Rosa Rubicondior: Refuting Evolution - Allopatric Evolution, Just as The Theory of Evolution Predicts

Tuesday, 21 October 2025

Refuting Evolution - Allopatric Evolution, Just as The Theory of Evolution Predicts

Map of the South China Sea showing the Ryuku Arc between Taiwan and Kyushu

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Natural Japanese and Taiwanese Hinoki Cypresses Genetically Differentiated 1 Million Years Ago | Research News - University of Tsukuba

Japanese plant geneticists, led by scientists from University of Tsukuba, have shown that the Japanese and Taiwanese Hinoki cypresses began to diverge around one million years ago, following the destruction of a land bridge that once connected Taiwan to the Japanese archipelago.

This is a textbook example of allopatric speciation, in which an isolated population diverges from its parent population through a combination of founder effects, genetic drift, and natural selection in response to different environmental pressures.

The now-vanished land bridge once linked Taiwan to the southern Japanese island of Kyushu. Its remnants form the Ryukyu Arc — a chain of small islands marking the south-eastern boundary of the South China Sea.

Faced with such clear evidence of speciation, creationists typically resort to a familiar tactic: redefining evolution into a straw man. They insist that “evolution” means one species turning in a single event into something utterly unrelated — for instance, that these cypresses should transform into daisies, cabbages, mammals, or birds. If such an absurd event ever occurred, it would in fact falsify evolutionary theory and throw the entire fields of biology and taxonomy into chaos. This is the standard creationist tactic on social media: misrepresent science, then demand that science defend the misrepresentation, and claim victory when it doesn’t.

The reality remains, however, that the divergence of these related species of cypress — and the fact that this divergence can be correlated precisely with geological change — stands as powerful evidence for Darwinian evolution. Charles Darwin knew nothing of genes, alleles, or genetic drift, yet his description of descent with modification through inherited traits is elegantly confirmed here by modern genetics and biogeography. The genus Chamaecyparis — commonly known as the false cypresses — is an evolutionarily interesting group of conifers in the cypress family Cupressaceae. Their distribution and divergence provide a good illustration of how geological change, climate oscillations, and geographic isolation have shaped the evolution of temperate conifers.

Evolution of the Chamaecyparis (false cypress).

Taxonomic and Phylogenetic Context

Family: Cupressaceae
Genus: Chamaecyparis (false cypresses)
Native to eastern Asia (Japan, Taiwan) and North America (Pacific Northwest and the eastern US).
Extant species include:

Chamaecyparis obtusa (Hinoki cypress – Japan)
Chamaecyparis pisifera (Sawara cypress – Japan)
Chamaecyparis formosensis (Formosan cypress – Taiwan)
Chamaecyparis lawsoniana (Port Orford cedar – Oregon and California, USA)
Chamaecyparis thyoides (Atlantic white cedar – eastern USA)

Phylogenetically, Chamaecyparis belongs to a clade within Cupressaceae that also includes Cupressus sensu lato, Fokienia, and Xanthocyparis. Molecular studies show that Chamaecyparis is a well-supported monophyletic genus.

Fossil Record and Biogeography

Fossil evidence indicates that Chamaecyparis-like ancestors were widespread across the Northern Hemisphere during the late Cretaceous and Paleogene.
The genus (or closely related lineages) appears to have originated in East Asia and later dispersed to North America via high-latitude land connections (Beringia).
A once-broader Holarctic distribution has been fragmented over time, leaving isolated relictual populations in East Asia and North America.

Divergence and Evolutionary Timeline

Molecular phylogenetic analyses (e.g., chloroplast and nuclear DNA markers) suggest:

The crown group of Chamaecyparis diversified during the late Miocene to early Pliocene, roughly 5–15 million years ago.
Divergence between the Asian (C. obtusa, C. pisifera, C. formosensis) and North American (C. lawsoniana, C. thyoides) lineages likely reflects vicariance following climatic cooling and the breakdown of boreal forest connections between the continents.
Within East Asia, the divergence between the Japanese and Taiwanese lineages — notably C. obtusa and C. formosensis — has been estimated at ~1 million years ago, coinciding with the destruction of the Ryukyu land bridge during glacial–interglacial sea-level changes. This is a clear case of allopatric speciation.

Pleistocene Climate Oscillations

The Pleistocene glacial cycles played a major role in shaping modern Chamaecyparis distribution:

Populations retreated to refugia during glacial maxima, then re-expanded during interglacial periods.
Genetic data reveal signatures of bottlenecks and expansions, especially in the East Asian taxa.
These climatic fluctuations likely reinforced isolation between island populations, further promoting speciation and genetic divergence.

Adaptive Traits and Ecological Niches

Chamaecyparis species are adapted to cool temperate or montane subtropical climates.
They show ecological specialisation:

C. obtusa prefers well-drained montane soils in Japan.
C. formosensis occupies high-elevation montane forests in Taiwan.
C. lawsoniana thrives in moist coastal forest of the Pacific Northwest.

Their tolerance of specific soil and climatic conditions, combined with limited seed dispersal, likely contributed to their restricted ranges and local endemism.

Molecular Evidence and Phylogenomics

Recent genomic studies, including plastid and mitochondrial genome sequencing, have:

Confirmed the monophyly of the genus.
Resolved interspecific relationships, showing a clear East Asia–North America split.
Provided molecular clock estimates consistent with Miocene–Pleistocene divergence events.
Indicated low gene flow between populations separated by water barriers, reinforcing the role of geographic isolation.

Evolutionary Significance

Chamaecyparis provides an elegant case study of:

Boreal-temperate disjunctions between East Asia and North America.
Island-driven speciation between Japan and Taiwan.
Survival of ancient conifer lineages in refugial habitats.

These patterns mirror those seen in other genera, such as Tsuga (hemlocks) and Taxus (yews), reflecting common biogeographic histories.

References and Key Studies

Farjon, A. (2010). A Handbook of the World's Conifers.
Mao, K. et al. (2012). "Distribution of living Cupressaceae reflects the breakup of Pangea." PNAS 109(20): 7793–7798.
Huang, S. et al. (2025). “Phylogeography of Hinoki cypress reveals divergence after the loss of the Ryukyu land bridge.” Ecology and Evolution.
Li, Z. et al. (2022). “Phylogenomic insights into Cupressaceae evolution.” Molecular Phylogenetics and Evolution 170: 107429.
Su, Y. et al. (2007). “Phylogeography of Chamaecyparis formosensis and C. obtusa in East Asia.” Botanical Studies.

The study is reported in the open-access journal Ecology and Evolution and summarised in a University of Tsukuba research news item.

Natural Japanese and Taiwanese Hinoki Cypresses Genetically Differentiated 1 Million Years Ago
Population genetic analysis conducted by researchers at University of Tsukuba have revealed that natural Japanese hinoki cypress (Chamaecyparis obtusa) and, its variety, Taiwanese hinoki cypress (C. obtuse var. formosana) diverged approximately 1 million years ago due to the geological separation of the Ryukyu Archipelago. The study also found that the Japanese variety has expanded over time, whereas the Taiwanese population has become fragmented and declined. Furthermore, the unique genetic characteristics of populations at the northern and southern distributional limits of Japan warrant high conservation priority.

Tsukuba, Japan — Hinoki cypress is a commercially vital species used as a high-quality building material, second only to sugi cedar in planted forest area and timber production in Japan. Natural hinoki cypress forests extend from Fukushima Prefecture in the north to Yakushima Island in the south. Taiwanese hinoki cypress is a variety and close relative of the Japanese hinoki, and its large-diameter timber was historically imported from Taiwan to Japan for constructing shrines and temples. By conducting a comprehensive population genetic analysis, this study aimed to elucidate genetic diversity, regional genetic structure, and evolutionary history across the entire natural distribution range of both species.

The results revealed clear genetic differentiation between Japanese and Taiwanese hinoki cypress, with divergence estimated to have occurred approximately 1 million years ago during the early Pleistocene epoch. The Ryukyu Arc, a chain of islands stretching from Southern Kyushu, Japan, to Taiwan, was once connected by a land bridge. Its eventual breakup led to geographic isolation between the two species. The study also indicates that Japanese hinoki is better adapted to warm, rainy summers, while Taiwanese hinoki cypress is suited to cold, rainy winters. Within Japan, genetic differences were observed among populations in Yakushima, central and western Honshu, and central and northern Honshu, with a generally increasing trend in population sizes. Populations at the northern (Fukushima) and southern (Yakushima) limits exhibited highly distinctive genetic characteristics, making them high-priority targets for conservation. On the other hand, in Taiwan, populations showed no clear geographic patterns of genetic differentiation and were estimated to be fragmented and declining.

The movement of Japanese hinoki cypress seedlings is currently regulated under the Forestry Seeds and Seedlings Transfer Act, which divides populations into three categories based primarily on climatic differences. However, the findings of this study signifiy the need for a revised classification system based on genetic regional characteristics. Outbreeding depression resulting from interbreeding between genetically distinct groups adapted to local environments may lead to reduced environmental adaptability. Therefore, conservation of natural forests as genetic resources requires careful management of seedling transfer to preserve local genetic integrity.

Publication:
Aihara, T., C.-H. Cheng, C.-P. Chen, et al. 2025.
The Historical Biogeography of Divergence in the Relict Cypress Chamaecyparis obtusa, and the Implications for Conservation and Management in East Asia.
Ecology and Evolution 15(10) : e72240. https://doi.org/10.1002/ece3.72240.

ABSTRACT
East Asia provides long-term stable refugia for relict plant species and supports high species richness. Chamaecyparis obtusa is a typical relict species that is now restricted to particularly warm, humid areas in East Asia, mainland Japan, and Taiwan. It is widely used for timber, and understanding its genetic characteristics within its natural range is important for appropriate management and conservation. This study used genome-wide single nucleotide polymorphisms (SNPs) to examine the historical biogeography as well as genetic characteristics of C. obtusa populations across its distribution range. High levels of genetic divergence were found between mainland Japan and Taiwan (0.673–0.717 FST). The initial divergence occurred around 1 million years ago (Ma) based on a neighbor-joining tree and 1.32 Ma (with a 95% confidence interval of 0.20–2.54 Ma) based on a DIYABC analysis, during the early Pleistocene when the land bridge connecting mainland Japan and Taiwan collapsed. Populations in mainland Japan exhibited higher genetic diversity, suggesting frequent gene flow and past population expansions. Within mainland Japan, both northern and southern marginal populations exhibited high levels of genetic distinctness and are considered to represent past refugia from the last glacial period. The populations in Taiwan exhibited lower genetic differentiation, even though infrequent gene flow was seen between them. All the C. obtusa populations studied exhibited random mating based on FIS values, and continuous conservation of restricted areas is indicated. The highly divergent populations emphasize the need for conservation, and seedling transfers between the different genetic clusters identified are not recommended.

1 Introduction
East Asia (EA) was generally not covered by ice sheets during the glacial periods of the Quaternary (2.6 million years ago (Ma)–present), allowing a greater persistence and higher species richness of vascular plants compared with other areas at the same latitude, such as North America (NA) and Europe (Kryshtofovich 1929; Latham and Ricklefs 1993; Qian and Ricklefs 2000). Accordingly, EA has provided long-term stable refugia for relict plant species (Qian and Ricklefs 2000; Manchester et al. 2009; Tang et al. 2018). Paleogene–Neogene relict species (referred to as Tertiary relict species) were distributed across a large part of the Northern Hemisphere during the Paleogene and Neogene, but today are restricted to limited areas. These species often show disjunct distribution patterns in the warm and wet climatic conditions that prevail over NA, southwest Eurasia, and EA (Milne and Abbott 2002). In EA, Paleogene–Neogene relict species can be divided into two distinct groups, ‘Pacific track’ pattern and ‘Atlantic track’ pattern, which reflect differences in divergence time and migration routes (Milne and Abbott 2002). Within the ‘Pacific track’ pattern, plant taxa that are distributed disjunctively in Japan and NA are thought to have migrated via the Bering land bridge (BLB) before it was broken (4.8–5.5 Ma; Marincovitch Jr. and Gladenov 1999).

Chamaecyparis (Cupressaceae) is a relict genus; fossils have been found across vast areas of the Northern Hemisphere, from the Paleogene and Neogene (Liu et al. 2009.1), and exhibit a typical EA–NA disjunct distribution (Farjon 2005). Within this genus, C. obtusa was thought to be a relict species in EA that had migrated via the BLB because a sister species exists in NA, C. lawsonia (Wang et al. 2022). Chamaecyparis obtusa is now restricted to particularly warm humid areas in EA, mainland Japan (C. obtusa s.s.; in this study, referred to as C. obtusa for convenience) and Taiwan (C. obtusa var. formosana). Chamaecyparis obtusa var. formosana in Taiwan is distinguished from C. obtusa in mainland Japan by its smaller and finer foliage and much smaller cones (Bailety 1914). It is known that more than 100 plant species are distributed across both mainland Japan and Taiwan (Hsieh 2003), even though these land masses have not been connected directly via the Ryukyu islands since the early Pleistocene (Ota 1998). The process of divergence in plant taxa between mainland Japan and Taiwan could be key to understanding the plant richness and refugia of relict species in EA.

Previous studies have suggested that C. obtusa in Japan and C. obtusa var. formosana in Taiwan diverged 1.3 Ma (Wang et al. 2003.1), and C. obtusa var. formosana is nested in the clade of C. obtusa (Liao et al. 2010). It therefore appears that the species migrated from mainland Japan to Taiwan (Huang 2014), although only limited sample numbers in Japan have been studied. However, Quercus glauca and Trochodendron aralioides, which also distribute disjunctively in mainland Japan, the Ryukyu islands, and Taiwan, exhibit higher genetic diversity in Taiwan than in Japan (Huang et al. 2002.1, 2004), suggesting that the Taiwanese populations are ancestral. Natural C. obtusa populations do not exist today in the Ryukyu islands, but the phylogeographic history of C. obtusa can be re-visited using modern molecular methods with samples from across the entire species range. Differences in the results of genetic diversity and structure of C. obtusa populations within Japan have been observed between molecular markers (Uchida et al. 1997; Tsumura et al. 2007; Matsumoto et al. 2010.1). Therefore, analyses of the genetic characteristics of C. obtusa using genome-wide molecular methods and abundant samples would be informative. Next-generation sequencing (NGS) technology (Metzker 2010.2), which has been developed over the last decade, offers an effective genotyping system for population biology, and deciphering regional population demographies and range shifts using NGS could provide a deeper insight into the biogeographical history of target species.

Chamaecyparis obtusa is important for its horticultural value; it is characterized by a pleasant scent, a very light, almost white color, strength, and resistance to humidity and decay. In Japan, the timber of this species has been used for house construction as well as temple and shrine construction since at least the Nara era (AD 710; Suzuki 2002.2). Both the amount of timber products and plantation area of C. obtusa in Japan are the second largest, after Cryptomeria japonica, representing about 3176 thousand m³ (about 6.5% of the net timber production) and 2568 thousand ha (about 6.8% of the national land area) in 2024 (Japan Forest Agency 2024). In Japan today, natural forests of this species are scattered in isolated locations (Figure 1a) ranging from the Fukushima Prefecture (37°10′ N) in northern Japan to Yakushima Island (30°15′ N) in southern Japan. In Taiwan, C. obtusa var. formosana grows in the northern and central cloud forests at an altitude between 1500 and 2500 m a.s.l. (Forestry and Nature Conservation Agency 2023), and includes huge trees that are more than 1000 years old (Figure 1b). Japan used to import large high-quality timber from natural forests in Taiwan for its own temple and shrine construction, before the Taiwanese government prohibited the logging of natural forests in 1990 (Editorial Committee of History of Precious Woods 1986; Mineo and Matsushita 2021). Elucidating the genetic properties of such natural forest populations is crucially important for the conservation and appropriate management of C. obtusa.

Chamaecyparis obtusa in Japan (a) (May 2025 in Chichibu) and C. obtusa var. formosana in Taiwan (b) (November 2023 in Heping District).

In this study, we aimed to examine the genetic characteristics of different populations across the whole species range of C. obtusa and C. obtusa var. formosana, and infer the populations' demographic history and any potential change in distribution since the last glacial maximum (LGM) by using molecular methods to analyze genome-wide regions. Finally, by looking at the divergence of the populations of C. obtusa and C. obtusa var. formosana, we discussed how they are restricted to those regions and the conservation and management of this species.

This elegant confirmation of the theory of evolution is also, incidentally and unintentionally, a refutation of creationism on several levels. Firstly, it reaffirms the validity of Darwinian evolution — the same scientific framework that creationists have been trying, and failing, to disprove for more than 160 years. Secondly, it demonstrates how multiple, independent strands of science converge on evolution as the explanation for biodiversity: in this case, the timing of the divergence aligns precisely with geological evidence for the isolation of the two populations. And thirdly, the divergence itself occurred roughly one million years before creationists believe the Earth existed, underscoring the incompatibility of their claims with physical reality.

In short, this single paper provides compelling evidence that life on Earth is the product of a long evolutionary process unfolding over deep time, shaped in part by the geological forces that continue to reshape the planet today. Earth is not "fine-tuned" for life; rather, life is "fine-tuned" Earth, and evolution is the mechanism that keeps it in tune.

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