A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids.
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ABSTRACT:
SUBMITTER: Allen R
PROVIDER: S-EPMC7341909 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:NLRPs (Nucleotide-binding oligomerization domain, Leucine rich Repeat and Pyrin domain containing Proteins) are members of NLR (Nod-like receptors) protein family. Recent researches have shown that NLRP genes play important roles in both mammalian innate immune system and reproductive system. Several of NLRP genes were shown to be specifically expressed in the oocyte in mammals. The aim of the present work was to study how these genes evolved and diverged after their duplication, as well as whether natural selection played a role during their evolution. RESULTS:By using in silico methods, we have evaluated the evolution and functional divergence of NLRP genes, in particular of mouse reproduction-related Nlrp genes. We found that (1) major NLRP genes have been duplicated before the divergence of mammals, with certain lineage-specific duplications in primates (NLRP7 and 11) and in rodents (Nlrp1, 4 and 9 duplicates); (2) tandem duplication events gave rise to a mammalian reproduction-related NLRP cluster including NLRP2, 4, 5, 7, 8, 9, 11, 13 and 14 genes; (3) the function of mammalian oocyte-specific NLRP genes (NLRP4, 5, 9 and 14) might have diverged during gene evolution; (4) recent segmental duplications concerning Nlrp4 copies and vomeronasal 1 receptor encoding genes (V1r) have been undertaken in the mouse; and (5) duplicates of Nlrp4 and 9 in the mouse might have been subjected to adaptive evolution. CONCLUSION:In conclusion, this study brings us novel information on the evolution of mammalian reproduction-related NLRPs. On the one hand, NLRP genes duplicated and functionally diversified in mammalian reproductive systems (such as NLRP4, 5, 9 and 14). On the other hand, during evolution, different lineages adapted to develop their own NLRP genes, particularly in reproductive function (such as the specific expansion of Nlrp4 and Nlrp9 in the mouse).
| S-EPMC2735741 | biostudies-literature
Project description:The five members of the mammalian G subfamily of ATP-binding cassette transporters differ greatly in their substrate specificity. Four members of the subfamily are important in lipid transport and the wide substrate specificity of one of the members, ABCG2, is of significance due to its role in multidrug resistance. To explore the origin of substrate selectivity in members 1, 2, 4, 5 and 8 of this subfamily, we have analysed the differences in conservation between members in a multiple sequence alignment of ABCG sequences from mammals. Mapping sets of residues with similar patterns of conservation onto the resolved 3D structure of ABCG2 reveals possible explanations for differences in function, via a connected network of residues from the cytoplasmic to transmembrane domains. In ABCG2, this network of residues may confer extra conformational flexibility, enabling it to transport a wider array of substrates.
| S-EPMC8001107 | biostudies-literature
Project description:Hybrid sterility is a major form of postzygotic reproductive isolation. Although reproductive isolation has been a key issue in evolutionary biology for many decades in a wide range of organisms, only very recently a few genes for reproductive isolation were identified. The Asian cultivated rice (Oryza sativa L.) is divided into two subspecies, indica and japonica. Hybrids between indica and japonica varieties are usually highly sterile. A special group of rice germplasm, referred to as wide-compatibility varieties, is able to produce highly fertile hybrids when crossed to both indica and japonica. In this study, we cloned S5, a major locus for indica-japonica hybrid sterility and wide compatibility, using a map-based cloning approach. We show that S5 encodes an aspartic protease conditioning embryo-sac fertility. The indica (S5-i) and japonica (S5-j) alleles differ by two nucleotides. The wide compatibility gene (S5-n) has a large deletion in the N terminus of the predicted S5 protein, causing subcellular mislocalization of the protein, and thus is presumably nonfunctional. This triallelic system has a profound implication in the evolution and artificial breeding of cultivated rice. Genetic differentiation between indica and japonica would have been enforced because of the reproductive barrier caused by S5-i and S5-j, and species coherence would have been maintained by gene flow enabled by the wide compatibility gene.
| S-EPMC2516230 | biostudies-literature
Project description:To invest in energetically demanding life history stages, individuals require a substantial amount of resources. Physiological traits, particularly those related to energetics, can be useful for examining variation in life history decisions and trade-offs because they result from individual responses to environmental variation. Leptin is a protein hormone found in mammals that is proportional to the amount of endogenous fat stores within an individual. Recently, researchers have confirmed that a mammalian leptin analogue (MLA), based on the mammalian sequence of leptin, is present with associated receptors and proteins in avian species, with an inhibitory effect on foraging and body mass gain at high circulating levels. While MLA has been both quantified and manipulated in avian species, little is currently known regarding whether plasma MLA in wild-living species and individuals is associated with key reproductive decisions. We quantified plasma MLA in wild, Arctic-nesting female common eiders (Somateria mollissima) at arrival on the breeding grounds and followed them to determine subsequent breeding propensity, and reproductive phenology, investment, and success. Common eiders are capital-income breeding birds that require the accumulation of substantial fat stores to initiate laying and successfully complete incubation. We found that females with lower plasma MLA initiated breeding earlier and in a shorter period of time. However, we found no links between plasma MLA levels and breeding propensity, clutch size, or reproductive success. Although little is still known about plasma MLA, based on these results and its role in influencing foraging behaviors and condition gain, plasma MLA appears to be closely linked to reproductive timing and is therefore likely to underlie trade-offs surrounding life history decisions.
| S-EPMC6374671 | biostudies-literature
Project description:BACKGROUND:The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change with the parental genetic divergence. However, there still no unanimous conclusion for this hypothesis. RESULTS:Three species of Camellia with a range of genetic divergence and their F1 hybrids were used to study the effect of parental genetic divergence on gene expression and regulatory patterns in hybrids by RNA-sequencing and allelic expression analysis. We found that though the proportion of differentially expressed genes (DEGs) between the hybrids and their parents did not increase, a greater proportion of DEGs would be non-additively (especially transgressively) expressed in the hybrids as genomes between the parents become more divergent. In addition, the proportion of genes with significant evidence of cis-regulatory divergence increased, whereas with trans-regulatory divergence decreased with parental genetic divergence. CONCLUSIONS:The discordance within hybrid would intensify as the parents become more divergent, manifesting as more DEGs would be non-additively expressed. Trans-regulatory divergence contributed more to the additively inherited genes than cis, however, its contribution to expression difference would be weakened as cis mutations accumulated over time; and this might be an important reason for that the more divergent the parents are, the greater proportion of DEGs would be non-additively expressed in hybrid.
| S-EPMC6842218 | biostudies-literature
Project description:Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage-specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.
| S-EPMC3538993 | biostudies-literature
Project description:Wild relatives of domesticated Capsicum represent substantial genetic diversity and thus sources of traits of potential interest. Furthermore, the hybridization compatibility between members of Capsicum species complexes remains unresolved. Improving our understanding of the relationship between Capsicum species relatedness and their ability to form hybrids is a highly pertinent issue. Through the development of novel interspecific hybrids in this study, we demonstrate interspecies compatibility is not necessarily reflected in relatedness according to established Capsicum genepool complexes. Based on a phylogeny constructed by genotyping using simple sequence repeat (SSR) markers and with a portion of the waxy locus, and through principal component analysis (PCA) of phenotypic data, we clarify the relationships among wild and domesticated Capsicum species. Together, the phylogeny and hybridization studies provide evidence for the misidentification of a number of species from the World Vegetable Center genebank included in this study. The World Vegetable Center holds the largest collection of Capsicum genetic material globally, therefore this may reflect a wider issue in the misidentification of Capsicum wild relatives. The findings presented here provide insight into an apparent disconnect between compatibility and relatedness in the Capsicum genus, which will be valuable in identifying candidates for future breeding programs.
| S-EPMC8508556 | biostudies-literature
Project description:Sexual reproduction in eukaryotes requires the fusion of two compatible gametes of opposite sexes or mating types. To meet the challenge of finding a mating partner with compatible gametes, evolutionary mechanisms such as hermaphroditism and self-fertilization have repeatedly evolved. Here, by combining the insights from comparative genomics, computer simulations and experimental evolution in fission yeast, we shed light on the conditions promoting separate mating types or self-compatibility by mating-type switching. Analogous to multiple independent transitions between switchers and non-switchers in natural populations mediated by structural genomic changes, novel switching genotypes readily evolved under selection in the experimental populations. Detailed fitness measurements accompanied by computer simulations show the benefits and costs of switching during sexual and asexual reproduction, governing the occurrence of both strategies in nature. Our findings illuminate the trade-off between the benefits of reproductive assurance and its fitness costs under benign conditions facilitating the evolution of self-compatibility.
| S-EPMC5915400 | biostudies-literature
Project description:BackgroundReproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI.ResultsBy augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI.ConclusionsThese results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.
| S-EPMC3225234 | biostudies-literature
Project description:Ecological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. Selection favouring gene regulatory divergence between species could result in transgressive levels of gene expression in F1 hybrids that may lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to identify patterns of hybrid gene misexpression that may be driven by adaptive regulatory divergence within a young radiation of Cyprinodon pupfishes, which consists of a dietary generalist and two trophic specialists-a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1,000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misexpressed in F1 hybrids. A subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length-the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can contribute to hybrid gene misexpression which may act as a reproductive barrier between nascent species.
| S-EPMC8209238 | biostudies-literature