Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

Inference of higher-order conifer relationships from a multi-locus plastid data setThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 658-669 ◽  
Author(s):  
Hardeep S. Rai ◽  
Patrick A. Reeves ◽  
Rod Peakall ◽  
Richard G. Olmstead ◽  
Sean W. Graham
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Bootstrap Support ◽  
Sister Group Relationship ◽  
Ribosomal Protein Genes ◽  
Conifer Species ◽  
Noncoding Regions ◽  
Selection Of

We reconstructed the broad backbone of conifer phylogeny from a survey of 15–17 plastid loci and associated noncoding regions from exemplar conifer species. Parsimony and likelihood analyses recover the same higher-order relationships, and we find strong support for most of the deep splits in conifer phylogeny, including those within our two most heavily sampled families, Araucariaceae and Cupressaceae. Our findings are broadly congruent with other recent studies, and are inferred with comparable or improved bootstrap support. The deepest phylogenetic split in conifers is inferred to be between Pinaceae and all other conifers (Cupressophyta). Our current gene and taxon sampling does not support a relationship between Pinaceae and Gnetales, observed in some published studies. Within the Cupressophyta clade, we infer well-supported relationships among Cephalotaxaceae, Cupressaceae, Sciadopityaceae, and Taxaceae. Our data support recent moves to recognize Cephalotaxus under Taxaceae, and we find strong support for a sister-group relationship between the two predominantly southern hemisphere conifer families, Araucariaceae and Podocarpaceae. A local hotspot of indel evolution shared by the latter two conifer families is identified in the coding portion of one of the plastid ribosomal protein genes. The removal of the most rapidly evolving plastid characters, as defined using a likelihood-based classification of substitution rates for the taxa considered here, is shown to have little to no effect on our inferences of higher-order conifer relationships.

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

2021 ◽  
Vol 46 (1) ◽  
pp. 162-174
Author(s):  
Ming-Hui Yan ◽  
Chun-Yang Li ◽  
Peter W. Fritsch ◽  
Jie Cai ◽  
Heng-Chang Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

Phylogenetic relationships of the African genera Alestes and Brycinus (Teleostei, Characiformes, Alestidae)

2002 ◽  
Vol 80 (11) ◽  
pp. 1887-1899 ◽  
Author(s):  
Alison M Murray ◽  
Kathlyn M Stewart
Keyword(s):  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Monophyletic Group ◽  
The Family ◽  
The Subject

The family Alestidae (also referred to as the African Characidae) comprises the African dwarf forms ("Petersiini") and the genera Alestes, Brycinus, Bryconaethiops, and Hydrocynus. Although several authors have presented characters to support the monophyly of the family, a cladistic analysis of the group has not been published. Furthermore, the interrelationships of the constituent groups are the subject of some controversy. A cladistic analysis of the Alestidae is presented, including characters to support the monophyly of the family. The results of this study indicate that several species should be removed from the genus Brycinus, that Hydrocynus is the sister group of Alestes s.str. (containing only five species), and that the dwarf alestids ("Petersiini") do not form a monophyletic group.

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
Author(s):  
Maria Heikkilä ◽  
Lauri Kaila ◽  
Marko Mutanen ◽  
Carlos Peña ◽  
Niklas Wahlberg
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bayesian Approaches ◽  
The Family ◽  
Family Level ◽  
Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

A new leaf-litter harvestman species of the genus Karos (Opiliones: Stygnopsidae: Karosinae), with a reanalysis of the morphological phylogeny of the genus

Zootaxa ◽  
2018 ◽  
Vol 4378 (4) ◽  
pp. 533 ◽  
Author(s):  
JESÚS A. CRUZ-LÓPEZ
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Leaf Litter ◽  
Endemic Species ◽  
Sister Group ◽  
Likelihood Methods ◽  
The Family ◽  
Maximum Likelihood Methods

Karos Goodnight & Goodnight, 1944 is the most diverse genus of the family Stygnopsidae. It contains seven micro-endemic species from the Huasteca region in eastern Mexico. In this paper, the new species Karos morronei sp. nov. is described based on the morphology of adults of both sexes. The new species is from Zacualtipán de Ángeles, Hidalgo State, which represents the southernmost record for the genus. Additionally, a reanalysis of the previous morphological phylogeny of the genus using both parsimony and maximum likelihood methods is provided. According to the morphological reanalysis, K. morronei sp. nov. exhibits an autapomorphy (males with femur IV thicker than females) and is the sister group of the clade that includes K. barbarikos, K. hexasetosus, K. monjarazi, K. parvus and K. singularis. Finally, information of barcoding (CO1) is provided for this new species. 

scholarly journals Restructuring the Ancorabolidae Sars (Copepoda, Harpacticoida) and Cletodidae T. Scott, with a new phylogenetic hypothesis regarding the relationships of the Laophontoidea T. Scott, Ancorabolidae and Cletodidae

2020 ◽  
Vol 96 (2) ◽  
pp. 455-498
Author(s):  
Kai Horst George
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characteristics ◽  
Sister Group ◽  
Morphological Characters ◽  
Sister Group Relationship ◽  
Phylogenetic Hypothesis ◽  
The Family ◽  
Swimming Leg

Uncovering the systematics of CopepodaHarpacticoida, the second-most abundant component of the meiobenthos after Nematoda, is of major importance for any further research dedicated especially to ecological and biogeographical approaches. Based on the evolution of the podogennontan first swimming leg, a new phylogenetic concept of the Ancorabolidae Sars and Cletodidae T. Scott sensu Por (Copepoda, Harpacticoida) is presented, using morphological characteristics. It confirms the polyphyletic status of the Ancorabolidae and its subfamily Ancorabolinae Sars and the paraphyletic status of the subfamily Laophontodinae Lang. Moreover, it clarifies the phylogenetic relationships of the so far assigned members of the family. An exhaustive phylogenetic analysis was undertaken using 150 morphological characters, resulting in the establishment of a now well-justified monophylum Ancorabolidae. In that context, the Ancorabolus-lineage sensu Conroy-Dalton and Huys is elevated to sub-family rank. Furthermore, the membership of Ancorabolina George in a rearranged monophylum Laophontodinae is confirmed. Conversely, the Ceratonotus-group sensu Conroy-Dalton is transferred from the hitherto Ancorabolinae to the Cletodidae. Within these, the Ceratonotus-group and its hypothesised sister-group Cletodes Brady are combined to form a monophyletic subfamily Cletodinae T. Scott, subfam. nov. Consequently, it was necessary to restructure the Ancorabolidae, Ancorabolinae and Laophontodinae and extend the Cletodidae to include the displacement and exclusion of certain taxa. Moreover, comparison of the Ancorabolidae, Cletodidae, Laophontoidea and other Podogennonta shows that the Ancorabolidae and Cletodidae form sister-groups in a monophylum Cletodoidea Bowman and Abele, which similarly has a sister-group-relationship with the Laophontoidea T. Scott. According to the present study, both taxa constitute a derived monophylum within the Podogennonta Lang.

Phylogenetic relationships among nassariid gastropods

2000 ◽  
Vol 74 (5) ◽  
pp. 839-852 ◽  
Author(s):  
D. M. Haasl
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Sister Group ◽  
Range Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Poor ◽  
The Family ◽  
Stratigraphic Position

Phylogenetic relationships within the neogastropod family Nassariidae are poorly understood as are relationships between the Nassariidae and other fossil and extant buccinid taxa. The poor resolution of nassariid and buccinoidean relationships is due to: 1) the complex distribution among these gastropods of characters commonly used in classification; 2) a number of Mesozoic and Paleogene genera whose relationships to extant buccinoidean lineages are poorly constrained; and 3) a lack of previous efforts to address these problems on a rigorous, phylogenetic basis.The results of a phylogenetic analysis of nassariid genera did not decisively support the monophyly of the family. The buccinid subfamily Photinae was an extant sister group to the Nassariinae in a phylogenetic analysis of extant taxa and on many cladograms from an analysis combining fossil and extant taxa. In addition, Buccitriton (representing the Paleogene Tritiaria group) was a sister taxon to the Nassariinae in all analyses in which it was included, regardless of the identity of the extant nassariine sister group. This suggests that the photines, which likely arose from a Tritiaria ancestor, are the closest living relatives to the Nassariinae. Many Paleogene fossil “buccinoid” taxa appear to be more distantly related to the Nassariinae and possibly to the rest of the nassariids as well. Stratigraphic range data combined with the results of this study suggest that the Nassariinae diversified rapidly in the early Miocene and achieved a cosmopolitan distribution early in their history. A largely Indo-Pacific subclade was consistently deeply-nested within the Nassariinae, suggesting that nassariines invaded the Indo-Pacific region most recently. The timing of this invasion is difficult to estimate but had occurred by the end of the Miocene. Further analyses using molecular sequence data, relative stratigraphic position, or focusing in more detail on the Paleogene taxa are required to resolve the identity of the sister group to the Nassariinae with greater confidence.

New contributions towards the understanding of the phylogenetic relationships among economically important fruit flies (Diptera: Tephritidae)

2006 ◽  
Vol 96 (3) ◽  
pp. 279-288 ◽  
Author(s):  
M.D. Segura ◽  
C. Callejas ◽  
M.P. Fernández ◽  
M.D. Ochando
Keyword(s):  
Phylogenetic Relationships ◽  
Fruit Flies ◽  
Bactrocera Cucurbitae ◽  
Likelihood Methods ◽  
Morphological Classification ◽  
Important Group ◽  
Tephritid Species ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
The Many

AbstractFruit flies (Diptera: Tephritidae) are a species-rich and economically important group. The phylogenetic relationships among the many taxa are still to be fully resolved and the monophyly of several groups is still to be confirmed. This paper reports a study of the phylogenetic relationships among 23 economically important tephritid species (representing several major lineages of the family) which examines the sequence of a region of mitochondrial DNA encompassing the cytb, tRNASer and ND1 genes. Substitutions characteristic of particular taxa were found that could help classify members of the family at any developmental stage. The trees obtained by the maximum parsimony, neighbour joining and maximum likelihood methods were generally compatible with present morphological classification patterns. However, the data reveal some characteristics of the phylogenetic relationships of this family that do not agree with present classifications. The results support the probable non-monophyletic nature of the subfamily Trypetinae and suggest that Bactrocera cucurbitae (Coquillet) is more closely related to the genus Dacus than to other species of Bactrocera.

scholarly journals Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Wanqing Zhao ◽  
Qing Zhao ◽  
Min Li ◽  
Jiufeng Wei ◽  
Xianhong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Rna Structures ◽  
Protein Coding ◽  
Transfer Rnas ◽  
The Family ◽  
Maximum Likelihood Methods

Abstract The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

Species delimitation, phylogenetic relationships, and two new species in the Cuscuta gracillima complex (Convolvulaceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 670-681 ◽  
Author(s):  
Mihai Costea ◽  
Fiona Aiston ◽  
Saša Stefanović
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Species Delimitation ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Conservation Status ◽  
Special Issue ◽  
Dna Sequence Data ◽  
F Region ◽  
Selection Of

Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL–F region and the nuclear internal transcribed spacer (ITS) regions were used to delimit the species of a recently circumscribed clade of Cuscuta (Convolvulaceae) and to investigate their phylogenetic relationships. This clade comprises the Cuscuta gracillima complex from Mexico, Central and northern South America, a group which is characterized by inflorescences that appear to emerge directly from the host stem. Eight lineages are recognized, with two of them described here as new species: Cuscuta punana Costea & Stefanović, sp. nov. from Ecuador and Cuscuta vandevenderi Costea & Stefanović, sp. nov. from Mexico. Cuscuta colombiana Yunck is redefined to include Cuscuta aristeguietae Yunck., and Cuscuta deltoidea Yunck. is broadened to encompass Cuscuta serruloba Yunck. A taxonomic treatment with an identification key, descriptions, and illustrations is provided; the biogeography and conservation status of the eight species are also discussed.

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