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Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies. [ABSTRACT FROM AUTHOR]

1.We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedent rate of decline.2.However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remains challenging.3.We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex.4.We found that the three sky‐island taxa formed three independently evolving units without detectable post‐divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid‐Pleistocene, have experienced episodes of demographic decline in the past.5.More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesised to impact the recent demographic history (<100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa.6.We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans. [ABSTRACT FROM AUTHOR]

Species delimitation can be difficult when the divergence between focal taxa is in the incipient stage of speciation, because conflicting results are expected among different data sets, and the species limits can differ depending on the species concept applied. We studied speciation history and investigated the impact on taxonomic decision-making when using different types of data in a Taiwanese endemic sister-species pair of stag beetles, Lucanus miwai and Lucanus yulaoensis , from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3%; however, L. miwai might not be monophyletic. The result of our multispecies coalescent-based species delimitation using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of the genealogical divergence index (gdi) corresponded to the ambiguous zone of species delimitation. We also showed that post-divergence gene flow is unlikely. Our study demonstrates challenges in the delineation of incipient species, but shows the importance of understanding the speciation history and adopting integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions. [ABSTRACT FROM AUTHOR]

Aim: The Southern Ocean landmasses have intrigued biologists for centuries because they share many taxonomic groups. Such disjunct taxa can provide insight into evolutionary processes that connect populations or drive divergence. The lichenized fungus Pseudocyphellaria glabra, for example, has a disjunct distribution—separated by the Tasman Sea and the Pacific Ocean—yet whether these locations should be genetically distinct is unclear. The large distances between continents may be expected to prohibit gene flow, but strong and sustained winds in the Southern Hemisphere and the small size of P. glabra propagules may facilitate migration. We compared support for these two hypotheses. Location: Southeastern Australia, Tasmania, New Zealand and Southern Chile. Taxon: Pseudocyphellaria glabra (Hook. f. & Taylor) C.W. Dodge, 1948 (Ascomycota, Peltigeraceae) Methods: We collected 371 samples across the disjunct range of P. glabra. We generated genomic data using restriction site‐associated DNA sequencing and reconstructed a Maximum Likelihood phylogeny using 29,098 unlinked SNPs. We then conducted population genomic analyses using 3,756 SNPs including a minimum‐spanning network, principal components analysis, discriminate analysis of principal components, and k‐means clustering. Results: Maximum likelihood analysis recovered multiple well‐supported clades that roughly corresponded to geography. Population genomic analyses identified genetic structuring that generally corresponded with geographic distance; however, some individuals from Chile and Australia were assigned to genetic clusters found in New Zealand, suggesting that recent dispersal events from New Zealand have successfully colonized Chile and Australia. Main conclusion: Populations of P. glabra from Australia, Chile and New Zealand are genetically distinct, but frequent long‐distance dispersal during the Quaternary probably prevented speciation. This study demonstrates the power of restriction‐site associated DNA sequencing for discernment between divergent and connective evolutionary forces that simultaneously influence the population structure of species with disjunct ranges in the Southern Ocean landmasses. [ABSTRACT FROM AUTHOR]