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Article ; Online: In the Spotlight-Established researcher.

Extavour, Cassandra G

Journal of experimental zoology. Part B, Molecular and developmental evolution

2021 Volume 336, Issue 8, Page(s) 589–590

Language	English
Publishing date	2021-06-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2103823-5
ISSN	1552-5015 ; 0022-104X ; 1552-5007
ISSN (online)	1552-5015
ISSN	0022-104X ; 1552-5007
DOI	10.1002/jez.b.23065
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Article ; Online: Phylotranscriptomics Reveals Discordance in the Phylogeny of Hawaiian Drosophila and Scaptomyza (Diptera: Drosophilidae).

Church, Samuel H / Extavour, Cassandra G

Molecular biology and evolution

2022 Volume 39, Issue 3

Abstract: Island radiations present natural laboratories for studying the evolutionary process. The Hawaiian Drosophilidae are one such radiation, with nearly 600 described species and substantial morphological and ecological diversification. These species are ... ...

Abstract	Island radiations present natural laboratories for studying the evolutionary process. The Hawaiian Drosophilidae are one such radiation, with nearly 600 described species and substantial morphological and ecological diversification. These species are largely divided into a few major clades, but the relationship between clades remains uncertain. Here, we present new assembled transcriptomes from 12 species across these clades, and use these transcriptomes to resolve the base of the evolutionary radiation. We recover a new hypothesis for the relationship between clades, and demonstrate its support over previously published hypotheses. We then use the evolutionary radiation to explore dynamics of concordance in phylogenetic support, by analyzing the gene and site concordance factors for every possible topological combination of major groups. We show that high bootstrap values mask low evolutionary concordance, and we demonstrate that the most likely topology is distinct from the topology with the highest support across gene trees and from the topology with highest support across sites. We then combine all previously published genetic data for the group to estimate a time-calibrated tree for over 300 species of drosophilids. Finally, we digitize dozens of published Hawaiian Drosophilidae descriptions, and use this to pinpoint probable evolutionary shifts in reproductive ecology as well as body, wing, and egg size. We show that by examining the entire landscape of tree and trait space, we can gain a more complete understanding of how evolutionary dynamics play out across an island radiation.
MeSH term(s)	Animals ; Biological Evolution ; Drosophila/genetics ; Drosophilidae/genetics ; Hawaii ; Phylogeny ; Wings, Animal
Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msac012
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Article ; Online: The evolution of ovary-biased gene expression in Hawaiian Drosophila.

Church, Samuel H / Munro, Catriona / Dunn, Casey W / Extavour, Cassandra G

PLoS genetics

2023 Volume 19, Issue 1, Page(s) e1010607

Abstract: With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across species. But to know ... ...

Abstract	With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across species. But to know when differences in gene expression across species are significant, we first need to know how much evolutionary variation in gene expression we expect to observe. Here we provide an answer by analyzing RNAseq data across twelve species of Hawaiian Drosophilidae flies, focusing on gene expression differences between the ovary and other tissues. We show that over evolutionary time, there exists a cohort of ovary specific genes that is stable and that largely corresponds to described expression patterns from laboratory model Drosophila species. Our results also provide a demonstration of the prediction that, as phylogenetic distance increases, variation between species overwhelms variation between tissue types. Using ancestral state reconstruction of expression, we describe the distribution of evolutionary changes in tissue-biased expression, and use this to identify gains and losses of ovary-biased expression across these twelve species. We then use this distribution to calculate the evolutionary correlation in expression changes between genes, and demonstrate that genes with known interactions in D. melanogaster are significantly more correlated in their evolution than genes with no or unknown interactions. Finally, we use this correlation matrix to infer new networks of genes that share evolutionary trajectories, and we present these results as a dataset of new testable hypotheses about genetic roles and interactions in the function and evolution of the Drosophila ovary.
MeSH term(s)	Animals ; Female ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Ovary ; Phylogeny ; Hawaii ; Genes, Insect ; Evolution, Molecular ; Drosophila/genetics ; Gene Expression
Language	English
Publishing date	2023-01-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1010607
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Article ; Online: Genomics and genome editing techniques of crickets, an emerging model insect for biology and food science.

Nakamura, Taro / Ylla, Guillem / Extavour, Cassandra G

Current opinion in insect science

2022 Volume 50, Page(s) 100881

Abstract: Most tools available for manipulating gene function in insects have been developed for holometabolous species. In contrast, functional genetics tools for the Hemimetabola are highly underdeveloped. This is a barrier both to understanding ancestral insect ...

Abstract	Most tools available for manipulating gene function in insects have been developed for holometabolous species. In contrast, functional genetics tools for the Hemimetabola are highly underdeveloped. This is a barrier both to understanding ancestral insect biology, and to optimizing contemporary study and manipulation of particular large hemimetabolous orders of crucial economic and agricultural importance like the Orthoptera. For orthopteran insects, including crickets, the rapid spread of next-generation sequencing technology has made transcriptome data available for a wide variety of species over the past decade. Furthermore, whole genome sequences of orthopteran insects with relatively large genome sizes are now available. With these new genome assemblies and the development of genome editing technologies such as the CRISPR-Cas9 system, it has become possible to create gene knock-out and knock-in strains in orthopteran insects. As a result, orthopteran species should become increasingly feasible for laboratory study not only in research fields that have traditionally used insects, but also in agricultural fields that use them as food and feed. In this review, we summarize these recent advances and their relevance to such applications.
MeSH term(s)	Animals ; Food Technology ; Gene Editing/methods ; Genomics ; Gryllidae/genetics ; Insecta/genetics
Language	English
Publishing date	2022-02-02
Publishing country	Netherlands
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2772833-X
ISSN	2214-5753 ; 2214-5745
ISSN (online)	2214-5753
ISSN	2214-5745
DOI	10.1016/j.cois.2022.100881
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Article ; Online: JEZB special issue on eggs.

Church, Samuel H / Donoughe, Seth / Extavour, Cassandra G

Journal of experimental zoology. Part B, Molecular and developmental evolution

2021 Volume 336, Issue 8, Page(s) 593–594

MeSH term(s)	Animals ; Ovum ; Periodicals as Topic
Language	English
Publishing date	2021-11-20
Publishing country	United States
Document type	Editorial
ZDB-ID	2103823-5
ISSN	1552-5015 ; 0022-104X ; 1552-5007
ISSN (online)	1552-5015
ISSN	0022-104X ; 1552-5007
DOI	10.1002/jez.b.23107
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Article ; Online: Null hypotheses for developmental evolution.

Church, Samuel H / Extavour, Cassandra G

Development (Cambridge, England)

2020 Volume 147, Issue 8

Abstract: How much evolutionary change in development do we expect? In this Spotlight, we argue that, as developmental biologists, we are in a prime position to contribute to the definition of a null hypothesis for developmental evolution: in other words, a ... ...

Abstract	How much evolutionary change in development do we expect? In this Spotlight, we argue that, as developmental biologists, we are in a prime position to contribute to the definition of a null hypothesis for developmental evolution: in other words, a hypothesis for how much developmental evolution we expect to observe over time. Today, we have access to an unprecedented array of developmental data from across the tree of life. Using these data, we can now consider development in the light of evolution, and vice versa, more deeply than ever before. As we do this, we may need to re-examine previous assumptions that appeared to serve us well when data points were fewer. Specifically, we think it is important to challenge assumptions that change is very rare for all developmental traits, especially if this assumption is used to sustain an erroneous view that evolution always optimizes adaptive traits toward increasing complexity.
MeSH term(s)	Animals ; Biological Evolution ; Gene Expression Regulation, Developmental ; Growth and Development ; Humans ; Insecta/genetics ; Models, Biological
Language	English
Publishing date	2020-04-27
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.178004
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Article ; Online: Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster.

Tarikere, Shreeharsha / Ylla, Guillem / Extavour, Cassandra G

G3 (Bethesda, Md.)

2021 Volume 12, Issue 2

Abstract: The survival and evolution of a species is a function of the number of offspring it can produce. In insects, the number of eggs that an ovary can produce is a major determinant of reproductive capacity. Insect ovaries are made up of tubular egg-producing ...

Abstract	The survival and evolution of a species is a function of the number of offspring it can produce. In insects, the number of eggs that an ovary can produce is a major determinant of reproductive capacity. Insect ovaries are made up of tubular egg-producing subunits called ovarioles, whose number largely determines the number of eggs that can be potentially laid. Ovariole number in Drosophila is directly determined by the number of cellular structures called terminal filaments, which are stacks of cells that assemble in the larval ovary. Elucidating the developmental and regulatory mechanisms of terminal filament formation is thus key to understanding the regulation of insect reproduction through ovariole number regulation. We systematically measured mRNA expression of all cells in the larval ovary at the beginning, middle, and end of terminal filament formation. We also separated somatic and germ line cells during these stages and assessed their tissue-specific gene expression during larval ovary development. We found that the number of differentially expressed somatic genes is highest during the late stages of terminal filament formation and includes many signaling pathways that govern ovary development. We also show that germ line tissue, in contrast, shows greater differential expression during early stages of terminal filament formation, and highly expressed germ line genes at these stages largely control cell division and DNA repair. We provide a tissue-specific and temporal transcriptomic dataset of gene expression in the developing larval ovary as a resource to study insect reproduction.
MeSH term(s)	Animals ; Drosophila Proteins/metabolism ; Drosophila melanogaster/physiology ; Female ; Gene Expression ; Germ Cells/metabolism ; Morphogenesis/genetics
Chemical Substances	Drosophila Proteins
Language	English
Publishing date	2021-12-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkab305
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Article ; Online: Evolutionary dynamics of sex-biased genes expressed in cricket brains and gonads.

Whittle, Carrie A / Kulkarni, Arpita / Extavour, Cassandra G

Journal of evolutionary biology

2021 Volume 34, Issue 8, Page(s) 1188–1211

Abstract: Sex-biased gene expression, particularly sex-biased expression in the gonad, has been linked to rates of protein sequence evolution (nonsynonymous to synonymous substitutions, dN/dS) in animals. However, in insects, sex-biased expression studies remain ... ...

Abstract	Sex-biased gene expression, particularly sex-biased expression in the gonad, has been linked to rates of protein sequence evolution (nonsynonymous to synonymous substitutions, dN/dS) in animals. However, in insects, sex-biased expression studies remain centred on a few holometabolous species. Moreover, other major tissue types such as the brain remain underexplored. Here, we studied sex-biased gene expression and protein evolution in a hemimetabolous insect, the cricket Gryllus bimaculatus. We generated novel male and female RNA-seq data for two sexual tissue types, the gonad and somatic reproductive system, and for two core components of the nervous system, the brain and ventral nerve cord. From a genome-wide analysis, we report several core findings. Firstly, testis-biased genes had accelerated evolution, as compared to ovary-biased and unbiased genes, which was associated with positive selection events. Secondly, although sex-biased brain genes were much less common than for the gonad, they exhibited a striking tendency for rapid protein sequence evolution, an effect that was stronger for the female than male brain. Further, some sex-biased brain genes were linked to sexual functions and mating behaviours, which we suggest may have accelerated their evolution via sexual selection. Thirdly, a tendency for narrow cross-tissue expression breadth, suggesting low pleiotropy, was observed for sex-biased brain genes, suggesting relaxed purifying selection, which we speculate may allow enhanced freedom to evolve adaptive protein functional changes. The findings of rapid evolution of testis-biased genes and male and female-biased brain genes are discussed with respect to pleiotropy, positive selection and the mating biology of this cricket.
MeSH term(s)	Animals ; Brain ; Female ; Gonads ; Male ; Ovary ; Sex Characteristics ; Testis
Language	English
Publishing date	2021-07-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1465318-7
ISSN	1420-9101 ; 1010-061X
ISSN (online)	1420-9101
ISSN	1010-061X
DOI	10.1111/jeb.13889
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Article: The Cricket Gryllus bimaculatus: Techniques for Quantitative and Functional Genetic Analyses of Cricket Biology.

Kulkarni, Arpita / Extavour, Cassandra G

Results and problems in cell differentiation

2019 Volume 68, Page(s) 183–216

Abstract: All extant species are an outcome of nature's "experiments" during evolution, and hence multiple species need to be studied and compared to gain a thorough understanding of evolutionary processes. The field of evolutionary developmental biology (evo-devo) ...

Abstract	All extant species are an outcome of nature's "experiments" during evolution, and hence multiple species need to be studied and compared to gain a thorough understanding of evolutionary processes. The field of evolutionary developmental biology (evo-devo) aspires to expand the number of species studied, because most functional genetic studies in animals have been limited to a small number of "traditional" model organisms, many of which belong to the same phylum (Chordata). The phylum Arthropoda, and particularly its component class Insecta, possesses many important characteristics that are considered favorable and attractive for evo-devo research, including an astonishing diversity of extant species and a wide disparity in body plans. The development of the most thoroughly investigated insect genetic model system to date, the fruit fly Drosophila melanogaster (a holometabolous insect), appears highly derived with respect to other insects and indeed with respect to most arthropods. In comparison, crickets (a basally branching hemimetabolous insect lineage compared to the Holometabola) are thought to embody many developmental features that make them more representative of insects. Here we focus on crickets as emerging models to study problems in a wide range of biological areas and summarize the currently available molecular, genomic, forward and reverse genetic, imaging and computational tool kit that has been established or adapted for cricket research. With an emphasis on the cricket species Gryllus bimaculatus, we highlight recent efforts made by the scientific community in establishing this species as a laboratory model for cellular biology and developmental genetics. This broad toolkit has the potential to accelerate many traditional areas of cricket research, including studies of adaptation, evolution, neuroethology, physiology, endocrinology, regeneration, and reproductive behavior. It may also help to establish newer areas, for example, the use of crickets as animal infection model systems and human food sources.
MeSH term(s)	Animals ; Drosophila melanogaster ; Food Supply ; Gryllidae/embryology ; Gryllidae/genetics ; Gryllidae/microbiology ; Gryllidae/physiology ; Models, Animal
Language	English
Publishing date	2019-10-09
Publishing country	Germany
Document type	Journal Article ; Review
ISSN	0080-1844
ISSN	0080-1844
DOI	10.1007/978-3-030-23459-1_8
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Article ; Online: Contrasting patterns of molecular evolution in metazoan germ line genes.

Whittle, Carrie A / Extavour, Cassandra G

BMC evolutionary biology

2019 Volume 19, Issue 1, Page(s) 53

Abstract: Background: Germ lines are the cell lineages that give rise to the sperm and eggs in animals. The germ lines first arise from primordial germ cells (PGCs) during embryogenesis: these form from either a presumed derived mode of preformed germ plasm ( ... ...

Abstract	Background: Germ lines are the cell lineages that give rise to the sperm and eggs in animals. The germ lines first arise from primordial germ cells (PGCs) during embryogenesis: these form from either a presumed derived mode of preformed germ plasm (inheritance) or from an ancestral mechanism of inductive cell-cell signalling (induction). Numerous genes involved in germ line specification and development have been identified and functionally studied. However, little is known about the molecular evolutionary dynamics of germ line genes in metazoan model systems. Results: Here, we studied the molecular evolution of germ line genes within three metazoan model systems. These include the genus Drosophila (N=34 genes, inheritance), the fellow insect Apis (N=30, induction), and their more distant relative Caenorhabditis (N=23, inheritance). Using multiple species and established phylogenies in each genus, we report that germ line genes exhibited marked variation in the constraint on protein sequence divergence (dN/dS) and codon usage bias (CUB) within each genus. Importantly, we found that de novo lineage-specific inheritance (LSI) genes in Drosophila (osk, pgc) and in Caenorhabditis (pie-1, pgl-1), which are essential to germ plasm functions under the derived inheritance mode, displayed rapid protein sequence divergence relative to the other germ line genes within each respective genus. We show this may reflect the evolution of specialized germ plasm functions and/or low pleiotropy of LSI genes, features not shared with other germ line genes. In addition, we observed that the relative ranking of dN/dS and of CUB between genera were each more strongly correlated between Drosophila and Caenorhabditis, from different phyla, than between Drosophila and its insect relative Apis, suggesting taxonomic differences in how germ line genes have evolved. Conclusions: Taken together, the present results advance our understanding of the evolution of animal germ line genes within three well-known metazoan models. Further, the findings provide insights to the molecular evolution of germ line genes with respect to LSI status, pleiotropy, adaptive evolution as well as PGC-specification mode.
MeSH term(s)	Animals ; Bees/genetics ; Caenorhabditis/genetics ; Cell Lineage ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genes, Insect ; Genetic Pleiotropy ; Germ Cells/cytology ; Germ Cells/metabolism ; Inheritance Patterns/genetics ; Phylogeny ; Sequence Analysis, Protein ; Species Specificity
Language	English
Publishing date	2019-02-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2041493-6
ISSN	1471-2148 ; 1471-2148
ISSN (online)	1471-2148
ISSN	1471-2148
DOI	10.1186/s12862-019-1363-x
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