Phylogeography of the Japanese giant flying squirrel, Petaurista leucogenys (Rodentia: Sciuridae): implication of glacial refugia in an arboreal small mammal in the Japanese Islands

To test the association between temperate forest dynamics and glacial refugia for arboreal small mammals, we studied the phylogeography of the Japanese giant flying squirrel ( Petaurista leucogenys ) using complete mitochondrial cytochrome b gene sequences (1140 bp). This squirrel is endemic to three of Japan's main islands: Honshu, Shikoku, and Kyushu. We examined 58 specimens of P. leucogenys collected from 40 localities in Japan. Additionally, two individuals with unknown sampling localities were included in phylogenetic analyses. There were 54 haplotypes of P. leucogenys. We found five major phylogroups (Northern, Central, South-eastern, South-western, and Southern). These phylogroups may have originated from glacial refugia during the Late Pleistocene. After the last glaciation, the Northern phylogroup, widely distributed in eastern Japan, could have extensively expanded northward from its refugia. By contrast, in western Japan, population expansion was restricted to western Japan. All members of four phylogroups existed in western Japan during glaciations. The complicated phylogeographical pattern of P. leucogenys populations originating from western Japan may have resulted from the long history.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 47–60.     

Estimating effects of global warming from past range changes for cold demanding refugial taxa: A case study on South-west Anatolian species Poecilimon birandi

Although changes in biodiversity and in ecosystems are surely caused by a range of interacting drivers, such as natural or human-induced factors, one of the important drivers having major impacts on climate and biodiversity and leading to range changes and fragmentation is global warming. Defining past range changes/fragmentations during interglacial periods may provide tools to understand possible impacts of global warming on present biodiversity. To test this assumption we studied a marker gene in the bush-cricket Poecilimon birandi, a species confined to South-west Anatolia that demands a cold climate. Haplotypes of P. birandi constituted three main phylogroups,West, East and Demre. All haplotypes are unique to the respective phylogroup. An AMOVA suggested considerable divergence at all hierarchical levels. Though there is a strong isolation between phylogroups, the East and West groups harbour considerable haplotype diversity. Most of the demographic analyses suggest stable historical populations for the West and East phylogroups, but a coalescent-based demographic analysis indicates a bottleneck for the West phylogroup. The main conclusions are; (i) P. birandi contains considerable phylogenetic signal in 16S rDNA, (ii) there were at least three contemporaneous radiations, which might have originated from isolated refugial populations during Pleistocene, (iii) within a refugium, range changes induced by climatic shifts may be only vertical through an altitudinal gradient, (iv) significant genetic structure can arise in a small heterogeneous area, if the species requires particular habitats and has weak dispersal ability, (v) climatic shifts may cause fragmentation or extinction of populations, but can also lead to divergence of populations suffering from fragmentation, and (vi) altitudinal heterogeneity plays a buffering role, allowing for survival of the refugial biodiversity.     

Historical vicariance and postglacial colonization effects on the evolution of genetic structure in Lophocereus,a Sonoran Desert columnar cactus

Distinguishing the historical effects of gene migration and vicariance on contemporary genetic structure is problematic without testable biogeographic hypotheses based on preexisting geological and environmental evidence. The availability of such hypotheses for North America's Sonoran Desert has contributed to our understanding of the effect of historical vicariance and dispersal events on the diversification of this region's vertebrate biota but have not yet been applied to its flora. In this paper we describe a detailed allozyme analysis of the population genetic structure and phylogeography of the Sonoran Desert columnar cactus, Lophocereus schottii (senita). Inferred phylogroup distributions reflect two historical vicariance events: (1) a middle Pliocene northward transgression of the Sea of Cortéz that is reflected in well-supported Baja California peninsular and continental phylogroups but not in current taxonomic treatments of the species; and (2) a late Pliocene transpeninsular seaway across southern Baja that is reflected in tentative support for peninsular and southern Cape Region phylogroups corresponding to taxonomic varieties L. schottii var. schottii and L. schottii var. australis, respectively. A middle Pleistocene midpeninsular seaway hypothesized to explain congruent phylogroup distributions in several vertebrate taxa is not reflected in L. s. var. schottii, nor is the distinction of a third variety, L. s. var. tenuis, from continental populations of L. s. var. schottii. Linear regression of pairwise estimates of interpopulation differentiation (M and F(ST)/[1 - F(ST)]) on interpopulation geographic distance revealed significant evidence of isolation by distance within peninsular and continental phylogroups but not between them, consistent with historical vicariance between but not within these regions. We also found significant evidence of isolation by distance between putative L. s. var. schottii and L. s. var. australis phylogroups, suggesting that reproductive isolation between peninsular and Cape Region forms is incomplete. Within peninsular, but not continental, phylogroups, northward range expansion from southern Pleistocene refugia is reflected in significant declines in genetic variation with increasing latitude and in an area phenogram in which populations are progressively nested from south (ancestral) to north (descendant) along the Baja peninsula. Although the geographic concordance of phylogenetic topologies suggests that ancient vicariance events, and not dispersal, have primarily influenced the biogeographic distributions of Baja's vertebrate biota, the phylogeographic structure of L. schottii suggests that Sonoran Desert plant species may exhibit genetic signatures of postglacial range expansion and gene flow as well as vicariance.     

Collation of data on the ploidy levels and mitochondrial DNA phylogenetic lineages in the silver crucian carp <Emphasis Type="Italic">Carassius auratus gibelio</Emphasis> from Far Eastern and Central Asian populations

The distribution of the diploid and triploid forms and the correspondence between ploidy and mitochondrial DNA (mtDNA) phylogenetic lineages of the silver crucian carp have been studied in Far Eastern water bodies and the Syr Darya River. Both diploid and triploid forms have been found in large river systems (the Amur, Suifun, Tumangan, and Syr Darya river basins). Only the diploid form has been detected in lakes of Bol’shoi Pelis Island (Peter the Great Bay of the Sea of Japan), Sakhalin Island, and the Kamchatka River basin (the Kamchatka Peninsula). It has been confirmed that there are two mtDNA phylogroups in the silver crucian carp in the area studied. Both mtDNA phylogenetic lineages are present in the Suifun and Tumangan river basins. Only one mtDNA phylogroup (characteristic of the gynogenetic form) has been detected in two samples from the Amur River and in the Syr Darya population. The other mtDNA phylogroup is predominant in insular populations and in Kamchatka. The gynogenetic form carries only mtDNA phylogroup I, whereas both phylogroups have been found in diploid bisexual fish. The existence of only two mtDNA phylogroups substantially differing from each other indicates that the gynogenetic form has emerged from the diploid form only once and evolved independently for a long time after that. The absence of haplotypes transitional between the two mtDNA phylogroups suggests that the secondary contact between the gynogenetic and bisexual forms in continental populations occurred within recent historical time. The obtained data confirm that genetic (though asymmetric) exchange between the two forms is possible, which explains the high morphological and, probably, genetic similarity between them.     

Mitochondrial DNA phylogeography of Semisulcospira libertina (Gastropoda: Cerithioidea: Pleuroceridae): implications the history of landform changes in Taiwan

The mitochondrial DNA cytochrome c oxidase subunit I sequences from 95 specimens of Semisulcospira libertina in Taiwan were identified as two major phylogroups, exhibiting a southern and northern distribution, north of Formosa Bank and south of Miaoli Plateau. The genetic distance between these two phylogroups was 12.20 %, and the distances within-phylogroups were 4.97 and 5.56 %. According to a molecular clock of 1.56 % per lineage per million years, the divergence time between these two major phylogroups was estimated at 4.94 million years ago (mya), with the two phylogroups forming at 3.64 and 3.75 mya, respectively. Moreover, the geological events have suggested that Taiwan Island emerged above sea level at 4–5 mya, and became its present shape at 2 mya. These results suggested that these two phylogroups might originate from two independent ancestral populations or divergent before colonizing Taiwan. Within South phylogroup, the initial colonization was hypothesized to be in Kaoping River (WT), followed by its northward. The high divergence between south- and north of WT River was influenced by the formation of the Kaoping foreland basins. Within North phylogroup, the colonization was from central sub-region through paleo-Miaoli Plateau to northern and northeastern sub-regions. This study showed that the landform changes might have shaped the genetic structure of S. libertina in concert. Apparently, two cryptic species or five different genetic stocks of S. libertina could be identified; these results are useful for the evaluation and conservation of S. libertina in Taiwan.     

Collation of data on the ploidy levels and mitochondrial DNA phylogenetic lineages in the silver crucian carp Carassius auratus gibelio from Far Eastern and Central Asian populations

The distribution of the diploid and triploid forms and the correspondence between ploidy and mitochondrial DNA (mtDNA) phylogenetic lineages of the silver crucian carp have been studied in Far Eastern water bodies and the Syr Darya River. Both diploid and triploid forms have been found in large river systems (the Amur, Suifun, Tumangan, and Syr Darya river basins). Only the diploid form has been detected in lakes of Bol'shoi Pelis Island (Peter the Great Bay of the Sea of Japan), Sakhalin Island, and the Kamchatka River basin (the Kamchatka Peninsula). It has been confirmed that there are two mtDNA phylogroups in the silver crucian carp in the area studied. Both mtDNA phylogenetic lineages are present in the Suifun and Tumangan river basins. Only one mtDNA phylogroup (characteristic of the gynogenetic form) has been detected in two samples from the Amur River and in the Syr Darya population. The other mtDNA phylogroup is predominant in insular populations and in Kamchatka. The gynogenetic form carries only mtDNA phylogroup I, whereas both phylogroups have been found in diploid bisexual fish. The existence of only two mtDNA phylogroups substantially differing from each other indicates that the gynogenetic form has emerged from the diploid form only once and evolved independently for a long time after that. The absence of haplotypes transitional between the two mtDNA phylogroups suggests that the secondary contact between the gynogenetic and bisexual forms in continental populations occurred within recent historical time. The obtained data confirm that genetic (though asymmetric) exchange between the two forms is possible, which explains the high morphological and, probably, genetic similarity between them.     

Mitochondrial DNA variation in diploid and triploid forms of silver crucian carp Carassius auratus gibelio

Variation of two mtDNA fragments amplified in polymerase chain reaction was compared by the RFLP method in a population of the sympatric bisexual (diploid) and gynogenetic (triploid) forms of silver crucian carp. The mtDNA haplotypes of all individuals differed in at least 2.5% of nucleotide substitutions and fall into two phylogroups. All gynogenetic individuals have haplotypes of a single phylogroup, whereas haplotypes of diploid fish belonged to both mtDNA phylogroups. This testifies to a possibility of transformation of gynogenetic individuals into a bisexual form, whereas the reverse process is either extremely rare or impossible.     

Late Pleistocene divergence and postglacial expansion in the Brazilian Atlantic Forest: multilocus phylogeography of Rhopias gularis (Aves: Passeriformes)

In the last decade, phylogeographic studies have revealed a complex evolutionary history of the Brazilian Atlantic Forest (AF) biota. Here, we investigated the evolutionary history of Rhopias gularis, an endemic bird of the AF, based on sequences of two mitochondrial genes and three nuclear introns from 64 specimens from 15 localities. We addressed three main questions: (1) Does the genetic diversity of R. gularis exhibit a distribution pattern congruent with the refuge hypothesis postulated for the AF? (2) Is the population genetic structure of R. gularis congruent with those observed in other AF species? (3) What were the possible historical events responsible for the population structure of this species? Our mtDNA data revealed two phylogroups: (1) phylogroup central‐south, with samples from the central and southern parts of the range; (2) and phylogroup north, which included individuals from southern Bahia. Nevertheless, nuclear loci did not reveal any evidence of population structure. Bottleneck tests indicated that the central‐south lineage experienced demographic expansion, starting around 20 kya, which coincides with the end of the last glacial maximum. However, there was no evidence of population growth in phylogroup north. Isolation with migration analysis indicated that these phylogroups split c.a. 304 kya, with limited gene flow among them. Palaeodistribution models indicated that R. gularis had a reduced distribution in the south and central AF during the last glacial maximum. Our results support a diversification scenario that is in accordance with proposed Pleistocene refugia. The phylogeographic results from our study exhibited spatial and temporal concordances and discordances with previous studies of organisms from the AF. Differences in habitat requirements of these species could be behind this complex scenario. Future studies correlating variables of the niche of these species with the observed phylogeographic patterns may help understand why there are congruent and incongruent results.     

Phylogeography of two sympatric giant flying squirrel subspecies,Petaurista alborufus lena and P. philippensis grandis (Rodentia: Sciuridae), in Taiwan

To test the association between Pleistocene forest dynamics relative to elevation and the population dynamics of arboreal small mammals, we examined the phylogeographical predictions for the genetic structure of the red and white giant flying squirrel (Petaurista alborufus lena) and the Indian giant flying squirrel (P. philippensis grandis) using complete mitochondrial control region sequences. Both giant flying squirrels are endemic subspecies to Taiwan and are sympatric in much of their range. In the phylogenetic analyses, we included 35 specimens of P. alborufus lena collected from 20 localities and five specimens with unknown sampling localities. Also, we phylogenetically examined 32 specimens of P. philippensis grandis from 18 localities and three specimens with unknown sampling localities. We identified 36 haplotypes of P. alborufus lena and 33 haplotypes of P. philippensis grandis. Although we did not recognize major phylogroups, we found several minor phylogroups in both subspecies, suggesting similar evolutionary histories. Phylogeographical and demographic tests showed distributions of these two subspecies expanded into coniferous and mixed forests that developed during glaciation in Taiwan's lowlands and middle lands. This suggests that these two Petaurista subspecies shifted elevation from mountainous areas to lowlands during glaciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 404–419.     

Phylogeographic analysis reveals two periods of divergence in large-scaled redfin Tribolodon hakonensis (Pisces, Cyprinidae)

Analysis of mtDNA variation in one of the amphidromic Far Eastern redfins, Tribolodon hakonensis, revealed the presence of three considerably genetically different mtDNA phylogroups in the individuals from the Russian part of the range. These data suggest the presence of the two periods of divergent evolution in the history of the species examined. Comparison of the haplotype distributions from different phylogroups over the species range revealed geographic localization of only one phylogroup in the population samples from southern continental coastal regions of the Sea of Japan. At the same time, two other phylogroups were found in almost equal ratios in northern continental samples and near the Sakhalin Island. These results suggest that the first stage of the divergent evolution, which occured between Pliocene and Pleistocene, resulted in the formation of genetically isolated form (probably, a species) in the region of the Sea of Japan. The second, later period of divergence, probably associated with the separation of the Sea of Okhotsk from the Pacific Ocean then ended with the integration of earlier genetically separated forms into one species with the common gene pool.