Genomic resolution of cryptic species diversity in chipmunks

Herrera, Nathanael D; Bell, Kayce C.; Callahan, Colin M.; Nordquist, Erin; Sarver, Brice A. J.; Sullivan, Jack; Demboski, John R.; Good, Jeffrey M.

doi:10.1111/evo.14546

Cited by 7 publications

(2 citation statements)

References 107 publications

(220 reference statements)

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“…An evaluation of nearly 600 bp of COI revealed that approximately 75% of Anastrepha species can successfully be identified using this approach, but it does not discriminate members of the A. fraterculus cryptic complex and some other closely related species of the fraterculus group (Barr et al, 2018 ; Bartolini et al, 2020 ). On the other hand, genomic data coupled with multispecies coalescent approaches have provided invaluable information on evolutionary histories of cryptic species complexes in a great variety of animal taxa, such as insects, mammals, reptiles, and birds (Dupuis, Bremer, et al, 2018 ; Herrera et al, 2022 ; Obiol et al, 2023 ; Singhal et al, 2018 ; Thawornwattana et al, 2018 ; Zhang et al, 2021 ), as well as plants, such as ferns and angiosperms (Kinosian et al, 2020 ; Wu et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Congrains,

Dupuis,

Rodriguez

et al. 2023

Evolutionary Applications

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Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus Anastrepha Schiner (Diptera: Tephritidae) include some of the most serious agricultural pests in the Americas, with the Anastrepha fraterculus (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across most of the New World tropics and subtropics. The eight morphotypes described for this complex as well as other closely related species are classified in the fraterculus species group, whose evolutionary relationships are unresolved due to incomplete lineage sorting and introgression. We performed multifaceted phylogenomic approaches using thousands of genes to unravel the evolutionary relationships within the A. fraterculus complex to provide a baseline for molecular diagnosis of these pests. We used a methodology that accommodates variable sources of data (transcriptome, genome, and whole‐genome shotgun sequencing) and developed a tool to align and filter orthologs, generating reliable datasets for phylogenetic studies. We inferred 3031 gene trees that displayed high levels of discordance. Nevertheless, the topologies of the inferred coalescent species trees were consistent across methods and datasets, except for one lineage in the A. fraterculus complex. Furthermore, network analysis indicated introgression across lineages in the fraterculus group. We present a robust phylogeny of the group that provides insights into the intricate patterns of evolution of the A. fraterculus complex supporting the hypothesis that this complex is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Despite this complex evolutionary scenario, our subsampling analysis revealed that a set of as few as 80 loci has a similar phylogenetic resolution as the genome‐scale dataset, offering a foundation to develop more efficient diagnostic tools in this species group.

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Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Congrains,

Dupuis,

Rodriguez

et al. 2023

Evolutionary Applications

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“…Tamias senex was long treated as a subspecies of T. townsendii , but the latter taxon is now recognized as four distinct species (Gannon and Forbes 1995). The sister taxon to the rest of the townsendii species group is the Long-eared Chipmunk ( T. quadrimaculatus ; Reid et al 2012; Herrera et al 2022). Restricted to the Sierra Nevada, the geographic range of T. quadrimaculatus is almost completely overlapped by that of T. senex (ca.…”

Section: Methodsmentioning

confidence: 99%

Niche conservatism versus niche differentiation in sympatric chipmunks in the northern Sierra Nevada

Kelt

Coppeto

Vuren

et al. 2023

Journal of Mammalogy

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Closely related species are predicted to have similar fundamental niches, and therefore to compete locally and possibly be constrained to occur allopatrically. Over time, niche differentiation should lead to divergent use of niche axes, such as food or habitat. Most studies of niche divergence or of niche conservatism have focused on multiple species at large spatial scales. We studied two species of closely related chipmunks at two spatial scales in the northern Sierra Nevada. The Long-eared Chipmunk (Tamias quadrimaculatus) and the Shadow Chipmunk (T. senex) are subcryptic species that exhibit extensive geographic overlap in the northern and central Sierra Nevada. Habitat use at the macrohabitat scale was similar, with both species reaching their highest mean abundance in Red Fir (Abies magnifica) forests, but exhibiting divergent secondary affinities. Additionally, macrohabitat associations of T. senex appear to differ from those reported 50 years ago within the same forest, suggesting flexibility in the face of structural habitat changes resulting from forest management actions, climate change, or other factors. At a finer spatial scale, habitat affinities of these chipmunks differed modestly, suggesting that local distribution emphasizes slightly different microhabitat characteristics. We conclude that these species exhibit niche conservatism overall, but whether microhabitat differences reflect competition or niche divergence requires further study. Because T. quadrimaculatus has the smallest geographic range of any Sierra Nevada sciurid, it may be at risk of local extirpation or substantial range restriction in the face of climate change, large-scale high-severity wildfires, and other stochastic threats; the present research sheds light on the ecology of these species, but has important relevance for regional resource managers as well.

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Ecological differentiation and sympatry of cryptic species in the Sphagnum magellanicum complex (Bryophyta)

Nieto‐Lugilde,

Piatkowski

et al. 2024

American J of Botany

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PremiseSphagnum magellanicum (Sphagnaceae, Bryophyta) has been considered to be a single semi‐cosmopolitan species, but recent molecular analyses have shown that it comprises a complex of at least seven reciprocally monophyletic groups, that are difficult or impossible to distinguish morphologically.MethodsNewly developed barcode markers and RADseq analyses were used to identify species among 808 samples from 119 sites. Molecular approaches were used to assess the geographic ranges of four North American species, the frequency at which they occur sympatrically, and ecological differentiation among them. Microhabitats were classified with regard to hydrology and shade. Hierarchical modelling of species communities was used to assess climate variation among the species. Climate niches were projected back to 22,000 years BP to assess the likelihood that the North American species had sympatric ranges during the late Pleistocene.ResultsThe species exhibited parallel morphological variation, making them extremely difficult to distinguish phenotypically. Two to three species frequently co‐occurred within peatlands. They had broadly overlapping microhabitat and climate niches. Barcode‐ versus RADseq‐based identifications were in conflict for 6% of the samples and always involved S. diabolicum vs. S. magniae.ConclusionsThese species co‐occur within peatlands at scales that could permit interbreeding, yet they remain largely distinct genetically and phylogenetically. The four cryptic species exhibited distinct geographic and ecological patterns. Conflicting identifications from barcode vs. RADseq analyses for S. diabolicum versus S. magniae could reflect incomplete speciation or hybridization. They comprise a valuable study system for additional work on climate adaptation.

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Genomic resolution of cryptic species diversity in chipmunks

Cited by 7 publications

References 107 publications

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Niche conservatism versus niche differentiation in sympatric chipmunks in the northern Sierra Nevada

Ecological differentiation and sympatry of cryptic species in the Sphagnum magellanicum complex (Bryophyta)

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