Evolutionary Ecology of Natural Comammox Nitrospira Populations

Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems.

A framework for defining livestock ecotypes based on ecological modelling and exploring genomic environmental adaptation: the example of Ethiopian village chicken

In evolutionary ecology, an ecotype is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining Ecological Niche Modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within- ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. A few biological pathways were shared amongst most ecotypes and the involved genes showed functions important for scavenging chickens, e.g. neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using Redundancy Analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype x environment (GxE) interactions.

Phylogenomic analyses using genomes and transcriptomes do not resolve relationships among major clades in Phrymaceae

Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons. Methods: We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events. Key results: Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. Conclusions: We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that genome-scale data do not always fully "resolve" phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.

Going all the way: The implications of life history and phenotype on reproductive success of the common triplefin, Forsterygion lapillum

<p>Identifying sources of variation in individual reproductive success is crucial to our understanding of population dynamics and evolutionary ecology. In many systems, the determinants of success are not well known. Where species have parental care, for example, determinants of success can be particularly challenging to partition between parents and offspring. In this thesis I investigate drivers and consequences of variable life histories, for a small reef fish that exhibits male parental care (the common triplefin Forsterygion lapillum). I examined the influence of individual life history, phenotype and behaviour on (1) the performance of recently settled juveniles, and (2) the reproductive success adult males. I made field-based observations of adult males during the breeding season, measured their phenotypic traits (body size and condition) and used their otoliths to reconstruct life history characteristics (hatch dates and mean growth rates). My life history trait reconstructions suggested two alternate pathways to ’success’ for adult males. Successful males hatched earlier and therefore had a developmental ’head start’ over less successful males (i.e., males with eggs > male territory holders without eggs > floaters). Alternatively, males can apparently achieve success by growing faster: for males born in the same month, those with eggs grew faster than those with territories and no eggs, and both groups grew faster than floaters. These results suggest that accelerated growth rate may mediate the effects of a later hatch date, and that both hatch dates and growth rates influence the success of adult males, likely through proximate effects on individual phenotypes. Identifying sources of variation in individual reproductive success is crucial to our understanding of population dynamics and evolutionary ecology. In many systems, the determinants of success are not well known. Where species have parental care, for example, determinants of success can be particularly challenging to partition between parents and offspring. Male parental care is common among fishes, where resources such as high quality territories and mates often may be limiting. In such systems, individual success of offspring may result from distinct life history pathways that are influenced by both parental effects (e.g., timing of reproduction) and by the offspring themselves (e.g., ’personalities’). These pathways, in turn, can induce phenotypic variation and affect success later in life. The drivers and consequences of variable life histories are not well understood in the context of reproductive success. In this thesis I investigate drivers and consequences of variable life histories, for a small reef fish that exhibits male parental care (the common triplefin Forsterygion lapillum). I examined the influence of individual life history, phenotype and behaviour on (1) the performance of recently settled juveniles, and (2) the reproductive success adult males. I made field-based observations of adult males during the breeding season, measured their phenotypic traits (body size and condition) and used their otoliths to reconstruct life history characteristics (hatch dates and mean growth rates). Some males showed no evidence of territorial defence and were defined as ’floaters’; others defended territories, and a subset of these also had nests with eggs present. Adult male body size was significantly higher for males that defended breeding territories, and body condition was significantly higher for the males that had eggs (i.e., had successfully courted females). My otolith-based reconstructions of life history traits suggested two alternate pathways to ’success’ for adult males. Successful males hatched earlier and therefore had a developmental ’head start’ over less successful males (i.e., males with eggs > male territory holders without eggs > floaters). Alternatively, males can apparently achieve success by growing faster: for males born in the same month, those with eggs grew faster than those with territories and no eggs, and both groups grew faster than floaters. These results suggest that accelerated growth rate may mediate the effects of a later hatch date, and that both hatch dates and growth rates influence the success of adult males, likely through proximate effects on individual phenotypes. I evaluated the effects of variable life history in a complimentary lab-based study. Specifically, I manipulated the developmental environments (feeding regime and temperature) for young fish and evaluated the direct effects on life history traits and phenotypes. Then, I conducted an assay to quantify the indirect effects of developmental environment, life history traits, and phenotypes on aggression and performance of young fish. These developmental environments did not have a clear, overall effect on juvenile phenotype or performance (i.e. behavioural aggression and the ability to dominate a resource). Instead, individuals (irrespective of developmental environment) that grew faster and/or longer pelagic larval durations had increased odds of dominating a limited resource. I attributed the non-significant direct effect of developmental environment to within-treatment mortality and variation among individuals in terms of their realised access to food (i.e., dominance hierarchies were apparent in rearing chambers, suggesting a non-uniform access to food). Fish that were more likely to dominate a resource were also more aggressive (i.e., more likely to engage in chasing behaviours). Fish that were larger and more aggressive established territories that were deemed to be of higher ’quality’ (inferred from percent cover of cobble resources). Overall, this study suggests a complex interplay between social systems, phenotype and life history. Developmental environments may influence phenotypes, although behavioural differences among individuals may moderate that effect, contributing to additional variation in phenotypes and life history traits which, in turn, shape the success of individuals. Collectively, my thesis emphasises the consequences of life history variability on success at multiple life stages. These results may be relevant to other species that exhibit male parental care or undergo intense competition for space during early life stages. In addition, my results highlight interactions between life history, phenotype and behaviour that can have important implications for population dynamics and evolutionary ecology.</p>

Going all the way: The implications of life history and phenotype on reproductive success of the common triplefin, Forsterygion lapillum

<p>Identifying sources of variation in individual reproductive success is crucial to our understanding of population dynamics and evolutionary ecology. In many systems, the determinants of success are not well known. Where species have parental care, for example, determinants of success can be particularly challenging to partition between parents and offspring. In this thesis I investigate drivers and consequences of variable life histories, for a small reef fish that exhibits male parental care (the common triplefin Forsterygion lapillum). I examined the influence of individual life history, phenotype and behaviour on (1) the performance of recently settled juveniles, and (2) the reproductive success adult males. I made field-based observations of adult males during the breeding season, measured their phenotypic traits (body size and condition) and used their otoliths to reconstruct life history characteristics (hatch dates and mean growth rates). My life history trait reconstructions suggested two alternate pathways to ’success’ for adult males. Successful males hatched earlier and therefore had a developmental ’head start’ over less successful males (i.e., males with eggs > male territory holders without eggs > floaters). Alternatively, males can apparently achieve success by growing faster: for males born in the same month, those with eggs grew faster than those with territories and no eggs, and both groups grew faster than floaters. These results suggest that accelerated growth rate may mediate the effects of a later hatch date, and that both hatch dates and growth rates influence the success of adult males, likely through proximate effects on individual phenotypes. Identifying sources of variation in individual reproductive success is crucial to our understanding of population dynamics and evolutionary ecology. In many systems, the determinants of success are not well known. Where species have parental care, for example, determinants of success can be particularly challenging to partition between parents and offspring. Male parental care is common among fishes, where resources such as high quality territories and mates often may be limiting. In such systems, individual success of offspring may result from distinct life history pathways that are influenced by both parental effects (e.g., timing of reproduction) and by the offspring themselves (e.g., ’personalities’). These pathways, in turn, can induce phenotypic variation and affect success later in life. The drivers and consequences of variable life histories are not well understood in the context of reproductive success. In this thesis I investigate drivers and consequences of variable life histories, for a small reef fish that exhibits male parental care (the common triplefin Forsterygion lapillum). I examined the influence of individual life history, phenotype and behaviour on (1) the performance of recently settled juveniles, and (2) the reproductive success adult males. I made field-based observations of adult males during the breeding season, measured their phenotypic traits (body size and condition) and used their otoliths to reconstruct life history characteristics (hatch dates and mean growth rates). Some males showed no evidence of territorial defence and were defined as ’floaters’; others defended territories, and a subset of these also had nests with eggs present. Adult male body size was significantly higher for males that defended breeding territories, and body condition was significantly higher for the males that had eggs (i.e., had successfully courted females). My otolith-based reconstructions of life history traits suggested two alternate pathways to ’success’ for adult males. Successful males hatched earlier and therefore had a developmental ’head start’ over less successful males (i.e., males with eggs > male territory holders without eggs > floaters). Alternatively, males can apparently achieve success by growing faster: for males born in the same month, those with eggs grew faster than those with territories and no eggs, and both groups grew faster than floaters. These results suggest that accelerated growth rate may mediate the effects of a later hatch date, and that both hatch dates and growth rates influence the success of adult males, likely through proximate effects on individual phenotypes. I evaluated the effects of variable life history in a complimentary lab-based study. Specifically, I manipulated the developmental environments (feeding regime and temperature) for young fish and evaluated the direct effects on life history traits and phenotypes. Then, I conducted an assay to quantify the indirect effects of developmental environment, life history traits, and phenotypes on aggression and performance of young fish. These developmental environments did not have a clear, overall effect on juvenile phenotype or performance (i.e. behavioural aggression and the ability to dominate a resource). Instead, individuals (irrespective of developmental environment) that grew faster and/or longer pelagic larval durations had increased odds of dominating a limited resource. I attributed the non-significant direct effect of developmental environment to within-treatment mortality and variation among individuals in terms of their realised access to food (i.e., dominance hierarchies were apparent in rearing chambers, suggesting a non-uniform access to food). Fish that were more likely to dominate a resource were also more aggressive (i.e., more likely to engage in chasing behaviours). Fish that were larger and more aggressive established territories that were deemed to be of higher ’quality’ (inferred from percent cover of cobble resources). Overall, this study suggests a complex interplay between social systems, phenotype and life history. Developmental environments may influence phenotypes, although behavioural differences among individuals may moderate that effect, contributing to additional variation in phenotypes and life history traits which, in turn, shape the success of individuals. Collectively, my thesis emphasises the consequences of life history variability on success at multiple life stages. These results may be relevant to other species that exhibit male parental care or undergo intense competition for space during early life stages. In addition, my results highlight interactions between life history, phenotype and behaviour that can have important implications for population dynamics and evolutionary ecology.</p>

Evolutionary Ecology of Lizards: Lessons from a Special Issue

Regardless of taxonomical disquisitions on its yet unraveled phylogenetic relationships within and among taxa [...]

Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology

The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.