Takahiro Yonezawa

In order to investigate the genetic diversity, differentiation, gene flows, and propagation routes of Island Southeast Asian (ISEA) goats, we genotyped 50K genome-wide SNPs in 57 Philippine and 30 Indonesian Katjang goats. Correlations of the distance from the domestication center and the genetic diversities of 21 Asian populations were significantly negative. A relatively high diversity of the Philippine population (He = 0.363) against the distance from the domestication center suggests a history of admixture, notably without large effects on their Katjang phenotype. This was confirmed by supervised PCA (Principal Component Analysis), f3 coancestry and f4 admixture analyses, Treemix-inferred migrations and model-based clustering (Admixture program). The inferred differential admixture of ISEA goats agreed with previously reported fixation of mtDNA haplogroup B in Indonesia, but not in the Philippines, and with high frequencies of African or European Y-chromosomal haplogroups that were not observed in Mainland Southeast Asia. We propose that admixture of cosmopolitan European and African goats into ISEA was mediated by a unique feature of the domestic goat, the maritime transport of goats during the colonial period as a source of provisions. This was followed by more recent imports of popular breeds such as Boer, and other cosmopolitan breeds.

East African cattle, including Malagasy native cattle (ZMA), are generally thought to have been shaped by admixture between African taurine and Asian indicine lineages, but the detailed position and formation history of ZMA within this broader diversity remain unclear. We analyzed worldwide SNP data from 145 cattle populations comprising 4093 individuals using principal component analysis (PCA), pairwise weighted F _ST , outgroup‐f3, f4, qpWave, and qpGraph. ZMA fell along the African taurine–Asian cattle axis in PCA. Although several West African taurine populations showed the highest absolute outgroup‐f3 values with ZMA, outgroup‐f3 profile comparisons showed that ZMA was most closely matched by East African cattle, especially East African Shorthorn Zebu, Boran, and Sheko, consistent with a shared African taurine ancestry background. However, f4, qpWave, and qpGraph showed that these relationships are not adequately explained by a simple clade‐like relationship or a single shared admixture event, but instead suggest multiple waves of gene flow from different Asian indicine populations. Our results refine African‐wide models of heterogeneous indicine ancestry by showing that, in the East African–Malagasy context, ZMA are best understood as part of a shared African taurine‐related ancestry background overlaid by later lineage‐specific and internally heterogeneous indicine‐related admixture histories.

Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae: Fordini) are obligate parasites that only use Rhus species (Anacardiaceae) as their primary host plants, and each aphid species feeds specifically on one or two sister Rhus species. Both aphids and Rhus hosts exhibit the same disjunct distribution pattern between East Asia and eastern North America. We assembled complete mitochondrial genomes and universal single‐copy nuclear genes for Rhus gall aphids using a genome skimming method and estimated their phylogeny from each dataset. Results strongly supported the monophyly of the Rhus gall aphids Fordini and two genera, Floraphis and Melaphis . However, the relationships among genera were inconsistent between the different datasets. We also estimated the relationships of Rhus host plants from published chloroplast genomes. The chloroplast phylogeny strongly supported Rhus monophyly and relationships among Rhus species. Dating analyses suggest that the most recent common ancestor of Rhus gall aphids was much older than that of their host plants. However, the divergence times and relationships among some Rhus gall aphid species, particularly those with more recent divergence times, were consistent with the ages and relationships of their corresponding primary host plants. This may suggest that Rhus gall aphids established an initial association with stem‐group ancestors of Anacardiaceae and acquired extant Rhus hosts as they evolved or through host switching from another plant group. Divergence time estimates implied that the separation of North America and Eurasia from the Laurasia supercontinent and the subsequent disappearance of the Bering Land Bridge, respectively, have played an important role in the divergence of the eastern North American Melaphis and the East Asian lineage. Our results provide new insights into the coevolution of insects and host plants.

Japanese native chickens (JNCs) comprise approximately 50 breeds, making Japan a diversity hotspot for native chicken breeds. JNCs were established through the repeated introduction of chickens from foreign countries. Jidori, which is the generic name of JNC breeds whose ancestral morphology resembles that of their wild progenitor (red junglefowls), is generally thought to have propagated from north East Asia (Korea and north China) to ancient Japan. However, mitochondrial haplogroup D, which is abundant in Island Southeast Asia (ISEA) as well as the Pacific but relatively rare in other regions, can be observed in some Jidori breeds (e.g., Tosa-Jidori, Tokuji-Jidori) with high frequency, leading to speculation that chickens from ISEA or the Pacific also contributed genetically to JNCs. To test this hypothesis, we sequenced the mitochondrial genomes of Jidori breeds and conducted phylogeographic analysis. Our results indicate that the JNC Haplogroup D belongs to Sub-haplogroup D2, which is currently only observed in Xinjiang, northwest China, and not to Sub-haplogroup D1, which is widely distributed in the ISEA-Pacific region. The other mitochondrial haplogroups of Jidori examined in this study also showed affinity to those of chickens native to north East Asia. Therefore, our findings support the north East Asian origin hypothesis for Jidori.

It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution.

We examined the weight distribution of skeletal muscles of the red jungle fowl, then compared these values with those of domesticated populations to determine how muscle distribution has changed by selecting breeding. Sonia, Fayoumi, and Rhode Island Red were selected for comparison from livestock breeds, while Japanese Shamo and Thai fighting cocks were selected from cockfighting groups. Principal component analysis was applied using body size‐free data. The mass distribution of muscles clearly differed between the wild, livestock, and cockfighting groups, demonstrating that muscle distribution has changed after selecting breeding, coupled with functional demands of each group. The red jungle fowl, which has the ability to fly, could be clearly distinguished from the flightless domesticated populations due to differences in flight pectoral muscle size. The cervical muscles in the wild population were smaller than in the domesticated groups; these do not contribute to flight. The gluteal muscles were larger in the fighting cock group, functionally coupled to their traditionally preferred upright posture. Wild bird populations typically exhibit reduced weight of their hind limbs, associated with flight, but as the red jungle fowl displays largely terrestrial behavior, these muscles are similar in arrangement and relative size to those of the livestock groups. We showed that the mass distribution pattern of skeletal muscles expresses selecting breeding strategy and clearly reflects the specific traits for each group.

Objective: In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, “Jidori”, “Shoukoku”, and “Shamo”. Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan.Methods: Maximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences. Results: This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that TosaJidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1.Conclusion: The sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.

Phylogenetic trees based on multiple genomic loci enable us to estimate the evolution of functional constraints that operate on genes based on lineage-specific fluctuation of the evolutionary rate at particular gene loci, “gene–branch interactions”. Using this information as predictors, our previous work inferred that the common ancestor of placental mammals was nocturnal, insectivorous, solitary, and bred seasonally. Here, we added seven new continuous traits including lifespan, bodyweight, and five reproduction-related traits and inferred the coevolution network of 14 core life history traits for 89 mammals. In this network, bodyweight and lifespan are not directly connected to each other; instead, their correlation is due to both of them coevolving with gestation period. Diurnal mammals are more likely to be monogamous than nocturnal mammals, while arboreal mammals tend to have a smaller litter size than terrestrial mammals. Coevolution between diet and the seasonal breeding behavior test shows that year-round breeding preceded the dietary change to omnivory, while seasonal breeding preceded the dietary change to carnivory. We also discuss the evolution of reproductive strategy of mammals. Genes selected as predictors were identified as well; for example, genes function as tumor suppressor were selected as predictors of weaning age.

The rock ptarmigan Lagopus muta is a grouse widely distributed in the arctic and subarctic regions of Eurasia and North America. The range of Japanese endemic subspecies (Japanese rock ptarmigans: L. m. japonica) is the southernmost of this species, but their origin is little known. Here, we determined the complete mitogenome of this subspecies and carried out the phylogenetic analysis. It was demonstrated that Japanese rock ptarmigans are old divergent lineage.