Biology subjects

Sheikh, S. I.

Publications and source records attributed to Sheikh, S. I..

9 recordsLinked to original sources

bioRxiv2026

Assessing positive selection in centromere-associated kinetochore proteins across Metazoan groups.

Centromeres are comprised of long stretches of repetitive DNA that evolve rapidly in organisms across the tree of life. Consistent selfish centromere evolution can also have cascading effects - driving rapid evolution in interacting kinetochore proteins - possibly to maintain centromere-kinetochore compatibility. Effects of selfishly evolving centromeres on interacting proteins are most heavily studied in the inner kinetochore and assembly proteins including the constitutive centromere-associated network proteins CENP-A and CENP-C with some exploration of the extended effects to other kinetochore-associated protein complexes. While rapid evolution of the centromere has been broadly studied in many organisms, studies assessing positive selection in centromere-associated kinetochore proteins have largely focused on Drosophila. Here, we tested the hypothesis that signatures of positive selection would be present in outer kinetochore and condensin genes in diverse animal groups. We selected two protein complexes -the Condensin I complex and the Mis12 Complex - to test for positive selection in parasitic wasps, two groups of ray-finned fishes (including the amazon molly an asexual diploid exempt from centromere drive), and two groups of primates. We did not find selection using any test in any protein in the amazon molly but did find sporadic positive selection in proteins in both complexes across all groups.

evolutionary biology↗

bioRxiv2025

A shared gene but distinct dynamics regulate mimicry polymorphisms in closely related species

Sex-limited polymorphisms, such as mating strategies in male birds and mimicry in female butterflies, are widespread across the tree of life and are frequently adaptive. Considerable work has been done exploring the ecological pressures and evolutionary forces that generate and maintain genetic variation resulting in alternative sex-limited morphs, yet little is known about their molecular and developmental genetic basis. A powerful system to investigate this is Papilio butterflies: within the subgenus Menelaides, multiple closely related species have female-limited mimicry polymorphism, with females developing either derived mimetic or ancestral non-mimetic wing color patterns. While mimetic color patterns are different between species, each polymorphism is controlled by allelic variation of doublesex (dsx). Across several species, we found that the mimetic and non-mimetic females develop male-like color patterns when we knockdown dsx expression, establishing that dsx controls both sexual dimorphism and polymorphism. We also found that mimetic dsx alleles have unique spatiotemporal expression patterns between two species, Papilio lowii and Papilio alphenor. To uncover the downstream genes involved in the color pattern switch between both species, we used RNA-seq in P. lowii and compared the results to previous work in P. alphenor. While some canonical wing patterning genes are differentially expressed in females of both species, the temporal patterns of differential expression are notably different. Our results indicate that, despite the putative ancestral co-option and shared use of dsx among closely related species, the mimicry switch functions through distinct underlying mechanisms. AUTHOR SUMMARYUnderstanding how a largely shared genome can encode the potential to develop multiple morphs while simultaneously restricting this potential to one sex has long been of interest to evolutionary and developmental biologists. This phenomenon, called sex-limited polymorphism, is widespread, occurring in organisms like crustaceans, insects, fish, birds, and mammals. Recent empirical work has begun to identify the genes controlling the switch between phenotypes, but the differences between developmental programs leading to those phenotypes remain unclear. Here we use a classic example of sex-limited polymorphism - female mimicry in swallowtail butterflies - to compare how closely related species have evolved to use the same gene, doublesex, in the development of multiple female morphs. Using a combination of functional experiments, we show that despite the shared use of doublesex, the developmental genetics underlying sex-limited polymorphism have evolved to function quite differently between two species that last shared a common ancestor approximately 15 million years ago.

evolutionary biology↗

bioRxiv2024

Supergene evolution via gain of auto-regulation

Development requires the coordinated action of many genes across space and time, yet numerous species have evolved the ability to develop multiple discrete, alternate phenotypes1-5. Such polymorphisms are often controlled by supergenes, sets of tightly-linked loci that function together to control development of a polymorphic phenotype6-10. Although theories of supergene evolution are well-established, the mutations that cause functional differences between supergene alleles have been difficult to identify. The doublesex gene is a master regulator of insect sexual differentiation but has been co-opted to function as a supergene in multiple Papilio swallowtail butterflies, where divergent dsx alleles control development of discrete non-mimetic or mimetic female wing shapes and color patterns11-15. Here we demonstrate that the Papilio alphenor supergene evolved via recruitment of six new cis-regulatory elements (CREs) that control allele-specific dsx expression. Most dsx CREs, including four of the six new CREs, are bound by the DSX transcription factor itself. Our findings provide experimental support to classic supergene theory and suggest that autoregulation may provide a simple route to supergene origination and to the co-option of pleiotropic genes into new developmental roles.

evolutionary biology↗

bioRxiv2023

Speciation in kleptoparasites of oak gall wasps often correlates with shifts into new tree habitats, tree organs, and gall morphospace

Host shifts to new plants can drive speciation for plant-feeding insects, but how commonly do host shifts also drive diversification for the parasites of those same insects? Oak gall wasps induce galls on oak trees and shifts to novel tree hosts and new tree organs have been implicated as drivers of oak gall wasp speciation. Gall wasps are themselves attacked by many insect parasites, which must find their hosts on the correct tree species and organ, but which also must navigate the morphologically variable galls with which they interact. Thus, we ask whether host shifts to new trees, organs, or gall morphologies correlate with gall parasite diversification. We delimit species and infer phylogenies for two genera of gall kleptoparasites, Synergus and Ceroptres, reared from a variety of North American oak galls. We find that most species were reared from galls induced by just one gall wasp species, and no parasite species was reared from galls of more than four species. Most kleptoparasite divergence events correlate with shifts to non-ancestral galls. These shifts often involved changes in tree habitat, gall location, and gall morphology. Host shifts are thus implicated in driving diversification for both oak gall wasps and their kleptoparasitic associates.

evolutionary biology↗

bioRxiv2022

Conserved signaling pathways antagonize and synergize with co-opted doublesex to control development of novel mimetic butterfly wing patterns

Novel phenotypes are increasingly recognized to have evolved by co-option of conserved genes into new developmental contexts, yet the impact of co-option on existing developmental programs remains obscure. Here we provide insight into this process by characterizing the consequences of doublesex co-option on wing color pattern development in Papilio swallowtail butterflies. doublesex is the master regulator of insect sex differentiation but has been co-opted to control the switch between discrete mimetic and non-mimetic, male-like color patterns in Papilio polytes and its close relatives. Here we show that development of the mimetic color pattern in P. polytes is caused by a pulse of dsx expression early in female wing development that results in a corresponding pulse of differential expression that both alters color pattern development and quickly becomes decoupled from dsx expression itself. Differentially expressed genes were enriched in canonical Wnt and Hedgehog signaling pathway genes, but case studies of key genes using RNAi and antibody stains suggested opposing, novel roles for the two pathways in mimetic color pattern development. The pulse of Dsx expression caused Engrailed, the key transcription factor effector of Hh signaling, to gain anterior expression in early pupal wing development. However, Dsx and En became decoupled by mid-pupal development when En pre-figured melanic and red patterns and Dsx pre-figured white patterns. In contrast, Wnt signaling antagonizes Dsx in restricted regions of the wing to refine the mimetic color pattern. Our results therefore provide strong experimental evidence that dsx co-option significantly altered spatiotemporal activities of conserved wing patterning pathways to promote and refine the development of a novel adaptive color pattern. Altogether, our findings provide strong evidence for how co-opted genes can both cause and elicit changes to established gene regulatory networks during the evolution and development of novel phenotypes.

evolutionary biology↗

bioRxiv2022

The arthropod associates of 155 North American cynipid oak galls

The identities of most arthropod associates of cynipid-induced oak galls in the western Palearctic are generally known. However, a comprehensive accounting of associates has been performed for only a small number of the galls induced by the estimated 700 species of cynipid gall wasp in the Nearctic. This gap in knowledge stymies many potential studies of diversity, coevolution, and community ecology, for which oak gall systems are otherwise ideal models. We report rearing records of insects and other arthropods from more than 527,306 individual galls representing 201 different oak gall types collected from 32 oak tree species in North America. Of the 201 gall types collected, 155 produced one or more animals. A total of 151,075 animals were found in association with these 155 gall types, and of these 61,044 (40.4%) were gall wasps while 90,031 (59.6%) were other arthropods. We identified all animals to superfamily, family, or, where possible, to genus. We provide raw numbers and summaries of collections, alongside notes on natural history, ecology, and previously published associations for each taxon. For eight common gall-associated genera (Synergus, Ceroptres, Euceroptres, Ormyrus, Torymus, Eurytoma, Sycophila, and Euderus), we also connect rearing records to gall wasp phylogeny, geography, and ecology - including host tree and gall location (host organ), and their co-occurrence with other insect genera. Though the diversity of gall wasps and the large size of these communities is such that many Nearctic oak gall-associated insects still remain undescribed, this large collection and identification effort should facilitate the testing of new and varied ecological and evolutionary hypotheses in Nearctic oak galls.

zoology↗

bioRxiv2022

Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both.

Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ~1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae, -- primarily the oaks (genus Quercus; ~435 sp). The association of oak gall wasps with oaks is ancient (~50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified a strong signal of host plant shifting among oak gall wasps. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich and where oaks are more phylogenetically diverse. We collected 86 species of Nearctic oak gall wasps from 10 of the 14 major clades of Nearctic oaks and sequenced >1000 Ultra Conserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than the analysis of previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Though formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.

evolutionary biology↗

bioRxiv2021

Ormyrus labotus Walker (Hymenoptera: Ormyridae): another generalist that should not be a generalist is not a generalist

Several recent reappraisals of supposed generalist parasite species have revealed hidden complexes of species, each with considerably narrower host ranges. Parasitic wasps that attack gall-forming insects on plants have life history strategies that are thought to promote specialization, and though many species are indeed highly specialized, others have been described as generalist parasites. Ormyrus labotus Walker (Hymenoptera: Ormyridae) is one such apparent generalist, with rearing records spanning more than 65 host galls associated with a diverse set of oak tree species and plant tissues. We pair a molecular approach with morphology, host ecology, and phenological data from across a wide geographic sample to test the hypothesis that this supposed generalist is actually a complex of several more specialized species. We find 16-18 putative species within the morphological species O. labotus, each reared from only 1-6 host gall types, though we identify no single unifying axis of specialization. We also find cryptic habitat specialists within two other named Ormyrus species. Our study suggests that caution should be applied when considering host ranges of parasitic insects described solely by morphological traits, particularly given their importance as biocontrol organisms and their role in biodiversity and evolutionary studies.

evolutionary biology↗

bioRxiv2020

Diversity, host ranges, and potential drivers of speciation among the inquiline enemies of oak gall wasps.

Animals that exploit an extended phenotype (e.g., residences, resources, etc.) of other animals are called inquilines. Not strictly parasites, inquilines may nevertheless possess specialized traits that adapt them to particular dimensions of the extended phenotype of their "host". These adaptations to host traits can in turn lead to fitness tradeoffs that restrict the host range of an inquiline such that shifts to novel hosts might trigger inquiline diversification. Speciation via host shifting has been studied in many animal parasites, but we know far less about the role of host shifts in inquiline speciation. Synergus (Hymenoptera: Cynipidae: Synergini) is a speciose but taxonomically-challenging group of inquilines that feed on the tissue of galls induced by oak gall wasps (Hymenoptera: Cynipidae: Cynipini). Currently too little is known about Nearctic Synergus diversity or host associations to evaluate whether and how host use affects their diversification. Here, we report on a large collection of Synergus reared from galls of 33 oak gall wasp species in the upper Midwestern United States. We integrated DNA barcodes, morphology, ecology, and phenology to delimit putative species of Synergus and describe their host ranges. We find evidence of at least 23 Synergus species associated with the 33 gall wasp hosts. At least five previously described Synergus species are each a complex of two to five species, while three species fit no prior description. We also find strong evidence that oak tree section and host gall morphology define axes of specialization for Synergus. Without over-interpreting our singlegene tree, it is clear that the North American Synergus have experienced several transitions among gall hosts and tree habitats and that host-use is correlated with reproductive isolation, though it remains too early to tell whether shifts to new hosts are the initiators of speciation events in Synergus inquilines of oak gall wasps, or if host shifts occur after reproductive isolation has already evolved.

evolutionary biology↗