Ancient DNA sequences reveal unsuspected phylogenetic relationships within New Zealand wrens (Acanthisittidae)

1994 ◽  
Vol 50 (6) ◽  
pp. 558-563 ◽  
Author(s):  
A. Cooper
Keyword(s):  
New Zealand ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
New Zealand Wrens

scholarly journals A Phylogenetic Investigation of the New Zealand  Pteridaceae Ferns

2021 ◽  
Author(s):  
◽  
Whitney L M Bouma
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Native Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxonomic Confusion ◽  
Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

scholarly journals Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

2015 ◽  
Vol 97 (2) ◽  
pp. 394-404 ◽  
Author(s):  
Juan F. Díaz-Nieto ◽  
Sharon A. Jansa ◽  
Robert S. Voss
Keyword(s):  
Soft Tissue ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Taxon ◽  
Evolutionary Relationships ◽  
Fresh Material

Abstract Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved. Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

scholarly journals A Phylogenetic Investigation of the New Zealand  Pteridaceae Ferns

2021 ◽  
Author(s):  
◽  
Whitney L M Bouma
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Native Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxonomic Confusion ◽  
Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

Reinstatement of Loxogramme dictyopteris, based on phylogenetic evidence, for the New Zealand endemic fern, Anarthropteris lanceolata (Polypodiaceae, Polypodiidae)

2006 ◽  
Vol 19 (4) ◽  
pp. 309 ◽  
Author(s):  
Hans-Peter Kreier ◽  
Harald Schneider
Keyword(s):  
New Zealand ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Morphological Evidence ◽  
Monotypic Genus

Phylogenetic relationships of the New Zealand endemic Anarthropteris lanceolata are inferred from DNA sequences of four chloroplast genome regions, rbcL, rps4, rps4–trnS IGS, and trnL–F IGS. In addition to a broad collection of polygrammoid ferns, the sampling includes two species of the genus Dictymia, five species of the genus Loxogramme, and one sample of the monotypic genus Anarthropteris. The latter is found to be nested within Loxogramme, and we reinstate it here as Loxogramme dictyopteris, to replace Anarthropteris lanceolata. These findings are not in conflict with morphological evidence. Phylogenetic evidence implies an isolation of L. dictyopteris from its closest relatives in Malesia. The five other species of Loxogramme included in this study fall either into an Asiatic-Malesian clade or in an Afro-Madagascan-Neotropical clade.

scholarly journals A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens

2002 ◽  
Vol 269 (1488) ◽  
pp. 235-241 ◽  
Author(s):  
Per G. P. Ericson ◽  
Les Christidis ◽  
Alan Cooper ◽  
Martin Irestedt ◽  
Jennifer Jackson ◽  
...  
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Passerine Birds ◽  
New Zealand Wrens

Description of Tripylella jianjuni sp. n. (Nematoda: Tripylidae) from New Zealand

Nematology ◽  
2018 ◽  
Vol 20 (8) ◽  
pp. 795-810
Author(s):  
Yumei Xu ◽  
Daniel Leduc ◽  
Weimin Ye ◽  
Zengqi Zhao
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Male Tail

Summary Tripylella jianjuni sp. n. (Tripylidae) is described from New Zealand. Females are characterised by a relatively long body (1743 (1675-1860) μm in the female and 1747 (1576-1979) μm in the male), outer labial setae (8-9 μm long) and cephalic setae (4-5 μm long) in a single circle, two large subventral teeth in two adjacent stomatal chambers, relatively short pharynx (b = 5.5 (5.4-5.6) in the female and 5.7 (5.3-6.1) in the male), vulva located slightly anterior to mid-body (V = 44 (43-46)), protuberant lips, and long filiform tail (461 (398-531) μm, c = 3.8 (3.3-4.2) and c′ = 23.2 (18-29) in the female, and 450 (362-511) μm, c = 3.9 (3.6-4.4) and c′ = 19.0 (16.0-20.8) in the male), tail with three ventromedian caudal setae. Males have arcuate spicules 37 (35-41) μm long, gubernaculum straight, 14 (12-16) μm long, three ventromedian supplementary papillae located anterior to the cloacal aperture, and a single plus four pairs of subventral caudal setae located posterior to the cloacal aperture on the tail. Preliminary analyses of phylogenetic relationships within the Triplonchida were done using the SSU and D2-D3 region of LSU DNA sequences.

New Zealand Wrens (Acanthisittidae)

2020 ◽  
Author(s):  
David W. Winkler ◽  
Shawn M. Billerman ◽  
Irby J. Lovette
Keyword(s):  
New Zealand ◽  
New Zealand Wrens

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

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