Recovering cryptic diversity and ancient drainage patterns in eastern North America: historical biogeography of the Notropis rubellus species group (Teleostei: Cypriniformes)

The Central Highlands of North America contain a strikingly diverse assemblage of temperate freshwater fishes and have long been a focus of biogeographic studies. The rosyface shiner complex, Notropis rubellus and related species, is a member of this fauna exhibiting a disjunct highlands distribution occurring in the unglaciated regions of the Central Highlands and glaciated regions of the Central Lowlands. Until recently, N. rubellus was considered a single, widespread species exhibiting geographic variation in morphological characters. However, several studies have revealed that N. rubellus is a multi-species complex with closely related species endemic to drainages within each highland region. We examined genetic variation of the N. rubellus complex using a complete mtDNA cytochrome b gene sequence data set and combined mtDNA and published allozyme data sets. Parsimony and Bayesian analyses of the mitochondrial data set and parsimony analyses of a combined mitochondrial and allozyme data sets were largely consistent. Results of these analyses revealed ancient cryptic diversity within the N. rubellus complex that existed prior to the onset of Pleistocene glaciations. We identified seven strongly supported clades within the N. rubellus complex. Four clades are diagnosed as separate species (N. percobromus, N. rubellus, N. micropteryx and N. suttkusi) and three clades may represent undescribed forms. Relationships among these groups and their biogeographical patterns provided significant inferences on ichthyofaunal distributions in southeastern North America. These include the timing of the origin of the diversity, ancient drainage patterns and barriers to dispersal in the Central Highlands. The observation of increased diversity in N. rubellus suggests there may be greater diversity within other taxa with a similar distribution.     

Phylogenetic perspective on ecological niche evolution in american blackbirds (Family Icteridae)

Analysis of ecological characters on phylogenetic frameworks has only recently appeared in the literature, with several studies addressing patterns of niche evolution, generally over relatively recent time frames. In the present study, we examined patterns of niche evolution for a broad radiation of American blackbird species (Family Icteridae), exploring more deeply into phylogenetic history. Within each of three major blackbird lineages, overlap of ecological niches in principal components analysis transformed environmental space varied from high to none. Comparative phylogenetic analyses of ecological niche characteristics showed a general pattern of niche conservatism over evolutionary time, with differing degrees of innovation among lineages. Although blackbird niches were evolutionarily plastic over differing periods of time, they diverged within a limited set of ecological possibilities, resulting in examples of niche convergence among extant blackbird species. Hence, an understanding of the patterns of ecological niche evolution on broad phylogenetic scales sets the stage for framing questions of evolutionary causation, historical biogeography, and ancestral ecological characteristics more appropriately.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 869–878.     

Rapid allopatric speciation in logperch darters (Percidae: Percina)

Theory predicts that clades diversifying via sympatric speciation will exhibit high diversification rates. However, the expected rate of diversification in clades characterized by allopatric speciation is less clear. Previous studies have documented significantly higher speciation rates in freshwater fish clades diversifying via sympatric versus allopatric modes, leading to suggestions that the geographic pattern of speciation can be inferred solely from knowledge of the diversification rate. We tested this prediction using an example from darters, a clade of approximately 200 species of freshwater fishes endemic to eastern North America. A resolved phylogeny was generated using mitochondrial DNA gene sequences for logperches, a monophyletic group of darters composed of 10 recognized species. Divergence times among logperch species were estimated using a fossil calibrated molecular clock in centrarchid fishes, and diversification rates in logperches were estimated using several methods. Speciation events in logperches are recent, extending from 4.20 +/- 1.06 million years ago (mya) to 0.42 +/- 0.22 mya, with most speciation events occurring in the Pleistocene. Diversification rates are high in logperches, at some nodes exceeding rates reported for well-studied adaptive radiations such as Hawaiian silverswords. The geographic pattern of speciation in logperches was investigated by examining the relationship between degree of sympatry and the absolute age of the contrast, with the result that diversification in logperches appears allopatric. The very high diversification rate observed in the logperch phylogeny is more similar to freshwater fish clades thought to represent examples of sympatric speciation than to clades representing allopatric speciation. These results demonstrate that the geographic mode of speciation for a clade cannot be inferred from the diversification rate. The empirical observation of high diversification rates in logperches demonstrates that allopatric speciation can occur rapidly.     

Population demography influences climatic niche evolution: evidence from diploid American Hordeum species (Poaceae)

In this study, we explore the interplay of population demography with the evolution of ecological niches during or after speciation in Hordeum. While large populations maintain a high level of standing genetic diversity, gene flow and recombination buffers against fast alterations in ecological adaptation. Small populations harbour lower allele diversity but can more easily shift to new niches if they initially survive under changed conditions. Thus, large populations should be more conservative regarding niche changes in comparison to small populations. We used environmental niche modelling together with phylogenetic, phylogeographic and population genetic analyses to infer the correlation of population demography with changes in ecological niche dimensions in 12 diploid Hordeum species from the New World, forming four monophyletic groups. Our analyses found both shifts and conservatism in distinct niche dimensions within and among clades. Speciation due to vicariance resulted in three species with no pronounced climate niche differences, while species originating due to long‐distance dispersals or otherwise encountering genetic bottlenecks mostly revealed climate niche shifts. Niche convergence among clades indicates a niche‐filling pattern during the last 2 million years in South American Hordeum. We provide evidence that species, which did not encounter population reductions mainly showed ecoclimatic niche conservatism, while major niche shifts occurred in species which have undergone population bottlenecks. Our data allow the conclusion that population demography influences adaptation and niche shifts or conservatism in South American Hordeum species.     

Niche conservatism and phylogenetic clustering in a tribe of arid‐adapted marsupial mice,the Sminthopsini

The progressive expansion of the Australian arid zone during the last 20 Ma appears to have spurred the diversification of several families of plants, vertebrates and invertebrates, yet such taxonomic groups appear to show limited niche radiation. Here, we test whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence in a tribe of marsupial mice (Sminthopsini; 23 taxa) that includes the most speciose genus of living dasyurids, the sminthopsins. To that end, we integrated phylogenetic data with ecological niche modelling, to enable us to reconstruct the evolution of climatic suitability within Sminthopsini. Niche overlap among species was low‐moderate (but generally higher than expected given environmental background similarity), and the degree of phylogenetic clustering increased with aridity. Climatic niche reconstruction illustrates that there has been little apparent evolution of climatic tolerance within clades. Accordingly, climatic disparity tends to be accumulated among clades, suggesting considerable niche conservatism. Our results also indicate that evolution of climatic tolerances has been heterogeneous across different dimensions of climate (temperature vs. precipitation) and across phylogenetic clusters (Sminthopsis murina group vs. other groups). Although some results point to the existence of shifts in climatic niches during the speciation of sminthopsins, our study provides evidence for substantial phylogenetic niche conservatism in the group. We conclude that niche diversification had a low impact on the speciation of this tribe of small, but highly mobile marsupials.     

Niche dynamics in the European ranges of two African carnivores reflect their dispersal and demographic histories

According to recent phylogeographical evidence, the common genet (Genetta genetta) and the Egyptian mongoose (Herpestes ichneumon) have dissimilar dispersal histories from Maghreb to south‐western Europe. Through comparative ecological niche modelling based on >1100 occurrences, we assessed whether the niche dynamics (i.e. niche shift versus conservatism) of the two species in their European ranges reflected DNA‐based demographic scenarios. Sensitivity analyses and projections of climatic niche models from the species' native ranges (Africa and Middle East) to Europe yielded support for (1) partial climatic niche shift in the northern European range of the common genet and (2) climatic niche conservatism in the Egyptian mongoose. Our results were consistent with demographic scenarios that predicted multiple introductions and demographic expansion in the common genet and long‐term, stable historical demography in the Egyptian mongoose. Our models further predicted a range expansion of the common genet in north‐western France and Italy, and progression of the Egyptian mongoose into Europe from the Near East. Overall, our study suggested a scenario of different niche dynamics in Europe for these two species of African carnivores, supporting the view that historical factors such as dispersal and demographic history may shape niche dynamics and thus distribution potential in colonized ranges. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 737–751.     

Global test of Eltonian niche conservatism of nonnative freshwater fish species between their native and introduced ranges

Despite growing evidence that biotic interactions limit the distribution of species and their potential redistribution under climate change, the recent surge of interest in niche conservatism has predominantly focused on the Grinellian (abiotic) niche, whereas few studies have attempted to quantify potential lability in the Eltonian (biotic or trophic) niche. Here, we test for conservatism in the Eltonian niche of 32 freshwater fish species between their introduced and native ranges from 435 populations across the globe. We used stable isotope data to quantify niche shifts along the horizontal (δ¹³C: indicating the origin of the resources consumed) and vertical (δ¹⁵N: describing the trophic position) dimensions of the isotopic niche, as well as shifts in overall isotopic niche breadth. Using an assemblage centroid standardized isotope vector analysis and controlling for phylogenetic relatedness among species, we demonstrated that introduced freshwater fishes exhibited flexibility in both resource use and trophic position that was beyond levels of natural variability observed in their native ranges. By contrast, niche breadth showed variability only within the limits recorded in native populations and varied independently from shifts in mean isotopic niche positions. Across all species and introduction histories, we found a consistent shift towards more balanced acquisition of resources with mixed origins and at intermediate trophic positions, suggesting a general mechanism by which fish species successfully establish into recipient communities. The mechanisms that promote or inhibit species from shifting their Eltonian niche remains unknown, but trophic flexibility is likely to contribute to both the success and the ecological impacts of invasive species and range shifts of native species under future global change.     

Phylogenetic relationships and ecological niche conservatism in killifish (Profundulidae) in Mesoamerica

The family Profundulidae is a group of small-sized fish species distributed between southern Mexico and Honduras, where they are frequently the only fish representatives at higher elevations in the basins where they occur. We characterized their ecological niche using different methods and metrics drawn from niche modelling and by re-examining phylogenetic relationships of a recently published molecular phylogeny of this family to gain a better understanding of its biogeographic and evolutionary history. We assessed both lines of evidence from the perspective of niche conservatism to set a foundation for discussing hypotheses about the processes underlying the distribution and evolution of the group. In fish clades where the species composition is not clear, we examined whether niche classification could be informative to discriminate groups geographically and ecologically consistent with any of the different hypotheses of valid species. The characterization of the ecological niche was carried out using the Maxent algorithm under different parameterizations and the projection of the presence on the main components of the most relevant environmental coverage, and the niche comparison was calculated with two indices (D and I), both in environmental space and in that projected geographically. With the molecular data, a species tree was generated using the *BEAST method. The comparison of these data was calculated with an age-overlap correlation test. Based on the molecular phylogeny and on niche overlap analyses, we uncovered strong evidence to support the idea that ecologically similar species are not necessarily sister species. The correlation analysis for genetic distance and niche overlap was not significant (P > 0.05). In clades with taxonomic conflicts, we only identified Profundulus oaxacae as a geographically and ecologically distinct group from P. punctatus. All the evidence considered leads us to propose that Profundulidae do not show evidence of niche conservatism and that there are reasons to consider P. oaxacae as a valid species. Our study suggests that niche divergence is a driving evolutionary force that caused the diversification and speciation processes of the Profundulidae, along with the geological and climatic events that promoted the expansion or contraction of suitable environments.     

Ecological niche differentiation in the Aphelocoma jays: a phylogenetic perspective

The Aphelocoma jays have become an important touchstone in behavioural ecology and biogeography – the corpus of studies of this genus makes it an important point of reference. Aphelocoma evolutionary history, nevertheless, has been the subject of two papers reaching opposite conclusions, even though they were based on the same allozyme data set. Herein, we present a second molecular data set – 500 bases of the ND2 gene – and analyse it cladistically to arrive at a new hypothesis of phylogenetic relationships. Recent hypotheses by other investigators of a hybrid origin of Aphelocoma populations are strongly contradicted. The ecological context within which these evolutionary processes are taking place is characterized using new tools for modelling ecological niches of species along a spectrum from humid tropical to dry temperate habitats. Evolutionary patterns of ecological niches are shown to consist of drastic departures from rate-uniformity and ecological niche conservatism.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 369–383.     

Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity

Aim Theoretical work suggests that species’ ecological niches should remain relatively constant over long‐term ecological time periods, but empirical tests are few. We present longitudinal studies of 23 extant mammal species, modelling ecological niches and predicting geographical distributions reciprocally between the Last Glacial Maximum and present to test this evolutionary conservatism. Location This study covered distributional shifts in mammal species across the lower 48 states of the United States. Methods We used a machine‐learning tool for modelling species’ ecological niches, based on known occurrences and electronic maps summarizing ecological dimensions, to assess the ability of ecological niches as modelled in one time period to predict the geographical distribution of the species in another period, and vice versa. Results High intertemporal predictivity between niche models and species’ occurrences indicate that niche conservatism is widespread among the taxa studied, particularly when statistical power is considered as a reason for failure of reciprocal predictions. Niche projections to the present for 8 mammal taxa that became extinct at the end of the Pleistocene generally increased in area, and thus do not support the hypothesis of niche collapse as a major driving force in their extinction. Main conclusions Ecological niches represent long‐term stable constraints on the distributional potential of species; indeed, this study suggests that mammal species have tracked consistent climate profiles throughout the drastic climate change events that marked the end of the Pleistocene glaciations. Many current modelling efforts focusing on anticipating climate change effects on species’ potential geographical distributions will be bolstered by this result — in essence, the first longitudinal demonstration of niche conservatism.     

What causes latitudinal gradients in species diversity? Evolutionary processes and ecological constraints on swallowtail biodiversity

The latitudinal diversity gradient (LDG) is one of the most striking ecological patterns on our planet. Determining the evolutionary causes of this pattern remains a challenging task. To address this issue, previous LDG studies have usually relied on correlations between environmental variables and species richness, only considering evolutionary processes indirectly. Instead, we use a phylogenetically integrated approach to investigate the ecological and evolutionary processes responsible for the global LDG observed in swallowtail butterflies (Papilionidae). We find evidence for the 'diversification rate hypothesis' with different diversification rates between two similarly aged tropical and temperate clades. We conclude that the LDG is caused by (1) climatically driven changes in both clades based on evidence of responses to cooling and warming events, and (2) distinct biogeographical histories constrained by tropical niche conservatism and niche evolution. This multidisciplinary approach provides new findings that allow better understanding of the factors that shape LDGs.     

Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution

Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of "niche conservatism" within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.     

Evolution of the climatic niche in scaly tree ferns (Cyatheaceae,Polypodiopsida)

Although climatic niche conservatism has been assumed by a large number of studies focused on climatic niche evolution, there are examples of climatic niche diversification and adaptation to changing climates. In this article, we reconstruct a climatic niche of scaly tree ferns (Cyatheaceae) using a rigorous analytical procedure which combines climatic niche modelling with reconstruction of continuous characters given a phylogenetic hypothesis. To estimate the limits to climatic niches of species, we used climate envelope modelling and ordination. Ancestral climatic niches of species were reconstructed by maximum likelihood and least‐squares analyses. We observed a trend towards niche conservatism with occasional events of niche transformations in scaly tree ferns. We discuss the implications of our study with respect to the potential and limitations for applications of niche modelling to evolutionary studies. We suggest that future studies of evolution of climatic niches could be considerably improved by employing approaches enabling reconstruction of continuous response to climatic gradients. Further progress may also be achieved by exploring models of character evolution other than the Brownian motion model. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 1–19.     

Climate niche conservatism does not explain restricted distribution patterns in Tynanthus (Bignonieae,Bignoniaceae)

Studies on niche evolution allow us to establish how species niches have changed over time and to identify how long‐term evolutionary processes have led to present‐day species distributions. Here, we investigate the patterns of climatic niche evolution in Tynanthus (Bignonieae, Bignoniaceae), a genus of narrowly distributed species. We test the hypothesis that niche conservatism has played an important role in the history of this group of Neotropical lianas. We perform univariate and multivariate comparisons between climatic niches of species and associated environmental data with information on phylogenetic relationships. We encountered considerable divergence in niches among species, indicating that niche conservatism in climatic variables does not seem to have played a key role in the history of the genus. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 95–109.     

Cryptic niche conservatism among evolutionary lineages of an invasive lizard

Aim There is increasing evidence that the quality and breadth of ecological niches vary among individuals, populations, evolutionary lineages and therefore also across the range of a species. Sufficient knowledge about niche divergence among clades might thus be crucial for predicting the invasion potential of species. We tested for the first time whether evolutionary lineages of an invasive species vary in their climate niches and invasive potential. Furthermore, we tested whether lineage‐specific models show a better performance than combined models. Location Europe. Methods We used species distribution models (SDMs) based on climatic information at native and invasive ranges to test for intra‐specific niche divergence among mitochondrial DNA (mtDNA) clades of the invasive wall lizard Podarcis muralis. Using DNA barcoding, we assigned 77 invasive populations in Central Europe to eight geographically distinct evolutionary lineages. Niche similarity among lineages was assessed and the predictive power of a combination of clade‐specific SDMs was compared with a combined SDM using the pooled records of all lineages. Results We recorded eight different invasive mtDNA clades in Central Europe. The analysed clades had rather similar realized niches in their native and invasive ranges, whereas inter‐clade niche differentiation was comparatively strong. However, we found only a weak correlation between geographic origin (i.e. mtDNA clade) and invasive occurrences. Clades with narrow realized niches still became successful invaders far outside their native range, most probably due to broader fundamental niches. The combined model using data for all invasive lineages achieved a much better prediction of the invasive potential. Conclusions Our results indicate that the observed niche differentiation among evolutionary lineages is mainly driven by niche realization and not by differences in the fundamental niches. Such cryptic niche conservatism might hamper the success of clade‐specific niche modelling. Cryptic niche conservatism may in general explain the invasion success of species in areas with apparently unsuitable climate.     

The ecological drivers of nuptial color evolution in darters (Percidae: Etheostomatinae)

Closely related animal lineages often vary in male coloration, and ecological selection is hypothesized to shape this variation. The role of ecological selection in inhibiting male color has been documented extensively at the population level, but relatively few studies have investigated the evolution of male coloration across a clade of closely related species. Darters are a diverse group of fishes that vary in the presence of elaborate male nuptial coloration, with some species exhibiting vivid color patterns and others mostly or entirely achromatic. We used phylogenetic logistic regression to test for correlations between the presence/absence of color traits across darter species and the ecological conditions in which these species occur. Environmental variables were correlated with the presence of nuptial color in darters with colorful species tending to inhabit environments that would support fewer predators and potentially transmit a broader spectrum of natural light compared to species lacking male coloration. We also tested the color preferences of a common darter predator, largemouth bass, and found that it exhibits a strong preference for red, providing further evidence of predation as a source of selection on color evolution in darters. Ecological selection therefore appears to be an important factor in dictating the presence or absence of male coloration in this group of fishes.     

Impact of ocean barriers, topography, and glaciation on the phylogeography of the catfish Trichomycterus areolatus (Teleostei: Trichomycteridae) in Chile

We examined the role of several earth history events on the phylogeographic distribution of the catfish Trichomycterus areolatus in Chile using the cytochrome b gene. We explored three biogeographic hypotheses: that sea level changes have resulted in the isolation of populations by drainages; that glaciation has impacted genetic diversity; and that ichthyological subprovince boundaries correspond to phylogeographic breaks in our focal species. We found seven well-supported clades within T. areolatus with high levels of genetic divergence. The strongest signal in our data was for an important role of sea level changes structuring populations. Five of the seven clades mapped cleanly to the geographic landscape and breaks corresponded closely to areas of narrowest continental shelf. In addition, few haplotypes were shared between rivers within clades, suggesting that only limited local movement of individuals has occurred. There was no relationship between the levels of genetic diversity and the proportion of individual drainages covered by glaciers during the last glacial maximum. Two phylogeographic breaks within T. areolatus did match the two previously identified faunal boundaries, but we found three additional breaks, which suggests that faunal breaks have only limited utility in explaining phylogeographic patterns. These results imply that the narrow continental shelf coupled with sea level changes had a strong influence on the obligate freshwater fishes in Chile.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 876–892.     

Indirect food web interactions increase growth of an algivorous stream fish

1. We tested the hypothesis that indirect food web interactions between some common, invertivorous fishes and their prey would positively affect growth of an algivorous fish species. Specifically, we predicted that orangethroat darter (Etheostoma spectabile) would increase periphyton biomass via a top‐down pathway, indirectly enhancing growth of the algivorous central stoneroller minnow (Campostoma anomalum). Moreover, we predicted that sand shiner (Notropis stramineus) would increase periphyton biomass via a bottom‐up pathway and indirectly enhance growth of the stoneroller minnow. 2. In an 83‐day experiment in large, outdoor, stream mesocosms, we stocked two fish species per mesocosm (stoneroller and either darter or shiner), estimated the effects of the invertivorous and grazing fishes on periphyton biomass and estimated growth of the algivorous fish. 3. The darter consumed grazing invertebrates, indirectly increasing periphyton biomass. The shiner consumed terrestrial insects as predicted, but it did not affect periphyton biomass. 4. In support of our hypothesis, the darter indirectly enhanced stoneroller growth. As predicted, stonerollers consumed the increased periphyton in streams with darters, resulting in greater growth, condition and gut fullness compared to streams without darters. No indirect interaction was observed between stonerollers and shiners. 5. Our study suggests that some invertivorous fish species can positively affect growth of algivorous fishes through indirect food web interactions. Thus, in stream communities, it is possible that the loss of a single, invertivorous fish taxon could have negative consequences on algivorous fish populations via the removal of positive indirect food web interactions.     

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

Ecologists are increasingly adopting an evolutionary perspective, and in recent years, the idea that closely related species are ecologically similar has become widespread. In this regard, phylogenetic signal must be distinguished from phylogenetic niche conservatism. Phylogenetic niche conservatism results when closely related species are more ecologically similar that would be expected based on their phylogenetic relationships; its occurrence suggests that some process is constraining divergence among closely related species. In contrast, phylogenetic signal refers to the situation in which ecological similarity between species is related to phylogenetic relatedness; this is the expected outcome of Brownian motion divergence and thus is necessary, but not sufficient, evidence for the existence of phylogenetic niche conservatism. Although many workers consider phylogenetic niche conservatism to be common, a review of case studies indicates that ecological and phylogenetic similarities often are not related. Consequently, ecologists should not assume that phylogenetic niche conservatism exists, but rather should empirically examine the extent to which it occurs.