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Foraminifera are important components of tropical marine benthic ecosystems and their recovery pattern from the end-Permian mass extinction can yield insights into the Mesozoic history of this group. Here we report the calcareous and agglutinated foraminifera recovered from five measured stratigraphic sections on the Great Bank of Guizhou, an uppermost Permian to Upper Triassic isolated carbonate platform in the Nanpanjiang Basin, south China. The material contains >100 Triassic species, including three that are newly described (Arenovidalina weiin. sp.,Meandrospira?enosin. sp., andSpinoendotebanella lehrmannin. gen., n. sp.), ranging from Griesbachian (Induan) to Cordevolian (Carnian) age. The species belong to the classes Miliolata, Textulariata, Fusulinata, Nodosariata, and to an unknown class housing all aragonitic forms of the orders Involutinida and Robertinida. Based on previously established conodont zones and carbon isotope chemostratigraphy, the Griesbachian (early Induan) through Illyrian (late Anisian) interval has been subdivided into 12 foraminiferal zones and two unnamed intervals devoid of foraminifera. Following the extinction at the Permian-Triassic boundary, habitable ecological niches of Griesbachian age were invaded by disaster taxa that subsequently became extinct during the Dienerian (late Induan) and left no younger descendants. The disaster taxa were replaced by Lazarus taxa with Permian origins, which were then decimated by the Smithian-Spathian (mid-Olenekian) boundary crisis. The tempo of recovery appears to have been modulated by environmental changes during the Griesbachian through Smithian that involved both climate change and expansion of anoxic ocean bottom waters. Uninterrupted and lasting recovery of benthic foraminifera did not begin until the Spathian.UUID:http://zoobank.org/2a6e9061-b163-402a-9098-8765a80576b3

Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121–130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.

The Vision and Change report called for the biology community to mobilize around teaching the core concepts of biology. This essay describes a collection of resources developed by several different groups that can be used to respond to the report’s call to transform undergraduate education at both the individual course and departmental levels. First, we present two frameworks that help articulate the Vision and Change core concepts, the BioCore Guide and the Conceptual Elements (CE) Framework, which can be used in mapping the core concepts onto existing curricula and designing new curricula that teach the biology core concepts. Second, we describe how the BioCore Guide and the CE Framework can be used alongside the Partnership for Undergraduate Life Sciences Education curricular rubric as a way for departments to self-assess their teaching of the core concepts. Finally, we highlight three sets of instruments that can be used to directly assess student learning of the core concepts: the Biology Card Sorting Task, the Biology Core Concept Instruments, and the Biology—Measuring Achievement and Progression in Science instruments. Approaches to using these resources independently and synergistically are discussed.

We describe the development of a new, freely available, online, programmatic-level assessment tool, Measuring Achievement and Progress in Science in Physiology, or Phys-MAPS ( http://cperl.lassp.cornell.edu/bio-maps ). Aligned with the conceptual frameworks of Core Principles of Physiology, and Vision and Change Core Concepts, Phys-MAPS can be used to evaluate student learning of core physiology concepts at multiple time points in an undergraduate physiology program, providing a valuable longitudinal tool to gain insight into student thinking and aid in the data-driven reform of physiology curricula. Phys-MAPS questions have a modified multiple true/false design and were developed using an iterative process, including student interviews and physiology expert review to verify scientific accuracy, appropriateness for physiology majors, and clarity. The final version of Phys-MAPS was tested with 2,600 students across 13 universities, has evidence of reliability, and has no significant statement biases. Over 90% of the physiology experts surveyed agreed that each Phys-MAPS statement was scientifically accurate and relevant to a physiology major. When testing each statement for bias, differential item functioning analysis demonstrated only a small effect size (

Mesomyzostoma Remscheid, 1918 currently includes three described species that live in the coelom and/or gonads of comatulid crinoids: Mesomyzostoma reichenspergeri Remscheid, 1918, Mesomyzostoma katoi Okada, 1933 and Mesomyzostoma lanterbecqae Summers and Rouse, 2014 in Summers, Al-Hakim et al. 2014. Here we describe four new species of Mesomyzostoma and assess their phylogenetic relationships using 18S rRNA, cytochrome oxidase subunit I and 16S rRNA sequence data. We also designate a neotype for M. katoi as the original types appear to be lost. We record M. reichenspergeri from the Australian Great Barrier Reef and from northern Papua New Guinea, but samples from the type locality (Aru Islands, Indonesia) and previously recorded host are needed for confirmation. The new species of Mesomyzostoma are one Japanese species: Mesomyzostoma okadai sp. nov., and three Australian species: Mesomyzostoma lobus sp. nov., Mesomyzostoma leukos sp. nov. and Mesomyzostoma botulus sp. nov. The first infects the c...

We provide a guide for identification of Comatulidae, a family of crinoid echinoderms, incorporating morphological and molecular evidence. A non-dichotomous key for all genera is included, as well as photographs of species most likely to be encountered in the tropical western Pacific Ocean. Based on sequencing of cytochrome oxidase subunit I (COI), and other genes when necessary, we identified four cases where taxonomic revision was needed. We synonymized Comaster nobilis under Comaster schlegelii, and Clarkcomanthus exilis under Clarkcomanthus comanthipinnus, and re-described Clarkcomanthus albinotus. We also showed the variation of COI sequences within and among species, which varies from lineage to lineage. In some cases, specimens with obvious morphological disparity possessed very little intraspecific molecular diversity (

The Vision and Change report provides a nationally agreed upon framework of core concepts that undergraduate biology students should master by graduation. While identifying these concepts was an important first step, departments also need ways to measure the extent to which students understand these concepts. Here, we present the General Biology–Measuring Achievement and Progression in Science (GenBio-MAPS) assessment as a tool to measure student understanding of the core concepts at key time points in a biology degree program. Data from more than 5000 students at 20 institutions reveal that this instrument distinguishes students at different stages of the curriculum, with an upward trend of increased performance at later time points. Despite this trend, we identify several concepts that advanced students find challenging. Linear mixed-effects models reveal that gender, race/ethnicity, English-language status, and first-generation status predict overall performance and that different institutions show distinct performance profiles across time points. GenBio-MAPS represents the first programmatic assessment for general biology programs that spans the breadth of biology and aligns with the Vision and Change core concepts. This instrument provides a needed tool to help departments monitor student learning and guide curricular transformation centered on the teaching of core concepts.

We report the presence of Mesorhizobium, a genus best known for its nitrogen-fixing symbiosis with terrestrial legumes, associated with the marine polychaete Meganerilla bactericola (Annelida: Nerillidae). Abundant epibionts were previously described as coating the exterior of M. bactericola, which is found within the anoxic sulfide-oxidizing microbial mats of the Santa Barbara Basin, California, USA. 16S rRNA investigation of the bacterial community associated with this polychaete discovered the presence of bacteria belonging to Mesorhizobium. We identified these bacteria using phylogenetic analyses of 16S rRNA and three additional functional genes, nifH, atpD and recA, and group-specific fluorescence in situ hybridization (FISH).

Delayed biotic recovery from the end-Permian mass extinction has long been interpreted to result from environmental inhibition. Recently, evidence of more rapid recovery has begun to emerge, suggesting the role of environmental inhibition was previously overestimated. However, there have been few high-resolution taxonomic and ecological studies spanning the full Early and Middle Triassic recovery interval, leaving the precise pattern of recovery and underlying mechanisms poorly constrained. In this study, we document Early and Middle Triassic trends in taxonomic diversity, assemblage evenness, and size distribution of benthic foraminifers on an exceptionally exposed carbonate platform in south China. We observe gradual increases in all metrics through Early Triassic and earliest Middle Triassic time, with stable values reached early in the Anisian. There is little support in our data set for a substantial Early Triassic lag interval during the recovery of foraminifers or for a stepwise recovery pattern. The recovery pattern of foraminifers on the GBG corresponds well with available global data for this taxon and appears to parallel that of many benthic invertebrate clades. Early Triassic diversity increase in foraminifers was more gradual than in ammonoids and conodonts. However, foraminifers continued to increase in diversity, size, and evenness into Middle Triassic time, whereas diversity of ammonoids and conodonts declined. These contrasts suggest decoupling of recovery between benthic and pelagic environments; it is unclear whether these discrepancies reflect inherent contrasts in their evolutionary dynamics or the differential impact of Early Triassic ocean anoxia or associated environmental parameters on benthic ecosystems.

A new assessment tool, Ecology and Evolution–Measuring Achievement and Progression in Science or EcoEvo-MAPS, measures student thinking in ecology and evolution during an undergraduate course of study. EcoEvo-MAPS targets foundational concepts in ecology and evolution and uses a novel approach that asks students to evaluate a series of predictions, conclusions, or interpretations as likely or unlikely to be true given a specific scenario. We collected evidence of validity and reliability for EcoEvo-MAPS through an iterative process of faculty review, student interviews, and analyses of assessment data from more than 3000 students at 34 associate’s-, bachelor’s-, master’s-, and doctoral-granting institutions. The 63 likely/unlikely statements range in difficulty and target student understanding of key concepts aligned with the Vision and Change report. This assessment provides departments with a tool to measure student thinking at different time points in the curriculum and provides data that can be used to inform curricular and instructional modifications.

An efficient protocol to identify and describe species of Myzostomida is outlined and demonstrated. This taxonomic approach relies on careful identification (facilitated by an included comprehensive table of available names with relevant geographical and host information) and concise descriptions combined with DNA sequencing, live photography, and accurate host identification. Twenty-one new species are described following these guidelines: Asteromyzostomum grygieri n. sp., Endomyzostoma scotia n. sp., Endomyzostoma neridae n. sp., Mesomyzostoma lanterbecqae n. sp., Hypomyzostoma jasoni n. sp., Hypomyzostoma jonathoni n. sp., Myzostoma debiae n. sp., Myzostoma eeckhauti n. sp., Myzostoma hollandi n. sp., Myzostoma indocuniculus n. sp., Myzostoma josefinae n. sp., Myzostoma kymae n. sp., Myzostoma laurenae n. sp., Myzostoma miki n. sp., Myzostoma pipkini n. sp., Myzostoma susanae n. sp., Myzostoma tertiusi n. sp., Protomyzostomum lingua n. sp., Protomyzostomum roseus n. sp., Pulvinomyzostomum inaki n. sp., and Pulvinomyzostomum messingi n. sp..

Background Myzostomids are marine annelids, nearly all of which live symbiotically on or inside echinoderms, chiefly crinoids, and to a lesser extent asteroids and ophiuroids. These symbionts possess a variety of adult body plans and lifestyles. Most described species live freely on the exterior of their hosts as adults (though starting life on the host inside cysts), while other taxa permanently reside in galls, cysts, or within the host’s mouth, digestive system, coelom, or gonads. Myzostomid lifestyles range from stealing incoming food from the host’s food grooves to consuming the host’s tissue directly. Previous molecular studies of myzostomids have had limited sampling with respect to assessing the evolutionary relationships within the group; therefore molecular data from 75 myzostomid taxa were analyzed using maximum likelihood and maximum parsimony methods. To compare relationships of myzostomids with their hosts, a phylogeny was inferred for 53 hosts and a tanglegram constructed with 88 associations. Results Gall- and some cyst-dwellers were recovered as a clade, while cyst-to-free-living forms were found as a grade including two clades of internal host-eaters (one infecting crinoids and the other asteroids and ophiuroids), mouth/digestive system inhabitants, and other cyst-dwellers. Clades of myzostomids were recovered that associated with asteroids, ophiuroids, and stalked or feather star crinoids. Co-phylogenetic analyses rejected a null-hypothesis of random associations at the global level, but not for individual associations. Event-based analyses relied most upon host-switching and duplication events to reconcile the association history. Conclusion Hypotheses were revised concerning the systematics and evolution of Myzostomida, as well their relationships to their hosts. We found two or three transitions between food-stealing and host-eating. Taxa that dwell within the mouth or digestive system and some cyst forms are arguably derived from cyst-to-free-living ancestors – possibly the result of a free-living form moving to the mouth and paedomorphic retention of the juvenile cyst. Phylogenetic conservatism in host use was observed among related myzostomid taxa. This finding suggests that myzostomids (which have a free-living planktonic stage) are limited to one or a few closely related hosts, despite most hosts co-occurring on the same reefs, many within physical contact of each other. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0170-7) contains supplementary material, which is available to authorized users.

Comatulidae Fleming, 1828 (previously, and incorrectly, Comasteridae A.H. Clark, 1908a), is a group of feather star crinoids currently divided into four accepted subfamilies, 21 genera and approximately 95 nominal species. Comatulidae is the most commonly-encountered and species-rich crinoid group on shallow tropical coral reefs, particularly in the Indo-western Pacific region (IWP). We conducted a molecular phylogenetic analysis of the group with concatenated data from up to seven genes for 43 nominal species spanning 17 genera and all subfamilies. Basal nodes returned low support, but maximum likelihood, maximum parsimony, and Bayesian analyses were largely congruent, permitting an evaluation of current taxonomy and analysis of morphological character transformations. Two of the four current subfamilies were paraphyletic, whereas 15 of the 17 included genera returned as monophyletic. We provide a new classification with two subfamilies, Comatulinae and Comatellinae n. subfamily Summers, Messing, & Rouse, the former containing five tribes. We revised membership of analyzed genera to make them all clades and erected Anneissia n. gen. Summers, Messing, & Rouse. Transformation analyses for morphological features generally used in feather star classification (e.g., ray branching patterns, articulations) and those specifically for Comatulidae (e.g., comb pinnule form, mouth placement) were labile with considerable homoplasy. These traditional characters, in combination, allow for generic diagnoses, but in most cases we did not recover apomorphies for subfamilies, tribes, and genera. New morphological characters that will be informative for crinoid taxonomy and identification are still needed. DNA sequence data currently provides the most reliable method of identification to the species-level for many taxa of Comatulidae.

We report the presence of Mesorhizobium, a genus best known for its nitrogen-fixing symbiosis with terrestrial legumes, associated with the marine polychaete Meganerilla bactericola (Annelida: Nerillidae). Abundant epibionts were previously described as coating the exterior of M. bactericola, which is found within the anoxic sulfide-oxidizing microbial mats of the Santa Barbara Basin, California, USA. 16S rRNA investigation of the bacterial community associated with this polychaete discovered the presence of bacteria belonging to Mesorhizobium. We identified these bacteria using phylogenetic analyses of 16S rRNA and three additional functional genes, nifH, atpD and recA, and group-specific fluorescence in situ hybridization (FISH).

An efficient protocol to identify and describe species of Myzostomida is outlined and demonstrated. This taxonomic approach relies on careful identification (facilitated by an included comprehensive table of available names with relevant geographical and host information) and concise descriptions combined with DNA sequencing, live photography, and accurate host identification. Twenty-one new species are described following these guidelines: Asteromyzostomum grygieri n. sp., Endomyzostoma scotia n. sp., Endomyzostoma neridae n. sp., Mesomyzostoma lanterbecqae n. sp., Hypomyzostoma jasoni n. sp., Hypomyzostoma jonathoni n. sp., Myzostoma debiae n. sp., Myzostoma eeckhauti n. sp., Myzostoma hollandi n. sp., Myzostoma indocuniculus n. sp., Myzostoma josefinae n. sp., Myzostoma kymae n. sp., Myzostoma laurenae n. sp., Myzostoma miki n. sp., Myzostoma pipkini n. sp., Myzostoma susanae n. sp., Myzostoma tertiusi n. sp., Protomyzostomum lingua n. sp., Protomyzostomum roseus n. sp., Pulvinomyzostomum inaki n. sp., and Pulvinomyzostomum messingi n. sp..