Shaghayegh Soudi - Academia.edu (original) (raw)

Papers by Shaghayegh Soudi

Research paper thumbnail of Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion

Local adaptation commonly involves alleles of large effect, which experience fitness advantages w... more 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:Helianthus annuus,H. argophyllus, andH. petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome h...

Research paper thumbnail of YIA23-002: Evolutionary Pressures Shape Soft Tissue Sarcoma Development and Response to Radiotherapy

Journal of the National Comprehensive Cancer Network

Research paper thumbnail of Constrained FL: A Genetically Distinct Subgroup of Follicular Lymphoma with Low Rates of Somatic Hypermutation and a Reduced Propensity for Histologic Transformation

Blood, 2021

Introduction: Follicular lymphoma (FL) is an indolent disease that undergoes histological transfo... more Introduction: Follicular lymphoma (FL) is an indolent disease that undergoes histological transformation (HT) to aggressive diffuse large B-cell lymphoma (DLBCL) in 8-15% of patients. FLs frequently share genetic features with DLBCL, especially those of the germinal center B-cell-like (GCB) cell-of-origin (COO) and the EZB/C3 genetic subgroup, and approximately 80% of transformed FL (tFL) are classified as GCB. Our current understanding of the genetics of FL and tFL is based on a variety of studies, most of which have sequenced tumors in small case numbers or using targeted approaches such that the potential role of non-coding mutations and aberrant somatic hypermutation (aSHM) in predicting HT have not previously been fully explored. Methods: Whole genome sequencing (WGS) data from 212 FL (including 24 from patients that subsequently underwent HT) and 241 de novo DLBCL were analyzed. Simple somatic mutations (SSMs) were called using an ensemble of somatic variant callers, while str...

Research paper thumbnail of Novel Genetic Subgroups Inform on Shared Pathobiology within Adult and Pediatric Burkitt Lymphoma

Blood, 2021

Introduction: Burkitt lymphoma (BL) accounts for approximately 50% of all pediatric non-Hodgkin l... more Introduction: Burkitt lymphoma (BL) accounts for approximately 50% of all pediatric non-Hodgkin lymphomas compared to 1-2% in adults. Adult BL (aBL) remains a poorly understood entity and its relationship to pediatric BL (pBL) and to DLBCL has not been fully elucidated. The variable treatment outcomes between these entities necessitate a more thorough understanding of the genetic and molecular features underlying their biology to enable better prognostication and more effective treatments. We sought to comprehensively determine genetic features shared with DLBCL and those that are unique to BL, to further delineate genetic subgroupings within each entity. Methods: Samples for this study were collected through the Burkitt Lymphoma Genome Sequencing Project (BLGSP). We sequenced the tumor genomes of 139 pBL and 92 aBL, consisting of both EBV-positive (EBV+) and EBV-negative (EBV-) BLs, and compared these to the genomes of 252 DLBCL patients. All cases were analyzed for simple somatic ...

Research paper thumbnail of Soudi_et_al_data_survival

Survival of individuals from both willow and birch host races of L. capreae leaf beetles and hybr... more Survival of individuals from both willow and birch host races of L. capreae leaf beetles and hybrids between them on willow and birc

Research paper thumbnail of Data from: Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetle Lochmaea capreae

The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because the... more 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 which 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

Research paper thumbnail of Host specialization and reproductive isolation in Lochmaea capreae leaf beetles

Soudi S. Host specialization and reproductive isolation in Lochmaea capreae leaf beetles. Bielefe... more Soudi S. Host specialization and reproductive isolation in Lochmaea capreae leaf beetles. Bielefeld; 2016

Research paper thumbnail of An Open-Source Toolkit That Powers the Genome-Wide Analysis of Mature B-Cell Lymphomas (GAMBL) Project

Blood, 2021

Introduction: Genome- and transcriptome-wide analyses continue to enhance our understanding of th... more Introduction: Genome- and transcriptome-wide analyses continue to enhance our understanding of the molecular pathogenesis of cancer. In lymphomas, this has enabled the identification of hundreds of recurrently mutated genes, highlighting genetic heterogeneity and relationships both within and among clinical entities. While the growing availability of lymphoma genomic data sets can be leveraged to integrate genomic analyses into diagnostic testing and clinical trials, the ability to rapidly process genomic data sets in a reproducible manner serves as a barrier to this goal. To this end, we developed a suite of tools Lymphoid Cancer Research modules (LCR-modules) to facilitate the discovery of novel drivers and molecular features in lymphoma cancers and perform quantitative comparisons between disease entities. We demonstrate here how this toolkit enabled a meta-analysis of lymphoma genomic data involving genome-wide profiles of 3330 patients. Methods: We assembled a collection of who...

Research paper thumbnail of Massive haplotypes underlie ecotypic differentiation in sunflowers

Species often include multiple ecotypes that are adapted to different environments. But how do ec... more Species often include multiple ecotypes that are adapted to different environments. But how do ecotypes arise, and how are their distinctive combinations of adaptive alleles maintained despite hybridization with non-adapted populations? Re-sequencing of 1506 wild sunflowers from three species identified 37 large (1-100 Mbp), non-recombining haplotype blocks associated with numerous ecologically relevant traits, and soil and climate characteristics. Limited recombination in these regions keeps adaptive alleles together, and we find that they differentiate several sunflower ecotypes; for example, they control a 77 day difference in flowering between ecotypes of silverleaf sunflower (likely through deletion of a FLOWERING LOCUS T homolog), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, associated with polymorphic structural variants, and often appear to represent introgressions from other, possibly...

Research paper thumbnail of Strong cryptic prezygotic isolation despite lack of behavioral isolation between sympatric host races of the leaf beetleLochmaea capreae

Evolution, 2016

One of the major goals in speciation research is to understand which isolation mechanisms form th... more 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.

Research paper thumbnail of Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetleLochmaea capreae

Evolution, 2016

The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because the... more 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.

Research paper thumbnail of Host associated divergence between the host races of the leaf feeding beetle Lochmaea capreae: Implications for local adaptation and reproductive isolation

Biological Journal of the Linnean Society, 2015

Research paper thumbnail of Genetic architecture underlying host choice differentiation in the sympatric host races of Lochmaea capreae leaf beetles

Genetica, 2016

Speciation in herbivorous insects has received considerable attention during the last few decades... more 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 jointscaling 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.

Research paper thumbnail of Host-associated divergence in sympatric host races of the leaf beetle Lochmaea capreae : implications for local adaptation and reproductive isolation

Biological Journal of the Linnean Society, 2015

Ecological specialization is widely recognized as a major determinant of the emergence and mainte... more Ecological specialization is widely recognized as a major determinant of the emergence and maintenance of biodiversity. We studied two critical facets of specializationlocal adaptation and habitat choicein 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.

Research paper thumbnail of Seasonal patterns of the thermal response in relation to sugar and polyol accumulation in overwintering adults of elm leaf beetle, Xanthogaleruca luteola (Coleoptera: Chrysomelidae)

Journal of Thermal Biology, 2012

Elm leaf beetle, Xanthogaleruca luteola (Muller), is one of the key pests of elm trees that survi... more 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 1C). 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 1C 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 1C 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.

Research paper thumbnail of Cold Tolerance and Supercooling Capacity in Overwintering Adults of Elm Leaf Beetle Xanthogaleruca luteola (Coleoptera: Chrysomelidae)

Environmental Entomology, 2011

Elm leaf beetle, Xanthogaleruca luteola (Muller) is one of the key pests of elm trees all over th... more Elm leaf beetle, Xanthogaleruca luteola (Muller) is one of the key pests of elm trees all over the world, and survives winter in reproductive diapause in sheltered locations. Seasonal variation of whole body supercooling points (SCP s), LT 50 (temperature at which 50% of the test individuals die) and survival rate after exposure to subzero temperatures were determined in Þeld collected adults during October 2008 to May 2009 and October 2009 to May 2010. The SCP of adults decreased signiÞcantly from October (median ϭ Ϫ13.8ЊC) to January (median ϭ Ϫ20.7ЊC) in Þrst year, relatively similar results was observed in the second year. The lowest LT 50 was observed in overwintering adults collected in January (Ϫ16.81ЊC) in the Þrst year and December (Ϫ15.59ЊC) in the second year. Mortality at Ϫ15ЊC for 24 h was Ͼ70% in early autumn in both years whereas it decreased to lower than 45% in early winter, the highest mortality (100%) was observed in adults collected in May in both years. Cold acclimated adults (30 d, 5ЊC) in November 2008 exhibited signiÞcantly higher SCP (Ϫ12.21 Ϯ 0.64ЊC) than nonacclimated adults (Ϫ15.57 Ϯ 1.35ЊC). A 30-d exposure to 5ЊC caused Ͼ20% mortality in November, while Ͻ9% mortality was observed in adults collected in December and January 2008. Overwintering adults died upon freezing and the lower lethal temperatures were within the range of SCP, indicating that X. luteola is a freeze intolerant insect.

Research paper thumbnail of Genomic signatures of local adaptation in recent invasiveAedes aegyptipopulations in California

Background: Rapid adaptation to new environments can facilitate species invasions and range expan... more 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 use whole-genome sequencing data from 103Aedes aegyptimosquitoes collected from various sites in southern and central California to infer the genetic structure of invasive populations. We integrate genome data with 25 topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principle components and admixture analysis, were consistent with three genetic clusters, likely resulting from multiple independent introductions. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic a...

Research paper thumbnail of Genetic Subgroups Inform on Pathobiology in Adult and Pediatric Burkitt Lymphoma

Burkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas (NHL) and is r... more Burkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas (NHL) and is relatively rare but significantly more lethal when diagnosed in adults. The global incidence is highest in Sub-Saharan Africa, where Epstein-Barr virus (EBV) positivity is observed in 95% of all tumors. Both pediatric (pBL) and adult (aBL) cases are known to share some driver mutations, for example MYC translocations, which are seen in > 90% of cases. Sequencing efforts have identified many common somatic alterations that cooperate with MYC in lymphomagenesis with approximately 30 significantly mutated genes (SMG) reported thus far. Recent analyses revealed non-coding mutation patterns in pBL that were attributed to aberrant somatic hypermutation (aSHM). We sought to identify genomic and molecular features that may explain clinical disparities within and between aBL and pBL in an effort to delineate BL subtypes that may allow for the stratification of patients with shared pathobiology....

Research paper thumbnail of Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion

Local adaptation commonly involves alleles of large effect, which experience fitness advantages w... more 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:Helianthus annuus,H. argophyllus, andH. petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome h...

Research paper thumbnail of YIA23-002: Evolutionary Pressures Shape Soft Tissue Sarcoma Development and Response to Radiotherapy

Journal of the National Comprehensive Cancer Network

Research paper thumbnail of Constrained FL: A Genetically Distinct Subgroup of Follicular Lymphoma with Low Rates of Somatic Hypermutation and a Reduced Propensity for Histologic Transformation

Blood, 2021

Introduction: Follicular lymphoma (FL) is an indolent disease that undergoes histological transfo... more Introduction: Follicular lymphoma (FL) is an indolent disease that undergoes histological transformation (HT) to aggressive diffuse large B-cell lymphoma (DLBCL) in 8-15% of patients. FLs frequently share genetic features with DLBCL, especially those of the germinal center B-cell-like (GCB) cell-of-origin (COO) and the EZB/C3 genetic subgroup, and approximately 80% of transformed FL (tFL) are classified as GCB. Our current understanding of the genetics of FL and tFL is based on a variety of studies, most of which have sequenced tumors in small case numbers or using targeted approaches such that the potential role of non-coding mutations and aberrant somatic hypermutation (aSHM) in predicting HT have not previously been fully explored. Methods: Whole genome sequencing (WGS) data from 212 FL (including 24 from patients that subsequently underwent HT) and 241 de novo DLBCL were analyzed. Simple somatic mutations (SSMs) were called using an ensemble of somatic variant callers, while str...

Research paper thumbnail of Novel Genetic Subgroups Inform on Shared Pathobiology within Adult and Pediatric Burkitt Lymphoma

Blood, 2021

Introduction: Burkitt lymphoma (BL) accounts for approximately 50% of all pediatric non-Hodgkin l... more Introduction: Burkitt lymphoma (BL) accounts for approximately 50% of all pediatric non-Hodgkin lymphomas compared to 1-2% in adults. Adult BL (aBL) remains a poorly understood entity and its relationship to pediatric BL (pBL) and to DLBCL has not been fully elucidated. The variable treatment outcomes between these entities necessitate a more thorough understanding of the genetic and molecular features underlying their biology to enable better prognostication and more effective treatments. We sought to comprehensively determine genetic features shared with DLBCL and those that are unique to BL, to further delineate genetic subgroupings within each entity. Methods: Samples for this study were collected through the Burkitt Lymphoma Genome Sequencing Project (BLGSP). We sequenced the tumor genomes of 139 pBL and 92 aBL, consisting of both EBV-positive (EBV+) and EBV-negative (EBV-) BLs, and compared these to the genomes of 252 DLBCL patients. All cases were analyzed for simple somatic ...

Research paper thumbnail of Soudi_et_al_data_survival

Survival of individuals from both willow and birch host races of L. capreae leaf beetles and hybr... more Survival of individuals from both willow and birch host races of L. capreae leaf beetles and hybrids between them on willow and birc

Research paper thumbnail of Data from: Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetle Lochmaea capreae

The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because the... more 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 which 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

Research paper thumbnail of Host specialization and reproductive isolation in Lochmaea capreae leaf beetles

Soudi S. Host specialization and reproductive isolation in Lochmaea capreae leaf beetles. Bielefe... more Soudi S. Host specialization and reproductive isolation in Lochmaea capreae leaf beetles. Bielefeld; 2016

Research paper thumbnail of An Open-Source Toolkit That Powers the Genome-Wide Analysis of Mature B-Cell Lymphomas (GAMBL) Project

Blood, 2021

Introduction: Genome- and transcriptome-wide analyses continue to enhance our understanding of th... more Introduction: Genome- and transcriptome-wide analyses continue to enhance our understanding of the molecular pathogenesis of cancer. In lymphomas, this has enabled the identification of hundreds of recurrently mutated genes, highlighting genetic heterogeneity and relationships both within and among clinical entities. While the growing availability of lymphoma genomic data sets can be leveraged to integrate genomic analyses into diagnostic testing and clinical trials, the ability to rapidly process genomic data sets in a reproducible manner serves as a barrier to this goal. To this end, we developed a suite of tools Lymphoid Cancer Research modules (LCR-modules) to facilitate the discovery of novel drivers and molecular features in lymphoma cancers and perform quantitative comparisons between disease entities. We demonstrate here how this toolkit enabled a meta-analysis of lymphoma genomic data involving genome-wide profiles of 3330 patients. Methods: We assembled a collection of who...

Research paper thumbnail of Massive haplotypes underlie ecotypic differentiation in sunflowers

Species often include multiple ecotypes that are adapted to different environments. But how do ec... more Species often include multiple ecotypes that are adapted to different environments. But how do ecotypes arise, and how are their distinctive combinations of adaptive alleles maintained despite hybridization with non-adapted populations? Re-sequencing of 1506 wild sunflowers from three species identified 37 large (1-100 Mbp), non-recombining haplotype blocks associated with numerous ecologically relevant traits, and soil and climate characteristics. Limited recombination in these regions keeps adaptive alleles together, and we find that they differentiate several sunflower ecotypes; for example, they control a 77 day difference in flowering between ecotypes of silverleaf sunflower (likely through deletion of a FLOWERING LOCUS T homolog), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, associated with polymorphic structural variants, and often appear to represent introgressions from other, possibly...

Research paper thumbnail of Strong cryptic prezygotic isolation despite lack of behavioral isolation between sympatric host races of the leaf beetleLochmaea capreae

Evolution, 2016

One of the major goals in speciation research is to understand which isolation mechanisms form th... more 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.

Research paper thumbnail of Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetleLochmaea capreae

Evolution, 2016

The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because the... more 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.

Research paper thumbnail of Host associated divergence between the host races of the leaf feeding beetle Lochmaea capreae: Implications for local adaptation and reproductive isolation

Biological Journal of the Linnean Society, 2015

Research paper thumbnail of Genetic architecture underlying host choice differentiation in the sympatric host races of Lochmaea capreae leaf beetles

Genetica, 2016

Speciation in herbivorous insects has received considerable attention during the last few decades... more 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 jointscaling 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.

Research paper thumbnail of Host-associated divergence in sympatric host races of the leaf beetle Lochmaea capreae : implications for local adaptation and reproductive isolation

Biological Journal of the Linnean Society, 2015

Ecological specialization is widely recognized as a major determinant of the emergence and mainte... more Ecological specialization is widely recognized as a major determinant of the emergence and maintenance of biodiversity. We studied two critical facets of specializationlocal adaptation and habitat choicein 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.

Research paper thumbnail of Seasonal patterns of the thermal response in relation to sugar and polyol accumulation in overwintering adults of elm leaf beetle, Xanthogaleruca luteola (Coleoptera: Chrysomelidae)

Journal of Thermal Biology, 2012

Elm leaf beetle, Xanthogaleruca luteola (Muller), is one of the key pests of elm trees that survi... more 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 1C). 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 1C 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 1C 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.

Research paper thumbnail of Cold Tolerance and Supercooling Capacity in Overwintering Adults of Elm Leaf Beetle Xanthogaleruca luteola (Coleoptera: Chrysomelidae)

Environmental Entomology, 2011

Elm leaf beetle, Xanthogaleruca luteola (Muller) is one of the key pests of elm trees all over th... more Elm leaf beetle, Xanthogaleruca luteola (Muller) is one of the key pests of elm trees all over the world, and survives winter in reproductive diapause in sheltered locations. Seasonal variation of whole body supercooling points (SCP s), LT 50 (temperature at which 50% of the test individuals die) and survival rate after exposure to subzero temperatures were determined in Þeld collected adults during October 2008 to May 2009 and October 2009 to May 2010. The SCP of adults decreased signiÞcantly from October (median ϭ Ϫ13.8ЊC) to January (median ϭ Ϫ20.7ЊC) in Þrst year, relatively similar results was observed in the second year. The lowest LT 50 was observed in overwintering adults collected in January (Ϫ16.81ЊC) in the Þrst year and December (Ϫ15.59ЊC) in the second year. Mortality at Ϫ15ЊC for 24 h was Ͼ70% in early autumn in both years whereas it decreased to lower than 45% in early winter, the highest mortality (100%) was observed in adults collected in May in both years. Cold acclimated adults (30 d, 5ЊC) in November 2008 exhibited signiÞcantly higher SCP (Ϫ12.21 Ϯ 0.64ЊC) than nonacclimated adults (Ϫ15.57 Ϯ 1.35ЊC). A 30-d exposure to 5ЊC caused Ͼ20% mortality in November, while Ͻ9% mortality was observed in adults collected in December and January 2008. Overwintering adults died upon freezing and the lower lethal temperatures were within the range of SCP, indicating that X. luteola is a freeze intolerant insect.

Research paper thumbnail of Genomic signatures of local adaptation in recent invasiveAedes aegyptipopulations in California

Background: Rapid adaptation to new environments can facilitate species invasions and range expan... more 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 use whole-genome sequencing data from 103Aedes aegyptimosquitoes collected from various sites in southern and central California to infer the genetic structure of invasive populations. We integrate genome data with 25 topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principle components and admixture analysis, were consistent with three genetic clusters, likely resulting from multiple independent introductions. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic a...

Research paper thumbnail of Genetic Subgroups Inform on Pathobiology in Adult and Pediatric Burkitt Lymphoma

Burkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas (NHL) and is r... more Burkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas (NHL) and is relatively rare but significantly more lethal when diagnosed in adults. The global incidence is highest in Sub-Saharan Africa, where Epstein-Barr virus (EBV) positivity is observed in 95% of all tumors. Both pediatric (pBL) and adult (aBL) cases are known to share some driver mutations, for example MYC translocations, which are seen in > 90% of cases. Sequencing efforts have identified many common somatic alterations that cooperate with MYC in lymphomagenesis with approximately 30 significantly mutated genes (SMG) reported thus far. Recent analyses revealed non-coding mutation patterns in pBL that were attributed to aberrant somatic hypermutation (aSHM). We sought to identify genomic and molecular features that may explain clinical disparities within and between aBL and pBL in an effort to delineate BL subtypes that may allow for the stratification of patients with shared pathobiology....