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Abstract Background Coral reefs are rapidly changing in response to local and global stressors. Research to better understand and inform the management of these stressors is burgeoning. However, in situ studies of coral reef ecology are constrained by complex logistics and limited resources. Many reef studies are also hampered by the scale-dependent nature of ecological patterns, and inferences made on causal relationships within coral reef systems are limited by the scales of observation. This is because most socio-ecological studies are conducted at scales relevant to the phenomenon of interest. However, management often occurs across a significantly broader, often geopolitical, range of scales. While there is a critical need for incisive coral reef management actions at relevant spatial and temporal scales, it remains unclear to what extent the scales of empirical study overlap with the scales at which management inferences and recommendations are made. This systematic map protocol will evaluate this potential scale mismatch with the goal of raising awareness about the significance of effectively addressing and reporting the scales at which researchers collect data and make assumptions. Methods We will use the Collaboration for Environmental Evidence (CEE) systematic mapping guidelines to identify relevant studies using a framework-based synthesis to summarise the spatial and temporal scales of coral reef fish ecology research and the scales at which management inferences or recommendations are made. Using tested predefined terms, we will search for relevant published academic and grey literature, including bibliographic databases, web-based search engines, and organisational websites. Inclusion criteria for the evidence map are empirical studies that focus on coral reef fish ecological organisation and processes, those informing management interventions and policy decisions, and management documents that cite coral reef research for management decision-making. Study results will be displayed graphically using data matrices and heat maps. This is the first attempt to systematically assess and compare the scales of socio-ecological research conducted on coral reef systems with their management.

Abstract An exceptionally large, hermatypic colony of Porites sp. has been identified and measured at Ta’u, American Samoa. This coral was measured in November 2019 as part of an effort to catalogue all large (≥ 2 m diameter) Porites colonies around Ta’u. Colonies exceeding 10 m in diameter were recorded on three different sides of the island with seasonally different wave exposures. The largest colony measured 8 m tall, 69 m in circumference and had a diameter of 22.4 m. To date, this is the biggest colony recorded in American Samoa, and one of the largest documented worldwide. It is currently unknown why such large corals exist around this particular island. Possible explanations include mild wave or atmospheric climates and minimal anthropogenic impacts. Physiologically, these colonies may be resistant and/or resilient to disturbances. Large, intact corals can help build past (century-scale) climatic profiles, and better understand coral persistence, particularly as coral communities worldwide are declining at rapid rates.

Monophyly, origin and systematics of the subfamily Chloridoideae have long been debated. We present evidence from the plastid matK gene sequences of 74 species representing 55 genera and all tribes, and from extensive outgroup survey to address these questions. The monophyly of the Chloridoideae and its origin from an arundinoid group with C4 photosynthesis are unequivocally ascertained by this study. Rooted with the arundinoid Centropodia, a basal polytomy was observed among Triraphis schlecteri and three strongly supported clades labeled A, B, and C. Clade A comprises the Pappophoreae, Uniolinae, and three Eragrostideae genera; clade B includes most representatives of subtribe Sporobolinae, Spartina, Zoysia, and some Eragrostis; and clade C encompasses the remaining taxa. The two largest tribes Eragrostideae and Chloridoideae are polyphyletic. Uniolinae, Orcuttieae and Triodiinae form strongly supported monophyletic entities. The taxonomic status of other tribes is discussed. Two large genera, Chloris and Eragrostis, do not appear monophyletic. A repeated pattern of segregation of Old World from New World taxa is evident. The results provide a framework for further detailed studies at the tribal and generic levels to reach a comprehensive systematic treatment of the Chloridoideae.

We analyzed DNA sequences of the plastid gene matK to infer phylogenetic relationships among angiosperms. Our sample includes seven monocot families (Anthericaceae, Asparagaceae, Convallariaceae, Joinvilleaceae, Poaceae, Restionaceae, and Trilliaceae) and 19 dicot families (Amborellaceae, Anthospermataceae, Brassicaceae, Calycanthaceae, Ericaceae, Fabaceae, Hamamelidaceae, Hernandiaceae, Illiciaceae, Lauraceae, Loganiaceae, Magnoliaceae, Monimiaceae, Nymphaeaceae, Paeoniaceae, Rosaceae, Rubiaceae, Saxifragaceae, and Scrophulariaceae). The tree is rooted with three families of conifers (Pinaceae, Cupressaceae, and Taxaceae) plus Gnetum (Gnetaceae). Including all species (AmboreIla and lllicium are missing the 5' one-third of the gene), the angiosperms are strongly supported as monophyletic. The base is a polytomy of six lineages: Amborella, Illicium, monocots, Nymphaeales, magnoliids, and tricolpates. Magnoliaceae are sister to all other members of the Magnoliid complex sampled. Saxifragales species form a clade with the rosids that is sister to the asterid clade. When Amborella and Illicium are excluded from the analysis, a single most parsimonious tree is recovered with a CI of 0.47 and an RI of 0.70 excluding uninformative characters. This tree shows Nymphaeales (bootstrap of 100%) as sister to the other angiosperms; the latter are divided into two large clades with the magnoliids (99%) sister to the tricolpates (97%). Additionally, the Nymphaeales are supported by a 12-bp insertion, the monocots by a different 12-bp insertion, and the tricolpates by a 9-bp deletion.

We used DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast gene matK to examine generic circumscriptions and infer phylogenetic relationships of the grass genus Chloris (Chloridinae: Chlorideae: Chloridoideae) and several related taxa. Our ITS and mark data sets include 36 and 29 species, respectively, and represent at least 13 genera plus three outgroups from the tribe Eragrostideae. Independent and combined analyses of both data sets firmly suggest that Chloris is polyphyletic and should be redefined. However, a clade containing 7-11 Chloris species, Enteropogon dolichostachys, and Lintonia nutans is strongly supported by bootstrap values of 99%. Thus, it appears that Lintonia nutans of subtribe Pommereullinae and Enteropogon dolichostachys should be included in Chloris. Species treated either as a separate genus (Eustachys) or as a subgenus of Chloris (except for C. retusa) form a monophyletic group that is distinct from Chloris and weakly associated with a clade comprising Cynodon + Brachyachne. The relationships among Eustachys, Cynodon-Brachyachne, and Chloris are not clear based on either data set alone or the combined analysis due to an internal polytomy. Additional taxa that have been treated in Chloris and as separate genera, such as Trichloris and Oxychloris, are distinct in these analyses and should be retained. This study forms the phylogenetic foundation for a taxonomic revision of Chloris.

We used DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast trnK intron, including the matK gene, to test monophyly and infer phylogenetic relationships of Rubus and its subgenera. Our ITS and trnK data sets include 17 species representing eight of the 12 Rubus subgenera, Dalibarda repens, and using Fallugia as an outgroup. Separate and combined parsimony analyses suggest that Rubus is paraphyletic because Dalibarda nests within it although bootstrap support is low. A clade including 12 of the species (excluding Dalibarda repens, Rubus pedatus, R. chamaemorus, R. deliciosus, and R. odoratus) is apparent in both the ITS and trnK analyses, and gains strong support (95%) in the combined analysis. This suggests that unarmed and primarily herbaceous, simple-leaved species are ancestral in Rubus. Within the clade of 12 species, several relationships are well supported in both separate and combined analyses. One includes four species of North American blackberries (subgenus Rubus) and another is the relationship between R. crataegifolius of subg. Idaeobatus and R. trifidus of subg. Anoplobatus. These results indicate that subg. Anoplobatus is polyphyletic because R. trifidus is more closely related to R. crataegifolius than to R. odoratus + R. deliciosus which form part of the basal complex in Rubus.

Hybridization has long been considered a source of taxonomic complexity in Rubus, but robust evidence of hybridization is meager. This study is the first to document natural hybridization in Rubus using molecular, morphological, and cytological data. Rubus idaeus (subgenus Idaeobatus, raspberries) is generally considered a sexual diploid (2n = 14), and R. caesius (subgenus Rubus, blackberries) is a tetraploid, facultative agamosperm. Both species are widespread in Europe. Putative hybrids of these two species have been identified morphologically in southern Sweden. We sequenced the nuclear ribosomal DNA internal transcribed spacer region (ITS) for one individual of R. caesius, two individuals of R. idaeus, and five putative hybrids. Rubus caesius differs from Swedish R. idaeus at 20 nucleotide positions and one indel. Four putative hybrids are polymorphic at all 20 sites and the indel, and one is polymorphic at most sites. For one hybrid individual we sequenced two clones and recovered both intact parental ITS sequences. Morphologically the hybrids are intermediate in carpel and leaf pubescence and resemble one of the parents in stipule shape and inflorescence glandularity. Ploidy of the parents has been confirmed in one individual each and the one hybrid plant we have sampled is tetraploid.