Biology subjects

Maestri, R.

Publications and source records attributed to Maestri, R..

10 recordsLinked to original sources

bioRxiv2024

Ancient DNA Clarifies the Identity and Geographic Origin of the holotype of the genus Ctenomys

Ctenomys Blainville 1826 ranks among the top ten most diverse mammal genera in terms of species richness. However, the taxonomic history of Ctenomys brasiliensis Blainville,1826, the corresponding type species, has long been obscured by a dearth of information regarding the collection data of the type material, compounded by an elusive geographic origin. Here, employing ancient DNA methodology, we sequenced the complete mitogenome of the remaining type specimen and conducted an extensive historical investigation to correlate originally described locality names with present-day locales in South America. Our analysis unequivocally confirms that the type specimen corresponds to the species currently designated as Ctenomys minutus Nehring, 1887. This resolution lays to rest a century-old debate surrounding the provenance of the type specimen, rejecting prior hypotheses that placed its collection site in southeastern Brazil or Uruguay. Instead, our evidence suggests it was likely obtained from a third location in southernmost Brazil. Previous analyses overlooked this new location due to confusion surrounding geographic nomenclature and labeling errors, issues rectified by our combined mitogenomic and historical approach. Furthermore, quantitative morphological analyses boost our findings, demonstrating a closer affinity between C. brasiliensis and C. minutus within the same species group. Accordingly, we validate C. brasiliensis and propose C. minutus as its junior synonym. Our study underscores the importance of robust DNA analyses in confirming the identity and geographic origins of type specimens, especially for Ctenomys species with similar phenotypes, and specimens collected centuries ago.

zoology↗

bioRxiv2023

From Fossils to Living Canids: Two Contrasting Perspectives on Biogeographic Diversification

The Canidae are an ecologically important group of dog-like carnivores that arose in North America and spread across the planet around 10 million years ago. The current distribution patterns of species, coupled with their phylogenetic structure, suggest that Canidae diversification may have occurred at varying rates across different biogeographic areas. However, such extant-only analyses undervalued the groups rich fossil history because of a limitation in methods development. Current State-dependent Speciation and Extinction (SSE) models are (i) often parameter-rich which hinders reliable application to relatively small clades such as the Caninae (the only extant subclade of the Canidae consisting of 36 extant species); and (ii) often assume as possible states only the states that extant species present. Here we extend the SSE method SecSSE to apply to phylogenies with extinct species as well (111 Caninae species) and compare the results to those of analyses with the extant-species-only phylogeny. The results on the extant-species tree suggest that distinct diversification patterns are related to geographic areas, but the results on the complete tree do not support this conclusion. Furthermore, our extant-species analysis yielded an unrealistically low estimate of the extinction rate. These contrasting findings suggest that information from extinct species is different from information from extant species. A possible explanation for our results is that extinct species may have characteristics (causing their extinction), which may be different from the characteristics of extant species that caused them to be extant. Hence, we conclude that differences in biogeographic areas probably did not contribute much to the variation in diversification rates in Caninae.

evolutionary biology↗

bioRxiv2023

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

Several coronaviruses infect humans, with three, including the SARS-CoV2, causing diseases. While coronaviruses are especially prone to induce pandemics, we know little about their evolutionary history, host-to-host transmissions, and biogeography. One of the difficulties lies in dating the origination of the family, a particularly challenging task for RNA viruses in general. Previous cophylogenetic tests of virus-host associations, including in the Coronaviridae family, have suggested a virus-host codiversification history stretching many millions of years. Here, we establish a framework for robustly testing scenarios of ancient origination and codiversification versus recent origination and diversification by host switches. Applied to coronaviruses and their mammalian hosts, our results support a scenario of recent origination of coronaviruses in bats and diversification by host switches, with preferential host switches within mammalian orders. Hotspots of coronavirus diversity, concentrated in East Asia and Europe, are consistent with this scenario of relatively recent origination and localized host switches. Spillovers from bats to other species are rare, but have the highest probability to be towards humans than to any other mammal species, implicating humans as the evolutionary intermediate host. The high host-switching rates within orders, as well as between humans, domesticated mammals, and non-flying wild mammals, indicates the potential for rapid additional spreading of coronaviruses across the world. Our results suggest that the evolutionary history of extant mammalian coronaviruses is recent, and that cases of long-term virus-host codiversification have been largely over-estimated.

evolutionary biology↗

bioRxiv2021

There and Back to the Present: An Evolutionary Tale on Biological Diversity

Ecologists often agree on the importance of macroevolution for niche-mediated distribution of biological diversity along environmental gradients. Yet, macroevolutionary diversification and dispersal in time and space generate uneven geographic distribution of phylogenetic pools, which affects the imprint let by macroevolution on local species pools. In this article we introduce an individual-based simulation approach coupled to Approximate Bayesian Computation (ABC) that allows to parameterize the adaptation rate of species niche positions along the evolution of a monophyletic lineage, and the intensity of dispersal limitation, associated with the distribution of biological diversity between assemblages potentially connected by dispersal (metacommunity). The analytical tool was implemented in an R package called mcfly. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate and dispersal limitation parameters. Further, we evaluated the role played by niche evolution and dispersal limitation on species diversity distribution of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and the distribution of biological diversity, and thereby improved our understanding of evolutionary imprints on ecological patterns. Perhaps more importantly, it offers new possibilities for solving the eco-evolutionary puzzle.

ecology↗

bioRxiv2021

The effect of climate change on the distribution of Canidae

Land use by humans and climate change have been seriously affecting the distribution of species resulting in a quarter of all known mammals currently threatened with extinction. Here, we modeled the present and future potential distributions of all 36 extant Canidae species to evaluate their response to future climate scenarios. In addition, we tested if canids were likely to experience evolutionary rescue, which could allow some species to adapt to climate change. Our results suggest that global warming will cause most species to lose or maintain their ranges, while a few will have the potential to benefit from future conditions and considerably expand their geographic distributions. Some canids have the potential to experience evolutionary rescue, but Atelocynus microtis and Chrysocyon brachyurus are two concerning cases that do not show this capacity to adapt given the current pace of climate change. We also reveal that most Canidae hotspot regions are outside protected areas, which may be useful for the identification of key areas for conservation.

ecology↗

bioRxiv2021

Competition and environmental gradients structure Canidae assemblages across the planet

The phylogenetic information of assemblages carries the signature of ecological and evolutionary processes that assembled these communities. Identifying the mechanisms that shape communities is not simple, as they can vary spatially. Here, we investigated how the phylogenetic structure of Canidae across the globe is affected by the environment and competition. We first identified phylogenetically clustered and overdispersed assemblages of canids over the planet taking into account regional pools of species in South and North America, Eurasia, and Africa. Then, we applied Structural Equation Models in these communities in order to identify the effect of temperature, vegetation cover, human impact, and body size dissimilarity on the spatial distribution of the phylogenetic information of canids. Only southern South America and the Middle East had strong phylogenetic clustered patterns, while the rest of the planet predominantly showed overdispersed assemblages. Body size dissimilarity and vegetation cover were the most important variables to explain the spatial patterns of phylogenetic structure in clustered and overdispersed communities, respectively. Canidae community composition across the world presents significant patterns of clustering and overdispersion, which vary following mainly the environmental gradient, suggesting habitat filtering as the main force acting on Canidae assemblages.

evolutionary biology↗

bioRxiv2021

Explosive diversification following continental colonizations by canids

Colonization of a new environment may trigger an explosive radiation process, defined as an accelerated accumulation of species in a short period of time. However, how often colonization events trigger explosive radiations is still an open question. We studied the worldwide dispersal of the subfamily Caninae, to investigate whether the invasion of new continents resulted in explosive radiations. We used a combination of phylogenetic analyses and ancestral area reconstructions to estimate ancestral ranges of 56 extant and extinct species of Caninae, as well as variation in speciation and extinction rates through time and across clades. Our findings indicate that canids experienced an explosive radiation event when lineages were able to cross the Bering Strait and the Isthmus of Panama to reach Eurasia and South America, respectively, around 11 million years ago. This large number of species arising in a short period of time suggests that canids experienced ecological opportunity events within the new areas, implying that the differences in the ecological settings between continents may be responsible for the variation in clade dynamics. We argue that interaction with other carnivores probably also affected the diversification dynamics of canids.

evolutionary biology↗

bioRxiv2019

Evoregions: Mapping Shifts in Phylogenetic Turnover Across Biogeographic Regions

Biogeographic regionalization offers context to the geographical evolution of clades. The positions of bioregions inform both the spatial location of clusters in species distribution and where their most important boundaries are. Nevertheless, defining bioregions based on species distribution alone only incidentally recovers regions that are important during the evolution of the focal group. The extent to which bioregions correspond to centers of independent diversification depends on how clusters of species composition naturally reflect the radiation of single clades, which is not the case when mixed colonization occurred. Here, we showed that using phylogenetic turnover based on fuzzy sets, instead of species composition, led to more adequate detection of evolutionary important bioregions, that is, regions that truly account for the independent diversification of lineages. Mapping those evoregions in the phylogenetic tree quickly reveals the timing and location of major shifts of biogeographic regions. Moreover, evolutionary transition zones are easily mapped, and permits the recognition of regions with high phylogenetic overlap. Our results using the global radiation of rats and mice (Muroidea) recovered four evoregions--three major evolutionary arenas corresponding to the Neotropics, a Nearctic-Siberian, and a Paleotropical-Australian evoregion, and a fourth and fuzzy Afro-Palearctic evoregion. In comparison, an analysis with a method considering species distribution alone found 52 bioregions. Evoregions is a useful framework whenever the question is related to the identification of the most important centers of a groups diversification history and its evolutionary transitions zones.

ecology↗

bioRxiv2018

HaploVectors: an integrative analytical tool for phylogeography

Sets of local populations show different degrees of gene flow due to dispersal barriers and environmental constraints, which renders genetic composition gradients among populations (genetic turnover). Unveiling biogeographic correlates of genetic turnover is paramount for phylogeography. While some processes (genetic drift, secondary contact) may erase the historical track of genetic turnover, vicariance or ancient dispersal likely leads to genetic divergence among populations. Yet available analyses do not permit direct inference about mechanisms driving genetic turnover. We propose a novel analytical approach called genvector analysis, which fulfills this gap by decomposing genetic compositional dissimilarities between populations based on either haplotypes or other genetic data into genetic eigenvectors. Such procedure allows exploring genetic turnover among sets of local populations, and analyzing their biogeographic correlates based on null model tests. We evaluate the statistical performance of the method on simulated datasets. We also analyzed biogeographic correlates of genetic turnover of Akodon cursor in the Brazilian Atlantic Forest. Results revealed that genvector analysis is robust to discriminate biogeographic drivers of genetic turnover. For Akodon cursor analysis, we observed that while for the entire species, all predictors considered (except for elevation) explained genetic turnover, within phylogroups some factors varied their importance. Genvector analysis was demonstrated to be useful for several different purposes in phylogeography, and complementary to classic analytical tools widely used by phylogeographers, such as AMOVA or DAPC. The role of ancient versus recent biogeographic events, the relationship between morphological divergence or abiotic variables and genetic turnover can easily be investigated using genvector analysis.

ecology↗

bioRxiv2018

Divergent genetic mechanisms lead to spiny hair in mammals

Spines, or modified hairs, have evolved multiple times in mammals, particularly in rodents. In this study, we investigated the evolution of spines in six rodent families. We first measured and compared the morphology and physical properties of hairs between paired spiny and non-spiny sister lineages. We found two distinct hair morphologies had repeatedly evolved in spiny rodents: hairs with a grooved cross-section and a second near cylindrical form. Compared to the ancestral elliptical-shaped hairs, spiny hairs had higher tension and stiffness, and overall, hairs with similar morphology had similar functional properties. To examine the genetic basis of this convergent evolution, we tested whether a single amino acid change (V370A) in the Ecdysoplasin A receptor (Edar) gene is associated with spiny hair, as this substitution causes thicker and straighter hair in East Asian human populations. We found that most mammals have the common amino acid valine at position 370, but two species, the kangaroo rat (non-spiny) and spiny pocket mouse (spiny), have an isoleucine. Importantly, none of the variants we identified are associated with differences in rodent hair morphology. Thus, the specific Edar mutation associated with variation in human hair does not seem to play a role in modifying hairs in wild rodents, suggesting that different mutations in Edar and/or other genes are responsible for variation in the spiny hair phenotypes we observed within rodents.

genetics↗