Paper Proposals

Paper Proposals

If you are interested in collaborating on one of the proposed papers read the Authorship Guidelines.  You have 6 weeks from the time of initial posting to contact the author with an outline of how you think you can contribute to the project. 

If you would like to propose your own paper go here for instructions


Patterns of Genetic Diversity

Leads – Libby Liggins (, Chris Bird, Michelle R. Gaither (May 9, 2016)


  • Are there hotspots of genetic diversity in the Indo-Pacific and do these correlate with patterns found in species diversity?
  • Do genetic diversity hotspots correlate with suggested environmental drivers?
  • Do genetic diversity hotspots correlate with known threats to biodiversity, and are they sufficiently protected in Marine Protected Areas?
  • Are patterns of genetic diversity concordant across species, and where geographically, and for what species, is there disparity in levels of genetic diversity?


Multispecies phylogeographic patterns across the Indo-Pacific

Leads – Michelle R. Gaither (, Chris Bird, Libby Liggins (March 27, 2014)

Question: Are there concordant patterns of genetic structure across the Indo-Pacific and which biogeographic classifications (those based on species distributions and taxonomy) most closely aligns with genetic partitions within species. Subsequently we can use this optimal model to ask what proportion of evolutionary divergence can be attributed to allopatric processes.


Inferring Indo-Pacific Migration Matrices

Lead – Eric Crandall ( (March 21, 2015)

Aim: Following on our work with the discrete diffusion model of phylogeography on Linckia laevigata in Crandall et al. 2014 in the special issue, I would like to propose to lead a paper wherein we use this method to infer migration matrices for >10 Indo-Pacific species that have been sampled for mtDNA across their ranges. This goal is both simple and largely descriptive but I think it should be relatively easily attainable and will provide a strong foundation for future work by our group.


Nestedness & turnover in genetic diversity in the Indo-Pacific

Lead – Libby Liggins ( (May 9, 2016)

Questions: I propose to: 1) reveal the significance of genetic nestedness and turnover in forming genetic breaks across the ranges of Indo-Pacific marine species, 2) describe genetic diversity gradients considering nestedness and turnover patterns. I predict that some genetic breaks identified using conventional measures (i.e. FST, ΦST) will constitute regions of high turnover, whereas others will reflect the nestedness of one region within another (i.e. a change in richness). I also expect that gradients in nestedness will underlie some genetic diversity gradients (based on haplotype and nucleotide diversity). However, in other cases I suspect that despite a reduction in population genetic diversity across an environmental gradient, there may be an increasing influence of genetic turnover in the composition of those populations, indicating genetic novelty.


Phylogenetic signal in population structure across the Indo-Pacific

Lead – Peter F Cowman ( (April 15, 2015)


Do closely related species share more similar level of population structure (or population diversity) than more distantly related species?

If there is phylogenetic signal in population structure across species, is this linked to the evolution of shared life history traits?

Do species share similar population structure because they share similar range characteristics (size, longitudinal extent, abundant or rare, widespread, endemic)


Testing for genetic breaks in the presence of isolation-by-distance

Lead – Sean R Connolly ( (April 17, 2015)

Main Question: Is it possible to improve the way that we account for IBD when testing for (or estimating the magnitude of) the effect of biogeographic boundaries on the genetic structure of boundary-crossers?

Key Idea: Permute the “region” assignment labels, which determines which pairs of sites are within vs between-region observations, while holding the genetic and geographic distance matrices constant. This preserves any IBD present in the data, while eliminating only any region effect.


Indo-Pacific priority areas to conserve multi-species marine genetic diversity

Lead – Maria Beger (

Background: Conservation of biodiversity is important, but everyone ignores genetic diversity when planning marine conservation areas.

Aim: Compare conservation priorities for genetic diversity for four objectives: genetic diversity representation, haplotype distributions, novelty (uniqueness), and structure.


Genetic disjunctions –strengths of “barriers” and species traits associated with permeability

Lead – Cynthia Riginos ( (April 22, 2015)

Questions: The geographic spread of sampling and large number of species in the DIPnet database allows us to move beyond simply identifying locations of genetic disjunctions (barriers) to ask how different geographic features quantitatively affect population genetic structure. Similarly, we can ask whether specific species traits accurately predict population genetic structure across barriers. To explore these issues, I will draw upon the isolation by distance method being developed by Sean Connolly (to estimate barrier strength by species) and compilations of relevant species traits (Cowman and others). The ideas outlined here could be incorporated into the first genetic structure paper or might be a stand alone paper – either outcome is ok with me.


Do population size and its proxies influence mtDNA diversity?

Leads – Chris Bird (, Libby Liggins, Eric Treml, Maria Beger

Aim: One key assumption when working with genetic diversity is that it scales with population size. Both Soule (1976) and Frankham (1996) found positive relationships between proxies of pop size and genetic diversity. Bazin et al (2006), however, determined that mtDNA diversity was not related to proxies of population size. With the DIPnet database, there is an extensive data set with which to determine if the diversity of mtDNA in marine species scales with proxies of population size.

(1) habitat area *** cooperating with Josh Copus and Libby Liggins

(2) species range

(3) body size

(4) chromosome evolution rate

(5) fish vs invert

(6) island vs mainland

(7) Endangered Species List /Redlist Level


Do spatio-temporal patterns of tropical marine habitat shape genetic diversity?

Leads – Joshua Copus (, Erik Franklin, Rob Toonen, and Brian Bowen (April 12, 2015)

Aim: These data will allow us to analyze how sea level change from the LGM to present has affected the patterns of genetic diversity we see today and shed light into how habitat influences the genetic connectivity of species across the Indo-Pacific. Further it will increase our understanding of the fundamental causal elements of marine biogeography by shedding light on an important historical geological pattern that may shape the population structure of marine organisms.


Photo: Michelle R. Gaither