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“Mother Nature's a MAD scientist, Jerry”

- Cosmo Kramer -

Our research integrates genetic, physiological, behavioral and biochemical approaches to address questions in multiple arenas of evolutionary biology.  Here are our most current research themes:

(1) What are the molecular mechanisms underlying reproductive isolating barriers in natural populations? 

Natural systems at the early stages of speciation are ideal for addressing this fundamental question.  

A powerful approach to investigate how two divergent genomes interact is to study recombinant hybrids formed between them.

Hybrid breakdown - Our lab is works on projects investigating the genetic causes of fitness breakdown in F2 hybrids in the marine copepod Tigriopus californicus. Populations along the coast show high levels of genetic divergence, and interpopulation crosses in the lab produce hybrids that suffer from impaired mitochondrial metabolism and reduced life-history fitness (low fecundity, slow development, etc). Studies focus on functional interactions between nuclear and mitochondrial genomes as sources of incompatibility. 

Male Tigriopus califonicus (Copepoda: Harpacticoida)

(Photo by Dan Schneck)

Copepods in a beaker (Photo by Dan Schneck)

Our work relies heavily on Next-generation high-throughput sequencing and computational methods to examine evolution at genome-wide scales. However, I strive to interpret genomic data from a functional perspective by incorporating biochemical and molecular assays to test new hypotheses.

Transcriptome divergence at the structural level

Synonymous and nonsynonymous divergence across the transcriptomes of San Diego and Santa Cruz copepods 

(N = 5897 protein-coding genes).

(From Barreto et al. 2011. Mol. Ecol.)

Mito-nuclear mismatch increases oxidative stress in hybrids

Levels of oxidative damage to DNA in hybrids and their parental populations. (From Barreto and Burton 2013. Proc. R. Soc. Lond. B)

Transcriptome divergence at the regulatory level

Transgressive gene expression in hybrids.

(From Barreto et al. 2015. Mol. Biol. Evol.)

Mitochondrial ribosomes are possible sites of mito-nuclear incompatibilities

Ribosomal proteins that function in mtDNA gene translation evolve faster than cytosolic ribosomal proteins. 

(From Barreto and Burton 2013. Mol. Biol. Evol.)

(2) How do genomes respond to environmental challenges, such as temperature and oxygen variations?

Geographic variation in thermal regimes across the range of a species can be a powerful selective force in shaping the genomes of isolated populations. Populations of several marine invertebrates often exhibit thermal tolerance that is correlated with their local temperature variations, but the genetic bases of such adaptations are often not known. Simply determining, for instance, that the same ‘functional group’ of genes responds to thermal stress across different geographic populations tells a very incomplete story about the evolution of those adaptations within each population. Results from recent projects in Tigriopus californicus suggest that populations exhibit fundamental differences in which genes they use, and how they use them, in response to environmental temperature changes.

Local adaptation - We are employing Next-Generation sequencing technologies to assess transcriptome-wide levels of divergence at the structural and gene regulatory levels in ecologically divergent populations of T. californicus. 

Differences in gene expression between T. californicus populations during acute thermal stress. Genes encoding heat shock proteins are in red.

(From Schoville et al. 2012. BMC Evol. Biol.)

Adaptation to local environmental conditions may permit the evolution of novel phenotypes via transgressive segregation.  Certain interpopulation crosses produce hybrids that are tolerant to temperatures otherwise lethal to their parental populations.

Transgressive segregation of thermal tolerance in hybrids between San Diego and La Jolla copepods.  Samples were exposed to acute thermal stress at 35OC for one hour.

(modified from Pereira et al. 2014. Evolution)

Genomic studies always generate new hypotheses. For hypotheses regarding gene expression, we have adapted the RNA interference (RNAi) technique to experimentally suppress expression of single target genes. By temporarily knocking down transcription, we can examine the gene’s phenotypic effects.

RNAi in T. californicus. 

(a) Knockdown of hsp-beta1 after dsRNA delivery by electroporation;

(b) Mortality of copepods after acute heat stress (36OC for 1 hr). 

Blue lines: control samples with NO hspb1 knockdown; Red lines: samples with hspb1 knockdown.

(From Barreto et al. 2015. Mol. Ecol. Res.)

Evolution of hypoxia response: We recently discovered that some subgroups of crustaceans, including harpacticoid copepods such as Tigriopus, have lost a gene that encodes the master regulator of hypoxia response, the HIFa protein. We are currently investigating what alternative mechanisms T. californicus uses to regulate physiological response to hypoxia. 

Maximum likelihood tree of bHLH-PAS-containing proteins. Tigriopus californicus has copies of every gene in this cluster except for HIF-alpha.

(From Graham and Barreto 2019, PNAS)

HIF tree.png

(3) How do intra-familial conflicts affect the evolution of mating systems and reproductive modes?

The ubiquity of mating promiscuity in nature creates chances for many levels of conflict, such as conflict between the sexes for care of offspring, conflict between parents and offspring for intensity of care, and conflict among siblings for quality of care.

Pycnogonid sea spiders exhibit exclusive paternal care of embryos, with males of most species carrying large broods for weeks to months.  Above are two common California intertidal pycnogonids: Pycnogonum stearnsi (left) and Ammothea hilgendorfi (right). (Collected by F. Barreto; Photos by P. Bryant)

Sea spiders (Class Pycnogonida) are arthropods that inhabit nearly all marine environments, including rocky intertidal zones, coral reefs, interstitial habitats and mud flats.  Their basic biology and natural history, however, are still poorly known. Perhaps the most intriguing aspect of their biology is the fact that this group exhibits exclusive paternal care of embryos, with males in most species carrying large clutches of eggs for weeks or even months.  This behavior is of great interest for studies of sexual selection and parental investment, since it is the rarest form of offspring care among animals.  I employed high-resolution microsatellite markers to quantify mating and reproductive successes in males and females across three species with varying levels of offspring housing and sexual size dimorphism (Barreto and Avise 2008, 2010, 2011).  Current projects aim at assessing the fitness costs, incurred by males, females and offspring, that result from the interplay between multiple mating and such prolonged parental care.  

We are also examining the mating system of other intertidal invertebrates to learn basic aspects about their reproductive biology in the wild. 

The sea star Leptasterias hexactis is a major predator in intertidal communities. Females of this species brood fertilized eggs until they become small sea stars and crawl away. We are currently using microsatellite DNA markers to assess levels of multiple mating in different populations of L. hexactis.

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