Takema Saitoh

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.

DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago

DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese‐breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour‐joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan‐specific cryptic species from trans‐Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans‐Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.

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.

Phylogenetic Relationship And Song Differences Between Closely Related Bush Warblers (Cettia seebohmi And C. diphone)

Abstract We investigated the phylogenetic relationship and differences in the song structure between the Philippine Bush Warbler (Cettia seebohmi) and the Japanese Bush Warbler (C. diphone). We compared complete sequences of the mitochondrial cyt-b gene of C. seebohmi to those of other Cettia taxa from GenBank and found C. seebohmi formed a monophyletic group with C. haddeni and C. diphone. The phylogenetic tree also suggests that C. seebohmi is more closely related to C. haddeni than to C. diphone although this was not strongly supported due to the low bootstrap values. The estimated nucleotide differences between C. seebohmi and C. haddeni (4.37%), and between C. seebohmi and C. diphone (3.87–4.37%) were larger than the inter-subspecific difference between C. diphone borealis and C. d. cantans (2.44%). Cettia seebohmi, C. haddeni, and C. diphone diverged prior to the subspecies divergences of C. diphone. The basic structure of songs was similar in C. seebohmi and C. diphone; all songs consisted of pure monotone whistles followed by variably modulated warbles. However, sonagraphic parameters showed statistically significant differences between species. It is reasonable to regard C. seebohmi and C. diphone as separate species.

Distribution of Two Distinctive Mitochondrial DNA Lineages of the Japanese Robin Luscinia akahige Across Its Breeding Range Around the Japanese Islands

The genetic structure of the Japanese robin Luscinia akahige across its breeding range was investigated based on mitochondrial cytochrome b and a control region sequence to reveal the phylogeographic history of this species, which is endemic to the islands around Japan. We obtained the 2,230-bp combined sequences of 77 robins from eight locations and identified 33 haplotypes. Of these, two phylogenetic clades, Ak and Tn, were evident in both maximum-likelihood and Bayesian analyses. Clade Ak was found throughout the range, whereas clade Tn was endemic to the Izu Islands, resulting in the mixture of both clades at this location. These two mtDNA lineages were inferred to have originated in different refugia during the mid-Pleistocene glacial period, probably one in southwestern Japan and the other in the Izu Islands. The population in the Izu Islands has been described as an independent subspecies, tanensis, and is known to be distinguished phenotypically from the nominotypical akahige. Therefore, the distribution pattern of the two mtDNA lineages may be better explained by past introgression of mitochondrial DNA rather than by assuming continuous hybridization with immigrants from the mainland. Future nuclear DNA analysis is needed to evaluate the effect of this introgression event on the genetic bases of the current Izu Islands population. Within clade Ak, the haplotype distribution pattern was inferred to be primarily a result of contiguous range expansion, reflecting the history of both range and population expansion after the last glacial period, with some effects of allopatric fragmentation in its southwestern range.

The complex systematics of the Acrocephalus of the Mariana Islands, western Pacific

Abstract The Nightingale Reed-Warbler (Acrocephalus luscinius) is known from six islands of the Mariana Archipelago in the Pacific Ocean. A recent phylogeny of the reed-warblers of the Pacific islands suggested however that the species was polyphyletic, the result of at least three independent colonisations. We present here a complete phylogeny of the Mariana reed-warblers that includes two populations, from Alamagan and Aguiguan, not yet studied using molecular techniques. Both of these populations belong to the Pacific Acrocephalus radiation, with birds from Alamagan closely related to the Saipan population, and those from Aguiguan having unresolved relationships within the Micronesian clade. These results suggest that the Mariana Islands experienced multiple colonisations by reed-warblers. We use a combination of molecular phylogeny and biometry of museum specimens to propose a new species-level taxonomy for Acrocephalus of the Marianas. These results have conservation implications for the two remaining populations, on Alamagan and Saipan, which probably belong to the same taxon, Acrocephalus hiwae (Nightingale Reed-Warbler).

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family

Abstract Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the worlds species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino‐Himalayan Mountains or these mountains and Central Asia–Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid‐Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo‐/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials—contrary to the usual view that glacial periods resulted mainly in fragmentations.