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- Hartop, Emily, 1983-
(författare)
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A multi-faceted approach to a "dark taxon" : The hyperdiverse and poorly known scuttle flies (Diptera: Phoridae)
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Most of the unknown animal biodiversity on earth is in groups of invertebrates that are hyperdiverse and abundant, yet poorly known (“dark taxa”). The study of these organisms requires a multi-faceted approach and methodologies designed to tackle large numbers of species and specimens. The scuttle flies (Diptera: Phoridae) are a classic example of a dark taxon and the focus of this thesis. Paper I is a molecular phylogeny of the phorid genus Megaselia based on one nuclear (28S rDNA) and three mitochondrial (ND1, COI and 16S) markers from 145 species of Nordic Megaselia. Molecular data was analysed with Bayesian analysis, maximum likelihood, and parsimony methods. Based on these results, and supporting morphological data, we divide Megaselia into 22 informal species groups, 20 of which fall into a monophyletic “core Megaselia”. We discuss implications for the future circumscription of Megaselia and associated genera. Paper II presents a pipeline for rapid and cost-effective species discovery using the Oxford Nanopore mobile sequencing technology MinION. This paper reveals the presence of ca. 650 species of Phoridae from a single Malaise trap placed in Kibale National Park, Uganda. Based on our data, we estimate that the phorid fauna of the Afrotropical region could be as high as 100 000 species: this figure dwarfs previous diversity estimates. The implications for species discovery and description are discussed, and a new species (Megaselia sepsioides sp. nov.) is described. Paper III outlines a large-scale integrative approach to species discovery and delimitation in hyperdiverse groups, exemplified using a dataset of 18 000 phorid flies from Sweden. COI minibarcodes (313 bp) were obtained for all specimens and classified into putative species using different clustering methods (objective clustering, Poisson tree process, automatic barcode gap discovery and refined single linkage). No clustering method was accurate enough to use for species delimitation without confirmation from additional data. We found that the stability of a cluster to change across genetic-distance thresholds and the genetic variation within a cluster both accurately predict clusters where morphology is likely to be incongruent with barcode data. With molecular clustering integrated with morphological validation, we found that we could examine less than 5% of specimens and still delimit all species fully and accurately. Paper IV addresses questions about the scuttle fly fauna of Sweden with data from 32 000 scuttle flies from 37 sites and 4 time periods. We estimate that the total Swedish fauna contains 652-713 (based on Chao 1 or CNE estimates, respectively) species of scuttle flies, 1.5 times the 372 species currently documented from Sweden. Ordination techniques show that scuttle fly communities are organized in a gradient across Sweden, which is well correlated with plant hardiness zones defined by the Swedish Horticultural Society. Hierarchical modelling of species communities (HMSC) reveals that phorid community composition is largely determined by climatic and temporal variables, but much of the variance remains unexplained by the models we explored. Comparison of our phorid data with that of species more commonly utilised for biodiversity assessments revealed that phorids may allow more fine-scaled analysis as they may exist in smaller ranges, and that they additionally may give unique patterns of distribution that are unlike those seen in other taxa.
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| 2. |
- Hartop, Emily, 1983-, et al.
(författare)
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Towards Large-Scale Integrative Taxonomy (LIT) : Resolving the Data Conundrum for Dark Taxa
- 2022
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 71:6, s. 1404-1422
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Tidskriftsartikel (refereegranskat)abstract
- New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa,” here defined as groups for which <<10%% of all species are described and the estimated diversity exceeds 1,000 species. Species delimitation for these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop large-scale integrative taxonomy (LIT), an explicit method where preliminary species hypotheses are generated based on inexpensive data that can be obtained quickly and cost-effectively. These hypotheses are then evaluated based on a more expensive type of “validation data” that is only obtained for specimens selected based on objective criteria applied to the preliminary species hypotheses. We here use this approach to sort 18,000 scuttle flies (Diptera: Phoridae) into 315 preliminary species hypotheses based on next-generation sequencing barcode (313 bp) clusters (using objective clustering [OC] with a 3%% threshold). These clusters are then evaluated with morphology as the validation data. We develop quantitative indicators for predicting which barcode clusters are likely to be incongruent with morphospecies by randomly selecting 100 clusters for in-depth validation with morphology. A linear model demonstrates that the best predictors for incongruence between barcode clusters and morphology are maximum p-distance within the cluster and a newly proposed index that measures cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that are incongruent with morphology. In our study, all morphospecies are true or disjoint subsets of the initial barcode clusters so that all incongruence can be eliminated by varying clustering thresholds. This leads to a discussion of when a third data source is needed to resolve incongruent grouping statements. The morphological validation step in our study involved 1,039 specimens (5.8%% of the total). The formal LIT protocol we propose would only have required the study of 915 (5.1%%: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of incongruence are similar across OC, Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Refined Single Linkage (RESL) (used by Barcode of Life Data System to assign Barcode Index Numbers [BINs]). OC and ABGD achieved a maximum congruence score with the morphology of 89%% while PTP was slightly less effective (84%%). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1,714 haplotypes were 86%% congruent with morphology while the values were 89%% for OC, 74%% for PTP, and 72%% for ABGD.
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