Evolutionary Distinctiveness Research Articles

Optimizing the NGS-based discrimination of multiple lung cancers from the perspective of evolution

Next-generation sequencing (NGS) offers a promising approach for differentiating multiple primary lung cancers (MPLC) from intrapulmonary metastasis (IPM), though panel selection and clonal interpretation remain challenging. Whole-exome sequencing (WES) data from 80 lung cancer samples were utilized to simulate MPLC and IPM, with various sequenced panels constructed through gene subsampling. Two clonal interpretation approaches primarily applied in clinical practice, MoleA (based on shared mutation comparison) and MoleB (based on probability calculation), were subsequently evaluated. ROC analysis highlighted MoleB’s superior performance, especially with the NCCNplus panel (AUC = 0.950 ± 0.002) and pancancer MoleA (AUC = 0.792 ± 0.004). In two independent cohorts (WES cohort, N = 42 and non-WES cohort, N = 94), NGS-based methodologies effectively stratified disease-free survival, with NCCNplus MoleB further predicting prognosis. Phylogenetic analysis further revealed evolutionary distinctions between MPLC and IPM, establishing an optimized NGS-based framework for differentiating multiple lung cancers.

Unraveling the impact of drought on waterbird community assembly and conservation strategies.

Drought-induced changes in lakes and wetlands, crucial habitats for migratory waterbirds, can greatly affect their foraging and habitat utilization. These changes lead to a decline in waterbird species richness and may cause shifts in community assembly from phylogenetic and functional trait perspectives. However, a gap remains between ecological mechanistic research about these changes and conservation applications. Here, we investigated the drought-induced phylogenetic and functional changes in waterbird community assembly over the past two decades in two lakes of the Yangtze River basin. Additionally, we explored conservation strategies to address the requirements of waterbirds during droughts. Results showed that drought modified the hydrological and phenological characteristics of waterbird habitats, leading to a decrease in waterbird species richness. As drought severity increased, species that were sensitive to drought exhibited higher degrees of similarity compared to the local species pool, leading to more divergent community assembly patterns. The mean values of body mass, tarsus length, bill length, and Evolutionary Distinctiveness (ED) of waterbirds in both lakes increased significantly under high drought stress conditions. Dabbling birds and small waders, which rely on habitats most susceptible to drought-induced changes, were the primary habitat preference groups affected. Additionally, the diversification of phylogenetic and functional community assembly in waterbirds and their associated conservation requirements indicated that effective conservation measures for waterbirds must be diversified and tailored to the specific requirements of different waterbird species, thereby preventing the loss of ecosystem functions and services. Conservation strategies should also be adaptive by incorporating periodic evaluations and adjustments to respond to environmental pressures and thus ensuring sustained effectiveness. In conclusion, as drought severity increased, functional and phylogenetic trait differences between species became more significant. Therefore, conservation measures must be diversified, tailored, and adaptive to effectively respond to the changes in waterbird community assembly.

Prioritizing future evidence needs for marine and freshwater mammal conservation action

AbstractMarine and freshwater mammals are increasingly threatened due to human activity. To improve conservation practice, decisions should be informed by the available evidence on the effectiveness of conservation actions. Using a systematically collated database of studies that test the effectiveness of actions to conserve marine and freshwater mammals, we investigated the gaps and biases in the available scientific evidence base. While there is a growing evidence base covering actions to address key threats (e.g. fisheries and bycatch) to marine and freshwater mammal populations, we identified large geographic and taxonomic biases. There was no relationship between the number of studies and marine mammal species per ecoregion and we found biases towards coastal areas of the Global North, with many regions and species having little or no evidence available. The number of studies per species did not correlate with (1) the threat level, (2) evolutionary distinctiveness or (3) the public ‘popularity’ of the study species. We also found a mismatch between actions tested and the actions suggested as needed in the International Union for the Conservation of Nature (IUCN) Red List. Several of these gaps and biases likely reflect the feasibility of researching marine mammal populations; many species can be difficult to access, with limited baseline information on populations and threats, and testing actions can require costly long‐term monitoring. Prioritizing the most cost‐effective conservation strategies for marine and freshwater mammal species will require a comprehensive evidence base on the effects of actions. Continuing to build the necessary baseline data, and focusing future research and funding towards the priority gaps identified in this study will be important to deliver this target.

Identification of biodiversity priority conservation areas in China by integrating genetic, species and ecosystem diversity

Genetic, species, and ecosystem diversity are the three fundamental levels of biodiversity, each crucial for identifying priority conservation areas (PCAs). Globally or regionally, the areas with the highest genetic, species, and ecosystem diversity are not necessarily the same. To comprehensively represent biodiversity, this study fully considers these three fundamental levels from the foundational concept of biodiversity. We applied systematic conservation planning theory to develop an integrated framework for identifying PCAs for key protected species in China. We used species richness (SR), weighted endemism (WE), phylogenetic diversity (PD), evolutionary distinctiveness (ED), phylogenetic endemism (PE), and ecosystem service value (ESV) as conservation indicators and built different scenarios in Zonation. The results show that the total area of PCAs is approximately 3.29 million km2, accounting for about 34.29 % of China's total land area. More than half (approximately 52.21 %) of existing protected areas (PAs) overlap with the PCAs, indicating that current PAs are somewhat effective in biodiversity protection. However, there are still some PCAs that are not located within PAs, suggesting a significant potential for expanding the PAs network. Additionally, the distribution of newly established national park pilot areas aligns well with that of the PCAs, demonstrating the effectiveness of national park policies in protecting biodiversity. This study bridges traditional ecological theory with practical conservation planning, offering new insights into the theoretical methods and practical applications for identifying PCAs. It also provides valuable guidance for the selection and adjustment of PCAs in other regions globally.

Phylogenetic Insights Into Canidae Trait Variation Across Continents

ABSTRACTAimUnderstanding the spatial structuring of ecological communities involves considering the interplay between evolutionary history and environmental factors. This study investigates how the phylogenetic structure of Canidae influences the geographical distribution and trait patterns of lineages globally, and how these patterns relate to Bergmann's and Rapoport's rules.LocationAmericas, Africa, Eurasia.Time Period12 million years ago—present.Major Taxa StudiedCanidae.MethodsUsing distribution data and phylogenetic information for 37 Canidae species, we analysed key ecological, functional and evolutionary variables. We applied phylogenetic fuzzy‐weighting via principal coordinates of phylogenetic structure (PCPS) and variance partitioning analysis (VPA) to assess the contributions of phylogenetic structure and environmental factors to trait variation among species.ResultsOur results revealed distinct global patterns in body size, body weight, range size, habitat use and evolutionary distinctiveness among lineages. We also identified the shared contributions of phylogenetic structure and temperature to trait variation using variance partitioning analysis. The PCPS axes highlighted the influence of phylogenetic relationships on Canidae assemblages, particularly in South America.Main ConclusionsImportantly, the study challenges the applicability of Bergmann's and Rapoport's rules across continents. The unique diversification history of Canidae in South America and Africa and their diverse environmental conditions likely contribute to the observed trait patterns that make both continents so distinguished when compared to North America and Eurasia. Our findings underscore the need to incorporate phylogenetic information in models assessing trait variation across geographic scales for unbiased estimates.

Evolutionary isolation of Canadian terrestrial vertebrate species

Conservation prioritization has become increasingly important as a practical response to ongoing biodiversity loss and limited resources. One tool, evolutionary distinctiveness (ED) is based on a measure of evolutionary isolation and has merit for identifying taxa with few close relatives. Here we present the first ever national-level ED scores for any jurisdiction, applying the measures to all Canadian tetrapods. We updated and pruned global dated phylogenies of all terrestrial vertebrates (amphibians, squamates, turtles, mammals, and birds) down to native Canadian species and calculated Canadian ED scores and rankings for each and compared them to their global ED ranks. Canada’s terrestrial ectotherm vertebrates (amphibians and reptiles) include most of Canada’s most evolutionarily isolated species and many score and rank higher nationally than globally in their ED scores. These taxa are also the most imperilled in Canada and so species with populations assessed as at-risk by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) represent, on average, more than expected national evolutionary history. Interestingly, several exotic species also have very high national ED scores. To the extent that evolutionary isolation captures aspects of local and national biodiversity worth preserving, our lists may provide useful input to conservation agencies engaging in conservation prioritization exercises.

The mitochondrial genome sequences of eleven leafhopper species of Batracomorphus (Hemiptera: Cicadellidae: Iassinae) reveal new gene rearrangements and phylogenetic implications.

Batracomorphus is the most diverse and widely distributed genus of Iassinae. Nevertheless, there has been no systematic analysis of the genome structure and phylogenetic relationships of the genus. To determine the characteristics of the mitogenomes of Batracomorphus species as well as the phylogenetic relationships between them, we sequenced and compared the mitogenomes of 11 representative Batracomorphus species. The results revealed that the mitogenomes of the 11 Batracomorphus species exhibited highly similar gene and nucleotide composition, and codon usage compared with other reported mitogenomes of Iassinae. Of these 11 species, we found that the mitogenomes of four species were rearranged in the region from trnI-trnQ-trnM to trnQ-trnI-trnM, whereas the remaining species presented a typical gene order. The topologies of six phylogenetic trees were in agreement. Eurymelinae consistently formed paraphyletic groups. Ledrinae and Evacanthinae formed sister taxa within the same clade. Similarly, Typhlocybinae and Mileewinae consistently clustered together. All phylogenetic trees supported the monophyly of Iassinae, indicating its evolutionary distinctiveness while also revealing its sister relationship with Coelidiinae. Notably, the nodes for all species of the genus Batracomorphus were well supported and these taxa clustered into a large branch that indicated monophyly. Within this large branch, four Batracomorphus species with a gene rearrangement (trnQ-trnI-trnM) exhibited distinctive clustering, which divided the large branch into three minor branches. These findings expand our understanding of the taxonomy, evolution, genetics, and systematics of the genus Batracomorphus and broader Iassinae groups.

Global primary predictors of extinction risk in primates.

Identifying the main predictors of species' extinction risk while accounting for the effects of spatial and phylogenetic structures in the data is key to preventing species loss in tropical forests through adequate conservation practices. We recorded 22 705 precise geographical locations of primate occurrence across four major geographic realms (Neotropics, mainland Africa, Madagascar and Asia) to assess predictors of threat status using a novel Bayesian spatio-phylogenetic approach. We estimated the relative contributions of fixed factors (forest amount, body mass, home range, diel activity, locomotion, evolutionary distinctiveness and climatic instability) and random factors (space and phylogeny) to primate extinction risk. Precipitation instability increased the extinction risk in the Neotropics but decreased it in mainland Africa and Madagascar. Forest amount was negatively associated with extinction risk in all realms except Madagascar. Body mass increased the extinction risk in the Neotropics and Madagascar, whereas home range increased the extinction risk in mainland Africa and decreased it in Asia. Evolutionary distinctiveness negatively influenced extinction risk only in mainland Africa. Our findings highlight the importance of climate change mitigation and forest protection strategies. Increasing the protection of large primates and reducing hunting are also essential.

Predicting yolk testosterone allocation using ecological contexts and species-specific traits.

The prenatal transfer of testosterone (T) from mother to offspring is an important source of phenotypic plasticity. In birds, exposure to ecologically relevant stimuli, such as social competition or an attractive mate, can cause females to deposit more T into their egg yolks. Exposure to elevated yolk T can modify the expression of several fitness-related traits in offspring (e.g. growth, immune function, secondary sex traits and behaviour). Despite some of these changes being potentially adaptive, not all studies find that yolk T levels change in response to ecologically relevant stimuli. This heterogeneity is currently unexplained, limiting our ability to predict inter-generational responses to ecological change. Here, we performed a systematic literature search and found 119 observations across 39 wild species that measured inter-female variation in yolk T allocation in response to various stimuli. We used boosted regression trees, a form of machine learning, to examine whether species-specific traits or variation in study-level variables could explain variation in yolk T allocation (i.e. statistically significant vs. non-significant responses). We found that both species-specific traits and study-level variables are important predictors of significant changes in yolk T levels. Geographic range (latitude and longitude), evolutionary distinctiveness, longevity, egg mass relative to female mass, sociality, migration status and time to fledge were among the top 10 most influential predictors of the 48 examined. We also found that studies measuring or manipulating social stimuli (e.g. competition and breeding density) or breeding date were more likely to detect changes in yolk T allocation compared with studies examining other ecological contexts. Overall, these data provide several testable hypotheses concerning yolk T allocation and its adaptive value across species and contexts. Additionally, these findings can help us predict how ecological changes will affect hormonal responses in females that can shape future generations.

Effects of trade and poaching pressure on extinction risk for cacti in the Atacama Desert.

In this era of a global biodiversity crisis, vascular plants are facing unprecedented extinction rates. We conducted an assessment of the extinction risk of 32 species and 7 subspecies of Copiapoa, a genus endemic to Chile's fog-dependent coastal Atacama Desert. We applied the International Union for Conservation of Nature Red List Categories and Criteria enhanced by expert insights and knowledge. Our primary aim was to analyze the impact of trade and poaching on their extinction risk. We employed machine learning models, including multinomial logistic regression (MLR), decision tree (DT), and random forest (RF), to analyze the relationships between conservation status and various factors. These factors encompassed trade and poaching activities, landscape condition, human footprint, monthly cloud frequency, and biological traits such as evolutionary distinctiveness and maximum diameter. Seven taxa had an area of occupancy (AOO) of <10km2, 10 additional taxa had an AOO of <20km2, and 16 taxa had an AOO of ≤100km2. This reassessment exposed a critical level of extinction risk for the genus; 92% of the taxa were classified as threatened, 41% as critically endangered, 41% as endangered, and 10% as vulnerable. MLR, DT, and RF exhibited accuracies of 0.784, 0.730, and 0.598, respectively, and identified trade and poaching pressure and landscape condition as the primary drivers of extinction risk. Our assessment of Copiapoa showed trade, poaching, habitat degradation, and their synergic impacts as the main drivers of the genus' extinction risk. Our results highlight the urgent need for nations to develop and enforce strategies to monitor and control trade and poaching pressure because these factors are crucial for the long-term persistence of desert plants.

Incorporating New Datatypes to Enhance Species Delimitation: A Case Study in Rice Paddy Snakes (Homalopsidae: Hypsiscopus).

Homalopsids (Old World Mud Snakes) include 59 semiaquatic species in Asia and Australasia that display an array of morphological adaptations, behaviors, and microhabitat preferences. These attributes make homalopsids an ideal model system for broader questions in evolutionary biology, but the diversity of this understudied group of snakes is still being described. Recognized species diversity in rice paddy snakes (Hypsiscopus) has recently doubled after nearly 200 years of taxonomic stability. However, the evolutionary distinctiveness of some populations remains in question. In this study, we compare mainland Southeast Asian populations of Hypsiscopus east and west of the Red River Basin in Vietnam, a known biogeographic barrier in Asia, using an iterative approach with molecular phylogenetic reconstruction, machine-learning morphological quantitative statistics, and ecological niche modeling. Our analyses show that populations west of the Red River Basin represent an independent evolutionary lineage that is distinct in genetics, morphospace, and habitat suitability, and so warrants species recognition. The holotype of H. wettsteini, a species originally described in error from Costa Rica, grouped morphometrically with the population at the Red River Basin and eastward, and those west of the Red River Basin are referred to the recently described H. murphyi. The two species may have diversified due to a variety of geological and environmental factors, and their recognition exemplifies the importance of multifaceted approaches in taxonomy for downstream biogeographic studies on speciation scenarios.

Crepuscular and small but not evolutionary unique species are the reptiles less affected by roadkill in Europe

We extensively reviewed scientific literature and extracted a large dataset with roadkill events for reptile species. We examined 300 articles from 33 European countries, gathering 1688 records of reptiles killed by vehicle traffic. A total of 125 taxa were found documented as roadkill (100 native and 25 exotic species). We calculated each species' occurrence frequency within the database (henceforth ‘relative roadkill frequency'). The relative roadkill of species was strongly and significantly correlated when comparing the whole dataset and the subset of systematic studies. We modelled the inter‐specific variation in relative roadkill frequency across the European reptilian phylogeny concerning species traits, evolutionary uniqueness, and distribution range using a phylogenetic generalized least squares (PGLS) model. Overall, reptile casualties are more pronounced for more closely related species. However, the relative roadkill frequency was unrelated to the level of evolutionary distinctiveness of European reptiles. Additionally, relative roadkill frequency was not correlated to the distribution range but was positively correlated with the species' body mass. The reptiles more frequently cited as road casualties were overall relatively large species: Montpellier snake Malpolon monspessulanus, European grass snake Natrix natrix, and Caspian whipsnake Dolichophis caspius. Additionally, more active species during the crepuscular hours were less affected by roadkill. From a conservation point of view, our results suggest that roadkill frequency is not more significant for evolutionary, more unique reptiles than for other species in Europe, while at the same time, widely distributed species are not the main target of roadkill events. Then, the main causes of roadkill in reptiles must be associated with other factors, such as behavioural traits or density of populations, rather than simply the size of their distribution range.Keywords: evolutionary uniqueness, phylogenetic signal, reptile species, roadkill incidence, wildlife conservation

Molecular analysis reveals the evolutionary distinctiveness of the Silver-backed Chevrotain within the genus Tragulus

Abstract The Silver-backed Chevrotain (Tragulus versicolor), a mammal endemic to the unique coastal arid ecosystem in south-central Vietnam, is an enigmatic mouse deer with little information available about its ecology and evolutionary history. The recent rediscovery of the species provides a rare opportunity to clarify its taxonomy and phylogenetic relationship within the genus Tragulus. In this study, we sequenced the complete mitochondrial cytochrome b gene for samples of T. versicolor and T. kanchil from Vietnam. Our molecular results show that the species forms a distinct evolutionary lineage sister to all other species in the genus, confirming the earlier hypothesis based on morphological evidence. However, further research is needed to assess the genetic diversity of the species and design appropriate conservation measures. As the species has not been secured over much of its range, it is recommended that the population in Nui Chua National Park, the only one covered by a protected area, be prioritized for conservation actions. Conserving the species in this unique and imperiled ecosystem will also benefits a suite of locally endemic and threatened species of fauna and flora.

Global distribution range of birds is negatively correlated with their level of diet specialization

AbstractAimUnderstanding the factors determining the size of a species distribution range is crucial to preventing the extinction of vulnerable species, particularly specialist species. Previous research has shown that climate and various traits of a species significantly affect its distribution range size. However, the impact of avian dietary specialization remains relatively unexplored and geographically restricted.LocationWorldwide.TaxonBirds.MethodsWe assessed the worldwide distribution range of 7416 bird species concerning the degree of diet specialization, including body mass size, daily activity and evolutionary distinctiveness (ED) as covariates. The phylogenetic generalized least squares (PGLS) model – including the avian phylogeny – was used to test the potential correlation between the distribution range size of bird species and the explored life history traits.ResultsWe found that, at a global scale, diet specialization negatively correlates with the distribution range size of bird species. Overall, diet specialist species displayed a distribution range of 60% smaller than generalist species.Main ConclusionsOur study demonstrates that an avian diet specialization is crucial in predicting its potential distribution range size. This information is essential for those species with narrow distribution ranges often threatened by global concerns.

Does nuclear DNA support the recognition of three species within the Splendid Fairywren Malurus splendens?

ABSTRACT The Splendid Fairywren Malurus splendens has four distinct phenotypic forms currently recognised as subspecies, although three species have been recognised within the group in the past. Here, we use multilocus nuclear DNA to test the recent hypothesis that the Splendid Fairywren represents three allopatric taxa with little to no modern-day contact, despite phenotypic evidence of periods of past contact and gene flow. Our nuclear dataset is concordant with earlier mtDNA-based data in supporting three distinct genetic groups within M. splendens. These genetic groups align with the three phenotypically distinct forms recently hypothesised to be allopatric and previously described at species-level – western M. splendens, central M. callainus and eastern M. melanotus. Nuclear gene flow does not appear to be rampant between the three forms; however, several individuals show signals of admixed nuclear ancestry, which we cannot distinguish as having resulted from incomplete lineage sorting, poor phylogenetic signal, or gene flow. Given changing modern taxonomic interpretations of the significance of gene flow in speciation, we argue that recognising three distinct species within the M. splendens complex might better represent their evolutionary distinctiveness, rather than continuing to treat these genetically and morphologically distinct forms as subspecies of a widespread polytypic species. Our study highlights the interesting complexity of determining species status when taxa are in the ‘grey zone’ near the subspecies/species continuum, and the value gained from adding perspectives from nuclear DNA.

Combining extinction probability and functional or phylogenetic distinctiveness to define conservation priorities

Given the current accelerating extinction rates, an increasing number of species-based conservation strategies have emerged because of the public interest in helping save particular species by funding rescue actions. Although public interest has focused mainly on well-studied, charismatic species, conservation scientists have developed tools to help prioritize species conservation from a more objective perspective, preserving ecosystem functioning and human well-being for future generations. For that purpose, species-centered biodiversity indicators that account not only for the extinction risk of a species but also for its evolutionary and/or functional distinctiveness have been developed. A species is considered irreplaceable and distinctive if it is isolated on the phylogenetic tree and/or if it has distinct traits, especially functional traits that determine the species' effects on ecosystems. The quantitative values representing extinction risk and distinctiveness of species have often been multiplied to define a quantitative conservation priority score. However, there is a plethora of ways to combine several conservation criteria into a single quantitative priority score, and the product of this multiplication is one such possibility. Each possible way of combining extinction risk and distinctiveness provides a different point of view on which of these should prevail to set conservation priorities. We set up an axiomatic framework on how a species' distinctiveness could be combined with its extinction risk via a tool used to define conservation priorities. By doing so, we show that further work is still needed to better communicate biodiversity indicators to the public and ensure an informed choice of indicators.

An assessment of methods to combine evolutionary history and conservation: A case study in the Brazilian campo rupestre.

Conservation policies typically focus on biodiversity hotspots. An alternative approach involves analyzing the evolutionary history of lineages in geographic areas along with their threat levels to guide conservation efforts. Mountains exhibit high levels of plant species richness and micro-endemism, and biogeographic studies commonly point to recent and rapid evolutionary radiations in these areas. Using a nearly endemic clade of legumes, our study evaluates conservation prioritization approaches in the campo rupestre, a Neotropical ecosystem associated with mountaintops that is located between two biodiversity hotspots. We compared the EDGE and EDGE2 metrics, which combine the evolutionary distinctiveness and the extinction risk of a species in a single value. These metrics are compared with traditional metrics used to assess conservation priority, such as phylogenetic diversity. The EDGE values reported are lower than those of other studies using this metric, mostly due to the prevalence of threatened species with short phylogenetic branch lengths (low values of evolutionary distinctiveness). Certain areas of campo rupestre with relatively high phylogenetic diversity and EDGE values do not correspond to areas with high species richness, agreeing with previous studies on biodiversity hotspots. Our study highlights the necessity of conservation of the campo rupestres as well as advantages and disadvantages of using EDGE, EDGE2, and phylogenetic diversity for appropriate selection of conservation areas with rapid evolutionary radiations. The selection of the metrics will depend primarily on the life history of the focus group and the data availability, as well as the conservation approach.

Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage.

Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species' evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). The genus Progne includes migrant and resident species, as well as geographically restricted taxa and widespread, intercontinentally distributed taxa, thus providing an ideal group in which to study the nature of niche divergence within a broad geographic mosaic. I obtained distributional information for the genus from publicly available databases and created ecological niche models for each species to create pairwise comparisons of environmental space. I combined these data with the most up-to-date phylogeny of Progne currently available to examine the patterns of niche evolution within the genus. I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, like extant basal Progne lineages, and several geographically localized descendant species occupy only portions of this larger ancestral niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages, and sheds light on the ways in which apparently divergent niches may arise through allopatry while not involving any true niche shifts through evolutionary time. Even taxa that appear unique in terms of habitat or behavior may not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.

Implications of gene tree heterogeneity on downstream phylogenetic analyses: A case study employing the Fair Proportion index.

Many questions in evolutionary biology require the specification of a phylogeny for downstream phylogenetic analyses. However, with the increasingly widespread availability of genomic data, phylogenetic studies are often confronted with conflicting signal in the form of genomic heterogeneity and incongruence between gene trees and the species tree. This raises the question of determining what data and phylogeny should be used in downstream analyses, and to what extent the choice of phylogeny (e.g., gene trees versus species trees) impacts the analyses and their outcomes. In this paper, we study this question in the realm of phylogenetic diversity indices, which provide ways to prioritize species for conservation based on their relative evolutionary isolation on a phylogeny, and are thus one example of downstream phylogenetic analyses. We use the Fair Proportion (FP) index, also known as the evolutionary distinctiveness score, and explore the variability in species rankings based on gene trees as compared to the species tree for several empirical data sets. Our results indicate that prioritization rankings among species vary greatly depending on the underlying phylogeny, suggesting that the choice of phylogeny is a major influence in assessing phylogenetic diversity in a conservation setting. While we use phylogenetic diversity conservation as an example, we suspect that other types of downstream phylogenetic analyses such as ancestral state reconstruction are similarly affected by genomic heterogeneity and incongruence. Our aim is thus to raise awareness of this issue and inspire new research on which evolutionary information (species trees, gene trees, or a combination of both) should form the basis for analyses in these settings.

Ecological characteristics explain neutral genetic variation of three coastal sparrow species.

Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.