Yoshimitsu Shigeta

Conflict between genetic and phenotypic differentiation: the evolutionary history of a 'lost and rediscovered' shorebird.

Understanding and resolving conflicts between phenotypic and genetic differentiation is central to evolutionary research. While phenotypically monomorphic species may exhibit deep genetic divergences, some morphologically distinct taxa lack notable genetic differentiation. Here we conduct a molecular investigation of an enigmatic shorebird with a convoluted taxonomic history, the White-faced Plover (Charadrius alexandrinus dealbatus), widely regarded as a subspecies of the Kentish Plover (C. alexandrinus). Described as distinct in 1863, its name was consistently misapplied in subsequent decades until taxonomic clarification ensued in 2008. Using a recently proposed test of species delimitation, we reconfirm the phenotypic distinctness of dealbatus. We then compare three mitochondrial and seven nuclear DNA markers among 278 samples of dealbatus and alexandrinus from across their breeding range and four other closely related plovers. We fail to find any population genetic differentiation between dealbatus and alexandrinus, whereas the other species are deeply diverged at the study loci. Kentish Plovers join a small but growing list of species for which low levels of genetic differentiation are accompanied by the presence of strong phenotypic divergence, suggesting that diagnostic phenotypic characters may be encoded by few genes that are difficult to detect. Alternatively, gene expression differences may be crucial in producing different phenotypes whereas neutral differentiation may be lagging behind.

Old divergences in a boreal bird supports long-term survival through the Ice Ages

BackgroundUnlike northern Europe and most of northern North America, the Eastern Palearctic and the northwesternmost tip of North America are believed to have been almost unglaciated during the Quarternary glacial periods. This could have facilitated long-term survival of many organisms in that area. To evaluate this, we studied the phylogeography in east Asia and Alaska of a boreal migratory passerine bird, the Arctic Warbler Phylloscopus borealis, and compared our results with published data on especially North American species.ResultsIn a sample of 113 individuals from 18 populations we identified 42 haplotypes of the mitochondrial cytochrome b gene, which separated into three clades: A - Alaska and mainland Eurasia (except Kamchatka); B - Kamchatka, Sakhalin and Hokkaido; and C - Honshu, Shikoku and Kyushu (i.e. Japan except Hokkaido). The oldest split among these clades, between A/B and C, is estimated to have taken place sometime between the mid Pliocene and early Pleistocene, and the second divergence, between clades A and B, in the early to mid Pleistocene. Within all of the three main clades, there are signs of population expansion.ConclusionsThe Arctic Warbler separated into three main clades in close succession around the Pliocene/Pleistocene border, with the two northern clades diverging last. All three clades probably experienced population bottlenecks during the Pleistocene as a result of range shifts and contractions, but nevertheless survived and maintained their integrities. Several other clades of Northeastern Palearctic birds are noted to have diversified during the Pliocene. In contrast, avian species or phylogroups presently occupying formerly glaciated North American ground are generally younger. The differences between these regions could be due to slower speciation rates in the Eastern Palearctic due to less fragmentation of forest habitats during glacial periods, or to longer survival of Eastern Palearctic clades as a result of less severe conditions in that region compared to northern North America. Several other Palearctic organisms show concordant biogeographical patterns to that of the Arctic Warbler, indicating common causes of their diversifications.

A Survey for Yersinia pseudotuberculosis in Migratory Birds in Coastal Japan

Yersinia pseudotuberculosis was isolated from three specimens of two species of birds, the black-faced bunting (Emberiza spodocephala) and pied wagtail (Motacilla alba), of 528 specimens of birds examined from coastal regions in Japan. The two isolated strains of Y. pseudotuberculosis were identified as serovar 4b and serovar 3. This is the first isolation of Y. pseudotuberculosis from birds in Japan. Yersinia enterocolitica was isolated from three specimens of the pied wagtail, one specimen of the reed bunting (Emberiza schoeniclus) and one specimen of the rustic bunting (Emberiza rustica). Yersinia frederiksenii was isolated from two specimens of the gray-rumped sandpiper (Heteroscelus brevipes). Yersinia intermedia was isolated from one specimen of the pied wagtail.

Morphological differences among populations of the Arctic Warbler with some intraspecific taxonomic notes

Abstract We studied the morphological differences among breeding populations of the Arctic Warbler Phylloscopus borealis across the Far East and Alaska. We previously identified three strong monophyletic clades of the Arctic Warbler based on molecular phylogeny using mitochondrial DNA (cytochrome b): Clade A (Alaska, Anadyr, and Magadan), Clade B (Kamchatka, Sakhalin, and Hokkaido), and Clade C (Honshu, Shikoku, and Kyushu). To identify whether there are external morphological differences among these three mitochondrial clades, we used canonical discriminant analysis (CDA) and principal component analysis (PCA). CDA showed that the morphological differences among populations corresponded well with each mtDNA clade, with classification accuracies of 94.55%. In particular, populations of Clade C differed distinctly from Clades A and B in their longest natural wing and P10-PC lengths. The measurements of Clades A and B partly overlapped. In contrast, PCA enabled us to identify all individuals of each population correctly. Arrangement of populations in order of body size based on PC1 were Honshu>Kamchatka>Hokkaido/Sakhalin>Magadan/Alaska. We also found a latitudinal trend in body size and P10-PC lengths, which became smaller with increasing latitude. This trend in body size provides an example of reversed Bergmanns rule in birds. The latitudinal trend of P10-PC lengths may be related to migration distance. Our morphometric analyses suggest that the Japanese subspecies P. b. xanthodryas (Honshu and Kyushu) is readily identifiable based on measurements, whereas although the subspecies P. b. examinandus and P. b. borealis/kennicotti are also identifiable, some individuals of the latter two clades are similar in morphology.

Current status of the Northern Goshawk Accipiter gentilis in Japan based on mitochondrial DNA

Abstract Although the Northern Goshawk Accipiter gentilis is not designated a threatened species in Japan, it is thought that its population once experienced a decrease. To evaluate the current status of the goshawk, we sequenced the mitochondrial DNA control region and determined its variation among individuals. Considering that part of the Japanese population migrates or moves seasonally, we divided the samples into two categories (breeding and non-breeding season, based on sampling dates) and then calculated indices of genetic diversity and statistics for each category. Among 145 samples, we found ten haplotypes, of which two were dominant in both frequency and range. Haplotype diversity and nucleotide diversity were 0.63±0.04SD and 0.0018±0.0014SD, respectively. Comparing this diversity with those of other species, we concluded that the status of the Northern Goshawk in Japan is neither urgent nor secure. Significant genetic distance was not detected between the breeding and non-breeding groups, thus we could find no evidence of seasonal movement. The long-term effective female population size was estimated at 3,000 to 30,000 individuals. A recent population decline was not detected from the mismatch distribution. Therefore, the past population decline of the goshawk may not have been very serious. Future studies should consider the genetic structure of goshawks that inhabit other areas near Japan.

Increasing the Number of Captured Migrant Buntings at an Autumn Stopover Site using Sound Lures

Abstract We compared the number of individuals and juvenile-to-adult ratio of Rustic Bunting Emberiza rustica, Black-faced Bunting E. spodocephala, and Reed Bunting E. schoeniclus captured in sound-lured and unlured mist nets at an autumn stopover site during October and November 2004–2011. The numbers of all three buntings captured and the proportion of juveniles of Black-faced and Reed buntings increased with sound luring. Use of sound luring could help further our understanding of migration ecology and conservation of the globally vulnerable Rustic Bunting and its congeners through increasing the number of individuals captured and banded.