- Groton CT
Paola Batta Lona
University of Connecticut, Marine Sciences, Faculty Member
Zooplankton play a pivotal role in sustaining the majority of marine ecosystems. The distribution patterns and diversity of zooplankton provide key information for understanding the functioning of these ecosystems. Nevertheless, due to... more
Zooplankton play a pivotal role in sustaining the majority of marine ecosystems. The distribution patterns and diversity of zooplankton provide key information for understanding the functioning of these ecosystems. Nevertheless, due to the numerous cryptic and sibling species and the lack of diagnostic characteristics for immature developmental stages, the identification of the global-to-local patterns of zooplankton biodiversity and biogeography remains a challenge in different research fields. Here, the spatial and temporal changes in the zooplankton community from the open waters of the southern section of the Gulf of Mexico were assessed using a multilocus sequence analysis and metabarcoding approach based on the genetic information of 18S and cytochrome oxidase c subunit I (COI) genes. Additionally, a multi-scale analysis was implemented to evaluate which environmental predictors may explain the variability in the structure of the zooplankton community. Our finding suggests tha...
Research Interests:
ABSTRACT Life histories in temperate habitats are highly cyclical, and include changes in physiology in response to seasonal or other environmental cues. With documented changes in global distribution of pelagic organisms, it has become... more
ABSTRACT Life histories in temperate habitats are highly cyclical, and include changes in physiology in response to seasonal or other environmental cues. With documented changes in global distribution of pelagic organisms, it has become important to understand their physiology and ability to adapt to environmental change. Here, we report on the development and application of molecular tools to investigate the physiological ecology of Calanus finmarchicus, a highly abundant North Atlantic calanoid copepod. Publicly available ESTs for C. finmarchicus were clustered into contigs and annotated using Blast2GO software. From these contigs, 1000 transcripts representing a range of biological processes were selected for inclusion in a species-specific microarray. Comparisons were made between pre-adult individuals collected during early summer (June) and fall (October) from the Gulf of Maine. Comparisons focused on determining physiological differences between morphotypes (lipid-rich vs. lipid poor), season (June vs. October) and depth (< 100 m vs. > 100 m depth). The largest expression differences were observed between individuals from the shallow vs. deep collection during October. A one-week experimental incubations at high (5000 algal cells ml-1) and low (500 algal cells ml-1) yielded moderate changes in expression (maximum 2-fold differences). These results suggest that expression studies could be a useful tool for studies on the physiological ecology of marine zooplankton. Further studies will be needed to interpret expression results within the context of organism-environment interactions.
A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an... more
A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely-related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936 bp genome sequence, covering more than 50% of the estimated 602 MB (±173 MB) genome size for S. thompsoni. Using a non-redundant set of
predicted proteins, more than 50% (16,823) of sequences showed significant homology to known proteins and ~38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously-estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution >1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these resources provide a
genomic foundation supporting S. thompsoni as a model species for further examination of the exceptional rates and patterns of genomic evolution shown by urochordates. Additionally, genomic data will allow for the development of molecular indicators of key life history events
and processes and afford new understandings and predictions of impacts of climate change on this key species of Antarctic pelagic ecosystems.
predicted proteins, more than 50% (16,823) of sequences showed significant homology to known proteins and ~38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously-estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution >1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these resources provide a
genomic foundation supporting S. thompsoni as a model species for further examination of the exceptional rates and patterns of genomic evolution shown by urochordates. Additionally, genomic data will allow for the development of molecular indicators of key life history events
and processes and afford new understandings and predictions of impacts of climate change on this key species of Antarctic pelagic ecosystems.
Research Interests:
Couch potato (CPO) is an RNA-binding protein involved in the regulation of nervous system development and adult diapause in insects. Within insects, this protein is highly conserved, yet it has not been identified in another large... more
Couch potato (CPO) is an RNA-binding protein involved in the regulation of nervous system development and adult diapause in insects. Within insects, this protein is highly conserved, yet it has not been identified in another large arthropod group, the Crustacea. Here, functional genomics was used to identify putative CPO homologs in the copepod Calanus finmarchicus, a planktonic crustacean that undergoes seasonal diapause. In silico mining of expressed sequence tag (EST) and 454 pyrosequencing data resulted in the identification of two full-length CPO proteins, each 205 amino acids long. The two C. finmarchicus CPOs (Calfi-CPO I and II) are identical in sequence with the exception of three amino acids, and are predicted to possess a single RNA recognition motif (RRM). Sequence comparison of the two Calfi-CPOs with those of insects shows high levels of amino acid conservation , particularly in their RRMs. Using the C. finmarchicus sequences as queries, ESTs encoding partial CPOs were identified from two other crustaceans, the parasitic copepod Lernaeocera branchialis and shrimp Penaeus monodon. Surprisingly, no convincing CPO-encoding transcripts were identified from crustacean species with very large (>100,000) EST datasets (e.g. Litopenaeus vannamei, Daphnia pulex and Lepeophtheirus salmonis), suggesting that CPO transcript/protein may be expressed at very low levels or absent in some crustaceans. RNA-Seq data suggested stage-specific expression of CPO in C. finmarchicus, with few transcripts present in eggs (which represent mixed embryonic stages) and adults, and high levels in nauplii and copepodites; stages exhibiting high CPO expression are consistent with a role for it in neuronal development.
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Aggregations of the salp Salpa thompsoni were encountered during the Antarctic krill and ecosystem-studies cruise on the RV “G.O. Sars” from 19 February to 27 March 2008. The salp’s in situ target strength (TS), size, number of... more
Aggregations of the salp Salpa thompsoni were encountered during the Antarctic krill and ecosystem-studies cruise on the RV “G.O. Sars” from 19 February to 27 March 2008. The salp’s in situ target strength (TS), size, number of individuals in aggregate chains, and chain angle of orientation were determined. Shipboard measurements were made of Salpa thompsoni’s material properties. Individual aggregates were mostly 45.5–60.6 mm in mean length; relatively rare solitaries were around 100 mm. Chains ranged from 3 to at least 121 individuals, and in surface waters (,20 m), they showed no preferred angle of orientation. Sound-speed contrast (h) ranged from 1.0060 to 1.0201 and density contrast (g) estimates between 1.0000 and 1.0039. The in situ TS distributions peaked between 275 and 276 dB at 38 kHz, with a secondary peak at approximately 265 dB. TS ranged between 285 and 265 dB at 120 and 200 kHz and peaked around 274 dB. The measured in situ TS of salps reasonably matched the theoretical scattering-model predictions based on multi-individual chains. The backscattering from aggregate salps gives rise to TS values that can be similar to krill and other zooplankton with higher density and sound-speed contrasts.