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. (2018) AnnotationBustR: an R package to extract subsequences from GenBank annotations. PeerJ 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

Advertisements

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.

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.

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.

 

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.

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

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.

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).

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.

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

New Paper in Science on the Lake Victoria Cichlid Extinction

Today our paper came out in Science investigating the actual causes of the Lake Victoria cichlid extinction event. Lake Victoria was home to around several hundred endemic cichlid species. However, introductions of the Nile perch (Lates niloticus) into Lake Victoria in the 1950’s caused a mass extinction of roughly 200 species of cichlids. As the Nile perch is a voracious predator that grows to six feet in length, it was long thought  high predation on the Lake Victorian cichlids (the largest of which only grow slightly over 12 inches in length)  by Nile perch best explained the extinction of so many species.

Our research group found that predation alone doesn’t explain the Lake Victorian cichlid extinction as we found that there was a non-random pattern of which cichlid species went extinct. Specifically, we found that the cichlids that were most impacted by the Nile perch were piscivorous (fish eating) species. The reason for this is that cichlids have highly modified pharyngeal jaws in their throat that function as a second set of jaws. These pharyngeal jaws are essentially a fused gill arch supported by muscles. Cichlids and other fish with this trait are known as “pharyngognathous fishes”. It has long been thought that pharyngognathy is evolutionary innovation as it allows the oral jaws to specialize in prey capture and the pharyngeal jaws in prey processing. When measuring the diameter of the oral jaws and the pharyngeal jaws we saw that the pharyngeal jaws were much smaller and imposed a limit on the prey size that could be swallowed by cichlids due to their bulkiness. Nile perch, which lack these specialized pharyngeal jaws had much larger gapes, meaning that they could swallow much larger prey.

Pharyngeal jaw gape of piscivorous cichlids from Lake Victoria and other geographic regions in comparison to Nile perch. Nile perch have much larger gapes than cichlids do.

 

Additionally, when we performed prey processing trials to see how long it took Lake Victorian cichlid piscivores and Nile perch to swallow fish prey, it took Victorian cichlids hours to process and swallow a fish that of comparable size would take Nile perch only several minutes! This indicates that when competing for the same prey resources, Nile perch are far superior to the native cichlids.

So what then explains the Lake Victorian extinction? While predation by Nile perch certainly played a role, our study highlights that competition for prey between Lake Victorian cichlid piscivores and Nile perch also played a critical role. So why then were so many cichlids in Lake Victoria piscivores if pharyngeal jaws limit them? There is pretty good evidence that the ancestor to all Lake Victorian cichlids was either a generalist or insectivore. Piscivory likely evolved in the lake because it was an open niche that had an abundance of prey resources. As the lake is dominated by cichlids, the main competitor to other cichlid piscivores before the Nile perch invasion was other piscivorous cichlids, so it was a leveled playing field in relation to prey processing. We show  support for this when looking at marine reef systems and evolutionary transitions to piscivory verses processing intensive prey (algae, mollusks, echinoderms) between other pharyngognathous fishes (wrasses, parrotfish, surf perches, damselfishes) and non-pharyngognathous fishes. We find that  non-pharyngognathous fish have far more transitions to piscivory than pharyngognathous fishes, indicating that pharyngognathy does restrict piscivory in marine systems as well. However, pharyngognathous fishes more commonly transition to processing intensive prey, highlighting that the pharyngeal jaws are extremely useful for processing these hard and tough to process items.

Transition into piscivory are uncommon in pharyngognathous fishes (red) relative to non-pharyngognathous fishes (blue). However, transitions to feeding on process intensive prey occur more often in pharyngognathous fishes.

Paper Citation & Link : McGee MD, Borstein SR, Neches RY, Buescher HH, Seehausen O, and Wainwright PC. 2015. A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids. Science 350:1077-1079. http://science.sciencemag.org/content/350/6264/1077