A supermatrix-based molecular phylogeny of the family Drosophilidae

Linde, Kim van der; Houle, David; Spicer, Greg S.; Steppan, Scott J.

doi:10.1017/s001667231000008x

Cited by 127 publications

(152 citation statements)

References 76 publications

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“…We inferred a phylogeny for major Drosophila lineages using DNA sequence alignments from a recent phylogenetic study of the genus (53). We trimmed the taxon set to include 94 species that we believed to be important for estimating the relative crown-clade age for each of nine major subclades for which we could obtain estimates of species richness (SI Materials and Methods).…”

Section: Methodsmentioning

confidence: 99%

Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

Rabosky

Matute

2013

Proc. Natl. Acad. Sci. U.S.A.

126

125

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The rate at which speciation occurs varies greatly among different kinds of organisms and is frequently assumed to result from species-or clade-specific factors that influence the rate at which populations acquire reproductive isolation. This premise leads to a fundamental prediction that has never been tested: Organisms that quickly evolve prezygotic or postzygotic reproductive isolation should have faster rates of speciation than organisms that slowly acquire reproductive isolation. We combined phylogenetic estimates of speciation rates from Drosophila and birds with a method for analyzing interspecific hybridization data to test whether the rate at which individual lineages evolve reproductive isolation predicts their macroevolutionary rate of species formation. We find that some lineages evolve reproductive isolation much more quickly than others, but this variation is decoupled from rates of speciation as measured on phylogenetic trees. For the clades examined here, reproductive isolation-especially intrinsic, postzygotic isolation-does not seem to be the rate-limiting control on macroevolutionary diversification dynamics. These results suggest that factors associated with intrinsic reproductive isolation may have less to do with the tremendous variation in species diversity across the evolutionary tree of life than is generally assumed. A central challenge at the interface between macroevolution and microevolution is to explain the population-level processes that contribute to biological variation in diversification rates and species richness (1). Phylogenetic evidence for biological variation in the rate of species diversification is widespread (2, 3), and numerous studies have now linked specific traits to the dynamics of speciation and extinction as realized over macroevolutionary timescales (2,4). At the population level, a microevolutionary research program on the biology of speciation has focused on the factors that lead to various forms of reproductive isolation (RI) between populations (5, 6). Explaining how and why RI evolves is generally considered to be the central and defining challenge in the study of speciation (2, 7-9), and recent studies have made great progress toward explaining the genetic and ecological basis for various forms of RI (7,8,10).Most microevolutionary research on speciation implicitly assumes that RI is the defining and rate-limiting step in the speciation process (7,8,11), but the evolution of RI need not bear any predictive relationship to rates of species diversification as realized over macroevolutionary timescales (12). This has long been recognized by the paleontological community, where "successful" speciation is believed to entail not only the evolution of reproductive isolation but also the persistence of incipient species (13-15). For example, speciation might be limited primarily by the rate at which lineages form allopatric isolates (6,16) or by the capacity for geographic range expansion (17, 18). Likewise, speciation might be limited more by factors that influe...

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Section: Methodsmentioning

confidence: 99%

Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

Rabosky

Matute

2013

Proc. Natl. Acad. Sci. U.S.A.

126

125

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“…Perhaps tropical conditions with stable climates relax naturally selective pressures on Drosophila and enable rapid evolutionary changes to behaviour through sexually selective mechanisms, resulting in convergence. Another possibility is that the relative density and variety of species in tropical regions require mate coordination that can communicate precisely at short distances without being influenced by surrounding messages (as could be the case with chemical signalling Linde et al (2010) were manually added based on molecular phylogenies from other sources (Kopp and True, 2002;Yu et al, 1999;Spicer and Jaenike, 1996;Perlman et al, 2003;Spicer and Bell, 2002). The distributions of species are mapped in four 'climatic categories' that summarizes their range the best.…”

Section: Visual Communicationmentioning

confidence: 99%

Phylogeny, environment and sexual communication across the Drosophila genus

Jezovit

Levine

Schneider

2017

Journal of Experimental Biology

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Social behaviour emerges from the local environment but is constrained by the animal's life history and its evolutionary lineage. In this perspective, we consider the genus Drosophila and provide an overview of how these constraints can shape how individuals interact. Our focus is restricted to visual and chemical signals and how their use varies across species during courtship -currently the only social behaviour well-studied across many Drosophila species. We broadly categorize species into four climatic groups -cosmopolitan, tropical, temperate and arid -which serve as discussion points as we review comparative behavioural and physiological studies and relate them to the abiotic conditions of a species environment. We discuss how the physiological and behavioural differences among many fly species may reflect life history differences as much as, or even more than, differences in phylogeny. This perspective serves not only to summarize what has been studied across drosophilids, but also to identify questions and outline gaps in the literature worth pursuing for progressing the understanding of behavioural evolution in Drosophila.

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“…Some studies placed it as a sister to all other Drosophila species [16,30], while others put it within the Drosophila subgenus [35]. This uncertainty in the phylogenetic position of D. busckii could have resulted from the small number of genes that were previously investigated, and we use whole-genome sequence alignments of representative Drosophila species and other Drosophilidae, to generate a phylogenomic tree.…”

Section: Phylogenetic Position Of D Busckiimentioning

confidence: 99%

“…This uncertainty in the phylogenetic position of D. busckii could have resulted from the small number of genes that were previously investigated, and we use whole-genome sequence alignments of representative Drosophila species and other Drosophilidae, to generate a phylogenomic tree. Our alignments include D. melanogaster, D. pseudoobscura and D. willistoni from the Sophophora subgenus; D. albomicans [11], D. grimshawi and D. virilis from the Drosophila subgenus, D. busckii and two recently sequenced Diptera species within the Drosophilidae family: Scaptodrosophila lebanonensis [36] and Phortica variegata [19] as outgroups to the Drosophila genus [35][36][37]. In total, we aligned CDS sequences of 6189 orthologous genes spanning a total of 19.1Mb from each species and acquired a consensus tree with high bootstrapping values (Fig 2).…”

Section: Phylogenetic Position Of D Busckiimentioning

confidence: 99%

Ancestral chromatin configuration constrains chromatin evolution on differentiating sex chromosomes inDrosophila

Zhou

Bachtrog

2015

Preprint

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Sex chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched for H3K9me2/3). Drosophila autosomes are typically mostly euchromatic but the small dot chromosome has evolved a heterochromatinlike milieu (enriched for H3K9me2/3) that permits the normal expression of dot-linked genes, but which is different from typical pericentric heterochromatin. In Drosophila busckii, the dot chromosomes have fused to the ancestral sex chromosomes, creating a pair of 'neo-sex' chromosomes. Here we collect genomic, transcriptomic and epigenomic data from D. busckii, to investigate the evolutionary trajectory of sex chromosomes from a largely heterochromatic ancestor. We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional. Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes. Despite rampant neo-Y degeneration, we find that the neo-X is deficient for the canonical histone modification mark of dosage compensation (H4K16ac), relative to autosomes or the compensated ancestral X chromosome, possibly reflecting constraints imposed on evolving hyperactive chromatin in an originally heterochromatic environment. Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X. Our data show that Y degeneration proceeds quickly after sex chromosomes become established through genomic and epigenetic changes, and are consistent with the idea that the evolution of sex-linked chromatin is influenced by its ancestral configuration. Data Availability Statement: All sequencing reads, the genome sequence assembly and annotation generated in this study are deposited at the National Center for Biotechnology Information Short Reads Archive (www.ncbi.nlm.nih.gov/sra) under the Bioproject accession no. PRJNA274996.Funding: This work was funded by NIH grants (R01GM076007, R01GM093182 and R01GM101255) to DB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author SummaryDNA is packaged with proteins into two general types of chromatin: the transcriptionally active euchromatin and repressive heterochromatin. Sex chromosomes typically evolve from a pair of euchromatic autosomes. The Y chromosome of Drosophila is gene poor and almost entirely heterochromatic; the X chromosome, in contrast, has evolved a hyperactive euchromatin structure and globally up-regulates its gene expression, to compensate for loss of activity from the homologous genes on the Y chromosome. The evolutionary trajectory along which sex chromosomes...

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A supermatrix-based molecular phylogeny of the family Drosophilidae

Cited by 127 publications

References 76 publications

Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

Phylogeny, environment and sexual communication across the Drosophila genus

Ancestral chromatin configuration constrains chromatin evolution on differentiating sex chromosomes inDrosophila

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