Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocomeandEudyptes moseleyi)

Abstract

Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.

Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)

“…The gdi values did not reach reciprocal significance within a pair of putative species in two instances ('sp9' vs. 'sp10' and 'sp5' vs. 'sp6+7';Figure 3, Table 2), which likely stems from the shortcomings of Cyclocosmia sampling. Such situation has been reported from frogs (Leaché et al, 2019) and penguins (Mays et al, 2019) as a consequence of differences in sample sizes between the compared species pair.…”

“…Low values thus correlate with intra‐specific diversity ( gdi < 0.2), while higher ones indicate ( gdi > 0.7) species‐level divergence (Jackson, Carstens, et al., 2017; Leaché et al., 2019). Although large portion of the spectrum represents an ambiguous outcome, gdi was effectively used in species delimitation of vertebrate taxa (Chan et al., 2020; Chan & Grismer, 2019; Jackson, Carstens, et al., 2017; Leaché et al., 2020; Mays et al., 2019). Implementation of the gdi estimation might be particularly useful in conservation where accurate species boundaries assessment and individual population differentiation is crucial for developing effective management strategies and protection plans (Coimbra et al., 2021; Devitt et al., 2019; Hosegood et al., 2020; Johnson et al., 2018).…”

Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

“…Although these thresholds were proposed in the literature from a small sample of species, work in other natural populations has shown that well-accepted species can fall into the ambiguous range of 0.2–0.7, including horned lizards (Leaché et al . 2021), penguins (Mays et al . 2019), and flying lizards (Reilly et al .…”

“…Although these thresholds were proposed in the literature from a small sample of species, work in other natural populations has shown that well-accepted species can fall into the ambiguous range of 0.2-0.7, including horned lizards (Leaché et al 2021), penguins (Mays et al 2019), and flying lizards (Reilly et al 2022). Furthermore, there appears to be significant variation in gdi within clades and between them.…”

“…To address this question, we turned to whole genome resequencing data and methods that quantitatively assess the degree to which taxa are independently evolving under a multispecies coalescent (MSC) framework (Zhang et al 2011, Jackson et al 2017, Morales et al 2018, Mays et al 2019, Leaché et al 2019, Marshall et al 2021. Here, we apply several of these methods of species delimitation to the Galapagos giant tortoises, and thereby provide an assessment of taxonomic considerations in this endangered clade.…”