KoT: an automatic implementation of the<i>K/θ</i>method for species delimitation

Spöri, Yann; Stoch, Fabio; Dellicour, Simon; Birky, C. William; Flot, Jean‐François

doi:10.1101/2021.08.17.454531

Cited by 13 publications

(11 citation statements)

References 26 publications

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“…The distance-based methods included three approaches: (1) a non-threshold method that uses a hierarchical clustering algorithm to identify a barcode gap (i.e. difference between intra and interspecific genetic distances)—ASAP (Assemble Species by Automatic Partitioning 67 ), (2) a threshold method that calculates the ratio between the average interspecific distance ( K ) of two clades and their intraspecific genetic diversity (θ)—KoT (K/θ 84 ), and (3) Barcode Index Number (BIN), which is an algorithm implemented in Barcode of Life Data Systems (BOLD; https://www.boldsystems.org/ ), where the newly submitted COI sequences are aligned and compared pairwise and also to each sequence already deposited in BOLD. The tree-based methods included three approaches: (1) a non-threshold method that distinguishes coalescent versus speciation processes on a phylogram assuming a Poisson distribution—PTP (Poisson Tree Processes 85 ), (2) a non-threshold method that determines the transition between species-level to population-level evolutionary processes by using a generalized Yule model—GMYC (Generalized Mixed Yule Coalescent 86 ), and (3) a proposed molecular threshold for crustaceans which assumes that clades separated by a patristic distance of at least 0.16 substitutions per site at the COI locus are likely different species—PDT (Patristic Distance Threshold 70 ).…”

Section: Methodsmentioning

confidence: 99%

A DNA barcode reference library for endemic Ponto-Caspian amphipods

Copilaş‐Ciocianu

Rewicz

Sands

et al. 2022

Sci Rep

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The Ponto-Caspian region is an endemicity hotspot that harbours several crustacean radiations, among which amphipods are the most diverse. These poorly known species are severely threatened in their native range, while at the same time they are invading European inland waters with significant ecological consequences. A proper taxonomic knowledge of this fauna is paramount for its conservation within the native region and monitoring outside of it. Here, we assemble a DNA barcode reference library for nearly 60% of all known Ponto-Caspian amphipod species. We use several methods to define molecular operational taxonomic units (MOTUs), based on two mitochondrial markers (COI and 16S), and assess their congruence with current species-level taxonomy based on morphology. Depending on the method, we find that 54–69% of species had congruent morpho-molecular boundaries. The cases of incongruence resulted from lumping distinct morphospecies into a single MOTU (7–27%), splitting a morphospecies into several MOTUs (4–28%), or both (4–11%). MOTUs defined by distance-based methods without a priori divergence thresholds showed the highest congruence with morphological taxonomy. These results indicate that DNA barcoding is valuable for clarifying the diversity of Ponto-Caspian amphipods, but reveals that extensive work is needed to resolve taxonomic uncertainties. Our study advances the DNA barcode reference library for the European aquatic biota, paving the way towards improved taxonomic knowledge needed to enhance monitoring and conservation efforts.

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Section: Methodsmentioning

confidence: 99%

A DNA barcode reference library for endemic Ponto-Caspian amphipods

Copilaş‐Ciocianu

Rewicz

Sands

et al. 2022

Sci Rep

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“…A median-joining haplotype network (haplonet) was constructed using HaplowebMaker (Spöri & Flot 2020) based on the COI sequence alignment, including in total 251 COI Corbicula sequences. The K/θ method is based on a comparison between intergroup and intragroup sequence diversity (Birky et al 2010;Birky 2013;Birky & Maughan 2021) as implemented in the online tool KoT (Spöri et al 2022). This method defines a new species when the gap between two clades cannot be caused by genetic drift (based on a threshold) and was shown efficient on asexual or clonal organisms (e.g.…”

Section: Sequence Editing Alignment and Species Delimitation Methodsmentioning

confidence: 99%

Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula

Vastrade¹,

Etoundi²,

Bournonville³

et al. 2022

Peer Community Journal

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Occasional" sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species.

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“…The K/θ method is based on a comparison between intergroup and intragroup sequence diversity (Birky et al . 2010; Birky 2013; Birky & Maughan, 2021) as implemented in the online tool KoT (Spöri & Flot, 2021). This method defines a new species when the gap between two clades cannot be caused by genetic drift (based on a threshold) and was shown efficient on asexual or clonal organisms ( e .…”

Section: Methodsmentioning

confidence: 99%

“…A median-joining haplotype network (haplonet) was constructed using HaplowebMaker (Spöri et al 2020) based on the COI sequence alignment, including in total 251 COI Corbicula sequences. The K/θ method is based on a comparison between intergroup and intragroup sequence diversity (Birky et al 2010;Birky 2013;Birky & Maughan, 2021) as implemented in the online tool KoT (Spöri & Flot, 2021). This method defines a new species when the gap between two clades cannot be caused by genetic drift (based on a threshold) and was shown efficient on asexual or clonal organisms (e.g.…”

Section: Because Mitochondrial and Nuclear Markers Potentially Have Different Inheritance Patterns Inmentioning

confidence: 99%

Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula

Vastrade

Etoundi

Bournonville³

et al. 2019

Preprint

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18Corbicula clams were introduced during the 20 th century into America and Europe, where they became 19 notoriously successful invaders with a widespread, global distribution. Their ability to reproduce clonally through 20 androgenesis ("all-male asexuality") has been determinant in their invasive success, with only four invasive clonal 21 lineages detected across Europe and America, one of which is very abundant and widespread on both continents. 22Due to their "all-male asexuality" and egg parasitism between distinct lineages, the evolutionary and geographic 23 origins of the invasive androgenetic lineages have been challenging to identify. We analyzed here the patterns of 24 allele sharing for different molecular markers among Corbicula individuals collected worldwide. We identify three 25 distinct genetic pools containing androgenetic Corbicula lineages. While one sexual Corbicula species forms a 26 distinct fourth genetic pool, the other sexual lineages cluster with the androgenetic ones based on shared alleles. 27One genetic pool contains most androgenetic lineages and sexual C. sandai from Lake Biwa in Japan, pointing to 28 this lake as a likely origin of androgenetic Corbicula lineages. Although three distinct biogeographic origins of 29Corbicula androgenetic lineages have been identified, their recent radiation and cross-lineage genetic mixing 30 hamper classical species delimitation within this clam genus. 31 32

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KoT: an automatic implementation of theK/θmethod for species delimitation

Cited by 13 publications

References 26 publications

A DNA barcode reference library for endemic Ponto-Caspian amphipods

A DNA barcode reference library for endemic Ponto-Caspian amphipods

Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula

Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula

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