Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae)

Biologists marvel at the powers of adaptive convergence, when distantly related animals look alike. While mimetic wing patterns of butterflies have fooled predators for millennia, entomologists inferred that mimics were distant relatives despite similar appearance. However, the obverse question has not been frequently asked. Who are the close relatives of mimetic butterflies and what are their features? As opposed to close convergence, divergence from a non-mimetic relative would also be extreme. When closely related animals look unalike, it is challenging to pair them. Genomic analysis promises to elucidate evolutionary relationships and shed light on molecular mechanisms of divergence. We chose the firetip skipper butterfly as a model due to its phenotypic diversity and abundance of mimicry. We sequenced and analysed whole genomes of nearly 120 representative species. Genomes partitioned this subfamily Pyrrhopyginae into five tribes (1 new), 23 genera and, additionally, 22 subgenera (10 new). The largest tribe Pyrrhopygini is divided into four subtribes (three new). Surprisingly, we found five cases where a uniquely patterned butterfly was formerly placed in a genus of its own and separately from its close relatives. In several cases, extreme and rapid phenotypic divergence involved not only wing patterns but also the structure of the male genitalia. The visually striking wing pattern difference between close relatives frequently involves disappearance or suffusion of spots and colour exchange between orange and blue. These differences (in particular, a transition between unspotted black and striped wings) happen recurrently on a short evolutionary time scale, and are therefore probably achieved by a small number of mutations.

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Genomes of skipper butterflies reveal extensive convergence of wing patterns

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1821304116 ◽

2019 ◽

Vol 116 (13) ◽

pp. 6232-6237 ◽

Cited By ~ 24

Author(s):

Wenlin Li ◽

Qian Cong ◽

Jinhui Shen ◽

Jing Zhang ◽

Winnie Hallwachs ◽

...

Keyword(s):

Phenotypic Traits ◽

Gene Markers ◽

Representative Species ◽

A Genome ◽

Wing Patterns ◽

Genomic Biology ◽

Similar Appearance ◽

Close Relatives ◽

Genomic Regions ◽

Distinct Morphology

For centuries, biologists have used phenotypes to infer evolution. For decades, a handful of gene markers have given us a glimpse of the genotype to combine with phenotypic traits. Today, we can sequence entire genomes from hundreds of species and gain yet closer scrutiny. To illustrate the power of genomics, we have chosen skipper butterflies (Hesperiidae). The genomes of 250 representative species of skippers reveal rampant inconsistencies between their current classification and a genome-based phylogeny. We use a dated genomic tree to define tribes (six new) and subtribes (six new), to overhaul genera (nine new) and subgenera (three new), and to display convergence in wing patterns that fooled researchers for decades. We find that many skippers with similar appearance are distantly related, and several skippers with distinct morphology are close relatives. These conclusions are strongly supported by different genomic regions and are consistent with some morphological traits. Our work is a forerunner to genomic biology shaping biodiversity research.

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Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese

BMC Genomics ◽

10.1186/s12864-021-07822-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yan Deng ◽

Shenqiang Hu ◽

Chenglong Luo ◽

Qingyuan Ouyang ◽

Li Li ◽

...

Keyword(s):

Molecular Mechanisms ◽

Protein Secondary Structure ◽

Genomic Analysis ◽

Production Performance ◽

Genetic Mechanism ◽

Farm Animals ◽

Practical Significance ◽

Genome Resequencing ◽

Genomic Analyses ◽

Whole Genome Resequencing

Abstract Background During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique appearance characteristic called knob, which is located at the base of the upper bill. However, neither the histomorphology nor the genetic mechanism of the knob phenotype has been revealed in geese. Results In the present study, integrated radiographic, histological, transcriptomic and genomic analyses revealed the histomorphological characteristics and genetic mechanism of goose knob. The knob skin was developed, and radiographic results demonstrated that the knob bone was obviously protuberant and pneumatized. Histologically, there were major differences in structures in both the knob skin and bone between geese owing knob (namely knob-geese) and those devoid of knob (namely non-knob geese). Through transcriptome analysis, 592 and 952 genes differentially expressed in knob skin and bone, and significantly enriched in PPAR and Calcium pathways in knob skin and bone, respectively, which revealed the molecular mechanisms of histomorphological differences of the knob between knob- and non-knob geese. Furthermore, integrated transcriptomic and genomic analysis contributed to the identification of 17 and 21 candidate genes associated with the knob formation in the skin and bone, respectively. Of them, DIO2 gene could play a pivotal role in determining the knob phenotype in geese. Because a non-synonymous mutation (c.642,923 G > A, P265L) changed DIO2 protein secondary structure in knob geese, and Sanger sequencing further showed that the AA genotype was identified in the population of knob geese, and was prevalent in a crossing population which was artificially selected for 10 generations. Conclusions This study was the first to uncover the knob histomorphological characteristics and genetic mechanism in geese, and DIO2 was identified as the crucial gene associated with the knob phenotype. These data not only expand and enrich our knowledge on the molecular mechanisms underlying the formation of head appendages in both mammalian and avian species, but also have important theoretical and practical significance for goose breeding.

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MoG+: a database of genomic variations across three mouse subspecies for biomedical research

Mammalian Genome ◽

10.1007/s00335-021-09933-w ◽

2021 ◽

Author(s):

Toyoyuki Takada ◽

Kentaro Fukuta ◽

Daiki Usuda ◽

Tatsuya Kushida ◽

Shinji Kondo ◽

...

Keyword(s):

Phenotypic Diversity ◽

Laboratory Mouse ◽

Genomic Analysis ◽

Inbred Strains ◽

Genetic Distances ◽

Mouse Strains ◽

Comparative Genomic ◽

Genome Database ◽

Data Resource ◽

Genomic Variations

AbstractLaboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m. domesticus-derived PGN2/Ms and BFM/Ms; M. m. castaneus-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M. m. musculus and M. m. castaneus. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.

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Phenotypic Divergence In Tomato Germplasm

SAARC Journal of Agriculture ◽

10.3329/sja.v17i2.45305 ◽

2020 ◽

Vol 17 (2) ◽

pp. 185-195

Author(s):

MZ Ullah ◽

L Hassan ◽

M Samsuzzaman ◽

MA Main

Keyword(s):

Multivariate Analysis ◽

Phenotypic Diversity ◽

Gene Bank ◽

Climatic Regions ◽

Phenotypic Divergence ◽

Locule Number ◽

Fruit Pericarp ◽

Pericarp Thickness ◽

Clustering Pattern ◽

Range Test

Phenotypic divergence was quantified by multivariate analysis among the 70 genotypes collected from different agro-climatic regions and was available in the gene bank of Energypac Agro Ltd., Gazipur, Bangladesh. Based on the phenotypic value of 11 characters, 70 genotypes were grouped into five clusters. The genotypes of tomato were distributed in different clusters suggesting that no association was found between geographical and phenotypic diversity. Cluster II consisted of maximum twenty three genotypes (32.86%) followed by cluster III of sixteen genotypes (22.85%). Cluster IV and Cluster V comprised of thirteen (18.57%) and ten genotypes (14.29%), respectively. Cluster I consisted of eight genotypes (11.43%). The highest intra-cluster divergence (0.061) for cluster I was invariably smaller than the lowest inter-cluster divergence between cluster IV and cluster V (2.83), thus authenticating the clustering pattern formed in this study. The intra-cluster divergence ranged from 0.007 to 0.061, whereas the inter-cluster divergence ranged from 2.83 to 8.34 between clusters IV and V and clusters III and V, respectively. The four characters that played the greatest role in differentiation were locule number per fruit, pericarp thickness, fruits per plant and days to 50% flowering. Twenty homozygous parents (15 female and five male) were selected from five clusters using range test among genotypes within cluster. From cluster I parents TM409, TM386 and TM528 and from cluster III parents TM403 and TM349 were selected as male. Parents TM356, TM361, TM368, TM371, TM377, TM384, TM422 and TM423 from cluster II; parents TM388, TM390, TM392 and TM410 from cluster IV and parents TM382, TM419 and TM360 from cluster V were selected as female. SAARC J. Agri., 17(2): 185-195 (2019)

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Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa396 ◽

2020 ◽

Vol 76 (1) ◽

pp. 91-100

Author(s):

Jorge Arca-Suárez ◽

Cristina Lasarte-Monterrubio ◽

Bruno-Kotska Rodiño-Janeiro ◽

Gabriel Cabot ◽

Juan Carlos Vázquez-Ucha ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Molecular Mechanisms ◽

Genomic Analysis ◽

Resistance Mechanisms ◽

Comparative Genomic ◽

Development Of Resistance ◽

Structural Impact ◽

Genetic Context

Abstract Background The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning. Objectives Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections. Methods Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes. Results The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold. Conclusions Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.

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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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Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.1663 ◽

2010 ◽

Vol 278 (1710) ◽

pp. 1306-1313 ◽

Cited By ~ 13

Author(s):

Brooks E. Miner ◽

Benjamin Kerr

Keyword(s):

Ultraviolet Radiation ◽

Environmental Variables ◽

Population Genetic ◽

Phenotypic Diversity ◽

Experimental Population ◽

Phenotypic Divergence ◽

Trade Offs ◽

Adaptive Processes ◽

Subdivided Populations ◽

Radiation Conditions

Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system.

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Implications of a genomic search for autophagy-related genes in trypanosomatids

Biochemical Society Transactions ◽

10.1042/bst0330972 ◽

2005 ◽

Vol 33 (5) ◽

pp. 972-974 ◽

Cited By ~ 8

Author(s):

D.J. Rigden ◽

M. Herman ◽

S. Gillies ◽

P.A.M. Michels

Keyword(s):

Transport System ◽

In Silico ◽

Molecular Mechanisms ◽

Genomic Analysis ◽

Genomic Search ◽

Similarities And Differences ◽

Related Proteins ◽

Cellular Components ◽

Putative Orthologues

Autophagy is the process by which cellular components are directed to and degraded in the vacuole or lysosome and has been studied largely in yeasts. We present here an in silico genomic analysis of trypanosomatid autophagy aimed at highlighting similarities and differences with autophagy in other organisms. Less than half of the yeast autophagy-related proteins examined have certain putative orthologues in trypanosomatids. A cytosol-to-vacuole transport system is clearly lacking in these organisms. Other absences are even more unexpected and have implications for our understanding of the molecular mechanisms of autophagy. The results are consistent with taxon-specific addition of components to a core autophagy machinery during evolution.

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