genetic differentiation between Farasan and mainland populations using eleven nuclear microsatellite loci and detected a distinct genetic cluster exclusively present on the archipelago, which we inferred to be separated from the mainland cluster for less than 2000 years. About 30% of sampled individuals from Farasan Islands showed assignment to a mainland cluster with signs of ongoing introgression. Analyses using the isolation‐with‐migration model confirmed recent (probably human‐induced) bidirectional exchange of gazelles between mainland and island populations. Hence, the surprisingly uniform island dwarfism most likely reflects phenotypic plasticity, that is, altered morphology as a direct consequence of harsh environmental conditions and resource limitation on the archipelago. Should a further decline of Arabian gazelles on the mainland necessitate restocking in the future, Farasan gazelles may thus become an additional source for captive breeding programmes.  相似文献   

11.
    
Unlike other migratory hummingbirds in North America, the broad‐tailed hummingbird (Selasphorus platycercus) exhibits both long‐distance migratory behaviour in the USA and sedentary behaviour in Mexico and Guatemala. We examined the evolution of migration linked to its northward expansion using a multiperspective approach. We analysed variation in morphology, mitochondrial and nuclear DNA, estimated migration rates between migratory and sedentary populations, compared divergence times with the occurrence of Quaternary climate events and constructed species distribution models to predict where migratory and sedentary populations resided during the Last Glacial Maximum (LGM) and Last Interglacial (LIG) events. Our results are consistent with a recent northward population expansion driven by migration from southern sedentary populations. Phylogeographical analyses and population genetics methods revealed that migratory populations in the USA and sedentary populations in Mexico of the platycercus subspecies form one admixed population, and that sedentary populations from southern Mexico and Guatemala (guatemalae) undertook independent evolutionary trajectories. Species distribution modelling revealed that the species is a niche tracker and that the climate conditions associated with modern obligate migrants in the USA were not present during the LIG, which provides indirect evidence for recent migratory behaviour in broad‐tailed hummingbirds on the temporal scale of glacial cycles. The finding that platycercus hummingbirds form one genetic population and that suitable habitat for migratory populations was observed in eastern Mexico during the LIG also suggests that the conservation of overwintering sites is crucial for obligate migratory populations currently facing climate change effects.  相似文献   

12.
    
Quantifying the role of gene flow during the divergence of closely related species is crucial to understanding the process of speciation. We collected DNA sequence data from 20 loci (one mitochondrial, 13 autosomal, and six sex‐linked) for population samples of Lazuli Buntings (Passerina amoena) and Indigo Buntings (Passerina cyanea) (Aves: Cardinalidae) to test explicitly between a strict allopatric speciation model and a model in which divergence occurred despite postdivergence gene flow. Likelihood ratio tests of coalescent‐based population genetic parameter estimates indicated a strong signal of postdivergence gene flow and a strict allopatric speciation model was rejected. Analyses of partitioned datasets (mitochondrial, autosomal, and sex‐linked) suggest the overall gene flow patterns are driven primarily by autosomal gene flow, as there is no evidence of mitochondrial gene flow and we were unable to reject an allopatric speciation model for the sex‐linked data. This pattern is consistent with either a parapatric divergence model or repeated periods of allopatry with gene flow occurring via secondary contact. These results are consistent with the low fitness of female avian hybrids under Haldane's rule and demonstrate that sex‐linked loci likely are important in the initial generation of reproductive isolation, not just its maintenance.  相似文献   

13.
    
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14.
    
Studies of gene flow between closely related taxa can provide insight into the genetic basis of speciation. To evaluate the importance of the X chromosome in reproductive isolation between subspecies of the European rabbit and to study the genomic scale over which islands of differentiation extend, we resequenced a total of 34 loci distributed along the X chromosome and chromosome 14. Previous studies based on few markers suggested that loci in centromeric regions were highly differentiated between rabbit subspecies, whereas loci in telomeric regions were less differentiated. Here, we confirmed this finding but also discovered remarkable variation in levels of differentiation among loci, with FST values from nearly 0 to 1. Analyses using isolation‐with‐migration models suggest that this range appears to be largely explained by differential levels of gene flow among loci. The X chromosome was significantly more differentiated than the autosomes. On chromosome 14, differentiation decayed very rapidly at increasing distances from the centromere, but on the X chromosome distinct islands of differentiation encompassing several megabases were observed both at the centromeric region and along the chromosome arms. These findings support the idea that the X chromosome plays an important role in reproductive isolation between rabbit subspecies. These results also demonstrate the mosaic nature of the genome at species boundaries.  相似文献   

15.
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 60years, 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 data set of eight 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 230,000-270,000years ago, while the split between the Mojave Desert and mainland Sonora-Arizona populations occurred one glacial cycle later, 117,000-135,000years 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.  相似文献   

16.
Complex aquatic systems of karst harbour a rich but little‐investigated biodiversity. In Croatia and Bosnia–Herzegovina karst, temporal springs are inhabited by a group of minnow‐like fishes that retreat to the associated ground water during dry seasons and spend several months underground. The most abundant species in this group is Delminichthys adspersus (Heckel 1843), which also has the most fragmented distribution range. To determine the population composition and dispersal patterns, and to detect potential underground migration, a large genetic data set comprising 544 specimens of D. adspersus covering most of its distribution area was analysed. Analysis of mitochondrial cytochrome b sequences (～1000 bp) and eight microsatellite loci showed that D. adspersus comprises at least three subpopulations with gene flow occurring among them. Coalescent‐based analysis revealed a complex migration pattern, with several unidirectional dispersal paths, including between temporal springs that share no surface connection. The results of this study suggest the existence of recurrent underground migration of fish in a karst environment and demonstrate the complexity of its hydrological network. The findings are relevant to conservation strategies for endemic karst organisms and karst ecosystems as a whole.  相似文献   

17.
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18.
Evaluating the impact of plant domestication on the population structure of the associated pathogens provides an opportunity to increase our understanding of how and why diseases emerge. Here, we investigated the evolution of the population structure of the apple scab fungus Venturia inaequalis in response to the domestication of its host. Inferences were drawn from multilocus microsatellite data obtained from samples collected on (i) the Central Asian Malus sieversii, the main progenitor of apple, (ii) the European crabapple, Malus sylvestris, a secondary progenitor of apple, and (iii) the cultivated apple, Malus×domestica, in orchards from Europe and Central Asia. Using clustering methods, we identified three distinct populations: (i) a large European population on domesticated and wild apples, (ii) a large Central Asian population on domesticated and wild apples in urban and agricultural areas, and (iii) a more geographically restricted population in M. sieversii forests growing in the eastern mountains of Kazakhstan. Unique allele richness and divergence time estimates supported a host‐tracking co‐evolutionary scenario in which this latter population represents a relict of the ancestral populations from which current populations found in human‐managed habitats were derived. Our analyses indicated that the domestication of apple induced a significant change in the genetic differentiation of populations of V. inaequalis in its centre of origin, but had little impact on its population dynamics and mating system. We discuss how the structure of the apple‐based agrosystem may have restricted changes in the population structure of the fungus in response to the domestication of its host.  相似文献   

19.
Genetic variation and evolutionary demography of the shrimp Fenneropenaeus chinensis were investigated using sequence data of the complete mitochondrial control region (CR). Fragments of 993 bp of the CR were sequenced for 93 individuals from five localities over most of the species' range in the Yellow Sea and the Bohai Sea. There were 84 variable sites defining 68 haplotypes. Haplotype diversity levels were very high (0.95 ± 0.03-0.99 ± 0.02) in F. chinensis populations, whereas those of nucleotide diversity were moderate to low (0.66 ± 0.36%-0.84 ± 0.46%). Analysis of molecular variance and conventional population statistics (F(ST) ) revealed no significant genetic structure throughout the range of F. chinensis. Mismatch distribution, estimates of population parameters and neutrality tests revealed that the significant fluctuations and shallow coalescence of mtDNA genealogies observed were coincident with estimated demographic parameters and neutrality tests, in implying important past-population size fluctuations or range expansion. Isolation with Migration (IM) coalescence results suggest that F. chinensis, distributed along the coasts of northern China and the Korean Peninsula (about 1000 km apart), diverged recently, the estimated time-split being 12,800 (7,400-18,600) years ago.  相似文献   

20.
    
Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow – a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co‐occur but are reproductively isolated solely due to their high specialization to a particular host plant. Genomewide amplified fragment‐length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genomewide divergence associated with both geographic distance and ecological divergence. However, a hybridization assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different host‐associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.  相似文献   

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