Phylogeographic Clades Research Articles

Vicariance and cryptic diversity revealed by molecular phylogenetic analyses of estuarine Gammarus species (Crustacea: Amphipoda) due to formation of the Labrador Current

The metapopulation of the estuarine species Gammarus tigrinus along the east coast of the United States has been hypothesised to represent two cryptic species divided biogeographically off the coast of North Carolina, USA. This divergence has been attributed to a strong temperature gradient created by the formation of the cold Labrador Current c. 3.0 million years ago. In addition, the northern phylogeographic clade of G. tigrinus has been demonstrated to be invasive in estuarine habitats across a large portion of northern Europe. Recent collections of G. tigrinus from Florida and Maryland, USA, allow for new approaches to test this hypothesis. Using the nuclear 18S and 28S rRNA, and mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes, species delimitation models provide support that the genetic divergence of the northern and southern clades is equivalent to species level. In addition, molecular clock data demonstrate that this phylogeographic divergence coincides with the formation of the Labrador Current. Furthermore, the collections of G. daiberi from Florida, a species with biogeographical and ecological characteristics similar to those of G. tigrinus, provide independent support for the hypothesis. The potential for invasive species to be cryptic highlights the need for accurate identification of taxa to ensure that appropriate biogeographical assessment of potential source populations and mechanisms of dispersal can be made.

The many faces of Candida auris: Phenotypic and strain variation in an emerging pathogen.

Candida auris is an emerging fungal pathogen with unusual evolutionary history-there are multiple distinct phylogeographic clades showing a near simultaneous transition from a currently unknown reservoir to nosocomial pathogen. Each of these clades has experienced different selective pressures over time, likely resulting in selection for genotypes with differential fitness or phenotypic consequences when introduced to new environments. We also observe diversification within clades, providing additional opportunities for phenotypic differences. These differences can have large impacts on pathogenic potential, drug resistance profile, evolutionary trajectory, and transmissibility. In recent years, there have been significant advances in our understanding of strain-specific behavior in other microbes, including bacterial and fungal pathogens, and we have an opportunity to take this strain variation into account when describing aspects of C. auris biology. Here, we critically review the literature to gain insight into differences at both the strain and clade levels in C. auris, focusing on phenotypes associated with clinical disease or transmission. Our goal is to integrate clinical and epidemiological perspectives with molecular perspectives in a way that would be valuable for both audiences. Identifying differences between strains and understanding which phenotypes are strain specific will be crucial for understanding this emerging pathogen, and an important caveat when describing the analysis of a singular isolate.

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains.

Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.

Nuclear phylogeography reveals strong impacts of gene flow in big brown bats

AbstractAimUnderstanding speciation mechanisms requires disentangling processes that promote and erode population‐level divergence. Three hypotheses are raised that contemporary population structure is mainly shaped by refugial isolation, gene flow or both. Testing these hypotheses requires range‐wide phylogeography and integrative analyses across scales. Here we aimed to (1) re‐estimate the previously unresolved nuclear divergence within a widespread bat; (2) test the above three phylogeographical hypotheses and (3) inform conservation management under climatic change.LocationNorth America including the Caribbean.TaxonThe big brown bat (Eptesicus fuscus).MethodsWe collected range‐wide samples and genome‐wide markers using restriction site‐associated DNA sequencing. Population structure was analysed by clustering methods and spatial estimations. Nuclear phylogeographical divergence was estimated using tree methods (concatenation and coalescence) and network analyses (TreeMix). Phylogeographical hypotheses were tested by comparing alternative evolutionary scenarios using demographic modelling. Species distribution modelling was used to help identify Pleistocene refugia and predict future range shifts under climatic change.ResultsWe identified three populations in the Caribbean, eastern and western North America. The western population further split into three phylogeographical clades: Pacific, southwestern North America and Mexico. Discordance among mitochondrial and nuclear topologies reflected strong impacts of gene flow without sex bias. Demographic modelling supported scenarios of historical isolation followed by secondary gene flow and estimated Holocene divergence times. Species distribution was essentially continuous during glaciation with possible regional isolation, and northward range shifts were predicted under future climatic change.Main ConclusionsContemporary population divergence of big brown bats was shaped by both historical isolation and secondary gene flow, supporting the third phylogeographical hypothesis. While climatic change likely triggered initial divergence, ongoing gene flow has largely impacted the dynamic within‐species evolution and generated population divergence without speciation.

Phylogeography of Patelloida pygmaea along the China coast

Patelloida pygmaea is one of the most abundantly distributed intertidal marine gastropods along the China coast. The mitochondrial (COI) and internal transcribed spacer 1 (ITS1) DNA of P. pygmaea, one hundred and thirty-seven samples collected from 13 localities along its distribution along the China coast, were used to investigate the phylogeographic patterns of P. pygmaea. Phylogeographic analysis revealed three distinct phylogeographic clades, the South China Sea (SCSC), the Bohai and Yellow Sea (BYSC), and the East China Sea (ECSC) clades. The results of AMOVA showed significant genetic differentiation (P 0.05). Phylogeographic patterns of P. pygmaea have been primarily affected by Pleistocene climatic oscillations and environmental conditions. During the glacial periods, the sea regressed and moist and warm conditions, characterizing glacial refugia, became prevalent in the region and caused isolated P. pygmaea populations to expand.

Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus)

BackgroundUlmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China.ResultsPolymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations.ConclusionsGeographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.

A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub-population of Helicobacter pylori from Australia.

We present a novel method for taxon selection, the aim being to minimize problems arising from highly recombinant species such as Helicobacter pylori. Helicobacter pylori has accompanied modern‐human migration out of Africa and is marked by a phylogeographic strain distribution, which has been exploited to add an extra layer of information about human migrations to that obtained from human sources. However, H. pylori's genome has high sequence heterogeneity combined with a very high rate of recombination, causing major allelic diversification across strains. On the other hand, recombination events that have become preserved in sub‐populations are a useful source of phylogenetic information. This creates a potential problem in selecting representative strains for particular genetic or phylogeographic clusters and generally ameliorating the impact on analyses of extensive low‐level recombination. To address this issue, we perform multiple population structure‐based analyses on core genomes to select exemplar strains, called ‘quintessents’, which exhibit limited recombination. In essence, quintessent strains are representative of their specific phylogenetic clades and can be used to refine the current MLST concatenation‐based population structure classification system. The use of quintessents reduces the noise due to local recombination events, while preserving recombination events that have become fixed in sub‐populations. We illustrate the method with an analysis of core genome concatenations from 185 H. pylori strains, which reveals a recent speciation event resulting from the recombination of strains from phylogeographic clade hpSahul, carried by Aboriginal Australians, and hpEurope, carried by some of the people who arrived in Australia over the past 200 years. The signal is much clearer when based on quintessent strains, but absent from the analysis based on MLST concatenations.

Influence of invasion history on rapid morphological divergence across island populations of an exotic bird.

There is increasing evidence that exotic populations may rapidly differentiate from those in their native range and that differences also arise among populations within the exotic range. Using morphological and DNA‐based analyses, we document the extent of trait divergence among native North American and exotic Hawaiian populations of northern cardinal (Cardinalis cardinalis). Furthermore, using a combination of historical records and DNA‐based analyses, we evaluate the role of founder effects in producing observed trait differences. We measured and compared key morphological traits across northern cardinal populations in the native and exotic ranges to assess whether trait divergence across the Hawaiian Islands, where this species was introduced between 1929 and 1931, reflected observed variation across native phylogeographic clades in its native North America. We used and added to prior phylogenetic analyses based on a mitochondrial locus to identify the most likely native source clade(s) for the Hawaiian cardinal populations. We then used Approximate Bayesian Computation (ABC) to evaluate the role of founder effects in producing the observed differences in body size and bill morphology across native and exotic populations. We found cardinal populations on the Hawaiian Islands had morphological traits that diverged substantially across islands and overlapped the trait space of all measured native North American clades. The phylogeographic analysis identified the eastern North American clade (C. cardinalis cardinalis) as the most likely and sole native source for all the Hawaiian cardinal populations. The ABC analyses supported written accounts of the cardinal's introduction that indicate the original 300 cardinals shipped to Hawaii were simultaneously and evenly released across Hawaii, Kauai, and Oahu. Populations on each island likely experienced bottlenecks followed by expansion, with cardinals from the island of Hawaii eventually colonizing Maui unaided. Overall, our results suggest that founder effects had limited impact on morphological trait divergence of exotic cardinal populations in the Hawaiian archipelago, which instead reflect postintroduction events.

Can treefrog phylogeographical clades and species' phylogenetic topologies be recovered by bioacoustical analyses?

Phenotypic traits, such as the frog advertisement call, are generally correlated with interspecific genetic variation, and, as a consequence of strong sexual selection, these behaviors may carry a phylogenetic signal. However, variation in acoustic traits is not always correlated with genetic differences between populations (intraspecific variation); phenotypic plasticity and environmental variables may explain part of such variation. For example, local processes can affect acoustic properties in different lineages due to differences in physical structure, climatic conditions, and biotic interactions, particularly when populations are isolated. However, acoustic traits can be used to test phylogenetic hypotheses. We analyzed the advertisement calls of Dendropsophus elegans males from 18 sites and compared them with those of four closely related congeneric species, in order to test for differences between inter and intraspecific variation. We analyzed 451 calls of 45 males of these five species. Because males from distant sites were grouped together without population congruence, differences found in advertisement calls among individuals were not correlated with phylogeographical clades. Phylogenetic and cluster analyses of the D. elegans clades and those of closely related species grouped all five species into the same topology, as reported by previous molecular and morphological phylogenies. However, the topology of the D. elegans phylogeographical clades did not match the topology previously reported. Acoustic communication in D. elegans seems to be conserved among populations, and the phylogeographical history of the species does not explain the variation among lineages in call properties, despite some congruent phylogenetic signals evident at the species level. Based on molecular clocks retrieved from the literature, it seems that more than 6.5 million years of divergence (late Miocene) are necessary to allow significant changes to occur in the acoustic properties of these treefrog calls, making it possible to recover their phylogenetic history only based on acoustic evidence.

Nuclear and Plastid DNA Sequence-based Molecular Phylogeography of Salvadora oleoides (Salvadoraceae) in Punjab, India Reveals Allopatric Speciation in Anthropogenic Islands Due to Agricultural Expansion

Salvadora oleiodes is a tropical tree species belonging to the little-known family Salvadoraceae and distributed in the arid regions of Africa and Asia. Aims of our study were to trace the microevolutionary legacy of this tree species with the help of sequence-based multi-local phylogeography and to find the comparative placement of family Salvadoraceae within angiosperm clade malvids. A total 20 geographical isolates were collected from different regions of North India, covering a major part of its species range within the Indian Subcontinent. Sequence data from nuclear-encoded Internal Transcribed Spacer region (ITS1-5.8S-ITS2) and plastid-encoded trnL-F spacer region, were generated for this species for the first time in the world. ITS-based Bayesian phylogeographic analysis revealed the existence of four clades while trnL-F spacer based Bayesian analysis revealed one clade for this species distributed in the Indian subcontinent. Between these two loci, ITS revealed more distinct phylogeographic clades, indicating the phylogeographic utility of this locus for the systematics of Salvadoraceae. Interestingly, the ITS phylogeny indicated the existence of allopatric speciation in this tree species. Factors such as habitat destruction through agricultural expansion of plains might have forced the remaining population of this threatened tree species to isolated patches of thorn forest biotas, the ‘anthropogenic islands’, analogous to an archipelago. Phylogenetic analyzes based on trnL-F spacer suggested a synonymy of this species with Salvadora angustifolia. Maximum Likelihood gene tree based on ITS sequence data revealed that Salvadoraceae belongs to Sapindales rather than Brassicales. However, in the gene tree based on trnL-F spacer sequence, this family clustered within Brassicales. An evolutionary congruence of S. oleoides isolates across its range in North India is revealed in this study. Given the conflicting results on the relative placement of Salvadoraceae in Brassicales and Sapindales, the need for further phylogenetic analyses of malvids using supermatrix approach is highlighted.

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae).

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.

Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association

Genetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA. Nei’s genetic distance calculated from core genome single nucleotide polymorphisms (SNPs) demonstrated that the animal isolates were from the same population. Investigation of the Shiga toxin bacteriophage and their insertion sites (SBI typing) revealed that cattle and sheep isolates had statistically indistinguishable rarefaction profiles, diversity and genotypes. In contrast, isolates from different countries exhibited significant differences in Nei’s genetic distance and SBI typing. Hence, after successful international transmission, which has occurred on multiple occasions, local genetic variation occurs, resulting in a global patchwork of continental and trans-continental phylogeographic clades. These findings are important for three reasons: first, understanding transmission and evolution of infectious diseases associated with multiple host reservoirs and multi-geographic locations; second, highlighting the relevance of the sheep reservoir when considering farm based interventions; and third, improving our understanding of why human disease incidence varies across the world.

High Rate of Simian Immunodeficiency Virus (SIV) Infections in Wild Chimpanzees in Northeastern Gabon.

The emergence of HIV-1 groups M, N, O, and P is the result of four independent cross-species transmissions between chimpanzees (cpz) and gorillas (gor) from central/south Cameroon and humans respectively. Although the first two SIVcpz were identified in wild-born captive chimpanzees in Gabon in 1989, no study has been conducted so far in wild chimpanzees in Gabon. To document the SIVcpz infection rate, genetic diversity, and routes of virus transmission, we analyzed 1458 faecal samples collected in 16 different locations across the country, and we conducted follow-up missions in two of them. We found 380 SIV antibody positive samples in 6 different locations in the north and northeast. We determined the number of individuals collected by microsatellite analysis and obtained an adjusted SIV prevalence of 39.45%. We performed parental analysis to investigate viral spread between and within communities and found that SIVs were epidemiologically linked and were transmitted by both horizontal and vertical routes. We amplified pol and gp41 fragments and obtained 57 new SIVcpzPtt strains from three sites. All strains, but one, clustered together within a specific phylogeographic clade. Given that these SIV positive samples have been collected nearby villages and that humans continue to encroach in ape’s territories, the emergence of a new HIV in this area needs to be considered.

Phylogeographic evidence for two mesic refugia in a biodiversity hotspot.

Phylogeographic studies of flora in species-rich south-western Australia point to complex evolutionary histories, reflecting patterns of persistence and resilience to climatic changes during the Pleistocene. We asked whether coastal areas of the mid-west and south, as well as granite outcrops and inland ranges, have acted as major refugia within this region during Pleistocene climatic fluctuations by analysing phylogeographic patterns in the shrub Calothamnus quadrifidus R.Br. (Myrtaceae). We determined variation in chloroplast DNA data for 41 populations across the geographic range. Relationships and major clades were resolved using parsimony and Bayesian analyses. We tested for demographic and spatial expansion of the major clades and estimated clade divergence dates using an uncorrelated, lognormal relaxed clock based on two conservative chloroplast mutation rates. Two distinct phylogeographic clades were identified showing divergence during the Pleistocene, consistent with other phylogeographic studies of south-west Australian flora, emphasising the impact of climatic oscillations in driving divergence in this landscape. The southern clade was more diverse, having higher haplotype diversity and greater genetic structure, while the northern clade showed evidence of fluctuation in population size. Regions of high haplotype diversity with adjacent areas of low diversity observed in each clade indicated the locations of two coastal refugia: one on the south coast and another along the mid-west coast. This is the first evidence for major Pleistocene refugia using chloroplast genetic data in a common, widespread species from this region.

High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery.

BackgroundSingle nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 60-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains.ResultsA total of 1581 chromosomal SNPs precisely establish the phylogenetic relationships existing between the French strains. Phylogeography patterns within the three canSNP sub-lineages present in France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One of the more remarkable findings was the identification of a variety of genotypes within the A.Br.011/009 sub-group that are persisting in the different regions of France. The 560 SNPs defining the A.Br.011/009- affiliated French strains split the Trans-Eurasian sub-group into six distinct branches without any intermediate nodes. Distinct sub-branches, with some geographic clustering, were resolved. The 345 SNPs defining the major B.Br CNEVA sub-lineage clustered three main phylogeographic clades, the Alps, the Pyrenees, and the Massif Central, with a small Saône-et-Loire sub-cluster nested within the latter group. The French strains affiliated to the minor A.Br.001/002 group were characterized by 226 SNPs. All recent isolates collected from the Doubs department were closely related. Identification of SNPs from whole-genome sequences facilitates high-resolution strain tracking and provides the level of discrimination required for outbreak investigations. Eight diagnostic SNPs, representative of the main French-specific phylogeographic clusters, were therefore selected and developed into high-resolution melting SNP discriminative assays.ConclusionsThis work has established one of the most accurate phylogenetic reconstruction of B. anthracis population structure in a country. An extensive next-generation sequencing (NGS) dataset of 122 French strains have been created that allowed the identification of novel diagnostic SNPs useful to rapidly determine the geographic origin of any strain found in France.

THE INFLUENCE OF POLLINATOR PHYLOGEOGRAPHY AND MATE PREFERENCE ON FLORAL DIVERGENCE IN A SEXUALLY DECEPTIVE DAISY

Divergent mate preferences and subsequent genetic differentiation between populations has been demonstrated, but its effects on interspecific interactions are unknown. Associated species exploiting these mate preferences, for example, may diverge to match local preferences. We explore this idea in the sexually deceptive, fly-mimicking daisy, Gorteria diffusa, by testing for association between genetic structure in the fly pollinator (a proxy for mate preference divergence) and geographic divergence in floral form. If genetic structure in flies influences interactions with G. diffusa, we expect phylogeographically distinct flies to be associated with different floral forms. Flies associated with forms exploiting only feeding behavior often belonged to several phylogeographic clades, whereas flies associated with forms exploiting male-mating behavior always belonged to distinct clades, indicating the possibility of pollinator-mediated floral divergence through phylogeographic variation in mating preferences of male flies. We tested this hypothesis with reciprocal presentations using male flies from distinct clades associated with separate floral forms. Results show that males from all clades exhibit similar preferences, making pollinator driven divergence through geographic variation in mate preference unlikely. Males, however, showed evidence of learned resistance to deceptive traits, suggesting antagonistic interactions between plants and pollinators may drive deceptive floral trait evolution in G. diffusa.

In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.

Sexual selection on song and cuticular hydrocarbons in two distinct populations of Drosophila montana.

Sexual selection has the potential to contribute to population divergence and speciation. Most studies of sexual selection in Drosophila have concentrated on a single signaling modality, usually either courtship song or cuticular hydrocarbons (CHCs), which can act as contact pheromones. We have examined the relationship between both signal types and reproductive success using F1–3 offspring of wild-collected flies, raised in the lab. We used two populations of the Holarctic species Drosophila montana that represent different phylogeographic clades that have been separate for ca. 0.5 million years (MY), and differ to some extent in both traits. Here, we characterize the nature and identify the targets of sexual selection on song, CHCs, and both traits combined within the populations. Three measures of courtship outcome were used as fitness proxies. They were the probability of mating, mating latency, and the production of rejection song by females, and showed patterns of association with different traits that included both linear and quadratic selection. Courtship song predicted courtship outcome better than CHCs and the signal modalities acted in an additive rather than synergistic manner. Selection was generally consistent in direction and strength between the two populations and favored males that sang more vigorously. Sexual selection differed in the extent, strength, and nature on some of the traits between populations. However, the differences in the directionality of selection detected were not a good predictor of population differences. In addition, a character previously shown to be important for species recognition, interpulse interval, was found to be under sexual selection. Our results highlight the complexity of understanding the relationship between within-population sexual selection and population differences. Sexual selection alone cannot predict differences between populations.

Small-scale genetic structure of American black bears illustrates potential postglacial recolonization routes

In the absence of obvious barriers to dispersal microsatellite studies of vagile mammalian carnivores frequently find panmictic-like genetic structure over wide scales, whereas high levels of differentiation at much finer scales are detected with mitochondrial DNA (mtDNA). Given the maternal inheritance of mtDNA, these differences are often attributed to male-biased dispersal, remnants of postglacial range expansion, or both. Based on such contrasting results, it is not always clear how to delineate contemporary populations. We investigated the genetic structure of American black bears (Ursus americanus) over a wide geographic area (.1,700 km) that has no obvious physiogeographic barriers to gene flow. We analyzed a 315-base pair fragment of the mtDNA control region from 660 individual bears from 23 regions of Ontario, Canada. Relative to black bear studies based on nuclear data, mitochondrial analyses revealed much stronger patterns of genetic structure among regions (0.09 , FST , 0.44), even at small-scale intervals (,150 km), which likely reflects strong female philopatry combined with male-biased dispersal. The patterns of genetic differentiation among regions were consistent with previously described historical patterns in black bears, specifically the division of the species into 2 phylogeographic clades (coastal and continental). We confirmed that further subdivision of the continental clade occurs in a region where obvious physiogeographic barriers do not exist. We postulate that this small-scale differentiation can be explained by residual patterns from postglacial recolonization routes on either side of the Great Lakes. We suggest that it was maintained through extreme female philopatry due to habitat saturation following the postglacial geographic expansion. Based on our results, we propose that a combination of several molecular markers can be more useful in defining population units for conservation and management decisions than biparentally inherited microsatellites.