scholarly journals Using community phylogenetics to assess phylogenetic structure in the Fitzcarrald region of Western Amazonia

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Jack M. Craig ◽  
Tiago P. Carvalho ◽  
Prosanta Chakrabarty ◽  
Valerie Derouen ◽  
Hernán Ortega ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Pool ◽  
Community Phylogenetics ◽  
River Channels ◽  
Terra Firme ◽  
Habitat Types ◽  
Phylogenetic Structure ◽  
Random Expectation ◽  
Extensive Collection ◽  
Southwestern Amazonia

ABSTRACT Here we explore the use of community phylogenetics as a tool to document patterns of biodiversity in the Fitzcarrald region, a remote area in Southwestern Amazonia. For these analyses, we subdivide the region into basin-wide assemblages encompassing the headwaters of four Amazonian tributaries (Urubamba, Yuruá, Purús and Las Piedras basins), and habitat types: river channels, terra firme (non-floodplain) streams, and floodplain lakes. We present a robust, well-documented collection of fishes from the region including 272 species collected from 132 field sites over 63 field days and four years, comprising the most extensive collection of fishes from this region to date. We conduct a preliminary community phylogenetic analysis based on this collection and recover results largely statistically indistinguishable from the random expectation, with only a few instances of phylogenetic structure. Based on these results, and of those published in other recent biogeographic studies, we conclude that the Fitzcarrald fish species pool accumulated over a period of several million years, plausibly as a result of dispersal from the larger species pool of Greater Amazonia.

Cladistic analysis of the Early Cambrian olenelloid trilobites

1998 ◽  
Vol 72 (1) ◽  
pp. 59-78 ◽  
Author(s):  
Bruce S. Lieberman
Keyword(s):  
Phylogenetic Analysis ◽  
Cladistic Analysis ◽  
Intraspecific Variability ◽  
Evolutionary Relationships ◽  
Early Cambrian ◽  
New Genera ◽  
Phylogenetic Structure ◽  
Major Clade ◽  
Lateral Margins

A phylogenetic analysis was used to determine evolutionary relationships within the Early Cambrian superfamily Olenelloidea Walcott, 1890. Phylogenetic patterns within the suborder Olenellina Walcott, 1890, which contains the Olenelloidea and the Fallotaspidoidea Hupé, 1953, are also discussed. The Olenelloidea are monophyletic, and synapomorphies uniting them include the condition of the ocular lobes where they intersect the frontal lobe of the glabella, and the condition of the lateral margins of the glabellar lobes. In contrast, taxa formerly assigned to the Fallotaspidoidea are shown to represent a paraphyletic grade of several genera, some more closely related to the Olenelloidea, and some more closely related to the Redlichiina Richter, 1933. Seventy-nine exoskeletal characters were coded for 26 taxa within the Olenellina. These included 22 ingroup Olenelloidea and four outgroup taxa that have traditionally been assigned to the Fallotaspidoidea. When subjected to parsimony analysis these character data yielded a single most parsimonious cladogram that provides an hypothesis of relationship for the generic clades within the superfamily. Two new genera are recognized herein, Fritzolenellus and Lochmanolenellus. It has been argued that genetic flexibility was so great and trilobite morphology was so plastic in the Early Cambrian that suprageneric classification of Early Cambrian trilobites is precluded. Although levels of intraspecific variability may have been slightly higher in the Early Cambrian relative to the mid Paleozoic, based on the extent of polymorphic character codings, it was not so high as to obviate attempts at recovering phylogenetic structure in a major clade of Early Cambrian taxa. In addition, the consistency index recovered by this analysis is not unduly low for a phylogenetic database of this size. The phylogenetic analysis also has bearing on patterns of allometric heterochrony, which have often been held to be significant in Early Cambrian trilobites. The paedomorphic retention of advanced genal spines into the adult probably evolved at least four times. Three of the episodes can be best described as neoteny, the fourth, as progenesis. Finally, based on the phylogeny, it is likely that rates of speciation in trilobites may have been two to three times higher in the Early Cambrian than in the mid Paleozoic.

scholarly journals Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK

2007 ◽  
Vol 57 (2) ◽  
pp. 276-286 ◽  
Author(s):  
Ivo M. Chelo ◽  
Líbia Zé-Zé ◽  
Rogério Tenreiro
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Phylogenetic Structure ◽  
The 16S Rrna Gene ◽  
Combined Data ◽  
Good Agreement

The phylogenetic structure of the Leuconostoc–Oenococcus–Weissella clade was evaluated by comparison of 16S rRNA gene, dnaA, gyrB, rpoC and dnaK sequence analysis. Phylogenies obtained with the different genes were in overall good agreement and a well-supported, almost fully resolved phylogenetic tree was obtained when the combined data were analysed in a Bayesian approach. A rapid basal diversification of the three genera is suggested. Evolutionary rates of the 16S rRNA gene in these genera seem to be different and specifically related to the evolution of this group, revealing the importance of this sequence in the constitution of the present taxonomy, but preventing its straightforward use in phylogenetic inference.

scholarly journals Predicting climate change effects on marine biodiversity: comparison of recent and fossil molluscan death assemblages

2002 ◽  
Vol 82 (5) ◽  
pp. 847-850 ◽  
Author(s):  
R.M. Warwick ◽  
S.M. Turk
Keyword(s):  
Climate Change ◽  
Species Composition ◽  
Sandy Beach ◽  
Species Pool ◽  
Marine Biodiversity ◽  
Taxonomic Distinctness ◽  
Habitat Types ◽  
Late Pliocene ◽  
Climate Change Effects ◽  
Regional Species Pool

The death assemblage of molluscs (gastropods and bivalves) from the sandy beach at Harlyn Bay, north Cornwall is shown to be fully representative of the biodiversity of the regional species pool from all habitat types. The biodiversity measures used are average taxonomic distinctness (Δ+, the average degree to which species in an assemblage are related to each other) and variation in taxonomic distinctness (Λ+, the evenness of the spread of taxa across the taxonomic spectrum). A late Pliocene fossil assemblage of molluscs from St Erth Pits, north Cornwall, UK, is also not significantly different in biodiversity, in these terms, from the present-day regional species pool. The climate in the late Pliocene was similar to the present-day Mediterranean, suggesting that predicted changes in climate, by the end of this century, will not affect molluscan biodiversity, although the species composition will undoubtedly change.

scholarly journals Community phylogenetics require phylogenies reconstructed from plastid genomes

2021 ◽  
Author(s):  
Lu Jin ◽  
Jia-Jia Liu ◽  
Tian-Wen Xiao ◽  
Qiao-Ming Li ◽  
Luxiang Lin ◽  
...  
Keyword(s):  
Functional Traits ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Maximum Height ◽  
Type I ◽  
Community Phylogenetics ◽  
Phylogenetic Structure ◽  
Plastid Genomes ◽  
A Genome ◽  
Genome Tree

Phylogenetic trees have been extensively used in community ecology. However, how the phylogenetic reconstruction affects ecological inferences is poorly understood. In this study, we reconstructed three different types of phylogenetic trees (a synthetic-tree generated using VPhylomaker, a barcode-tree generated using rbcL+matK+trnH-psbA and a genome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the genome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith’s PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the genome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and genome-tree detected phylogenetic signal in maximum height, but only the genome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the outperformance of genome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of Type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

scholarly journals Two New Russula Species (Fungi) from Dry Dipterocarp Forest in Thailand Suggest Niche Specialization to This Habitat Type

2021 ◽  
Author(s):  
Komsit Wisitrassameewong ◽  
Cathrin Manz ◽  
Felix Hampe ◽  
Brian P. Looney ◽  
Thitiya Boonpratuang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Habitat Type ◽  
Habitat Types ◽  
Spore Ornamentation ◽  
Dipterocarp Forest ◽  
Niche Specialization ◽  
Edible Species ◽  
Dipterocarp Forests ◽  
Dry Dipterocarp Forest

Abstract Dry dipterocarp forests are among the most common habitat types in Thailand. Russulaceae are known as common ectomycorrhizal symbionts of Dipterocarpaceae trees in this type of habitat. The present study aims to identify collections of Russula subsection Amoeninae Buyck from dry dipterocarp forests in Thailand. A multi-locus phylogenetic analysis placed Thai Amoeninae collections in two novel lineages, and they are described here as Russula bellissima sp. nov. and R. luteonana sp. nov. The closest identified relatives of both species were sequestrate species suggesting that they may belong to drought-adapted lineages. The analysis of publicly available ITS sequences in R. subsect. Amoeninae did not confirm evidence of any of the new species occurring in other Asian regions, indicating that dry dipterocarp forests might harbor a novel community of ectomycorrhizal fungi. Macromorphological characters are variable and are not totally reliable for distinguishing the new species from other previously described Asian Amoeninae species. Both new species are defined by a combination of differentiated micromorphological characteristics in spore ornamentation, hymenial cystidia and hyphal terminations in the pileipellis. The new Amoeninae species may correspond to some Russula species collected for consumption in Thailand, and the detailed description of the new species can be used for better identification of edible species and food safety in the region.

scholarly journals Phylogenetic structure of local communities predicts the size of the regional species pool

2008 ◽  
Vol 96 (4) ◽  
pp. 709-712 ◽  
Author(s):  
Pille Gerhold ◽  
Meelis Pärtel ◽  
Jaan Liira ◽  
Kristjan Zobel ◽  
Andreas Prinzing
Keyword(s):  
Local Communities ◽  
Species Pool ◽  
Phylogenetic Structure ◽  
Regional Species Pool

scholarly journals Additive effects of connectivity provided by different habitat types drive plant assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Léa Uroy ◽  
Cendrine Mony ◽  
Aude Ernoult
Keyword(s):  
Empirical Studies ◽  
Agricultural Landscapes ◽  
Plant Responses ◽  
Herbaceous Plant ◽  
Habitat Types ◽  
Plant Assemblage ◽  
Dispersal Vectors ◽  
Random Expectation ◽  
Plant Assemblages ◽  
Primary Dispersal

Abstract How connectivity affects plant assemblages is a central issue in landscape ecology. So far, empirical studies have produced contradictory results, possibly because studies: (1) inaccurately assess connectivity by prioritizing the respective effect of the type of habitat on plant assemblages and (2) omit the range of possible plant responses to connectivity depending on dispersal vectors. We focused on three dominant habitat types in agricultural landscapes (woodland, grassland and cropland), and analysed the effect of connectivity on herbaceous plant assemblage similarity for three primary dispersal modes (animal-dispersed, wind-dispersed and unassisted). Using circuit theory, we measured connectivity provided by woodland, grassland and cropland habitats independently. The similarity of plant assemblages was evaluated relative to the random expectation based on the regional pool. Overall, plant assemblage similarity in woodlands and temporary grasslands was dependent on connectivity, but not in wheat croplands. Only animal-dispersed species responded to connectivity. The similarity of animal-dispersed assemblages in woodlands was increased by the connectivity provided by woodland habitats, but was reduced by cropland habitats, whereas in temporary grasslands, similarity was increased by the connectivity provided by cropland habitats. Our results suggest that animal-dispersed species supplement their dispersal pathways, thus improving our knowledge of plant assembly rules in fragmented landscapes.

Tachigali amarumayu (Leguminosae), a new species from terra firme forests of Southwestern Amazonia

Brittonia ◽  
2018 ◽  
Vol 71 (1) ◽  
pp. 39-48 ◽  
Author(s):  
Isau Huamantupa-Chuquimaco ◽  
Haroldo C. De Lima ◽  
Domingos B. O. S. Cardoso ◽  
Raúl Yuca-Rivas ◽  
José Antonio Ochoa ◽  
...  
Keyword(s):  
New Species ◽  
Terra Firme ◽  
Southwestern Amazonia ◽  
A New Species

scholarly journals Re-evaluation of Mycoleptodiscus species and morphologically similar fungi

2019 ◽  
Vol 42 (1) ◽  
pp. 205-227 ◽  
Author(s):  
M. Hernández-Restrepo ◽  
J.D.P. Bezerra ◽  
Y.P. Tan ◽  
N. Wiederhold ◽  
P.W. Crous ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Type Species ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Leaf Spots ◽  
The Usa ◽  
Extensive Collection ◽  
One New Species ◽  
Type Strains

Mycoleptodiscus includes plant pathogens, animal opportunists, saprobic and endophytic fungi. The present study presents the first molecular phylogeny and revision of the genus based on four loci, including ITS, LSU, rpb2, and tef1. An extensive collection of Mycoleptodiscus cultures, including ex-type strains from the CBS, IMI, MUCL, BRIP, clinical isolates from the USA, and fresh isolates from Brazil and Spain, was studied morphologically and phylogenetically to resolve their taxonomy. The study showed that Mycoleptodiscus sensu lato is polyphyletic. Phylogenetic analysis places Mycoleptodiscus in Muyocopronales (Dothideomycetes), together with Arxiella, Leptodiscella, Muyocopron, Neocochlearomyces, and Paramycoleptodiscus. Mycoleptodiscus terrestris, the type species, and M. sphaericus are reduced to synonyms, and one new species is introduced, M. suttonii. Mycoleptodiscus atromaculans, M. coloratus, M. freycinetiae, M. geniculatus, M. indicus, M. lateralis (including M. unilateralis and M. variabilis as its synonyms) and M. taiwanensis belong to Muyocopron (Muyocopronales, Dothideomycetes), and M. affinis, and M. lunatus to Omnidemptus (Magnaporthales, Sordariomycetes). Based on phylogenetic analyses we propose Muyocopron alcornii sp. nov., a fungus associated with leaf spots on Epidendrum sp. (Orchidaceae) in Australia, Muyocopron zamiae sp. nov. associated with leaf spots on Zamia (Zamiaceae) in the USA, and Omnidemptus graminis sp. nov. isolated from a grass (Poaceae) in Spain. Furthermore, Neomycoleptodiscus venezuelense gen. & sp. nov. is introduced for a genus similar to Mycoleptodiscus in Muyocopronaceae.

scholarly journals Strong influence of regional species pools on continent-wide structuring of local communities

2011 ◽  
Vol 279 (1727) ◽  
pp. 266-274 ◽  
Author(s):  
Jean-Philippe Lessard ◽  
Michael K. Borregaard ◽  
James A. Fordyce ◽  
Carsten Rahbek ◽  
Michael D. Weiser ◽  
...  
Keyword(s):  
Community Structure ◽  
Local Communities ◽  
Species Pool ◽  
Ant Communities ◽  
Phylogenetic Structure ◽  
Structure Of Communities ◽  
Species Pools ◽  
Regional Source ◽  
Regional Species Pool ◽  
Definition Of

There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.

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