Genetics and the origin of bird species

The Rules of Variation Expanded, Implications for the Research on Compatible Genomics

The main focus of this article is to present the practical aspect of the code rules of variation and the search for a second set of genomic rules, including comparison of sequences to understand how to preserve compatible organisms in danger of extinction and how to generate biodiversity. Three new rules of variation are introduced: 1) homologous recombination, 2) a healthy fertile offspring, and 3) comparison of compatible genomes. The novel search in the natural world for fully compatible genomes capable of homologous recombination is explored by using examples of human polymorphisms in the LDLRAP1 gene, and by the production of fertile offspring by crossbreeding. Examples of dogs, llamas and finches will be presented by a rational control of: natural crossbreeding of organisms with compatible genomes (something already happening in nature), the current work focuses on the generation of new varieties after a careful plan. This study is presented within the context of biosemiotics, which studies the processing of information, signaling and signs by living systems. I define a group of organisms having compatible genomes as a single theme: the genomic species or population, able to speak the same molecular language through different accents, with each variety within a theme being a different version of the same book. These studies have a molecular, compatible genetics context. Population and ecosystem biosemiotics will be exemplified by a possible genetic damage capable of causing mutations by breaking the rules of variation through the coordinated patterns of atoms present in the 9/11 World Trade Center contaminated dust (U, Ba, La, Ce, Sr, Rb, K, Mn, Mg, etc.), combination that may be able to overload the molecular quality control mechanisms of the human body. I introduce here the balance of codons in the circular genetic code: 2[1(1)+1(3)+1(4)+4(2)]=2[2(2)+3(4)].

Asymmetric response patterns to subspecies-specific song differences in allopatry and parapatry in the gray-breasted wood-wren

Song divergence between closely related taxa may play a critical role in the evolutionary processes of speciation and hybridization. We explored song variation between two Ecuadorian subspecies of the gray-breasted wood-wren (Henicorhina leucophrys) and tested the impact of song divergence on response behaviors. Songs were significantly different between the two subspecies, even between two parapatric populations 10 km apart. Playback experiments revealed an asymmetric response pattern to these divergent subspecies specific songs; one subspecies responded more to songs of its own subspecies than to the other subspecies' songs, whereas the second responded equally strongly to songs of both subspecies. While song parameters revealed a mixed pattern of divergence between allopatric and parapatric populations, the majority of spectral characteristics showed increased divergence in parapatry, suggestive of character displacement. This increased song divergence in parapatry appeared to affect behavioral responses to playback as discriminating responses were most prominent in parapatry and against parapatric songs. The clear behavioral impact of subspecies-specific song differences supports a potential role for song as an acoustic barrier to gene flow. The asymmetric nature of the responses suggests that song divergence could affect the direction of gene flow and the position of the subspecies-specific transition.

Under which conditions is character displacement a likely outcome of secondary contact?

Sympatric character displacement is one possible mechanism that prevents competitive exclusion. This mechanism is thought to be behind the radiation of Darwin's finches, where character displacement is assumed to have followed secondary contact of ecologically similar species. We use a model to evaluate under which ecological and environmental conditions this mechanism is likely. Using the adaptive dynamics theory, we analyse different ecological models embedded in the secondary contact scenario. We highlight two necessary conditions for character displacement in sympatry: (i) very strong premating isolation between the two populations, and (ii) secondary contact to occur at an evolutionary branching point. Character displacement is then driven by adaptation to interspecific competition. We determine how ecological and environmental parameters influence the probability of ecological divergence. Finally, we discuss the likelihood of sympatric character displacement under disruptive selection in natural populations.

Speciation genetics: current status and evolving approaches

The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues.

Contemporary cultural evolution of a conspecific recognition signal following serial translocations

The divergence of conspecific recognition signals (CRS) among isolated populations facilitates the evolution of behavioral barriers to gene flow. The influence of CRS evolution on signal effectiveness in isolated populations can be assessed by testing the salience of changes in CRS from surviving ancestral populations but founder events are rarely detected. The population history of the North Island (NI) saddleback Philesturnus rufusater is absolutely known following conservation translocations which increased the number of populations from 1 to 15. With one exception there is no gene flow between these populations. The translocations have generated interisland divergence of male rhythmical song (MRS), a culturally transmitted CRS. We conducted an experimental test of behavioral discrimination in NI saddlebacks exposed to familiar and unfamiliar MRS and found that responses were significantly stronger for familiar MRS, consistent with a model of contemporary cultural evolution leading to discrimination between geographic song variants. Significantly, this result demonstrates the rapid tempo with which discrimination of CRS might evolve within isolated populations and supports both bottleneck and cultural mutation hypotheses in CRS evolution. The evolutionary implications of contemporary cultural evolution in the production and perception of CRS merit debate on the time frames over which conservation management is evaluated.

A hybrid zone revisited: molecular and morphological analysis of the maintenance, movement, and evolution of a Great Plains avian (Cardinalidae: Pheucticus) hybrid zone

Black-headed grosbeaks (Pheucticus melanocephalus) and rose-breasted grosbeaks (Pheucticus ludovicianus) are passerine bird species known to hybridize in the Great Plains of North America. Both extrinsic (environmental) and intrinsic factors (pre- and postzygotic reproductive isolation) have been credited for the generation and maintenance of the grosbeak hybrid zone, but little is known about the genetic characteristics of this hybrid zone. To investigate the stability and extent of the grosbeak hybrid zone, we constructed clines from both molecular sequence data (mtDNA, three autosomal intron loci, and one Z-linked locus) and morphological data (morphometric analyses and hybrid index scores) to determined zone centre and width. Hybrid zone centre and width were also determined for samples collected across the zone 40 years ago from morphological data. The present and past clines were compared and provided support for stability in hybrid zone location and width, and the evolutionary implications of this are discussed. Three models of hybrid zone maintenance were investigated to consider the influence of intrinsic and extrinsic factors on this zone. Our results suggest low hybrid frequencies, a stable zone location and narrow width, and reduced hybrid fitness over the past 40 years best categorize the grosbeak hybrid zone as a tension zone.

Phylogeography and taxonomy of White-chinned and Spectacled Petrels

The genus Procellaria traditionally consists of four species, two restricted to New Zealand and two widespread in the Southern Ocean. All four are threatened because of incidental mortality on longlines and other fishing gear. The White-chinned Petrel P. aequinoctialis is the seabird killed in largest numbers by fisheries in the Southern Ocean. A spectacled form recently has been elevated to species status, Spectacled Petrel P. conspicillata, based on differences in morphometrics, vocalisations and breeding phenology. Cytochrome b sequences support species status for the Spectacled Petrel and show that the White-chinned Petrel has two regional populations, one around New Zealand and one throughout the South Atlantic and Indian Oceans. White-chinned and Spectacled Petrels segregated approximately 0.90 million years ago by allopatric fragmentation, and the two populations within White-chinned Petrels diverged approximately 0.35 million years ago. Climate changes and corresponding changes in ocean currents are most likely responsible for these patterns.

The genetic architecture of insect courtship behavior and premating isolation

The genetic architecture underlying reproductively isolating traits may have substantial impacts on the likelihood and pace of speciation. Recent studies of a key premating barrier, courtship, provide sufficient data to assess the degree to which behaviorally isolating traits are controlled by many or few loci, and help to investigate whether the same loci underlie both intraspecific and interspecific behavioral differences. Of the behavioral courtship traits examined, 69% (25 of 36) were found to be mediated by few loci of relatively large effect. This apparent prevalence of major loci suggests that changes in courtship behavior may often evolve quickly, which in turn may drive rapid speciation through premating isolation. Although both intraspecific and interspecific courtship differences are commonly controlled by major loci, intraspecific and interspecific differences usually involve different loci or traits. This finding provides evidence that different sets of processes and genetic changes characterize microevolutionary change in courtship-related traits, in contrast to change during speciation.

Fission and fusion of Darwin's finches populations

This study addresses the causes and evolutionary consequences of introgressive hybridization in the sympatric species of Darwin's ground finches (Geospiza) on the small island of Daphne Major in the Galápagos archipelago. Hybridization occurs rarely (less than 2% of breeding pairs) but persistently across years, usually as a result of imprinting on the song of another species. Hybrids survive well under some ecological conditions, but not others. Hybrids mate according to song type. The resulting introgression increases phenotypic and genetic variation in the backcrossed populations. Effects of introgression on beak shape are determined by the underlying developmental genetic pathways. Introgressive hybridization has been widespread throughout the archipelago in the recent past, and may have been a persistent feature throughout the early history of the radiation, episodically affecting both the speed and direction of evolution. We discuss how fission through selection and fusion through introgression in contemporary Darwin's finch populations may be a reflection of processes occurring in other young radiations. We propose that introgression has the largest effect on the evolution of interbreeding species after they have diverged in morphology, but before the point is reached when genetic incompatibilities incur a severe fitness cost.

Lack of premating isolation at the base of a phylogenetic tree

Darwin's finches in the Galápagos archipelago are an unusual example of adaptive radiation in that the basal split separates two lineages of warbler finches (Certhidea olivacea and Certhidea fusca) believed until recently to be only one species. The large genetic difference between them contrasts with their similarity in plumage, size, shape, and courtship behavior. They differ in song, which is a key factor in premating isolation of other sympatric Darwin's finches. We conducted playback experiments to see whether members of the population of C. olivacea on Santa Cruz Island would respond to songs of C. fusca from two islands, Genovesa and Pinta, and songs of C. olivacea from another island (Isabela). Another set of experiments was performed, using the same playback tapes, with C. fusca on Genovesa. Some members of both populations responded to all playbacks; therefore, the hypothesis of complete premating isolation on the basis of song is rejected. Discrimination between songs of the two lineages was inconsistent. We conclude that premating barriers to interbreeding among the tested populations have not arisen in the 1.5-2.0 m.yr. of their geographical isolation on different islands. This contrasts with strong premating barriers between more recently derived sympatric species. Early learning of song associated with morphology is later used in mate recognition. This explains why sympatric species that are vocally and morphologically distinct yet genetically less differentiated than Certhidea do not interbreed, whereas the Certhidea lineages that are genetically well differentiated but vocally and morphologically similar have no apparent premating barrier. We discuss this unusual situation in terms of the forces that have produced similarities and differences in song, morphology, and ecology and their relevance to phylogenetic and biological species concepts. Neither principles nor details are unique to Darwin's finches, and we conclude by pointing out strong parallels with some continental birds.

Isolation-by-distance and outbreeding depression are sufficient to drive parapatric speciation in the absence of environmental influences

A commonly held view in evolutionary biology is that speciation (the emergence of genetically distinct and reproductively incompatible subpopulations) is driven by external environmental constraints, such as localized barriers to dispersal or habitat-based variation in selection pressures. We have developed a spatially explicit model of a biological population to study the emergence of spatial and temporal patterns of genetic diversity in the absence of predetermined subpopulation boundaries. We propose a 2-D cellular automata model showing that an initially homogeneous population might spontaneously subdivide into reproductively incompatible species through sheer isolation-by-distance when the viability of offspring decreases as the genomes of parental gametes become increasingly different. This simple implementation of the Dobzhansky-Muller model provides the basis for assessing the process and completion of speciation, which is deemed to occur when there is complete postzygotic isolation between two subpopulations. The model shows an inherent tendency toward spatial self-organization, as has been the case with other spatially explicit models of evolution. A well-mixed version of the model exhibits a relatively stable and unimodal distribution of genetic differences as has been shown with previous models. A much more interesting pattern of temporal waves, however, emerges when the dispersal of individuals is limited to short distances. Each wave represents a subset of comparisons between members of emergent subpopulations diverging from one another, and a subset of these divergences proceeds to the point of speciation. The long-term persistence of diverging subpopulations is the essence of speciation in biological populations, so the rhythmic diversity waves that we have observed suggest an inherent disposition for a population experiencing isolation-by-distance to generate new species.

Climate-driven diversification in two widespread Galerida larks

BACKGROUND

The major impact of Plio-Pleistocene climatic oscillations on the current genetic structure of many species is widely recognised but their importance in driving speciation remains a matter of controversies. In addition, since most studies focused on Europe and North America, the influence of many other biogeographic barriers such as the Sahara remains poorly understood. In this paper, climate-driven diversification was investigated by using a comparative phylogeographic approach in combination with phenotypic data in two avian species groups distributed on both sides of the deserts belt of Africa and Asia. In particular, we tested whether: 1) vicariance diversification events are concomitant with past climatic events; and 2) current ecological factors (using climate and competition as proxies) contribute to phenotypic divergence between allopatric populations.

RESULTS

Mitochondrial and nuclear sequence data indicated that the crested and Thekla lark species groups diverged in the early Pliocene and that subsequent speciation events were congruent with major late Pliocene and Pleistocene climatic events. In particular, steep increase in aridity in Africa near 2.8 and 1.7 million years ago were coincident with two north-south vicariance speciation events mediated by the Sahara. Subsequent glacial cycles of the last million years seem to have shaped patterns of genetic variation within the two widespread species (G. cristata and G. theklae). The Sahara appears to have allowed dispersal from the tropical areas during climatic optima but to have isolated populations north and south of it during more arid phases. Phenotypic variation did not correlate with the history of populations, but was strongly influenced by current ecological conditions. In particular, our results suggested that (i) desert-adapted plumage evolved at least three times and (ii) variation in body size was mainly driven by interspecific competition, but the response to competition was stronger in more arid areas.

CONCLUSION

Climatic fluctuations of the Plio-Pleistocene strongly impacted diversification patterns in the Galerida larks. Firstly, we found that cladogenesis coincides with major climatic changes, and the Sahara appears to have played a key role in driving speciation events. Secondly, we found that morphology and plumage were strongly determined by ecological factors (interspecific competition, climate) following vicariance.

The evolution of functionally referential meaning in a structured world

Animal communication systems serve to transfer both motivational information--about the intentions or emotional state of the signaler--and referential information--about external objects. Although most animal calls seem to deal primarily with motivational information, those with a substantial referential component are particularly interesting because they invite comparison with words in human language. We present a game-theoretic model of the evolution of communication in a "structured world", where some situations may be more similar to one another than others, and therefore require similar responses. We find that breaking the symmetry in this way creates the possibility for a diverse array of evolutionarily stable communication systems. When the number of signals is limited, as in alarm calling, the system tends to evolve to group together situations which require similar responses. We use this observation to make some predictions about the situations in which primarily motivational or referential communication systems will evolve.

Differentiation of sympatric populations of the band-rumped storm-petrel in the Galapagos Islands: an examination of genetics, morphology, and vocalizations

In each of at least two locations within the Galapagos Islands, breeding band-rumped storm-petrels (Oceanodroma castro) form two distinct populations that use the same colony site at separate times of the year for reproduction. Temporal segregation of these populations raises the possibility that they are reproductively isolated and represent cryptic species. We examined variation in mitochondrial DNA, morphology, and vocalizations of storm-petrel populations nesting 6 months apart on the islet of Plaza Norte in the Galapagos. Seasonal populations displayed low but significant levels of differentiation in the mitochondrial control region, five morphological variables, and one feature of male vocalizations. Breeding populations appear to have been separated for approximately 1700 years. Given the recent divergence date and relatively high effective population sizes (4000-5600 females each), seasonal populations are unlikely to be in genetic equilibrium. As a result, the low divergence estimate probably reflects historical association and not contemporary genetic exchange. These populations are not sufficiently differentiated to be considered cryptic species. However, they are probably in the early stages of divergence. Consequently, we recommend that cool- and hot season populations on Plaza Norte be recognized as separate management units.

POPULATION DIFFERENTIATION IN THE BEETLE TRIBOLIUM CASTANEUM. II. HALDANE'S RULE AND INCIPIENT SPECIATION

The heterogametic sex tends to be rare, absent, sterile, or deformed in F1 hybrid crosses between species, a pattern called Haldane's rule (HR). The introgression of single genes or chromosomal regions from one drosophilid species into the genetic background of another have shown that HR is most often associated with fixed genetic differences in inter-specific crosses. However, because such introgression studies have involved species diverged several hundred thousand generations from a common ancestor, it is not clear whether HR attends the speciation process or results from the accumulation of epistatically acting genes postspeciation. We report the first evidence for HR prior to speciation in crosses between two populations of the red flour beetle, Tribolium castaneum, collected 931 km apart in Colombia and Ecuador. In this cross, HR is manifested as an increase in the proportion of deformed males compared to females and the expression of HR is temperature dependent. Neither population, when crossed to a geographically distant population from Japan, exhibits HR at any rearing temperature. Using joint-scaling analysis and additional data from backcrosses and F2's, we find that the hybrid incompatibilities and the emergence of HR are concurrent processes involving interactions between X-linked and autosomal genes. However, we also find many examples of incompatibilities manifest by F2 and backcross hybrids but not by F1 hybrids and most incompatibilities are not sex different in their effects, even when they involve both X-autosomal interactions and genotype-by-environment interactions. We infer that incipient speciation in flour beetles can occur with or without HR and that significant hybrid incompatibilities result from the accumulation of epistatically acting gene differences between populations without differentially affecting the heterogametic sex in F1 hybrids. The temperature dependence of the incompatibilities supports the inference that genotype-by-environment interactions and adaptation to different environments contribute to the genetic divergence important to postzygotic reproductive isolation.

The Causes of Evolutionary Radiations in Archipelagoes: Passerine Birds in the Lesser Antilles

To investigate why some lineages undergo evolutionary radiation, we compare the passerine avifaunas of the Hawaiian and Galapagos archipelagoes, which have supported well-known radiations of birds, with those of the Lesser Antilles, which have not. We focus on four steps required for the buildup of diversity through allopatric speciation and secondary sympatry: genetic divergence in isolation, persistence of island populations, recolonization of source islands, and ecological compatibility in secondary sympatry. Analysis of genetic divergence among island populations in the Lesser Antilles reveals evidence of both prolonged independent evolution and re-expansion of differentiated island populations through the archipelago but little evidence of secondary sympatry of divergent genetic lineages. Archipelagoes with high rates of colonization from continental or nearby large-island sources might fail to promote evolutionary radiations because colonists fill ecological space and constrain diversification through competition. However, morphological analysis demonstrated similar divergence between allopatric populations in species in Hawaii, Galapagos, and the Lesser Antilles, although the rate of divergence between secondarily sympatric species evidently is more rapid in Hawaii and the Galapagos. Alternatively, endemic buildup of diversity might be facilitated by the relative absence of pathogens in Hawaii and Galapagos that otherwise could prevent the secondary sympatry of populations owing to disease-mediated competition.

Uniform genetic diversity, low differentiation, and neutral evolution characterize contemporary refuge populations of Taiwan fir (Abies kawakamii, Pinaceae)

Based on fossil pollen, the distribution range of Taiwan fir [Abies kawakamii (Hay.) Ito] (Pinaceae) is smaller than it was 50 000 years ago. To characterize the present refuge populations of A. kawakamii, which survive only in subalpine forests in Taiwan, we surveyed nuclear genes and chloroplast intergenic spacers to assess the genetic diversity of Taiwan fir. Populations maintain high genetic diversity and contain similar numbers of haplotypes for the GapC (cytosolic glyceraldehyde 3-phosphate dehydrogenase) fragment. Haplotypes for GapC are generally widespread, and population-specific haplotypes accounted for 2.5% of the total. Differentiation among populations is very low (G(ST) = 0.01). Only three haplotypes were detected for the cpDNA marker, and every population had one or two haplotypes. In a neutrality test, the variation in nucleotides did not deviate from that expected with neutral evolution for either marker. A retreat route to higher elevations was not evident from either the GapC or cpDNA markers. Hsuehshan was the site of the most divergent population in Taiwan. We concluded that uniform genetic diversity, low differentiation, low numbers of population-specific haplotypes, and neutral evolution characterize contemporary refuge populations of Taiwan fir.

Genetic divergence and phylogeography in the genus Nyctalus (Mammalia, Chiroptera): implications for population history of the insular bat Nyctalus azoreum

We used three mitochondrial DNA fragments with different substitution rates (ND1, Cyt b and the CR) to infer phylogenetic relationships among six species of the genus Nyctalus, and compare levels of genetic divergence between the insular, vulnerable Nyctalus azoreum and its continental counterpart to assess the origins of the Azorean bat. The larger species found throughout the Palaearctic region (N. lasiopterus, N. aviator and N. noctula) share a unique chromosome formula (2n=42) and form a monophyletic clade in our reconstructions. Nyctalus plancyi (=velutinus), a Chinese taxon with 2n=36 chromosomes, is sometimes included in N. noctula, but is genetically very divergent from the latter and deserves full species status. All Cyt b and CR haplotypes of N. azoreum are closely related and only found in the Azores archipelago, but when compared to continental sequences of N. leisleri, levels of mtDNA divergence are unusually low for mammalian species. This contrasts with the high level of differentiation that N. azoreum has attained in its morphology, ecology, and echolocation calls, suggesting a recent split followed by fast evolutionary change. The molecular data suggest that N. azoreum originated from a European population of N. leisleri, and that the colonisation of the Azores occurred at the end of the Pleistocene. The Madeiran populations of N. leisleri also appear to have a European origin, whereas those of the Canary Islands probably came from North Africa. In spite of its recent origin and low genetic divergence, the Azorean bat is well differentiated and consequently represents a unique evolutionary unit with great conservation value.

Hybridization increases measures of innate and cell-mediated immunity in an endangered bird species

1. Given the increasing threat of 'emerging infectious diseases' (EIDs), and the vulnerability of small inbred populations to such novel challenges (at least partly through compromised immunity), a degree of interspecific hybridization may improve the viability of endangered species by enriching depauperate gene pools. 2. To investigate this hypothesis, we quantified indicators of the strength of both innate and cell-mediated immunity in wild populations of hybridizing parakeets on the Chatham Islands, New Zealand. 3. We show that both measures of immune function are markedly higher in the cosmopolitan red-crowned parakeet Cyanoramphus novaezelandiae than in the island endemic Forbes' parakeet C. forbesi, as is to be expected when comparing relatively outbred vs. relatively inbred species. 4. In addition, we show that both measures of immune function are higher in Forbes'x red-crowned parakeet hybrids than in the Forbes' parakeet. Even those individuals with few red-crowned characteristics, suggesting they are the products of matings between hybrids and Forbes' parakeets, have significantly higher measures of immune function. 5. As at least one of the immune indicators measured correlates directly with both survivorship and the viability of small bird populations, this study reveals a potential management option for hybridizing species of conservation concern, where an increase in resilience to novel disease challenges could outweigh some loss of genetic integrity.

Song similarity predicts hybridization in flycatchers

Given that population divergence in sexual signals is an important prerequisite for reproductive isolation, a key prediction is that cases of signal convergence should lead to hybridization. However, empirical studies that quantitatively demonstrate links between phenotypic characters of individuals and their likelihood to hybridize are rare. Here we show that song convergence between sympatric pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) influence social and sexual interactions between the two species. In sympatry, the majority of male pied flycatchers (65%) include various parts of collared flycatcher song in their song repertoire (but not vice versa). Playback experiments on male interactions demonstrate that male collared flycatchers respond similarly to this 'mixed' song as to conspecific song. Long-term data on pairing patterns show that males singing a converged song attract females of the other species: female collared flycatchers only pair with male pied flycatchers if the males sing the mixed song type. From the perspective of a male pied flycatcher, singing a mixed song type is associated with 30% likelihood of hybridization. This result, combined with our estimates of the frequency of mixed singers, accurately predicts the observed occurrence of hybridization among male pied flycatchers in our study populations (20.45% of 484 pairs; predicted 19.5%). Our results support the suggestion that song functions as the most important prezygotic isolation mechanism in many birds.

LANDSCAPE BIOACOUSTICS ALLOW DETECTION OF THE EFFECTS OF HABITAT PATCHINESS ON POPULATION STRUCTURE

Landscape structure may affect individual dispersal abilities, thus influencing the genotypic and phenotypic composition of populations. We analyzed the interplay among landscape, behavior, and evolutionary processes by correlating habitat patchiness to the variability in vocalizations of Dupont's Lark Chersophilus duponti, one of the most habitat-selective and rare European songbirds. We tape-recorded males throughout the species distribution in Spain, analyzed the spatial patterns of territorial call variation at different scales (individuals, populations, and broad geographic areas), and related acoustic variability to patterns of isolation by geographic distance and by landscape unsuitability (calculated by building a predictive model of habitat suitability). The differentiation of spectro-temporal call features resulted from both isolation by distance and isolation by landscape unsuitability mechanisms. Landscape connectivity was often a better determinant of call differentiation than simple straight-line distance between individuals, providing the first evidence that call transmission can be limited by the presence and distribution of patches of adequate habitat, which likely mediates bird dispersal. Landscape patchiness resulted in a reduction of acoustic diversity (repertoire size) within populations, and a parallel increase in differentiation among populations. Landscape bioacoustics can represent a promising tool for estimating population structure, although the study of animal communication cannot be viewed as an alternative, but a source of complementary information to genetics, given that it provides evidence of male-male transmission and social and cultural phenomena that are currently undetectable from molecular data.

A molecular phylogeny of New Zealand's Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences

The New Zealand robin (Petroica australis), tomtit (P. macrocephala), and Chatham Island black robin (P. traversi) are members of the Petroicidae family of Australo-Papuan robins, found throughout Australasia and the western Pacific. In the nearly 200 years since the New Zealand members of Petroicidae were first described, the division of species, subspecies, and even genera has undergone many changes. In this study, we investigate whether molecular phylogenies based on mitochondrial DNA sequences support current taxonomic classifications based on morphology. Petroica traversi, P. australis, and P. macrocephala form distinct clades in phylogenetic trees constructed from Cytochrome b and control region sequences, however the position of the black robin is at odds with the morphological and behavioral data. The black robin does not appear to be a derivative of the New Zealand robin, instead it groups strongly with the tomtit, indicating that lineage sorting and/or introgressive hybridization may have occurred. There is some evidence to support the hypothesis that two invasions of Petroica from Australia have occurred, however additional data from Australian Petroica taxa are required to confirm this. Control region sequences confirm a deep split between the North and South Island P. australis lineages, but suggest a recent radiation of P. macrocephala.

Source populations of Quercus glauca in the last glacial age in Taiwan revealed by nuclear microsatellite markers

In this work, we attempted to study genetic differentiation between populations of Quercus glauca in Taiwan using nuclear microsatellite markers to infer the potential refugium in the last glaciation stage. Four microsatellite loci for 20 individuals each in 10 populations of Taiwan were analyzed. We found that Q. glauca has relatively high within-population diversity (H(E) = 0.741) and low population differentiation (F(ST) = 0.042) but shows isolation by distance. The most divergent populations, according to the average F(ST) for individual populations in comparison with every other population, were found in populations Cy, Sa, and Hy in southern Taiwan and Pa in north-central Taiwan. Moreover, populations Cy, Sa, and Pa were recognized as being the source populations for gene recolonization after the last glaciation stage. In addition, the three sites of Wu, Ym, and Cy exhibited the highest gene diversities that coincided with populations with the highest chloroplast DNA variations. This may have resulted from an admixture of colonization routes. In conclusion, observations of the most divergent populations and source populations suggest that southern and probably north-central Taiwan may have potentially been refugia for Q. glauca in the last glaciation. This agrees with the possible refugium in southern Taiwan revealed by a previous study using chloroplast DNA markers.

Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela Island

Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals.

Hybrid origin of a swordtail species (Teleostei: Xiphophorus clemenciae) driven by sexual selection

The swordlike exaggerated caudal fin extensions of male swordtails are conspicuous traits that are selected for through female choice. Swords are one of only few examples where the hypothesis of a pre-existing bias is believed to apply for the evolution of a male trait. Previous laboratory experiments demonstrated that females prefer males with longer swords and even females from some swordless species show an affiliation for males of sworded species. Earlier phylogenetic studies based on maternally inherited mitochondrial DNA placed the sworded southern swordtail Xiphophorus clemenciae with swordless platies, contradicting its morphology-based evolutionary affinities. The analyses of new nuclear DNA markers now recover its traditional phylogenetic placement with other southern swordtails, suggesting that this species was formed by an ancient hybridization event. We propose that sexual selection through female choice was the likely process of hybrid speciation, by mating of platy females with males of an ancestral swordtail lineage. In artificial crosses of descendent species from the two potential ancestral lineages of X. clemenciae the hybrid and backcross males have swords of intermediate lengths. Additionally, mate choice experiments demonstrate that hybrid females prefer sworded males. These experimental lines of evidence make hybridization through xeno-specific sexual selection by female choice the likely mechanism of speciation.