| 1. |
- Roslin, Tomas, et al.
(författare)
-
A molecular-based identification resource for the arthropods of Finland
- 2022
-
Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 22:2, s. 803-822
-
Tidskriftsartikel (refereegranskat)abstract
- To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.
|
|
| 2. |
- Heikkilä, Maria, et al.
(författare)
-
Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera).
- 2015
-
Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 15:1
-
Tidskriftsartikel (refereegranskat)abstract
- Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only.
|
|
| 3. |
- Lee, Kyung Min, et al.
(författare)
-
Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus
- 2018
-
Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 67:6, s. 925-939
-
Tidskriftsartikel (refereegranskat)abstract
- A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.
|
|
| 4. |
- Parmesan, Camille, et al.
(författare)
-
Poleward shifts in geographical ranges of butterfly species associated with regional warming
- 1999
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 399:6736, s. 579-583
-
Tidskriftsartikel (refereegranskat)abstract
- Mean global temperatures have risen this century, and further warming is predicted to continue for the next 50–100 years. Some migratory species can respond rapidly to yearly climate variation by altering the timing or destination of migration, but most wildlife is sedentary and so is incapable of such a rapid response. For these species, responses to the warming trend should be slower, reflected in poleward shifts of the range. Such changes in distribution would occur at the level of the population, stemming not from changes in the pattern of individuals' movements, but from changes in the ratios of extinctions to colonizations at the northern and southern boundaries of the range. A northward range shift therefore occurs when there is net extinction at the southern boundary or net colonization at the northern boundary. However, previous evidence has been limited to a single species or to only a portion of the species' range. Here we provide the first large-scale evidence of poleward shifts in entire species' ranges. In a sample of 35 non-migratory European butterflies, 63% have ranges that have shifted to the north by 35–240 km during this century, and only 3% have shifted to the south.
|
|
| 5. |
- Rajaei, Hossein, et al.
(författare)
-
Catalogue of the lepidoptera of Iran
- 2023
-
Ingår i: Integrative Systematics. - : Stuttgart State Museum of Natural History. - 2628-2380. ; 6:SP1, s. 121-459
-
Tidskriftsartikel (refereegranskat)
|
|
| 6. |
- Rota, Jadranka, et al.
(författare)
-
The unresolved phylogenomic tree of butterflies and moths (Lepidoptera) : Assessing the potential causes and consequences
- 2022
-
Ingår i: Systematic Entomology. - : Wiley. - 0307-6970 .- 1365-3113. ; 47:4, s. 531-550
-
Tidskriftsartikel (refereegranskat)abstract
- The field of molecular phylogenetics is being revolutionized with next-generation sequencing technologies making it possible to sequence large numbers of genomes for non-model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. Here, we focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera), whose phylogeny remains unresolved despite several recent phylogenomic studies. In this study, we assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein-coding genes and the alignment length over 290,000 base pairs, including 200 taxa representing 83% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias and possible other model violations. Furthermore, we employed a series of analyses to dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much – but not all – of the lepidopteran tree of life. The relationships among superfamilies within Ditrysia, the most species rich lepidopteran clade containing 98% of the extant species, remain poorly resolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.
|
|
| 7. |
- Rönkä, Katja, et al.
(författare)
-
Putting Parasemia in its phylogenetic place : A molecular analysis of the subtribe Arctiina (Lepidoptera)
- 2016
-
Ingår i: Systematic Entomology. - : Wiley. - 0307-6970 .- 1365-3113. ; 41:4, s. 844-853
-
Tidskriftsartikel (refereegranskat)abstract
- Despite being popular among amateur and professional lepidopterologists and posing great opportunities for evolutionary research, the phylogenetic relationships of tiger moths (Erebidae: Arctiinae) are not well resolved. Here we provide the first phylogenetic hypothesis for the subtribe Arctiina with the basic aim of clarifying the phylogenetic position of the Wood Tiger Moth Parasemia plantaginis Hübner, a model species in evolutionary ecology. We sampled 89 species in 52 genera within Arctiina s.l., 11 species of Callimorphina and two outgroup species. We sequenced up to seven nuclear genes (CAD, GAPDH, IDH, MDH, Ef1α, RpS5, Wingless) and one mitochondrial gene (COI) including the barcode region (a total of 5915 bp). Both maximum likelihood and Bayesian inference resulted in a well-resolved phylogenetic hypothesis, consisting of four clades within Arctiina s.s. and a clade comprising spilosomine species in addition to Callimorphina and outgroups. Based on our results, we present a new classification, where we consider the Diacrisia clade, Chelis clade, Apantesis clade, Micrarctia Seitz and Arctia clade as valid genera within Arctiina s.s., whereas Rhyparia Hübner syn.n. and Rhyparioides Butler syn.n. are synonymized with Diacrisia Hübner; Neoarctia Neumoegen & Dyar syn.n., Tancrea Püngeler syn.n., Hyperborea Grum-Grshimailo syn.n., Palearctia Ferguson syn.n., Holoarctia Ferguson syn.n., Sibirarctia Dubatolov syn.n. and Centrarctia Dubatolov syn.n. are synonymized with Chelis Rambur; Grammia Rambur syn.n., Orodemnias Wallengren syn.n., Mimarctia Neumoegen & Dyar syn.n., Notarctia Smith syn.n. and Holarctia Smith syn.n. are synonymized with Apantesis Walker; and Epicallia Hübner syn.n., Eucharia Hübner syn.n., Hyphoraia Hübner syn.n., Parasemia Hübner syn.n., Pericallia Hübner syn.n., Nemeophila Stephens syn.n., Ammobiota Wallengren syn.n., Platarctia Packard syn.n., Chionophila Guenée syn.n., Eupsychoma Grote syn.n., Gonerda Moore syn.n., Platyprepia Dyar syn.n., Preparctia Hampson syn.n., Oroncus Seitz syn.n., Acerbia Sotavalta syn.n., Pararctia Sotavalta syn.n., Borearctia Dubatolov syn.n., Sinoarctia Dubatolov syn.n. and Atlantarctia Dubatolov syn.n. are synonymized with Arctia Schrank, leading to 33 new genus-level synonymies. Our focal species Arctia plantaginis comb.n. is placed as sister to Arctia festiva comb.n., another widespread aposematic species showing wing pattern variation. Our molecular hypothesis can be used as a basis when adding more species to the tree and tackling interesting evolutionary questions, such as the evolution of warning signalling and mimicry in tiger moths.
|
|
