Evolutionary history of the honey bee Apis mellifera inferred from mitochondrial DNA analysis

Variability of mitochondrial DNA (mtDNA) of the honey bee Apis mellifera L. has been investigated by restriction and sequence analyses on a sample of 68 colonies from ten different subspecies. The 19 mtDNA types detected are clustered in three major phylogenetic lineages. These clades correspond well to three groups of populations with distinct geographical distributions: branch A for African subspecies (intermissa, monticola, scutellata, andansonii and capensis), branch C for North Mediterranean subspecies (caucasica, carnica and ligustica) and branch M for the West European populations (mellifera subspecies). These results partially confirm previous hypotheses based on morphometrical and allozymic studies, the main difference concerning North African populations, now assigned to branch A instead of branch M. The pattern of spatial structuring suggests the Middle East as the centre of dispersion of the species, in accordance with the geographic areas of the other species of the same genus. Based on a conservative 2% divergence rate per Myr, the separation of the three branches has been dated at about 1 Myr BP.     

Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets

Aim We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location Neotropical lowlands, including dry and humid forests. Methods Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well‐supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time‐frame as previously found for Pionus and Pyrilia. Main conclusions The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes.     

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp – Cyprinus carpio haematopterus , Yuanjiang River wild common carp – Cyprinus carpio rubrofuscus and Volga River wild common carp – Cyprinus carpio carpio ) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus , C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus , most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus ) to 1.47%(between C. c. carpio and C. c. rubrofuscus ). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus . Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus .     

Estimation of molecular clocks for ITS and 28S rDNA in Erysiphales

Based on a comparative phylogenetic analysis of Goloviomyces and their host tribes of the Asteraceae, we speculate that Golovinomyces first acquired parasitism to the Asteraceae after migration of the family into the Northern Hemisphere and before the divergence of the tribe Carduaeae. The divergence time of the Carduaeae is estimated to be 25.2Myr ago based on the molecular clock of rbcL sequences of the Asteraceae. When 25.2Myr is given at the node of the first split of the phylogenetic tree of Golovinomyces, nucleotide substitution rates of the Erysiphales are calculated to be 2.52 × 10^–9 per site per year (0.01D = 3.97Myr) in the ITS region and 6.5 × 10^–10 per site per year (0.01D = 15.4Myr) in the D1 and D2 regions of the 28S rDNA.     

Polymorphism analysis of <Emphasis Type="Italic">csd</Emphasis> gene in six <Emphasis Type="Italic">Apis mellifera</Emphasis> subspecies

The complementary sex determination (csd) gene is the primary gene determining the gender of honey bees (Apis spp). In this study we analyzed the polymorphism of csd gene in six Apis mellifera subspecies. The genomic region 3 of csd gene in these six A. mellifera was cloned, and identified. A total of 79 haplotypes were obtained from these six subspecies. Analysis showed that region 3 of csd gene has a high level of polymorphism in all the six A. mellifera subspecies. The A. m. anatolica subspecies has a slightly higher nucleotide diversity (π) than other subspecies, while the π values showed no significant difference among the other five subspecies. The phylogenetic tree showed that all the csd haplotypes from different A. mellifera subspecies are scattered throughout the tree, without forming six different clades. Population differentiation analysis showed that there are significant genetic differentiations among some of the subspecies. The NJ phylogenetic tree showed that the A. m. caucasica and A. m. carnica have the closest relationship, followed by A. m. ssp, A. m. ligustica, A. m. carpatica and A. m. anatolica that were gathered in the tree in turn.     

Did the Quaternary climatic fluctuations really influence the tempo and mode of diversification in European rodents?

The objective of this study was to establish whether the Quaternary climatic fluctuations influenced the tempo and mode of diversification in European rodents. Our case study is the subgenus Microtus (Terricola) distributed from western Europe to the Caucasus. Mitochondrial cytochrome b gene sequences from several representatives of all the species were used to generate maximum‐likelihood and Bayesian phylogenetic trees, to estimate divergence times, to identify biogeographic ancestral areas and to study the rate of diversification. Results showed that phylogenetic tree topologies were similar to previous published studies but with a better resolution at some nodes. The origin of Microtus (Terricola) is dated back to approximately 4.05 Myr in the Early Pliocene, and molecular dating for most Terricola species corresponds to several glacial periods of the Pleistocene. Results of the biogeographic ancestral area reconstruction suggest that Microtus (Terricola) diversified from the Caucasus/Turkey/Iran area through western Europe. Several periods of diversity variation were highlighted as follows: two period of diversity increase, between 3 and 2 Myr, and after 1 Myr; two periods of diversity decrease, before 3 Myr, and between 2 and 1 Myr. The diversification rate of Microtus (Terricola) was 0.353 ± 0.004 event/Myr, a rate similar to that of the Muridae family. To conclude, although the Pleistocene glacial conditions had an impact on the speciation events, the Quaternary does not appear however as a period with an exceptional rate of diversification for European rodents.     

Taxonomy of the bean goose-pink-footed goose

The bean goose Anser fabalis and the pink-footed goose A. brachyrhynchus breed in the tundra and taiga zones of Eurasia and eastern Greenland, and the taxonomy of the group based on morphology has been controversial. We investigated the phylogenetic relationships within the bean goose–the pink-footed goose complex using mitochondrial control region sequences of 199 individuals collected from the breeding areas in the Palaearctic and Eastern Nearctic. We found three mitochondrial clades geographically distributed to (1) Greenland, Iceland and Svalbard (A. brachyrhynchus), (2) the eastern taiga zone (former subspecies A. fabalis middendorffii), and (3) the western taiga and the tundra zone (subspecies A. fabalis rossicus, serrirostris and fabalis). MtDNA phylogeny suggests that morphological affinities between the taxa, e.g. in the bill structure, result from convergent evolution due to adaptation to similar habitats. Although a latitudinal cline in morphology was observed, clear phylogenetic discontinuities exist in the taiga and tundra zones supporting a species status for brachyrhynchus and middendorffii.     

The chromosomal distribution of the major and minor satellite is not conserved in the genusMus

The cytological distribution of the major and minor satellite first identified inMus musculus was studied in the karyotypes of three related subspecies and two other species of the genusMus. Both the major and minor satellite showed species dependent hybridization patterns. The major satellite is confined to the centromere region inM. musculus and related subspecies. However, inM spretus andM. caroli, the chromosomal arm regions contain this sequence class. In contrast the minor satellite is found at the kinetochore region inM. musculus and related subspecies but is distributed throughout the entire centromeric domain inM. spretus and appears to be excluded from the chromosomes ofM. caroli. There is an apparent correlation between the chromosomal location of these satellites and their phylogenetic relationship. Determination of the biological roles of the major and minor satellites fromM. musculus must take into account their differential chromosomal distribution in otherMus species.     

GEOLOGICALLY DATED SEA BARRIERS CALIBRATE A PROTEIN CLOCK FOR AEGEAN WATER FROGS

Reliable estimates of phylogenetic relationships and divergence times are a crucial requirement for many evolutionary studies, but are usually difficult because fossils are scarce and their interpretation is often uncertain. Frogs are fresh water animals that generally are unable to cross salt water barriers (their skin is readily permeable to both salt and water). The geologically determined ages of salt water barriers that isolate related frog populations thus provide an independent measure of the minimum date of genetic divergence between pairs of such populations. For the genetically well-studied western Palearctic water frogs (Rana esculenta group), the Aegean region provides an ideal area for determining the relationship between genetic divergence and time of spatial isolation, using a nested set of geologically determined isolation times (12,000 yr, 200,000 yr, 1.8 Myr, 2–3 Myr, and 5.2 Myr). Using 31 electrophoretic loci for 33 pairs of neighboring frog populations, a linear relationship between geologically determined isolation time and Hillis' modified Nei genetic distance was found: D^*_Nei = (0.04 ± 0.01) + (0.10 ± 0.01) isolation time [Myr] corresponding to an average divergence rate (“molecular clock” pace) of 0.10 D^*_Nei/Myr (0.10 D_Nei/Myr). This rate is in the range of previous estimates reported for protein electrophoretic data; the value is conservative because relatively few of the loci used are “fast evolvers” (13%; sAAT, ALB, EST-5, MPI). Removing these fast evolvers from the analysis results in 0.08 D^*_Nei/Myr (0.08 D_Nei/Myr). The confidence limits for estimation of the divergence time given the genetic distance are large, but unusually narrow for this kind of study; they permit us to estimate divergence times during the Pliocene and Miocene. Few previous studies, including sequence analyses, have provided reasonable estimates of divergence time for the Pliocene. A test using the outgroup taxa Rana perezi and Rana saharica (also isolated for 5.2 Myr by the Strait of Gibraltar) fits the calibration well: observed genetic Nei distance D^*_Nei = 0.55, expected D^*_Nei = 0.56. The calculated divergence times, based on this absolute molecular clock, suggest a series of speciation events after the Messinian (5.2 Myr), possibly triggered by the rapid ecological changes accompanying the desiccation and refilling of the Mediterranean Basin.     

High phylogenetic diversity of the cat flea (Ctenocephalides felis) at two mitochondrial DNA markers

The cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae) (Bouché), is the most common flea species found on cats and dogs worldwide. We investigated the genetic identity of the cosmopolitan subspecies C. felis felis and evaluated diversity of cat fleas from Australia, Fiji, Thailand and Seychelles using mtDNA sequences from cytochrome c oxidase subunit I (cox1) and II (cox2) genes. Both cox1 and cox2 confirmed the high phylogenetic diversity and paraphyletic origin of C. felis felis. The African subspecies C. felis strongylus (Jordan) is nested within the paraphyletic C. felis felis. The south East Asian subspecies C. felis orientis (Jordan) is monophyletic and is supported by morphology. We confirm that Australian cat fleas belong to C. felis felis and show that in Australia they form two distinct phylogenetic clades, one common with fleas from Fiji. Using a barcoding approach, we recognize two putative species within C. felis (C. felis and C. orientis). Nucleotide diversity was higher in cox1 but COX2 outperformed COX1 in amino acid diversity. COX2 amino acid sequences resolve all phylogenetic clades and provide an additional phylogenetic signal. Both cox1 and cox2 resolved identical phylogeny and are suitable for population structure studies of Ctenocephalides species.     

Quantitative Analysis of Genetic Parameters in Populations of European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) Roe Deer with RAPD Markers

A technique for obtaining unbiased estimates of genetic parameters (allelic frequencies of RAPD loci, heterozygosity (H), Wright's Fstatistic, and Nei's genetic distances) in populations of the European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) roe deer is presented. The technique employs jackknifing and multiple comparative analysis based on a modified Holmes's procedure for Bonferroni's test. It was demonstrated that samples from local groups of roe deer in the Trans-Ural region did not differ significantly in allelic frequencies (0.8, 0.81, and 0.78; P > 0.447) or Nei's genetic distances (0.0056, 0.0273, and 0.0218; P = 0.26), but they could be differentiated based on Wright's F statistic (0.0346, 0.0519, and 0.0450; P = 10^–9). The parameters of within-population heterozygosity formed a gradient from the east to the west. Calibration estimates of molecular evolution rate in the family Cervidae obtained based on published data and Jukes–Cantor genetic distances estimated in this study demonstrated that the Siberian roe deer has split into two subspecies, C. pygargus pygargusPall. and C. pygargus tianschanicusSatunin in the interval between 229 and 462.3 thousand years ago. The species formation of the Siberian and European roe deer was dated between 1.375 and 2.75 Myr ago. Based on the results obtained we recommend the approaches used in the study for analysis of population genetic structure and phylogenetic relationships between populations, subspecies, species, and higher taxa.     

Genetic constitution and phylogenetic relationships of Japanese crucian carps (Carassius)

The genetic constitution and phylogenetic relationships among the proposed species and subspecies of the crucian carp complex in Japan (Carassius cuvieri, C. auratus subspp. 1 and 2, C. a. grandoculis, C. a. buergeri, and C. a. langsdorfii) were investigated based on analyses of the partial nucleotide sequences of the mitochondrial DNA control region and amplified fragment length polymorphisms of nuclear DNA. Our results demonstrate that C. cuvieri and C. auratus are different entities. However, although several distinct lineages were observed for C. auratus, none corresponded to the proposed subspecies. Moreover, the five subspecies of C. auratus were not necessarily separated genetically from each other. Triploid fish, which are currently classified as a single subspecies (C. a. langsdorfii) but are sometimes treated as an independent species, fell into various clades along with diploid individuals of other subspecies that have the same or similar mitochondrial haplotypes. This suggests that gynogenetic triploid crucian carps distributed throughout the Japanese Archipelago have polyphyletic maternal origins. Our results indicate that Japanese crucian carps are a much more complex assemblage than previously believed.     

PHYLOGEOGRAPHY OF SPOTTED OWL (STRIX OCCIDENTALIS) POPULATIONS BASED ON MITOCHONDRIAL DNA SEQUENCES: GENE FLOW,GENETIC STRUCTURE,AND A NOVEL BIOGEOGRAPHIC PATTERN

Mitochondrial DNA control region sequences of spotted owls (Strix occidentalis) allowed us to investigate gene flow, genetic structure, and biogeographic relationships among these forest-dwelling birds of western North America Estimates of gene flow based on genetic partitioning and the phylogeography of haplotypes indicate substantial dispersal within three long-recognized subspecies. However, patterns of individual phyletic relationships indicate a historical absence of gene flow among the subspecies, which are essentially monophyletic. The pattern of haplotype coalescence enabled us to identify the approximate timing and direction of a recent episode of gene flow from the Sierra Nevada to the northern coastal ranges. The three subspecies comprise phylogenetic species, and the northern spotted owl (S. o. caurina) is sister to a clade of California (S. o. occidentalis) plus Mexican spotted owls (S o lucida); this represents a novel biogeographic pattern within birds. The California spotted owl had substantially lower nucleotide diversity than the other two subspecies; this result is inconsistent with present patterns of population density A causal explanation requires postulating a severe bottleneck or a selective sweep, either of which was confined to only one geographic region.     

Phylogeography of a Palaearctic sedentary passerine,the willow tit (Parus montanus)

We analysed variation of the mitochondrial control region from willow tits through its Palaearctic distribution range. Although we found high amount of genetic variation (π=1.114%), there was almost no differentiation between subspecies or geographical localities. This may be because of a combination of several ecological and genetic factors, including a relatively homogenic habitat through the distribution range, lack of geographical barriers, high gene flow and a large long‐term effective population size. On the contrary, in the songar tit, which is sometimes considered to be conspecific with the willow tit, the mitochondrial lineages seem to correlate with the geographical locality and are clearly distinct from the willow tit. We concluded that the common ancestors of willow and songar tits existed some 1.5–2 Myr ago in the south‐eastern Asia. After the last Ice Ages, the willow tit expanded all through the Palaearctic, whereas the songar tit remained in eastern Asia.     

Molecular evidence for the subspecific differentiation of blue sheep (Pseudois nayaur) and polyphyletic origin of dwarf blue sheep (Pseudois schaeferi)

Blue sheep (Pseudois nayaur), a Central Asian ungulate with restricted geographic distribution, exhibits unclear variation in morphology and phylogeographic structure. The composition of species and subspecies in the genus Pseudois is controversial, particularly with respect to the taxonomic designation of geographically restricted populations. Here, 26 specimens including 5 dwarf blue sheep (Pseudois schaeferi), which were collected from a broad geographic region in China, were analyzed for 2 mitochondrial DNA fragments (cytochrome b and control region sequences). In a pattern consistent with geographically defined subspecies, we found three deeply divergent mitochondrial lineages restricted to different geographic regions. The currently designated two subspecies of blue sheep, Pseudois nayaur nayaur and Pseudois nayaur szechuanensis, were recognized in the phylogenetic trees. In addition, the Helan Mountain population showed distinct genetic characteristics from other geographic populations, and thus should be classified as a new subspecies. In contrast, dwarf blue sheep clustered closely with some blue sheep from Sichuan Province in the phylogenetic trees. Therefore, dwarf blue sheep appear to be a subset of Pseudois nayaur szechuanensis. After considering both population genetic information and molecular clock analysis, we obtained some relevant molecular phylogeographic information concerning the historical biogeography of blue sheep. These results also indicate that western Sichuan was a potential refugium for blue sheep during the Quaternary period.     

Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae)

• Premise of the study: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. • Methods: We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana, and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high-read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor-net network analyses. • Key results: Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis, are polyphyletic occurring within and between diploid subspecies groups. • Conclusions: Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.     

Phylogenetic analysis of the Lacerta agilis subspecies complex

The Sand lizard Lacerta agilis inhabits a huge area across Eurasia with several subspecies. Nine subspecies are generally approved, L. a. agilis, L. a. argus, L. a. bosnica; L. a. chersonensis, L. a. exigua, L. a. grusinica, L. a. iorinensis, L. a. brevicaudata and L. a. boemica, but several more have been described. The emergence of this large number of subspecies is connected with the phylogeographic history of this species, defined by geographic and climatic processes. A study revealing phylogenetic relationships of this species was already conducted with a broad taxon sampling and coverage. However, the latter study was based solely on the cytochrome b gene and, furthermore, the Balkan Peninsula inhabited by the subspecies L. a. bosnica was underrepresented. This peninsula is a centre of European herpetofaunal endemism with high levels of phenotypic and genotypic variation. Therefore, the inclusion of the subspecies L. a. bosnica is important to clarify the overall view of the phylogenetic relations within the Lacerta agilis subspecies complex and to investigate the level of population differentiation within this highly diverse area. Thus, the aim of the present study was a more thorough analysis of the Balkan Peninsula with a broader taxon sampling. Furthermore, we extended the available datasets by adding the mitochondrial d-loop region and by further samples of different areas of the distribution range apart from the Balkan Peninsula. Our study reveals that the Balkan Peninsula is apparently inhabited by several differentiated lineages, whereby the Central Greek lineage might deserve subspecies status. Furthermore, the distribution area of the two subspecies L. a. agilis and L. a. argus should be revised, as the results of our study raise doubt about the commonly assumed distribution of both subspecies. As the most important outcome our results support that L. a. boemica deserves species status.     

Genetic variation among Corsican and continental populations of the Eurasian treecreeper (Aves: Certhia familiaris) reveals the existence of a palaeoendemic mitochondrial lineage

In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia familiaris), a forest passerine with a wide Palaearctic range including Corsica, using three mitochondrial genes and three nuclear introns, and its phylogeographic history using the COI gene. Our phylogenetic results, including eight of the ten sub‐species currently recognized, support the monophyly of C. familiaris with respect to its Indo‐Asian sister species C. hodgsoni. C. familiaris comprises two lineages that diverged during the mid‐Pleistocene (c. 1 Myr): one palaeoendemic lineage has an allopatric range nowadays restricted to the Corsica island and the Caucasus region whereas the second one, more recent and widespread, is distributed over most of Eurasia and in northern China. The most likely scenario that may explain such a pattern is a double colonization of the western Palaearctic from the eastern range of the species. During the middle Pleistocene period, a first lineage expanded its range up into Europe but did not persist through glacial cycles except in Corsica and the Caucasus region. Later, during the upper Pleistocene, a second lineage began to diversify around 0.09 Myr, spreading towards the western Palaearctic from a unique refuge likely located in the eastern Palaearctic [correction added on 6 March 2015 after first online publication: 0.9 Myr amended to 0.09 Myr]. Apart from C. f. corsa, our results do not suggest any distinct evolutionary history for other sub‐species previously described on morphological grounds in Europe. Our study highlights the important conservation value of the Corsican treecreeper and emphasizes the major role of mature pine forests in the evolution of endemic bird taxa in Corsica. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 134–153.     

Testing historical explanations for gradients in species richness in heliconiine butterflies of tropical America

We compiled a large database of 58 059 point locality records for 70 species and 434 subspecies of heliconiine butterflies and used these data to test evolutionary hypotheses for their diversification. To study geographical patterns of diversity and contact zones, we mapped: (1) species richness; (2) mean molecular phylogenetic terminal branch length; (3) subspecies richness and the proportion of specimens that were subspecific hybrids, and (4) museum sampling effort. Heliconiine species richness is high throughout the Amazon region and peaks near the equator in the foothills and middle elevations of the eastern Andes. Mean phylogenetic terminal branch length is lowest in the eastern Andes and tends to be low in species‐rich areas. By contrast, areas of high subspecies richness, where subspecies overlap in range and/or hybridize, are concentrated along the course of the Amazon River, with the eastern Andes slopes and foothills relatively depauperate in terms of local intraspecific phenotypic diversity. Spatial gradients in heliconiine species richness in the Neotropics are consistent with the hypothesis that species richness gradients are driven at least in part by variation in speciation and/or extinction rates, resulting in observed gradients in mean phylogenetic branch length, rather than via evolutionary age or niche conservatism alone. The data obtained in the present study, coupled with individual case studies of recently evolved Heliconius species, suggest that the radiation of heliconiine butterflies occurred predominantly on the eastern slopes of the Andes in Colombia, Ecuador, and Peru, as well as in the upper/middle Amazon basin. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 479–497.     

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.