Interspecific Territoriality by a Rufous-Tailed Hummingbird (Amazilia tzacatl): Effects of Intruder Size and Resource Value1

I studied two aspects of interspecific territoriality in a Costa Rican nectarivorous bird, the rufous-tailed hummingbird (Amazilia tzacatl). First, I examined variation in the response of the territory holder to four species of intruding hummingbirds by quantifying the proportion of intruders chased from the territory. This measure of territory defense varied significantly among species of intruders and was negatively related to the intruding species’body mass, possibly due to potential costs associated with becoming involved in escalated contests with larger individuals. Second, I tested for an effect of resource manipulation on territory defense. I increased the resource value of the territory by injecting extant natural flowers with artificial sucrose solution. While the frequency of territorial intrusions did not change, the proportion of intruders chased by the territory holder increased. Apparently, nectar supplementation changed the territory holder's perception of resource value but had little impact on the intruders’perception.     

The complex phylogeography of the Indo‐Malayan Alophoixus bulbuls with the description of a putative new ring species complex

The Indo‐Malayan bioregion has provided some of the most spectacular discoveries of new vertebrate species (e.g. saola, khanyou, bare‐faced bulbul) over the last 25 years. Yet, very little is known about the processes that led to the current biodiversity in this region. We reconstructed the phylogeographic history of a group of closely related passerines, the Alophoixus bulbuls. These birds are continuously distributed in Indo‐Malaya around the Thailand lowlands such that their distribution resembles a ring. Our analyses revealed a single colonization event of the mainland from Sundaland with sequential divergence of taxa from southwest to northeast characterized by significant gene flow between parapatric taxa, and reduced or ancient gene flow involving the two taxa at the extremities of the ring. We detected evidence of population expansion in two subspecies, including one that was involved in the closing of the ring. Hence, our analyses indicate that the diversification pattern of Alophoixus bulbuls fits a ring species model driven by geographic isolation. To our knowledge, the Alophoixus bulbuls represent the first case of a putative broken ring species complex in Indo‐Malaya. We also discuss the implications of our results on our understanding of the biogeography in Indo‐Malaya.     

Mimicry on the QT(L): genetics of speciation in Mimulus

Ecological studies suggest that hummingbird-pollinated plants in North America mimic each other to increase visitation by birds. Published quantitative trait locus (QTL) data for two Mimulus species indicate that floral traits associated with hummingbird versus bee pollination results from a few loci with major effects on morphology, as predicted by classical models for the evolution of mimicry. Thus, the architecture of genetic divergence associated with speciation may depend on the ecological context.     

Time-activity budgets and behaviour of the Amazilia hummingbird, Amazilia amazilia (Apodiformes: Trochilidae) in an urban environment

This study deals with the time-activity budgets of Amazilia amazilia, a territorial hummingbird, and its preferences for different flower species and perches in the gardens of Lima (Peru) in September 2001. A. amazilia spent an important part of its time resting on perches (ca. 80%) and only 15.5% for foraging, devoted essentially to flower visitation and only 0.3% for hunting and drinking water. Territorial defence accounted for 2% of total time, mostly against Coereba flaveola, an introduced nectarivorous species that seem to be an important competitor of A. amazilia. Flower use is not directly related to flower abundance (chi(2)9, = 1,546, p<0.0001), with Justicia brandegeana and red-flowered Salvia splendens being selected and Impatiens balsamina being rejected. The large amount of time spent on the perches makes them an important element of the habitat. The perches selected are typically on trees, close to the flowers visited, and in a low vertical and middle horizontal position, surrounded by low foliage density, probably to minimize heat loss.     

Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex

Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (10(4) km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average F(ST) = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (F(ST) = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.     

Hybrid zones and the speciation continuum in Heliconius butterflies

Tropical butterflies in the genus Heliconius have long been models in the study of the stages of speciation. Heliconius are unpalatable to predators, and many species are notable for multiple geographic populations with striking warning colour pattern differences associated with Müllerian mimicry. A speciation continuum is evident in Heliconius hybrid zones. Examples range from hybrid zones across which (a) there is little genetic differentiation other than at mimicry loci, but where hybrids are common, (b) to ‘bimodal‘ hybrid zones with strong genetic divergence and few hybrids, (c) through to ‘good’ sympatric species, with hybridization extremely rare or absent. Now, in this issue of Molecular Ecology, Arias et al. ( 2012 ) have found an intermediate case in Colombian Heliconius cydno showing evidence for assortative mating and molecular differences, but where hybrids are abundant.     

Re-examination of a proposed case of stasipatric speciation: phylogeography of the Australian morabine grasshoppers (Vandiemenella viatica species group)

Karyotypic differences have been used for delimiting populations or species, although whether these mutations provide strong barriers to gene flow between populations and promote speciation remains contentious. In this study, we assessed whether 11 chromosomal races of Australian morabine grasshoppers ( Vandiemenella viatica species group) represent genetically distinct populations by analyses of cytological and allozyme (35 loci) data and DNA sequences of the elongation factor-1 alpha ( EF -1α), anonymous Mvia11 , and mitochondrial cytochrome c oxidase subunit I ( COI ) loci. While the Vandiemenella chromosomal taxa generally represent genetically distinct units, a substantial portion of the total genetic variation in our samples was not explained by the chromosomal variation. Mantel tests indicated that Vandiemenella populations were spatially structured and have maintained gene flow at a local scale within each of the taxa. The group was subdivided into 13 genetic clusters; four chromosomal taxa comprised single exclusive clusters, while others comprised more than one cluster or clusters shared with other taxa. Boundaries of these cryptic population subdivisions correspond with several biogeographical barriers, such as straits, gulfs, the Murray River, and an ancient mega-lake, Lake Bungunnia. The viatica species group was previously proposed to have diversified without major geographical separation based on the stasipatric speciation model; however, the present study suggests the involvement of allopatric fragmentation. Given extensive nonmonophyly of chromosomal taxa and incomplete barriers to gene flow among taxa, all Vandiemenella chromosomal taxa and genetically distinct populations within chromosomal taxa, except Vandiemenella pichirichi , should be regarded as populations of one species: Vandiemenella viatica .     

Gene flow across secondary contact zones of the Emys orbicularis complex in the Western Mediterranean and evidence for extinction and re‐introduction of pond turtles on Corsica and Sardinia (Testudines: Emydidae)

European pond turtles represent a phylogeographically deeply structured complex of distinct taxa. Here, we use mitochondrial DNA sequences (cytochrome b gene) and eight polymorphic microsatellite loci to investigate genetic differentiation and gene flow of Sicilian, Corsican and Sardinian pond turtles and of subspecies involved in two secondary contact zones in the Pyrenean region and Southern Italy. Mitochondrial and microsatellite differentiation is largely concordant in populations from the core regions of the distribution ranges of the studied taxa. Both marker systems provide no evidence for gene flow between Sicilian pond turtles (Emys trinacris) and Southern Italian subspecies of E. orbicularis. By contrast, in the contact zones limited gene flow occurs between distinct subspecies of E. orbicularis. Although the Southern Italian contact zone is significantly older than the Pyrenean contact zone of Holocene age, patterns of asymmetric introgression are similar. Introgressive hybridization leads to the exchange of mitochondria, but microsatellite data indicate only a few individuals with mixed ancestry. This suggests that incipient isolating mechanisms maintain largely discrete nuclear genomic gene pools. Furthermore, this implies that Southern Italy acted as a hotspot rather than as a melting pot of genetic diversity during the last glacial. Pond turtles from Corsica and Sardinia are not differentiated from continental populations of the subspecies E. o. galloitalica, neither in the mitochondrial nor in the quickly evolving microsatellite markers. As the fossil record argues for a continuous presence of pond turtles on both islands since the Middle Pleistocene, this suggests that the native island populations became extinct and the extant turtles were later introduced by prehistoric settlers. The lack of genetic differentiation of pond turtles from Corsica and Sardinia supports the view that the subspecies described from these islands are not valid.     

Differential gene flow of mitochondrial and nuclear DNA markers among chromosomal races of Australian morabine grasshoppers (Vandiemenella, viatica species group)

Recent theoretical developments have led to a renewed interest in the potential role of chromosomal rearrangements in speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) provide an excellent study system to test this potential role of chromosomal rearrangements because they show extensive chromosomal variation and formed the basis of a classic chromosomal speciation model. There are three chromosomal races, viatica19, viatica17, and P24(XY), on Kangaroo Island, South Australia, forming five parapatric populations with four putative contact zones among them. We investigate the extent to which chromosomal variation among these populations may be associated with barriers to gene flow. Population genetic and phylogeographical analyses using 15 variable allozyme loci and the elongation factor-1alpha (EF-1alpha) gene indicate that the three races represent genetically distinct taxa. In contrast, analyses of the mitochondrial cytochrome c oxidase subunit I (COI) gene show the presence of three distinctive and geographically localized groups that do not correspond with the distribution of the chromosomal races. These discordant population genetic patterns are likely to result from introgressive hybridization between the chromosomal races and range expansions/contractions. Overall, these results suggest that reduction of nuclear gene flow may be associated with chromosomal variation, or underlying genetic variation linked with chromosomal variation, whereas mitochondrial gene flow appears to be independent of this variation in these morabine grasshoppers. The identification of an intact contact zone between P24(XY) and viatica17 offers considerable potential for further investigation of molecular mechanisms that maintain distinct nuclear genomes among the chromosomal races.     

Nuclear locus divergence at the early stages of speciation in the Orchard Oriole complex

As two lineages diverge from one another, mitochondrial DNA should evolve fixed differences more rapidly than nuclear DNA due to its smaller effective population size and faster mutation rate. As a consequence, molecular systematists have focused on the criteria of reciprocal monophyly in mitochondrial DNA for delimiting species boundaries. However, mitochondrial gene trees do not necessarily reflect the evolutionary history of the taxa in question, and even mitochondrial loci are not expected to be reciprocally monophyletic when the speciation event happened very recently. The goal of this study was to examine mitochondrial paraphyly within the Orchard Oriole complex, which is composed of Icterus spurius (Orchard Oriole) and Icterus fuertesi (Fuertes' Oriole). We increased the geographic sampling, added four nuclear loci, and used a range of population genetic and coalescent methods to examine the divergence between the taxa. With increased taxon sampling, we found evidence of clear structure between the taxa for mitochondrial DNA. However, nuclear loci showed little evidence of population structure, indicating a very recent divergence between I. spurius and I. fuertesi. Another goal was to examine the genetic variation within each taxon to look for evidence of a past founder event within the I. fuertesi lineage. Based on the high amounts of genetic variation for all nuclear loci, we found no evidence of such an event – thus, we found no support for the possible founding of I. fuertesi through a change in migratory behavior, followed by peripheral isolates speciation. Our results demonstrate that these two taxa are in the earliest stages of speciation, at a point when they have fixed differences in plumage color that are not reflected in monophyly of the mitochondrial or nuclear DNA markers in this study. This very recent divergence makes them ideal for continued studies of species boundaries and the earliest stages of speciation.     

Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus)

We investigated the genetic population structure and species status of a relatively sedentary bird that is a permanent resident of western North American forests, the blue grouse (Dendragapus obscurus). Phylogenetic analysis of complete mitochondrial control region DNA sequences resulted in the identification of three basal clades of haplotypes that were largely congruent with well-known biogeographical regions. These clades corresponded to the parapatric sooty (D. o. fuliginosus) and dusky (D. o. obscurus) subspecies groups of blue grouse plus a previously unrecognized division between northern and southern dusky grouse populations; the latter does not correspond closely to any currently recognized subspecies boundary. Approximately 66% of the total genetic variation was distributed among these three regions. Maximum likelihood estimates of gene flow between the regions were low or asymmetric; gene flow has been insufficient to prevent genetic divergence between dusky and sooty grouse. Estimates of gene flow among populations within sooty grouse were large except across the Columbia River valley. Among populations of dusky grouse, estimates of gene flow were heterogeneous and asymmetrical, reflecting large-scale fragmentation of the distribution due to landscape features and associated vegetation. Genetic, morphological and behavioural evidence suggest that sooty and dusky grouse are species-level taxa; the specific status of a third clade remains ambiguous.     

Increasing evidence of the role of gene flow in animal evolution: hybrid speciation in the yellow-rumped warbler complex

In this issue of Molecular Ecology, Brelsford et al. (2011) present strong evidence for a case of hybrid speciation within the yellow-rumped warbler complex. Although homoploid hybrid speciation has now been documented in many animals (Mallet 2007), it seems rare in tetrapods (Mavárez & Linares 2008) and it has barely even been mentioned in birds (Price 2008). Brelsford and colleagues thus present the first detailed molecular evidence suggesting that hybrid speciation can occur in birds. Brelsford et al. (2011) posit that Audubon's warbler (Dendroica auduboni) constitutes a hybrid species originating from the admixture of two distinct parental lineages, represented today by myrtle warbler (D. coronata) and black-fronted warbler (D. nigrifrons). The authors present three major lines of molecular evidence suggesting that this is not simply a case of a hybrid swarm or limited introgression.     

Influences of gene flow on adaptive speciation in the Dubautia arborea--D. ciliolata complex

Mechanisms of reproductive isolation during plant speciation are often unclear because distinct species often experience high levels of gene flow and hybridization. Adaptive radiations such as the Hawaiian silversword alliance (HSA) provide unique opportunities to study the interactions of selection, gene flow and isolating mechanisms during the speciation process. We examined patterns of phenotypic and genetic differentiation in Dubautia arborea and Dubautia ciliolata, two parapatric HSA taxa that show marked morphological divergence but evidence of weak molecular differentiation, in order to estimate genome-wide differentiation and gene flow patterns. We scored 166 amplified fragment length polymorphism markers in a set of 89 plants from two populations each of D. arborea and D. ciliolata and phenotypically D. arborea-like and D. ciliolata-like plants from a natural hybrid zone. Analyses of population subdivision showed low levels of differentiation between the two species (F(ST) = 0.089) and evidence that the phenotypically parental hybrid zone plants were largely of parental species rather than of hybrid origin. A Bayesian analysis of population ancestry identified a number of plants with admixed D. arborea and D. ciliolata ancestry, even in nonhybrid-zone populations. These results suggest that genome-wide low levels of differentiation between D. arborea and D. ciliolata are in part due to gene flow, and favour models of genic speciation and collective evolution in which gene flow has different effects on selected loci vs. nonselected genomic regions. We discuss ecological and climatic factors that may have shaped patterns of differentiation in this species complex.     

Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces

Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.     

Molecular Assessment and Taxonomic Status of the Rapid Racerunner （Eremias velox complex） with Particular Attention to the Populations in Northwestern China

The rapid racerunner,Eremias velox,is a widely distributed lizard from the northern Caucasus across entire Central Asia eastward to China.It is increasingly common to accept E.velox as a species complex in its entire range.To date,published morphological and molecular systematic hypotheses of this complex are only partially congruent,and its taxonomic status and evolutionary history are still far from clear.The mitochondrial cytochrome b gene and12S rRNA sequences were used to evaluate the taxonomy of this complex,with particular attention to the phylogenetic placement of populations in northwestern China.Examination of the phylogenetic analyses recovers seven distinct,biogeographically discrete,and well-supported clades,revealing genetically identifiable populations corresponding to some previously morphology-defined subspecies.Chinese E.v.roborowskii appears to have split from other Central Asian rapid racerunner lizards well before differentiation occurred among the latter taxa.Specifically,we corroborate that there are two subspecies occurring in China,i.e.,E.v.velox and E.v.roborowskii.We recommend a novel subspecific status for the phenotypically and genetically distinct populations in southern Aral Sea region of Uzbekistan previously assigned to E.v.velox.Finally,each of the three independently evolving lineages from Iranian Plateau should be recognized as three species new to science under the general lineage concept.     

Glacial refuges and cryptic speciation in a Southern Palearctic tiger beetle (Coleoptera: Cicindelidae)

Pleistocene glaciations had a determining role for shaping the current distribution and diversity of organisms, especially in the Palearctic region. In this work, we carry out a phylogeographic analysis of Iberian and two Eastern European populations of the tiger beetle Calomera littoralis (Fabricius, 1787) in order to infer the processes that may have affected their evolutionary history. According to our results, the genetic diversity of central Iberian C. littoralis populations is very low. The haplotype networks also suggest that these populations experienced a genetic bottleneck in the past, possibly related to the last glacial maxima, similar to that observed in other cicindelid taxa. These results highlight the remarkable dispersal capacity of this species, being able to move freely from one locality to another, despite the relatively long distances of sub-optimal habitat that separates them. The genetic data of central Iberian populations contrast with those of the Eastern European populations, with higher genetic diversity and no hints of any past bottleneck. This can be explained by the different characteristics of both (Iberian and Pontic) glacial refuges. The high degree of genetic differentiation between the three C. littoralis clades, and the inclusion of C. lunulata between them, suggests that the three analysed populations could be considered as different cryptic species. In that case, C. littoralis may correspond to a species complex that is still undergoing a process of speciation, similar to that observed in Cicindela campestris.     

Phylogeography and speciation in the <Emphasis Type="Italic">Pseudocrenilabrus philander</Emphasis> species complex in Zambian Rivers

Haplochromine cichlids form the most species-rich lineage of cichlid fishes that both colonized almost all river systems in Africa and radiated to species flocks in several East African lakes. The enormous diversity of lakes is contrasted by a relatively poor albeit biogeographically clearly structured species diversity in rivers. The present study analyzed the genetic structure and phylogeographic history of species and populations of the genus Pseudocrenilabrus in Zambian rivers that span two major African drainage systems, the Congo- and the Zambezi-system. The mtDNA phylogeny identifies four major lineages, three of which occur in the Congo-system and one in the Zambezi system. Two of the Congo-clades (Lake Mweru and Lunzua River) comprise distinct albeit yet undescribed species, while the fish of the third Congo-drainage clade (Chambeshi River and Bangweulu swamps), together with the fish of the Zambezi clade (Zambezi and Kafue River) are assigned to Pseudocrenilabrus philander. Concerning the intraspecific genetic diversity observed in the sampled rivers, most populations are highly uniform in comparison to lacustrine haplochromines, suggesting severe founder effects and/or bottlenecking during their history. Two bursts of diversification are reflected in the structure of the linearized tree. The first locates at about 3.9% mean sequence divergence and points to an almost simultaneous colonization of the sampled river systems. Subsequent regional diversification (with about 1% mean sequence divergence) occurred contemporaneously within the Kafue River and the Zambezi River. The clear-cut genetic biogeographic structure points to the dominance of geographic speciation in this lineage of riverine cichlid fishes, contrasting the importance of in situ diversification observed in lake cichlids.     

Reconstruction of caribou evolutionary history in Western North America and its implications for conservation

The role of Beringia as a refugium and route for trans-continental exchange of fauna during glacial cycles of the past 2million years are well documented; less apparent is its contribution as a significant reservoir of genetic diversity. Using mitochondrial DNA sequences and 14 microsatellite loci, we investigate the phylogeographic history of caribou (Rangifer tarandus) in western North America. Patterns of genetic diversity reveal two distinct groups of caribou. Caribou classified as a Northern group, of Beringian origin, exhibited greater number and variability in mtDNA haplotypes compared to a Southern group originating from refugia south of glacial ice. Results indicate that subspecies R. t. granti of Alaska and R. t. groenlandicus of northern Canada do not constitute distinguishable units at mtDNA or microsatellites, belying their current status as separate subspecies. Additionally, the Northern Mountain ecotype of woodland caribou (presently R. t. caribou) has closer kinship to caribou classified as granti or groenlandicus. Comparisons of mtDNA and microsatellite data suggest that behavioural and ecological specialization is a more recently derived life history characteristic. Notably, microsatellite differentiation among Southern herds is significantly greater, most likely as a result of human-induced landscape fragmentation and genetic drift due to smaller population sizes. These results not only provide important insight into the evolutionary history of northern species such as caribou, but also are important indicators for managers evaluating conservation measures for this threatened species.     

Inter‐specific gene flow dynamics during the Pleistocene‐dated speciation of forest‐dependent mosquitoes in Southeast Asia

Tropical forests have undergone repeated fragmentation and expansion during Pleistocene glacial and interglacial periods, respectively. The effects of this repeated forest fragmentation in driving vicariance in tropical taxa have been well studied. However, relatively little is known about how often this process results in allopatric speciation, since it may be inhibited by recurrent gene flow during repeated secondary contact, or to what extent Pleistocene‐dated speciation results from ecological specialization in the face of gene flow. Here, divergence times and gene flow between three closely‐related mosquito species of the Anopheles dirus species complex endemic to the forests of Southeast Asia, are inferred using coalescent based Bayesian analysis. An Isolation with Migration model is applied to sequences of two mitochondrial and three nuclear genes, and 11 microsatellites. The divergence of An. scanloni has occurred despite unidirectional nuclear gene flow from this species into An. dirus. The inferred asymmetric gene flow may result from the unique evolutionary adaptation of An. scanloni to limestone karst habitat, and therefore the fitness advantage of this species over An. dirus in regions of sympatry. Mitochondrial introgression has led to the complete replacement of An. dirus haplotypes with those of An. baimaii through a recent (～62 kya) selective sweep. Speciation of An. baimaii and An. dirus is inferred to have involved allopatric divergence throughout much of the Pleistocene. Secondary contact and bidirectional gene flow has occurred only within the last 100 000 years, by which time the process of allopatric speciation seems to have been largely completed.