The geography and ecology of plant speciation: range overlap and niche divergence in sister species

A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under ‘budding’ speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister–non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities.     

Population differentiation and restricted gene flow in Spanish crossbills: not isolation-by-distance but isolation-by-ecology

Divergent selection stemming from environmental variation may induce local adaptation and ecological speciation whereas gene flow might have a homogenizing effect. Gene flow among populations using different environments can be reduced by geographical distance (isolation-by-distance) or by divergent selection stemming from resource use (isolation-by-ecology). We tested for and encountered phenotypic and genetic divergence among Spanish crossbills utilizing different species of co-occurring pine trees as their food resource. Morphological, vocal and mtDNA divergence were not correlated with geographical distance, but they were correlated with differences in resource use. Resource diversity has now been found to repeatedly predict crossbill diversity. However, when resource use is not 100% differentiated, additional characters (morphological, vocal, genetic) must be used to uncover and validate hidden population structure. In general, this confirms that ecology drives adaptive divergence and limits neutral gene flow as the first steps towards ecological speciation, unprevented by a high potential for gene flow.     

Latitudinal variation in genetic divergence of populations and the potential for future speciation

The increase in biological diversity with decreasing latitude is widely appreciated but the cause of the pattern is unknown. This pattern reflects latitudinal variation in both the origin of new species (cladogenesis) and the number of species that coexist. Here we address latitudinal variation in species origination, by examining population genetic processes that influence speciation. Previous data suggest a greater number of speciation events at lower latitudes. If speciation events occur more frequently at lower latitudes, we predicted that genetic divergence among populations within species, an important component of cladogenesis, should be greater among lower latitude populations. We tested this prediction using within-species patterns of mtDNA variation across 60 vertebrate species that collectively spanned six continents, two oceans, and 119 degrees latitude. We found greater genetic divergence of populations, controlling for geographic distance, at lower latitudes within species. This pattern remained statistically significant after removing populations that occur in localities previously covered by continental glaciers during the last glaciation. Results suggest that lower latitude populations within species exhibit greater evolutionary independence, increasing the likelihood that mutation, recombination, selection, and/or drift will lead to divergence of traits important for reproductive isolation and speciation. Results are consistent with a greater influence of seasonality, reduced energy, and/or glacial (Milankovitch) cycles acting on higher latitude populations, and represent one of the few tests of predictions of latitudinal variation in speciation rates using population genetic data.     

Genetic structure among populations in the endemic Hawaiian Plantago lineage: insights from microsatellite variation

Endemic Hawaiian species in the genus Plantago show considerable morphological and ecological diversity. Despite their variation, a recent phylogenetic analysis based on DNA sequence data showed that the group is monophyletic and that sequence variation among species and morphotypes is low. This lack of sequence polymorphisms resulted in an inability to resolve species and population affinities within the most recently derived clade of this lineage. To assess species boundaries, population genetic structure and interpopulation connectivity among the morphologically and ecologically distinct populations within this clade, genetic variation was examined using eight microsatellite loci. Within‐population genetic diversity was found to be lowest in the Maunaiu, Hawai'i population of the endangered P. hawaiensis, and highest in the large P. pachyphylla population from 'Eke, West Maui. Isolation by distance across the range of populations was detected and indicated restricted dispersal. This result is likely to be attributable to few interisland dispersal events in the evolutionary history of this lineage. Genetic differentiation within islands tended to be higher among populations occurring in contrasting bog and woodland habitats, suggesting ecological barriers to gene flow and the potential role of ecological divergence in population diversification. Overall, these results are consistent with findings from phylogenetic analysis of the entire lineage. Our data bring new insights regarding patterns of dispersal and population genetic structure to this endemic and endangered group of island taxa. As island environments become increasingly fragmented, information of this type has important implications for the successful management of these fragile populations and habitats.     

Comparative phylogeography of Nearctic and Palearctic fishes

Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.     

Rivers,refuges and population divergence of fire‐eye antbirds (Pyriglena) in the Amazon Basin

The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white‐backed fire‐eye (Pyriglena leuconota) populations along the Tocantins River valley in the south‐eastern Amazon Basin, and we confront the predictions of the river and the Pleistocene refuge hypotheses with patterns of genetic variation observed in these populations. We also investigated whether these patterns reflect the recently detected shift in the course of the Tocantins River. We sampled a total of 32 individuals east of, and 52 individuals west of, the Tocantins River. Coalescent simulations and phylogeographical and population genetics analytical approaches revealed that mtDNA variation observed for fire‐eye populations provides little support for the hypothesis that populations were isolated in glacial forest refuges. Instead, our data strongly support a key prediction of the river hypothesis. Our study shows that the Tocantins River has probably been the historical barrier promoting population divergence in fire‐eye antbirds. Our results have important implications for a better understanding of the importance of large Amazonian rivers in vertebrate diversification in the Neotropics.     

Multilocus phylogeography of Australian teals (Anas spp.): a case study of the relationship between vagility and genetic structure

Biogeographic barriers potentially restrict gene flow but variation in dispersal or vagility can influence the effectiveness of these barriers among different species and produce characteristic patterns of population genetic structure. The objective of this study was to investigate interspecific and intraspecific genetic structure in two closely related species that differ in several life‐history characteristics. The grey teal Anas gracilis is geographically widespread throughout Australia with a distribution that crosses several recognized biogeographic barriers. This species has high vagility as its extensive movements track broad‐scale patterns in rainfall. In contrast, the closely related chestnut teal A. castanea is endemic to the mesic southeastern and southwestern regions of Australia and is more sedentary. We hypothesized that these differences in life‐history characteristics would result in more pronounced population structuring in the chestnut teal. We sequenced five nuclear loci (nuDNA) for 49 grey teal and 23 chestnut teal and compared results to published mitochondrial DNA (mtDNA) sequences. We used analysis of molecular variance to examine population structure, and applied coalescent based approaches to estimate demographic parameters. As predicted, chestnut teal were more strongly structured at both mtDNA and nuDNA (Φ_ST= 0.163 and 0.054, respectively) than were grey teal (Φ_ST < 0.0001 for both sets of loci). Surprisingly, a greater proportion of the total genetic variation was partitioned among populations within species (Φ_SC= 0.014 and 0.047 for nuDNA and mtDNA, respectively) than between the two species (Φ_CT < 0.0001 for both loci). The ‘Isolation with Migration’ coalescent model suggested a late Pleistocene divergence between the taxa, but remarkably, a deeper divergence between the southeastern and southwestern populations of chestnut teal. We conclude that dispersal potential played a prominent role in the structuring of populations within these species and that divergent selection associated with ecology and life history traits likely contributed to rapid and recent speciation in this pair.     

Widespread geographical distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika

The spectacularly diverse cichlid fish species flocks of the East African Rift Lakes have elicited much debate on the potential evolutionary mechanisms responsible for the origin of these adaptive radiations. An historical perspective on population structure may offer insights into the processes driving population differentiation and possibly speciation. Here, we examine mitochondrial DNA (mtDNA) sequence variation in two endemic species of rock-dwelling cichlids, Simochromis babaulti and S. diagramma , from Lake Tanganyika. Phylogeographic analyses were used to infer what factors might have been important in the genetic structuring of Simochromis populations. Patterns of mtDNA differentiation in Simochromis were compared to those of other rock-dwelling cichlids to distinguish between competing hypotheses concerning the processes underlying their evolution. In striking contrast to previous findings, populations of Simochromis , even those separated by up to 300 km, were found to share mitochondrial DNA haplotypes. There is no correspondence between mtDNA genealogies and the geographical distribution of populations. Only S. babaulti , but not S. diagramma was found to have a significant association between genetic and geographical distance. These phylogeographic patterns suggest that the evolutionary effects of abiotic and biotic factors shaping population genetic structure may differ substantially even among closely related species of rock-dwelling cichlids. Physical events and barriers to gene flow that are believed to have had a major impact on the geographical distribution and intralacustrine speciation of Tropheus do not seem to have equally strongly affected its close relative Simochromis . These findings emphasize that no single mechanism can be responsible for the formation of population structure, speciation, and the adaptive radiation of all cichlid fishes.     

Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae)

The diversity of geographic scales at which marine organisms display genetic variation mirrors the biophysical and ecological complexity of dispersal by pelagic larvae. Yet little is known about the effect of larval ecology on genetic population patterns, partly because detailed data of larval ecology do not yet exist for most taxa. One species for which this data is available is Eleutheronema tetradactylum, a tropical Indo-West Pacific shorefish. Here, we use a partial sequence mitochondrial cytochrome oxidase subunit 1 (COI) marker and five microsatellite loci to survey the genetic structure of E. tetradactylum across northern Australia. Structure was found throughout the range and isolation by distance was strong, explaining approximately 87 and 64% of the genetic variation in microsatellites and mtDNA, respectively. Populations separated by as little as 15 km also showed significant genetic structure, implying that local populations are mainly insular and self-seeding on an ecological time frame. Because the larvae of E. tetradactylum have lower swimming performance and poor orientation compared with other tropical fishes, even modest larval abilities may permit self-recruitment rather than passive dispersal.     

SPECIATION AND POPULATION GENETIC STRUCTURE IN TROPICAL PACIFIC SEA URCHINS

Unlike populations of many terrestrial species, marine populations often are not separated by obvious, permanent barriers to gene flow. When species have high dispersal potential and few barriers to gene flow, allopatric divergence is slow. Nevertheless, many marine species are of recent origin, even in taxa with high dispersal potential. To understand the relationship between genetic structure and recent species formation in high dispersal taxa, we examined population genetic structure among four species of sea urchins in the tropical Indo-West Pacific that have speciated within the past one to three million years. Despite high potential for gene flow, mtDNA sequence variation among 200 individuals of four species in the urchin genus Echinometra shows a signal of strong geographic effects. These effects include (1) substantial population heterogeneity; (2) lower genetic variation in peripheral populations; and (3) isolation by distance. These geographic patterns are especially strong across scales of 5000-10,000 km, and are weaker over scales of 2500-5000 km. As a result, strong geographic patterns would not have been readily visible except over the wide expanse of the tropical Pacific. Surface currents in the Pacific do not explain patterns of gene flow any better than do patterns of simple spatial proximity. Finally, populations of each species tend to group into large mtDNA regions with similar mtDNA haplotypes, but these regional boundaries are not concordant in different species. These results show that all four species have accumulated mtDNA differences over similar spatial and temporal scales but that the precise geographic pattern of genetic differentiation varies for each species. These geographic patterns appear much less deterministic than in other well-known coastal marine systems and may be driven by chance and historical accident.     

Phylogeography of Aglais urticae (Lepidoptera) based on DNA sequences of the mitochondrial COI gene and control region

Mitochondrial DNA (mtDNA) sequences of the COI gene and the control region were used to examine the genetic population structure of Aglais urticae L. (Lepidoptera) over its entire geographic range, i.e., the Palaearctic. The phylogenetic relationships within and between A. urticae subspecies were determined and patterns of mtDNA divergence and ecological differentiation were compared. High gene flow together with a recent and sudden population expansion characterise the genetic population structure of this species. No geographically induced differentiation was observed, nor were subspecies identified as separate evolutionary units. The discrepancy between the genetic and ecological variation is most likely due to the slower rate of mtDNA evolution compared to ecological differentiation. The control region proved to be a less useful molecular marker for the population genetics and the phylogenetic reconstruction of closely related taxa in A. urticae than it has for other species. The extreme bias in adenine and thymine content (A+T=90.91%) probably renders this region highly susceptible to homoplasy, resulting in a less informative molecular marker.     

Fine-scale genetic structure, estuarine colonization and incipient speciation in the marine silverside fish Odontesthes argentinensis

The identification of incipient ecological species represents an opportunity to investigate current evolutionary process where adaptive divergence and reproductive isolation are associated. In this study we analysed the genetic structure of marine and estuarine populations of the silverside fish Odontesthes argentinensis using nine microsatellite loci and 396 bp of the mitochondrial DNA (mtDNA) control region. Our main objective was to investigate the relationship among estuarine colonization, divergent selection and speciation in silversides. Significant genetic structure was detected among all marine and estuarine populations. Despite the low phylogeographic structure in mtDNA haplotypes, there was clear signal of local radiations of haplotypes in more ancient populations. Divergence among marine populations was interpreted as a combined result of homing behaviour, isolation by distance and drift. On the other hand, ecological shifts due to the colonization of estuarine habitats seem to have promoted rapid adaptive divergence and reproductive isolation in estuarine populations, which were considered as incipient ecological species. This conclusion is supported by the existence of a set of environmental factors required for successful reproduction of estuarine ecotypes. The pattern of genetic structure indicates that phenotypic and reproductive divergence evolved in the face of potential gene flow between populations. We suggest that the 'divergence-with-gene-flow' model of speciation may account for the diversification of estuarine populations. The approach used can potentially identify 'incipient estuarine species', being relevant to the investigation of the evolutionary relationships of silversides in several coastal regions of the world.     

Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and Omocestus navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean‐montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome‐wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent‐based phylogenetic reconstructions, integrative Bayesian model‐based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species.     

Phylogenetic and phylogeographic analysis of Iberian lynx populations

The Iberian lynx (Lynx pardinus), one of the world's most endangered cat species, is vulnerable due to habitat loss, increased fragmentation of populations, and precipitous demographic reductions. An understanding of Iberian lynx evolutionary history is necessary to develop rational management plans for the species. Our objectives were to assess Iberian lynx genetic diversity at three evolutionary timescales. First we analyzed mitochondrial DNA (mtDNA) sequence variation to position the Iberian lynx relative to other species of the genus LYNX: We then assessed the pattern of mtDNA variation of isolated populations across the Iberian Peninsula. Finally we estimated levels of gene flow between two of the most important remaining lynx populations (Do?ana National Park and the Sierra Morena Mountains) and characterized the extent of microsatellite locus variation in these populations. Phylogenetic analyses of 1613 bp of mtDNA sequence variation supports the hypothesis that the Iberian lynx, Eurasian lynx, and Canadian lynx diverged within a short time period around 1.53-1.68 million years ago, and that the Iberian lynx and Eurasian lynx are sister taxa. Relative to most other felid species, genetic variation in mtDNA genes and nuclear microsatellites were reduced in Iberian lynx, suggesting that they experienced a fairly severe demographic bottleneck. In addition, the effects of more recent reductions in gene flow and population size are being manifested in local patterns of molecular genetic variation. These data, combined with recent studies modeling the viability of Iberian lynx populations, should provide greater urgency for the development and implementation of rational in situ and ex situ conservation plans.     

The evolutionary enigma of bonefishes (Albula spp.): cryptic species and ancient separations in a globally distributed shorefish

Many examples of cryptic marine species have been demonstrated with biochemical and molecular studies. In most cases, a broadly distributed taxon is actually a group of sibling species that can be distinguished (upon closer examination) by ecological or morphological characters. Fishes of the family Albulidae constitute a notable exception. Bonefish (Albula spp.) morphology and ecology are highly conserved around the globe, and their extended pelagic larval stage could allow population connections on a vast geographic scale. Based on this perceived homogeneity, bonefishes were classified as a single pantropical species, A. vulpes. However, allozyme studies of Hawaiian populations indicated that two sympatric species (A. glossodonta and A. neoguinaica) are included in the synonymy of A. vulpes. To ascertain the number and distribution of evolutionary partitions in Albula, we surveyed 564 bp of mitochondrial DNA (mtDNA) cytochrome b from 174 individuals collected at 26 locations. Sequence comparisons reveal eight deep lineages (d = 5.56-30.6%) and significant population structure within three of the four lineages that could be tested (phiST = 0.047-0.678). These findings confirm the genetic distinctiveness of the three species noted above and invoke the possibility of five additional species. Clock estimates for mtDNA indicate that these putative species arose 4-20 million years ago. Distinct evolutionary lineages coexist in several sample locations, yet show little morphological or ecological differentiation in sympatry. Thus, bonefish species seem to defy the evolutionary conventions of morphological differentiation over time and ecological displacement in sympatry. Despite multiple cases of sympatry, sister-taxa relationships inferred from mtDNA indicate that divergence in allopatry has been the predominant speciation mechanism in Albula. Stabilizing selection in the homogeneous habitat occupied by bonefishes (tropical sand flats) could promote the retention of highly conserved morphology and ecology.     

A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity

The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys are urgently needed to avoid underestimating tropical diversity, and the use of mtDNA markers can be instrumental in identifying and prioritizing taxa for species discovery.     

Spatial and ecological population genetic structures within two island‐endemic Aeonium species of different niche width

The Crassulacean genus Aeonium is a well‐known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra‐island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island‐endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci–environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.     

DOES NICHE CONSERVATISM PROMOTE SPECIATION? A CASE STUDY IN NORTH AMERICAN SALAMANDERS

Recent speciation research has generally focused on how lineages that originate in allopatry evolve intrinsic reproductive isolation, or how ecological divergence promotes nonallopatric speciation. However, the ecological basis of allopatric isolation, which underlies the most common geographic mode of speciation, remains poorly understood and largely unstudied. Here, we explore the ecological and evolutionary factors that promote speciation in Desmognathus and Plethodon salamanders from temperate eastern North America. Based on published molecular phylogenetic estimates and the degree of geographic range overlap among extant species, we find strong evidence for a role for geographic isolation in speciation. We then examine the relationship between climatic variation and speciation in 16 sister-taxon pairs using geographic information system maps of climatic variables, new methods for modeling species' potential geographic distributions, and data on geographic patterns of genetic variation. In contrast to recent studies in tropical montane regions, we found no evidence for parapatric speciation along climatic gradients. Instead, many montane sister taxa in the Appalachian Highlands inhabit similar climatic niches and seemingly are allopatric because they are unable to tolerate the climatic conditions in the intervening lowlands. This temporal and spatial-ecological pattern suggests that niche conservatism, rather than niche divergence, plays the primary role in promoting allopatric speciation and montane endemism in this species-rich group of vertebrates. Our results demonstrate that even the relatively subtle climatic differences between montane and lowland habitats in eastern North America may play a key role in the origin of new species.     

Applications of mitochondrial DNA analysis in conservation: a critical review

Patterns of variation in mitochondrial DNA (mtDNA) increasingly are being investigated in threatened or managed species, but not always with clearly defined goals for conservation. In this review I identify uses of mtDNA analysis which fall into two different areas: (i) 'gene conservation' - the identification and management of genetic diversity, and (ii) 'molecular ecology' - the use of mtDNA variation to guide and assist demographic studies of populations. These two classes of application have different conceptual bases, conservation goals and time-frames. Gene conservation makes extensive use of phylogenetic information and is, in general, most relevant to long-term planning. Appropriate uses here include identification of Evolutionarily Significant Units and assessment of conservation priority of taxa or areas from an evolutionary perspective. Less appropriate are inferences about fitness from within-population diversity and about species boundaries. Molecular ecology makes more use of allele frequencies and provides information useful for short-term management of populations. Powerful applications are to identify Management Units and to define and use naturally occurring genetic tags. Estimating demographic parameters, e.g migration rate and population size, from patterns of mtDNA diversity is fraught with difficulty, particularly where populations are fluctuating, and is unlikely to produce quantitative estimates sufficiently accurate to be useful for practical management of contemporary populations. However, through comparative studies, mtDNA analysis can provide qualitative signals of population changes, allowing efficient targeting of resource-intensive ecological studies. Thus, there are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long-term planning and short-term execution of species recovery plans.     

Radiation and divergence in the Rhagoletis pomonella species complex: inferences from DNA sequence data

Here, we investigate the evolutionary history and pattern of genetic divergence in the Rhagoletis pomonella (Diptera: Tephritidae) sibling species complex, a model for sympatric speciation via host plant shifting, using 11 anonymous nuclear genes and mtDNA. We report that DNA sequence results largely coincide with those of previous allozyme studies. Rhagoletis cornivora was basal in the complex, distinguished by fixed substitutions at all loci. Gene trees did not provide reciprocally monophyletic relationships among US populations of R. pomonella, R. mendax, R. zephyria and the undescribed flowering dogwood fly. However, private alleles were found for these taxa for certain loci. We discuss the implications of the results with respect to identifiable genetic signposts (stages) of speciation, the mosaic nature of genomic differentiation distinguishing formative species and a concept of speciation mode plurality involving a biogeographic contribution to sympatric speciation in the R. pomonella complex.