Ecological speciation

Ecological interactions shape the evolution of flower color in communities across a temperate biodiversity hotspot

Processes driving the divergence of floral traits may be integral to the extraordinary richness of flowering plants and the assembly of diverse plant communities. Several models of pollinator-mediated floral evolution have been proposed; floral divergence may (i) be directly involved in driving speciation or may occur after speciation driven by (ii) drift or local adaptation in allopatry or (iii) negative interactions between species in sympatry. Here, we generate predictions for patterns of trait divergence and community assembly expected under these three models, and test these predictions in Hakea (Proteaceae), a diverse genus in the Southwest Australian biodiversity hotspot. We quantified functional richness for two key floral traits (pistil length and flower color), as well as phylogenetic distances between species, across ecological communities, and compared these to patterns generated from null models of community assembly. We also estimated the statistical relationship between rates of trait evolution and lineage diversification across the phylogeny. Patterns of community assembly suggest that flower color, but not floral phenology or morphology, or phylogenetic relatedness, is more divergent in communities than expected. Rates of lineage diversification and flower color evolution were negatively correlated across the phylogeny and rates of flower colour evolution were positively related to branching times. These results support a role for diversity-dependent species interactions driving floral divergence during the Hakea radiation, contributing to the development of the extraordinary species richness of southwest Australia.

Multi-locus genetic analyses of Quasipaa from throughout its distribution

Montane frogs of the genus Quasipaa Dubois, 1992 occur from southern China to Southeast Asia (Frost 2021). Analyses of mtDNA (Cytb) and nuDNA data (Rag1, Rag2, Rhod, Tyr) for samples from 93 localities throughout its distribution yield a phylogeny. Clades A and B occur in Southeast Asia, clade C in northern Yangtze River, China, clade D in southwestern China, and clades E and F in southeastern China. Results place Q. yei within monophyletic Quasipaa and identify two new species. Based on nuDNA data, the basal split of clade A and B indicates an Indochinese origin of Quasipaa. The west-east diversification of five species across South China (Q. spinosa, Q. exilispinosa, Q. jiulongensis, Q. shini, Q. boulengeri) corresponds to topographic terrains II and III of China. Divergence of species from southeastern China (Q. shini, Q. jiulongensis, Q. spinosa, Q. exilispinosa) and southwestern China (Q. boulengeri) dates to 15.30-16.56 Ma (million years ago). A principal component analysis (PCA) and t-test involving 19 bioclimatic variables identifies significantly different environmental conditions between the two regions. Species' distribution models (SDM) for Q. spinosa and Q. boulengeri identify the best areas to be eastern and western South China, respectively. Thus, environmental variation appears to have influenced the genetic divergence and distributions of Quasipaa in South China. Mito-nuclear discordance indicates that some individuals of Q. exilispinosa and Q. spinosa hybridized historically.

Temporal resource partitioning mitigates interspecific competition and promotes coexistence among insect parasites

A key to understanding life's great diversity is discerning how competing organisms divide limiting resources to coexist in diverse communities. While temporal resource partitioning has long been hypothesized to reduce the negative effects of interspecific competition, empirical evidence suggests that time may not often be an axis along which animal species routinely subdivide resources. Here, we present evidence to the contrary in the world's most biodiverse group of animals: insect parasites (parasitoids). Specifically, we conducted a meta-analysis of 64 studies from 41 publications to determine if temporal resource partitioning via variation in the timing of a key life-history trait, egg deposition (oviposition), mitigates interspecific competition between species pairs sharing the same insect host. When competing species were manipulated to oviposit at (or near) the same time in or on a single host in the laboratory, competition was common, and one species was typically inherently superior (i.e. survived to adulthood a greater proportion of the time). In most cases, however, the inferior competitor could gain a survivorship advantage by ovipositing earlier (or in a smaller number of cases later) into shared hosts. Moreover, this positive (or in a few cases negative) priority advantage gained by the inferior competitor increased as the interval between oviposition times became greater. The results from manipulative experiments were also correlated with patterns of life-history timing and demography in nature: the more inherently competitively inferior a species was in the laboratory, the greater the interval between oviposition times of taxa in co-occurring populations. Additionally, the larger the interval between oviposition times of competing taxa, the more abundant the inferior species was in populations where competitors were known to coexist. Overall, our findings suggest that temporal resource partitioning via variation in oviposition timing may help to facilitate species coexistence and structures diverse insect communities by altering demographic measures of species success. We argue that the lack of evidence for a more prominent role of temporal resource partitioning in promoting species coexistence may reflect taxonomic differences, with a bias towards larger-sized animals. For smaller species like parasitic insects that are specialized to attack one or a group of closely related hosts, have short adult lifespans and discrete generation times, compete directly for limited resources in small, closed arenas and have life histories constrained by host phenology, temporal resource subdivision via variation in life history may play a critical role in allowing species to coexist by alleviating the negative effects of interspecific competition.

Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae)

Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.

Why are there not more herbivorous insect species?

Insect species richness is estimated to exceed three million species, of which roughly half is herbivorous. Despite the vast number of species and varied life histories, the proportion of herbivorous species among plant-consuming organisms is lower than it could be due to constraints that impose limits to their diversification. These include ecological factors, such as vague interspecific competition; anatomical and physiological limits, such as neural limits and inability of handling a wide range of plant allelochemicals; phylogenetic constraints, like niche conservatism; and most importantly, a low level of concerted genetic variation necessary to a phyletic conversion. It is suggested that diversification ultimately depends on what we call the intrinsic trend of diversification of the insect genome. In support of the above, we survey the major types of host-specificity, the mechanisms and constraints of host specialization, possible pathways of speciation, and hypotheses concerning insect diversification.

Context-Dependent Reproductive Isolation: Host Plant Variability Drives Fitness of Hybrid Herbivores

AbstractThe role of divergent selection between alternative environments in promoting reproductive isolation (RI) between lineages is well recognized. However, most studies view each divergent environment as homogenous, thereby overlooking the potential role within-environment variation plays in RI between differentiating lineages. Here, we test the importance of microenvironmental variation in RI by using individual trees of two host plants, each harboring locally adapted populations of the cynipid wasp Belonocnema treatae. We compared the fitness surrogate (survival) of offspring from hybrid crosses with resident crosses across individual trees on each of two primary host plants, Quercus virginiana and Q. geminata. We found evidence of weak hybrid inviability between host-associated lineages of B. treatae despite strong genomic differentiation. However, averaging across environments masked great variation in hybrid fitness on individual trees, where hybrids performed worse than, equal to, or better than residents. Thus, considering the environmental context of hybridization is critical to improving the predictability of divergence under variable selection.

Reinforcement and the Proliferation of Species

Adaptive radiations are characterized by the rapid proliferation of species. Explaining how adaptive radiations occur therefore depends, in part, on identifying how populations become reproductively isolated-and ultimately become different species. Such reproductive isolation could arise when populations adapting to novel niches experience selection to avoid interbreeding and, consequently, evolve mating traits that minimize such hybridization via the process of reinforcement. Here, we highlight that a downstream consequence of reinforcement is divergence of conspecific populations, and this further divergence can instigate species proliferation. Moreover, we evaluate when reinforcement will-and will not-promote species proliferation. Finally, we discuss empirical approaches to test what role, if any, reinforcement plays in species proliferation and, consequently, in adaptive radiation. To date, reinforcement's downstream effects on species proliferation remain largely unknown and speculative. Because the ecological and evolutionary contexts in which adaptive radiations occur are conducive to reinforcement and its downstream consequences, adaptive radiations provide an ideal framework in which to evaluate reinforcement's role in diversification.

Isolation of Metrosideros ('Ohi'a) Taxa on O'ahu Increases with Elevation and Extreme Environments

Species radiations should be facilitated by short generation times and limited dispersal among discontinuous populations. Hawaii's hyper-diverse, landscape-dominant tree, Metrosideros, is unique among the islands' radiations for its massive populations that occur continuously over space and time within islands, its exceptional capacity for gene flow by both pollen and seed, and its extended life span (ca. >650 years). Metrosideros shows the greatest phenotypic and microsatellite DNA diversity on O'ahu, where taxa occur in tight sympatry or parapatry in mesic and montane wet forest on 2 volcanoes. We document the nonrandom distributions of 12 taxa (including unnamed morphotypes) along elevation gradients, measure phenotypes of ~6-year-old common-garden plants of 8 taxa to verify heritability of phenotypes, and examine genotypes of 476 wild adults at 9 microsatellite loci to compare the strengths of isolation across taxa, volcanoes, and distance. All 8 taxa retained their diagnostic phenotypes in the common garden. Populations were isolated by taxon to a range of degrees (pairwise FST between taxa: 0.004-0.267), and there was no pattern of isolation by distance or by elevation; however, significant isolation between volcanoes was observed within monotypic species, suggesting limited gene flow between volcanoes. Among the infraspecific taxa of Metrosideros polymorpha, genetic diversity and isolation significantly decreased and increased, respectively, with elevation. Overall, 5 of the 6 most isolated taxa were associated with highest elevations or otherwise extreme environments. These findings suggest a principal role for selection in the origin and maintenance of the exceptional diversity that occurs within continuous Metrosideros stands on O'ahu.

A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence

Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.

Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically-relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights into the abiotic and biotic mechanisms that structure populations and drive the accumulation of phenotypic and taxonomic diversity. Low-vagility organisms whose distributions span ephemeral geographic barriers present the ideal evolutionary context within which to address these questions. Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians (Amphibia: Gymnophiona) endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north-to-south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Consequently, in contrast to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island. Our study joins a growing number of systems demonstrating lineage divergence on volcanic islands with stark environmental transitions across small geographic distances.

Genetic, Morphological, and Environmental Differentiation of an Arid-Adapted Oak with a Disjunct Distribution

The patterns of genetic and morphological diversity of a widespread species can be influenced by environmental heterogeneity and the degree of connectivity across its geographic distribution. Here, we studied Quercus havardii Rydb., a uniquely adapted desert oak endemic to the Southwest region of the United States, using genetic, morphometric, and environmental datasets over various geographic scales to quantify differentiation and understand forces influencing population divergence. First, we quantified variation by analyzing 10 eastern and 13 western populations from the disjunct distribution of Q. havardii using 11 microsatellite loci, 17 morphological variables, and 19 bioclimatic variables. We then used regressions to examine local and regional correlations of climate with genetic variation. We found strong genetic, morphological and environmental differences corresponding with the large-scale disjunction of populations. Additionally, western populations had higher genetic diversity and lower relatedness than eastern populations. Levels of genetic variation in the eastern populations were found to be primarily associated with precipitation seasonality, while levels of genetic variation in western populations were associated with lower daily temperature fluctuations and higher winter precipitation. Finally, we found little to no observed environmental niche overlap between regions. Our results suggest that eastern and western populations likely represent two distinct taxonomic entities, each associated with a unique set of climatic variables potentially influencing local patterns of diversity.

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics

Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (d_XY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.

Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini)

Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species Φ_ST > 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species - the Steller's eider (Polysticta stelleri) - via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories.

Biological and biochemical diversity in different biotypes of spotted stem borer, Chilo partellus (Swinhoe) in India

Because of variation in incidence and severity of damage by Chilo partellus (Swinhoe) in different geographical regions, it is difficult to identify stable sources of resistance against this pest. Therefore, the present studies were undertaken on biological attributes (damage in resistant and susceptible genotypes, survival and development) and biochemical profiles (amino acids and lipophilic compound) of C. partellus populations from eight geographical regions to understand it's population structure in India. There was a significant variation in biological attributes and biochemical profiles of C. partellus populations from different geographical regions. Based on virulence and biological attributes, similarity index placed the C. partellus populations in five groups. Likewise, lipophilic and amino acid profiling also placed the C. partellus populations in five groups. However, the different clusters based on biological and biochemical attributes did not include populations from the same regions. Similarity index based on virulence, biological attributes, and amino acids and lipophilic profiles placed the C. partellus populations in six groups. The C. partellus populations from Hisar, Hyderabad, Parbhani and Coimbatore were distinct from each other, indicating that there are four biotypes of C. partellus in India. The results suggested that sorghum and maize genotypes need to be tested against these four populations to identify stable sources of resistance. However, there is a need for further studies to establish the restriction in gene flow through molecular approaches across geographical regions to establish the distinctiveness of different biotypes of C. partellus in India.

Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution

When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selection through adaptation, sexual selection, and inter-sexual conflict, in addition to cryptic evolution under stabilizing selection. Dysfunctional sex-biased gene expression, in particular, may provide an important source of sexually-dimorphic genetic incompatibilities. Here, we characterize and compare male and female/hermaphrodite transcriptome profiles for sibling nematode species Caenorhabditis briggsae and C. nigoni, along with allele-specific expression in their F1 hybrids, to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, misexpression of sex-biased genes pervades F1 hybrids of both sexes. This finding implicates greater fragility of male genetic networks to produce dysfunctional organismal phenotypes. Spermatogenesis genes are especially prone to high divergence in both expression and coding sequences, consistent with a "faster male" model for Haldane's rule and elevated sterility of hybrid males. Moreover, underdominant expression pervades male-biased genes compared to female-biased and sex-neutral genes and an excess of cis-trans compensatory regulatory divergence for X-linked genes underscores a "large-X effect" for hybrid male expression dysfunction. Extensive regulatory divergence in sex determination pathway genes likely contributes to demasculinization of XX hybrids. The evolution of genetic incompatibilities due to regulatory versus coding sequence divergence, however, are expected to arise in an uncorrelated fashion. This study identifies important differences between the sexes in how regulatory networks diverge to contribute to sex-biases in how genetic incompatibilities manifest during the speciation process.

Drivers of population divergence and species differentiation in a recent group of indigenous orchids (Vanilla spp.) in Madagascar

With over 25,000 species, orchids are among families with remarkable high rate of diversification. Since Darwin's time, major advances attributed the exceptional diversity of orchids to plant-pollinator interactions. However, unraveling the processes and factors that determine the phenotypic and genotypic variation of natural orchid populations remains a challenge. Here, we assessed genetic population structure and floral differentiation in recently diverged leafless Vanilla species in a world biodiversity hotspot, Madagascar, using seven microsatellite loci and 26 morphometric variables. Additionally, analyses were performed to test for the occurrence of any patterns of isolation by distance, isolation by environment, and isolation by adaptation and to detect possible physical barriers that might have caused genetic discontinuities between populations. Positive inbreeding coefficients detected in 22 populations were probably due to the presence of null alleles, geitonogamy and/or some admixture (sympatric species). In contrast, the only high-altitude population showed an important rate of clonality leading to heterozygote excess. Genetic diversity was maximum in western populations, suggesting a postglacial colonization to the north and south. Clustering analyses identified seven genetic groups characterized by specific floral traits that matched five botanical descriptions in the literature. A contribution of montane refugia and river barriers on population differentiation was detected. We also detected combined effects of IBD/IBE and IBE/IBA on genetic differentiation and suggested this pattern is more likely determined by ecological isolation, although pollinator-mediated divergent selection could not be ruled out for some of the species. Overall, this study provides further insights on speciation in orchids, a group for which Madagascar shows one of the world's highest level of endemism and confirms the importance of the peculiar biogeography of the island in shaping species differentiation.

Seven Questions on the Chemical Ecology and Neurogenetics of Resource-Mediated Speciation

Adaptation to different environments can result in reproductive isolation between populations and the formation of new species. Food resources are among the most important environmental factors shaping local adaptation. The chemosensory system, the most ubiquitous sensory channel in the animal kingdom, not only detects food resources and their chemical composition, but also mediates sexual communication and reproductive isolation in many taxa. Chemosensory divergence may thus play a crucial role in resource-mediated adaptation and speciation. Understanding how the chemosensory system can facilitate resource-mediated ecological speciation requires integrating mechanistic studies of the chemosensory system with ecological studies, to link the genetics and physiology of chemosensory properties to divergent adaptation. In this review, we use examples of insect research to present seven key questions that can be used to understand how the chemosensory system can facilitate resource-mediated ecological speciation in consumer populations.

Depth-dependent parental effects create invisible barriers to coral dispersal

Historically, marine populations were considered to be interconnected across large geographic regions due to the lack of apparent physical barriers to dispersal, coupled with a potentially widely dispersive pelagic larval stage. Recent studies, however, are providing increasing evidence of small-scale genetic segregation of populations across habitats and depths, separated in some cases by only a few dozen meters. Here, we performed a series of ex-situ and in-situ experiments using coral larvae of three brooding species from contrasting shallow- and deep-water reef habitats, and show that their settlement success, habitat choices, and subsequent survival are substantially influenced by parental effects in a habitat-dependent manner. Generally, larvae originating from deep-water corals, which experience less variable conditions, expressed more specific responses than shallow-water larvae, with a higher settlement success in simulated parental-habitat conditions. Survival of juvenile corals experimentally translocated to the sea was significantly lower when not at parental depths. We conclude that local adaptations and parental effects alongside larval selectivity and phenotype-environment mismatches combine to create invisible semipermeable barriers to coral dispersal and connectivity, leading to habitat-dependent population segregation.

Tom Shlesinger and Yossi Loya use ex-situ and in-situ experiments with coral larvae of three brooding species from contrasting shallow- and deep-water habitats and show that larvae originating from deep-water corals have narrower tolerances and higher habitat-specificity in simulated parental-habitat conditions. They also show that survival of juvenile corals experimentally translocated to the sea was significantly lower when not at parental depths. Together these results demonstrate that local adaptations and parental effects interact with larval selectivity and phenotype-environment mismatches to create semipermeable barriers to coral dispersal and connectivity.

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Genomic divergence landscape in recurrently hybridizing Chironomus sister taxa suggests stable steady state between mutual gene flow and isolation

Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component-based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence-simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.

Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus)

Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.

Colonization of a novel host by fleas: changes in egg production and egg size

We studied the success of fleas, Synosternus cleopatrae and Xenopsylla ramesis, in switching to a novel host by establishing experimental lines maintained on different hosts for 18 generations. Fleas fed on principal (P-line) or novel hosts, either sympatric with (S-line) or allopatric to (A-line) a flea and its principal host, then we assessed their reproductive performance via the number and size of eggs. We compared reproductive performance between hosts within a line and between lines within a host asking: (a) whether fleas adapt to a novel host species after multiple generations; (b) if yes, whether the pattern of adaptation differs between novel host species sympatric with or allopatric to a flea and its principal host; and (c) adaptation to a novel host is accompanied with a loss of success in exploitation of an original host. Fleas from the S- and A-lines increased their egg production on a novel host (except X. ramesis from the S-line). S. cleopatrae from the S-line but not the A-line increased egg size on a novel host, whereas X. ramesis from the A-line but not the S-line produced larger eggs from a novel host. We found no indication of a loss of reproductive performance on the original host while adapting to a novel host. We conclude that fleas are able to switch rapidly to a new host with the pattern of a switch to either sympatric or an allopatric host depending on the identities of both flea and host species.

Ecological niche differentiation in Chiroxiphia and Antilophia manakins (Aves: Pipridae)

Species distribution models are useful for identifying the ecological characteristics that may limit a species' geographic range and for inferring patterns of speciation. Here, we test a hypothesis of niche conservatism across evolutionary time in a group of manakins (Aves: Pipridae), with a focus on Chiroxiphia boliviana, and examine the degree of ecological differentiation with other Chiroxiphia and Antilophia manakins. We tested whether allopatric sister species were more or less similar in environmental space than expected given their phylogenetic distances, which would suggest, respectively, ecological niche conservatism over time or ecologically mediated selection (i.e. niche divergence). We modeled the distribution of nine manakin taxa (C. boliviana, C. caudata, C. lanceolata, C. linearis, C. p. pareola, C. p. regina, C. p. napensis, Antilophia galeata and A. bokermanni) using Maxent. We first performed models for each taxon and compared them. To test our hypothesis we followed three approaches: (1) we tested whether C. boliviana could predict the distribution of the other manakin taxa and vice versa; (2) we compared the ecological niches by using metrics of niche overlap, niche equivalency and niche similarity; and (3) lastly, we tested whether niche differentiation corresponded to phylogenetic distances calculated from two recent phylogenies. All models had high training and test AUC values. Mean AUC ratios were high (>0.8) for most taxa, indicating performance better than random. Results suggested niche conservatism, and high niche overlap and equivalency between C. boliviana and C. caudata, but we found very low values between C. boliviana and the rest of the taxa. We found a negative, but not significant, relationship between niche overlap and phylogenetic distance, suggesting an increase in ecological differentiation and niche divergence over evolutionary time. Overall, we give some insights into the evolution of C. boliviana, proposing that ecological selection may have influenced its speciation.

Asymmetric, but opposing reductions in immigrant viability and fecundity promote reproductive isolation among host-associated populations of an insect herbivore

Immigrant inviability can contribute to reproductive isolation (RI) during ecological speciation by reducing the survival of immigrants in non-native environments. However, studies that assess the fitness consequence of immigrants moving from native to non-native environments typically fail to explore the potential role of concomitant reductions in immigrant fecundity despite recent evidence suggesting its prominent role during local adaptation. Here, we evaluate the directionality and magnitude of both immigrant viability and fecundity to RI in a host-specific gall-forming wasp, Belonocnema treatae. Using reciprocal transplant experiments replicated across sites, we measure immigrant viability and fecundity by comparing differences in the incidence of gall formation (viability) and predicted the number of eggs per female (fecundity) between residents and immigrants in each of two host-plant environments. Reduced immigrant viability was found in one host environment while reduced immigrant fecundity was found in the other. Such habitat-dependent barriers resulted in asymmetric RI between populations. By surveying recent literature on local adaptation, we find that asymmetry in immigrant viability and fecundity are widespread across disparate taxa, which highlights the need to combine estimates of both common and overlooked barriers in cases of potential bi-directional gene flow to create a more comprehensive view of the evolution of RI.

Genomics Reveals Widespread Ecological Speciation in Flightless Insects

Recent genomic analyses have highlighted parallel divergence in response to ecological gradients, but the extent to which altitude can underpin such repeated speciation remains unclear. Wing reduction and flight loss have apparently evolved repeatedly in montane insect assemblages and have been suggested as important drivers of hexapod diversification. We test this hypothesis using genomic analyses of a widespread wing-polymorphic stonefly species complex in New Zealand. We identified over 50,000 polymorphic genetic markers generated across almost 200 Zelandoperla fenestrata stonefly specimens using a newly generated plecopteran reference genome, to reveal widespread parallel speciation between sympatric full-winged and wing-reduced ecotypes. Rather than the existence of a single, widespread, flightless taxon (Zelandoperla pennulata), evolutionary genomic data reveal that wing-reduced upland lineages have speciated repeatedly and independently from full-winged Z. fenestrata. This repeated evolution of reproductive isolation between local ecotype pairs that lack mitochondrial DNA differentiation suggests that ecological speciation has evolved recently. A cluster of outlier single-nucleotide polymorphisms detected in independently wing-reduced lineages, tightly linked in an approximately 85 kb genomic region that includes the developmental “supergene” doublesex, suggests that this “island of divergence” may play a key role in rapid ecological speciation. [Ecological speciation; genome assembly; genomic island of differentiation; genotyping-by-sequencing; incipient species; plecoptera; wing reduction.]

The Evolutionary Genomics of Serpentine Adaptation

Serpentine barrens are among the most challenging settings for plant life. Representing a perfect storm of hazards, serpentines consist of broadly skewed elemental profiles, including abundant toxic metals and low nutrient contents on drought-prone, patchily distributed substrates. Accordingly, plants that can tolerate the challenges of serpentine have fascinated biologists for decades, yielding important insights into adaptation to novel ecologies through physiological change. Here we highlight recent progress from studies which demonstrate the power of serpentine as a model for the genomics of adaptation. Given the moderate - but still tractable - complexity presented by the mix of hazards on serpentine, these venues are well-suited for the experimental inquiry of adaptation both in natural and manipulated conditions. Moreover, the island-like distribution of serpentines across landscapes provides abundant natural replicates, offering power to evolutionary genomic inference. Exciting recent insights into the genomic basis of serpentine adaptation point to a partly shared basis that involves sampling from common allele pools available from retained ancestral polymorphism or via gene flow. However, a lack of integrated studies deconstructing complex adaptations and linking candidate alleles with fitness consequences leaves room for much deeper exploration. Thus, we still seek the crucial direct link between the phenotypic effect of candidate alleles and their measured adaptive value - a prize that is exceedingly rare to achieve in any study of adaptation. We expect that closing this gap is not far off using the promising model systems described here.

Allopatric and Sympatric Drivers of Speciation in Alviniconcha Hydrothermal Vent Snails

Despite significant advances in our understanding of speciation in the marine environment, the mechanisms underlying evolutionary diversification in deep-sea habitats remain poorly investigated. Here, we used multigene molecular clocks and population genetic inferences to examine processes that led to the emergence of the six extant lineages of Alviniconcha snails, a key taxon inhabiting deep-sea hydrothermal vents in the Indo-Pacific Ocean. We show that both allopatric divergence through historical vicariance and ecological isolation due to niche segregation contributed to speciation in this genus. The split between the two major Alviniconcha clades (separating A. boucheti and A. marisindica from A. kojimai, A. hessleri, and A. strummeri) probably resulted from tectonic processes leading to geographic separation, whereas the splits between co-occurring species might have been influenced by ecological factors, such as the availability of specific chemosynthetic symbionts. Phylogenetic origin of the sixth species, Alviniconcha adamantis, remains uncertain, although its sister position to other extant Alviniconcha lineages indicates a possible ancestral relationship. This study lays a foundation for future genomic studies aimed at deciphering the roles of local adaptation, reproductive biology, and host–symbiont compatibility in speciation of these vent-restricted snails.

Niche specificity influences gene flow across fine-scale habitat mosaics in Succulent Karoo plants

While the tempo of diversification in biodiversity hotspots has received much attention, the spatial scale of diversification has often been overlooked. Addressing this deficiency requires understanding the drivers of population divergence and the spatial scales at which they operate in species-rich clades and ecosystems. South Africa's Succulent Karoo (SK) hotspot provides an excellent system for such research, being both compact (ca. 110,000 km² ) and home to spectacular in-situ radiations, such as the ruschioid Aizoaceae. Here we use GBS to document genetic structure in two co-occurring ruschioid species, at both coarse (>10 km) and fine (<500 m) spatial scales. Where Ruschia burtoniae shows strong between-population genetic differentiation and no gene flow, Conophytum calculus shows weak differentiation, with high levels of admixture suggesting recent or ongoing gene flow. Community analysis and transplant experiments reveal that R. burtoniae occupies a narrow, low-pH edaphic niche, and at scales of a few hundred metres, areas of elevated genetic turnover correspond to patches of edaphically unsuitable habitat. In contrast, C. calculus occupies a broader niche and exhibits isolation-by-distance without a habitat effect. We suggest that edaphic specialisation, coupled with highly restricted seed and pollen dispersal in heterogeneous landscapes, has played a major role in driving rapid diversification at small spatial scales in this system. However, the contrasting patterns in our study species show that these factors do not influence all organisms uniformly, being strongly modulated by lineage-specific traits that influence both the spatial scale of gene flow and habitat specificity.

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system

How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing β-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.

Ecological and morphological determinants of evolutionary diversification in Darwin's finches and their relatives

Darwin's finches are a classic example of adaptive radiation, a process by which multiple ecologically distinct species rapidly evolve from a single ancestor. Such evolutionary diversification is typically explained by adaptation to new ecological opportunities. However, the ecological diversification of Darwin's finches following their dispersal to Galápagos was not matched on the same archipelago by other lineages of colonizing land birds, which diversified very little in terms of both species number and morphology. To better understand the causes underlying the extraordinary variation in Darwin's finches, we analyze the evolutionary dynamics of speciation and trait diversification in Thraupidae, including Coerebinae (Darwin's finches and relatives) and, their closely related clade, Sporophilinae. For all traits, we observe an early pulse of speciation and morphological diversification followed by prolonged periods of slower steady-state rates of change. The primary exception is the apparent recent increase in diversification rate in Darwin's finches coupled with highly variable beak morphology, a potential key factor explaining this adaptive radiation. Our observations illustrate how the exploitation of ecological opportunity by contrasting means can produce clades with similarly high diversification rate yet strikingly different degrees of ecological and morphological differentiation.

Moniliophthora perniciosa, the mushroom causing witches' broom disease of cacao: Insights into its taxonomy, ecology and host range in Brazil

Witches' broom caused by Moniliophthora perniciosa is the main disease of cacao (Theobroma cacao) in Brazil. The fungus is known to occur on other host families and these populations have been addressed in the literature as biotypes: C (Malvaceae); H (Malpighiaceae); L (Bignoniaceae) and S (Solanaceae). No complete elucidation of the phylogenetic relationships of isolates obtained from this disparate host range appears in the literature. One member of H (ex Heteropterys acutifolia) has been described as a distinct species. But should other biotypes be also recognized as distinct taxa? In the present study, a survey yielding 24 isolates of M. perniciosa from ten hosts and covering a wide range of geographic regions in Brazil was undertaken. These isolates were compared with those from T. cacao using three DNA regions for the phylogenetic analyses: ITS, LSU and RPB1. Morphology was also examined. All isolates in this study were found to belong to M. perniciosa, including the population from H. acutifolia, formerly treated as Moniliophthora brasiliensis but reduced here to a synonym of M. perniciosa. This species ranged from pathogenic to a previously unreported occurrence as a non-pathogenic endophyte in the Atlantic rainforest tree Allophylus edulis (Sapindaceae). M. perniciosa was recorded on a range of solanaceous hosts (16 species) over a wide variety of ecosystems. The ecological and evolutionary significance of these novel findings are discussed.

Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish

Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune responses can be of relevance in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes have often relied on only one pair of populations, targeted the expression of only a subset of genes or used wild-caught individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological abilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish Astatotilapia burtoni. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond set-up. In all investigated population pairs, lake fish were more heavily parasitized than river fish, in terms of both parasite taxon composition and infection abundance. The innate immune response in the wild was higher in lake than in river populations and was elevated in a river population exposed to lake parasites in the pond set-up. Environmental differences between lake and river habitat and their distinct parasite communities have shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond set-up were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimatized to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.

Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity

Adaptation to different environments can directly and indirectly generate reproductive isolation between species. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are sister species that have diverged across a salinity gradient and are reproductively isolated by habitat, behavioural, extrinsic and intrinsic post-zygotic isolation. We asked if salinity adaptation contributes indirectly to other forms of reproductive isolation via linked selection and hypothesized that low recombination regions, such as sex chromosomes or chromosomal rearrangements, might facilitate this process. We conducted QTL mapping in backcrosses between L. parva and L. goodei to explore the genetic architecture of salinity tolerance, behavioural isolation and intrinsic isolation. We mapped traits relative to a chromosome that has undergone a centric fusion in L. parva (relative to L. goodei). We found that the sex locus appears to be male determining (XX-XY), was located on the fused chromosome and was implicated in intrinsic isolation. QTL associated with salinity tolerance were spread across the genome and did not overly co-localize with regions associated with behavioural or intrinsic isolation. This preliminary analysis of the genetic architecture of reproductive isolation between Lucania species does not support the hypothesis that divergent natural selection for salinity tolerance led to behavioural and intrinsic isolation as a by-product. Combined with previous studies in this system, our work suggests that adaptation as a function of salinity contributes to habitat isolation and that reinforcement may have contributed to the evolution of behavioural isolation instead, possibly facilitated by linkage between behavioural isolation and intrinsic isolation loci on the fused chromosome.

Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island

A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.

The signature of competition in ecomorphological traits across the avian radiation

Competition for shared resources represents a fundamental driver of biological diversity. However, the tempo and mode of phenotypic evolution in deep-time has been predominantly investigated using trait evolutionary models which assume that lineages evolve independently from each other. Consequently, the role of species interactions in driving macroevolutionary dynamics remains poorly understood. Here, we quantify the prevalence for signatures of competition between related species in the evolution of ecomorphological traits across the bird radiation. We find that mechanistic trait models accounting for the effect of species interactions on phenotypic divergence provide the best fit for the data on at least one trait axis in 27 out of 59 clades ranging between 21 and 195 species. Where it occurs, the signature of competition generally coincides with positive species diversity-dependence, driven by the accumulation of lineages with similar ecologies, and we find scarce evidence for trait-dependent or negative diversity-dependent phenotypic evolution. Overall, our results suggest that the footprint of interspecific competition is often eroded in long-term patterns of phenotypic diversification, and that other selection pressures may predominantly shape ecomorphological diversity among extant species at macroevolutionary scales.

Model-Based Inference of Punctuated Molecular Evolution

In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.

Appendicular skeletal morphology of North American Martes reflect independent modes of evolution in conjunction with Pleistocene glacial cycles

Pleistocene glacial cycles are thought to have driven ecological niche shifts, including novel niche formation. North American pine martens, Martes americana and M. caurina, are exemplar taxa thought to have diverged molecularly and morphologically during Pleistocene glaciation. Previous research found correlations between Martes limb morphology with biome and climate, suggesting that appendicular evolution may have occurred via adaptation to selective pressures imposed by novel and shifting habitats. Such variation can also be achieved through non-adaptive means such as genetic drift. Here, we evaluate whether regional genetic differences reflect limb morphology differences among populations of M. americana and M. caurina by analyzing evolutionary tempo and mode of six limb elements. Our comparative phylogenetic models indicate that genetic structure predicts limb shape better than size. Marten limb size has low phylogenetic signal, and the best supported model of evolution is punctuational (kappa), with morphological and genetic divergence occurring simultaneously. Disparity through time analysis suggests that the tempo of limb evolution in Martes tracks Pleistocene glacial cycles, such that limb size may be responding to shifting climates rather than population genetic structure. Contrarily, we find that limb shape is strongly tied to genetic relationships, with high phylogenetic signal and a lambda mode of evolution. Overall, this pattern of limb size and shape variation may be the result of geographic isolation during Pleistocene glacial advance, while declines in disparity suggest hybridization during interglacial periods. Future inclusion of extinct populations of Martes, which were more morphologically and ecologically diverse, may further clarify Martes phenotypic evolution.

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāne'ohe Bay Hawai'i during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.

A non-exhaustive survey revealed possible genetic similarity in mitochondrial adaptive evolution of marine fish species in the northwestern Pacific

Mitochondrial coding genes involved in the oxidative phosphorylation pathway play vitally important roles in energy production and thermal adaptation. Investigating the underlying molecular mechanism of mitochondrial adaptive evolution is crucial for understanding biodiversity and ecological radiation. In this study, we collated population genetic studies of marine fish species in the northwestern Pacific based on mitochondrial cytochrome b gene sequences, to investigate whether similar patterns could be detected in mitochondrial adaptive evolution. After filtering, nine studies containing eight marine fish species (Ammodytespersonatus, Boleophthalmuspectinirostris, Larimichthyspolyactis, Mugilcephalus, Pampusargenteus, Platycephalus sp.1, Sebastiscusmarmoratus, and Trachidermusfasciatus) belonging to eight different families were retained. Multiple codon-based approaches were used to identify potential sites under selection in each species. By comparison, our results showed that the posterior part of the mitochondrial cytochrome b gene (particularly codon 372 and its neighboring sites) seemed to be involved in the adaptive evolution process, suggesting potential genetic similarity among distantly related species. We also summarized four types of adaptive patterns in the reviewed species, and suggest that the level of genetic differentiation and mitochondrial adaptive evolution might be correlated. Further studies are needed to confirm such relationship by detecting RNA-level evidence and investigating more species and samples.

Small-scale population divergence is driven by local larval environment in a temperate amphibian

Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small-scale natural systems even when population sizes are small, and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16,707 ddRAD-seq SNPs, relating levels of differentiation with local environments, as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment, and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape, and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small-scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system, leading to observable population differentiation.