Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity

de, Adrián Nieto‐Montes; Barley, Anthony J.; Meza-Lázaro, Rubí N.; García‐Vázquez, Uri Omar; Zamora-Ábrego, Joan Gastón; Thomson, Robert C.; Leaché, Adam D.

doi:10.1016/j.ympev.2016.09.001

Cited by 61 publications

(40 citation statements)

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“…On the basis of analyses of ddRADseq data for the genus Xenosaurus with a variety of species delimitation methods, Nieto-Montes de Oca et al (2017) suggested that populations from the Huehuetla region represent a distinct, evolutionary independent (yet undescribed) lineage of Xenosaurus . In this study, we documented that populations of Xenosaurus from the Huehuetla region also are morphologically diagnosable from all other described species of the genus, including X. tzacualtipantecus , with which they have been likely confused (see above).…”

Section: Discussionmentioning

confidence: 99%

“…Lizards of the Middle American genus Xenosaurus Peters, 1861 occur from southwestern Tamaulipas and extreme southeastern Guerrero, on the Caribbean and Pacific versants of Mexico, respectively, south and east to Alta Verapaz, Guatemala (King and Thompson 1968; Smith and Iverson 1993; Ballinger et al 2000; Pérez-Ramos et al 2000; Nieto-Montes de Oca et al 2001; Canseco-Márquez 2005; Zamora-Abrego 2009; Nieto-Montes de Oca et al 2013, 2017). Species of Xenosaurus occur in a considerable elevational range (ca.…”

Section: Introductionmentioning

confidence: 99%

“…The taxonomic history of the genus and the geographic distribution of its species have been recently summarized by Nieto-Montes de Oca et al (2013) and Nieto-Montes de Oca et al (2017, Fig. 2).…”

Section: Introductionmentioning

confidence: 99%

“…In addition to the above species, a recent phylogenetic analysis of the genus Xenosaurus based on RADseq data (Nieto-Montes de Oca et al 2017) provided evidence that its diversity has been substantially underestimated, and that several species remain to be described. Given the usually restricted distributions of these species and the destruction of their habitats, such description is a pressing matter.…”

Section: Introductionmentioning

confidence: 99%

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A new species of knob-scaled lizard (Xenosauridae, Xenosaurus) from the Sierra Madre Oriental of Puebla, Mexico

de¹,

Sánchez-Vega²,

Durán-Fuentes³

2018

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A new species of Xenosaurus in the X. tzacualtipantecus clade is described from the Sierra Madre Oriental of northern Puebla, Mexico. The new species differs from all of its congeners in possessing a unique combination of characters. The new species appears to be allopatric and fills in the geographic gap between the geographic distributions of X. tzacualtipantecus and the species in the newmanorum clade to the north and northwest and those of the species in the grandis and rackhami clades to the south and southeast. The new species occurs between approximately 880 m and 1470 m of elevation, and appears to be restricted to cloud forest, which has been replaced by coffee plantations in many areas. An updated key to the species of Xenosaurus is provided.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A new species of knob-scaled lizard (Xenosauridae, Xenosaurus) from the Sierra Madre Oriental of Puebla, Mexico

de¹,

Sánchez-Vega²,

Durán-Fuentes³

2018

Self Cite

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“…The double‐digest RADseq (ddRADseq; Peterson, Weber, Kay, Fisher, & Hoekstra, 2012), a variation of the original method (Baird et al., 2008), improves on depth of coverage per locus by optimizing sequencing effort and reducing missing genotypes. The protocol is flexible, allowing for easy optimization for different organisms, genome sizes, genetic diversity, and scientific questions (Mastretta‐Yanes et al., 2015; Nieto‐Montes de Oca et al., 2017; Recknagel, Elmer, & Meyer, 2013; Zhou et al., 2014). Consequently, numerous modifications or improvements of ddRADseq are being continually proposed (Franchini, Parera, Kautt, & Meyer, 2017; Heffelfinger et al., 2014; Recknagel, Jacobs, Herzyk, & Elmer, 2015).…”

Section: Introductionmentioning

confidence: 99%

Double‐digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

Salas‐Lizana

Oono

2018

Ecology and Evolution

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The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low‐cost double‐digest restriction site‐associated DNA sequencing (ddRADseq) protocol to reveal among‐ and within‐species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded adapters and incorporates universal indexes for multiplexing. We tested for reproducibility and functionality by comparing shared loci from sample replicates and assessed the effects of numbers of ambiguous sites and clustering thresholds on coverage depths, number of shared loci among samples, and phylogenetic reconstruction. Errors between technical replicates were minimal. Relaxing the quality‐filtering criteria increased the mean coverage depth per locus and the number of loci recovered within a sample, but had little effect on the number of shared loci across samples. Increasing clustering threshold decreased the mean coverage depth per cluster and increased the number of loci recovered within a sample but also decreased the number of shared loci across samples, especially among distantly related species. The combination of low similarity clustering (70%) and relaxed quality‐filtering (allowing up to 30 ambiguous sites per read) performed the best in phylogenetic analyses at both recent and deep genetic divergences. Hence, this method generated sufficient number of shared homologous loci to investigate the evolutionary relationships among divergent fungal lineages with small haploid genomes. The greater genetic resolution also revealed new structure within species that correlated with ecological traits, providing valuable insights into their cryptic life histories.

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A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity

Wilson

Rossetto

Bain

et al. 2022

American J of Botany

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Premise: Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. Methods: To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. Results: Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. Conclusions: The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.

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Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity

Cited by 61 publications

References 39 publications

A new species of knob-scaled lizard (Xenosauridae, Xenosaurus) from the Sierra Madre Oriental of Puebla, Mexico

A new species of knob-scaled lizard (Xenosauridae, Xenosaurus) from the Sierra Madre Oriental of Puebla, Mexico

Double‐digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity

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