Seminar Talk 2/21/19 @ University of Tennessee

I will be giving a lightning talk on February 21, 2019 at the University of Tennessee about my research on the role of pharyngeal jaws in acanthomorph fish diversity. The talk will occur at 3:30 in the 307 SERF (Science & Engineering Building) on the University of Tennessee, Knoxville campus.

PJAsize

Specialized pharyngeal jaws are found in six families of fish, including the cichlids. Above is a distribution of size-corrected (for body size) diameter of the pharyngeal gape.

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AnnotationBustR Paper Published in PeerJ

I’m happy to announce that the paper describing the R package AnnotationBustR Brian O’Meara and I created has been accepted at PeerJ. This package extracts subsequences from GenBank Annotations. For more details about the R package, check out the previous blog-post: AnnotationBustR, a New R Package and Pre-Print That Extracts Sequence Data From GenBank Annotations.

Paper Citation and Link: Borstein SR, O’Meara BC. (2018AnnotationBustR: an R package to extract subsequences from GenBank annotationsPeerJ 6:e5179.
https://doi.org/10.7717/peerj.5179

For a link to the R package on CRAN: https://cran.r-project.org/web/packages/AnnotationBustR/index.html

GitHub Development Repo: https://github.com/sborstein/AnnotationBustR

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New Paper on Cichlid Feeding Kinematic Efficiency Published in Evolution

A paper I collaborated on with Christopher Martinez on Malawi and Tanganyikan cichlid kinematics was recently published in Evolution. This paper builds upon a kinematic dataset and paper I worked on that you can find more information about on my site here. Most fish (including cichlids) can be categorized as either suction feeders or biters. Suction feeders by protruding their jaws, depressing their hyoid bone, and abducting the operculum (gill plate) generate a suction force to suck their prey into their mouth. Biters directly contact and forcefully remove the prey with their jaws.

In this paper, we track how the feeding apparatus changes during a feeding event mapping its morphology (see below photo) and investigated how it relates to exploiting functionally different prey. The linearity of the mapped trajectory can then be used to assess how efficient the strike is, with a more linear strike being more efficient.

2018 Cichlid Kinematic Efficiency.pdf - Adobe Acrobat Pro DC1

The above depicts how the craniofacial (head and face) morphology of Lamprologus lemairii, a fish and crustacean predator that employs suction feeding to capture prey, changes throughout prey capture. The figure shows how we tracked kinesis and the overall trajectory as the head moves from the beginning (teal dot) of a feeding event to the maximum expansion of the jaws during a feeding event (red dot). Light blue dots are individual morphological landmarks tracked throughout the strike while the yellow dots are along a curve tracked throughout the strike. Dark blue dots and associated photos show how these landmarks move at roughly evenly spaced out intervals throughout the strike. The dotted line depicts the overall kinematic trajectory.

We find that fish that feed on evasive prey items, fish that typically employ suction feeding to capture prey, have more cranial kinesis during a strike, as the jaws protrude to aid in generating suction force (see the below photo). While the jaws and other aspects of the head do undergo a vast amount of kinesis during feeding, we find that they have much more kinematically efficient (i.e. more linear) than species that employ biting (algae, sponge, mollusk feeders, etc.) and have far less jaw kinesis. Our study highlights underappreciated aspect of jaw protrusion, how it aids in kinematic efficiency, which may help in understanding the origins and diversity of jaw morphology in ray-finned fishes.

2018 Cichlid Kinematic Efficiency.pdf - Adobe Acrobat Pro DC

Phylogeny of Lake Malawi and Tanganyikan cichlids depicting the diet of species, the amount of cranial kinesis, and with representative photos showing how morphology changes during feeding. Branch colors of the phylogeny depict the amount of cranial kinesis, with species on cooler colored branches having more cranial kinesis and species on warmer colored branches having less cranial kinesis. Colored dots next to species names represent one of the six diet classifications used to categorize species (i.e. fish, zoobenthos, aufwuchs, etc.). From the various pictures of fish heads, it is easy to see that species that feed on more evasive prey items (fish, zoobenthos 2 (which includes shrimps) have more cranial kinesis than species that employ biting to feed on non-evasive prey items (aufwuchs, zoobenthos 1 (which includes snails and bivalves).

The citation and link to the paper:

Martinez CM, McGee MD, Borstein SR, and Wainwright PC. 2018. Feeding ecology underlies the evolution of cichlid jaw mobility. Evolution.
 https://doi.org/10.1111/evo.13518.

 

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AnnotationBustR, a New R Package and Pre-Print That Extracts Sequence Data From GenBank Annotations

I have recently published a new R package, AnnotationBustR, and a Preprint of our paper that is submitted at PeerJ. Sequence data can be difficult to work with sometimes as sequences may be concatenated or a sequence of interest may be in a genome and not available by itself on GenBank. Additionally, the same gene may be annotated may be annotated differently among records,  making it difficult to extract data from a lot of records. AnnotationBustR was written to make this process easier and as users can supply a list of accessions and a set of terms they want to extract and get FASTA formatted files returned. We provide a vignette tutorial within the R package or on CRAN (see link below) on how to use the software.

The R package is developed on GitHub and  interfaces to GenBank through the R package seqinr. You can see the GitHub repo, CRAN page, and pre-print of our paper in the links below:

GitHub: https://github.com/sborstein/AnnotationBustR

CRAN: https://cran.r-project.org/web/packages/AnnotationBustR/index.html

PeerJ Preprint citation and link: Borstein, S. R., & O’Meara, B. C. (2017). AnnotationBustR: An R package to extract subsequences from GenBank annotations. PeerJ Preprints, e2920v1, https://doi.org/10.7287/peerj.preprints.2920v1.

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I’ve Been Awarded an NSF DDIG!

I have been awarded a National Science Foundation Doctoral Dissertation Improvement Grant for my research on the morphological consequences of trophic evolution. I look forward to providing information on the research products produced by this funding on this site in the future. A brief summary of my project can be found here: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1701913&HistoricalAwards=false

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Presentation at SICB 2017 New Orleans, LA

I will be presenting a talk at this years Society of Integrative and Comparative Biologists annual meeting January 7th, 2017 in New Orleans. The talk “The evolution of diet breadth in coral reef fishes” will discuss how diet breadth effects phenotypic evolution in reef fishes. The talk is in the convention center room 217 at 11:15 AM.

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New Paper in Proceedings of the Royal Society B on Biting and Suction Feeding in Rift Lake Cichlids

I’m happy to announce a paper I collaborated on investigating how feeding modes effect jaw kinesis in cichlids was recently published in Proceedings of the Royal Society B: Biological Sciences.

In this paper we used a combination of ultra-conserved element sequencing (UCE) and high-speed video to investigate if the mode at which fish procure their food effects the evolution of jaw protrusion in Lake Malawi and Tanganyikan fishes. A distinctive feature of ray-finned fishes (which include cichlids) is that many of them are able to protrude the upper jaw when feeding. This jaw protrusion is especially useful when feeding on evasive prey items as it enhances the suction force and aides in sucking the prey into the mouth. For the most part, fish feed by two methods. Suction feeding, where prey is obtained by the method described above or biting, where prey is forcefully removed/captured by the jaws themselves (e.x. fish feeding of algae/sponged off rocks, scale eaters, mollusk shellers).

2016 Cichlid replicated divergence mirrors ver.pdf - Adobe Acrobat Pro DC

Lamprologus lemairii, a fish and crustacean predator that employs suction feeding, showing how the jaw bones protrude during feeding. The above photo shows the position of the bones before a strike while the bottom shows where the same points have moved to once prey is captured.

Our results showed that species that obtain prey via biting have much less jaw protrusion and overall movement of the cranial bones during a feeding event relative to suction feeders. This is not necessarily surprising as biting fish face certain functional demands on the jaws, like stress placed by forcible contact to extract prey, where additional jaw protrusion would be ineffective. Our results highlight  the contrasting functional demands and trade-offs both modes of feeding have and how these demands have shaped the evolution of head morphology and feeding ecology in the Malawi and Tanganyikan cichlid radiations.

Kinesis

A phylogeny constructed from ultra-conserved elements of 56 Malawi and Tanganyikan cichlids used in the study. Feeding mode has transitioned numerous times through the evolution of these fishes as can be seen by the different colors of the branches of the phylogeny, with biting species highlighted in warmer colors and suction feeding species by cooler colors.

Paper Citation & Link : McGee MD, Faircloth BC, Borstein SR, Zheng J, Hulsey CD, Wainwright PC, and Alfaro ME. 2016. Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Proceedings of the Royal Society B: Biological Sciences 283. http://dx.doi.org/10.1098/rspb.2015.1413

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