Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae)

Leavitt, Dean H.; Starrett, James; Westphal, Michael F.; Hedin, Marshal

doi:10.1016/j.ympev.2015.05.016

Cited by 61 publications

(47 citation statements)

References 61 publications

(35 reference statements)

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“…; Leavitt et al . ). Few studies have examined absolute divergence time estimates for the arachnid species we sequenced, but Derkarabetian et al .…”

Section: Discussionmentioning

confidence: 97%

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Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Burns

Starrett

Derkarabetian

et al. 2016

Molecular Ecology Resources

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Next-generation sequencing technologies now allow researchers of non-model systems to perform genome-based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) by generating reduced representation genome-wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non-model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6-base pair cutter EcoRI combined with methylated site-specific 4-base pair cutter MspI produced, on average, the greatest numbers of intra-individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non-linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable.

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“…; Leavitt et al . ). Few studies have examined absolute divergence time estimates for the arachnid species we sequenced, but Derkarabetian et al .…”

Section: Discussionmentioning

confidence: 97%

“…), Calisoga (Leavitt et al . ) and Hypochilus (Keith & Hedin ). COI sequence data were compiled and imported into Geneious Pro v. 8.1.7 (http://www.geneious.com, Kearse et al .…”

Section: Methodsmentioning

confidence: 99%

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Burns

Starrett

Derkarabetian

et al. 2016

Molecular Ecology Resources

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“…; Leavitt et al . ). In some cases, researchers have cited genetic distances equivalent to or greater than those observed among already described species as evidence that populations likely represent distinct species (e.g.…”

Section: Introductionmentioning

confidence: 97%

Assessing the performance of DNA barcoding using posterior predictive simulations

Barley

Thomson

2016

Molecular Ecology

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Accurate estimates of biodiversity are required for research in a broad array of biological subdisciplines including ecology, evolution, systematics, conservation and biodiversity science. The use of statistical models and genetic data, particularly DNA barcoding, has been suggested as an important tool for remedying the large gaps in our current understanding of biodiversity. However, the reliability of biodiversity estimates obtained using these approaches depends on how well the statistical models that are used describe the evolutionary process underlying the genetic data. In this study, we utilize data from the Barcode of Life Database and posterior predictive simulations to assess the performance of DNA barcoding under commonly used substitution models. We demonstrate that the success of DNA barcoding varies widely across DNA substitution models and that model choice has a substantial impact on the number of operational taxonomic units identified (changing results by ~4-31%). Additionally, we demonstrate that the widely followed practice of a priori assuming the Kimura 2-parameter model for DNA barcoding is statistically unjustified and should be avoided. Using both data-based and inference-based test statistics, we detect variation in model performance across taxonomic groups, clustering algorithms, genetic divergence thresholds and substitution models. Taken together, these results illustrate the importance of considering both model selection and model adequacy in studies quantifying biodiversity.

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“…Many exemplar dispersal limited salamanders, such as Batrachoseps attenuatus (Martinez‐Solano et al, ), Ensatina eschscholtzii xanthoptica (Kutcha, Parks, Mueller, & Wake, ), and Aneides lugubris (Lapointe & Rissler, ) and mygalomorph spiders like Calisoga (Leavitt et al, ), Antrodiaetus (Hedin et al, ; Starrett & Hedin, ), and Aliatypus (Satler et al, ) exhibit a disjunct distribution at latitudes near the San Francisco Bay dated to around the Mid‐Pleistocene. Additionally, present‐day populations of Batrachoseps persist on the valley floor north of the San Francisco Bay (Jockusch & Wake, ).…”

Section: Discussionmentioning

confidence: 99%

Systematics and evolution of Kibramoa Chamberlin 1924 (Araneae: Plectreuridae) from the California Floristic Province

Garcia

Griswold

Esposito

2020

J Zool Syst Evol Res

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The eight‐eyed haplogyne spider family Plectreuridae Simon, 1893 is one of the oldest of spider families, currently comprising two genera (Kibramoa and Plectreurys), 30 extant species and one subspecies. Plectreuridae have not been rigorously examined since 1958, with only three new species added to Plectreurys. This study revisited a subset of taxa from the genus Kibramoa using a combined morphological and multilocus phylogenetic analysis. Species distribution modeling (SDM) was used to investigate the current and paleo distributional patterns of the genus Kibramoa throughout the biodiverse region of the California Floristic Province (CFP). A reexamination of genitalic morphology reflected cryptic species, yet multilocus Bayesian and maximum likelihood analyses of mitochondrial (COI, 16S) and nuclear (ITS1, 28S) markers consistently suggested several divergent lineages. A time‐calibrated phylogeny indicated that the most recent common ancestor of Kibramoa appeared in the Mid‐Miocene and continued to diversify throughout the Plio‐Pleistocene. Xerophilic Kibramoa, as inferred by SDM, had a much wider distribution during the Mid‐Holocene, when climate was at its warmest. This body of work uncovered novel findings regarding the evolution of plectreurids, provided the first phylogeny of the family, and demonstrated similar biogeographic patterns displayed in other CFP taxa.

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Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae)

Cited by 61 publications

References 61 publications

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Assessing the performance of DNA barcoding using posterior predictive simulations

Systematics and evolution of Kibramoa Chamberlin 1924 (Araneae: Plectreuridae) from the California Floristic Province

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