Biology subjects

Huang, J.-P.

Publications and source records attributed to Huang, J.-P..

5 recordsLinked to original sources

bioRxiv2025

Eco-genomic analysis uncovers precision-conservation targets for the western Pacific's southernmost salmonid

Understanding how isolated small populations persist and adapt in adverse environments is instrumental to evolutionary and conservation biology. We combine a chromosome-level genome assembly, population resequencing and forward-time simulations to reconstruct the history and viability of the Formosan landlocked salmon (Oncorhynchus formosanus), now restricted to a handful of high-mountain headwaters in Taiwan. We estimate that this lineage has diverged from Japanese masu salmon over one million years ago and has no detectable gene flow for [~]50,000 years. It has accumulated extensive chromosome fusions and expansions of cold-adaptation gene families, qualifying it as a new species rather than a subspecies of Japanese masu salmon. Whole-stream sampling reveals an overlooked Hehuan-Creek population that retains high heterozygosity and has gained unique alleles. Life-table simulations show that the Hehuan population has a notably lower extinction risk and can persist or even grow under low-to-moderate typhoon frequency, whereas Qijiawan-Creek population would decline precipitously under the same or higher frequency . These findings contradict the notion that peripheral populations are likely genetically depleted and support stream-specific "precision conservation" in place of broad, untargeted translocations that could erode local adaptation potential. Thus, our genomic-ecological analysis has uncovered hidden strong resilience in a critically endangered, climate-threatened salmonid lineage.

genomics↗

bioRxiv2023

Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)

In recent years, parasite conservation has become a globally significant issue. Because of this, there is a need for standardised methods for inferring population status and possible cryptic diversity. However, given the lack of molecular data for some groups, it is challenging to establish procedures for genetic diversity estimation. Therefore, universal tools, such as double digest restriction-site associated DNA sequencing (ddRADseq), could be useful when conducting conservation genetic studies on rarely studied parasites. Here, we generated a ddRADseq dataset that includes all three described Taiwanese horsehair worms (Phylum Nematomorpha), possibly one of the most understudied animal groups. Additionally, we produced data for a fragment of the cytochrome c oxidase subunit I (COXI) for said species. We used the COXI dataset in combination with previously published sequences of the same locus for inferring the effective population size (Ne) trends and possible population structure. We found that a larger and geographically broader sample size combined with more sequenced loci resulted in a better estimation of changes in Ne. We were able to detect demographic changes associated with Pleistocene events in all the species. Furthermore, the ddRADseq dataset for Chordodes formosanus did not reveal a genetic structure based on geography, implying a great dispersal ability, possibly due to its hosts. We showed that different molecular tools can be used to reveal genetic structure and demographic history at different historical times and geographical scales, which can help with conservation genetic studies in rarely studied parasites.

zoology↗

bioRxiv2021

Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories

The ecology and genetic diversity of model yeast Saccharomyces cerevisiae prior to human domestication remain poorly understood. Taiwan is regarded as part of this yeasts geographic birthplace where the most divergent natural lineage was discovered. Here, we deep sampled the broad-leaf forests across this continental island to probe the ancestral species diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages, the highest known in any region. Three lineages are endemic to Taiwan and six are widespread in Asia. Molecular dating placed the divergence of the Taiwanese and Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Extensive historical and recent admixture events were detected between natural lineages. In particular, the genetic component from a lineage associated with fruits that spanned the widest geographical range was present in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We detected prevalent purifying selection genome-wide, with lineage-specific signals of positive or directional selection independent between lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.

genomics↗

bioRxiv2019

Macroevolutionary integration of phenotypes within and across ant worker castes

Phenotypic traits are often integrated into evolutionary modules: sets of organismal parts that evolve together. In social insect colonies the concepts of integration and modularity apply to sets of traits both within and among functionally and phenotypically differentiated castes. On macroevolutionary timescales, patterns of integration and modularity within and across castes can be clues to the selective and ecological factors shaping their evolution and diversification. We develop a set of hypotheses describing contrasting patterns of worker integration and apply this framework in a broad (246 species) comparative analysis of major and minor worker evolution in the hyperdiverse ant genus Pheidole. Using geometric morphometrics in a phylogenetic framework, we inferred fast and tightly integrated evolution of mesosoma shape between major and minor workers, but slower and more independent evolution of head shape between the two worker castes. Thus, Pheidole workers are evolving as a mixture of intra- and inter-caste integration and rate heterogeneity. The decoupling of homologous traits across worker castes may represent an important process facilitating the rise of social complexity.

evolutionary biology↗

bioRxiv2018

Evolution of the latitudinal diversity gradient in the hyperdiverse ant genus Pheidole

AimThe latitudinal diversity gradient is the dominant pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyper-rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (>1100 species) ant radiation, Pheidole, and evaluate the roles of three general explanations for the latitudinal gradient: variation in diversification rate, tropical conservatism, and ecological regulation.\n\nLocationGlobal.\n\nTime PeriodThe past 35 million years.\n\nMajor taxa studiedThe hyperdiverse ant genus Pheidole Westwood.\n\nMethodsWe assembled geographic data for 1499 species and morphospecies, and inferred a dated phylogeny of Pheidole of 449 species, including 150 species newly sequenced for this study. We tested correlations between diversification rate and latitude with BAMM, HiSSE, GeoSSE, and FiSSE, and examined patterns of diversification as Pheidole spread around the globe.\n\nResultsWe found that Pheidole diversification occurred in series of bursts when new continents were colonized, followed by a slowdown in each region. There was no evidence of systematic variation of net diversification rates with latitude across any of the methods. Additionally, we found latitudinal affinity is moderately conserved with a Neotropical ancestor and phylogenetic inertia alone is sufficient to produce the gradient pattern.\n\nMain ConclusionsOverall our results are consistent with tropical conservatism explaining the diversity gradient, while providing no evidence that diversification rate varies systematically with latitude. There is evidence of ecological regulation on continental scales through the pattern of diversification after colonization. These results shed light on the mechanisms underlying the diversity gradient, while contributing toward a much-needed invertebrate perspective on global biodiversity dynamics.

evolutionary biology↗