The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.

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Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders

BMC Ecology and Evolution ◽

10.1186/s12862-021-01779-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Cory A. Berger ◽

Michael S. Brewer ◽

Nobuaki Kono ◽

Hiroyuki Nakamura ◽

Kazuharu Arakawa ◽

...

Keyword(s):

Genetic Basis ◽

Adaptive Traits ◽

Deep Time ◽

Selective Pressures ◽

Silk Production ◽

Silk Glands ◽

Genetic Mechanisms ◽

Orb Web ◽

Short Time ◽

Web Building

Abstract Background A striking aspect of evolution is that it often converges on similar trajectories. Evolutionary convergence can occur in deep time or over short time scales, and is associated with the imposition of similar selective pressures. Repeated convergent events provide a framework to infer the genetic basis of adaptive traits. The current study examines the genetic basis of secondary web loss within web-building spiders (Araneoidea). Specifically, we use a lineage of spiders in the genus Tetragnatha (Tetragnathidae) that has diverged into two clades associated with the relatively recent (5 mya) colonization of, and subsequent adaptive radiation within, the Hawaiian Islands. One clade has adopted a cursorial lifestyle, and the other has retained the ancestral behavior of capturing prey with sticky orb webs. We explore how these behavioral phenotypes are reflected in the morphology of the spinning apparatus and internal silk glands, and the expression of silk genes. Several sister families to the Tetragnathidae have undergone similar web loss, so we also ask whether convergent patterns of selection can be detected in these lineages. Results The cursorial clade has lost spigots associated with the sticky spiral of the orb web. This appears to have been accompanied by loss of silk glands themselves. We generated phylogenies of silk proteins (spidroins), which showed that the transcriptomes of cursorial Tetragnatha contain all major spidroins except for flagelliform. We also found an uncharacterized spidroin that has higher expression in cursorial species. We found evidence for convergent selection acting on this spidroin, as well as genes involved in protein metabolism, in the cursorial Tetragnatha and divergent cursorial lineages in the families Malkaridae and Mimetidae. Conclusions Our results provide strong evidence that independent web loss events and the associated adoption of a cursorial lifestyle are based on similar genetic mechanisms. Many genes we identified as having evolved convergently are associated with protein synthesis, degradation, and processing, which are processes that play important roles in silk production. This study demonstrates, in the case of independent evolution of web loss, that similar selective pressures act on many of the same genes to produce the same phenotypes and behaviors.

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Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies

Nutrients ◽

10.3390/nu12092689 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2689

Author(s):

Augusto Anguita-Ruiz ◽

Concepción M. Aguilera ◽

Ángel Gil

Keyword(s):

Genetic Basis ◽

Human Populations ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genotype Frequencies ◽

Genetic Mechanisms ◽

Visualization Tools ◽

Available Information ◽

Static World ◽

Interactive Resources

In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.

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On the role of enemies in divergence and diversification of prey: a review and synthesis

Canadian Journal of Zoology ◽

10.1139/z05-063 ◽

2005 ◽

Vol 83 (7) ◽

pp. 894-910 ◽

Cited By ~ 105

Author(s):

Steven M Vamosi

Keyword(s):

Visual Cues ◽

Phenotypic Diversity ◽

Theoretical Models ◽

Ecological Interactions ◽

Closely Related Species ◽

Diversification Rates ◽

Extinction Rates ◽

Phenotypic Divergence ◽

Experimental Approaches

Understanding the contribution of ecological interactions to the origin and maintenance of diversity is a fundamental challenge for ecologists and evolutionary biologists, and one that is currently receiving a great deal of attention. Natural enemies (e.g., predators, parasites, and herbivores) are ubiquitous in food webs and are predicted to have significant impacts on phenotypic diversity and on speciation, and extinction rates of their prey. Spurred by the development of a theoretical framework beginning in the late 1970s, there is now a growing body of literature that addresses the effects of enemy–prey interactions on the evolution of prey. A number of theoretical models predict that enemies can produce phenotypic divergence between closely related species, even in the absence of interspecific competition for resources. Effects on diversification of prey are more variable, and enemies may either enhance or depress speciation and extinction rates of their prey. Empirical evidences from a number of study systems, notably those involving predators and prey in aquatic environments and interactions between insects and flowering plants, confirm both predictions. There is now considerable evidence for the role of enemies, especially those that are size-selective or use visual cues when identifying suitable prey, on phenotypic divergence of sympatric and allopatric taxa. Enemies may spur diversification rates in certain groups under some circumstances, and hinder diversification rates in other cases. I suggest that further research should focus on the role of enemies in diversification of prey, with significant insights likely to be the product of applying traditional experimental approaches and emerging comparative phylogenetic methods.

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Understanding the Genetic Basis of C4 Kranz Anatomy with a View to Engineering C3 Crops

Annual Review of Genetics ◽

10.1146/annurev-genet-120417-031217 ◽

2018 ◽

Vol 52 (1) ◽

pp. 249-270 ◽

Cited By ~ 27

Author(s):

Olga V. Sedelnikova ◽

Thomas E. Hughes ◽

Jane A. Langdale

Keyword(s):

Genetic Basis ◽

Genetic Regulation ◽

Crop Productivity ◽

Research Field ◽

Leaf Cell ◽

Cell Type ◽

Kranz Anatomy ◽

Genetic Mechanisms ◽

Metabolic Reactions ◽

Type Specification

One of the most remarkable examples of convergent evolution is the transition from C3 to C4 photosynthesis, an event that occurred on over 60 independent occasions. The evolution of C4 is particularly noteworthy because of the complexity of the developmental and metabolic changes that took place. In most cases, compartmentalized metabolic reactions were facilitated by the development of a distinct leaf anatomy known as Kranz. C4 Kranz anatomy differs from ancestral C3 anatomy with respect to vein spacing patterns across the leaf, cell-type specification around veins, and cell-specific organelle function. Here we review our current understanding of how Kranz anatomy evolved and how it develops, with a focus on studies that are dissecting the underlying genetic mechanisms. This research field has gained prominence in recent years because understanding the genetic regulation of Kranz may enable the C3-to-C4 transition to be engineered, an endeavor that would significantly enhance crop productivity.

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Genetic analyses of several Drosophila ananassae-complex species show a low-frequency major gene for parthenogenesis that maps to chromosome 2

Genetics Research ◽

10.1017/s0016672303006657 ◽

2004 ◽

Vol 83 (2) ◽

pp. 83-89 ◽

Cited By ~ 7

Author(s):

MUNEO MATSUDA ◽

YOSHIKO N. TOBARI

Keyword(s):

Related Species ◽

Genetic Basis ◽

Present Report ◽

Major Gene ◽

American Samoa ◽

Species Group ◽

Drosophila Ananassae ◽

Chromosome 2 ◽

Closely Related Species ◽

Complex Species

Parthenogenetic strains of several species have been found in the genus Drosophila. The mode of diploidization in the eggs of females has been found to be post-meiotic nuclear fusion. The genetic basis for this parthenogenesis is not understood but is believed to be under the control of a complex polygenic system. We found parthenogenetic females in an isofemale strain (LAE345) of D. pallidosa-like collected in 1981 at Lae, Papua New Guinea, and established a parthenogenetically reproducing strain. Parthenogenetic strains of D. ananassae and D. pallidosa collected at Taputimu, American Samoa had also been established by Futch (1972). D. ananassae, D. pallidosa and D. pallidosa-like are very closely related species belonging to the ananassae complex of the ananassae species subgroup of the melanogaster species group. Using these three species, we found that more than 80% of females from parthenogenetic strains produced progeny parthenogenetically and that inter-specific hybrid females also produced impaternate progeny. In the present report, we demonstrate that the mode of parthenogenesis of D. ananassae appears to be the post-meiotic nuclear doubling of a single meiotic product, and that a major gene responsible for the parthenogenesis maps to the left arm of the second chromosome of D. ananassae. We also suggest that the genetic basis for parthenogenesis capacity may be identical among the three closely related species. We discuss the function of the gene required for parthenogenesis and its significance for the evolutionary process.

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Multiple roles for laccase2 in butterfly wing pigmentation, scale development, and cuticle tanning

10.1101/858167 ◽

2019 ◽

Author(s):

Ceili L. Peng ◽

Anyi Mazo-Vargas ◽

Benjamin J. Brack ◽

Robert D. Reed

Keyword(s):

Scale Development ◽

Multiple Roles ◽

Melanin Pigmentation ◽

Lepidopteran Insect ◽

Genetic Mechanisms ◽

Nymphalid Butterfly ◽

Encoding Gene ◽

Mutant Phenotypes ◽

Insight Into ◽

Wing Scales

ABSTRACTLepidopteran wing scales play important roles in a number of functions including color patterning and thermoregulation. Despite the importance of wing scales, however, we still have a limited understanding of the genetic mechanisms that underlie scale patterning, development, and coloration. Here we explore the function of the phenoloxidase-encoding gene laccase2 in wing and scale development in the nymphalid butterfly Vanessa cardui. Somatic deletion mosaics of laccase2 generated by CRISPR/Cas9 genome editing presented several distinct mutant phenotypes. Consistent with work in other non-lepidopteran insect groups, we observed reductions in melanin pigmentation and defects in cuticle formation. We were also surprised, however, to see distinct effects on scale development including complete loss of wing scales. This work highlights laccase2 as a gene that plays multiple roles in wing and scale development and provides new insight into the evolution of lepidopteran wing coloration.

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Divergent evolutionary trajectories shape the postmating transcriptional profiles of conspecific and heterospecifically mated females

10.1101/2021.11.07.467655 ◽

2021 ◽

Author(s):

Fernando Diaz ◽

Allan W. Carson ◽

Xingsen Chen ◽

Joshua M. Coleman ◽

Jeremy M. Bono ◽

...

Keyword(s):

Sexual Selection ◽

Genetic Basis ◽

Intron Retention ◽

Transcriptional Response ◽

Isolated Populations ◽

Closely Related Species ◽

Transcriptional Profiles ◽

Future Studies ◽

Evolutionary Forces ◽

Evolutionary Trajectories

Postmating-prezygotic (PMPZ) reproductive isolation is hypothesized to result from divergent coevolutionary trajectories of sexual selection and/or sexual conflict in isolated populations (coevolutionary divergence model). However, the genetic basis of PMPZ incompatibilities between species is poorly understood. Here, we use a comparative framework to test predictions of the coevolutionary divergence model using a large transcriptomic dataset generated from con- and heterospecifically mated Drosophila mojavensis and D. arizonae female reproductive tracts. We found striking divergence between the species in the female postmating transcriptional response to conspecific mating, including differences in differential expression (DE), alternative splicing (AS), and intron retention (IR). As predicted, heterospecific matings produced disrupted transcriptional profiles, but the overall patterns of misregulation were different between the reciprocal crosses. Moreover, we found a positive correlation between postmating transcriptional divergence between species and levels of transcriptional disruption in heterospecific crosses, indicating that mating-responsive genes that have diverged more in expression also have more disrupted transcriptional profiles in heterospecifically mated females. Overall, our results are consistent with predictions of the coevolutionary divergence model and lay the foundation for future studies aimed at identifying specific genes involved in PMPZ incompatibilities and the evolutionary forces that have contributed to their divergence in closely related species.

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Differential Expression of Myogenic and Calcium Signaling-Related Genes in Broilers Affected With White Striping

Frontiers in Physiology ◽

10.3389/fphys.2021.712464 ◽

2021 ◽

Vol 12 ◽

Author(s):

Caroline Michele Marinho Marciano ◽

Adriana Mércia Guaratini Ibelli ◽

Jorge Augusto Petroli Marchesi ◽

Jane de Oliveira Peixoto ◽

Lana Teixeira Fernandes ◽

...

Keyword(s):

Oxidative Stress ◽

Calcium Signaling ◽

Genetic Basis ◽

Fiber Type ◽

Biological Pathways ◽

Pcr Analysis ◽

Poultry Production ◽

Qrt Pcr ◽

White Striping ◽

Genetic Mechanisms

White Striping (WS) has been one of the main issues in poultry production in the last years since it affects meat quality. Studies have been conducted to understand WS and other myopathies in chickens, and some biological pathways have been associated to the prevalence of these conditions, such as extracellular calcium level, oxidative stress, localized hypoxia, possible fiber-type switching, and cellular repairing. Therefore, to understand the genetic mechanisms involved in WS, 15 functional candidate genes were chosen to be analyzed by quantitative PCR (qPCR) in breast muscle of normal and WS-affected chickens. To this, the pectoral major muscle (PMM) of 16 normal and 16 WS-affected broilers were collected at 42 days of age and submitted to qRT-PCR analysis. Out of the 15 genes studied, six were differentially expressed between groups. The CA2, CSRP3, and PLIN1 were upregulated, while CALM2, DNASE1L3, and MYLK2 genes were downregulated in the WS-affected when compared to the normal broilers. These findings highlight that the disruption on muscle and calcium signaling pathways can possibly be triggering WS in chickens. Improving our understanding on the genetic basis involved with this myopathy might contribute for reducing WS in poultry production.

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The role of APETALA1 in petal number robustness

eLife ◽

10.7554/elife.39399 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 8

Author(s):

Marie Monniaux ◽

Bjorn Pieper ◽

Sarah M McKim ◽

Anne-Lise Routier-Kierzkowska ◽

Daniel Kierzkowski ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Genetic Variation ◽

Reproductive Success ◽

Genetic Basis ◽

Phenotypic Expression ◽

Specific Difference ◽

Closely Related Species ◽

Epistatic Interactions ◽

Species Specific

Invariant floral forms are important for reproductive success and robust to natural perturbations. Petal number, for example, is invariant in Arabidopsis thaliana flowers. However, petal number varies in the closely related species Cardamine hirsuta, and the genetic basis for this difference between species is unknown. Here we show that divergence in the pleiotropic floral regulator APETALA1 (AP1) can account for the species-specific difference in petal number robustness. This large effect of AP1 is explained by epistatic interactions: A. thaliana AP1 confers robustness by masking the phenotypic expression of quantitative trait loci controlling petal number in C. hirsuta. We show that C. hirsuta AP1 fails to complement this function of A. thaliana AP1, conferring variable petal number, and that upstream regulatory regions of AP1 contribute to this divergence. Moreover, variable petal number is maintained in C. hirsuta despite sufficient standing genetic variation in natural accessions to produce plants with four-petalled flowers.

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The Loci of Behavioral Evolution: Evidence That Fas2 and tilB Underlie Differences in Pupation Site Choice Behavior between Drosophila melanogaster and D. simulans

Molecular Biology and Evolution ◽

10.1093/molbev/msz274 ◽

2019 ◽

Vol 37 (3) ◽

pp. 864-880

Author(s):

Alison Pischedda ◽

Michael P Shahandeh ◽

Thomas L Turner

Keyword(s):

Drosophila Melanogaster ◽

X Chromosome ◽

Related Species ◽

Choice Behavior ◽

Genetic Basis ◽

Association Studies ◽

Single Gene ◽

Closely Related Species ◽

Environmentally Sensitive ◽

Pupation Site

Abstract The behaviors of closely related species can be remarkably different, and these differences have important ecological and evolutionary consequences. Although the recent boom in genotype–phenotype studies has led to a greater understanding of the genetic architecture and evolution of a variety of traits, studies identifying the genetic basis of behaviors are, comparatively, still lacking. This is likely because they are complex and environmentally sensitive phenotypes, making them difficult to measure reliably for association studies. The Drosophila species complex holds promise for addressing these challenges, as the behaviors of closely related species can be readily assayed in a common environment. Here, we investigate the genetic basis of an evolved behavioral difference, pupation site choice, between Drosophila melanogaster and D. simulans. In this study, we demonstrate a significant contribution of the X chromosome to the difference in pupation site choice behavior between these species. Using a panel of X-chromosome deficiencies, we screened the majority of the X chromosome for causal loci and identified two regions associated with this X-effect. We then collect gene disruption and RNAi data supporting a single gene that affects pupation behavior within each region: Fas2 and tilB. Finally, we show that differences in tilB expression correlate with the differences in pupation site choice behavior between species. This evidence associating two genes with differences in a complex, environmentally sensitive behavior represents the first step toward a functional and evolutionary understanding of this behavioral divergence.

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