Projects in this area use a combination of phylogenetic and population genomic methods to understand how cephalopod species have evolved and to gain insight on their spatial and temporal dynamics at the population level. Ongoing and past projects include:

Big fin reef squid (Sepioteuthis cf. lessoniana)
Cephalopod fisheries in Southeast Asia and the Coral Triangle constitute a major source of income and protein to thousands of coastal communities. However, little basic information is known about these fisheries, much less about their evolution and population dynamics. In particular, the big fin reef squid (S. cf. lessoniana, Family: Loliginidae) is a heavily harvested species throughout the Indian and Pacific Oceans. Existing evidence suggests that there are actually multiple morphologically similar species that are lumped together as S. cf. lessoniana. Understanding how many species there are and what distinguishes them is critical for informing effective management and conservation of these commercial stocks. Using a suite of molecular markers, we examined the distribution and evolution of a species complex of bigfin reef squid (Sepioteuthis cf. lessoniana) throughout the global center of marine biodiversity, the Coral Triangle, and adjacent areas. Phylogenetic analyses and species delimitation methods unequivocally demonstrate the presence of at least three reciprocally monophyletic cryptic lineages sympatrically distributed throughout the region (see Cheng et al. 2014). This information indicates that management of these species must take into account species identity.Differences in life history, particularly in dispersal life history, is a major factor in driving different patterns of connectivity, or the exchange of genes, over space and time. Understanding patterns of connectivity is vital to informing spatial management of these squid stocks, particularly as they range over the fishing regions of multiple nations. Using genome-wide markers, we examine patterns of population structure over the Coral Triangle and adjacent regions to identify important processes shaping both genetic and demographic connectivity in two of these cryptic species. We are using a RAD sequencing method called 2b-RAD (see Misha Matz and Eli Meyer‘s lab sites) to generate these markers.

California market squid (Doryteuthis opalescens)
Within California, one of the most highly valued fisheries is for market squid (Doryteuthis opalescens). This fishery has long been hypothesized to be two separate stocks due to different spawning peaks and areas. However, previous studies using various methodologies have not been able to conclusively delineate populations structure. Using genome-wide SNPs (generated with 2b-RAD) and a rigorous temporal sampling scheme, we are examining this question in collaboration with California Fish and Wildlife. This project is funded by Save Our Coasts.

Evolution of diversity in reef fishes – phylogeny of Chrysiptera damsels
One of the most well-studied groups in coral reef ecosystems are the colorful Pomacentridae reef fishes. These fishes are characterized by a wide range of coloration patterns, ecological niches, and morphological diversity. Within this group, the genus Chrysiptera has at least 35 known species, but whose evolutionary history is rather complex. Previous phylogenetic studies of Pomacentridae indicate that Chrysiptera is not a monophyletic group, despite indications from morphology. Furthermore, genetic evidence suggests that multiple species complexes exist, with many cryptic species featuring subtle color polymorphisms and possible endemism. Given this complex evolutionary scenario, we are conducting an in-depth, multi-gene phylogenetic examination into Chrysiptera in order to illuminate the evolutionary history of this extremely diverse group. This project is being conducted in collaboration with Hayley Nuetzel at University of California-Santa Cruz.

Phylogeography of co-distributed mantis shrimps
The Coral Triangle is an area of the Indo-Australian Archipelago that hosts the world’s greatest concentration of marine biodiversity. This small region lies at the confluence of the Pacific and Indian Oceans, and is characterized by complex oceanographic currents, thousands of islands, and a tumultuous geological history – creating a diverse fabric of evolutionary processes. Researchers have long debated the origins of this biodiversity hotspot – as a center of origin, center of overlap or center of survival (see Bellwood et al. 2001, Briggs 2000, Barber 2009). The long-standing assumption in marine divergence and speciation theory posits that due the prevalence of a pelagic larval dispersal stage in a vast and fluid environment, very strong barriers are necessary for divergence to occur in marine populations. Using three species of co-distributed mantis shrimp (Stomatopoda) species, we take a phylogeographic approach to understanding processes that drive diversification in the Coral Triangle. We find a shared genetic break over the marine Wallace’s line as proposed by Barber 2000 in all three species, but evidence of dramatically different fine-scale population divergence patterns indicating that subtle differences in life history likely play a much larger role that previously expected. – Barber, P.H., Cheng, S.H., Erdmann M.V., Tenggardjaja, K., Ambariyanto 2011.