In the benthic oceanic environment, space is often at a premium. Because space is so limited, a process called fusion has evolved in many types of marine invertebrates. Fusion is two separate individuals physically joining to become a single individual. Through the process of allorecognition, individuals can determine whether or not a neighboring individual is closely related. In the ascidian Botryllus schlosseri, fusion is controlled by two adjacent genes, FuHC secreted and FuHC transmembrane (Nydam et al. 2013a). Individuals that share one or more FuHC secreted alleles will fuse. Individuals can discriminate kin from hundreds of unrelated neighbors, and FuHC is therefore highly polymorphic.  My students and I found evidence for balancing selection maintaining the polymorphism in this gene (Nydam and De Tomaso 2011, Nydam et al. 2012, Nydam et al. 2017c).  We have also studied the evolution of three other groups of genes within the FuHC locus: the fester loci (Nydam and De Tomaso 2012), Hsp40-L (Nydam et al. 2013b), and BHF (Taketa et al. 2015).  Fester and the C-terminal end of the Hsp40-L protein experience selection, but we found no evidence for selection acting on BHF (Nydam and De Tomaso 2012, Nydam et al. 2013b, Taketa et al. 2015).

Photo 72 - Ciona savignyi
Crowded benthic environment in Santa Barbara, CA


In order to study allorecognition at a large taxonomic scale, I received a $25,000 grant from the National Science Foundation’s Experimental Program to Stimulate Competitive Research (EPSCoR).  I am currently developing a comprehensive phylogeny of the botryllids (51 described species) in collaboration with Sarah Cohen at San Francisco State University and the Center for Anchored Phylogenomics at Florida State University.  We sequenced the genomes of seven species in the group, and used the aligned genomes to design 100 phylogenetically informatively loci.  We then constructed genomic libraries for 55 samples, enriched the libraries for the 100 loci, and sequenced the libraries using an Illumina HiSeq2500 with paired end 150 bp reads.  The resulting phylogeny is well-resolved, and I am currently engaged in morphological descriptions of preserved tissue samples to confirm species identifications (including several new species).  I received funding from the LUCE Initiative for Asian Studies and the Environment to travel to Japan in 2018 to collect additional species for the phylogeny.

Botryllus sp. from Heron Island, Australia.  Collected by Tony De Tomaso.
Botryllus sp. from Bocas del Toro, Panama
Botryllus sp. from Bocas del Toro, Panama (Closeup)
Botrylloides sp. from Bocas del Toro, Panama.  Bright orange and rust color morphs also exist.
Botrylloides sp. from Bocas del Toro, Panama (Closeup).  Bright orange and rust color morphs also exist.

Origin and Dispersal of Invasive Species

Ascidians (“sea squirts”) are a large group of invertebrates which occupy a central role in the ecology of marine benthic communities. Many ascidian species have become successfully introduced around the world via anthropogenic vectors, with a few species causing extensive ecological and economic damage. Invasive ascidians have effected declines in native species richness, altered benthic community structure, and disrupted the link between pelagic and benthic communities.  Despite the central positions that ascidians will occupy in the marine ecosystems of the future, their evolutionary histories are not well known.  By determining the origins and dispersal patterns of ascidians, we can begin to predict the composition and function of future marine benthic communities.

I used mitochondrial cytochrome oxidase (mtCOI) to examine the spread of Ciona robusta and Botryllus schlosseri Clade A from Asia to the majority of the world’s temperate oceans (Nydam and Harrison 2010b, Nydam et al. 2017a, Nydam et al. 2017b), Ciona intestinalis from Europe to the east coast of the United States (Nydam and Harrison 2010b), Botryllus schlosseri Clade E from the Mediterranean throughout European waters (Nydam et al. 2017a).  

Median Joining Network for Botryllus schlosseri Clade A.  Nucleotide diversity and Approximate Bayesian Computation analyses support a Pacific origin, with two likely dispersal scenarios that both show the northwestern Atlantic populations establishing early in the history of the species.
4 locations Median Joining Network for publication
Median Joining Network for Botryllus schlosseri Clade E.  Both Discrete Phylogeographic Analysis and Approximate Bayesian Computation support an origin on the French side of the English Channel.

I am now focusing on tropical and sub-tropical invasive ascidians.  In collaboration with Susanna Lopez-Legentil and Bailey Counts at the University of North Carolina, Wilmington and Lauren Stefaniak at Coastal Carolina University, I conducted a rapid assessment survey of invasive ascidians in Florida in 2017. Invasive ascidian species distribution and abundance is not well studied in Florida.  These data will be compared to a study done by Gretchen Lambert in 2004, to determine which species are new to Florida waters, and are therefore dispersing quickly.

Aplidium stellatum
Aplidium stellatum, St. Petersburg, FL (native)
Botrylloides nigrum, St. Petersburg, FL (cryptogenic, likely native)
Distaplia bermudensis, St. Petersburg, FL (native)
Distaplia bermudensis - 2 colonies fusing
Distaplia bermudensis –
2 colonies fusing, Tampa, FL (native)
Ecteinascidia turbinata
Ecteinascidia turbinata,
St. Petersburg, FL (cryptogenic, likely native)
Herdmania pallida
Herdmania pallida, Miami, FL (cryptogenic, likely non-native)
Microcosmus exasperatus
Microcosmus exasperatus, Miami, FL (cryptogenic, likely non-native)
Polyandrocarpa anguinea,
Miami, FL (cryptogenic, likely non-native)
Styela plicata
Styela plicata, Tampa, FL (cryptogenic, likely non-native)


Marine broadcast spawners release gametes into the water column, where fertilization occurs. Because copulatory and other behavioral barriers are absent in these animals, reproductive isolation often occurs as a byproduct of the rapid evolution of sperm and egg proteins. Therefore, studying the evolution of these proteins lends direct insight into the speciation process.

My study organisms are ascidians, specifically two species in the genus Ciona: Ciona intestinalis and Ciona robusta (Nydam and Harrison 2007). Ciona robusta is native to the Western Pacific Ocean and has invaded many of the world’s temperate oceans. Ciona intestinalis is native to the Northeast Atlantic Ocean and has invaded the Northwest Atlantic Ocean. These two types exhibit partial post-mating prezygotic and postzygotic reproductive isolation.         

IMG_0056_edited                                OLYMPUS DIGITAL CAMERA

 Ciona intestinalis                                       Ciona robusta

I examined the previously unknown genealogical relationships among Ciona species using mitochondrial (Nydam and Harrison 2007) and nuclear (Nydam and Harrison 2010a) markers. My students and I then investigated the distribution of Ciona robusta and Ciona intestinalis in the zone of sympatry (the English Channel and the Atlantic coast of France) in 2007, 2009 and 2013. We found that these species exhibit low levels of introgression despite substantial divergence (Nydam and Harrison 2010b, Nydam et al. 2017b).  In 2014, we identified a second hybrid zone on the northern coast of Spain (Nydam et al. 2017b).  While a subsequent genome-wide study revealed that the gene flow between these species may the result of secondary contact 15,500 years ago, these two species had been geographically separated for >3 million years prior to secondary contact.  Therefore, Ciona intestinalis and Ciona robusta show that reproductive barriers in marine broadcast spawners may be weaker than in other groups of organisms.

All Ciona Europe - All data
Distribution of C. intestinalis (blue) and C. robusta (yellow) in European waters.  The pie charts do not reflect proportions of the two species; pie charts that are blue and yellow denote locations where both species have been found.


English Channel and Bay of Biscay with Pie Charts
 Proportions of pure C. intestinalis (blue), pure C. robusta (yellow), and introgressed individuals (green) in two hybrid zones: English Channel and southern Bay of Biscay  

Microcosmus exasperatus