scholarly journals Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line

2020 ◽  
Vol 69 (6) ◽  
pp. 1039-1051 ◽  
Author(s):  
Damien Esquerré ◽  
Stephen Donnellan ◽  
Ian G Brennan ◽  
Alan R Lemmon ◽  
Emily Moriarty Lemmon ◽  
...  
Keyword(s):  
Body Shape ◽  
Habitat Preferences ◽  
Ecological Niches ◽  
Mitochondrial Genomes ◽  
Phenotypic Evolution ◽  
Conservative Group ◽  
Anchored Hybrid Enrichment ◽  
Nuclear Loci ◽  
Wallace’S Line ◽  
Diverse Groups

Abstract Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace’s and Lyddeker’s lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pythons, is distributed across these lines, and are remarkably more diverse in phenotype and ecology east of Lydekker’s line in Australo-Papua. We used an anchored hybrid enrichment approach, with near complete taxon sampling, to extract mitochondrial genomes and 376 nuclear loci to resolve and date their phylogenetic history. Biogeographic reconstruction demonstrates that they originated in Asia around 38-45 Ma and then invaded Australo-Papua around 23 Ma. Australo-Papuan pythons display a sizeable expansion in morphological space, with shifts towards numerous new adaptive optima in head and body shape, coupled with the evolution of new micro-habitat preferences. We provide an updated taxonomy of pythons and our study also demonstrates how ecological opportunity following colonization of novel environments can promote morphological diversification in a formerly ecomorphologically conservative group. [Adaptive radiation; anchored hybrid enrichment; biogeography; morphometrics; snakes.]

scholarly journals Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

2020 ◽  
Author(s):  
Zachary D. Blount ◽  
Rohan Maddamsetti ◽  
Nkrumah A. Grant ◽  
Sumaya T. Ahmed ◽  
Tanush Jagdish ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Transposable Elements ◽  
Copy Number ◽  
Ecological Niches ◽  
Phenotypic Evolution ◽  
Aerobic Growth ◽  
E Coli ◽  
Number Variation ◽  
Control Set ◽  
Resource Environment

ABSTRACTEvolutionary innovations allow populations to colonize new, previously inaccessible ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in a population of Escherichia coli during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ can grow in citrate-only medium (DM0), which is a novel environment for E. coli. To study adaptation to this new niche, we evolved one set of Cit+ populations for 2,500 generations in DM0 and a control set in DM25. We identified numerous parallel mutations, many mediated by transposable elements. Several lineages evolved multi-copy amplifications containing the maeA gene, constituting up to ∼15% of the genome. We also found substantial cell death in ancestral and evolved clones. Our results demonstrate the importance of copy-number variation and transposable elements in the refinement of the Cit+ trait. However, the observed mortality suggests a persistent evolutionary mismatch between E. coli physiology and a citrate-only environment.

scholarly journals Ectodysplasin signalling genes and phenotypic evolution in sculpins ( Cottus )

2015 ◽  
Vol 282 (1815) ◽  
pp. 20150746 ◽  
Author(s):  
Jie Cheng ◽  
Fritz Sedlazek ◽  
Janine Altmüller ◽  
Arne W. Nolte
Keyword(s):  
Body Shape ◽  
Morphological Evolution ◽  
Genomic Region ◽  
Phenotypic Evolution ◽  
Natural Hybrid ◽  
Microevolutionary Change ◽  
Trait Locus ◽  
Locus Mapping ◽  
Edar Gene

Despite their deeply conserved function among vertebrates, ectodysplasin (Eda) signalling genes are involved in microevolutionary change in humans and sticklebacks. If such a dual role is common, Eda signalling genes constitute hotspots for morphological evolution. Variation in sculpin ( Cottus ) skin prickling and body shape resembles patterns caused by variation in Eda signalling in sticklebacks. We mapped Eda signalling genes and performed quantitative trait locus mapping in crosses between Cottus rhenanus and Cottus perifretum . A genomic region containing the Eda receptor (Edar) was strongly associated with prickling and contributed to shape. The expression of Edar in developing prickles and skeletal elements in Cottus was confirmed by in situ hybridization. Coding sequence changes between Edar alleles in C. rhenanus and C. perifretum exceeded sequence differentiation in other vertebrates. However, it is likely that additional genetic elements besides coding changes affect the phenotypic variation. Although the phenotype in a natural hybrid lineage between C. rhenanus and C. perifretum resembles C. perifretum , the respective coding Edar alleles are not fully fixed (88.6%). Hence, our results support an involvement of Eda signalling in microevolutionary changes, but imply that the Edar gene is affected by multiple evolutionary processes that vary among freshwater sculpins.

scholarly journals Morphology, Ecology, and Biogeography of Independent Origins of Cleaning Behavior Around the World

2019 ◽  
Vol 59 (3) ◽  
pp. 625-637 ◽  
Author(s):  
Vikram B Baliga ◽  
Rita S Mehta
Keyword(s):  
Body Shape ◽  
Morphological Evolution ◽  
Small Body ◽  
Character Displacement ◽  
Phenotypic Evolution ◽  
Ecological Specialization ◽  
Selective Pressures ◽  
Cleaning Behavior ◽  
Marine Habitats ◽  
The Caribbean

Abstract Members of an ecological guild may be anticipated to show morphological convergence, as similar functional demands exert similar selective pressures on phenotypes. Nature is rife with examples, however, where such taxa instead exhibit ‘incomplete’ convergence or even divergence. Incorporating factors such as character displacement by other guild members or variation in ecological specialization itself may therefore be necessary to gain a more complete understanding of what constrains or promotes diversity. Cleaning, a behavior in which species remove and consume ectoparasites from “clientele,” has been shown to exhibit variation in specialization and has evolved in a variety of marine habitats around the globe. To determine the extent to which specialization in this tropic strategy has affected phenotypic evolution, we examined the evolution of cleaning behavior in five marine fish families: Labridae, Gobiidae, Pomacanthidae, Pomacentridae, and Embiotocidae. We used a comparative framework to determine patterns of convergence and divergence in body shape and size across non-cleaning and cleaning members within these five clades. Highly specialized obligate cleaning, found in the Indo-Pacific and the Caribbean, evolved in the Labridae and Gobiidae at strikingly similar times. In these two regions, obligate cleaning evolves early, shows convergence on an elongate body shape, and is restricted to species of small body size. Facultative cleaning, shown either throughout ontogeny or predominately in the juvenile phase, exhibits a much more varied phenotype, especially in geographic regions where obligate cleaning occurs. Collectively, our results are consistent with varying extents of an ecological specialization constraining or spurring morphological evolution in recurrent ways across regions.

scholarly journals Testing for phylogenetic signal in claws suggests great influence of ecology on Caribbean intertidal arthropods (Acari, Oribatida)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michaela Kerschbaumer ◽  
Tobias Pfingstl
Keyword(s):  
Phylogenetic Signal ◽  
Habitat Preferences ◽  
Great Influence ◽  
Ecological Niches ◽  
Ecological Aspects ◽  
Perfect Model ◽  
Wide Range ◽  
Claw Morphology ◽  
Selective Forces ◽  
Caribbean Populations

AbstractClaws are common biological attachment devices that can be found in a wide variety of animal groups. Their curvature and size are supposed to be parameters related to ecological aspects. Mites, known as very small arthropods, occupy a wide range of ecological niches and are a perfect model system to investigate correlations of claw morphology with ecology. There is only one study regarding this question in littoral mites but the phylogenetic impact, which plays an important role in the evolution of morphological traits, was not tested. We investigated claw shapes of different Caribbean populations of five species showing different substrate/habitat preferences. We used geometric morphometrics to quantify claw shape and tested for phylogenetic signal within this morphological trait. Even in closely related populations, we found clear claw shapes for hard versus soft substrate, confirming previous findings. Surprisingly, we found no phylogenetic signal within the trait, which demonstrates that ecology (different surfaces and substrates) has acted as one of the primary selective forces in the diversification of claw shapes. Considering that the basic claw design may be the same in the majority of arthropods, our results have important implications for further investigations of claw morphology and its ecological relevance within this phylum.

scholarly journals Foraminiferal stratigraphy and palaeoecological implications in turbidite-like deposits from the Early Tortonian (Late Miocene) of Greece

2007 ◽  
Vol 26 (2) ◽  
pp. 145-158 ◽  
Author(s):  
H. Drinia ◽  
A. Antonarakou ◽  
N. Tsaparas ◽  
M. D. Dermitzakis
Keyword(s):  
Habitat Preferences ◽  
High Energy ◽  
Environmental Stability ◽  
Ecological Niches ◽  
Feeding Strategies ◽  
Sedimentary Environments ◽  
Bottom Waters ◽  
Broad Variety ◽  
Consistent Picture ◽  
Of Greece

Abstract. The Lower Tortonian Ag. Giannis section, in Gavdos Island, Greece, consists of an outer neritic to upper bathyal, marly hemipelagic sequence which is interrupted by thick turbidite-like sandy deposits. During deposition of the marly intervals, reworking was considerably reduced.This paper contributes to knowledge concerning benthic foraminiferal response to dynamic sedimentary environments. Important palaeoecological information for benthic foraminiferal assemblages was gathered and analyzed in order to create a regionally consistent picture of the palaeoenvironment. Samples were analyzed statistically in order to identify the different palaeoenvironmental settings during turbiditic sedimentation. Undisturbed basal marls of the section are characterized by the predominance of a diversified Uvigerina striatissima assemblage typified by a broad variety of morphotypes with different inferred habitat preferences and feeding strategies, indicating rather well-oxygenated bottom waters. This environmental stability was subsequently disrupted by recurrent deposition of turbidite-like sands. A low-diversity Valvulineria complanata-Globobulimina sp. assemblage is dominant in this part of the succession, as these specialized endobenthic species could keep pace with high-energy sedimentary settings. Just above the turbidites, a “recolonization” fauna (Bolivina alata assemblage), composed entirely of infaunal elements is observed, indicating a nutrient-rich substrate. This oligotypic fauna is later replaced by a more diversified microfauna capable of occupying a wider range of ecological niches.

scholarly journals Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Zachary D Blount ◽  
Rohan Maddamsetti ◽  
Nkrumah A Grant ◽  
Sumaya T Ahmed ◽  
Tanush Jagdish ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Death ◽  
Transposable Elements ◽  
Ecological Niches ◽  
Phenotypic Evolution ◽  
Glucose Medium ◽  
Aerobic Growth ◽  
E Coli ◽  
Resource Environment ◽  
Minimal Glucose Medium

Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.

scholarly journals Shared ecological traits influence shape of the skeleton in flatfishes (Pleuronectiformes)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8919
Author(s):  
Corinthia R. Black ◽  
Peter B. Berendzen
Keyword(s):  
Body Shape ◽  
Middle Miocene ◽  
Linear Models ◽  
Phylogenetic Signal ◽  
X Rays ◽  
Ecological Traits ◽  
Body Depth ◽  
Primary Focus ◽  
Diverse Groups ◽  
Fin Length

In the age of phylogenetic comparative methods, evolutionary biologists have been able to explore evolutionary trends in form in unique and extraordinarily diverse groups of animals. Pleuronectiformes, commonly known as flatfishes, is a diverse and specialized order of fishes that have remarkable asymmetry induced by ocular migration and a benthic life style. Although flatfishes are unique from other fishes, species within the group are morphologically diverse. The origin of ocular migration has been a primary focus of research; however, little is known about overall shape diversification among the flatfishes. In this study, we use integrative methods to examine how body shape evolved within the flatfishes. Shape was quantified from X-rays using geometric morphometrics for 389 individuals across 145 species. The most recent and robust phylogeny was overlaid onto the morphospace and phylogenetic signal was calculated to ascertain convergence in the morphospace. In addition, phylogenetic linear models were employed to determine if ecological traits were correlated with shape and if size had an effect on overall body shape. Results revealed that the majority of variation evolved recently, within the past 15–10-million-years in the middle Miocene, and is highly variable within the flatfishes. These changes are best summarized by body depth, jaw length and medial fin length. Dorsal and anal fin length are correlated, which may be due to the unique mode of locomotion used by flatfishes. A phylogenetic linear model and phylomorphospace analysis suggested that several ecological traits are correlated with shape, which indicates an ecological role in the diversification of flatfishes.

scholarly journals Following The Niche: Reconstructing 32,000 Years Of Niche Dynamics In Four European Ungulate Species

2020 ◽  
Author(s):  
Michela Leonardi ◽  
Francesco Boschin ◽  
Paolo Boscato ◽  
Andrea Manica
Keyword(s):  
Last Glacial Maximum ◽  
Habitat Preferences ◽  
Glacial Maximum ◽  
Habitat Modification ◽  
Ecological Niches ◽  
Climatic Fluctuations ◽  
Last Glacial ◽  
The Future ◽  
The Last Glacial Maximum ◽  
The Last Glacial

AbstractAn understanding of how ecological niches can change through time is key to predicting the effect of future global change. Past climatic fluctuations provide a natural experiment to assess the extent to which species can change their niche. Here we use an extensive archaeological database to formally test whether the niche of four European ungulates changed between 40 and 8 kya (i.e. before major anthropogenic habitat modification and excluding the confounding effect of domestication). We find that niche change depended on habitat. Horse and aurochs, which are adapted to open environment, changed their niche after the Last Glacial Maximum, and it is unclear whether this was the result of adaptation, or an expansion of the realized niche as a response to the extinction of other megafauna (competitors and predators) that shared the same habitat preferences. On the other hand, red deer and wild boar, which prefer close and semi-close habitats, did not change their niche during the same period; possibly because these habitats have experienced fewer extinctions. Irrespective of the mechanism that might have led to the observed niche changes, the fact that large mammals with long generation times can change their niche over the time period of thousands of years cautions against assuming a constant niche when predicting the future.Significance statementWhen predicting species responses to future change, it is often assumed that their habitat preferences (i.e. their niche) will not change. However, it is strongly debated whether this is reasonable. Here we show that two out of four species of large European ungulates changed their niche following the Last Glacial Maximum, possibly as a response to the reorganization of animal communities that resulted from numerous megafauna extinctions. This finding cautions against the assumption of a constant niche, highlighting that, to predict the future, we will ultimately need to understand the mechanisms that underpin the success of a given species under different climatic conditions.

scholarly journals Shifted distribution baselines: neglecting long-term biodiversity records risks overlooking potentially suitable habitat for conservation management

2019 ◽  
Vol 374 (1788) ◽  
pp. 20190215 ◽  
Author(s):  
Sophie Monsarrat ◽  
Peter Novellie ◽  
Ian Rushworth ◽  
Graham Kerley
Keyword(s):  
Habitat Suitability ◽  
Potential Distribution ◽  
Habitat Preferences ◽  
Ecological Niches ◽  
Suitable Habitat ◽  
Ecological Data ◽  
Distribution Models ◽  
Mammal Species ◽  
Occurrence Records

Setting appropriate conservation measures to halt the loss of biodiversity requires a good understanding of species' habitat requirements and potential distribution. Recent (past few decades) ecological data are typically used to estimate and understand species’ ecological niches. However, historical local extinctions may have truncated species–environment relationships, resulting in a biased perception of species' habitat preferences. This may result in incorrect assessments of the area potentially available for their conservation. Incorporating long-term (centuries-old) occurrence records with recent records may provide better information on species–environment relationships and improve the modelling and understanding of habitat suitability. We test whether neglecting long-term occurrence records leads to an underestimation of species’ historical niche and potential distribution and identify which species are more vulnerable to this effect. We compare outputs of species distribution models and niche hypervolumes built using recent records only with those built using both recent and long-term (post-1500) records, for a set of 34 large mammal species in South Africa. We find that, while using recent records only is adequate for some species, adding historical records in the analyses impacts estimates of the niche and habitat suitability for 12 species (34%) in our dataset, and that this effect is significantly higher for carnivores. These results show that neglecting long-term biodiversity records in spatial analyses risks misunderstanding, and generally underestimating, species' niches, which in turn may lead to ill-informed management decisions, with significant implications for the effectiveness of conservation efforts. This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’

Sign in / Sign up

Export Citation Format

Share Document