BMC Ecology and Evolution

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EISSN : 2730-7182
Current Publisher: Springer Science and Business Media LLC (10.1186)
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Total articles ≅ 105
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Rong Huang, Yu Wang, Kuan Li,
BMC Ecology and Evolution, Volume 21, pp 1-13; doi:10.1186/s12862-021-01853-2

Abstract:
Background There has always been controversy over whether clonal plants have lower genetic diversity than plants that reproduce sexually. These conflicts could be attributed to the fact that few studies have taken into account the mating system of sexually reproducing plants and their phylogenetic distance. Moreover, most clonal plants in these previous studies regularly produce sexual progeny. Here, we describe a study examining the levels of genetic diversity and differentiation within and between local populations of fully clonal Zingiber zerumbet at a microgeographical scale and compare the results with data for the closely related selfing Z. corallinum and outcrossing Z. nudicarpum. Such studies could disentangle the phylogenetic and sexually reproducing effect on genetic variation of clonal plants, and thus contribute to an improved understanding in the clonally reproducing effects on genetic diversity and population structure. Results The results revealed that the level of local population genetic diversity of clonal Z. zerumbet was comparable to that of outcrossing Z. nudicarpum and significantly higher than that of selfing Z. corallinum. However, the level of microgeographic genetic diversity of clonal Z. zerumbet is comparable to that of selfing Z. corallinum and even slightly higher than that of outcrossing Z. nudicarpum. The genetic differentiation among local populations of clonal Z. zerumbet was significantly lower than that of selfing Z. corallinum, but higher than that of outcrossing Z. nudicarpum. A stronger spatial genetic structure appeared within local populations of Z. zerumbet compared with selfing Z. corallinum and outcrossing Z. nudicarpum. Conclusions Our study shows that fully clonal plants are able not only to maintain a high level of within-population genetic diversity like outcrossing plants, but can also maintain a high level of microgeographic genetic diversity like selfing plant species, probably due to the accumulation of somatic mutations and absence of a capacity for sexual reproduction. We suggest that conservation strategies for the genetic diversity of clonal and selfing plant species should be focused on the protection of all habitat types, especially fragments within ecosystems, while maintenance of large populations is a key to enhance the genetic diversity of outcrossing species.
Yunong Wang, Li Zhou, Lele Wu, Changbin Song, Xiaona Ma, Shihong Xu, Tengfei Du, , Jun Li
BMC Ecology and Evolution, Volume 21, pp 1-12; doi:10.1186/s12862-021-01837-2

Abstract:
Background As flatfish, turbot undergo metamorphosis as part of their life cycle. In the larval stage, turbot live at the ocean surface, but after metamorphosis they move to deeper water and turn to benthic life. Thus, the light environment differs greatly between life stages. The visual system plays a great role in organic evolution, but reports of the relationship between the visual system and benthic life are rare. In this study, we reported the molecular and evolutionary analysis of opsin genes in turbot, and the heterochronic shifts in opsin expression during development. Results Our gene synteny analysis showed that subtype RH2C was not on the same gene cluster as the other four green-sensitive opsin genes (RH2) in turbot. It was translocated to chromosome 8 from chromosome 6. Based on branch-site test and spectral tuning sites analyses, E122Q and M207L substitutions in RH2C, which were found to be under positive selection, are closely related to the blue shift of optimum light sensitivities. And real-time PCR results indicated the dominant opsin gene shifted from red-sensitive (LWS) to RH2B1 during turbot development, which may lead to spectral sensitivity shifts to shorter wavelengths. Conclusions This is the first report that RH2C may be an important subtype of green opsin gene that was retained by turbot and possibly other flatfish species during evolution. Moreover, E122Q and M207L substitutions in RH2C may contribute to the survival of turbot in the bluish colored ocean. And heterochronic shifts in opsin expression may be an important strategy for turbot to adapt to benthic life.
, Manuel Curto, , Gernot K. Englmaier, Papius Dias Tibihika, Esayas Alemayehu, Abebe Getahun, Harald Meimberg
BMC Ecology and Evolution, Volume 21, pp 1-14; doi:10.1186/s12862-021-01829-2

Abstract:
Background Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques. Results The samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High F ST values (Global F ST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq. Conclusions The results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.
, , Fanbing Meng, YanShuang Shi,
BMC Ecology and Evolution, Volume 21, pp 1-11; doi:10.1186/s12862-021-01844-3

Abstract:
Background In contrast to the explosive increase of a population following biological invasion, natural dispersal, i.e., when a population disperses from its original range into a new range, is a passive process that is affected by resources, the environment, and other factors. Natural dispersal is also negatively impacted by genetic drift and the founder effect. Although the fates of naturally dispersed populations are unknown, they can adapt evolutionarily over time to the new environment. Can naturally dispersed populations evolve beneficial adaptive strategies to offset these negative effects to maintain their population in a stable state? Results The current study addressed this question by focusing on the toad Bombina orientalis, the population of which underwent natural dispersal following the Last Glacial Maximum in Northeast Asia. Population genetic approaches were used to determine the genetic structure, dispersal pattern, and mating system of the population of B. orientalis in northeast China (Northern population). The results showed that this northern population of B. orientalis is a typical naturally dispersed population, in which the stable genetic structure and high level of genetic diversity of the population have been maintained through the long-distance biased dispersal behavior of males and the pattern of promiscuity within the population. Conclusions Our findings suggest that naturally dispersed populations can evolve effective adaptive strategies to maintain a stable population. Different species may have different strategies. The relevance of these maintenance mechanisms for naturally dispersed populations provide a new perspective for further understanding the processes of speciation and evolution.
Correction
, Gerald O. Gunderson, Ronald C. Meyer
BMC Ecology and Evolution, Volume 21, pp 1-1; doi:10.1186/s12862-021-01843-4

Abstract:
An amendment to this paper has been published and can be accessed via the original article.
Xiao-Lin Chu,
BMC Ecology and Evolution, Volume 21, pp 1-8; doi:10.1186/s12862-021-01846-1

Abstract:
Background Mutation accumulation (MA) has profound ecological and evolutionary consequences. One example is that accumulation of conditionally neutral mutations leads to fitness trade-offs among heterogenous habitats which cause population divergence. Here we suggest that temperature, which controls the rates of all biochemical and biophysical processes, should play a crucial role for determining mutational effects. Particularly, warmer temperatures may mitigate the effects of some, not all, deleterious mutations and cause stronger environmental dependence in MA effects. Results We experimentally tested the above hypothesis by measuring the growth performance of ten Escherichia coli genotypes on six carbon resources across ten temperatures, where the ten genotypes were derived from a single ancestral strain and accumulated spontaneous mutations. We analyzed resource dependence of MA consequences for growth yields. The MA genotypes typically showed reduced growth yields relative to the ancestral type; and the magnitude of reduction was smaller at intermediate temperatures. Stronger resource dependence in MA consequences for growth performance was observed at higher temperatures. Specifically, the MA genotypes were more likely to show impaired growth performance on all the six carbon resources when grown at lower temperatures; but suffered growth performance loss only on some, not all the six, carbon substrates at higher temperatures. Conclusions Higher temperatures increase the chance that MA causes conditionally neutral fitness effects while MA is more likely to cause fitness loss regardless of available resources at lower temperatures. This finding has implications for understanding how geographic patterns in population divergence may emerge, and how conservation practices, particularly protection of diverse microhabitats, may mitigate the impacts of global warming.
BMC Ecology and Evolution, Volume 21, pp 1-14; doi:10.1186/s12862-021-01841-6

Abstract:
Background Mendelian inheritance is a fundamental law of genetics. When we consider two genomes in a diploid cell, a heterozygote’s phenotype is dominated by a particular homozygote according to the law of dominance. Classical Mendelian dominance is concerned with which proteins are dominant, and is usually based on simple genotype–phenotype relationship in which one gene regulates one phenotype. However, in reality, some interactions between genes can exist, resulting in deviations from Mendelian dominance. Whether and how Mendelian dominance is generalized to the phenotypes of gene expression determined by gene regulatory networks (GRNs) remains elusive. Results Here, by using the numerical evolution of diploid GRNs, we discuss whether the dominance of phenotype evolves beyond the classical Mendelian case of one-to-one genotype–phenotype relationship. We examine whether complex genotype–phenotype relationship can achieve Mendelian dominance at the expression level by a pair of haplotypes through the evolution of the GRN with interacting genes. This dominance is defined via a pair of haplotypes that differ from each other but have a common phenotype given by the expression of target genes. We numerically evolve the GRN model for a diploid case, in which two GRN matrices are added to give gene expression dynamics and simulate evolution with meiosis and recombination. Our results reveal that group Mendelian dominance evolves even under complex genotype–phenotype relationship. Calculating the degree of dominance shows that it increases through the evolution, correlating closely with the decrease in phenotypic fluctuations and the increase in robustness to initial noise. We also demonstrate that the dominance of gene expression patterns evolves concurrently. This evolution of group Mendelian dominance and pattern dominance is associated with phenotypic robustness against meiosis-induced genome mixing, whereas sexual recombination arising from the mixing of genomes from the parents further enhances dominance and robustness. Due to this dominance, the robustness to genetic differences increases, while optimal fitness is sustained to a significant difference between the two genomes. Conclusion Group Mendelian dominance and gene-expression pattern dominance are achieved associated with the increase in phenotypic robustness to noise.
, C. D. Bacon, D. J. Bennett, B. E. Pfeil, B. Oxelman, A. Antonelli
BMC Ecology and Evolution, Volume 21, pp 1-13; doi:10.1186/s12862-021-01751-7

Abstract:
Background The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.
Leila Alickovic, Kevin P. Johnson, Bret M. Boyd
BMC Ecology and Evolution, Volume 21, pp 1-11; doi:10.1186/s12862-021-01840-7

Abstract:
Background Feather feeding lice are abundant and diverse ectoparasites that complete their entire life cycle on an avian host. The principal or sole source of nutrition for these lice is feathers. Feathers appear to lack four amino acids that the lice would require to complete development and reproduce. Several insect groups have acquired heritable and intracellular bacteria that can synthesize metabolites absent in an insect’s diet, allowing insects to feed exclusively on nutrient-poor resources. Multiple species of feather feeding lice have been shown to harbor heritable and intracellular bacteria. We expected that these bacteria augment the louse’s diet with amino acids and facilitated the evolution of these diverse and specialized parasites. Heritable symbionts of insects often have small genomes that contain a minimal set of genes needed to maintain essential cell functions and synthesize metabolites absent in the host insect’s diet. Therefore, we expected the genome of a bacterial endosymbiont in feather lice would be small, but encode pathways for biosynthesis of amino acids. Results We sequenced the genome of a bacterial symbiont from a feather feeding louse (Columbicola wolffhuegeli) that parasitizes the Pied Imperial Pigeon (Ducula bicolor) and used its genome to predict metabolism of amino acids based on the presence or absence of genes. We found that this bacterial symbiont has a small genome, similar to the genomes of heritable symbionts described in other insect groups. However, we failed to identify many of the genes that we expected would support metabolism of amino acids in the symbiont genome. We also evaluated other gene pathways and features of the highly reduced genome of this symbiotic bacterium. Conclusions Based on the data collected in this study, it does not appear that this bacterial symbiont can synthesize amino acids needed to complement the diet of a feather feeding louse. Our results raise additional questions about the biology of feather chewing lice and the roles of symbiotic bacteria in evolution of diverse avian parasites.
Xiangyun Li, Xiaoan Zuo, Ping Yue, Xueyong Zhao, Ya Hu, Xinxin Guo, Aixia Guo, Chong Xu, Qiang Yu
BMC Ecology and Evolution, Volume 21, pp 1-13; doi:10.1186/s12862-021-01842-5

Abstract:
Background Increasing drought induced by global climate changes is altering the structure and function of grassland ecosystems. However, there is a lack of understanding of how drought affects the trade-off of above- and belowground biomass in desert steppe. We conducted a four-year (2015–2018) drought experiment to examine the responses of community above-and belowground biomass (AGB and BGB) to manipulated drought and natural drought in the early period of growing season (from March to June) in a desert steppe. We compared the associations of drought with species diversity (species richness and density), community-weighted means (CWM) of five traits, and soil factors (soil Water, soil carbon content, and soil nitrogen content) for grass communities. Meanwhile, we used the structural equation modeling (SEM) to elucidate whether drought affects AGB and BGB by altering species diversity, functional traits, or soil factors. Results We found that manipulated drought affected soil water content, but not on soil carbon and nitrogen content. Experimental drought reduced the species richness, and species modified the CWM of traits to cope with a natural drought of an early time in the growing season. We also found that the experimental and natural drought decreased AGB, while natural drought increased BGB. AGB was positively correlated with species richness, density, CWM of plant height, and soil water. BGB was negatively correlated with CWM of plant height, CWM of leaf dry matter content, and soil nitrogen content, while was positively correlated with CWM of specific leaf area, CWM of leaf nitrogen content, soil water, and soil carbon content. The SEM results indicated that the experimental and natural drought indirectly decreased AGB by reducing species richness and plant height, while natural drought and soil nitrogen content directly affected BGB. Conclusions These results suggest that species richness and functional traits can modulate the effects of drought on AGB, however natural drought and soil nitrogen determine BGB. Our findings demonstrate that the long-term observation and experiment are necessary to understand the underlying mechanism of the allocation and trade-off of community above-and belowground biomass.
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