Publications by authors named "Kiwoong Nam"

24 Publications

  • Page 1 of 1

A novel reference dated phylogeny for the genus Spodoptera Guenée (Lepidoptera: Noctuidae: Noctuinae): new insights into the evolution of a pest-rich genus.

Mol Phylogenet Evol 2021 Mar 29:107161. Epub 2021 Mar 29.

DGIMI, Univ Montpellier, INRAE, Montpellier, France. Electronic address:

The noctuid genus Spodoptera currently consists of 31 species with varied host plant breadths, ranging from monophagous and oligophagous non-pest species to polyphagous pests of economic importance. Several of these pest species have become major invaders, colonizing multiple continents outside their native range. Such is the case of the infamous fall armyworm, Spodoptera frugiperda (J.E. Smith), which includes two recognized host strains that have not been treated as separate species. Following its accidental introduction to Africa in 2016, it quickly spread through Africa and Asia to Australia. Given that half the described Spodoptera species cause major crop losses, comparative genomics studies of several Spodoptera species have highlighted major adaptive changes in genetic architecture, possibly relating to their pest status. Several recent population genomics studies conducted on two species enable a more refined understanding of their population structures, migration patterns and invasion processes. Despite growing interest in the genus, the taxonomic status of several Spodoptera species remains unstable and evolutionary studies suffer from the absence of a robust and comprehensive dated phylogenetic framework. We generated mitogenomic data for 14 Spodoptera taxa, which are combined with data from 15 noctuoid outgroups to generate a resolved mitogenomic backbone phylogeny using both concatenation and multi-species coalescent approaches. We combine this backbone with additional mitochondrial and nuclear data to improve our understanding of the evolutionary history of the genus. We also carry out comprehensive dating analyses, which implement three distinct calibration strategies based on either primary or secondary fossil calibrations. Our results provide an updated phylogenetic framework for 28 Spodoptera species, identifying two well-supported ecologically diverse clades that are recovered for the first time. Well-studied larvae in each of these clades are characterized by differences in mandibular shape, with one clade's being more specialized on silica-rich C grasses. Interestingly, the inferred timeframe for the genus suggests an earlier origin than previously thought for the genus: about 17-18 million years ago.
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http://dx.doi.org/10.1016/j.ympev.2021.107161DOI Listing
March 2021

Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm.

BMC Evol Biol 2020 11 13;20(1):152. Epub 2020 Nov 13.

DGIMI, Univ Montpellier, INRAE, Montpellier, France.

Background: The process of speciation involves differentiation of whole genome sequences between a pair of diverging taxa. In the absence of a geographic barrier and in the presence of gene flow, genomic differentiation may occur when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host-plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that genomic differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for genomic differentiation in the fall armyworm.

Results: These two strains exhibit a low level of genomic differentiation (F = 0.0174), while 99.2% of 200 kb windows have genetically differentiated sequences (F > 0). We found that the combined effect of mild positive selection and genetic linkage to selectively targeted loci are responsible for the genomic differentiation. However, a single event of very strong positive selection appears not to be responsible for genomic differentiation. The contribution of chromosomal inversions or tight genetic linkage among positively selected loci causing reproductive barriers is not supported by our data. Phylogenetic analysis shows that the genomic differentiation occurred by sub-setting of genetic variants in one strain from the other.

Conclusions: From these results, we concluded that genomic differentiation may occur at the early stage of a speciation process in the fall armyworm and that mild positive selection targeting many loci alone is sufficient evolutionary force for generating the pattern of genomic differentiation. This genomic differentiation may provide a condition for accelerated genomic differentiation by synergistic effects among linkage disequilibrium generated by following events of positive selection. Our study highlights genomic differentiation as a key evolutionary factor connecting positive selection to divergent selection.
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http://dx.doi.org/10.1186/s12862-020-01715-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7663868PMC
November 2020

Adaptation by copy number variation increases insecticide resistance in the fall armyworm.

Commun Biol 2020 Nov 12;3(1):664. Epub 2020 Nov 12.

DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France.

Understanding the genetic basis of insecticide resistance is a key topic in agricultural ecology. The adaptive evolution of multi-copy detoxification genes has been interpreted as a cause of insecticide resistance, yet the same pattern can also be generated by the adaptation to host-plant defense toxins. In this study, we tested in the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), if adaptation by copy number variation caused insecticide resistance in two geographically distinct populations with different levels of resistance and the two host-plant strains. We observed a significant allelic differentiation of genomic copy number variations between the two geographic populations, but not between host-plant strains. A locus with positively selected copy number variation included a CYP gene cluster. Toxicological tests supported a central role for CYP enzymes in deltamethrin resistance. Our results indicate that copy number variation of detoxification genes might be responsible for insecticide resistance in fall armyworm and that evolutionary forces causing insecticide resistance could be independent of host-plant adaptation.
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http://dx.doi.org/10.1038/s42003-020-01382-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661717PMC
November 2020

Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China.

Mol Ecol Resour 2020 Nov 20;20(6):1682-1696. Epub 2020 Jul 20.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

The rapid wide-scale spread of fall armyworm (Spodoptera frugiperda) has caused serious crop losses globally. However, differences in the genetic background of subpopulations and the mechanisms of rapid adaptation behind the invasion are still not well understood. Here we report the assembly of a 390.38-Mb chromosome-level genome of fall armyworm derived from south-central Africa using Pacific Bioscience (PacBio) and Hi-C sequencing technologies, with scaffold N50 of 12.9 Mb and containing 22,260 annotated protein-coding genes. Genome-wide resequencing of 103 samples and strain identification were conducted to reveal the genetic background of fall armyworm populations in China. Analysis of genes related to pesticide- and Bacillus thuringiensis (Bt) resistance showed that the risk of fall armyworm developing resistance to conventional pesticides is very high. Laboratory bioassay results showed that insects invading China carry resistance to organophosphate and pyrethroid pesticides, but are sensitive to genetically modified maize expressing the Bt toxin Cry1Ab in field experiments. Additionally, two mitochondrial fragments were found to be inserted into the nuclear genome, with the insertion event occurring after the differentiation of the two strains. This study represents a valuable advance toward improving management strategies for fall armyworm.
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http://dx.doi.org/10.1111/1755-0998.13219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7689805PMC
November 2020

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.

Genome Biol Evol 2018 04;10(5):1282-1297

CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.

Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05-79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep's recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.
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http://dx.doi.org/10.1093/gbe/evy085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963296PMC
April 2018

Nocturnal Desaturation is Associated With Neurological Deterioration Following Ischemic Stroke: A Retrospective Observational Study.

J Clin Sleep Med 2017 Nov 15;13(11):1273-1279. Epub 2017 Nov 15.

Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea.

Study Objectives: The mechanism of early neurological deterioration (END) in patients with stroke remains unclear. We assessed the relationship between nocturnal oxygen desaturation (NOD) in the stroke unit (SU) and END, especially occurring at nighttime, following acute stroke.

Methods: A retrospective analysis was performed on a total of 276 patients with ischemic stroke who were admitted to the SU between July 2013 and June 2015. The oxygen desaturation index was calculated from pulse oximetry data sampled every 1 minute during 9 hours on the first night (10:00 PM to 7:00 AM) after admission, and NOD was defined as oxygen desaturation index ≥ 5 events/h. END was defined as an increase of ≥ 2 points from the baseline National Institutes of Health Stroke Scale during 7 days after onset. We compared clinical characteristics and NOD between patients with and without END.

Results: Among the included patients (mean age 69.2; male 55.4%), 42 patients (15.2%) experienced END. The proportion of NOD was significantly greater in the END group (45.2% versus 12.8%, < .001). After adjusting for confounders, NOD was independently associated with END (odds ratio 7.57; 95% confidence interval 3.14-18.27). Among END patients, 47.6% patients (n = 20) had END during nighttime. Moreover, NOD was more frequent in patients with END during nighttime compared to those with END during daytime (73.7% versus 26.1%, = .002).

Conclusions: NOD in the SU was associated with END, especially during nighttime, after ischemic stroke. This suggests that treatment of sleep-disordered breathing could be a modifiable factor to possibly reduce the risk of neurological worsening among acute stroke patients.
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http://dx.doi.org/10.5664/jcsm.6796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656476PMC
November 2017

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.

Sci Rep 2017 09 25;7(1):11816. Epub 2017 Sep 25.

DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France.

Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world's worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains ("C" and "R") that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
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http://dx.doi.org/10.1038/s41598-017-10461-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613006PMC
September 2017

Evidence that the rate of strong selective sweeps increases with population size in the great apes.

Proc Natl Acad Sci U S A 2017 02 30;114(7):1613-1618. Epub 2017 Jan 30.

Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark;

Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.
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http://dx.doi.org/10.1073/pnas.1605660114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320968PMC
February 2017

Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans.

Sci Rep 2017 01 11;7:40233. Epub 2017 Jan 11.

Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Haeanro 787, Ansan 15627, Republic of Korea.

Cetacean body structure and physiology exhibit dramatic adaptations to their aquatic environment. Fibroblast growth factors (FGFs) are a family of essential factors that regulate animal development and physiology; however, their role in cetacean evolution is not clearly understood. Here, we sequenced the fin whale genome and analysed FGFs from 8 cetaceans. FGF22, a hair follicle-enriched gene, exhibited pseudogenization, indicating that the function of this gene is no longer necessary in cetaceans that have lost most of their body hair. An evolutionary analysis revealed signatures of positive selection for FGF3 and FGF11, genes related to ear and tooth development and hypoxia, respectively. We found a D203G substitution in cetacean FGF9, which was predicted to affect FGF9 homodimerization, suggesting that this gene plays a role in the acquisition of rigid flippers for efficient manoeuvring. Cetaceans utilize low bone density as a buoyancy control mechanism, but the underlying genes are not known. We found that the expression of FGF23, a gene associated with reduced bone density, is greatly increased in the cetacean liver under hypoxic conditions, thus implicating FGF23 in low bone density in cetaceans. Altogether, our results provide novel insights into the roles of FGFs in cetacean adaptation to the aquatic environment.
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http://dx.doi.org/10.1038/srep40233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225608PMC
January 2017

Selective Sweeps across Twenty Millions Years of Primate Evolution.

Mol Biol Evol 2016 12 22;33(12):3065-3074. Epub 2016 Sep 22.

Bioinformatics Research Centre, Aarhus University, C. F. Møllers Alle, Denmark.

The contribution from selective sweeps to variation in genetic diversity has proven notoriously difficult to assess, in part because polymorphism data only allows detection of sweeps in the most recent few hundred thousand years. Here, we show how linked selection in ancestral species can be quantified across evolutionary timescales by analyzing patterns of incomplete lineage sorting (ILS) along the genomes of closely related species. We show that sweeps in the human-chimpanzee and human-orangutan ancestors can be identified as depletions of ILS in regions in excess of 100 kb in length. Sweeps predicted in each ancestral species, as well as recurrent sweeps predicted in both species, often overlap sweeps predicted in humans. This suggests that many genomic regions experience recurrent selective sweeps. By comparing the ILS patterns along the genomes of the closely related human-chimpanzee and human-orangutan ancestors, we are further able to quantify the impact of selective sweeps relative to that of background selection. Compared with the human-orangutan ancestor, the human-chimpanzee ancestor shows a strong excess of regions depleted of ILS as well as a stronger reduction in ILS around genes. We conclude that sweeps play a strong role in reducing diversity along the genome and that sweeps have reduced diversity in the human-chimpanzee ancestor much more than in the human-orangutan ancestor.
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http://dx.doi.org/10.1093/molbev/msw199DOI Listing
December 2016

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

Genome Biol Evol 2016 07 3;8(6):2020-30. Epub 2016 Jul 3.

Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.
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http://dx.doi.org/10.1093/gbe/evw124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943195PMC
July 2016

Nocturnal Desaturation in the Stroke Unit Is Associated With Wake-Up Ischemic Stroke.

Stroke 2016 07 24;47(7):1748-53. Epub 2016 May 24.

From the Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea (T.J.K., S.-B.K., H.-G.J., K.N., H.M., S.J.A., B.-W.Y.); Clinical Research Center, Asan Medical Center, Seoul, Republic of Korea (J.S.L.); Department of Neruology, Korea University Guro Hospital, Seoul, Republic of Korea (C.K.K.); Department of Neurology, Bucheon St. Mary's Hospital, Gyeonggi-do, Republic of Korea (Y.K.); and Department of Neurology and Neurosurgery, The Mischer Neuroscience Institute, Memorial Hermann of Texas Medical Center, Houston, TX (H.A.C.).

Background And Purpose: Wake-up stroke (WUS) represents a quarter of all ischemic strokes and may be a specific subgroup. Nocturnal desaturation secondary to sleep-disordered breathing is an independent risk factor for stroke, but the association between nocturnal desaturation and WUS remains unclear. We investigated the relationship between nocturnal desaturation using oxygen desaturation index and WUS in patients with acute stroke in the stroke unit.

Methods: A total of 298 patients admitted for acute ischemic stroke to the stroke unit between July 2013 and May 2015 were enrolled. The oxygen desaturation index was calculated using pulse oximetry data sampled every 1 minute during 9 hours on the first night (10:00 pm-7:00 am) of the stroke unit admission, and nocturnal desaturation was defined as an oxygen desaturation index of 5 at least per hour. We compared the clinical characteristics and nocturnal desaturations between patients with and without WUS.

Results: Among all patients (age, 67.7±12.6 years; male, 54.4%), 26.5% patients had WUS. The proportion of nocturnal desaturation was significantly greater in patients admitted with WUS (29.1% versus 12.3%, P=0.001). The age, sex, risk factors except for hyperlipidemia, stroke severity, and stroke mechanisms were similar between the 2 groups. After adjustment for covariates, it was found that nocturnal desaturation was significantly more common in the WUS group (odds ratio, 3.25; 95% confidence interval, 1.63-6.46).

Conclusions: Nocturnal desaturation was more frequently observed in patients admitted with WUS during the first night in the stroke unit. This suggests that nocturnal desaturation is a possible modifiable risk factor for the occurrence of WUS.
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http://dx.doi.org/10.1161/STROKEAHA.116.013266DOI Listing
July 2016

Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence.

PLoS Genet 2015 Aug 14;11(8):e1005451. Epub 2015 Aug 14.

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark; Department of Bioscience, Aarhus University, Aarhus, Denmark.

The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence. We study incomplete lineage sorting patterns between humans, chimpanzees and gorillas to show that this low divergence can be entirely explained by megabase-sized regions comprising one-third of the X chromosome, where polymorphism in the human-chimpanzee ancestral species was severely reduced. We show that background selection can explain at most 10% of this reduction of diversity in the ancestor. Instead, we show that several strong selective sweeps in the ancestral species can explain it. We also report evidence of population specific sweeps in extant humans that overlap the regions of low diversity in the ancestral species. These regions further correspond to chromosomal sections shown to be devoid of Neanderthal introgression into modern humans. This suggests that the same X-linked regions that undergo selective sweeps are among the first to form reproductive barriers between diverging species. We hypothesize that meiotic drive is the underlying mechanism causing these two observations.
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http://dx.doi.org/10.1371/journal.pgen.1005451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537231PMC
August 2015

Extreme selective sweeps independently targeted the X chromosomes of the great apes.

Proc Natl Acad Sci U S A 2015 May 4;112(20):6413-8. Epub 2015 May 4.

Bioinformatics Research Centre and Department of Bioscience, Aarhus University, Aarhus 8000, Denmark;

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis.
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http://dx.doi.org/10.1073/pnas.1419306112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443357PMC
May 2015

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

Gigascience 2014 12;3(1):27. Epub 2014 Dec 12.

China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100 Denmark.

Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri].

Results: Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology.

Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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http://dx.doi.org/10.1186/2047-217X-3-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322438PMC
February 2015

Recombination drives vertebrate genome contraction.

PLoS Genet 2012 3;8(5):e1002680. Epub 2012 May 3.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

Selective and/or neutral processes may govern variation in DNA content and, ultimately, genome size. The observation in several organisms of a negative correlation between recombination rate and intron size could be compatible with a neutral model in which recombination is mutagenic for length changes. We used whole-genome data on small insertions and deletions within transposable elements from chicken and zebra finch to demonstrate clear links between recombination rate and a number of attributes of reduced DNA content. Recombination rate was negatively correlated with the length of introns, transposable elements, and intergenic spacer and with the rate of short insertions. Importantly, it was positively correlated with gene density, the rate of short deletions, the deletion bias, and the net change in sequence length. All these observations point at a pattern of more condensed genome structure in regions of high recombination. Based on the observed rates of small insertions and deletions and assuming that these rates are representative for the whole genome, we estimate that the genome of the most recent common ancestor of birds and lizards has lost nearly 20% of its DNA content up until the present. Expansion of transposable elements can counteract the effect of deletions in an equilibrium mutation model; however, since the activity of transposable elements has been low in the avian lineage, the deletion bias is likely to have had a significant effect on genome size evolution in dinosaurs and birds, contributing to the maintenance of a small genome. We also demonstrate that most of the observed correlations between recombination rate and genome contraction parameters are seen in the human genome, including for segregating indel polymorphisms. Our data are compatible with a neutral model in which recombination drives vertebrate genome size evolution and gives no direct support for a role of natural selection in this process.
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http://dx.doi.org/10.1371/journal.pgen.1002680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342960PMC
September 2012

Molecular evolution of genes in avian genomes.

Genome Biol 2010 23;11(6):R68. Epub 2010 Jun 23.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, S-752 36, Sweden.

Background: Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species.

Results: We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an over-representation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton.

Conclusions: Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between omega and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes.
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http://dx.doi.org/10.1186/gb-2010-11-6-r68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911116PMC
November 2010

The genome of a songbird.

Nature 2010 Apr;464(7289):757-62

The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
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http://dx.doi.org/10.1038/nature08819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626PMC
April 2010

The recombination landscape of the zebra finch Taeniopygia guttata genome.

Genome Res 2010 Apr 31;20(4):485-95. Epub 2010 Mar 31.

Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.

Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.
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http://dx.doi.org/10.1101/gr.101410.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847751PMC
April 2010

Ontogenetic complexity of sexual dimorphism and sex-specific selection.

Mol Biol Evol 2010 Jul 8;27(7):1570-8. Epub 2010 Feb 8.

Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom.

Sex-biased gene expression is becoming an increasingly important way to study sexual selection at the molecular genetic level. However, little is known about the timing, persistence, and continuity of gene expression required in the creation of distinct male and female phenotypes, and even less about how sex-specific selection pressures shift over the life cycle. Here, we present a time-series global transcription profile for autosomal genes in male and female chicken, beginning with embryonic development and spanning to reproductive maturity, for the gonad. Overall, the amount and magnitude of sex-biased expression increased as a function of age, though sex-biased gene expression was surprisingly ephemeral, with very few genes exhibiting continuous sex bias in both embryonic and adult tissues. Despite a large predicted role of the sex chromosomes in sexual dimorphism, our study indicates that the autosomes house the majority of genes with sex-biased expression. Most interestingly, sex-specific evolutionary pressures shifted over the course of the life cycle, acting equally strongly on female-biased genes and male-biased genes but at different ages. Female-biased genes exhibited high rates of divergence late in embryonic development, shortly before arrested meiosis halts oogenesis. The level of divergence on female-biased late embryonic genes is similar to that seen in male-biased genes expressed in adult gonads, which correlates with the onset of spermatogenesis. These analyses reveal that sex-specific selection pressure varies over the life cycle as a function of male and female biology.
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http://dx.doi.org/10.1093/molbev/msq042DOI Listing
July 2010

Molecular and biochemical characterizations of a novel arthropod endo-beta-1,3-glucanase from the Antarctic springtail, Cryptopygus antarcticus, horizontally acquired from bacteria.

Comp Biochem Physiol B Biochem Mol Biol 2010 Apr 16;155(4):403-12. Epub 2010 Jan 16.

Korea Ocean Research and Development Institute, Seoul, Republic of Korea.

Collembolan species have been known to have beta-1,3-glucanase activity and yet the genes coding such enzymes have not been demonstrated. We report here a novel arthropod endo-beta-1,3-glucanase gene CaLam from the Antarctic springtail, Cryptopygus antarcticus. The open reading frame consists of 813bp encoding 270 amino acids with a putative signal peptide and a typical motif of glycosyl hydrolase family 16 (GHF16), E-I-D-I-T-E. The recombinant protein expressed in E. coli shows the hydrolytic activity toward laminarin (K(m) approximately 9.98mg/mL) with an optimal temperature 50 degrees C and an optimal pH 6.0. CaLam digests laminarin and laminarioligosaccharides except laminaribiose as an endo-beta-1,3-glucanase, releasing glucose, laminaribiose and laminaritriose as the major products. Analyses of molecular phylogeny of CaLam and its protein structure reveal that CaLam is closely related with bacterial beta-1,3-glucanases more than with the eukaryotic homologues. Even so, the genomic structure of the CaLam gene consisting of six exons interspersed with approximately 57 to 63bp introns confirms that it is endogenous in the genome of the Antarctic springtail. These results suggest that CaLam should have been transferred from bacteria to the lineage of the Collembolan species by horizontal gene transfer.
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http://dx.doi.org/10.1016/j.cbpb.2010.01.003DOI Listing
April 2010

Faster-Z evolution is predominantly due to genetic drift.

Mol Biol Evol 2010 Mar 18;27(3):661-70. Epub 2009 Nov 18.

Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom.

Genes linked to sex chromosomes may show different levels of functional change than autosomal genes due to different evolutionary pressures. We used whole-genome data from zebra finch-chicken orthologs to test for Faster-Z evolution, finding that Z-linked genes evolve up to 50% more rapidly than autosomal genes. We combined these divergence data with information about sex-specific expression patterns in order to determine whether the Faster-Z Effect that we observe was predominantly the result of positive selection of recessive beneficial mutations in the heterogametic sex or primarily due to genetic drift attributable to the lower effective population size of the Z chromosome compared with an autosome. The Faster-Z Effect was no more prevalent for genes expressed predominantly in females; therefore, our data indicate that the largest source of Faster-Z Evolution is the increased levels of genetic drift on the Z chromosome. This is likely a product of sexual selection acting on males, which reduces the effective population size of the Z relative to that of the autosomes. Additionally, this latter result suggests that the relative evolutionary pressures underlying Faster-Z Evolution are different from those in analogous Faster-X Evolution.
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http://dx.doi.org/10.1093/molbev/msp282DOI Listing
March 2010

Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection.

Genome Biol Evol 2009 Aug 13;1:308-19. Epub 2009 Aug 13.

Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.

Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the mode and strength of selection. To control for regional variation in substitution rates, the proportionate number of nonsynonymous differences (d(N)) is divided by the proportionate number of synonymous differences (d(S)). The resulting ratio (d(N)/d(S)) is a widely used indicator for functional divergence to identify particular genes that underwent positive selection. With the ever-growing amount of genome data, summary statistics like mean d(N)/d(S) allow gathering information on the mode of evolution for entire species. Both applications hinge on the assumption that d(S) and mean d(S) (approximately branch length) are neutral and adequately control for variation in substitution rates across genes and across organisms, respectively. We here explore the validity of this assumption using empirical data based on whole-genome protein sequence alignments between human and 15 other vertebrate species and several simulation approaches. We find that d(N)/d(S) does not appropriately reflect the action of selection as it is strongly influenced by its denominator (d(S)). Particularly for closely related taxa, such as human and chimpanzee, d(N)/d(S) can be misleading and is not an unadulterated indicator of selection. Instead, we suggest that inconsistencies in the behavior of d(N)/d(S) are to be expected and highlight the idea that this behavior may be inherent to taking the ratio of two randomly distributed variables that are nonlinearly correlated. New null hypotheses will be needed to adequately handle these nonlinear dynamics.
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http://dx.doi.org/10.1093/gbe/evp030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817425PMC
August 2009

The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata.

Genetics 2008 Oct 14;180(2):1131-6. Epub 2008 Sep 14.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden.

Birds have female heterogamety with Z and W sex chromosomes. These evolved from different autosomal precursor chromosomes than the mammalian X and Y. However, previous work has suggested that the pattern and process of sex chromosome evolution show many similarities across distantly related organisms. Here we show that stepwise restriction of recombination between the protosex chromosomes of birds has resulted in regions of the chicken Z chromosome showing discrete levels of divergence from W homologs (gametologs). The 12 genes analyzed fall into three levels of estimated divergence values, with the most recent divergence (d(S) = 0.18-0.21) displayed by 6 genes in a region on the Z chromosome corresponding to the interval 1-11 Mb of the assembled genome sequence. Another 4 genes show intermediate divergence (d(S) = 0.27-0.38) and are located in the interval 16-53 Mb. Two genes (at positions 42 and 50 Mb) with higher d(S) values are located proximal to the most distal of the 4 genes with intermediate divergence, suggesting an inversion event. The distribution of genes and their divergence indicate at least three evolutionary strata, with estimated times for cessation of recombination between Z and W of 132-150 (stratum 1), 71-99 (stratum 2), and 47-57 (stratum 3) million years ago. An inversion event, or some other form of intrachromosomal rearrangement, subsequent to the formation of strata 1 and 2 has scrambled the gene order to give rise to the nonlinear arrangement of evolutionary strata currently seen on the chicken Z chromosome. These observations suggest that the progressive restriction of recombination is an integral feature of sex chromosome evolution and occurs also in systems of female heterogamety.
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http://dx.doi.org/10.1534/genetics.108.090324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567362PMC
October 2008