Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: <i>Rhinichthys osculus</i>) of the Greater Death Valley ecosystem

Mussmann, Steven M.; Douglas, Michael E.; Oakey, David D.

doi:10.1002/ece3.6736

Cited by 17 publications

(38 citation statements)

References 121 publications

(128 reference statements)

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“…As with prior studies (Derkarabetian et al 2019; Mussmann et al 2020), we also found considerable variation among methods, some of which can be attributed either to idiosyncrasies in the data or to algorithms and their implementation. For example, among RF methods iso MDS generally yielded smaller K (Figure 3d), attributed by Derkarabetian et al (2019) to the retention of only two dimensions.…”

Section: Discussionsupporting

confidence: 80%

“…In contrast to Derkarabetian et al (2019), we found t -SNE the most inclined to produce inconsistent groupings, a pattern most prevalent with the gap statistic (Supplementary Information B1-B60). Mussmann et al (2020) concurred, although in their case it was PAM+HMSW. We see this as an inherent problem relating to data structure.…”

Section: Discussionmentioning

confidence: 89%

“…By comparison, BFD* partitioned all groups, which may reflect a vulnerability to local structure at the population level, as reported by others for MSC methods (Sukumaran & Knowles 2017). BFD* and VAE partitioned equally in Mussmann et al . (2020), although their populations were relictual and without contemporary connectivity, whereas Terrapene reflects both historical (Figure 3d) and contemporary gene flow (Martin et al .…”

Section: Discussionmentioning

confidence: 99%

“…Some algorithms are robust to gene flow (Derkarabetian et al 2019; Newton et al 2020; Smith & Carstens 2020), yet a greater number of tests must be performed across diverse systems so as to understand which parameters impinge upon performance. Potentials include: Data quantity (Newton et al 2020), the proportion missing (Mussmann et al 2020), as well as its evolutionary complexity (Austerlitz et al 2009). Here, we employ species-delimitation algorithms relative to coalescent methods such as BFD* (Leaché et al 2014) as vehicles to parse a taxonomically recalcitrant biodiversity clade.…”

Section: Introductionmentioning

confidence: 99%

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The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapenespp.)

Martin

Chafin

Douglas

et al. 2020

Preprint

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Model-based approaches to species delimitation are constrained both by 22 computational capacities as well as by algorithmic assumptions that are frequently violated when 23 applied to biologically complex systems. An alternate approach, demonstrated herein, employs 24 machine learning (=ML) approaches from which species limits are derived without an explicit 25 definition of an underlying species model. By doing so, we demonstrate the capacity of these 26 approaches to designate phylogenomically and biologically relevant groups, using North 27 American box turtles (Terrapene spp.) as an example. Several different ML-based and traditional 28 species delimitation algorithms were invoked to parse a large SNP dataset derived from ddRAD 29 sequencing. Our results illuminate two major findings. First, more traditional model-based 30 approaches perform poorly, a likely reflection of systematic biases inherent in their formulation. 31Multispecies coalescent methods consistently over-split Terrapene, particularly given prior 32 evidence and our own phylogenetic results. Second, results from ML and clustering algorithms 33 consistently reiterated the presence of clades that were well-supported in prior species tree 34 analyses. In summary, we highlight both the strengths and limitations of ML algorithms, and in 35 doing so, explore appropriate approaches to data manipulation and model fit. Our study was 36 accomplished within the context of a well-characterized empirical system that allowed a direct 37 contrast between ML versus traditional approaches. It allowed the utility of ML-methods to be 38 underscored for species delimitation and serves as a study case from which guidelines implicit to 39 ML methods could be applied to other study systems. 40 41

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Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapenespp.)

Martin

Chafin

Douglas

et al. 2020

Preprint

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“…Speciation in the Karnali River Basin could thus be poorly resolved with respect to mitochondrial divergence, with a genetic signal likely obscured by the limited framework within which ancestral alleles could sort, allowing novel haplotypes to arise. More refined molecular approaches, such as reduced-representation genomics [32,33,34,49,50], could potentially provide the necessary resolution, although it will again be compounded by the rampant polyploidy found in Cyprininae.…”

Section: Macrophthalmus S Nepalensis S Raraensis) Occupy Separatementioning

confidence: 99%

The Himalayan Uplift and the Evolution of Aquatic Biodiversity Across Asia: Snowtrout (Cyprininae: Schizothorax) as a Test Case

Regmi

Douglas

Edds

et al. 2020

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The Himalayan uplift, a tectonic event of global importance, seemingly disseminated aquatic biodiversity broadly across Asia. But surprisingly, this hypothesis has yet to be tested. We do so herein by sequencing 1,140 base-pair of mtDNA cytochrome-b for 72 tetraploid Nepalese/Bhutanese Snowtrout (Schizothorax spp.), combining those data with 67 GENBANK sequences (59 ingroup/8 outgroup), then reconstructing phylogenetic relationships using maximum likelihood/ Bayesian analyses. Results indicate Snowtrout originated in Central Asia, dispersed across the Qinghai-Tibetan Plateau (QTP), then into Bhutan via south-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). The headwaters of five large Asian rivers provided dispersal corridors into southeast Asia. South of the Himalaya, the YLTR transitions into a westward-flowing Brahmaputra River that facilitated successive colonization of Himalayan drainages: First Bhutan, then Nepal, followed by far-western drainages subsequently captured by the Indus River. We found greater species-divergences across rather than within-basins, implicating vicariant evolution as a driver. The Himalaya is a component of the third-pole [largest (but rapidly shrinking) glacial reservoir outside the Arctic/Antarctic]. Its unique aquatic biodiversity must not only be recognized (as herein) but also conserved through broad, trans-national collaborations. Our results effectively contrast phylogeography with taxonomy as a necessary first step in this process.

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Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California

Moyle

Campbell

et al. 2022

Trans Am Fish Soc

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Objective: Speckled Dace Rhinichthys osculus is small cyprinoid fish that is widespread in western North America. In California and elsewhere it is currently treated as a single species with multiple subspecies, many undescribed. However, these subspecies may represent evolutionary lineages that are cryptic species because they cannot be distinguished using standard morphometric techniques. In this study, we attempt to determine evolutionary lineages within California populations of Speckled Dace using the population genetic and genomic information. Methods: We used restriction site-associated DNA sequencing to extract thousands of single-nucleotide polymorphisms across the genome to identify genetic differences among all the samples from 38 locations in the western USA, with a focus on California. We performed principal component analysis, admixture analysis, estimated pairwise values of the genetic differentiation index F ST , and constructed molecular phylogenies to characterize population genetic and phylogenetic relationships among sampled Speckled Dace populations. Result: Our analyses detected three major lineages of Speckled Dace in California that align with geography: (1) Sacramento River, central California coast, Klamath River, and Warner Basin; (2) Death Valley and Lahontan Basin; and (3) Santa Ana River basin, in southern California. These lineages fit well with the geologic history of California, which has promoted long isolation of populations of Speckled Dace and other fishes. Conclusion: The presence of distinct evolutionary lineages indicates that SpeckledDace in California should be managed with distinct population segments to preserve within-species diversity. This study highlights the importance of genetic analyses for conservation and management of freshwater fishes.

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Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus) of the Greater Death Valley ecosystem

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 17 publications

References 121 publications

The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapenespp.)

The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapenespp.)

The Himalayan Uplift and the Evolution of Aquatic Biodiversity Across Asia: Snowtrout (Cyprininae: Schizothorax) as a Test Case

Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California

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