Genetic structure and relationships of 16 Asian and European cattle populations using DigiTag2 assay

In this study, we genotyped 117 autosomal single nucleotide polymorphisms using a DigiTag2 assay to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations, including nine cattle breeds and seven native cattle. Phylogenetic and principal component analyses showed that Bos taurus and Bos indicus populations were clearly distinguished, whereas Japanese Shorthorn and Japanese Polled clustered with European populations. Furthermore, STRUCTURE analysis demonstrated the distinct separation between Bos taurus and Bos indicus (K=2), and between European and Asian populations (K=3). In addition, Japanese Holstein exhibited an admixture pattern with Asian and European cattle (K=3‐5). Mongolian (K=13‐16) and Japanese Black (K=14‐16) populations exhibited admixture patterns with different ancestries. Bos indicus populations exhibited a uniform genetic structure at K=2‐11, thereby suggesting that there are close genetic relationships among Bos indicus populations. However, the Bhutan and Bangladesh populations formed a cluster distinct from the other Bos indicus populations at K=12‐16. In conclusion, our study could sufficiently explain the genetic construction of Asian cattle populations, including: (i) the close genetic relationships among Bos indicus populations; (ii) the genetic influences of European breeds on Japanese breeds; (iii) the genetic admixture in Japanese Holstein, Mongolian and Japanese Black cattle; and (iv) the genetic subpopulations in Southeast Asia.     

Long-term recovery of stream habitat structure and benthic invertebrate communities from in-stream restoration

Headwater streams channelized for water transport of timber in Finland are being restored to their pre-channelization state. The primary motivation is the enhancement of sport fisheries, but restoration probably has profound impacts also on other stream organisms. We assessed how such “single-goal” restorations affect benthic macroinvertebrate communities. We revisited the streams sampled by Laasonen et al. [Aquatic Conservation: Marine and Freshwater Ecosystems 8 (1998)] in the early 1990s when the streams had been recently restored. In 1997, the recovery period of these streams ranged from 4 to 8 years. Habitat structure among the stream types represented a distinct recovery gradient, with streams restored 1 month before sampling and natural streams being the endpoints of a gradient in moss cover (highest in natural, lowest in recently restored streams). Channelized streams supported a characteristic set of indicator species, whereas shifts in species composition between restored and natural streams were more gradual. Macroinvertebrate communities in unmodified streams changed little between the two surveys, whereas communities in restored streams had undergone considerable changes. In-stream restoration is an unpredictable disturbance, to which stream biota cannot have any evolved responses. Therefore, the relatively rapid recovery of habitat structure and macroinvertebrate communities in restored streams is encouraging. However, long-term monitoring of benthic communities in both restored and natural streams is needed to assess whether restoring rivers by these techniques will enhance the recovery of benthic biodiversity in boreal streams.     

Low mitochondrial DNA diversity of Japanese Polled and Kuchinoshima feral cattle

This study aims to estimate the mitochondrial genetic diversity and structure of Japanese Polled and Kuchinoshima feral cattle, which are maintained in small populations. We determined the mitochondrial DMA (mtDNA) displacement loop (D‐loop) sequences for both cattle populations and analyzed these in conjunction with previously published data from Northeast Asian cattle populations. Our findings showed that Japanese native cattle have a predominant, Asian‐specific mtDNA haplogroup T4 with high frequencies (0.43–0.81). This excluded Kuchinoshima cattle (32 animals), which had only one mtDNA haplotype belonging to the haplogroup T3. Japanese Polled showed relatively lower mtDNA diversity in the average sequence divergence (0.0020) than other Wagyu breeds (0.0036–0.0047). Japanese Polled have been maintained in a limited area of Yamaguchi, and the population size is now less than 200. Therefore, low mtDNA diversity in the Japanese Polled could be explained by the decreasing population size in the last three decades. We found low mtDNA diversity in both Japanese Polled and Kuchinoshima cattle. The genetic information obtained in this study will be useful for maintaining these populations and for understanding the origin of Japanese native cattle.