Douglas J. Eernisse

Bio: Douglas J. Eernisse is an academic researcher from California State University, Fullerton. The author has contributed to research in topics: Polyplacophora & Chiton. The author has an hindex of 22, co-authored 46 publications receiving 2194 citations. Previous affiliations of Douglas J. Eernisse include Natural History Museum of Los Angeles County & University of Michigan.

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences.

Abstract: Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1,000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.

Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology.

Abstract: Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the available character evidence. Explicit or implicit use of taxonomic congruence is usually employed when an investigator either has both molecular and morphological data sets or has different gene-, rRNA-, or protein-sequence data sets available. Indeed, a taxonomic congruence rationale is frequently used as the basis for exploring classes of data, thus allowing comparison between the phylogenetic signal emerging from a particular data set and those of other such classes. Problematic aspects of employing the taxonomic congruence approach include the potentially misleading and arbitrary choices of both a consensus method and the division of characters into subsets. If the goal of an analysis is to provide the best estimate of genealogy afforded by the available character evidence, then taxonomic congruence is substantially more arbitrary than a total evidence approach. The theoretical advantages of phylogenetic estimates based on total evidence are argued in the present study and are illustrated with an example of amniote relationships. We report conflicting results from total evidence and taxonomic congruence approaches, with analyses of previously reported data from both fossil and living amniotes and from both morphology and molecules, the latter including available 18S rRNA, 28S rRNA, and protein sequences. We conclude that a more highly resolved and robust phylogenetic hypothesis of amniotes, the traditional one, emerges when a total evidence approach is employed.

Annelida and Arthropoda are Not Sister Taxa: A Phylogenetic Analysis of Spiralian Metazoan Morphology

Abstract: ?Annelids and arthropods have long been considered to be each other's closest relatives, as evidenced by similarities in their segmented body plans. In the first cladistic analysis of metazoan morphology accompanied by an explicit data matrix, Schram (Meglitsch and Schram, 1991, Invertebrate zoology, 3rd edition, Oxford Univ. Press, New York) suggested tentative support for this conventional "Articulata" hypothesis. Our reanalysis of the Schram data matrix yielded weak support for an alternative "Eutrochozoa" grouping of annelids, molluscs, and certain other spiralian phyla, exclusive of arthropods. Likewise, recent 18S ribosomal RNA se? quence comparisons have favored the Eutrochozoa hypothesis. This study presents a new analysis of 141 independently assembled characters, purported to represent the current state of knowledge of metazoan morphology and embryology. This maximum parsimony analysis resulted in robust support of Eutrochozoa. For this data compilation and method of analysis, the Articulata hy? pothesis could only be supported by adding multiple ad hoc proposals of evolutionary events. Instead, the more parsimonious Eutrochozoa hypothesis is favored as the best-supported current reconstruction of higher level animal genealogy. [Phylogeny; Metazoa; animal; Arthropoda; Annelida; Mollusca; morphology; embryology; RNA.] An enormous literature of descriptive and experimental work on the ontogeny and morphology of animals has accumu? lated over the last century and a half. Much is now known about the life history, anat? omy, and genetic organization of species in most of the more than 30 recognized animal phyla. Our modern interpretation of character homology rests on the results of these studies and on the understanding of animal evolution they make possible. The recent emphasis of cladistic methods in systematic biology, however, has fo? cused new attention on the evidential basis for asserting hypotheses of homology among characters (Wiley, 1981; Patterson, 1982). The criteria for homology formal? ized by Remane (1956) involve evaluation of similarities of ontogeny, composition, and anatomical position on a case-by-case basis. These similarities are now regarded by many systematists to be preliminary to the test of character congruence on a dadogram (Hennig, 1966; Patterson, 1982), and only shared derived characters (synapomorphies) are considered candidates for homology. Other similarities that result from independent or parallel evolution (homoplasies) or are retained from more ancient evolutionary transformation (plesiomorphies) are not considered relevant even when they are phenotypically iden? tical. Studies on the early evolution of major animal lineages and on the origins of im? portant features in their structural design have only recently begun to incorporate the character congruence approach of eval? uating phenotypic similarities. One ex? ample is the investigation of genealogical relationships among spiralian metazoans, including Arthropoda, Mollusca, Anneli? da, and several other less speciose phyla. Spiralians comprise >90% of all living metazoan (multicellular animal) species (Barnes, 1987; Brusca and Brusca, 1990), yet the genealogical relationships among many of them remain undocumented by phylo? genetic criteria. Members of the Spiralia have also been grouped as Protostomia by 1 Present address: Institute of Marine Sciences and Biology Department, University of California, Santa Cruz, California 95064, USA.

Photoperiodic regulation of gametogenesis and gonadal growth in the sea star Pisaster ochraceus

Abstract: A photoperiod regime 6 mo out of phase between December 1978 and August 1980 resulted in gametogenesis, gonadal growth, and spawning in laboratory-maintained sea stars [Pisaster ochraceus (Brandt)] 6 mo out of phase with individuals in the field or laboratory on normal celestial photoperiods at Santa Cruz, California (USA). The seasonal fluctuation of pyloric cecum size also was shifted when the sea stars were held on the out-of-phase photoperiod regime. Phase shift of all these events was evident within 6 to 9 mo. Long daylengths (or short nightlengths) in spring and summer apparently synchronize or entrain the initiaion of gametogenesis and gonadal growth in fall.

Gaps as Characters in Sequence-Based Phylogenetic Analyses

Abstract: In the analysis of sequence-based data matrices, the use of different methods of treating gaps has been demonstrated to in? fluence the resulting phylogenetic hypothe? ses (e.g., Eernisse and Kluge, 1993; Vogler and DeSalle, 1994; Simons and Mayden, 1997). Despite this influence, a well-justi? fied, uniformly applied method of treating gaps is lacking in sequence-based phyloge? netic studies. Treatment of gaps varies widely from secondarily mapping gaps onto the tree inferred from base characters

The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'.

Abstract: SUMMARY Physiological studies can help predict effects of climate change through determining which species currently live closest to their upper thermal tolerance limits, which physiological systems set these limits, and how species differ in acclimatization capacities for modifying their thermal tolerances. Reductionist studies at the molecular level can contribute to this analysis by revealing how much change in sequence is needed to adapt proteins to warmer temperatures — thus providing insights into potential rates of adaptive evolution — and determining how the contents of genomes — protein-coding genes and gene regulatory mechanisms — influence capacities for adapting to acute and long-term increases in temperature. Studies of congeneric invertebrates from thermally stressful rocky intertidal habitats have shown that warm-adapted congeners are most susceptible to local extinctions because their acute upper thermal limits (LT 50 values) lie near current thermal maxima and their abilities to increase thermal tolerance through acclimation are limited. Collapse of cardiac function may underlie acute and longer-term thermal limits. Local extinctions from heat death may be offset by in-migration of genetically warm-adapted conspecifics from mid-latitude ‘hot spots’, where midday low tides in summer select for heat tolerance. A single amino acid replacement is sufficient to adapt a protein to a new thermal range. More challenging to adaptive evolution are lesions in genomes of stenotherms like Antarctic marine ectotherms, which have lost protein-coding genes and gene regulatory mechanisms needed for coping with rising temperature. These extreme stenotherms, along with warm-adapted eurytherms living near their thermal limits, may be the major ‘losers’ from climate change.

Evidence for a clade of nematodes, arthropods and other moulting animals.

Abstract: The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other.

REPuter: the manifold applications of repeat analysis on a genomic scale.

Abstract: The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.