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Article ; Online: Genomic signatures of local adaptation in recent invasive Aedes aegypti populations in California.

Soudi, Shaghayegh / Crepeau, Marc / Collier, Travis C / Lee, Yoosook / Cornel, Anthony J / Lanzaro, Gregory C

2023 Volume 24, Issue 1, Page(s) 311

Abstract: Background: Rapid adaptation to new environments can facilitate species invasions and range expansions. Understanding the mechanisms of adaptation used by invasive disease vectors in new regions has key implications for mitigating the prevalence and ... ...

Abstract	Background: Rapid adaptation to new environments can facilitate species invasions and range expansions. Understanding the mechanisms of adaptation used by invasive disease vectors in new regions has key implications for mitigating the prevalence and spread of vector-borne disease, although they remain relatively unexplored. Results: Here, we integrate whole-genome sequencing data from 96 Aedes aegypti mosquitoes collected from various sites in southern and central California with 25 annual topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principal components and admixture analysis, were consistent with three genetic clusters. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic and environmental variation, we identified 112 genes showing strong signals of local environmental adaptation associated with one or more topo-climate factors. Some of them have known effects in climate adaptation, such as heat-shock proteins, which shows selective sweep and recent positive selection acting on these genomic regions. Conclusions: Our results provide a genome wide perspective on the distribution of adaptive loci and lay the foundation for future work to understand how environmental adaptation in Ae. aegypti impacts the arboviral disease landscape and how such adaptation could help or hinder efforts at population control.
MeSH term(s)	Animals ; Aedes/genetics ; Mosquito Vectors/genetics ; Genomics ; Adaptation, Physiological/genetics ; California
Language	English
Publishing date	2023-06-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-023-09402-5
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Article ; Online: Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion.

Soudi, Shaghayegh / Jahani, Mojtaba / Todesco, Marco / Owens, Gregory L / Bercovich, Natalia / Rieseberg, Loren H / Yeaman, Sam

eLife

2023 Volume 12

Abstract: Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally ... ...

Abstract	Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower:
MeSH term(s)	Helianthus/genetics ; Genome-Wide Association Study ; Genomics ; Linkage Disequilibrium ; Genotype
Language	English
Publishing date	2023-12-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.88604
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Article ; Online: Strong cryptic prezygotic isolation despite lack of behavioral isolation between sympatric host races of the leaf beetle Lochmaea capreae.

Soudi, Shaghayegh / Reinhold, Klaus / Engqvist, Leif

Evolution; international journal of organic evolution

2016 Volume 70, Issue 12, Page(s) 2889–2898

Abstract: One of the major goals in speciation research is to understand which isolation mechanisms form the first barriers to gene flow. This requires examining lineages that are still in the process of divergence or incipient species. Here, we investigate the ... ...

Abstract	One of the major goals in speciation research is to understand which isolation mechanisms form the first barriers to gene flow. This requires examining lineages that are still in the process of divergence or incipient species. Here, we investigate the presence of behavioral and several cryptic barriers between the sympatric willow and birch host races of Lochmaea capreae. Behavioral isolation did not have any profound effect on preventing gene flow. Yet despite pairs mating indiscriminately, no offspring were produced from the heterospecific matings between birch females and willow males due to the inability of males to transfer sperm to females. We found evidence for differences in genital morphology that may contribute to failed insemination attempts during copulation. The heterospecific matings between willow females and birch males resulted in viable offspring. Yet fecundity and hatchability was remarkably reduced, which is likely the result of lower efficiency in sperm transportation and storage and lower survival of sperm in the foreign reproductive tract. Our results provide evidence for the contribution of several postmating-prezygotic barriers that predate behavioral isolation and act as primary inhibitors of gene flow in this system. This is a surprising, yet perhaps often overlooked feature of barriers acting early in sympatric speciation process.
MeSH term(s)	Animals ; Coleoptera/genetics ; Coleoptera/physiology ; Feeding Behavior ; Female ; Gene Flow ; Genetic Speciation ; Hybridization, Genetic ; Male ; Reproductive Isolation ; Sympatry
Language	English
Publishing date	2016-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2036375-8
ISSN	1558-5646 ; 0014-3820
ISSN (online)	1558-5646
ISSN	0014-3820
DOI	10.1111/evo.13083
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Article ; Online ; Research data: (with research data) Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetle Lochmaea capreae.

Soudi, Shaghayegh / Reinhold, Klaus / Engqvist, Leif

Evolution; international journal of organic evolution

2016 Volume 70, Issue 2, Page(s) 471–479

Abstract: The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because they fall between ecological niches due to their intermediate phenotypes ("extrinsic isolation"). Here, we present data from several crosses (parental crosses, ... ...

Abstract	The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because they fall between ecological niches due to their intermediate phenotypes ("extrinsic isolation"). Here, we present data from several crosses (parental crosses, F1, F2, and backcrosses) between the two host races of Lochmaea capreae on willow and birch to test for extrinsic isolation, intrinsic isolation, and environmentally dependent genetic incompatibilities. We employed a reciprocal transplant design in which offspring were raised on either host plant and their survival was recorded until adulthood. We also applied joint-scaling analysis to determine the genetic architecture of hybrid inviability. The relative fitness of the backcrosses switched between environments; furthermore, the additive genetic-environment interaction was detected as the strongest effect in our analysis. These results provide strong evidence that divergent natural selection has played a central role in the evolution of hybrid dysfunction between host races. Joint-scaling analysis detected significant negative epistatic effects that are most evident in the poor performance of F2-hybrids on willow, indicating signs of intrinsic isolation. We did not find any evidence that genetic incompatibilities are manifested independently of environmental conditions. Our findings suggest the outcome of natural hybridization between these host races is mainly affected by extrinsic isolation and a weak contribution of intrinsic isolation.
MeSH term(s)	Animals ; Coleoptera/genetics ; Environment ; Epistasis, Genetic ; Evolution, Molecular ; Female ; Genetic Fitness ; Genetic Speciation ; Hybridization, Genetic ; Male ; Models, Genetic ; Reproductive Isolation ; Selection, Genetic ; Sympatry ; Zygote/growth & development
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article
ZDB-ID	2036375-8
ISSN	1558-5646 ; 0014-3820 ; 0014-3820
ISSN (online)	1558-5646
ISSN	0014-3820
DOI	10.1111/evo.12846
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Article ; Online: Genetic architecture underlying host choice differentiation in the sympatric host races of Lochmaea capreae leaf beetles.

Soudi, Shaghayegh / Reinhold, Klaus / Engqvist, Leif

Genetica

2016 Volume 144, Issue 2, Page(s) 147–156

Abstract: Speciation in herbivorous insects has received considerable attention during the last few decades. Much of this group's diversity originates from adaptive population divergence onto different host plants, which often involves the evolution of specialized ...

Abstract	Speciation in herbivorous insects has received considerable attention during the last few decades. Much of this group's diversity originates from adaptive population divergence onto different host plants, which often involves the evolution of specialized patterns of host choice behaviour. Differences in host choice often translates directly into divergence in mating sites, and therefore positive assortative mating will be created which will act as a strong barrier to gene flow. In this study, we first explored whether host choice is a genetically determined trait in the sympatric willow and birch host races of the leaf feeding beetle Lochmaea capreae, or whether larval experience influences adult host choice. Once we had established that host choice is a genetically based trait we determined its genetic architecture. To achieve this, we employed a reciprocal transplant design in which offspring from pure willow and birch cross-types, F1, F2 and backcrosses were raised on each host plant and their preference was determined upon reaching adulthood. We then applied joint-scaling analysis to uncover the genetic architecture of host preference. Our results suggest that rearing host does not have a pronounced effect on adult's host choice; rather the segregation pattern implies the existence of genetic loci affecting host choice in these host races. The joint-scaling analysis revealed that population differences in host choice are mainly influenced by the contribution of additive genetic effects and also maternally inherited cytoplasmic effects. We explore the implications of our findings for evolutionary dynamics of sympatric host race formation and speciation.
MeSH term(s)	Animals ; Betula ; Choice Behavior ; Coleoptera/genetics ; Crosses, Genetic ; Feeding Behavior ; Female ; Genetics, Population ; Larva ; Linear Models ; Male ; Models, Genetic ; Oviposition ; Salix ; Sympatry
Language	English
Publishing date	2016-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2165-9
ISSN	1573-6857 ; 0016-6707
ISSN (online)	1573-6857
ISSN	0016-6707
DOI	10.1007/s10709-016-9885-2
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Article: Host‐associated divergence in sympatric host races of the leaf beetle Lochmaea capreae: implications for local adaptation and reproductive isolation

Soudi, Shaghayegh / Reinhold, Klaus / Engqvist, Leif

Biological journal of the Linnean Society. 2015 Sept., v. 116, no. 1

2015

Abstract: Ecological specialization is widely recognized as a major determinant of the emergence and maintenance of biodiversity. We studied two critical facets of specialization – local adaptation and habitat choice – in the host races of the leaf beetle Lochmaea ...

Abstract	Ecological specialization is widely recognized as a major determinant of the emergence and maintenance of biodiversity. We studied two critical facets of specialization – local adaptation and habitat choice – in the host races of the leaf beetle Lochmaea capreae on willow and birch. Our results revealed that there is asymmetric disruptive selection for host use traits, and host races achieved different adaptive sets of life history traits through association with their host plant. Beetles from each host race exhibited food and oviposition preference for their own host plant. Reciprocal transplant displayed significant variation in host acceptance and performance: all families from the willow race rejected the alternative host plant before initiation of feeding and all died on this host plant. By contrast, all families from the birch race accepted willow for feeding, but they consumed less and performed less well. Intriguingly, families that performed well on birch also performed well on willow, suggesting positive genetic correlation rather than genetic trade‐offs. Our results suggest that the major proximal determinant of host specialization in the willow race is the behavioural acceptance of a plant rather than the toxicity of the food resource. However, in the birch race a combination of behavioural host acceptance and performance may play a role in specialization. Our study sheds light on the mechanisms by which divergent host adaptation might influence the evolution of reproductive isolation between herbivorous populations.
Keywords	Betula ; Lochmaea ; biodiversity ; evolution ; genetic correlation ; habitats ; herbivores ; host plants ; host preferences ; life history ; oviposition ; population ; races ; reproductive isolation
Language	English
Dates of publication	2015-09
Size	p. 169-182.
Publishing place	Published for the Linnean Society of London by Blackwell [etc.]
Document type	Article
ZDB-ID	1461865-5
ISSN	1095-8312 ; 0024-4066
ISSN (online)	1095-8312
ISSN	0024-4066
DOI	10.1111/bij.12547
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Article: Seasonal patterns of the thermal response in relation to sugar and polyol accumulation in overwintering adults of elm leaf beetle, Xanthogaleruca luteola (Coleoptera: Chrysomelidae)

Soudi, Shaghayegh / Moharramipour, Saeid

Journal of thermal biology. 2012 Aug., v. 37, no. 5

2012

Abstract: Elm leaf beetle, Xanthogaleruca luteola (Muller), is one of the key pests of elm trees that survive winter in reproductive diapause in sheltered locations. Overwintering adults of the elm leaf beetle showed a complex sugar/polyol cryoprotectant system. ... ...

Abstract	Elm leaf beetle, Xanthogaleruca luteola (Muller), is one of the key pests of elm trees that survive winter in reproductive diapause in sheltered locations. Overwintering adults of the elm leaf beetle showed a complex sugar/polyol cryoprotectant system. The major components of the multiple systems were glucose, myo-inositol and trehalose. In this study, we investigated the seasonal profile of low molecular weight compounds and glycogen in natural population and also in response to thermal constant regimes (5 and 15°C). Among these components, a remarkable seasonal pattern of accumulation/depletion was observed in myo-inositol over the course of hibernation with the development of diapause progress. Incubating at 5°C only elicited a strong response in myo-inositol synthesis during diapause. It suggests that the elm leaf beetle accumulates myo-inositol not only in relation to entering diapause but also in response to low temperatures and their interactions. The laboratory acclimation experiments showed that adults exposed to 15°C had no chance for accumulation of low molecular weight carbohydrate even during diapause. The results of this study illustrated that overwintering adults of elm leaf beetle produce myo-inositol as the primary substance which plays a specific role in some biochemical adjustments in overwintering adults of X. luteola.
Keywords	Pyrrhalta luteola ; Ulmus ; acclimation ; adults ; cryoprotectants ; diapause ; glucose ; glycogen ; hibernation ; molecular weight ; myo-inositol ; overwintering ; pests ; seasonal variation ; temperature ; trehalose ; winter
Language	English
Dates of publication	2012-08
Size	p. 384-391.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1498364-3
ISSN	1879-0992 ; 0306-4565
ISSN (online)	1879-0992
ISSN	0306-4565
DOI	10.1016/j.jtherbio.2012.02.003
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Article ; Online: Massive haplotypes underlie ecotypic differentiation in sunflowers.

Nature

2020 Volume 584, Issue 7822, Page(s) 602–607

Abstract: Species often include multiple ecotypes that are adapted to different ... ...

Abstract	Species often include multiple ecotypes that are adapted to different environments
MeSH term(s)	Acclimatization/genetics ; Alleles ; Ecotype ; Flowers/genetics ; Haplotypes ; Helianthus/anatomy & histology ; Helianthus/genetics ; Helianthus/growth & development ; Phylogeny ; Seeds/genetics
Language	English
Publishing date	2020-07-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2467-6
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Article ; Online: Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma.

Thomas, Nicole / Dreval, Kostiantyn / Gerhard, Daniela S / Hilton, Laura K / Abramson, Jeremy S / Ambinder, Richard F / Barta, Stefan / Bartlett, Nancy L / Bethony, Jeffrey / Bhatia, Kishor / Bowen, Jay / Bryan, Anthony C / Cesarman, Ethel / Casper, Corey / Chadburn, Amy / Cruz, Manuela / Dittmer, Dirk P / Dyer, Maureen A / Farinha, Pedro /

Gastier-Foster, Julie M / Gerrie, Alina S / Grande, Bruno M / Greiner, Timothy / Griner, Nicholas B / Gross, Thomas G / Harris, Nancy L / Irvin, John D / Jaffe, Elaine S / Henry, David / Huppi, Rebecca / Leal, Fabio E / Lee, Michael S / Martin, Jean Paul / Martin, Marie-Reine / Mbulaiteye, Sam M / Mitsuyasu, Ronald / Morris, Vivian / Mullighan, Charles G / Mungall, Andrew J / Mungall, Karen / Mutyaba, Innocent / Nokta, Mostafa / Namirembe, Constance / Noy, Ariela / Ogwang, Martin D / Omoding, Abraham / Orem, Jackson / Ott, German / Petrello, Hilary / Pittaluga, Stefania / Phelan, James D / Ramos, Juan Carlos / Ratner, Lee / Reynolds, Steven J / Rubinstein, Paul G / Sissolak, Gerhard / Slack, Graham / Soudi, Shaghayegh / Swerdlow, Steven H / Traverse-Glehen, Alexandra / Wilson, Wyndham H / Wong, Jasper / Yarchoan, Robert / ZenKlusen, Jean C / Marra, Marco A / Staudt, Louis M / Scott, David W / Morin, Ryan D

Blood

2023 Volume 141, Issue 8, Page(s) 904–916

Abstract: Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), ... ...

Abstract	Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), leaving its relationship to adult BL (aBL) and other adult lymphomas not fully explored. We sought to more thoroughly identify the somatic changes that underlie lymphomagenesis in aBL and any molecular features that associate with clinical disparities within and between pBL and aBL. Through comprehensive whole-genome sequencing of 230 BL and 295 diffuse large B-cell lymphoma (DLBCL) tumors, we identified additional significantly mutated genes, including more genetic features that associate with tumor Epstein-Barr virus status, and unraveled new distinct subgroupings within BL and DLBCL with 3 predominantly comprising BLs: DGG-BL (DDX3X, GNA13, and GNAI2), IC-BL (ID3 and CCND3), and Q53-BL (quiet TP53). Each BL subgroup is characterized by combinations of common driver and noncoding mutations caused by aberrant somatic hypermutation. The largest subgroups of BL cases, IC-BL and DGG-BL, are further characterized by distinct biological and gene expression differences. IC-BL and DGG-BL and their prototypical genetic features (ID3 and TP53) had significant associations with patient outcomes that were different among aBL and pBL cohorts. These findings highlight shared pathogenesis between aBL and pBL, and establish genetic subtypes within BL that serve to delineate tumors with distinct molecular features, providing a new framework for epidemiologic, diagnostic, and therapeutic strategies.
MeSH term(s)	Child ; Humans ; Adult ; Burkitt Lymphoma/pathology ; Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; Lymphoma, Large B-Cell, Diffuse/pathology ; Mutation
Language	English
Publishing date	2023-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	80069-7
ISSN	1528-0020 ; 0006-4971
ISSN (online)	1528-0020
ISSN	0006-4971
DOI	10.1182/blood.2022016534
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