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1.
Bruce E. Deagle Cassandra Faux So Kawaguchi Bettina Meyer Simon N. Jarman 《Molecular ecology》2015,24(19):4943-4959
Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA‐based analyses have focused on a limited number of markers and have covered only part of their circum‐Antarctic range. We used mitochondrial DNA and restriction site‐associated DNA sequencing (RAD‐seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD‐seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD‐seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist. 相似文献
2.
Alan Brelsford Christophe Dufresnes Nicolas Perrin 《Evolution; international journal of organic evolution》2016,70(4):840-847
Empirical studies on the relative roles of occasional XY recombination versus sex‐chromosome turnover in preventing sex‐chromosome differentiation may shed light on the evolutionary forces acting on sex‐determination systems. Signatures of XY recombination are difficult to distinguish from those of homologous transitions (i.e., transitions in sex‐determination systems that keep sex‐chromosome identity): both models predict X and Y alleles at sex‐linked genes to cluster by species. However, the XY‐recombination model specifically predicts the reverse pattern (clustering by gametologs) for those genes that are directly involved in sex determination. Hence, the latter model can only be validated by identification of an ancestral sex‐determining region (SDR) with trans‐species polymorphism associated to sex. Here we combine a candidate‐gene approach with a genome scan to identify a small SDR shared by four species of a monophyletic clade of European tree frogs. This SDR encompasses at least the N‐terminal part of Dmrt1 and immediate upstream sequences. Our findings provide definitive evidence that sex‐chromosome homomorphy in this clade results only from XY recombination, and take an important step toward the identification of the sex‐determining locus. Moreover, the sex‐diagnostic markers we identify will enable research on environmental sex reversal in a wider range of frog species. 相似文献
3.
Wenlu Yang Deyan Wang Yiling Li Zhiyang Zhang Shaofei Tong Mengmeng Li Xu Zhang Lei Zhang Liwen Ren Xinzhi Ma Ran Zhou Brian J Sanderson Ken Keefover-Ring Tongming Yin Lawrence B Smart Jianquan Liu Stephen P DiFazio Matthew Olson Tao Ma 《Molecular biology and evolution》2021,38(3):968
Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems. 相似文献
4.
Daniela H. Palmer Thea F. Rogers Rebecca Dean Alison E. Wright 《Molecular ecology》2019,28(21):4709-4724
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non‐model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research. 相似文献
5.
为检验阿尔泰林蛙(Rana altaica)的系统发育地位及其物种有效性,该文运用线粒体细胞色素b基因,应用贝叶斯分析和最大简约方法构建了欧哑人陆分布的部分林蛙的系统发育关系.两种分析方法均支持阿尔泰林蛙在田野林蛙(R.arvalis)这一分支的内部.单倍型网络图显示来自阿尔泰地区和中西伯利亚地区所谓的阿尔泰林蛙与田野林蛙有共享单倍型.通过该文母系遗传发育分析结果显爪阿尔泰林蛙种级地位不成立,是田野林蛙的同物异名.另外,该文实验分析结果提示,对中国分布的林蛙内部种组划分应建立在系统进化关系的基础上重新进行评估. 相似文献
6.
William R. Stovall Helen R. Taylor Michael Black Stefanie Grosser Kim Rutherford Neil J. Gemmell 《Molecular ecology resources》2018,18(2):179-190
Establishing the sex of individuals in wild systems can be challenging and often requires genetic testing. Genotyping‐by‐sequencing (GBS) and other reduced‐representation DNA sequencing (RRS) protocols (e.g., RADseq, ddRAD) have enabled the analysis of genetic data on an unprecedented scale. Here, we present a novel approach for the discovery and statistical validation of sex‐specific loci in GBS data sets. We used GBS to genotype 166 New Zealand fur seals (NZFS, Arctocephalus forsteri) of known sex. We retained monomorphic loci as potential sex‐specific markers in the locus discovery phase. We then used (i) a sex‐specific locus threshold (SSLT) to identify significantly male‐specific loci within our data set; and (ii) a significant sex‐assignment threshold (SSAT) to confidently assign sex in silico the presence or absence of significantly male‐specific loci to individuals in our data set treated as unknowns (98.9% accuracy for females; 95.8% for males, estimated via cross‐validation). Furthermore, we assigned sex to 86 individuals of true unknown sex using our SSAT and assessed the effect of SSLT adjustments on these assignments. From 90 verified sex‐specific loci, we developed a panel of three sex‐specific PCR primers that we used to ascertain sex independently of our GBS data, which we show amplify reliably in at least two other pinniped species. Using monomorphic loci normally discarded from large SNP data sets is an effective way to identify robust sex‐linked markers for nonmodel species. Our novel pipeline can be used to identify and statistically validate monomorphic and polymorphic sex‐specific markers across a range of species and RRS data sets. 相似文献
7.
Hans Recknagel Arne Jacobs Pawel Herzyk Kathryn R. Elmer 《Molecular ecology resources》2015,15(6):1316-1329
Research in evolutionary biology involving nonmodel organisms is rapidly shifting from using traditional molecular markers such as mtDNA and microsatellites to higher throughput SNP genotyping methodologies to address questions in population genetics, phylogenetics and genetic mapping. Restriction site associated DNA sequencing (RAD sequencing or RADseq) has become an established method for SNP genotyping on Illumina sequencing platforms. Here, we developed a protocol and adapters for double‐digest RAD sequencing for Ion Torrent (Life Technologies; Ion Proton, Ion PGM) semiconductor sequencing. We sequenced thirteen genomic libraries of three different nonmodel vertebrate species on Ion Proton with PI chips: Arctic charr Salvelinus alpinus, European whitefish Coregonus lavaretus and common lizard Zootoca vivipara. This resulted in ~962 million single‐end reads overall and a mean of ~74 million reads per library. We filtered the genomic data using Stacks, a bioinformatic tool to process RAD sequencing data. On average, we obtained ~11 000 polymorphic loci per library of 6–30 individuals. We validate our new method by technical and biological replication, by reconstructing phylogenetic relationships, and using a hybrid genetic cross to track genomic variants. Finally, we discuss the differences between using the different sequencing platforms in the context of RAD sequencing, assessing possible advantages and disadvantages. We show that our protocol can be used for Ion semiconductor sequencing platforms for the rapid and cost‐effective generation of variable and reproducible genetic markers. 相似文献
8.
N. Rodrigues C. Betto‐Colliard H. Jourdan‐Pineau N. Perrin 《Journal of evolutionary biology》2013,26(7):1569-1577
In sharp contrast with birds and mammals, the sex chromosomes of ectothermic vertebrates are often undifferentiated, for reasons that remain debated. A linkage map was recently published for Rana temporaria (Linnaeus, 1758) from Fennoscandia (Eastern European lineage), with a proposed sex‐determining role for linkage group 2 (LG2). We analysed linkage patterns in lowland and highland populations from Switzerland (Western European lineage), with special focus on LG2. Sibship analyses showed large differences from the Fennoscandian map in terms of recombination rates and loci order, pointing to large‐scale inversions or translocations. All linkage groups displayed extreme heterochiasmy (total map length was 12.2 cM in males, versus 869.8 cM in females). Sex determination was polymorphic within populations: a majority of families (with equal sex ratios) showed a strong correlation between offspring phenotypic sex and LG2 paternal haplotypes, whereas other families (some of which with female‐biased sex ratios) did not show any correlation. The factors determining sex in the latter could not be identified. This coexistence of several sex‐determination systems should induce frequent recombination of X and Y haplotypes, even in the absence of male recombination. Accordingly, we found no sex differences in allelic frequencies on LG2 markers among wild‐caught male and female adults, except in one high‐altitude population, where nonrecombinant Y haplotypes suggest sex to be entirely determined by LG2. Multifactorial sex determination certainly contributes to the lack of sex‐chromosome differentiation in amphibians. 相似文献
9.
The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low‐cost double‐digest restriction site‐associated DNA sequencing (ddRADseq) protocol to reveal among‐ and within‐species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded adapters and incorporates universal indexes for multiplexing. We tested for reproducibility and functionality by comparing shared loci from sample replicates and assessed the effects of numbers of ambiguous sites and clustering thresholds on coverage depths, number of shared loci among samples, and phylogenetic reconstruction. Errors between technical replicates were minimal. Relaxing the quality‐filtering criteria increased the mean coverage depth per locus and the number of loci recovered within a sample, but had little effect on the number of shared loci across samples. Increasing clustering threshold decreased the mean coverage depth per cluster and increased the number of loci recovered within a sample but also decreased the number of shared loci across samples, especially among distantly related species. The combination of low similarity clustering (70%) and relaxed quality‐filtering (allowing up to 30 ambiguous sites per read) performed the best in phylogenetic analyses at both recent and deep genetic divergences. Hence, this method generated sufficient number of shared homologous loci to investigate the evolutionary relationships among divergent fungal lineages with small haploid genomes. The greater genetic resolution also revealed new structure within species that correlated with ecological traits, providing valuable insights into their cryptic life histories. 相似文献
10.
RAD‐tag is a powerful tool for high‐throughput genotyping. It relies on PCR amplification of the starting material, following enzymatic digestion and sequencing adaptor ligation. Amplification introduces duplicate reads into the data, which arise from the same template molecule and are statistically nonindependent, potentially introducing errors into genotype calling. In shotgun sequencing, data duplicates are removed by filtering reads starting at the same position in the alignment. However, restriction enzymes target specific locations within the genome, causing reads to start in the same place, and making it difficult to estimate the extent of PCR duplication. Here, we introduce a slight change to the Illumina sequencing adaptor chemistry, appending a unique four‐base tag to the first index read, which allows duplicate discrimination in aligned data. This approach was validated on the Illumina MiSeq platform, using double‐digest libraries of ants (Wasmannia auropunctata) and yeast (Saccharomyces cerevisiae) with known genotypes, producing modest though statistically significant gains in the odds of calling a genotype accurately. More importantly, removing duplicates also corrected for strong sample‐to‐sample variability of genotype calling accuracy seen in the ant samples. For libraries prepared from low‐input degraded museum bird samples (Mixornis gularis), which had low complexity, having been generated from relatively few starting molecules, adaptor tags show that virtually all of the genotypes were called with inflated confidence as a result of PCR duplicates. Quantification of library complexity by adaptor tagging does not significantly increase the difficulty of the overall workflow or its cost, but corrects for differences in quality between samples and permits analysis of low‐input material. 相似文献
11.
Genotyping‐by‐sequencing (GBS) and related methods are increasingly used for studies of non‐model organisms from population genetic to phylogenetic scales. We present GIbPSs, a new genotyping toolkit for the analysis of data from various protocols such as RAD, double‐digest RAD, GBS, and two‐enzyme GBS without a reference genome. GIbPSs can handle paired‐end GBS data and is able to assign reads from both strands of a restriction fragment to the same locus. GIbPSs is most suitable for population genetic and phylogeographic analyses. It avoids genotyping errors due to indel variation by identifying and discarding affected loci. GIbPSs creates a genotype database that offers rich functionality for data filtering and export in numerous formats. We performed comparative analyses of simulated and real GBS data with GIbPSs and another program, pyRAD. This program accounts for indel variation by aligning homologous sequences. GIbPSs performed better than pyRAD in several aspects. It required much less computation time and displayed higher genotyping accuracy. GIbPSs retained smaller numbers of loci overall in analyses of real GBS data. It nevertheless delivered more complete genotype matrices with greater locus overlap between individuals and greater numbers of loci sampled in all individuals. 相似文献
12.
Terry D. Beacham Colin G. Wallace Kim Jonsen Brenda McIntosh John R. Candy Katherine Horst Cheryl Lynch David Willis Wilf Luedke Lee Kearey Eric B. Rondeau 《Evolutionary Applications》2021,14(5):1365-1389
Wild Pacific salmon, including Chinook salmon Oncorhynchus tshawytscha, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest, mitigation for hydroelectric development, and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. For policy implementation, a new approach to the assessment and management of Chinook salmon and the associated hatchery production and fisheries management are needed. Implementation of genetic stock identification (GSI) and parentage-based tagging (PBT) for marine fisheries assessment may overcome problems associated with coded-wire tag-based (CWT) assessment and management of Chinook salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. GSI and PBT were used to identify Chinook salmon sampled in 2018 and 2019 marine fisheries (18,819 individuals genotyped) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 391 single nucleotide polymorphisms via direct sequencing of amplicons. Very high accuracy of assignment to population and age (>99.5%) via PBT was observed for 1994 Chinook salmon of ages 2–4 years, with a 105,722–individual, 380–population baseline available for assignment. Application of a GSI-PBT system of identification to individuals in 2019 fisheries provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, with fishery exploitation rates directly comparable to those provided by CWTs for 13 populations. GSI and PBT provide an alternate, cheaper, and more effective method in the assessment and management of Canadian-origin Chinook salmon relative to CWTs, and an opportunity for a genetics-based system to replace the current CWT system for salmon assessment. 相似文献
13.
中亚林蛙的核型,C带和银带研究及田野林蛙起源的探讨 总被引：6，自引：1，他引：6
中亚林蛙（Ranaasialica）的核型为2n＝26,NF＝52．第2号染色体短臂有一条近端着丝粒区C带。第10号染色体长臂上有一对标准NORs。本文认为,田野林蛙（Ranaarvalis）起源于欧洲,是欧洲林蛙群与亚洲2n＝24的林蛙群间的过渡种类。 相似文献
14.
15.
性染色体进化及性别决定机制是脊椎动物进化研究的热点,近些年更是提出了性别组学的概念。脊椎动物各类群的性别决定机制呈现出多种形式,尤其是具有年青性染色体系统的类群的演化模式更为多样。由于年青性染色体在核型形态上差异不大,传统的研究方法难以识别,因此本文从细胞遗传学方法、性染色体上的DNA序列/RNA序列及其表达、蛋白质表达等多个维度阐述了年青性染色体和性别决定系统的鉴定方法。在高通量测序技术的基础上结合基因组学、蛋白质组学和代谢组学对性别决定系统进行更深层次的研究,从而形成性别组学,并最终解答性别决定的方式多样性及其背后的进化动力和分子途径。 相似文献
16.
Catherine A. Wilson Samantha K. High Braedan M. McCluskey Angel Amores Yi-lin Yan Tom A. Titus Jennifer L. Anderson Peter Batzel Michael J. Carvan III Manfred Schartl John H. Postlethwait 《Genetics》2014,198(3):1291-1308
Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this “RAD-sex” method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, “male genotypes” became males and some “female genotypes” also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture. 相似文献
17.
Richard P. Meisel 《BioEssays : news and reviews in molecular, cellular and developmental biology》2020,42(9):1900212
Sex chromosomes can differ between species as a result of evolutionary turnover, a process that can be driven by evolution of the sex determination pathway. Canonical models of sex chromosome turnover hypothesize that a new master sex determining gene causes an autosome to become a sex chromosome or an XY chromosome pair to switch to a ZW pair (or vice versa). Here, a novel paradigm for the evolution of sex determination and sex chromosomes is presented, in which there is an evolutionary transition in the master sex determiner, but the X chromosome remains unchanged. There are three documented examples of the novel paradigm, and it is hypothesized that a similar process could happen in a ZW sex chromosome system. Three other taxa are also identified where the novel paradigm may have occurred, and how it could be distinguished from canonical trajectories in these and additional taxa is also described. 相似文献
18.
Urban environments are warmer, have higher levels of atmospheric CO2 and have altered patterns of disturbance and precipitation than nearby rural areas. These differences can be important for plant growth and are likely to create distinct selective environments. We planted a common garden experiment with seeds collected from natural populations of the native annual plant Lepidium virginicum, growing in five urban and nearby rural areas in the northern United States to determine whether and how urban populations differ from those from surrounding rural areas. When grown in a common environment, plants grown from seeds collected from urban areas bolted sooner, grew larger, had fewer leaves, had an extended time between bolting and flowering, and produced more seeds than plants grown from seeds collected from rural areas. Interestingly, the rural populations exhibited larger phenotypic differences from one another than urban populations. Surprisingly, genomic data revealed that the majority of individuals in each of the urban populations were more closely related to individuals from other urban populations than they were to geographically proximate rural areas – the one exception being urban and rural populations from New York which were nearly identical. Taken together, our results suggest that selection in urban environments favors different traits than selection in rural environments and that these differences can drive adaptation and shape population structure. 相似文献
19.
Many amphibian species are known to form leks during breeding season, yet it has seldom been tested which evolutionary forces are likely to act on lek formation in this taxon. We tested the kin selection hypothesis for lek formation by using eight variable microsatellite loci to compare the genetic relationship of 203 males in seven Rana arvalis leks. The results indicate that moor frog males do not lek with kin: their relatedness within leks was not higher than expected by chance. Furthermore, spatially distinct leks within same water bodies could not be distinguished from each other as separate units. These results are not expected if kin selection underlie lek formation. On the basis of these results and general knowledge of anuran breeding biology, we suggest that lek formation in explosively breeding amphibians might have evolved by female choice for breeding aggregations, combined with female choice of habitat. Future work should aim at predicting aggregations based on rules of phonotaxis over different spatial scales, and empirical work should document visitation rates not only for leks of a specific size, but also for different travel distances that visiting females may have had to cover. 相似文献
20.
Sex reversal has been suggested to have profound implications for the evolution of sex chromosomes and population dynamics in ectotherms. Occasional sex reversal of genetic males has been hypothesized to prevent the evolutionary decay of nonrecombining Y chromosomes caused by the accumulation of deleterious mutations. At the same time, sex reversals can have a negative effect on population growth rate. Here, we studied phenotypic and genotypic sex in the common frog (Rana temporaria) in a subarctic environment, where strongly female‐biased sex ratios have raised the possibility of frequent sex reversals. We developed two novel sex‐linked microsatellite markers for the species and used them with a third, existing marker and a Bayesian modelling approach to study the occurrence of sex reversal and to determine primary sex ratios in egg clutches. Our results show that a significant proportion (0.09, 95% credible interval: 0.04–0.18) of adults that were genetically female expressed the male phenotype, but there was no evidence of sex reversal of genetic males that is required for counteracting the degeneration of Y chromosome. The primary sex ratios were mostly equal, but three clutches consisted only of genetic females and three others had a significant female bias. Reproduction of the sex‐reversed genetic females appears to create all‐female clutches potentially skewing the population level adult sex‐ratio consistent with field observations. However, based on a simulation model, such a bias is expected to be small and transient and thus does not fully explain the observed female‐bias in the field. 相似文献