Billie J. Swalla is the Director of Friday Harbor Laboratories in the College of the Environment and also Professor of Biology in the College of Arts and Sciences at the University of Washington. She is an expert in Invertebrate Development and Marine Genomics. She moved to the University of Washington from Penn State University in 1999 in order to work on the diversity of marine invertebrates that inhabit Puget Sound and the Salish Sea. Professor Swalla began her career at the University of Iowa, working on cartilage and muscle differentiation and limb patterning in chicken embryos with Professor Michael Solursh for her M.S. and Ph.D. A summer taking Embryology at the Marine Biological Laboratory in 1983 changed her life and she moved to Postdoctoral studies with Professor William R. Jeffery at the University of Texas at Austin and Bodega Marine Lab at the University of California at Davis. During Postdoctoral research made possible grant from the American Association of University Women, Billie became interested in the role that gender, race and cultures play in science and society. The Swalla lab uses transcriptomics and genomics to investigate the evolution of animal body plans by comparing gene expression between different animal embryos. Specific interests are the Evolution and Development of ctenophores, tunicates and hemichordates. Supervisors: Professor Michael Solursh and Professor William R. Jeffery
This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured wi... more This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured with or without notochord in explant cultures. Histological sections of the cultures were stained with a trichrome stain to identify the different kinds of connective tissues formed. Both anterior and posterior (epithelial) somites made muscle, cartilage and loose connective tissue in explant culture. The extent of cartilage differentiation was enhanced by the presence of the notochord, confirming earlier studies. The presence of 1 mM-dibutyryl cAMP in the culture medium increased the amount of muscle found in the explants but by histological criteria did not inhibit chondrogenesis, contrary to earlier reports. The addition of quail ectoderm to the explants stimulated loose connective tissue to form directly beneath it, suggesting for the first time a role of the ectoderm in dermatome differentiation. These results suggest that the epithelial somite has the capacity to differentiate into a...
This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured wi... more This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured with or without notochord in explant cultures. Histological sections of the cultures were stained with a trichrome stain to identify the different kinds of connective tissues formed. Both anterior and posterior (epithelial) somites made muscle, cartilage and loose connective tissue in explant culture. The extent of cartilage differentiation was enhanced by the presence of the notochord, confirming earlier studies. The presence of 1 mM-dibutyryl cAMP in the culture medium increased the amount of muscle found in the explants but by histological criteria did not inhibit chondrogenesis, contrary to earlier reports. The addition of quail ectoderm to the explants stimulated loose connective tissue to form directly beneath it, suggesting for the first time a role of the ectoderm in dermatome differentiation. These results suggest that the epithelial somite has the capacity to differentiate into a...
This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured wi... more This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured with or without notochord in explant cultures. Histological sections of the cultures were stained with a trichrome stain to identify the different kinds of connective tissues formed. Both anterior and posterior (epithelial) somites made muscle, cartilage and loose connective tissue in explant culture. The extent of cartilage differentiation was enhanced by the presence of the notochord, confirming earlier studies. The presence of 1 mM-dibutyryl cAMP in the culture medium increased the amount of muscle found in the explants but by histological criteria did not inhibit chondrogenesis, contrary to earlier reports. The addition of quail ectoderm to the explants stimulated loose connective tissue to form directly beneath it, suggesting for the first time a role of the ectoderm in dermatome differentiation. These results suggest that the epithelial somite has the capacity to differentiate into a...
This symposium undertakes to examine some historical background relevant to the renaissance in bi... more This symposium undertakes to examine some historical background relevant to the renaissance in biological studies linking evolution and development, to review the current status of research in this rapidly changing area (especially the problem of forging links between disciplines that have gone in divergent directions), to address the benefits and difficulties that arise from molecular studies of the relationship between evolution and development, and to help set the research agenda in evolutionary developmental biology in the next few years. Rather than introducing the individual contributions that follow, this paper aims to set some historical background for the topics they cover. I argue that old questions about the relationship of development to evolution, raised by such figures as William Bateson and Richard Goldschmidt, remain relevant to contemporary work, though they require major reformulation in light of subsequent developments. Many older questions, long set aside as intractable, remain open. Recently developed techniques may enable us to answer some of them. Accordingly, I suggest, it is worth reviewing the work of several historical figures in setting current research agendas.
tunicates is accompanied by dramatic developmental changes that affect morphology and reproductio... more tunicates is accompanied by dramatic developmental changes that affect morphology and reproduction. We compared vasa expression in a solitary ascidian and a closely related colonial ascidian, in an effort to uncover developmental mechanisms important during the evolution of these contrasting life histories, including the ability to reproduce by budding. In this study, we explored the origin of germ cells in new buds developing by asexual reproduction in a colonial ascidian, Botrylloides violaceus and compared it to the source of germ cells in a solitary ascidian Boltenia villosa. We studied expression by in situ hybridization of vasa, a DEAD box RNA helicase gene found in germ cells across the metazoans. In B. villosa, bv-vasa mRNA was expressed in putative germ cells and oocytes of adult gonads, and was sequestered into a posterior lineage during embryogenesis. In mature colonies of the ascidian B. violaceus, bot-vasa mRNA was expressed in putative spermatogonia, in oocytes of zooids, and in some circulating cells in the zooids and differentiating buds. We propose that expression of vasa in cells other than gonadal germ cells of zooids in a colonial ascidian may serve as a source of germ-line stem cells in the colony.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2009
Colonial ascidians are the only chordates to undergo whole body regeneration (WBR), the ability t... more Colonial ascidians are the only chordates to undergo whole body regeneration (WBR), the ability to form an entirely new individual from the peripheral vasculature. Here we describe WBR in Botrylloides violaceus, a colonial ascidian that reliably regenerates after ablation of all zooids and buds of young colonies. During early regeneration several buds develop within the tunic vasculature, but only one continues development into a complete zooid. We describe some of the first events of vascular budding leading to the vesicle stage with phase contrast microscopy, time-lapse video recording and detailed histological studies of regenerating colonies. The first conspicuous stage of vascular budding is when a single-layered sphere of cells becomes enclosed by vascular epithelium. We report the appearance of Piwi-positive cells in hemocytes surrounding the regenerates. We observed an increase of proliferating cell nuclear antigen (PCNA)-positive cells in circulatory hemocytes in late regenerates, and found double-labeled nuclear expression with Piwi in a subset of large circulatory cells. We rarely found Piwi or PCNA in differentiating tissues during vascular budding, suggesting that cells that form the epithelial tissues during budding and WBR originate mostly from circulatory hemocyte precursors. We propose that multiple stem cell types are circulating within B. violaceus and that they undergo proliferation in the peripheral vasculature before differentiating into epithelial tissues for all three germ layers during WBR.
In many taxa, germline precursors segregate from somatic lineages during embryonic development an... more In many taxa, germline precursors segregate from somatic lineages during embryonic development and are irreversibly committed to gametogenesis. However, in animals that can propagate asexually, germline precursors can originate in adults. Botryllus schlosseri is a colonial ascidian that grows by asexual reproduction, and on a weekly basis regenerates all somatic and germline tissues. Embryonic development in solitary ascidians is the classic example of determinative specification, and we are interested in both the origins and the persistence of stem cells responsible for asexual development in colonial ascidians. In this study, we characterized vasa as a putative marker of germline precursors. We found that maternally deposited vasa mRNA segregates early in development to a posterior lineage of cells, suggesting that germline formation is determinative in colonial ascidians. In adults, vasa expression was observed in the gonads, as well as in a population of mobile cells scattered throughout the open circulatory system, consistent with previous transplantation/reconstitution results. vasa expression was dynamic during asexual development in both fertile and infertile adults, and was also enriched in a population of stem cells. Germline precursors in juveniles could contribute to gamete formation immediately upon transplantation into fertile adults, thus vasa expression is correlated with the potential for gamete formation, which suggests that it is a marker for embryonically specified, long-lived germline progenitors. Transient vasa knockdown did not have obvious effects on germline or somatic development in adult colonies, although it did result in a profound heterochrony, suggesting that vasa might play a homeostatic role in asexual development.
Summary
Background
The question of how many marine species exist is important because it provide... more Summary Background
The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered.
Results
There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science.
Conclusions
Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century.
Highlights
► ∼226,000 described eukaryotic marine species are accepted and ∼170,000 are not ► Experts and statistics predict that fewer than one million marine species exist ► 70,000 species may already be in specimen collections, waiting to be described ► Most of marine life may be discovered this century
Animals are complex systems operating at multiple spatial and temporal scales, facing the challen... more Animals are complex systems operating at multiple spatial and temporal scales, facing the challenge of how to change in appropriate ways, degrees, and times, in response to the diverse internal and external influences to which they are exposed. Discovering the system-level attributes of organisms that make them resilient or robust-or sensitive or fragile-to change presents a grand challenge for biology. Knowledge of these attributes and the underlying mechanisms controlling them is crucially needed to predict how organisms will respond to short-and long-term changes in internal and external environments, including those driven by climate change. Organismal biologists require novel approaches that extend beyond traditional disciplinary boundaries, especially when they partner with mathematicians and engineers. Pursuing this research enterprise will not only give us a deeper understanding of how organisms will face future challenges, but it will also reveal nature-inspired solutions in complex engineered systems, both of which will benefit science and society.
Journal of experimental zoology. Part B, Molecular and developmental evolution, 2013
Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic int... more Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic interrelationships amongst the constituent taxa. Although the monophyly and interrelationships among the three principal groups-the chordates, the echinoderms, and the hemichordates-are well established, as are the internal relationships among the echinoderm and chordate taxa, the interrelationships among the principal groups of hemichordates-the harrimaniid enteropneusts, the ptychoderid enteropneusts, and the pterobranchs-remain unresolved. Depending on the study some find enteropneusts paraphyletic with pterobranchs (e.g., Cephalodiscus) more closely related to the harrimaniid enteropneusts (e.g., Saccoglossus) than either are to the ptychoderid enteropneusts (e.g., Ptychodera), whereas other studies support a monophyletic Enteropneusta. To try and resolve between these two competing hypotheses, we turned to microRNAs, small ∼22 nt non-coding RNA genes that have been shown to shed insigh...
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2013
Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic int... more Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic interrelationships amongst the constituent taxa. Although the monophyly and interrelationships among the three principal groups-the chordates, the echinoderms, and the hemichordates-are well established, as are the internal relationships among the echinoderm and chordate taxa, the interrelationships among the principal groups of hemichordates-the harrimaniid enteropneusts, the ptychoderid enteropneusts, and the pterobranchs-remain unresolved. Depending on the study some find enteropneusts paraphyletic with pterobranchs (e.g., Cephalodiscus) more closely related to the harrimaniid enteropneusts (e.g., Saccoglossus) than either are to the ptychoderid enteropneusts (e.g., Ptychodera), whereas other studies support a monophyletic Enteropneusta. To try and resolve between these two competing hypotheses, we turned to microRNAs, small $22 nt non-coding RNA genes that have been shown to shed insight into particularly difficult phylogenetic questions. Using deep sequencing we characterized the small RNA repertoires of two hemichordate species, Cephalodiscus hodgsoni and Ptychodera flava, and the crinoid echinoderm Antedon mediterranea, and combined our results with the described complements of the hemichordate Saccoglossus kowalevskii, the sea urchin Strongylocentrotus purpuratus, and the starfish Patiria miniata. Our data unambiguously support the monophyly of Enteropneusts as S. kowalevskii shares 12 miRNA sequences with P. flava that are not present in the C. hodgsoni or A. mediterranea libraries, and have never been reported from another metazoan taxon. Thus, these data resolve the phylogenetic position of pterobranchs, ultimately allowing for a better understanding of body plan evolution throughout the deuterostomes. J. Exp. Zool.
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organ... more Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
The small brooding ascidian Molgula citrina Alder and Hancock, 1848 has long been known as a comm... more The small brooding ascidian Molgula citrina Alder and Hancock, 1848 has long been known as a common inhabitant of shallow waters on both sides of the north Atlantic on subtidal natural hard substrates and also as a fouler of floating docks. There are published records from the White Sea (NW Russia), but none from the north Pacific. In May and August 2008, a number of adult brooding Molgula sp. specimens were collected from floating docks at the small fishing village of Seldovia on the Kenai Peninsula at Kachemak Bay, Alaska. Morphologically these individuals exactly match Atlantic specimens of Molgula citrina in all characters that were examined. The unique constellation of characters for this species differentiates it from all other Molgula species, as noted by . In addition, the full-length 18S and 28S rDNA sequences are identical for both the Alaska specimens and New England M. citrina. Is this a new invasion, or is M. citrina a northern circumpolar species that was somehow overlooked? If this new record indicates a natural distribution, why has it not been collected before? If it is a recent introduction, it is unlikely that M. citrina, an inhabitant of cold waters, could survive in sea chests of ships from the N. Atlantic arriving in Alaska via the Panama Canal, but the intriguing idea exists of transport from Atlantic to Pacific through the Northwest or Northeast Passages. As global warming diminishes the ice cover in this region, more and more ships are traversing the Northwest Passage across northern Canada as well as the NE Passage across northern Russia, representing significant new routes for anthropogenic transport of marine species. The tadpoles of this small brooder are retained for some time after hatching, resulting in an extremely short free larval life, but could survive as metamorphosed juveniles attached in sea chests or free-floating in ballast water. They have a wide temperature tolerance and once they metamorphose can live free-floating in sea water for some time. They become very sticky and will ultimately stick to whatever they contact. Thus they could conceivably live for many generations in sea chests and sustain a viable population from which to invade new habitats.
This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured wi... more This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured with or without notochord in explant cultures. Histological sections of the cultures were stained with a trichrome stain to identify the different kinds of connective tissues formed. Both anterior and posterior (epithelial) somites made muscle, cartilage and loose connective tissue in explant culture. The extent of cartilage differentiation was enhanced by the presence of the notochord, confirming earlier studies. The presence of 1 mM-dibutyryl cAMP in the culture medium increased the amount of muscle found in the explants but by histological criteria did not inhibit chondrogenesis, contrary to earlier reports. The addition of quail ectoderm to the explants stimulated loose connective tissue to form directly beneath it, suggesting for the first time a role of the ectoderm in dermatome differentiation. These results suggest that the epithelial somite has the capacity to differentiate into a...
This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured wi... more This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured with or without notochord in explant cultures. Histological sections of the cultures were stained with a trichrome stain to identify the different kinds of connective tissues formed. Both anterior and posterior (epithelial) somites made muscle, cartilage and loose connective tissue in explant culture. The extent of cartilage differentiation was enhanced by the presence of the notochord, confirming earlier studies. The presence of 1 mM-dibutyryl cAMP in the culture medium increased the amount of muscle found in the explants but by histological criteria did not inhibit chondrogenesis, contrary to earlier reports. The addition of quail ectoderm to the explants stimulated loose connective tissue to form directly beneath it, suggesting for the first time a role of the ectoderm in dermatome differentiation. These results suggest that the epithelial somite has the capacity to differentiate into a...
This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured wi... more This paper examines the differentiation of somites from stage-16 or -17 chick embryos cultured with or without notochord in explant cultures. Histological sections of the cultures were stained with a trichrome stain to identify the different kinds of connective tissues formed. Both anterior and posterior (epithelial) somites made muscle, cartilage and loose connective tissue in explant culture. The extent of cartilage differentiation was enhanced by the presence of the notochord, confirming earlier studies. The presence of 1 mM-dibutyryl cAMP in the culture medium increased the amount of muscle found in the explants but by histological criteria did not inhibit chondrogenesis, contrary to earlier reports. The addition of quail ectoderm to the explants stimulated loose connective tissue to form directly beneath it, suggesting for the first time a role of the ectoderm in dermatome differentiation. These results suggest that the epithelial somite has the capacity to differentiate into a...
This symposium undertakes to examine some historical background relevant to the renaissance in bi... more This symposium undertakes to examine some historical background relevant to the renaissance in biological studies linking evolution and development, to review the current status of research in this rapidly changing area (especially the problem of forging links between disciplines that have gone in divergent directions), to address the benefits and difficulties that arise from molecular studies of the relationship between evolution and development, and to help set the research agenda in evolutionary developmental biology in the next few years. Rather than introducing the individual contributions that follow, this paper aims to set some historical background for the topics they cover. I argue that old questions about the relationship of development to evolution, raised by such figures as William Bateson and Richard Goldschmidt, remain relevant to contemporary work, though they require major reformulation in light of subsequent developments. Many older questions, long set aside as intractable, remain open. Recently developed techniques may enable us to answer some of them. Accordingly, I suggest, it is worth reviewing the work of several historical figures in setting current research agendas.
tunicates is accompanied by dramatic developmental changes that affect morphology and reproductio... more tunicates is accompanied by dramatic developmental changes that affect morphology and reproduction. We compared vasa expression in a solitary ascidian and a closely related colonial ascidian, in an effort to uncover developmental mechanisms important during the evolution of these contrasting life histories, including the ability to reproduce by budding. In this study, we explored the origin of germ cells in new buds developing by asexual reproduction in a colonial ascidian, Botrylloides violaceus and compared it to the source of germ cells in a solitary ascidian Boltenia villosa. We studied expression by in situ hybridization of vasa, a DEAD box RNA helicase gene found in germ cells across the metazoans. In B. villosa, bv-vasa mRNA was expressed in putative germ cells and oocytes of adult gonads, and was sequestered into a posterior lineage during embryogenesis. In mature colonies of the ascidian B. violaceus, bot-vasa mRNA was expressed in putative spermatogonia, in oocytes of zooids, and in some circulating cells in the zooids and differentiating buds. We propose that expression of vasa in cells other than gonadal germ cells of zooids in a colonial ascidian may serve as a source of germ-line stem cells in the colony.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2009
Colonial ascidians are the only chordates to undergo whole body regeneration (WBR), the ability t... more Colonial ascidians are the only chordates to undergo whole body regeneration (WBR), the ability to form an entirely new individual from the peripheral vasculature. Here we describe WBR in Botrylloides violaceus, a colonial ascidian that reliably regenerates after ablation of all zooids and buds of young colonies. During early regeneration several buds develop within the tunic vasculature, but only one continues development into a complete zooid. We describe some of the first events of vascular budding leading to the vesicle stage with phase contrast microscopy, time-lapse video recording and detailed histological studies of regenerating colonies. The first conspicuous stage of vascular budding is when a single-layered sphere of cells becomes enclosed by vascular epithelium. We report the appearance of Piwi-positive cells in hemocytes surrounding the regenerates. We observed an increase of proliferating cell nuclear antigen (PCNA)-positive cells in circulatory hemocytes in late regenerates, and found double-labeled nuclear expression with Piwi in a subset of large circulatory cells. We rarely found Piwi or PCNA in differentiating tissues during vascular budding, suggesting that cells that form the epithelial tissues during budding and WBR originate mostly from circulatory hemocyte precursors. We propose that multiple stem cell types are circulating within B. violaceus and that they undergo proliferation in the peripheral vasculature before differentiating into epithelial tissues for all three germ layers during WBR.
In many taxa, germline precursors segregate from somatic lineages during embryonic development an... more In many taxa, germline precursors segregate from somatic lineages during embryonic development and are irreversibly committed to gametogenesis. However, in animals that can propagate asexually, germline precursors can originate in adults. Botryllus schlosseri is a colonial ascidian that grows by asexual reproduction, and on a weekly basis regenerates all somatic and germline tissues. Embryonic development in solitary ascidians is the classic example of determinative specification, and we are interested in both the origins and the persistence of stem cells responsible for asexual development in colonial ascidians. In this study, we characterized vasa as a putative marker of germline precursors. We found that maternally deposited vasa mRNA segregates early in development to a posterior lineage of cells, suggesting that germline formation is determinative in colonial ascidians. In adults, vasa expression was observed in the gonads, as well as in a population of mobile cells scattered throughout the open circulatory system, consistent with previous transplantation/reconstitution results. vasa expression was dynamic during asexual development in both fertile and infertile adults, and was also enriched in a population of stem cells. Germline precursors in juveniles could contribute to gamete formation immediately upon transplantation into fertile adults, thus vasa expression is correlated with the potential for gamete formation, which suggests that it is a marker for embryonically specified, long-lived germline progenitors. Transient vasa knockdown did not have obvious effects on germline or somatic development in adult colonies, although it did result in a profound heterochrony, suggesting that vasa might play a homeostatic role in asexual development.
Summary
Background
The question of how many marine species exist is important because it provide... more Summary Background
The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered.
Results
There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science.
Conclusions
Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century.
Highlights
► ∼226,000 described eukaryotic marine species are accepted and ∼170,000 are not ► Experts and statistics predict that fewer than one million marine species exist ► 70,000 species may already be in specimen collections, waiting to be described ► Most of marine life may be discovered this century
Animals are complex systems operating at multiple spatial and temporal scales, facing the challen... more Animals are complex systems operating at multiple spatial and temporal scales, facing the challenge of how to change in appropriate ways, degrees, and times, in response to the diverse internal and external influences to which they are exposed. Discovering the system-level attributes of organisms that make them resilient or robust-or sensitive or fragile-to change presents a grand challenge for biology. Knowledge of these attributes and the underlying mechanisms controlling them is crucially needed to predict how organisms will respond to short-and long-term changes in internal and external environments, including those driven by climate change. Organismal biologists require novel approaches that extend beyond traditional disciplinary boundaries, especially when they partner with mathematicians and engineers. Pursuing this research enterprise will not only give us a deeper understanding of how organisms will face future challenges, but it will also reveal nature-inspired solutions in complex engineered systems, both of which will benefit science and society.
Journal of experimental zoology. Part B, Molecular and developmental evolution, 2013
Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic int... more Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic interrelationships amongst the constituent taxa. Although the monophyly and interrelationships among the three principal groups-the chordates, the echinoderms, and the hemichordates-are well established, as are the internal relationships among the echinoderm and chordate taxa, the interrelationships among the principal groups of hemichordates-the harrimaniid enteropneusts, the ptychoderid enteropneusts, and the pterobranchs-remain unresolved. Depending on the study some find enteropneusts paraphyletic with pterobranchs (e.g., Cephalodiscus) more closely related to the harrimaniid enteropneusts (e.g., Saccoglossus) than either are to the ptychoderid enteropneusts (e.g., Ptychodera), whereas other studies support a monophyletic Enteropneusta. To try and resolve between these two competing hypotheses, we turned to microRNAs, small ∼22 nt non-coding RNA genes that have been shown to shed insigh...
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2013
Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic int... more Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic interrelationships amongst the constituent taxa. Although the monophyly and interrelationships among the three principal groups-the chordates, the echinoderms, and the hemichordates-are well established, as are the internal relationships among the echinoderm and chordate taxa, the interrelationships among the principal groups of hemichordates-the harrimaniid enteropneusts, the ptychoderid enteropneusts, and the pterobranchs-remain unresolved. Depending on the study some find enteropneusts paraphyletic with pterobranchs (e.g., Cephalodiscus) more closely related to the harrimaniid enteropneusts (e.g., Saccoglossus) than either are to the ptychoderid enteropneusts (e.g., Ptychodera), whereas other studies support a monophyletic Enteropneusta. To try and resolve between these two competing hypotheses, we turned to microRNAs, small $22 nt non-coding RNA genes that have been shown to shed insight into particularly difficult phylogenetic questions. Using deep sequencing we characterized the small RNA repertoires of two hemichordate species, Cephalodiscus hodgsoni and Ptychodera flava, and the crinoid echinoderm Antedon mediterranea, and combined our results with the described complements of the hemichordate Saccoglossus kowalevskii, the sea urchin Strongylocentrotus purpuratus, and the starfish Patiria miniata. Our data unambiguously support the monophyly of Enteropneusts as S. kowalevskii shares 12 miRNA sequences with P. flava that are not present in the C. hodgsoni or A. mediterranea libraries, and have never been reported from another metazoan taxon. Thus, these data resolve the phylogenetic position of pterobranchs, ultimately allowing for a better understanding of body plan evolution throughout the deuterostomes. J. Exp. Zool.
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organ... more Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
The small brooding ascidian Molgula citrina Alder and Hancock, 1848 has long been known as a comm... more The small brooding ascidian Molgula citrina Alder and Hancock, 1848 has long been known as a common inhabitant of shallow waters on both sides of the north Atlantic on subtidal natural hard substrates and also as a fouler of floating docks. There are published records from the White Sea (NW Russia), but none from the north Pacific. In May and August 2008, a number of adult brooding Molgula sp. specimens were collected from floating docks at the small fishing village of Seldovia on the Kenai Peninsula at Kachemak Bay, Alaska. Morphologically these individuals exactly match Atlantic specimens of Molgula citrina in all characters that were examined. The unique constellation of characters for this species differentiates it from all other Molgula species, as noted by . In addition, the full-length 18S and 28S rDNA sequences are identical for both the Alaska specimens and New England M. citrina. Is this a new invasion, or is M. citrina a northern circumpolar species that was somehow overlooked? If this new record indicates a natural distribution, why has it not been collected before? If it is a recent introduction, it is unlikely that M. citrina, an inhabitant of cold waters, could survive in sea chests of ships from the N. Atlantic arriving in Alaska via the Panama Canal, but the intriguing idea exists of transport from Atlantic to Pacific through the Northwest or Northeast Passages. As global warming diminishes the ice cover in this region, more and more ships are traversing the Northwest Passage across northern Canada as well as the NE Passage across northern Russia, representing significant new routes for anthropogenic transport of marine species. The tadpoles of this small brooder are retained for some time after hatching, resulting in an extremely short free larval life, but could survive as metamorphosed juveniles attached in sea chests or free-floating in ballast water. They have a wide temperature tolerance and once they metamorphose can live free-floating in sea water for some time. They become very sticky and will ultimately stick to whatever they contact. Thus they could conceivably live for many generations in sea chests and sustain a viable population from which to invade new habitats.
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Papers by Billie Swalla
Background
The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered.
Results
There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science.
Conclusions
Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century.
Highlights
► ∼226,000 described eukaryotic marine species are accepted and ∼170,000 are not ► Experts and statistics predict that fewer than one million marine species exist ► 70,000 species may already be in specimen collections, waiting to be described ► Most of marine life may be discovered this century
Background
The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered.
Results
There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science.
Conclusions
Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century.
Highlights
► ∼226,000 described eukaryotic marine species are accepted and ∼170,000 are not ► Experts and statistics predict that fewer than one million marine species exist ► 70,000 species may already be in specimen collections, waiting to be described ► Most of marine life may be discovered this century