Publications by authors named "Scott R Santos"

57 Publications

Infection of mosquitoes with midgut-attenuated Sindbis virus reduces, but does not eliminate, disseminated infection.

J Virol 2021 Apr 14. Epub 2021 Apr 14.

Division of Biology, Kansas State University, Manhattan, Kansas 66503

Arboviruses are transmitted by specific vectors and the reasons for this specificity are not fully understood. One contributing factor is the existence of tissue barriers within the vector such as the midgut escape barrier. We used miRNA targeting of Sindbis virus (SINV) to study how replication in midgut cells contributes to overcoming this barrier in the mosquito SINV constructs were designed to be attenuated specifically in midgut cells by inserting binding sites for midgut-specific miRNAs into either the 3' untranslated region (MRE3'miRT) or the structural open reading frame (MRE-ORFmiRT) of the SINV genome. Both miRNA-targeted viruses replicated less efficiently than control viruses in the presence of these miRNAs. When mosquitoes were given infectious blood meals containing miRNA-targeted viruses, only around 20% (MRE3'miRT) or 40% (MRE-ORFmiRT) of mosquitoes developed disseminated infection. In contrast, dissemination occurred in almost all mosquitoes fed control viruses. Deep sequencing of virus populations from individual mosquitoes ruled out selection for mutations in the inserted target sequences as being the cause for dissemination in these mosquitoes. In mosquitoes that became infected with miRNA-targeted viruses, titers were equivalent to control virus in both the midgut and the carcass and there was no evidence of a threshold titer necessary for dissemination. Instead, it appeared that if infection was successfully established in the midgut, replication and dissemination were largely normal. Our results support the hypothesis that replication is an important factor in allowing SINV to overcome the midgut escape barrier, but hint that other factors are also likely involved.When a mosquito ingests an arbovirus during a blood meal, the arbovirus must escape from the midgut of the vector and infect the salivary glands in order to be transmitted to a new host. We used tissue-specific miRNA targeting to examine the requirement for Sindbis virus (SINV) to replicate in midgut epithelium in order to cause disseminated infection in the mosquito Our results indicate that specifically reducing the ability of SINV to replicate in the mosquito midgut reduces its overall ability to establish infection in the mosquito, but if infection is established, replication and dissemination occur normally. These results are consistent with an importance for replication in the midgut epithelium in aiding arboviruses in crossing the midgut barrier.
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http://dx.doi.org/10.1128/JVI.00136-21DOI Listing
April 2021

Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library.

Front Microbiol 2020 7;11:585398. Epub 2020 Dec 7.

Department of Biological Sciences, Auburn University, Auburn, AL, United States.

Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.
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http://dx.doi.org/10.3389/fmicb.2020.585398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750434PMC
December 2020

Red Coloration in an Anchialine Shrimp: Carotenoids, Genetic Variation, and Candidate Genes.

Biol Bull 2020 04 15;238(2):119-130. Epub 2020 Apr 15.

Red coloration is a widely distributed phenotype among animals, yet the pigmentary and genetic bases for this phenotype have been described in relatively few taxa. Here we show that the Hawaiian endemic anchialine shrimp is red because of the accumulation of astaxanthin. Laboratory colonies of phylogenetically distinct lineages of have colony-specific amounts of astaxanthin that are developmentally, and likely genetically, fixed. Carotenoid supplementation and restriction experiments failed to change astaxanthin content from the within-colony baseline levels, suggesting that dietary limitation is not a major factor driving coloration differences. A possible candidate gene product predicted to be responsible for the production of astaxanthin in and other crustaceans is closely related to the bifunctional cytochrome P450 family 3 enzyme found in fungi. However, homologs to the enzyme thought to catalyze ketolation reactions in birds and turtles, , were not found. This work is one of the first steps in linking phenotypic variation in red coloration of to genotypic variation. Future work should focus on (1) pinpointing the genes that function in the bioconversion of dietary carotenoids to astaxanthin, (2) examining what genomic variants might drive variation in coloration among discrete lineages, and (3) testing more explicitly for condition-dependent carotenoid coloration in crustaceans.
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http://dx.doi.org/10.1086/708625DOI Listing
April 2020

Phenotypic Comparability from Genotypic Variability among Physically Structured Microbial Consortia.

Integr Comp Biol 2020 08;60(2):288-303

Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, Auburn, AL 36849, USA.

Microbiomes represent the collective bacteria, archaea, protist, fungi, and virus communities living in or on individual organisms that are typically multicellular eukaryotes. Such consortia have become recognized as having significant impacts on the development, health, and disease status of their hosts. Since understanding the mechanistic connections between an individual's genetic makeup and their complete set of traits (i.e., genome to phenome) requires consideration at different levels of biological organization, this should include interactions with, and the organization of, microbial consortia. To understand microbial consortia organization, we elucidated the genetic constituents among phenotypically similar (and hypothesized functionally-analogous) layers (i.e., top orange, second orange, pink, and green layers) in the unique laminated orange cyanobacterial-bacterial crusts endemic to Hawaii's anchialine ecosystem. High-throughput amplicon sequencing of ribosomal RNA hypervariable regions (i.e., Bacteria-specific V6 and Eukarya-biased V9) revealed microbial richness increasing by crust layer depth, with samples of a given layer more similar to different layers from the same geographic site than to their phenotypically-analogous layer from different sites. Furthermore, samples from sites on the same island were more similar to each other, regardless of which layer they originated from, than to analogous layers from another island. However, cyanobacterial and algal taxa were abundant in all surface and bottom layers, with anaerobic and chemoautotrophic taxa concentrated in the middle two layers, suggesting crust oxygenation from both above and below. Thus, the arrangement of oxygenated vs. anoxygenated niches in these orange crusts is functionally distinct relative to other laminated cyanobacterial-bacterial communities examined to date, with convergent evolution due to similar environmental conditions a likely driver for these phenotypically comparable but genetically distinct microbial consortia.
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http://dx.doi.org/10.1093/icb/icaa022DOI Listing
August 2020

Disparate responses to salinity across species and organizational levels in anchialine shrimps.

J Exp Biol 2019 12 12;222(Pt 24). Epub 2019 Dec 12.

Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849, USA.

Environmentally induced plasticity in gene expression is one of the underlying mechanisms of adaptation to habitats with variable environments. For example, euryhaline crustaceans show predictable changes in the expression of ion-transporter genes during salinity transfers, although studies have typically been limited to specific genes, taxa and ecosystems of interest. Here, we investigated responses to salinity change at multiple organizational levels in five species of shrimp representing at least three independent invasions of the anchialine ecosystem, defined as habitats with marine and freshwater influences with spatial and temporal fluctuations in salinity. Although all five species were generally strong osmoregulators, salinity-induced changes in gill physiology and gene expression were highly species specific. While some species exhibited patterns similar to those of previously studied euryhaline crustaceans, instances of distinct and atypical patterns were recovered from closely related species. Species-specific patterns were found when examining: (1) numbers and identities of differentially expressed genes, (2) salinity-induced expression of genes predicted to play a role in osmoregulation, and (3) salinity-induced expression of orthologs shared among all species. Notably, ion transport genes were unchanged in the atyid while genes normally associated with vision and light perception were among those most highly upregulated. Potential reasons for species-specific patterns are discussed, including variation among anchialine habitats in salinity regimes and divergent evolution in anchialine taxa. Underexplored mechanisms of osmoregulation in crustaceans revealed here by the application of transcriptomic approaches to ecologically and taxonomically understudied systems are also explored.
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http://dx.doi.org/10.1242/jeb.211920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955204PMC
December 2019

Na /K -ATPase gene duplications in clitellate annelids are associated with freshwater colonization.

J Evol Biol 2019 06 11;32(6):580-591. Epub 2019 Apr 11.

Department of Zoology, Southern Illinois University, Carbondale, Illinois.

Major habitat transitions, such as those from marine to freshwater habitats or from aquatic to terrestrial habitats, have occurred infrequently in animal evolution and may represent a barrier to diversification. Identifying genomic events associated with these transitions can help us better understand mechanisms that allow animals to cross these barriers and diversify in new habitats. Study of the Capitella telata and Helobdella robusta genomes allows examination of one such habitat transition (marine to freshwater) in Annelida. Initial examination of these genomes indicated that the freshwater leech H. robusta contains many more copies (12) of the sodium-potassium pump alpha-subunit (Na /K -ATPase) gene than does the marine polychaete C. telata (2). The sodium-potassium pump plays a key role in maintenance of cellular ionic balance and osmoregulation, and Na /K -ATPase duplications may have helped annelids invade and diversify in freshwater habitats. To assess whether the timing of Na /K -ATPase duplications coincided with the marine-to-freshwater transition in Clitellata, we used transcriptomic data from 18 annelid taxa, along with the two genomes, to infer a species phylogeny and identified Na /K -ATPase gene transcripts in order to infer the timing of gene duplication events using tree-based methods. The inferred timing of Na /K -ATPase duplication events is consistent with the timing of the initial marine-to-freshwater transition early in the history of clitellate annelids, supporting the hypothesis that gene duplications may have played a role in the annelid diversification into freshwater habitats.
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http://dx.doi.org/10.1111/jeb.13439DOI Listing
June 2019

Revisiting "Genetic Diversity of Symbiotic Dinoflagellates in the Genus Symbiodinium".

Protist 2018 11 6;169(5):784-787. Epub 2018 Jul 6.

Department of Geology, Graduate Program in Evolution, Ecology and Behavior, State University of New York at Buffalo, Buffalo, NY 14260, USA.

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http://dx.doi.org/10.1016/j.protis.2018.06.008DOI Listing
November 2018

Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts.

Curr Biol 2018 08 9;28(16):2570-2580.e6. Epub 2018 Aug 9.

Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849, USA.

The advent of molecular data has transformed the science of organizing and studying life on Earth. Genetics-based evidence provides fundamental insights into the diversity, ecology, and origins of many biological systems, including the mutualisms between metazoan hosts and their micro-algal partners. A well-known example is the dinoflagellate endosymbionts ("zooxanthellae") that power the growth of stony corals and coral reef ecosystems. Once assumed to encompass a single panmictic species, genetic evidence has revealed a divergent and rich diversity within the zooxanthella genus Symbiodinium. Despite decades of reporting on the significance of this diversity, the formal systematics of these eukaryotic microbes have not kept pace, and a major revision is long overdue. With the consideration of molecular, morphological, physiological, and ecological data, we propose that evolutionarily divergent Symbiodinium "clades" are equivalent to genera in the family Symbiodiniaceae, and we provide formal descriptions for seven of them. Additionally, we recalibrate the molecular clock for the group and amend the date for the earliest diversification of this family to the middle of the Mesozoic Era (∼160 mya). This timing corresponds with the adaptive radiation of analogs to modern shallow-water stony corals during the Jurassic Period and connects the rise of these symbiotic dinoflagellates with the emergence and evolutionary success of reef-building corals. This improved framework acknowledges the Symbiodiniaceae's long evolutionary history while filling a pronounced taxonomic gap. Its adoption will facilitate scientific dialog and future research on the physiology, ecology, and evolution of these important micro-algae.
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http://dx.doi.org/10.1016/j.cub.2018.07.008DOI Listing
August 2018

Crossing the Divide: Admixture Across the Antarctic Polar Front Revealed by the Brittle Star Astrotoma agassizii.

Biol Bull 2017 06 1;232(3):198-211. Epub 2017 Sep 1.

The Antarctic Polar Front (APF) is one of the most well-defined and persistent oceanographic features on the planet and serves as a barrier to dispersal between the Southern Ocean and lower latitudes. High levels of endemism in the Southern Ocean have been attributed to this barrier, whereas the accompanying Antarctic Circumpolar Current (ACC) likely promotes west-to-east dispersal. Previous phylogeographic work on the brittle star Astrotoma agassizii Lyman, 1875 based on mitochondrial genes suggested isolation across the APF, even though populations in both South American waters and the Southern Ocean are morphologically indistinguishable. Here, we revisit this finding using a high-resolution 2b-RAD (restriction-site-associated DNA) single-nucleotide polymorphism (SNP)-based approach, in addition to enlarged mitochondrial DNA data sets (16S rDNA, COI, and COII), for comparison to previous work. In total, 955 biallelic SNP loci confirmed the existence of strongly divergent populations on either side of the Drake Passage. Interestingly, genetic admixture was detected between South America and the Southern Ocean in five individuals on both sides of the APF, revealing evidence of recent or ongoing genetic contact. We also identified two differentiated populations on the Patagonian Shelf with six admixed individuals from these two populations. These findings suggest that the APF is a strong but imperfect barrier. Fluctuations in location and strength of the APF and ACC due to climate shifts may have profound consequences for levels of admixture or endemism in this region of the world.
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http://dx.doi.org/10.1086/693460DOI Listing
June 2017

Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms.

BMC Evol Biol 2017 05 30;17(1):123. Epub 2017 May 30.

Department of Biology, University of Iowa, Iowa City, Iowa, 52242, USA.

Background: Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved.

Methods: In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion.

Results And Discussion: We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea.

Conclusions: These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.
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http://dx.doi.org/10.1186/s12862-017-0973-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5450073PMC
May 2017

Discovery and evolution of novel hemerythrin genes in annelid worms.

BMC Evol Biol 2017 03 23;17(1):85. Epub 2017 Mar 23.

Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA.

Background: Despite extensive study on hemoglobins and hemocyanins, little is known about hemerythrin (Hr) evolutionary history. Four subgroups of Hrs have been documented, including: circulating Hr (cHr), myohemerythrin (myoHr), ovohemerythrin (ovoHr), and neurohemerythrin (nHr). Annelids have the greatest diversity of oxygen carrying proteins among animals and are the only phylum in which all Hr subgroups have been documented. To examine Hr diversity in annelids and to further understand evolution of Hrs, we employed approaches to survey annelid transcriptomes in silico.

Results: Sequences of 214 putative Hr genes were identified from 44 annelid species in 40 different families and Bayesian inference revealed two major clades with strong statistical support. Notably, the topology of the Hr gene tree did not mirror the phylogeny of Annelida as presently understood, and we found evidence of extensive Hr gene duplication and loss in annelids. Gene tree topology supported monophyly of cHrs and a myoHr clade that included nHrs sequences, indicating these designations are functional rather than evolutionary.

Conclusions: The presence of several cHrs in early branching taxa suggests that a variety of Hrs were present in the common ancestor of extant annelids. Although our analysis was limited to expressed-coding regions, our findings demonstrate a greater diversity of Hrs among annelids than previously reported.
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http://dx.doi.org/10.1186/s12862-017-0933-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363010PMC
March 2017

Geographic structure in the Southern Ocean circumpolar brittle star (Ophiuridae) revealed from mtDNA and single-nucleotide polymorphism data.

Ecol Evol 2017 Jan 16;7(2):475-485. Epub 2016 Dec 16.

Department of Biological Sciences Auburn University Auburn AL USA.

Marine systems have traditionally been thought of as "open" with few barriers to gene flow. In particular, many marine organisms in the Southern Ocean purportedly possess circumpolar distributions that have rarely been well verified. Here, we use the highly abundant and endemic Southern Ocean brittle star to examine genetic structure and determine whether barriers to gene flow have existed around the Antarctic continent. possesses feeding planktotrophic larvae with presumed high dispersal capability, but a previous study revealed genetic structure along the Antarctic Peninsula. To test the extent of genetic differentiation within , we sampled from the Ross Sea through the eastern Weddell Sea. Whereas two mitochondrial DNA markers (16S rDNA and COI) were employed to allow comparison to earlier work, a 2b-RAD single-nucleotide polymorphism (SNP) approach allowed sampling of loci across the genome. Mitochondrial data from 414 individuals suggested three major lineages, but 2b-RAD data generated 1,999 biallelic loci that identified four geographically distinct groups from 89 samples. Given the greater resolution by SNP data, can be divided into geographically distinct populations likely representing multiple species. Specific historical scenarios that explain current population structure were examined with approximate Bayesian computation (ABC) analyses. Although the Bransfield Strait region shows high diversity possibly due to mixing, our results suggest that within the recent past, dispersal processes due to strong currents such as the Antarctic Circumpolar Current have not overcome genetic subdivision presumably due to historical isolation, questioning the idea of large open circumpolar populations in the Southern Ocean.
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http://dx.doi.org/10.1002/ece3.2617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243193PMC
January 2017

Classification of a Hypervirulent Pathotype Responsible for Epidemic Outbreaks in Warm-Water Fishes.

Front Microbiol 2016 18;7:1615. Epub 2016 Oct 18.

Department of Biological Sciences, Auburn University Auburn, AL, USA.

Lineages of hypervirulent (vAh) are the cause of persistent outbreaks of motile septicemia in warm-water fishes worldwide. Over the last decade, this virulent lineage of has resulted in annual losses of millions of tons of farmed carp and catfish in the People's Republic of China and the United States (US). Multiple lines of evidence indicate US catfish and Asian carp isolates of affiliated with sequence type 251 (ST251) share a recent common ancestor. To address the genomic context for the putative intercontinental transfer and subsequent geographic spread of this pathogen, we conducted a core genome phylogenetic analysis on 61 spp. genomes, of which 40 were affiliated with , with 26 identified as epidemic strains. Phylogenetic analyses indicate all ST251 strains form a coherent lineage affiliated with . Within this lineage, conserved genetic loci unique to were identified, with some genes present in consistently higher copy numbers than in non-epidemic isolates. In addition, results from analyses of representative ST251 isolates support the conclusion that multiple lineages are present within US vAh isolated from Mississippi, whereas vAh isolated from Alabama appear clonal. This is the first report of genomic heterogeneity within US vAh isolates, with some Mississippi isolates showing closer affiliation with the Asian grass carp isolate ZC1 than other vAh isolated in the US. To evaluate the biological significance of the identified heterogeneity, comparative disease challenges were conducted with representatives of different vAh genotypes. These studies revealed that isolate ZC1 yielded significantly lower mortality in channel catfish, relative to Alabama and Mississippi vAh isolates. Like other Asian vAh isolates, the ZC1 lineage contains all core genes for a complete type VI secretion system (T6SS). In contrast, more virulent US isolates retain only remnants of the T6SS (, and ) which may have functional implications. Collectively, these results characterize a hypervirulent pathotype that affects farmed fish on multiple continents.
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http://dx.doi.org/10.3389/fmicb.2016.01615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5067525PMC
October 2016

Developmental Transcriptomics of the Hawaiian Anchialine Shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae).

Integr Comp Biol 2016 12 8;56(6):1170-1182. Epub 2016 Jul 8.

*Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg, Auburn, AL 36849, USA

Many crustacean species progress through a series of metamorphoses during the developmental transition from embryo to adult. The molecular genetic basis of this transition, however, is not well characterized for a large number of crustaceans. Here, we employ multiple RNA-Seq methodologies to identify differentially expressed genes (DEGs) between "early" (i.e., Z - Z) as well as "late" (i.e., Z - Z) larval and adult developmental stages of Halocaridina rubra Holthuis (1963), an atyid shrimp endemic to the environmentally variable anchialine ecosystem of the Hawaiian Islands. Given the differences in salinity tolerance (narrow vs. wide range), energy acquisition (maternal yolk-bearing vs. microphagous grazing), and behavior (positively phototactic vs. not) between larvae and adults, respectively, of this species, we hypothesized the recovery of numerous DEGs belonging to functional categories relating to these characteristics. Consistent with this and regardless of methodology, hundreds of DEGs were identified, including upregulation of opsins and other light/stimulus detection genes and downregulation of genes related to ion transport, digestion, and reproduction in larvae relative to adults. Furthermore, isoform-switching, which has been largely unexplored in crustacean development, appears to be pervasive between H. rubra larvae and adults, especially among structural and oxygen-transport genes. Finally, by comparing RNA-Seq methodologies, we provide recommendations for future crustacean transcriptomic studies, including a demonstration of the pitfalls associated with identifying DEGs from single replicate samples as well as the utility of leveraging "prepackaged" bioinformatics pipelines.
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http://dx.doi.org/10.1093/icb/icw003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6281345PMC
December 2016

Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015.

Integr Comp Biol 2016 12 8;56(6):1055-1066. Epub 2016 Jul 8.

Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg, Auburn, AL 36849, USA.

Despite their economic, ecological, and experimental importance, genomic resources remain scarce for crustaceans. In lieu of genomes, many researchers have taken advantage of technological advancements to instead sequence and assemble crustacean transcriptomes de novo However, there is little consensus on what standard operating procedures are, or should be, for the field. Here, we systematically reviewed 53 studies published during 2014-2015 that utilized transcriptomic resources from this taxonomic group in an effort to identify commonalities as well as potential weaknesses that have applicability beyond just crustaceans. In general, these studies utilized RNA-Seq data, both novel and publicly available, to characterize transcriptomes and/or identify differentially expressed genes (DEGs) between treatments. Although the software suite Trinity was popular in assembly pipelines and other programs were also commonly employed, many studies failed to report crucial details regarding bioinformatic methodologies, including read mappers and the utilized parameters in identifying and characterizing DEGs. Annotation percentages for assembled transcriptomic contigs were low, averaging 32% overall. While other metrics, such as numbers of contigs and DEGs reported, correlated with the number of sequence reads utilized per sample, these did reach apparent saturation with increasing sequencing depth. Most disturbingly, a number of studies (55%) reported DEGs based on non-replicated experimental designs and single biological replicates for each treatment. Given this, we suggest future RNA-Seq experiments targeting transcriptome characterization conduct deeper (i.e., 50-100 M reads) sequencing while those examining differential expression instead focus more on increased biological replicates at shallower (i.e., ∼10-20 M reads/sample) sequencing depths. Moreover, the community must avoid submitting for review, or accepting for publication, non-replicated differential expression studies. Finally, mining the ever growing publicly available transcriptomic data from crustaceans will allow future studies to focus on hypothesis-driven research instead of continuing to simply characterize transcriptomes. As an example of this, we utilized neurotoxin sequences from the recently described remipede venom gland transcriptome in conjunction with publicly available crustacean transcriptomic data to derive preliminary results and hypotheses regarding the evolution of venom in crustaceans.
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http://dx.doi.org/10.1093/icb/icw061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6281346PMC
December 2016

Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics.

Comp Biochem Physiol Part D Genomics Proteomics 2016 09 11;19:34-44. Epub 2016 Jun 11.

Department of Biological Sciences, Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, AL 36849, USA.

Decapods represent one of the most ecologically diverse taxonomic groups within crustaceans, making them ideal to study physiological processes like osmoregulation. However, prior studies have failed to consider the entire transcriptomic response of the gill - the primary organ responsible for ion transport - to changing salinity. Moreover, the molecular genetic differences between non-osmoregulatory and osmoregulatory gill types, as well as the hormonal basis of osmoregulation, remain underexplored. Here, we identified and characterized differentially expressed genes (DEGs) via RNA-Seq in anterior (non-osmoregulatory) and posterior (osmoregulatory) gills during high to low salinity transfer in the blue crab Callinectes sapidus, a well-studied model for crustacean osmoregulation. Overall, we confirmed previous expression patterns for individual ion transport genes and identified novel ones with salinity-mediated expression. Notable, novel DEGs among salinities and gill types for C. sapidus included anterior gills having higher expression of structural genes such as actin and cuticle proteins while posterior gills exhibit elevated expression of ion transport and energy-related genes, with the latter likely linked to ion transport. Potential targets among recovered DEGs for hormonal regulation of ion transport between salinities and gill types included neuropeptide Y and a KCTD16-like protein. Using publically available sequence data, constituents for a "core" gill transcriptome among decapods are presented, comprising genes involved in ion transport and energy conversion and consistent with salinity transfer experiments. Lastly, rarefication analyses lead us to recommend a modest number of sequence reads (~10-15M), but with increased biological replication, be utilized in future DEG analyses of crustaceans.
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http://dx.doi.org/10.1016/j.cbd.2016.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987279PMC
September 2016

Evolution of Sulfur Binding by Hemoglobin in Siboglinidae (Annelida) with Special Reference to Bone-Eating Worms, Osedax.

J Mol Evol 2016 05 21;82(4-5):219-29. Epub 2016 Apr 21.

Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA.

Most members of Siboglinidae (Annelida) harbor endosymbiotic bacteria that allow them to thrive in extreme environments such as hydrothermal vents, methane seeps, and whale bones. These symbioses are enabled by specialized hemoglobins (Hbs) that are able to bind hydrogen sulfide for transportation to their chemosynthetic endosymbionts. Sulfur-binding capabilities are hypothesized to be due to cysteine residues at key positions in both vascular and coelomic Hbs, especially in the A2 and B2 chains. Members of the genus Osedax, which live on whale bones, do not have chemosynthetic endosymbionts, but instead harbor heterotrophic bacteria capable of breaking down complex organic compounds. Although sulfur-binding capabilities are important in other siboglinids, we questioned whether Osedax retained these cysteine residues and the potential ability to bind hydrogen sulfide. To answer these questions, we used high-throughput DNA sequencing to isolate and analyze Hb sequences from 8 siboglinid lineages. For Osedax mucofloris, we recovered three (A1, A2, and B1) Hb chains, but the B2 chain was not identified. Hb sequences from gene subfamilies A2 and B2 were translated and aligned to determine conservation of cysteine residues at previously identified key positions. Hb linker sequences were also compared to determine similarity between Osedax and siboglinids/sulfur-tolerant annelids. For O. mucofloris, our results found conserved cysteines within the Hb A2 chain. This finding suggests that Hb in O. mucofloris has retained some capacity to bind hydrogen sulfide, likely due to the need to detoxify this chemical compound that is abundantly produced within whale bones.
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http://dx.doi.org/10.1007/s00239-016-9739-7DOI Listing
May 2016

Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure.

Front Microbiol 2016 23;7:284. Epub 2016 Mar 23.

Department of Biological Sciences, Auburn University Auburn, AL, USA.

Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ(13)C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH4 (+)) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability.
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http://dx.doi.org/10.3389/fmicb.2016.00284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803750PMC
April 2016

Reproduction and development in Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae) clarifies larval ecology in the Hawaiian anchialine ecosystem.

Biol Bull 2015 Oct;229(2):134-42

Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, Alabama 36849.

Larvae in aquatic habitats often develop in environments different from those they inhabit as adults. Shrimp in the Atyidae exemplify this trend, as larvae of many species require salt or brackish water for development, while adults are freshwater-adapted. An exception within the Atyidae family is the "anchialine clade," which are euryhaline as adults and endemic to habitats with subterranean fresh and marine water influences. Although the Hawaiian anchialine atyid Halocaridina rubra is a strong osmoregulator, its larvae have never been observed in nature. Moreover, larval development in anchialine species is poorly studied. Here, reproductive trends in laboratory colonies over a 5-y period are presented from seven genetic lineages and one mixed population of H. rubra; larval survivorship under varying salinities is also discussed. The presence and number of larvae differed significantly among lineages, with the mixed population being the most prolific. Statistical differences in reproduction attributable to seasonality also were identified. Larval survivorship was lowest (12% settlement rate) at a salinity approaching fresh water and significantly higher in brackish and seawater (88% and 72%, respectively). Correlated with this finding, identifiable gills capable of ion transport did not develop until metamorphosis into juveniles. Thus, early life stages of H. rubra are apparently excluded from surface waters, which are characterized by lower and fluctuating salinities. Instead, these stages are restricted to the subterranean (where there is higher and more stable salinity) portion of Hawaii's anchialine habitats due to their inability to tolerate low salinities. Taken together, these data contribute to the understudied area of larval ecology in the anchialine ecosystem.
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http://dx.doi.org/10.1086/BBLv229n2p134DOI Listing
October 2015

Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific duplications, and homologs with low sequence identity.

J Mol Evol 2015 Apr 11;80(3-4):193-208. Epub 2015 Mar 11.

Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, USA,

Cyclooxygenase (COX) enzymatically converts arachidonic acid into prostaglandin G/H in animals and has importance during pregnancy, digestion, and other physiological functions in mammals. COX genes have mainly been described from vertebrates, where gene duplications are common, but few studies have examined COX in invertebrates. Given the increasing ease in generating genomic data, as well as recent, although incomplete descriptions of potential COX sequences in Mollusca, Crustacea, and Insecta, assessing COX evolution across Metazoa is now possible. Here, we recover 40 putative COX orthologs by searching publicly available genomic resources as well as ~250 novel invertebrate transcriptomic datasets. Results suggest the common ancestor of Cnidaria and Bilateria possessed a COX homolog similar to those of vertebrates, although such homologs were not found in poriferan and ctenophore genomes. COX was found in most crustaceans and the majority of molluscs examined, but only specific taxa/lineages within Cnidaria and Annelida. For example, all octocorallians appear to have COX, while no COX homologs were found in hexacorallian datasets. Most species examined had a single homolog, although species-specific COX duplications were found in members of Annelida, Mollusca, and Cnidaria. Additionally, COX genes were not found in Hemichordata, Echinodermata, or Platyhelminthes, and the few previously described COX genes in Insecta lacked appreciable sequence homology (although structural analyses suggest these may still be functional COX enzymes). This analysis provides a benchmark for identifying COX homologs in future genomic and transcriptomic datasets, and identifies lineages for future studies of COX.
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http://dx.doi.org/10.1007/s00239-015-9670-3DOI Listing
April 2015

Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida).

Mol Phylogenet Evol 2015 Apr 24;85:221-9. Epub 2015 Feb 24.

Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA. Electronic address:

Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts.
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http://dx.doi.org/10.1016/j.ympev.2015.02.008DOI Listing
April 2015

Phylogenomic resolution of the hemichordate and echinoderm clade.

Curr Biol 2014 Dec 6;24(23):2827-32. Epub 2014 Nov 6.

Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA. Electronic address:

Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced transcriptomes for 14 hemichordates as well as 8 echinoderms and complemented these with existing data for a total of 33 ambulacrarian operational taxonomic units (OTUs). Examination of leaf stability values revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus canadensis were unstable in placement; therefore, analyses were also run without these taxa. Analyses of 185 genes resulted in reciprocal monophyly of Enteropneusta and Pterobranchia, placed the deep-sea family Torquaratoridae within Ptychoderidae, and confirmed the position of ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa hypothesis). These results are consistent with earlier perspectives concerning plesiomorphies of Ambulacraria, including pharyngeal gill slits, a single axocoel, and paired hydrocoels and somatocoels. The resolved ambulacrarian phylogeny will help clarify the early evolution of chordate characteristics and has implications for our understanding of major fossil groups, including graptolites and somasteroideans.
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http://dx.doi.org/10.1016/j.cub.2014.10.016DOI Listing
December 2014

Nemertean toxin genes revealed through transcriptome sequencing.

Genome Biol Evol 2014 Nov 27;6(12):3314-25. Epub 2014 Nov 27.

Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, Alabama

Nemerteans are one of few animal groups that have evolved the ability to utilize toxins for both defense and subduing prey, but little is known about specific nemertean toxins. In particular, no study has identified specific toxin genes even though peptide toxins are known from some nemertean species. Information about toxin genes is needed to better understand evolution of toxins across animals and possibly provide novel targets for pharmaceutical and industrial applications. We sequenced and annotated transcriptomes of two free-living and one commensal nemertean and annotated an additional six publicly available nemertean transcriptomes to identify putative toxin genes. Approximately 63-74% of predicted open reading frames in each transcriptome were annotated with gene names, and all species had similar percentages of transcripts annotated with each higher-level GO term. Every nemertean analyzed possessed genes with high sequence similarities to known animal toxins including those from stonefish, cephalopods, and sea anemones. One toxin-like gene found in all nemerteans analyzed had high sequence similarity to Plancitoxin-1, a DNase II hepatotoxin that may function well at low pH, which suggests that the acidic body walls of some nemerteans could work to enhance the efficacy of protein toxins. The highest number of toxin-like genes found in any one species was seven and the lowest was three. The diversity of toxin-like nemertean genes found here is greater than previously documented, and these animals are likely an ideal system for exploring toxin evolution and industrial applications of toxins.
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http://dx.doi.org/10.1093/gbe/evu258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986456PMC
November 2014

Taking their breath away: metabolic responses to low-oxygen levels in anchialine shrimps (Crustacea: Atyidae and Alpheidae).

Comp Biochem Physiol A Mol Integr Physiol 2014 Dec 1;178:109-20. Epub 2014 Sep 1.

Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.

Crustaceans generally act as oxy-regulators, maintaining constant oxygen uptake as oxygen partial pressures decrease, but when a critical low level is reached, ventilation and aerobic metabolism shut down. Cave-adapted animals, including crustaceans, often show a reduced metabolic rate possibly owing in part to the hypoxic nature of such environments. However, metabolic rates have not been thoroughly explored in crustaceans from anchialine habitats (coastal ponds and caves), which can experience variable oxygenic regimes. Here, an atypical oxy-conforming pattern of oxygen uptake is reported in the Hawaiian anchialine atyid Halocaridina rubra, along with other unusual metabolic characteristics. Ventilatory rates are near-maximal in normoxia and did not increase appreciably as PO₂ declined, resulting in a decline in VO₂ during progressive hypoxia. Halocaridina rubra maintained in anoxic waters survived for seven days (the duration of the experiment) with no measureable oxygen uptake, suggesting a reliance on anaerobic metabolism. Supporting this, lactate dehydrogenase activity was high, even in normoxia, and oxygen debts were quickly repaid by an unusually extreme increase in oxygen uptake upon exposure to normoxia. In contrast, four related anchialine shrimp species from the Ryukyu Islands, Japan, exhibited physiological properties consistent with previously studied crustaceans. The unusual respiratory patterns found in H. rubra are discussed in the context of a trade-off in gill morphology for osmoregulatory ion transport vs. diffusion of respiratory gasses. Future focus on anchialine species may offer novel insight into the diversity of metabolic responses to hypoxia and other physiological challenges experienced by crustaceans.
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http://dx.doi.org/10.1016/j.cbpa.2014.08.015DOI Listing
December 2014

Expanding the population genetic perspective of cnidarian-Symbiodinium symbioses.

Authors:
Scott R Santos

Mol Ecol 2014 Sep;23(17):4185-7

Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA; Cellular and Molecular Biosciences Program, Auburn University, Auburn, AL, 36849, USA.

The modern synthesis was a seminal period in the biological sciences, establishing many of the core principles of evolutionary biology that we know today. Significant catalysts were the contributions of R.A. Fisher, J.B.S. Haldane and Sewall Wright (and others) developing the theoretical underpinning of population genetics, thus demonstrating adaptive evolution resulted from the interplay of forces such as natural selection and mutation within groups of individuals occupying the same space and time (i.e. a population). Given its importance, it is surprising that detailed population genetic data remain lacking for numerous organisms vital to many ecosystems. For example, the coral reef ecosystem is well recognized for its high biodiversity and productivity, numerous ecological services and significant economic and societal values (Moberg & Folke 1999;Cinner 2014). Many coral reef invertebrates form symbiotic relationships with single-celled dinoflagellates within the genus Symbiodinium Freudenthal (Taylor 1974), with hosts providing these (typically) intracellular symbionts with by-products of metabolism and in turn receiving photosynthetically fixed carbon capable of meeting hosts' respiratory demands (Falkowski et al. 1984; Muscatine et al. 1984). Unfortunately, the health and integrity of the coral reef ecosystem has been significantly and negatively impacted by onslaughts like anthropogenic eutrophication and disease in addition to global climate change, with increased incidences of 'bleaching' events (characterized as the loss of photosynthetic pigments from the algal cell or massive reduction of Symbiodinium density from hosts' tissue) and host mortality leading to staggering declines in geographic coverage (Bruno & Selig 2007) that have raised questions on the viability of this ecosystem as we know it (Bellwood et al. 2004; Parmesan 2006). One avenue towards anticipating the future of the coral reef ecosystem is by developing a broader and deeper understanding of the current genotypic diversity encompassed within and between populations of their keystone species, the scleractinian corals and dinoflagellate symbionts, as they potentially possess functional variation (either singularly or in combination) that may come under selection due to the ongoing and rapid environmental changes they are experiencing. However, such studies, especially for members of the genus Symbiodinium, are sparse. In this issue, Baums et al. (2014) provide a significant contribution by documenting the range-wide population genetics of Symbiodinium 'fitti' (Fig.1 ) in the context of complementary data from its host, the endangered Caribbean elkhorn coral Acropora palmata (Fig. 2). Notable results of this study include a single S. 'fitti' genotype typically dominates an individual A. palmata colony both spatially and temporally, gene flow among coral host populations is a magnitude higher to that of its symbiont populations, and the partners possess disparate patterns of genetic differentiation across the Greater Caribbean. The implications of such findings are discussed herein.
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http://dx.doi.org/10.1111/mec.12865DOI Listing
September 2014

Genomic Resources Notes accepted 1 June 2014 - 31 July 2014.

Mol Ecol Resour 2014 Nov 5;14(6):1322. Epub 2014 Sep 5.

This article documents the public availability of transcriptome sequence data, assembled contigs and annotated contigs and ORFS for five anchialine shrimp species (Crustacea: Atyidae and Alpheidae).
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http://dx.doi.org/10.1111/1755-0998.12315DOI Listing
November 2014

Osmoregulation in the Hawaiian anchialine shrimp Halocaridina rubra (Crustacea: Atyidae): expression of ion transporters, mitochondria-rich cell proliferation and hemolymph osmolality during salinity transfers.

J Exp Biol 2014 Jul 17;217(Pt 13):2309-20. Epub 2014 Apr 17.

Department of Biological Sciences and Cellular and Molecular Biosciences Program, Auburn University, Auburn, AL 36849, USA.

Studies of euryhaline crustaceans have identified conserved osmoregulatory adaptions allowing hyper-osmoregulation in dilute waters. However, previous studies have mainly examined decapod brachyurans with marine ancestries inhabiting estuaries or tidal creeks on a seasonal basis. Here, we describe osmoregulation in the atyid Halocaridina rubra, an endemic Hawaiian shrimp of freshwater ancestry from the islands' anchialine ecosystem (coastal ponds with subsurface freshwater and seawater connections) that encounters near-continuous spatial and temporal salinity changes. Given this, survival and osmoregulatory responses were examined over a wide salinity range. In the laboratory, H. rubra tolerated salinities of ~0-56‰, acting as both a hyper- and hypo-osmoregulator and maintaining a maximum osmotic gradient of ~868 mOsm kg(-1) H2O in freshwater. Furthermore, hemolymph osmolality was more stable during salinity transfers relative to other crustaceans. Silver nitrate and vital mitochondria-rich cell staining suggest all gills are osmoregulatory, with a large proportion of each individual gill functioning in ion transport (including when H. rubra acts as an osmoconformer in seawater). Additionally, expression of ion transporters and supporting enzymes that typically undergo upregulation during salinity transfer in osmoregulatory gills (i.e. Na(+)/K(+)-ATPase, carbonic anhydrase, Na(+)/K(+)/2Cl(-) cotransporter, V-type H(+)-ATPase and arginine kinase) were generally unaltered in H. rubra during similar transfers. These results suggest H. rubra (and possibly other anchialine species) maintains high, constitutive levels of gene expression and ion transport capability in the gills as a means of potentially coping with the fluctuating salinities that are encountered in anchialine habitats. Thus, anchialine taxa represent an interesting avenue for future physiological research.
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http://dx.doi.org/10.1242/jeb.103051DOI Listing
July 2014

Illuminating the base of the annelid tree using transcriptomics.

Mol Biol Evol 2014 Jun 23;31(6):1391-401. Epub 2014 Feb 23.

Zoological Research Museum Alexander Koenig, Bonn, Germany.

Annelida is one of three animal groups possessing segmentation and is central in considerations about the evolution of different character traits. It has even been proposed that the bilaterian ancestor resembled an annelid. However, a robust phylogeny of Annelida, especially with respect to the basal relationships, has been lacking. Our study based on transcriptomic data comprising 68,750-170,497 amino acid sites from 305 to 622 proteins resolves annelid relationships, including Chaetopteridae, Amphinomidae, Sipuncula, Oweniidae, and Magelonidae in the basal part of the tree. Myzostomida, which have been indicated to belong to the basal radiation as well, are now found deeply nested within Annelida as sister group to Errantia in most analyses. On the basis of our reconstruction of a robust annelid phylogeny, we show that the basal branching taxa include a huge variety of life styles such as tube dwelling and deposit feeding, endobenthic and burrowing, tubicolous and filter feeding, and errant and carnivorous forms. Ancestral character state reconstruction suggests that the ancestral annelid possessed a pair of either sensory or grooved palps, bicellular eyes, biramous parapodia bearing simple chaeta, and lacked nuchal organs. Because the oldest fossil of Annelida is reported for Sipuncula (520 Ma), we infer that the early diversification of annelids took place at least in the Lower Cambrian.
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http://dx.doi.org/10.1093/molbev/msu080DOI Listing
June 2014

Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data.

PLoS One 2014 8;9(1):e84080. Epub 2014 Jan 8.

Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, Alabama, United States of America ; Cellular and Molecular Biosciences Program, Auburn University, Auburn, Alabama, United States of America.

Mitochondrial (mt) genes are some of the most popular and widely-utilized genetic loci in phylogenetic studies of metazoan taxa. However, their linked nature has raised questions on whether using the entire mitogenome for phylogenetics is overkill (at best) or pseudoreplication (at worst). Moreover, no studies have addressed the comparative phylogenetic utility of mitochondrial genes across individual lineages within the entire Metazoa. To comment on the phylogenetic utility of individual mt genes as well as concatenated subsets of genes, we analyzed mitogenomic data from 1865 metazoan taxa in 372 separate lineages spanning genera to subphyla. Specifically, phylogenies inferred from these datasets were statistically compared to ones generated from all 13 mt protein-coding (PC) genes (i.e., the "supergene" set) to determine which single genes performed "best" at, and the minimum number of genes required to, recover the "supergene" topology. Surprisingly, the popular marker COX1 performed poorest, while ND5, ND4, and ND2 were most likely to reproduce the "supergene" topology. Averaged across all lineages, the longest ∼2 mt PC genes were sufficient to recreate the "supergene" topology, although this average increased to ∼5 genes for datasets with 40 or more taxa. Furthermore, concatenation of the three "best" performing mt PC genes outperformed that of the three longest mt PC genes (i.e, ND5, COX1, and ND4). Taken together, while not all mt PC genes are equally interchangeable in phylogenetic studies of the metazoans, some subset can serve as a proxy for the 13 mt PC genes. However, the exact number and identity of these genes is specific to the lineage in question and cannot be applied indiscriminately across the Metazoa.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084080PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891902PMC
January 2015