Patterns Of Gene Evolution Research Articles

Identification of novel proteins regulating lipid droplet biogenesis in filamentous fungi.

Lipid droplets (LDs) are storage organelles for neutral lipids which are critical for lipid homeostasis. Current knowledge of fungal LD biogenesis is largely limited to budding yeast, while LD regulation in multinucleated filamentous fungi which exhibit considerable metabolic activity remains unexplored. In this study, 19 LD-associated proteins were identified in the multinucleated species Aspergillus oryzae using a colocalization screening of a previously established enhanced green fluorescent protein (EGFP) fusion library. Functional screening identified 12 lipid droplet-regulating (LDR) proteins whose loss of function resulted in irregular LD biogenesis, particularly in terms of LD number and size. Bioinformatics analysis, targeted mutagenesis, and microscopy revealed four LDR proteins that localize to LD via the putative amphipathic helices (AHs). Further analysis revealed that LdrA with an Opi1 domain is essential for cytoplasmic and nuclear LD biogenesis involving a novel AH. Phylogenetic analysis demonstrated that the patterns of gene evolution were predominantly based on gene duplication. Our study identified a set of novel proteins involved in the regulation of LD biogenesis, providing unique molecular and evolutionary insights into fungal lipid storage.

Comparative analysis of adipokinetic hormones and their receptors in Blattodea reveals novel patterns of gene evolution.

Adipokinetic hormone (AKH) is a neuropeptide produced in the insect corpora cardiaca that plays an essential role in mobilising carbohydrates and lipids from the fat body to the haemolymph. AKH acts by binding to a rhodopsin-like G protein-coupled receptor (GPCR), the adipokinetic hormone receptor (AKHR). In this study, we tackle AKH ligand and receptor gene evolution as well as the evolutionary origins of AKH gene paralogues from the order Blattodea (termites and cockroaches). Phylogenetic analyses of AKH precursor sequences point to an ancient AKH gene duplication event in the common ancestor of Blaberoidea, yielding a new group of putative decapeptides. In total, 16 different AKH peptides from 90 species were obtained. Two octapeptides and seven putatively novel decapeptides are predicted for the first time. AKH receptor sequences from 18 species, spanning solitary cockroaches and subsocial wood roaches as well as lower and higher termites, were subsequently acquired using classical molecular methods and in silico approaches employing transcriptomic data. Aligned AKHR open reading frames revealed 7 highly conserved transmembrane regions, a typical arrangement for GPCRs. Phylogenetic analyses based on AKHR sequences support accepted relationships among termite, subsocial (Cryptocercus spp.) and solitary cockroach lineages to a large extent, while putative post-translational modification sites do not greatly differ between solitary and subsocial roaches and social termites. Our study provides important information not only for AKH and AKHR functional research but also for further analyses interested in their development as potential candidates for biorational pest control agents against invasive termites and cockroaches.

Unusual Dependence between Gene Expression and Negative Selection in Euplotes

In most of the studied organisms, gene expression is associated with a number of evolutionary features pertaining to the protein-coding sequences. In particular, gene expression positively correlates with the average intensity of negative selection and influences codon usage. Here, we study the connection between gene expression and selection patterns in two species of ciliate protists of the genus Euplotes. We find that codon usage is influenced by gene expression in these organisms, pointing at additional evolutionary constraints on mutations in heavily expressed genes relative to the genes expressed at lower rates. At the same time, at the level of synonymous vs. non-synonymous substitutions we observe a stronger constraint on the genes expressed at lower rates relative to those with higher rates of expression. Our study adds to the discussion about the general evolutionary patterns and opens new questions about the mechanisms of control of gene expression in ciliates.

Marine species turnover but not richness, peaks at the Equator

Turnover in species composition, also called beta diversity, can indicate natural habitat diversity and fragmentation of populations due to environmental stress, such as heatwaves. Latitudinal gradients in species diversity help synthesise local diversity into more general evolutionary and climatic patterns. Recently it has been shown that local (alpha) and regional (gamma) measures of marine species richness do not peak but dip at and peak on either side of the Equator, and decline in higher latitudes, creating a bimodal gradient. Here we show that for a dataset of 50,113 marine animal species, that species turnover peaked at the Equator. Thus, species richness declined where turnover was highest. This high turnover but dip in species richness at the Equator may indicate population fragmentation due to thermal stress. Such fragmentation could be the mechanism behind declining marine species richness in latitudes with an annual mean temperature > 25 °C.One Sentence Summary: The latitudinal gradient in species turnover but not species richness is unimodal, with a peak at the Equator.

EVOLUÇÃO DA ICTIOFAUNA DE RIACHOS SUL-AMERICANOS (CASTRO, 1999) REVISITADO APÓS MAIS DE DUAS DÉCADAS

A little more than 20 years after the first publication of Castro (1999), the knowledge of the South American freshwater ichthyofauna, especially that of Brazil, has increased dramatically. This increase occurred both in terms of knowledge of its taxonomic diversity - in 1999, based on various sources in the scientific literature, a total of 2,800 species of South American freshwater fish was estimated, and a total of near 3,500 species it is currently known from Brazil alone - as to the knowledge of its evolution and also ecology. Consequently, all the hypotheses originally proposed in that paper are reexamined and critically discussed here considering this new knowledge accumulated in the past nearly two decades. Although the original 1999 hypothesis that the small adult size of their respective species is a general evolutionary pattern shared by the South American stream ichthyofauna has been firmly corroborated by several studies carried out in many regions of Brazil, the different patterns associated with most of the species of stream fish originally proposed are discussed in this chapter in the light of the new accumulated knowledge about their biology and ecology. Likewise, the possible role of heterochrony in their respective evolution is critically analyzed in the context of the great advance that has occurred in understanding the phylogenetic relationships of component taxa of freshwater neotropical ichthyofauna, using mainly the family Characidae as a possible model. Finally, a recent intriguing idea of the role of respiratory physiology in determining both the maximum size of teleost fish and their patterns of environmental occupation is examined in relation to its possible effect in the evolution of South American stream ichthyofauna.

Remarkable sexually dimorphic features ofConiceromyia(Diptera: Phoridae): evolution in the light of phylogeny and comparative evidence about their function

AbstractConiceromyia is a genus of 100 species of phorid flies mostly distributed in the Neotropical region. The genus is distinguishable based on several male-exclusive features in different parts of the body, many of which are unique among the Phoridae. In addition, many species of Coniceromyia have nearly identical morphology of their male copulatory apparatus (i.e. hypopygium). The co-occurrence of these unusual characteristics suggests an evolutionary correlation between them. To investigate this possible correlation and to understand other aspects of the evolution of these puzzling male-exclusive characters, we performed the first phylogenetic analysis of Coniceromyia, based on morphological and molecular data. Ancestral state reconstructions and comparative analyses then allowed us to infer the evolution of these characters and search for general evolutionary patterns and correlated histories. We demonstrate that these male-exclusive features varied from highly homoplastic to uniquely derived on the phylogenetic history of Coniceromyia. For some characters, we found evidence of a biased evolution favouring gains over losses of the feature, but no male characteristics were significantly correlated with hypopygium morphology. The evolutionary patterns of the male-exclusive features and comparative evidence with other better known groups suggest possible functions for these features related to sexual selection.

The evolutionary pattern of language in scientific writings: A case study of Philosophical Transactions of Royal Society (1665\u20131869)

Scientific writings, as one essential part of human culture, have evolved over centuries into their current form. Knowing how scientific writings evolved is particularly helpful in understanding how trends in scientific culture developed. It also allows us to better understand how scientific culture was interwoven with human culture generally. The availability of massive digitized texts and the progress in computational technologies today provide us with a convenient and credible way to discern the evolutionary patterns in scientific writings by examining the diachronic linguistic changes. The linguistic changes in scientific writings reflect the genre shifts that took place with historical changes in science and scientific writings. This study investigates a general evolutionary linguistic pattern in scientific writings. It does so by merging two credible computational methods: relative entropy; word-embedding concreteness and imageability. It thus creates a novel quantitative methodology and applies this to the examination of diachronic changes in the Philosophical Transactions of Royal Society (PTRS, 1665–1869). The data from two computational approaches can be well mapped to support the argument that this journal followed the evolutionary trend of increasing professionalization and specialization. But it also shows that language use in this journal was greatly influenced by historical events and other socio-cultural factors. This study, as a “culturomic” approach, demonstrates that the linguistic evolutionary patterns in scientific discourse have been interrupted by external factors even though this scientific discourse would likely have cumulatively developed into a professional and specialized genre. The approaches proposed by this study can make a great contribution to full-text analysis in scientometrics.

Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum.

Plasticity and evolution are two processes allowing populations to respond to environmental changes, but how both are related and impact each other remains controversial. We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after exposure of the beetles to new environments that differed from ancestral conditions in temperature, humidity or both. Using experimental evolution with 10 replicated lines per condition, we were able to demonstrate adaptation after 20 generations. We measured whole-transcriptome gene expression with RNA-sequencing to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between the proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line.

Patterns of gene evolution following duplications and speciations in vertebrates.

BackgroundEukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting.MethodsTo provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa.ResultsOverall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

Kinetics of Chemical Precipitation: General Evolutionary Patterns in Different Models

The trends, general patterns, and stages of evolutionary processes, in particular, the evolution of solid matter in crystallization processes, have been considered. The role of the logistic (sigmoid) function in the description of the kinetics of evolutionary processes has been shown. Mathematical modeling of the chemical precipitation of slightly soluble salts has been performed taking into account the rates of crystal growth and nucleation. It has been found that different models lead to the S-shaped dependence of the same form, which adequately describes the formation of crystalline precipitates of slightly soluble calcium salts from supersaturated aqueous solutions.

The modular nature of protein evolution: domain rearrangement rates across eukaryotic life

BackgroundModularity is important for evolutionary innovation. The recombination of existing units to form larger complexes with new functionalities spares the need to create novel elements from scratch. In proteins, this principle can be observed at the level of protein domains, functional subunits which are regularly rearranged to acquire new functions.ResultsIn this study we analyse the mechanisms leading to new domain arrangements in five major eukaryotic clades (vertebrates, insects, fungi, monocots and eudicots) at unprecedented depth and breadth. This allows, for the first time, to directly compare rates of rearrangements between different clades and identify both lineage specific and general patterns of evolution in the context of domain rearrangements. We analyse arrangement changes along phylogenetic trees by reconstructing ancestral domain content in combination with feasible single step events, such as fusion or fission. Using this approach we explain up to 70% of all rearrangements by tracing them back to their precursors. We find that rates in general and the ratio between these rates for a given clade in particular, are highly consistent across all clades. In agreement with previous studies, fusions are the most frequent event leading to new domain arrangements. A lineage specific pattern in fungi reveals exceptionally high loss rates compared to other clades, supporting recent studies highlighting the importance of loss for evolutionary innovation. Furthermore, our methodology allows us to link domain emergences at specific nodes in the phylogenetic tree to important functional developments, such as the origin of hair in mammals.ConclusionsOur results demonstrate that domain rearrangements are based on a canonical set of mutational events with rates which lie within a relatively narrow and consistent range. In addition, gained knowledge about these rates provides a basis for advanced domain-based methodologies for phylogenetics and homology analysis which complement current sequence-based methods.

REVISION OF THE MIOCENE CAVIOMORPH RODENTS FROM THE RÍO SANTA CRUZ (ARGENTINEAN PATAGONIA)

Fossil rodents from the Río Santa Cruz (RSC) classic localities (Santa Cruz Formation, Early–Middle Miocene) are known by the works of F. Ameghino and W.B. Scott since the end of the 19th and beginning of the 20th centuries. These caviomorph rodents have not been comprehensively reviewed since then. In this contribution, we studied new fossil specimens from the cliffs of the RSC (Province of Santa Cruz, Argentina) collected with accurate stratigraphic and geographic data during fieldtrips in 2013 and 2014. An increase in the caviomorph taxonomic richness is observed, based upon our taxonomic study of caviomorphs previously recorded in the RSC. Also, these fieldworks recovered for the first time several taxa previously found in other Santacrucian and even older Patagonian localities (Colhuehuapian, Early Miocene). As a general evolutionary pattern, we note an increase of derived euhypsodont taxa (Prolagostomus, Pliolagostomus, Schistomys, and Eocardia) in Segundas Barrancas Blancas (16.47–15.3 Ma). In addition, a taxonomic replacement of Phanomys by Schistomys is noted between Barrancas Blancas (17.21–16.3 Ma) and Segundas Barrancas Blancas, as well as a notably increase in the abundance of the large Perimys onustus in the latter locality. The present study provides a revision of the caviomorph systematics, and intends to be the starting point to understand the diversity (in all its aspects) and the evolution of this group during the Santacrucian, a major event in the South American mammalian history.

Flap-Footed Lizards (Gekkota: Pygopodidae) Have Forelimbs, Albeit During Embryonic Development

Limb reduction among squamate clades is common; limbless (forelimbs, hindlimbs, or both) forms have had at least 25 independent origins among snakes and lizards. The general evolutionary pattern is the gradual loss of limb elements proceeding from the toes to the shoulder or hip. In contrast, forelimbs are not known to have ever existed in snakes. Forelimbs are not known for either stem or crown snakes; snake fossils lack forelimbs and the embryos of modern snakes lack the signaling pathways that initiate forelimb development. Both fossil and developmental data thus imply an abrupt loss of forelimbs. In contrast, the well-developed hindlimbs of the oldest fossil snakes and vestigial hindlimbs of some basal clades of modern snakes imply the historical presence of hindlimbs, and their gradual reduction during snake evolution. In contrast, observations on limb-reduced lizards are in accord with gradual reduction of both fore- and hindlimbs; embryos of even limbless species initiate limb development. The question then arises, have any clades of limbless lizards become limbless abruptly, as have snakes? To address this question, I examined limb development in the family Pygopodidae. Like basal snakes, pygopodids are characterized by the absence of forelimbs and by vestigial hindlimbs. My observations on the development of forelimb buds in Delma molleri support gradual limb reduction, as do observations on other limbless lizards. Nonetheless, many clades of limbless lizards are yet to be studied and hence provide a wealth of opportunities to address modes of limb reduction and loss in squamate reptiles.

The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals.

The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Sequencing was performed on blood cells as they are amongst the most accessible, stable and abundant sources of the different sncRNA classes. We evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. While the distribution of sncRNAs in the different RNA classes varied significantly, general evolutionary patterns were maintained. In particular, miRNA sequences and expression were found to be even more conserved than previously assumed. To make the results available for other researchers, all data, including expression profiles at the species and family levels, and different tools for viewing, filtering and searching the data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/.

Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers

Different human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example, hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The "pygmy" phenotype (small adult body size), characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent versus population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes of two pairs of populations: Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda and Andamanese rainforest hunter-gatherers and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the rainforest hunter-gatherers across the set of genes with "growth factor binding" functions ([Formula: see text]). Unexpectedly, for the rainforest groups, we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g., "cardiac muscle tissue development"; [Formula: see text]). We hypothesize that the growth hormone subresponsiveness likely underlying the adult small body-size phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, in the agriculturalist populations, we did not observe similar patterns of positive selection on sets of genes associated with growth or cardiac development, indicating our results most likely reflect a history of convergent adaptation to the similar ecology of rainforests rather than a more general evolutionary pattern.

Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome.

Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in plants.

BEBAIMĖ KULTŪRINIO HEROJAUS PRAEITIS (PROMETĖJAS, LOKIS, SYRDONAS…KOJOTAS…)

The paper compares Loki of the Scandinavian and Syrdon of the Caucasian material (the Nart epic tradition) with the evolution of the character of Prometheus as described in the early texts (Theogony and Works and Days by Hesiod) and with his later transformation as described in Prometheus Bound by Aeschilus. This comparison makes it possible to demonstrate the general pattern of evolution which can be described as (chthonian) deity → trickster → culture hero. In this we do not agree with Eleazar Meletinskij’s statemwent, according to which the culture hero – Demiurge – is the most ancient character in the world folklore, while the trickster is a subsequent transformation of the image of the culture hero. Employing the Greek model (Hesiod’s Theogony) as our starting point, we will argue that an intriguer / a trickster is the most ancient mythological character, while the culture hero emerges as a result of later developments.

Morphometric analysis of graphoglyptid trace fossils in two dimensions: implications for behavioral evolution in the deep sea

AbstractGraphoglyptids are deep-marine trace fossils, often found preserved as casts in positive relief on the base of turbidites. Previous analyses of the behavioral evolution of graphoglyptids suggested they were slowly diversifying, becoming optimized, and getting smaller over time until the Late Cretaceous, when a sudden increase in diversification occurred. This current study quantifies the morphology of approximately 400 different graphoglyptid specimens, ranging in age from the Cambrian to the present, in order to evaluate the behavioral evolutionary interpretations made previously. Results from this study indicate that although some general evolutionary patterns can be discerned, they are not as straightforward as previously reported.Different topological categories of trace fossils represent organisms’ responses to evolutionary pressures in unique ways. While burrow widths of meandering traces were becoming smaller over time, as predicted by previous workers, the burrow widths of the network traces were becoming smaller only until the Late Cretaceous, when they started to get larger again. The times of significant evolutionary changes in behavior were not consistent among various topological categories, with some morphological features being affected in the Late Cretaceous and others during the beginning of the Eocene. It is likely that the behavioral evolution of graphoglyptids was influenced by deep-marine global influences linked to climate change, glaciation, and deep-ocean warming. These influences affected each topological group uniquely, suggesting that different species or genera of trace makers were creating each of the topological categories. This is contrary to the hypothesis that all graphoglyptids were created by closely related species.

Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects.

Epigenetic information is widely appreciated for its role in gene regulation in eukaryotic organisms. However, epigenetic information can also influence genome evolution. Here, we investigate the effects of epigenetic information on gene sequence evolution in two disparate insects: the fly Drosophila melanogaster, which lacks substantial DNA methylation, and the ant Camponotus floridanus, which possesses a functional DNA methylation system. We found that DNA methylation was positively correlated with the synonymous substitution rate in C. floridanus, suggesting a key effect of DNA methylation on patterns of gene evolution. However, our data suggest the link between DNA methylation and elevated rates of synonymous substitution was explained, in large part, by the targeting of DNA methylation to genes with signatures of transcriptionally active chromatin, rather than the mutational effect of DNA methylation itself. This phenomenon may be explained by an elevated mutation rate for genes residing in transcriptionally active chromatin, or by increased structural constraints on genes in inactive chromatin. This result highlights the importance of chromatin structure as the primary epigenetic driver of genome evolution in insects. Overall, our study demonstrates how different epigenetic systems contribute to variation in the rates of coding sequence evolution.

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene-Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.