bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Influence of Smolt Age on Freshwater and Early Marine Behavior and Survival of Migrating Juvenile Sockeye Salmon
Authors: Stevenson Christine F. , Hinch Scott G. , Porter Aswea D. , Rechisky Erin L. , Welch David W. , Healy Stephen J. , Lotto Andrew G. , Furey Nathan B. 
Published: February 2019

AbstractSockeye Salmon Oncorhynchus nerka smolts typically experience high mortality during out‐migration through freshwater and the early marine environment. Due to tag burden (tag mass relative to fish mass) constraints, telemetry studies investigating migration survival have focused on tracking hatchery smolts or larger individuals within wild populations. However, hatchery and larger wild smolts may not represent the majority of migrants. We used miniaturized acoustic transmitters (VEMCO V4) to track age‐1 Sockeye Salmon smolts (n = 200) for the first time over approximately 950 km from Chilko Lake, British Columbia, Canada, through the coastal environment by using large‐scale receiver arrays. We compared their survival with that of concomitantly tracked age‐2 smolts (n = 100) by using VEMCO V7 acoustic transmitters. Freshwater survival of tagged age‐1 smolts was double the age‐2 survival (56% versus 28%), potentially due to higher proportional tag burdens on age‐2 smolts. Age‐1 smolt cumulative survival was 16% to the last array capable of detecting age‐1 smolts (944 km from release) and was within the range of cumulative survival reported for age‐2 Chilko Lake Sockeye Salmon smolts in previous telemetry studies. Age‐2 smolt minimum cumulative survival to the final arrays (944 and 1,041 km) was about 2% and was lower than survival in previous years. Although survival differed between age‐classes in 2016, both experienced similar trends in landscape‐specific survival relative to age‐2 smolts tracked in previous years. Survival was particularly low in the upper Fraser River tributaries for age‐1 and age‐2 smolts (76% and 53%, respectively, over 13 km from release) and after ocean entry for age‐1 smolts (36% over 217 km). Migration rates of both age‐classes among landscapes were within the range observed for age‐2 smolts in earlier studies. Our study highlights the importance of expanding research to include smaller age‐1 smolts and provides survival estimates for an indicator population of Fraser River Sockeye Salmon.
Consolida and Aconitella are an annual clade of Delphinium (Ranunculaceae) that diversified in the Mediterranean basin and the Irano‐Turanian region
Authors: Jabbour Florian , Renner Susanne S. 
Published: February 2019

AbstractThe Mediterranean and Irano‐Turanian biogeographic regions are biodiversity hotspots for mesophytic and xerophytic species, including many Delphinieae. This phylogenetically poorly understood tribe of Ranunculaceae consists of Consolida and Aconitella, with together ca. 52 species, and Delphinium and Aconitum, each with ca. 300 species. To infer the phylogeny of Consolida and Aconitella, we analyzed nuclear and chloroplast DNA sequences from 39 of their species and subspecies (44 taxa) plus a set of 30 exemplar species of Delphinium and Aconitum. We used a Bayesian relaxed clock model to estimate divergence times and a maximum likelihood approach to reconstruct ancestral areas. Aconitella forms a clade embedded in Consolida, and the latter is embedded in Delphinium. Consolida s.l. (including Aconitella) comprises two clades in the Irano‐ Turanian region and three in the Mediterranean basin. The latter clades’ inferred crown ages of 5.1, 4.4, and 2.8 Ma suggests that the repeated drying‐up of the Mediterranean, concomitant with and following the Messinian salinity crisis (5.96–5.33 Ma), may have facilitated their westward expansion. While there is clear geographic structure towards the tips of the Consolida s.l. tree, a likely ancestral area could not be inferred. However, the initial diversification of Consolida s.l., which occurred ca. 17 Ma ago, falls in a period when the climate in the Anatolian region became more arid, which may have favoured the annual life cycle that characterizes all species in this clade. To achieve a classification of mutually monophyletic genera in Delphinieae may require transferring the species of Aconitella and Consolida into Delphinium.
Molecular phylogeny of the Neotropical sections of Bulbophyllum (Orchidaceae) using nuclear and plastid spacers
Authors: Smidt Eric C. , Borba Eduardo L. , Gravendeel Barbara , Fischer Gunter A. , van den Berg Cássio 
Published: February 2019

AbstractThe systematic utility of sequences from two non‐coding regions of plastid DNA, psbA‐trnH and trnS‐trnG, and one nuclear region, nrITS, was examined in an assessment of phylogenetic relationships among Neotropical sections of Bulbophyllum Thouars (Orchidaceae, Epidendroideae, Dendrobieae). The nrITS region was 6 to 7 times more variable than the two cpDNA regions. No major incongruencies between the nuclear and cpDNA datasets were detected. The combined analysis revealed a well‐resolved phylogeny at sectional level based on both maximum parsimony and Bayesian approaches. Six sections of Bulbophyllum are recognized for the Neotropics. Five of these were pre‐existent but needed to be recircumscribed and one is proposed as new. We did not find disagreements between maximum parsimony and Bayesian analyses, but the latter showed better resolved relationships between the sections, which are supported by morphological features. Of the two main clades of Neotropical Bulbophyllum species, one has two lineages and occurs predominantly north of the Equator. The second contains four lineages which are highly diverse in southeastern Brazil. Our results suggest a single colonization event in the Neotropics, from Africa to northern South America, followed by dispersion through the Andes to southeastern Brazil.
Phylogeny of the "Ifloga clade" (Asteraceae, Gnaphalieae), a lineage occurring disjointly in the Northern and Southern Hemisphere, and inclusion of Trichogyne in synonymy with Ifloga
Authors: Bergh Nicola G. , Trisos Christopher H. , Verboom George A. 
Published: February 2019

AbstractIfloga and Trichogyne constitute a small but biologically interesting lineage within the tribe Gnaphalieae (Asteraceae). Species are distributed mainly in the semi‐arid parts of southern Africa, but there is a disjunction to the Saharo‐Sindian region where three species occur. Due partly to an unusual capitulum structure, the phylogenetic position of the group has been little understood. In addition, the monophyly of the genera has not been assessed using phylogenetic methods. A species‐level phylogenetic hypothesis is presented, based on one nuclear and two chloroplast DNA regions, analysed with parsimony and Bayesian methods. Ifloga + Trichogyne constitute the “Ifloga clade” that forms one of the early‐diverging lineages within Gnaphalieae. These lineages constitute a basal grade with many poorly supported nodes, precluding robust hypotheses of relationships amongst the lineages. A sister lineage to the Ifloga clade could thus not be identified, although it diverges amongst taxa formerly united in subtribe Relhaniinae. Although this subtribe is now known to be non‐monophyletic, members of the Ifloga clade share with former members of Relhaniinae a previously overlooked set of leaf characters. The genus Trichogyne is monophyletic, but Ifloga is paraphyletic with respect to Trichogyne. To retain generic monophyly, all species are here transferred to the genus Ifloga. Although two of the Northern‐Hemisphere species were not included in the analysis, morphological characters suggest that the three species from this region are monophyletic, in which case the Saharo‐Sindian distribution is the result of a single dispersal northwards from Southern Africa. A new combination and an updated key to the species are presented.
Smilax ligneoriparia sp. nov.: A link between herbaceous and woody Smilax (Smilacaceae) based on morphology, karyotype and molecular phylogenetic data
Authors: Li Pan , Qi Zhechen , Chen Shichao , Cameron Kenneth M. , Fu Chengxin 
Published: February 2019

AbstractA population of Smilax found in southeastern Yunnan was originally considered to be a local race of S. riparia with unusual woody, perennial stems, but its status as a distinct species is supported here by morphology, karyology, and molecular phylogenetics. This new species, Smilax ligneoriparia C.X. Fu & P. Li, shares several unique morphological characteristics with S. riparia, such as ovate herbaceous leaves and smooth stem lacking prickles, but its stem is "woody" and its chromosome number is 2n = 32, unlike that of S. riparia (2n = 30). Molecular phylogenetic analysis also confirms that it is distinct, but tentatively supports the position of this new taxon as sister to a clade of woody Asian species, which in turn is sister to the herbaceous, annually emergent Smilax clade. Herbarium specimens show that S. ligneoriparia has been collected in at least three locations in southeastern Yunnan and southern Zhejiang Provinces, but we suspect that the population from Xichou, occurring on limestone mountain slopes at 1550–1600 m, may be the only extant population.
Names of Chinese seed plants validly published in A Catalogue of Type Specimens (Cormophyta) in the Herbaria of China and its two supplements
Authors: Yu Wen-Bin , Wang Hong , Li De-Zhu 
Published: February 2019

AbstractAt least 41 names of Chinese seed plants from 17 families were not validly published in their original publications because the type was not indicated in accordance with one or more of the requirements of Art. 37. They are validated in A Catalogue of Type Specimens (Cormophyta) in the Herbaria of China and its two supplements edited by Shu‐Ying Jin and Yi‐Lin Chen (1994, 1999, 2007). However, most of botanists were presumably unaware of these validations. As it is necessary to know this information when using these names in subsequent publications, the correct citation of the 41 names is provided here.
Report of the Nomenclature Committee for Fungi: 18
Authors: Norvell Lorelei L. 
Published: February 2019

AbstractThe following specific names are recommended for conservation: Olivea tectonae (T.S. Ramakr. & K. Ramakr.) R.L. Mulder against O. tectonae (Racib.) Thirum.; Craterellus cinereus (Pers. : Fr.) Donk with a conserved type against Craterellus cinereus Pers.; Botrytis brongniartii Sacc. with a conserved type; Buellia subcanescens against B. leptina, Lichen flavicans Sw. against Lichen flavicans Lam.; and it is recommended that Cortinarius speciosissimus not be conserved against C. rubellus. Conservation of Boletus applanatus against B. lipsiense, reconsidered in light of a published rebuttal, remains strongly recommended. The withdrawn proposal to conserve the name Aspicilia farinosa with a conserved type is removed from further consideration. In light of an even split on three ballots, the proposal to conserve Agaricus rachodes with that spelling is referred to the General Committee for a final decision. Finally, the Committee notes the need for the correction of "Lecidea euphorea (Flörke) Nyl.", nom. cons. (1858) to L. euphorea (Flörke) Sommerf. (1826) to reflect an earlier combination.
Micromitriaceae: A new family of highly reduced mosses
Authors: Goffinet Bernard , Budke Jessica M. , Newman Leah C. 
Published: February 2019

AbstractMorphological complexity tends to increase at a macroevolutionary scale among land plants, but reversals or loss of previously acquired complex traits occurs across various lineages and in particular in bryophytes. In mosses reduction may pertain to the leafy gametophyte and the architecture of the sporophyte, and is often considered linked to shifts in habitats. Reduction in morphological complexity may obscure the phylogenetic affinities of the taxa, in particular when multiple derived characters are lost. Ephemeraceae comprise two genera, Ephemerum and Micromitrium, growing typically on disturbed, seasonally moist soils. The hypothesis of a shared ancestry of these genera is drawn from the similarities in their highly reduced morphologies: their ephemeral gametophytes are tiny, bearing few leaves composed of typically smooth cells, and their capsules lack a differentiated lid and are nearly sessile. The family was historically included in Funariidae, but recent phylogenetic inferences revealed that Ephemeraceae likely arose within Dicranidae and may be of polyphyletic origin. Phylogenetic inferences based on eight loci confirm that both genera belong to Dicranidae, and reconstructions of the familial relationships within this subclass corroborate the independent origins of the ephemeral life history and associated character losses, with Ephemerum diverging from a pottiaceous ancestor and Micromitrium sharing a unique common ancestor with Leucobryaceae (Dicranales). Micromitrium is thus excluded from Ephemeraceae and accommodated within its own newly described family, Micromitriaceae. This study strengthens the hypothesis that homoplasy is recurrent throughout the evolutionary history of bryophytes and that phylogenetic inferences from DNA sequences are essential to test the systematic concepts based on morphological characters, and particularly in cases of taxa with the most simple architectures and life histories.
Evidence for radiations of cheilanthoid ferns in the Greater Cape Floristic Region
Authors: Eiserhardt Wolf L. , Rohwer Jens G. , Russell Stephen J. , Yesilyurt Jovita C. , Schneider Harald 
Published: February 2019

AbstractThe Greater Cape Floristic Region (GCFR) of southern Africa is characterised by large, endemic radiations of flowering plants, the so‐called 'Cape Clades', but it is unknown whether such radiations are also found in non‐angiosperms. We hypothesise that GCFR‐endemic lineages exist in the xeric adapted cheilanthoid ferns. To test this hypothesis with special emphasis on the alternative hypothesis of frequent colonization, the phylogenetic relations, divergence times, and ancestral areas of the cheilanthoid ferns of the GCFR and adjacent regions are investigated. The dataset includes 22 cheilanthoid fern species occurring in the GCFR. With two exceptions, all GCFR‐endemics are part of two clades that diversified in the Afro‐Madagascan region. The GCFR‐endemics are further concentrated in three high‐endemism subclades that did not originate simultaneously, but within the timeframe of angiosperm Cape Clades diversification. According to ancestral area reconstructions the ancestors of the two larger Afro‐Madagascan clades were likely GCFR‐endemic, and a substantial part of the diversification history of these clades took place in the GCFR. The high diversity of cheilanthoids in the GCFR appears to stem primarily from in situ diversification, not from immigration. This pattern resembles the numerous radiations of angiosperm clades in the GCFR, and may be caused by the same factors. We did not find evidence for rapid, synchronised radiations as documented for some, albeit not all, angiosperm Cape Clades. High diversification within and dispersal out of the GCFR has likely enriched cheilanthoid diversity in the Afro‐Madagascan region.
Molecular systematics and incongruent gene trees of Urophylleae (Rubiaceae)
Authors: Smedmark Jenny E.E. , Bremer Birgitta 
Published: February 2019

AbstractThe phylogeny of the Pantropical tribe Urophylleae is poorly understood. Earlier phylogenetic work has identified major evolutionary lineages within the group, each geographically restricted to a single continent, but relationships among taxa within these lineages are so far largely unresolved. This study uses parsimony and Bayesian phylogenetic analyses of chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) to resolve phylogenetic relationships within Urophylleae. The results show that there are conflicts between cpDNA and nrDNA regarding species‐level relationships within Pauridiantha, Urophyllum, and Amphidasya, which provides evidence of a complex genetic history. Different types of tests are used to explore the magnitude of the incongruence and locate the exact nodes in the two gene trees that are in conflict. This approach makes it possible to use the topology from the combined analysis, despite the separate datasets being strongly incongruent, since areas of the tree that are free from conflict can be identified. Based on the results presented in this study, Urophylleae is indicated to consist of Temnopteryx, Raritebe, Amphidasya, Urophyllum s.l., Pauridiantha s.l., and Pentaloncha. Several genera are shown to be nested inside Pauridiantha, two of which have already been included in Pauridiantha based on other data (Pamplethantha, Commitheca), and two which are included in this genus here (Poecilocalyx, Stelechantha). Likewise, three genera are shown to be ingroups in Urophyllum (Pravinaria, Maschalocorymbus, Pleiocarpidia), and are therefore subsumed under this genus. New combinations under Pauridiantha are proposed for three species in Poecilocalyx and three species in Stelechantha, as well as new combinations under Urophyllum for two species in Pravinaria and 17 species in Pleiocarpidia. For one of the latter species a new name is presented to avoid homonymy.
Phylogenetic affinities ofPolyalthiaspecies (Annonaceae) with columellar‐sulcate pollen: Enlarging the Madagascan endemic genusFenerivia
Authors: Saunders Richard M.K. , Su Yvonne C.F. , Xue Bine 
Published: February 2019

AbstractThe genusPolyalthia(Annonaceae) has been demonstrated to be polyphyletic, with the Asian species with columellar‐sulcate pollen recently segregated to form a new genus,Maasia. The phylogenetic affinities of the otherPolyalthiaspecies with columellar‐sulcate pollen, which occur in Madagascar, are investigated using maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses of three chloroplast DNA markers (trnL‐F, matK, rbcL). The species are shown to form a well‐supported clade which warrants taxonomic recognition as a distinct genus. The nameFeneriviais adopted, considerably expanding the application of this formerly monotypic name, with nine new nomenclatural combinations validated. The genus is hypothesised to have undergone a homeotic mutation in which the outermost whorl of stamens develop as inner petals (presumed andropetals), and the calyx is reduced to a vestigial flange.
Next–generation sequencing and systematics: What can a billion base pairs of DNA sequence data do for you?
Authors: Harrison Nicola , Kidner Catherine Anne 
Published: February 2019

AbstractThe increasing speed and decreasing cost of generating DNA sequence data has transformed experimental approaches in many fields of biology. In this review we describe some of the new technologies commercially available and in development, and discuss how plant taxonomy could benefit from the possible data generated. These benefits include better resolved phylogenies, potential for dealing with the difficulties posed by polyploidy and hybridisation, and new options for studying species boundaries and species relationships in recent radiations.
Incongruence among morphological species circumscriptions and two molecular datasets in Sarmentypnum (Bryophyta: Calliergonaceae)
Authors: Hedenäs Lars 
Published: February 2019

AbstractRelationships among species in Sarmentypnum, and Warnstorfia, are investigated based on the nuclear ITS and the chloroplast markers trnL–trnF, rpl16, and tRNA–Gly of up to 237 specimens. Six specimens in which morphology agrees with ITS sequences have chloroplast markers belonging to other species, whereas in two specimens morphology agrees with the chloroplast markers but have ITS sequences belonging to other species. Although hybridization has been recorded in Sarmentypnum, such incongruence could also be a result of other processes, including rapid morphological differentiation and incomplete lineage sorting. ITS and the chloroplast markers partly agree with the morphological species, although some of the latter appear to be polyphyletic or paraphyletic. Sarmentypnum exannulatum consists of two to three haplotype groups that are connected to S. sarmentosum, but not with each other. Sarmentypnum sarmentosum haplotypes are connected with haplotypes of most other species and may have played a central role in the genus' diversification. The trnL–trnF spacer inversion shows patterns congruent with other chloroplast information; it is therefore clearly informative. The incongruence among mainly non–coding molecular datasets and partial disagreement with morphological species could possibly be attributable to the special history of the boreal to arctic environments where Sarmentypnum is predominantly found. The species must be young in terms of number of generations and have experienced large–scale climatic oscillations during the Pleistocene. Incomplete lineage sorting in combination with rapid morphological evolution that is not reflected in the non–coding markers and an unknown frequency of hybridization most likely explains the observed incongruence.
Phylogeny of Polygoneae (Polygonaceae: Polygonoideae)
Authors: Schuster Tanja M. , Reveal James L. , Kron Kathleen A. 
Published: February 2019

AbstractGenera included in Polygoneae such as Atraphaxis, Duma, Fallopia, Muehlenbeckia, Polygonella, Polygonum, Oxygonum, and Reynoutria are investigated using a molecular framework. Previous morphological studies had indicated that Polygonum is composed of sections Duravia, Polygonum, and Pseudomollia with the genus Polygonella included as a subsection of Polygonum sect. Duravia. One nuclear (nrITS) and three chloroplast (matK, ndhF, trnL–trnF) regions were analyzed with Maximum Parsimony and Maximum Likelihood methods to address evolutionary relationships within the tribe. The results show that Polygoneae is composed of three main clades: Knorringia as sister to all other taxa within Polygoneae, a clade of Reynoutria and Fallopia+Muehlenbeckia, and their sister clade of Atraphaxis, Duma, and Polygonum. The currently accepted sections within Polygonum are recovered and Polygonum sect. Duravia is sister to sections Polygonum and Pseudomollia. With Polygonella included in Polygonum, the appropriate new combinations and names are proposed. In addition, a few species of Polygonum are transferred to Atraphaxis. Oxygonum is not supported as a member of Polygoneae and its exact position awaits additional data.
Phylogenetics of Piptatherum s.l. (Poaceae: Stipeae): Evidence for a new genus, Piptatheropsis, and resurrection of Patis
Authors: Romaschenko Konstantin , Peterson Paul M. , Soreng Robert J. , Futorna Oksana , Susanna Alfonso 
Published: February 2019

AbstractHistorically, there has been taxonomic confusion among agrostologists regarding the short–spikeleted Stipeae. We refer to these as the Oryzopsis/Piptatherum complex which consists of short–spikeleted species with coriaceous to cartilaginous and often caducous–awned lemmas, and florets with a blunt callus. We conducted a phylogenetic analysis of 53 species that have been associated with this complex using four plastid regions (ndhF, rpl32–trnL, rps16–trnK, rps16 intron) in combination with lemma micromorphology to infer evolutionary relationships. Piptatherum as currently circumscribed is polyphyletic and is found in five strongly supported clades in our maximum likelihood tree. Based on our phylogenetic and morphological evidence we recognize a Eurasian Piptatherum s.str., propose a new genus, Piptatheropsis, to include five North American species, and resurrect the genus Patis to include three species, two from Eurasia and one from North America. We provide morphological descriptions of Patis, Piptatherum, and Piptatheropsis, and provide keys to the genera and species of the Oryzopsis/Piptatherum complex. The following new combinations are made: Patis obtusa, Patis racemosa, Piptatheropsis canadensis, Piptatheropsis exigua, Piptatheropsis micrantha, Piptatheropsis pungens, Piptatheropsis shoshoneana, Piptatherum brachycladum, and Piptatherum kopetdagense.