Characterizing the multivariate physiogenomic response to environmental change

Global change is altering the climate that species have historically adapted to – in some cases at a pace not recently experienced in their evolutionary history – with cascading effects on all taxa. A central aim in global change biology is to understand how specific populations may be “primed” for global change, either through acclimation or adaptive standing genetic variation. It is therefore an important goal to link physiological measurements to the degree of stress a population experiences (Annual Review of Marine Science, 2012, 4, 39). Although “omic” approaches such as gene expression are often used as a proxy for the amount of stress experienced, we still have a poor understanding of how gene expression affects ecologically and physiologically relevant traits in non‐model organisms. In a From the Cover paper in this issue of Molecular Ecology, Griffiths, Pan and Kelley (Molecular Ecology, 2019, 28) link gene expression to physiological traits in a temperate marine coral. They discover population‐specific responses to ocean acidification for two populations that originated from locations with different histories of exposure to acidification. By integrating physiological and gene expression data, they were able to elucidate the mechanisms that explain these population‐specific responses. Their results give insight into the physiogenomic feedbacks that may prime organisms or make them unfit for ocean global change.     

Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA‐defined Operational Taxonomic Units, OTUs) across 108 globally‐distributed surface ocean stations. We grouped taxa based on their SpAD shape (“normal‐like”‐ abundant and ubiquitous; “logistic”‐ globally rare, present in few sites; and “bimodal”‐ abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan “normal‐like” OTUs, yet there was a gradual shift towards assemblages dominated by “logistic” taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer “normal‐like” shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.     

Explaining ecological shifts: the roles of temperature and primary production in the long‐term dynamics of benthic faunal composition

Predicting the ecological consequences of environmental change requires that we can identify the drivers of long‐term ecological variation. Biological assemblages can exhibit abrupt deviations from temporal trends, potentially resulting in irreversible shifts in species composition over short periods of time. Such dynamics are hypothesised to occur as gradual forcing eventually causes biological thresholds to be crossed, but could also be explained by biota simply tracking abrupt changes to their environment. Here, we modelled temporal variation in a North Sea benthic faunal assemblage over a 40‐year period (1972–2012) to test for changes to temporal trends of biota and determine whether they could be explained by underlying patterns in sea temperature and primary production. These extrinsic factors were postulated to influence community dynamics through their roles in determining and sustaining the metabolic demands of organisms, respectively. A subset of mainly large and long‐lived taxa (those loaded on the first principal component of taxa densities) exhibited two significant changes to their temporal trends, which culminated in a shift in assemblage composition. These changes were explained by an increase in pelagic primary production, and hence detrital food input to the seabed, but were unrelated to variation in sea temperature. A second subset of mainly small and short‐lived taxa (those loaded on the second principal component) did not experience any significant changes to their temporal trends, as enhanced pelagic primary production appeared to mitigate the impact of warming on these organisms. Our results suggest that abrupt ecological shifts can occur as biota track underlying variation in extrinsic factors, in this case primary production. Changes to the structure of ecosystems may therefore be predictable based on environmental change projections.     

Quantifying ecological change through discriminant analysis: a paleoecological example from the Peruvian Amazon

Question: Can discriminant analysis be used to quantify ecological change? Can fossil pollen data be used as a proxy to quantify moisture availability change through discriminant analysis? Location: Lake Sauce, Amazonian piedmont of Peru. Methods: A linear discriminant function was used to classify taxa found through pollen analysis into wet and dry indicators. The data set was filtered to exclude rare taxa from the analysis. Given that after application of the filter there were more variables (samples) than observations (taxa), the model was “de‐saturated” through simulation of samples based on the existing data set. Results: The inclusion of taxa that have a relative abundance of 1% or more in at least 5% of the samples reduces noise in the data set. Application of discriminant analysis to pollen data gave an error of 18% when classifying taxa by affinity with dry or wet conditions. The inferred moisture availability curve shows consistency with independent proxies from the same core and with identified local and sub‐continental moisture patterns. Conclusions: The method provides a reliable means to reduce a complex paleoecological data set to proportional change in a single pre‐defined variable. The output is a relative scale of change of a defined environmental gradient through time, without reliance on an extensive array of modern analogues. The results appear to provide a comparable quality of information to that of isotopic analysis derived from speleothem or sedimentary records.     

Species: kinds of individuals or individuals of a kind

The “species‐as‐individuals” thesis takes species, or taxa, to be individuals. On grounds of spatiotemporal boundedness, any biological entity at any level of complexity subject to evolutionary processes is an individual. From evolutionary theory flows an ontology that does not countenance universal properties shared by evolving entities. If austere nominalism were applied to evolving entities, however, nature would be reduced to a mere flow of passing events, each one a blob in space–time and hence of passing interest only. Yet if there is genuine biodiversity in nature, if nature is genuinely carved into species, and taxa, then these evolutionary entities will be genuinely differentiated into specific kinds, each species being one of its kind. Given the fact that evolving entities have un‐sharp boundaries, an appropriately weak, “non‐essentialist” concept of natural kind has to be invoked that does not allow for strong identity conditions. The thesis of this paper is that species are not either individuals, or natural kinds. Instead, species are complex wholes (particulars, individuals) that instantiate a specific natural kind. © The Willi Hennig Society 2007.     

Deconstructing the long-standing a priori assumption that serial homology generally involves ancestral similarity followed by anatomical divergence

It has long been assumed that serial homologues are ancestrally similar—polysomerism resulting from a “duplication” or “repetition” of forms—and then often diverge—anisomerism, for example, as they become adapted to perform different tasks as is the case with the forelimb and hind limbs of humans. However, such an assumption, with crucial implications for comparative, evolutionary, and developmental biology, and for evolutionary developmental biology, has in general not really been tested by a broad analysis of the available empirical data. Perhaps not surprisingly, more recent anatomical comparisons, as well as molecular knowledge of how, for example, serial appendicular structures are patterned along with different anteroposterior regions of the body axis of bilateral animals, and how “homologous” patterning domains do not necessarily mark “homologous” morphological domains, are putting in question this paradigm. In fact, apart from showing that many so-called “serial homologues” might not be similar at all, recent works have shown that in at least some cases some “serial” structures are indeed more similar to each other in derived taxa than in phylogenetically more ancestral ones, as pointed out by authors such as Owen. In this article, we are taking a step back to question whether such assumptions are actually correct at all, in the first place. In particular, we review other cases of so-called “serial homologues” such as insect wings, arthropod walking appendages, Dipteran thoracic bristles, and the vertebrae, ribs, teeth, myomeres, feathers, and hairs of chordate animals. We show that: (a) there are almost never cases of true ancestral similarity; (b) in evolution, such structures—for example, vertebra—and/or their subparts—for example, “transverse processes”—many times display trends toward less similarity while in many others display trends toward more similarity, that is, one cannot say that there is a clear, overall trend to anisomerism.     

Phylogeny of Mysis (Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data

We studied the phylogenetic history of opossum shrimps of the genus Mysis Latreille, 1802 (Crustacea: Mysida) using parsimony analyses of morphological characters, DNA sequence data from mitochondrial (16S, COI and CytB) and nuclear genes (ITS2, 18S), and eight allozyme loci. With these data we aimed to resolve a long‐debated question of the origin of the non‐marine (continental) taxa in the genus, i.e., “glacial relicts” in circumpolar postglacial lakes and “arctic immigrants” in the Caspian Sea. A simultaneous analysis of the data sets gave a single tree supporting monophyly of all continental species, as well as monophyly of the taxa from circumpolar lakes and from the Caspian Sea. A clade of three circumarctic marine species was sister group to the continental taxa, whereas Atlantic species had more distant relationships to the others. Small molecular differentiation among the morphologically diverse endemic species from the Caspian Sea suggested their recent speciation, while the phenotypically more uniform “glacial relict” species from circumpolar lakes (Mysis relicta group) showed deep molecular divergences. For the length‐variable ITS2 region both direct optimization and a priori alignment procedures gave similar topologies, although the former approach provided a better overall resolution. In terms of partitioned Bremer support (PBS), mitochondrial protein coding genes provided the largest contribution (83%) to the total tree resolution. This estimate however, appears to be partly spurious, due to the concerted inheritance of mitochondrial characters and probable cases of introgression or ancestral polymorphism. © The Willi Hennig Society 2005.     

Unusual adhesive production system in the barnacle Lepas anatifera: An ultrastructural and histochemical investigation

Adhesives that are naturally produced by marine organisms are potential sources of inspiration in the search for medical adhesives. Investigations of barnacle adhesives are at an early stage but it is becoming obvious that barnacles utilize a unique adhesive system compared to other marine organisms. The current study examined the fine structure and chemistry of the glandular system that produces the adhesive of the barnacle Lepas anatifera. All components for the glue originated from large single‐cell glands (70–180 μm). Staining (including immunostaining) showed that L ‐3,4‐dihydroxyphenylalanine and phosphoserine were not present in the glue producing tissues, demonstrating that the molecular adhesion of barnacles differs from all other permanently gluing marine animals studied to date. The glandular tissue and adhesive secretion primarily consisted of slightly acidic proteins but also included some carbohydrate. Adhesive proteins were stored in cytoplasmic granules adjacent to an intracellular drainage canal (ICC); observations implicated both merocrine and apocrine mechanisms in the transport of the secretion from the cell cytoplasm to the ICC. Inside the ICC, the secretion was no longer contained within granules but was a flocculent material which became “clumped” as it traveled through the canal network. Hemocytes were not seen within the adhesive “apparatus” (comprising of the glue producing cells and drainage canals), nor was there any structural mechanism by which additions such as hemocytes could be made to the secretion. The unicellular adhesive gland in barnacles is distinct from multicellular adhesive systems observed in marine animals such as mussels and tubeworms. Because the various components are not physically separated in the apparatus, the barnacle adhesive system appears to utilize completely different and unknown mechanisms for maintaining the liquid state of the glue within the body, as well as unidentified mechanisms for the conversion of extruded glue into hard cement. J. Morphol., 2012. © 2012 Wiley Periodicals, Inc.     

Effects of dredging on critical ecological processes for marine invertebrates,seagrasses and macroalgae,and the potential for management with environmental windows using Western Australia as a case study

Dredging can have significant impacts on benthic marine organisms through mechanisms such as sedimentation and reduction in light availability as a result of increased suspension of sediments. Phototrophic marine organisms and those with limited mobility are particularly at risk from the effects of dredging. The potential impacts of dredging on benthic species depend on biological processes including feeding mechanism, mobility, life history characteristics (LHCs), stage of development and environmental conditions. Environmental windows (EWs) are a management technique in which dredging activities are permitted during specific periods throughout the year; avoiding periods of increased vulnerability for particular organisms in specific locations. In this review we identify these critical ecological processes for temperate and tropical marine benthic organisms; and examine if EWs could be used to mitigate dredging impacts using Western Australia (WA) as a case study. We examined LHCs for a range of marine taxa and identified, where possible, their vulnerability to dredging. Large gaps in knowledge exist for the timing of LHCs for major species of marine invertebrates, seagrasses and macroalgae, increasing uncertainty around their vulnerability to an increase in suspended sediments or light attenuation. We conclude that there is currently insufficient scientific basis to justify the adoption of generic EWs for dredging operations in WA for any group of organisms other than corals and possibly for temperate seagrasses. This is due to; 1) the temporal and spatial variation in the timing of known critical life history stages of different species; and 2) our current level of knowledge and understanding of the critical life history stages and characteristics for most taxa and for most areas being largely inadequate to justify any meaningful EW selection. As such, we suggest that EWs are only considered on a case-by-case basis to protect ecologically or economically important species for which sufficient location-specific information is available, with consideration of probable exposures associated with a given mode of dredging.     

Species concepts and the recognition of ancestors

Whether or not ancestral species can be recognised depends on the species concept adopted. A “metaspecies”; is a species that completely lacks autapomorphies, and which might (or might not) be ancestral to other species. Such taxa have been identified among both living and fossil organisms. Under the most commonly‐used species concepts (biological, evolutionary, phenetic, phylogenetic, ecological, recognition and cohesion), “metaspecies”; can be assumed to be ancestral. Even if the known members of a metaspecies are not ancestral to anything, parsimony dictates that the (as yet unknown) ancestral lineage is identical to the metaspecies and, under these species concepts, assignable to the same species. Only the cladistic and monophyletic species concepts would deny “metaspecies”; ancestral status, but these species concepts are problematical and have never been used by practising systematists.     

Do saline taxa evolve faster? Comparing relative rates of molecular evolution between freshwater and marine eukaryotes

The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline versus freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein‐coding and noncoding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein‐coding genes in freshwater taxa—the comparisons mainly involving bony fish—compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms.     

Effects of fasting and nutritional restriction on the isotopic ratios of nitrogen and carbon: a meta‐analysis

Many organisms experience fasting in their life time, and this physiological process has the potential to alter stable isotope values of organisms, and confound interpretation of food web studies. However, previous studies on the effects of fasting and starvation on stable isotopes show disparate results, and have never been quantitatively synthesized. We performed a laboratory experiment and meta‐analysis to determine how stable isotopes of δ¹⁵N and δ¹³C change with fasting, and we tested whether moderators such as taxa and tissue explain residual variation. We collected literature data from a wide variety of taxa and tissues. We surveyed over 2000 papers, and of these, 26 met our selection criteria, resulting in 51 data points for δ¹⁵N, and 43 data points for δ¹³C. We determine that fasting causes an average increase in the isotopic value of organisms of 0.5‰ for δ¹⁵N and that the only significant moderator is tissue type. We find that the overall effect size for δ¹³C is not significant, but when the significant moderator of tissue is considered, significant increases in blood and whole organisms are seen with fasting. Our results show that across tissues and taxa, the nutritional status of an organism must be considered when interpreting stable isotope data, as fasting can cause large differences in stable isotope values that would be otherwise attributed to other factors.     

The potential role of public gardens as sentinels of plant invasion

Public gardens can help prevent detrimental effects of plant invasions by collecting and sharing data on taxa spreading from cultivation early in the invasion process, thereby acting as sentinels of plant invasion. Existing initiatives have called for public gardens to adopt measures preventing plant invasion, but it is unclear what actions individual gardens are implementing, as there is no formal mechanism for communicating their progress. This study used internal lists of escaping taxa from seven public gardens in the Midwestern United States and Canada to demonstrate how public gardens can collectively contribute data that is critical to assessing potential invasiveness. It also reveals methodological differences in how gardens develop their lists of escaping plants, leading to recommendations for standardization. Data pooled across gardens yielded 769 species spreading from cultivation at one or more gardens. Eight woody species were listed by all gardens despite not consistently being recognized as invasive by states and provinces containing the gardens; some species recorded by multiple gardens did not appear on any invasive lists. While it may be premature to call taxa escaping from cultivation at a few public gardens “invasive” or even “potentially invasive”, these plants should be monitored and evaluated with this information shared to facilitate stronger conclusions about risk. Thus, public gardens have a unique expertise in assisting invasive plant efforts as sentinels, particularly if challenges related to methodological inconsistencies and data sharing are suitably addressed, which is herein recommended through the adoption of a set of standardized guidelines.

     

From Sea to Sea: Canada's Three Oceans of Biodiversity

Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada''s three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada''s three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada''s natural heritage.     

Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing

Soleglad and Fet's (2003a) attempt to reconstruct the phylogeny of Recent (including extant) scorpions, the revised classification derived from it, and recent emendations, mostly published in their self‐edited online journal, Euscorpius, are deficient. Separate analyses of three independent matrices (morphology, 16S rDNA, 18S rDNA) were presented. In the morphological matrix, 52 binary and 10 tristate trichobothrial characters were replaced with one character comprising six ordered states representing trichobothrial “types”. The remaining matrix of 105 characters was further reduced to 33 “fundamental” characters (20% of the morphological dataset), the analysis of which appears to be the basis for the revised classification presented. The taxon sample for the morphological analysis included 14 supraspecific terminal taxa representing genera, the monophyly of only 7 (12.5%) of which has been confirmed. A composite terminal, assembled from the fragments of fossils that may not be confamilial let alone monophyletic, was created for the Palaeopisthacanthidae, employed as the primary outgroup for the analysis. Other important outgroup taxa, notably eurypterids, xiphosurans and other arachnids, were omitted entirely. The morphological characters presented contained numerous unjustifiable assumptions of character polarity and phylogenetic relationship. An approach to character coding, deliberately adopted to reduce “homoplasy”, biased the analysis towards a preconceived result. Structurally and topographically similar features in different taxa were explicitly assigned separate (often autapomorphic) states according to presumed phylogenetic relationships among the taxa in which they were observed. Putative “reversals” were coded as separate characters or states. Character transformation was forced by ordering, additive coding or Sankoff optimization through allegedly intermediate states for which there is no empirical evidence. Many characters were defined in a manner that demonstrates either a lack of understanding of, or disregard for, established methods and standards of morphological character coding. Some states display overlapping variation whereas others subsume variation that is not structurally or topographically similar. Polymorphic “states” were created for terminals with interspecific variation and unknown “states” for terminals that should have been scored unknown. Many characters were not evaluated for particular terminal taxa, but merely scored inapplicable although the structures and, consequently, the characters in question are present and therefore applicable to them. In view of the significant theoretical and empirical problems with the approach to cladistics taken by Soleglad and Fet, we find no justification for accepting either the results of their analyses or the revised classification derived from them. Pending the outcome of a rigorous phylogenetic analysis, published according to acceptable standards of scholarship in a peer‐reviewed journal, we revert to the suprageneric classification of Scorpiones reflected by the most recent peer‐reviewed, published treatments and reject all changes to the classification proposed by Soleglad, Fet and colleagues since 2001. We argue that an analysis and revised classification of the kind presented in various papers by these authors could not survive the peer‐review process of a mainstream scientific journal. The poor scholarship exemplified by these and other papers published in Euscorpius emphasize the importance of quality control associated with the emergent infrastructure of online publishing. A centralized register of taxa may be the only solution for ensuring quality control in the taxonomy of the future. © The Willi Hennig Society 2005.